Reproducibility of CT bone dosimetry: Operator versus automated ROI definition

International Nuclear Information System (INIS)

Louis, O.; Luypaert, R.; Osteaux, M.; Kalender, W.

1988-01-01

Intrasubject reproducibility with repeated determination of vertebral mineral density from a given set of CT images was investigated. The region of interest (ROI) in 10 patient scans was selected by four independent operators either manually or with an automated procedure separating cortical and spongeous bone, the operators being requested to interact in ROI selection. The mean intrasubject variation was found to be much lower with the automated process (0.3 to 0.6%) than with the conventional method (2.5 to 5.2%). In a second study, 10 patients were examined twice to determine the reproducibility of CT slice selection by the operator. The errors were of the same order of magnitude as in ROI selection. (orig.)

Effect of single-visit VIA and cryotherapy cervical cancer prevention program in Roi Et, Thailand: a preliminary report.

Science.gov (United States)

Chumworathayi, Bandit; Blumenthal, Paul D; Limpaphayom, Khunying Kobchitt; Kamsa-Ard, Supot; Wongsena, Metee; Supaatakorn, Pongsatorn

2010-02-01

To assess the effect of introducing visual inspection with acetic acid and cryotherapy on cervical cancer incidence rates in Roi Et province over time, between 1997 and 2006, and compare this with two nearby provinces. Data from two cancer registration units, one in Srinagarind Hospital and another in Ubon Ratchathani Cancer Center (to which all cervical cancer patients were referred from the three study provinces) were registered, extracted, combined and analyzed using a generalized estimation equation. Cervical cancer detection rates improved. These are represented by the apparent increased incidence rates in Roi Et province during the study period compared with two nearby provinces (P = 0.01), equivalent to a doubling of the previously reported age-standardized incidence ratio and three times its baseline in 2006. A single-visit approach to cervical cancer prevention in Roi Et province using visual inspection with acetic acid and cryotherapy appeared to have an effect in revealing an increased cervical cancer incidence rate by achieving higher coverage, resulting in increased case finding.

Medical Ultrasound Video Coding with H.265/HEVC Based on ROI Extraction.

Science.gov (United States)

Wu, Yueying; Liu, Pengyu; Gao, Yuan; Jia, Kebin

2016-01-01

High-efficiency video compression technology is of primary importance to the storage and transmission of digital medical video in modern medical communication systems. To further improve the compression performance of medical ultrasound video, two innovative technologies based on diagnostic region-of-interest (ROI) extraction using the high efficiency video coding (H.265/HEVC) standard are presented in this paper. First, an effective ROI extraction algorithm based on image textural features is proposed to strengthen the applicability of ROI detection results in the H.265/HEVC quad-tree coding structure. Second, a hierarchical coding method based on transform coefficient adjustment and a quantization parameter (QP) selection process is designed to implement the otherness encoding for ROIs and non-ROIs. Experimental results demonstrate that the proposed optimization strategy significantly improves the coding performance by achieving a BD-BR reduction of 13.52% and a BD-PSNR gain of 1.16 dB on average compared to H.265/HEVC (HM15.0). The proposed medical video coding algorithm is expected to satisfy low bit-rate compression requirements for modern medical communication systems.

Medical Ultrasound Video Coding with H.265/HEVC Based on ROI Extraction.

Directory of Open Access Journals (Sweden)

Yueying Wu

Full Text Available High-efficiency video compression technology is of primary importance to the storage and transmission of digital medical video in modern medical communication systems. To further improve the compression performance of medical ultrasound video, two innovative technologies based on diagnostic region-of-interest (ROI extraction using the high efficiency video coding (H.265/HEVC standard are presented in this paper. First, an effective ROI extraction algorithm based on image textural features is proposed to strengthen the applicability of ROI detection results in the H.265/HEVC quad-tree coding structure. Second, a hierarchical coding method based on transform coefficient adjustment and a quantization parameter (QP selection process is designed to implement the otherness encoding for ROIs and non-ROIs. Experimental results demonstrate that the proposed optimization strategy significantly improves the coding performance by achieving a BD-BR reduction of 13.52% and a BD-PSNR gain of 1.16 dB on average compared to H.265/HEVC (HM15.0. The proposed medical video coding algorithm is expected to satisfy low bit-rate compression requirements for modern medical communication systems.

Roi Vaara tähendussõnad

Index Scriptorium Estoniae

2003-01-01

10. II oli Tallinna Kunstihoones soome kunstniku Roi Vaara performance Tallinna Kunstihoone uue juhataja Reiu Tüüri, kuraatorite Andres Härmi ja Reet Varblase inauguratsiooni ning TK interneti lehekülje esitluse puhul. Uue ühtse nimekuju KU autorit Edith Parist autasustati 1934 krooniga

SU-F-J-19: Robust Region-Of-Interest (ROI) for Consistent Registration On Deteriorated Surface Images

Energy Technology Data Exchange (ETDEWEB)

Kang, H; Malin, M; Chmura, S; Hasan, Y; Al-Hallaq, H [The Department of Radiation and Cellular Oncology, The University of Chicago Medicine, Chicago, IL (United States)

2016-06-15

Purpose: For African-American patients receiving breast radiotherapy with a bolus, skin darkening can affect the surface visualization when using optical imaging for daily positioning and gating at deep-inspiration breath holds (DIBH). Our goal is to identify a region-of-interest (ROI) that is robust against deteriorating surface image quality due to skin darkening. Methods: We study four patients whose post-mastectomy surfaces are imaged daily with AlignRT (VisionRT, UK) for DIBH radiotherapy and whose surface image quality is degraded toward the end of treatment. To simulate the effects of skin darkening, surfaces from the first ten fractions of each patient are systematically degraded by 25–35%, 40–50% and 65–75% of the total area of the clinically used ROI-ipsilateral-chestwall. The degraded surfaces are registered to the reference surface in six degrees-of-freedom. To identify a robust ROI, three additional reference ROIs — ROI-chest+abdomen, ROI-bilateral-chest and ROI-extended-ipsilateral-chestwall are created and registered to the degraded surfaces. Differences in registration using these ROIs are compared to that using ROI-ipsilateral-chestwall. Results: For three patients, the deviations in the registrations to ROI-ipsilateral-chestwall are > 2.0, 3.1 and 7.9mm on average for 25–35%, 40–50% and 65–75% degraded surfaces, respectively. Rotational deviations reach 11.1° in pitch. For the last patient, registration is consistent to within 2.6mm even on the 65–75% degraded surfaces, possibly because the surface topography has more distinct features. For ROI-bilateral-chest and ROI-extended-ipsilateral-chest registrations deviate in a similar pattern. However, registration on ROI-chest+abdomen is robust to deteriorating image qualities to within 4.2mm for all four patients. Conclusion: Registration deviations using ROI-ipsilateral-chestwall can reach 9.8mm on the 40–50% degraded surfaces. Caution is required when using AlignRT for patients

The evaluation of the automatic setting of ROI to SPECT measuring cerebral blood flow

International Nuclear Information System (INIS)

Mizuno, Hiroshi; Takahashi, Masaaki; Yoshioka, Katsunori

2007-01-01

It has been pointed out that the manual settings of region of interest (ROI) to the single-photon-emission-computed-tomography (SPECT) slice lacked objectivity when the fixed quantity value of regional cerebral blood flow (rCBF) was measured previously. Therefore, we jointly developed software Brain ROI'' with Daiichi Radioisotope Laboratories, Ltd. (DRL) that normalized an individual brain to a standard brain template by using Statistical Parametric Mapping 2 (SPM 2) of easy Z-score Imaging System ver. 3.0 (eZIS Ver. 3.0), and, ROI template was set to a specific slice. In this paper, we evaluated the accuracy of this software with ROI template that we made the useful size of the shape, in some clinical samples. As a result, the method of the automatic setting of ROI was the objectively. However, we thought that we should use the shape of ROI template without an influence of Brain atrophy. Moreover, we should see Normalizing individual brain and confirm the accuracy of normalization. When failing in normalization, we should partially correct ROI or set all by the manual operation of the operator. However, it was thought that this software was useful if the tendency was understood because the failure example was few. (author)

A direct ROI quantification method for inherent PVE correction: accuracy assessment in striatal SPECT measurements

Energy Technology Data Exchange (ETDEWEB)

Vanzi, Eleonora; De Cristofaro, Maria T.; Sotgia, Barbara; Mascalchi, Mario; Formiconi, Andreas R. [University of Florence, Clinical Pathophysiology, Florence (Italy); Ramat, Silvia [University of Florence, Neurological and Psychiatric Sciences, Florence (Italy)

2007-09-15

The clinical potential of striatal imaging with dopamine transporter (DAT) SPECT tracers is hampered by the limited capability to recover activity concentration ratios due to partial volume effects (PVE). We evaluated the accuracy of a least squares method that allows retrieval of activity in regions of interest directly from projections (LS-ROI). An Alderson striatal phantom was filled with striatal to background ratios of 6:1, 9:1 and 28:1; the striatal and background ROIs were drawn on a coregistered X-ray CT of the phantom. The activity ratios of these ROIs were derived both with the LS-ROI method and with conventional SPECT EM reconstruction (EM-SPECT). Moreover, the two methods were compared in seven patients with motor symptoms who were examined with N-3-fluoropropyl-2-{beta}-carboxymethoxy-3-{beta}-(4-iodophenyl) (FP-CIT) SPECT, calculating the binding potential (BP). In the phantom study, the activity ratios obtained with EM-SPECT were 3.5, 5.3 and 17.0, respectively, whereas the LS-ROI method resulted in ratios of 6.2, 9.0 and 27.3, respectively. With the LS-ROI method, the BP in the seven patients was approximately 60% higher than with EM-SPECT; a linear correlation between the LS-ROI and the EM estimates was found (r = 0.98, p = 0.03). The LS-ROI PVE correction capability is mainly due to the fact that the ill-conditioning of the LS-ROI approach is lower than that of the EM-SPECT one. The LS-ROI seems to be feasible and accurate in the examination of the dopaminergic system. This approach can be fruitful in monitoring of disease progression and in clinical trials of dopaminergic drugs. (orig.)

Measuring the ROI on Knowledge Management Systems.

Science.gov (United States)

Wickhorst, Vickie

2002-01-01

Defines knowledge management and corporate portals and provides a model that can be applied to assessing return on investment (ROI) for a knowledge management solution. Highlights include leveraging knowledge in an organization; assessing the value of human capital; and the Intellectual Capital Performance Measurement Model. (LRW)

ROI en medios sociales: campañas de marketing en bibliotecas

OpenAIRE

González-Fernández-Villavicencio, Nieves

2015-01-01

Social media marketing must be a part of a digital marketing plan. Although marketing traditionally has been associated with obtaining an economic ROI (return on investment), it also can be measured in terms of social ROI (return on influence, return on relationships, reputation, branding, etc.). This study addresses the use of digital marketing campaigns by libraries for social profitability. Concepts related to digital marketing and social media marketing, and the way different types of org...

Automated PET-only quantification of amyloid deposition with adaptive template and empirically pre-defined ROI

Science.gov (United States)

Akamatsu, G.; Ikari, Y.; Ohnishi, A.; Nishida, H.; Aita, K.; Sasaki, M.; Yamamoto, Y.; Sasaki, M.; Senda, M.

2016-08-01

Amyloid PET is useful for early and/or differential diagnosis of Alzheimer’s disease (AD). Quantification of amyloid deposition using PET has been employed to improve diagnosis and to monitor AD therapy, particularly in research. Although MRI is often used for segmentation of gray matter and for spatial normalization into standard Montreal Neurological Institute (MNI) space where region-of-interest (ROI) template is defined, 3D MRI is not always available in clinical practice. The purpose of this study was to examine the feasibility of PET-only amyloid quantification with an adaptive template and a pre-defined standard ROI template that has been empirically generated from typical cases. A total of 68 subjects who underwent brain 11C-PiB PET were examined. The 11C-PiB images were non-linearly spatially normalized to the standard MNI T1 atlas using the same transformation parameters of MRI-based normalization. The automatic-anatomical-labeling-ROI (AAL-ROI) template was applied to the PET images. All voxel values were normalized by the mean value of cerebellar cortex to generate the SUVR-scaled images. Eleven typical positive images and eight typical negative images were normalized and averaged, respectively, and were used as the positive and negative template. Positive and negative masks which consist of voxels with SUVR  ⩾1.7 were extracted from both templates. Empirical PiB-prone ROI (EPP-ROI) was generated by subtracting the negative mask from the positive mask. The 11C-PiB image of each subject was non-rigidly normalized to the positive and negative template, respectively, and the one with higher cross-correlation was adopted. The EPP-ROI was then inversely transformed to individual PET images. We evaluated differences of SUVR between standard MRI-based method and PET-only method. We additionally evaluated whether the PET-only method would correctly categorize 11C-PiB scans as positive or negative. Significant correlation was observed between the SUVRs

Return on investment. What is ROI and how to use it.

Science.gov (United States)

Cotter, Steve

2014-08-01

Formulated and interpreted correctly, ROI tools and techniques can be very useful for EMS managers when evaluating various competing projects and initiatives within the organization. More so, decision makers and elected bodies responsible for approving the financial support of these initiatives are demanding that they be presented with a more complete picture of the return for any dollars allocated under ever-tightening financial considerations that all organizations face today. ROI can be a powerful tool in supporting your organization when competing for limited dollars.

The hands-on project office guaranteeing ROI and on-time delivery

CERN Document Server

Kesner, Richard M

2003-01-01

THE THREE PILLARS OF IT DELIVERY - PROBLEM RESOLUTION, SERVICE REQUESTS, AND PROJECTSIntroduction The Business Context The Internal Economy for Investing in IT Services and ProjectsThe Three Pillars of IT Delivery Managing Service DeliveryManaging Project Commitments IT Metrics and Reporting Tools THE PROJECT MANAGEMENT OFFICE BUSINESS MODELIntroduction: Revisiting the IT Organization IT Service and Project Delivery RolesThe Role of the Project Management Office: Measuring its ROI The PMO Value Proposition: An Initial ROI Estimate ALIGNMENT AND PLANNING - DOING THE RIGHT THINGS Introduction Ge

Application of a semi-automatic ROI setting system for brain PET images to animal PET studies

International Nuclear Information System (INIS)

Kuge, Yuji; Akai, Nobuo; Tamura, Koji

1998-01-01

ProASSIST, a semi-automatic ROI (region of interest) setting system for human brain PET images, has been modified for use with the canine brain, and the performance of the obtained system was evaluated by comparing the operational simplicity for ROI setting and the consistency of ROI values obtained with those by a conventional manual procedure. Namely, we created segment maps for the canine brain by making reference to the coronal section atlas of the canine brain by Lim et al., and incorporated them into the ProASSIST system. For the performance test, CBF (cerebral blood flow) and CMRglc (cerebral metabolic rate in glucose) images in dogs with or without focal cerebral ischemia were used. In ProASSIST, brain contours were defined semiautomatically. In the ROI analysis of the test image, manual modification of the contour was necessary in half cases examined (8/16). However, the operation was rather simple so that the operation time per one brain section was significantly shorter than that in the manual operation. The ROI values determined by the system were comparable with those by the manual procedure, confirming the applicability of the system to these animal studies. The use of the system like the present one would also merit the more objective data acquisition for the quantitative ROI analysis, because no manual procedure except for some specifications of the anatomical features is required for ROI setting. (author)

Effects of ROI definition and reconstruction method on quantitative outcome and applicability in a response monitoring trial

International Nuclear Information System (INIS)

Krak, Nanda C.; Boellaard, R.; Hoekstra, Otto S.; Hoekstra, Corneline J.; Twisk, Jos W.R.; Lammertsma, Adriaan A.

2005-01-01

Quantitative measurement of tracer uptake in a tumour can be influenced by a number of factors, including the method of defining regions of interest (ROIs) and the reconstruction parameters used. The main purpose of this study was to determine the effects of different ROI methods on quantitative outcome, using two reconstruction methods and the standard uptake value (SUV) as a simple quantitative measure of FDG uptake. Four commonly used methods of ROI definition (manual placement, fixed dimensions, threshold based and maximum pixel value) were used to calculate SUV (SUV [MAN] , SUV 15 mm , SUV 50 , SUV 75 and SUV max , respectively) and to generate ''metabolic'' tumour volumes. Test-retest reproducibility of SUVs and of ''metabolic'' tumour volumes and the applicability of ROI methods during chemotherapy were assessed. In addition, SUVs calculated on ordered subsets expectation maximisation (OSEM) and filtered back-projection (FBP) images were compared. ROI definition had a direct effect on quantitative outcome. On average, SUV [MAN] , SUV 15 mm , SUV 50 and SUV 75 , were respectively 48%, 27%, 34% and 15% lower than SUV max when calculated on OSEM images. No statistically significant differences were found between SUVs calculated on OSEM and FBP reconstructed images. Highest reproducibility was found for SUV 15 mm and SUV [MAN] (ICC 0.95 and 0.94, respectively) and for ''metabolic'' volumes measured with the manual and 50% threshold ROIs (ICC 0.99 for both). Manual, 75% threshold and maximum pixel ROIs could be used throughout therapy, regardless of changes in tumour uptake or geometry. SUVs showed the same trend in relative change in FDG uptake after chemotherapy, irrespective of the ROI method used. The method of ROI definition has a direct influence on quantitative outcome. In terms of simplicity, user-independence, reproducibility and general applicability the threshold-based and fixed dimension methods are the best ROI methods. Threshold methods are in

What's the ROI for resolving the nursing faculty shortage?

Science.gov (United States)

Kowalski, Karren; Kelley, Brian M

2013-01-01

The nursing faculty shortage will have a fundamental impact on the ability to produce nurses. For most nursing schools and states, however, concerns about the relative merits of different solutions to the nursing faculty shortage are misplaced. Without significantly increased visibility and definition, accompanied by a clear public, private, and health care organization return on investment (ROI), proposing solutions to the nursing faculty shortage is at best premature and at worst irrelevant. There is simply too much competition for resources to expect that a vaguely defined and invisible problem with no rationale for increased investment will receive sufficient support from critical decision makers and constituencies. First must come problem definition, visibility, and ROI. Only then can the case be made for implementing solutions to the nursing faculty shortage.

Oil palm fresh fruit bunch ripeness classification based on rule- based expert system of ROI image processing technique results

International Nuclear Information System (INIS)

Alfatni, M S M; Shariff, A R M; Marhaban, M H; Shafie, S B; Saaed, O M B; Abdullah, M Z; BAmiruddin, M D

2014-01-01

There is a processing need for a fast, easy and accurate classification system for oil palm fruit ripeness. Such a system will be invaluable to farmers and plantation managers who need to sell their oil palm fresh fruit bunch (FFB) for the mill as this will avoid disputes. In this paper,a new approach was developed under the name of expert rules-based systembased on the image processing techniques results of thethree different oil palm FFB region of interests (ROIs), namely; ROI1 (300x300 pixels), ROI2 (50x50 pixels) and ROI3 (100x100 pixels). The results show that the best rule-based ROIs for statistical colour feature extraction with k-nearest neighbors (KNN) classifier at 94% were chosen as well as the ROIs that indicated results higher than the rule-based outcome, such as the ROIs of statistical colour feature extraction with artificial neural network (ANN) classifier at 94%, were selected for further FFB ripeness inspection system

Examining Brain Morphometry Associated with Self-Esteem in Young Adults Using Multilevel-ROI-Features-Based Classification Method

Directory of Open Access Journals (Sweden)

Bo Peng

2017-05-01

Full Text Available Purpose: This study is to exam self-esteem related brain morphometry on brain magnetic resonance (MR images using multilevel-features-based classification method.Method: The multilevel region of interest (ROI features consist of two types of features: (i ROI features, which include gray matter volume, white matter volume, cerebrospinal fluid volume, cortical thickness, and cortical surface area, and (ii similarity features, which are based on similarity calculation of cortical thickness between ROIs. For each feature type, a hybrid feature selection method, comprising of filter-based and wrapper-based algorithms, is used to select the most discriminating features. ROI features and similarity features are integrated by using multi-kernel support vector machines (SVMs with appropriate weighting factor.Results: The classification performance is improved by using multilevel ROI features with an accuracy of 96.66%, a specificity of 96.62%, and a sensitivity of 95.67%. The most discriminating ROI features that are related to self-esteem spread over occipital lobe, frontal lobe, parietal lobe, limbic lobe, temporal lobe, and central region, mainly involving white matter and cortical thickness. The most discriminating similarity features are distributed in both the right and left hemisphere, including frontal lobe, occipital lobe, limbic lobe, parietal lobe, and central region, which conveys information of structural connections between different brain regions.Conclusion: By using ROI features and similarity features to exam self-esteem related brain morphometry, this paper provides a pilot evidence that self-esteem is linked to specific ROIs and structural connections between different brain regions.

Attention to detail helps Clarian measure ROI.

Science.gov (United States)

2007-01-01

Clarian Health takes a risk and embarks on a branding strategy. Taking a multi-integrated approach, with The Heavy Weights in Indianapolis, Clarian started managing its marketing by tracking return on investment (ROI) and making the most of a CRM database. In a groundbreaking approach, it found that it was actually able to turn its marketing effort into a money-maker, leading higher-ups to see its outreach efforts as necessity.

Influence of ROI selection on Resting Functional Connectivity: An Individualized Approach for Resting fMRI Analysis

Directory of Open Access Journals (Sweden)

William Seunghyun Sohn

2015-08-01

Full Text Available The differences in how our brain is connected are often thought to reflect the differences in our individual personalities and cognitive abilities. Individual differences in brain connectivity has long been recognized in the neuroscience community however it has yet to manifest itself in the methodology of resting state analysis. This is evident as previous studies use the same region of interest (ROIs for all subjects. In this paper we demonstrate that the use of ROIs which are standardized across individuals leads to inaccurate calculations of functional connectivity. We also show that this problem can be addressed by taking an individualized approach by using subject-specific ROIs. Finally we show that ROI selection can affect the way we interpret our data by showing different changes in functional connectivity with ageing.

Low-Cost Small Satellite Atmospheric Rotating Solar Occultation Imager (ROI)

Data.gov (United States)

National Aeronautics and Space Administration — Utilizing a unique, new occultation technique involving imaging, the ROI concept will meet or exceed the quality of SAGE measurements at a small fraction of the...

A multilevel-ROI-features-based machine learning method for detection of morphometric biomarkers in Parkinson's disease.

Science.gov (United States)

Peng, Bo; Wang, Suhong; Zhou, Zhiyong; Liu, Yan; Tong, Baotong; Zhang, Tao; Dai, Yakang

2017-06-09

Machine learning methods have been widely used in recent years for detection of neuroimaging biomarkers in regions of interest (ROIs) and assisting diagnosis of neurodegenerative diseases. The innovation of this study is to use multilevel-ROI-features-based machine learning method to detect sensitive morphometric biomarkers in Parkinson's disease (PD). Specifically, the low-level ROI features (gray matter volume, cortical thickness, etc.) and high-level correlative features (connectivity between ROIs) are integrated to construct the multilevel ROI features. Filter- and wrapper- based feature selection method and multi-kernel support vector machine (SVM) are used in the classification algorithm. T1-weighted brain magnetic resonance (MR) images of 69 PD patients and 103 normal controls from the Parkinson's Progression Markers Initiative (PPMI) dataset are included in the study. The machine learning method performs well in classification between PD patients and normal controls with an accuracy of 85.78%, a specificity of 87.79%, and a sensitivity of 87.64%. The most sensitive biomarkers between PD patients and normal controls are mainly distributed in frontal lobe, parental lobe, limbic lobe, temporal lobe, and central region. The classification performance of our method with multilevel ROI features is significantly improved comparing with other classification methods using single-level features. The proposed method shows promising identification ability for detecting morphometric biomarkers in PD, thus confirming the potentiality of our method in assisting diagnosis of the disease. Copyright © 2017 Elsevier B.V. All rights reserved.

Cloud computing and ROI a new framework for it strategy

CERN Document Server

Mohapatra, Sanjay

2014-01-01

This book develops an IT strategy for cloud computing that helps businesses evaluate their readiness for cloud services and calculate the ROI. The framework provided helps reduce risks involved in transitioning from traditional "on site" IT strategy to virtual "cloud computing." Since the advent of cloud computing, many organizations have made substantial gains implementing this innovation. Cloud computing allows companies to focus more on their core competencies, as IT enablement is taken care of through cloud services. Cloud Computing and ROI includes case studies covering retail, automobile and food processing industries. Each of these case studies have successfully implemented the cloud computing framework and their strategies are explained. As cloud computing may not be ideal for all businesses, criteria?are also offered to help determine if this strategy should be adopt.

Region-of-interest analyses of one-dimensional biomechanical trajectories: bridging 0D and 1D theory, augmenting statistical power

Directory of Open Access Journals (Sweden)

Todd C. Pataky

2016-11-01

Full Text Available One-dimensional (1D kinematic, force, and EMG trajectories are often analyzed using zero-dimensional (0D metrics like local extrema. Recently whole-trajectory 1D methods have emerged in the literature as alternatives. Since 0D and 1D methods can yield qualitatively different results, the two approaches may appear to be theoretically distinct. The purposes of this paper were (a to clarify that 0D and 1D approaches are actually just special cases of a more general region-of-interest (ROI analysis framework, and (b to demonstrate how ROIs can augment statistical power. We first simulated millions of smooth, random 1D datasets to validate theoretical predictions of the 0D, 1D and ROI approaches and to emphasize how ROIs provide a continuous bridge between 0D and 1D results. We then analyzed a variety of public datasets to demonstrate potential effects of ROIs on biomechanical conclusions. Results showed, first, that a priori ROI particulars can qualitatively affect the biomechanical conclusions that emerge from analyses and, second, that ROIs derived from exploratory/pilot analyses can detect smaller biomechanical effects than are detectable using full 1D methods. We recommend regarding ROIs, like data filtering particulars and Type I error rate, as parameters which can affect hypothesis testing results, and thus as sensitivity analysis tools to ensure arbitrary decisions do not influence scientific interpretations. Last, we describe open-source Python and MATLAB implementations of 1D ROI analysis for arbitrary experimental designs ranging from one-sample t tests to MANOVA.

Ludwig, un roi sur la lune : l’histoire d’un roi fou jouée par des comédien.ne.s en situation de handicap mental

Directory of Open Access Journals (Sweden)

Marie Astier

2017-12-01

Full Text Available Ludwig, un roi sur la lune, spectacle mis en scène par Madeleine Louarn avec les comédien.ne.s professionnels en situation de handicap mental de l’Atelier Catalyse et présenté lors de la dernière édition du Festival d’Avignon n’est pas une reconstitution historique de la vie de Louis II de Bavière, roi du XIXe siècle diagnostiqué paranoïaque et destitué pour être interné, mais une tentative de transcrire théâtralement la perception du monde d’un homme amoureux de l’Art, de la nature et des hommes, mais qui devait être Roi. Ce n’est ni un personnage ni des comédien.ne.s « handicapé.e.s » que nous sommes invités à voir, mais les visions de Ludwig incarnées par des comédien.ne.s qui se trouvent être en situation de handicap mental. Dans ce spectacle, la « folie » devenue plus tard « handicap mental » apparaît sous les traits de la non-conformité bien plus que sous ceux de la pathologie.

Computerized analysis of mammographic parenchymal patterns for assessing breast cancer risk: Effect of ROI size and location

International Nuclear Information System (INIS)

Li Hui; Giger, Maryellen L.; Huo Zhimin; Olopade, Olufunmilayo I.; Lan Li; Weber, Barbara L.; Bonta, Ioana

2004-01-01

The long-term goal of our research is to develop computerized radiographic markers for assessing breast density and parenchymal patterns that may be used together with clinical measures for determining the risk of breast cancer and assessing the response to preventive treatment. In our earlier studies, we found that women at high risk tended to have dense breasts with mammographic patterns that were coarse and low in contrast. With our method, computerized texture analysis is performed on a region of interest (ROI) within the mammographic image. In our current study, we investigate the effect of ROI size and ROI location on the computerized texture features obtained from 90 subjects (30 BRCA1/BRCA2 gene-mutation carriers and 60 age-matched women deemed to be at low risk for breast cancer). Mammograms were digitized at 0.1 mm pixel size and various ROI sizes were extracted from different breast regions in the craniocaudal (CC) view. Seventeen features, which characterize the density and texture of the parenchymal patterns, were extracted from the ROIs on these digitized mammograms. Stepwise feature selection and linear discriminant analysis were applied to identify features that differentiate between the low-risk women and the BRCA1/BRCA2 gene-mutation carriers. ROC analysis was used to assess the performance of the features in the task of distinguishing between these two groups. Our results show that there was a statistically significant decrease in the performance of the computerized texture features, as the ROI location was varied from the central region behind the nipple. However, we failed to show a statistically significant decrease in the performance of the computerized texture features with decreasing ROI size for the range studied

Diffusion-weighted magnetic resonance imaging in the characterization of testicular germ cell neoplasms: Effect of ROI methods on apparent diffusion coefficient values and interobserver variability

Energy Technology Data Exchange (ETDEWEB)

Tsili, Athina C., E-mail: a_tsili@yahoo.gr [Department of Clinical Radiology, Medical School, University of Ioannina, University Campus, 45110, Ioannina (Greece); Ntorkou, Alexandra, E-mail: alexdorkou@hotmail.com [Department of Clinical Radiology, Medical School, University of Ioannina, University Campus, 45110, Ioannina (Greece); Astrakas, Loukas, E-mail: astrakas@uoi.gr [Department of Medical Physics, Medical School, University of Ioannina, University Campus, 45110, Ioannina (Greece); Xydis, Vasilis, E-mail: vxydis@cc.uoi.gr [Department of Clinical Radiology, Medical School, University of Ioannina, University Campus, 45110, Ioannina (Greece); Tsampalas, Stavros, E-mail: stamp@gmail.com [Department of Urology, Medical School, University of Ioannina, University Campus, 45110, Ioannina (Greece); Sofikitis, Nikolaos, E-mail: akrosnin@hotmail.com [Department of Urology, Medical School, University of Ioannina, University Campus, 45110, Ioannina (Greece); Argyropoulou, Maria I., E-mail: margyrop@cc.uoi.gr [Department of Clinical Radiology, Medical School, University of Ioannina, University Campus, 45110, Ioannina (Greece)

2017-04-15

Highlights: • Seminomas have lower mean ADC compared to NSGCNs. • Round ROI is accurate in characterizing TGCNS. • ROI shape has no significant effect on interobserver variability. - Abstract: Introduction: To evaluate the difference in apparent diffusion coefficient (ADC) measurements at diffusion-weighted (DW) magnetic resonance imaging of differently shaped regions-of-interest (ROIs) in testicular germ cell neoplasms (TGCNS), the diagnostic ability of differently shaped ROIs in differentiating seminomas from nonseminomatous germ cell neoplasms (NSGCNs) and the interobserver variability. Materials and methods: Thirty-three TGCNs were retrospectively evaluated. Patients underwent MR examinations, including DWI on a 1.5-T MR system. Two observers measured mean tumor ADCs using four distinct ROI methods: round, square, freehand and multiple small, round ROIs. The interclass correlation coefficient was analyzed to assess interobserver variability. Statistical analysis was used to compare mean ADC measurements among observers, methods and histologic types. Results: All ROI methods showed excellent interobserver agreement, with excellent correlation (P < 0.001). Multiple, small ROIs provided the lower mean ADC in TGCNs. Seminomas had lower mean ADC compared to NSGCNs for each ROI method (P < 0.001). Round ROI proved the most accurate method in characterizing TGCNS. Conclusion: Interobserver variability in ADC measurement is excellent, irrespective of the ROI shape. Multiple, small round ROIs and round ROI proved the more accurate methods for ADC measurement in the characterization of TGCNs and in the differentiation between seminomas and NSGCNs, respectively.

Single-shot full resolution region-of-interest (ROI) reconstruction in image plane digital holographic microscopy

Science.gov (United States)

Singh, Mandeep; Khare, Kedar

2018-05-01

We describe a numerical processing technique that allows single-shot region-of-interest (ROI) reconstruction in image plane digital holographic microscopy with full pixel resolution. The ROI reconstruction is modelled as an optimization problem where the cost function to be minimized consists of an L2-norm squared data fitting term and a modified Huber penalty term that are minimized alternately in an adaptive fashion. The technique can provide full pixel resolution complex-valued images of the selected ROI which is not possible to achieve with the commonly used Fourier transform method. The technique can facilitate holographic reconstruction of individual cells of interest from a large field-of-view digital holographic microscopy data. The complementary phase information in addition to the usual absorption information already available in the form of bright field microscopy can make the methodology attractive to the biomedical user community.

Radiologic-pathologic analysis of quantitative 3D tumour enhancement on contrast-enhanced MR imaging: a study of ROI placement

International Nuclear Information System (INIS)

Chockalingam, Arun; Duran, Rafael; Sohn, Jae Ho; Schernthaner, Ruediger; Chapiro, Julius; Lee, Howard; Sahu, Sonia; Nguyen, Sonny; Geschwind, Jean-Francois; Lin, MingDe

2016-01-01

To investigate the influence of region-of-interest (ROI) placement on 3D tumour enhancement [Quantitative European Association for the Study of the Liver (qEASL)] in hepatocellular carcinoma (HCC) patients treated with transcatheter arterial chemoembolization (TACE). Phase 1: 40 HCC patients had nine ROIs placed by one reader using systematic techniques (3 ipsilateral to the lesion, 3 contralateral to the lesion, and 3 dispersed throughout the liver) and qEASL variance was measured. Intra-class correlations were computed. Phase 2: 15 HCC patients with histosegmentation were selected. Six ROIs were systematically placed by AC (3 ROIs ipsilateral and 3 ROIs contralateral to the lesion). Three ROIs were placed by 2 radiologists. qEASL values were compared to histopathology by Pearson's correlation, linear regression, and median difference. Phase 1: The dispersed method (abandoned in phase 2) had low consistency and high variance. Phase 2: qEASL correlated strongly with pathology in systematic methods [Pearson's correlation coefficient = 0.886 (ipsilateral) and 0.727 (contralateral)] and in clinical methods (0.625 and 0.879). However, ipsilateral placement matched best with pathology (median difference: 5.4 %; correlation: 0.89; regression CI: [0.904, 0.1409]). qEASL is a robust method with comparable values among tested placements. Ipsilateral placement showed high consistency and better pathological correlation. (orig.)

The Study on Bone Mineral Density Measurement Error in Accordance with Change in ROI by Utilizing Dual Energy X-ray Absorptiometry

Energy Technology Data Exchange (ETDEWEB)

Lee, Yun Hong [Dept. of Diagnostic Radiology, Korea University Guro Hospital, Seoul (Korea, Republic of); Lee, In Ja [Dept. of Radiological Technology, Dongnam Health College, Suwon (Korea, Republic of); Yong, Hyung Jin [Dept. of Medicine Physics, The Graduate School of Biomedical Science Korea University, Seoul (Korea, Republic of)

2012-03-15

Dual Energy X-ray Absorptiometry(DEXA) is commonly used to diagnose Osteoporosis. The errors of DEXA bone density operation are caused by operator, bone mineral density meter, blood testing, patient. We focus on operator error then study about how much influence operator's region of intest(ROI) in bone testing result. During from March to July in 2011. 50 patients ware selected respectively from 30, 40, 50, 60, and 70 age groups who came to Korea University Medical Center(KUMC) for their Osteoporosis treatment. A-test was performed with usually ROI and B-test was performed with most widely ROI. Then, We compare A-test and B-test for find maximum difference of T-score error which occurred operator ROI controlling. Standard deviation of T-score of B-test showed 0.1 higher then A-test in femur neck. Standard deviation of B-test showed 0.2 higher then A-test in Ward's area which in Greater trocanter and Inter trocanter. Standard deviation of B-test showed 0,1 lower then A-test in L-1. Bone density testing about Two hundred patients results are as follow. When operator ROI was changed wider than normal ROI, bone density of femur was measured more higher but bone density of L-spine was measured more lower then normal bone density. That means, sometime DEXA bone density testing result is dependent by operator ROI controlling. This is relevant with the patient's medicine and health insurance, thus, tester always keep the size of ROI for to prevent any problem in the patient.

Language pathway tracking: comparing nTMS-based DTI fiber tracking with a cubic ROIs-based protocol.

Science.gov (United States)

Negwer, Chiara; Sollmann, Nico; Ille, Sebastian; Hauck, Theresa; Maurer, Stefanie; Kirschke, Jan S; Ringel, Florian; Meyer, Bernhard; Krieg, Sandro M

2017-03-01

OBJECTIVE Diffusion tensor imaging (DTI) fiber tracking (FT) has been widely used in glioma surgery in recent years. It can provide helpful information about subcortical structures, especially in patients with eloquent space-occupying lesions. This study compared the newly developed navigated transcranial magnetic stimulation (nTMS)-based DTI FT of language pathways with the most reproducible protocol for language pathway tractography, using cubic regions of interest (ROIs) for the arcuate fascicle. METHODS Thirty-seven patients with left-sided perisylvian lesions underwent language mapping by repetitive nTMS. DTI FT was performed using the cubic ROIs-based protocol and the authors' nTMS-based DTI FT approach. The same minimal fiber length and fractional anisotropy were chosen (50 mm and 0.2, respectively). Both protocols were performed with standard clinical tractography software. RESULTS Both methods visualized language-related fiber tracts (i.e., corticonuclear tract, arcuate fascicle, uncinate fascicle, superior longitudinal fascicle, inferior longitudinal fascicle, arcuate fibers, commissural fibers, corticothalamic fibers, and frontooccipital fascicle) in all 37 patients. Using the cubic ROIs-based protocol, 39.9% of these language-related fiber tracts were detected in the examined patients, as opposed to 76.0% when performing nTMS-based DTI FT. For specifically tracking the arcuate fascicle, however, the cubic ROIs-based approach showed better results (97.3% vs 75.7% with nTMS-based DTI FT). CONCLUSIONS The cubic ROIs-based protocol was designed for arcuate fascicle tractography, and this study shows that it is still useful for this intention. However, superior results were obtained using the nTMS-based DTI FT for visualization of other language-related fiber tracts.

Aznar, Hanotin, and May (eds., À la place du roi. Vice-rois, gouverneurs et ambassadeurs dans les monarchies française et espanole (Casa de Velázquez, 2014

Directory of Open Access Journals (Sweden)

Lisandra Estevez

2016-06-01

Full Text Available The French and Spanish courts were two of the most powerful cultural and political institutions in seventeenth-century Europe.  Both rivals and allies, the French and Spanish crowns were bound by disputes and diplomacy.  This anthology examines the Gallic and Iberian court systems from a comparative approach, filling an important lacuna in early modern political studies and diplomatic history.  It is based on the proceedings of a seminar held at the Casa de Velázquez, Madrid in June 2010. Edited by Daniel Aznar, Guillaume Hanotin and Niels F. May, À la place du roi. Vice-rois, gouverneurs et ambassadeurs dans les monarchies française et espanole (XVIe-XVIIIe siècles unites ten essays by leading scholars of seventeenth-century French and Spanish history.

Safety of drinking water supplies to suburban Paris: analysis and control of radioactivity at Choisy-le-Roi

International Nuclear Information System (INIS)

Rapinat, M.; Philipot, J.M.; Cadet, J.L.

1990-01-01

The Syndicat des Eaux d'Ile de France and the Compagnie des Eaux have undertaken several stringent actions, to analyse and control radioactivity at Cholsy-le-Roi, 150 KM downstream from Nogent/s/Seine:- founding in 1985 a new laboratory branch for radioactivity measurement. - adding new elements to the existing alarm network (automatic analysis of the raw water quality). - studies for the treatability of radioelements. - using protected resources (ground water). -set up of a second treated water feeder between the river Seine and the river Marne areas. Others projects are under study, such as the creation of a raw water reservoir and increasing the capacity of treated water stockage. (author)

Maximizing ROI (return on information)

Energy Technology Data Exchange (ETDEWEB)

McDonald, B.

2000-05-01

The role and importance of managing information are discussed, underscoring the importance by quoting from the report of the International Data Corporation, according to which Fortune 500 companies lost $ 12 billion in 1999 due to inefficiencies resulting from intellectual re-work, substandard performance , and inability to find knowledge resources. The report predicts that this figure will rise to $ 31.5 billion by 2003. Key impediments to implementing knowledge management systems are identified as : the cost and human resources requirement of deployment; inflexibility of historical systems to adapt to change; and the difficulty of achieving corporate acceptance of inflexible software products that require changes in 'normal' ways of doing business. The author recommends the use of model, document and rule-independent systems with a document centered interface (DCI), employing rapid application development (RAD) and object technologies and visual model development, which eliminate these problems, making it possible for companies to maximize their return on information (ROI), and achieve substantial savings in implementation costs.

Data from the Roi Removal Project, West Hawaii, 2010-2011 (NODC Accession 0082197

Data.gov (United States)

National Oceanic and Atmospheric Administration, Department of Commerce — In situ observations of the introduced predatory grouper roi (Cephalopholis argus) were taken within the coral reef ecosystem of Puako, northwest side of the Island...

Efficient random access high resolution region-of-interest (ROI) image retrieval using backward coding of wavelet trees (BCWT)

Science.gov (United States)

Corona, Enrique; Nutter, Brian; Mitra, Sunanda; Guo, Jiangling; Karp, Tanja

2008-03-01

Efficient retrieval of high quality Regions-Of-Interest (ROI) from high resolution medical images is essential for reliable interpretation and accurate diagnosis. Random access to high quality ROI from codestreams is becoming an essential feature in many still image compression applications, particularly in viewing diseased areas from large medical images. This feature is easier to implement in block based codecs because of the inherent spatial independency of the code blocks. This independency implies that the decoding order of the blocks is unimportant as long as the position for each is properly identified. In contrast, wavelet-tree based codecs naturally use some interdependency that exploits the decaying spectrum model of the wavelet coefficients. Thus one must keep track of the decoding order from level to level with such codecs. We have developed an innovative multi-rate image subband coding scheme using "Backward Coding of Wavelet Trees (BCWT)" which is fast, memory efficient, and resolution scalable. It offers far less complexity than many other existing codecs including both, wavelet-tree, and block based algorithms. The ROI feature in BCWT is implemented through a transcoder stage that generates a new BCWT codestream containing only the information associated with the user-defined ROI. This paper presents an efficient technique that locates a particular ROI within the BCWT coded domain, and decodes it back to the spatial domain. This technique allows better access and proper identification of pathologies in high resolution images since only a small fraction of the codestream is required to be transmitted and analyzed.

Can state-of-the-art HVS-based objective image quality criteria be used for image reconstruction techniques based on ROI analysis?

Science.gov (United States)

Dostal, P.; Krasula, L.; Klima, M.

2012-06-01

Various image processing techniques in multimedia technology are optimized using visual attention feature of the human visual system. Spatial non-uniformity causes that different locations in an image are of different importance in terms of perception of the image. In other words, the perceived image quality depends mainly on the quality of important locations known as regions of interest. The performance of such techniques is measured by subjective evaluation or objective image quality criteria. Many state-of-the-art objective metrics are based on HVS properties; SSIM, MS-SSIM based on image structural information, VIF based on the information that human brain can ideally gain from the reference image or FSIM utilizing the low-level features to assign the different importance to each location in the image. But still none of these objective metrics utilize the analysis of regions of interest. We solve the question if these objective metrics can be used for effective evaluation of images reconstructed by processing techniques based on ROI analysis utilizing high-level features. In this paper authors show that the state-of-the-art objective metrics do not correlate well with subjective evaluation while the demosaicing based on ROI analysis is used for reconstruction. The ROI were computed from "ground truth" visual attention data. The algorithm combining two known demosaicing techniques on the basis of ROI location is proposed to reconstruct the ROI in fine quality while the rest of image is reconstructed with low quality. The color image reconstructed by this ROI approach was compared with selected demosaicing techniques by objective criteria and subjective testing. The qualitative comparison of the objective and subjective results indicates that the state-of-the-art objective metrics are still not suitable for evaluation image processing techniques based on ROI analysis and new criteria is demanded.

Feeding biology of the introduced fish roi, and its impact on Hawaiian reef fishes, January 2004 and January 2005, (NODC Accession 0002172)

Data.gov (United States)

National Oceanic and Atmospheric Administration, Department of Commerce — Feeding biology of the introduced fish roi (Cephalopholis argus), and its impact on Hawaiian reef fishes and fisheries between January 2004 and January 2005. Roi...

Usefulness of a three-dimensional stereotaxic ROI template on anatomically standardised {sup 99m}Tc-ECD SPET

Energy Technology Data Exchange (ETDEWEB)

Takeuchi, Ryo [Department of Internal Medicine, Division of Nuclear Medicine, Nishi-Kobe Medical Center, Kobe (Japan); Yonekura, Yoshiharu [Biomedical Imaging Research Center, Fukui Medical University, Fukui (Japan); Matsuda, Hiroshi [Department of Radiology, National Center Hospital for Mental, Tokyo (Japan); Konishi, Junji [Department of Nuclear Medicine and Diagnostic Imaging, Graduate School of Medicine, Kyoto University, Kyoto (Japan)

2002-03-01

We have constructed a three-dimensional stereotaxic ROI template (3DSRT) on anatomically standardised cerebral blood flow (CBF) single-photon emission tomography (SPET) images to objectively estimate regional CBF (rCBF). The 3DSRT is composed of 259 regions of interest (ROIs) in 11 segments (1, superior frontal; 2, middle and inferior frontal; 3, primary sensorimotor; 4, parietal; 5, angular; 6, temporal; 7, occipital; 8, pericallosal; 9, lenticular nucleus; 10, thalamus; 11, hippocampus) on each side. We measured the rCBF values of the 518 ROIs and calculated the area-weighted average (segmental CBF; sCBF) of the 22 segments based on the rCBF in each ROI. We compared vascular reserve before and after revascularisation surgery using sCBF on anatomically standardised resting and acetazolamide (Acz)-challenged CBF SPET images, which were obtained using an equal-volume-split dual-injection single-day protocol [resting and vascular reserve (RVR) method] in 13 patients who had not suffered any major stroke but did have significant cerebrovascular stenosis. Prior to the evaluation, we examined the sCBF values of 16 subjects with various cerebrovascular conditions (8, normal; 3, lacunar infarction; 2, chronic infarction; 2, meningioma; 1, aneurysm) using physiological saline instead of Acz (placebo study) in order to confirm the reproducibility of the RVR method. In the placebo study we observed excellent linearity (y=1.444+0.964x) between the 352 pairs of baseline (x) and post-placebo (y) sCBF values in the 16 subjects, irrespective of the segment location. In all of the 13 patients, estimation of sCBF demonstrated impaired vascular reserve pre-operatively and improved vascular reserve postoperatively. We conclude that the 3DSRT, which could be identically set on the anatomically standardised images obtained at baseline and after Acz injection, allowed objective assessment of the pre- and postoperative vascular reserve, which was not easy with conventional ROI settings

Les marbriers des Bâtiments du roi : organisation et réalisations

Directory of Open Access Journals (Sweden)

Sophie Mouquin

2012-09-01

Full Text Available Matériau noble, symbole de beauté, de pouvoir et d’éternité, le marbre est sous l’Ancien Régime, et particulièrement sous le règne de Louis XIV et la Régence, un matériau royal. Toutes les maisons royales reçoivent pavements, lambris et cheminées réalisés dans des marbres aux couleurs vives, provenant pour la plupart de carrières du royaume. Leur origine répond ainsi à la politique royale du marbre français que les directeurs des Bâtiments du roi s’efforcent de mettre en place et de consolider. Tous ces travaux ont leurs artisans : Derbais, Dezègre, Pasquier, Ménard, Mathaut, Lisquy, Tarlé, Trouard, etc., autant de noms indissociables des réalisations marbrières dans les maisons royales, mais si souvent oubliés. Ils jouent pourtant, dans ce domaine, un rôle de premier plan à tous niveaux, de la carrière au chantier. L’exposé présente l’organisation de ce corps de métier, sa place au sein des Bâtiments du roi et son rôle dans la politique marbrière. Il s’appuie sur les principales réalisations versaillaises, comme l’appartement des bains, l’escalier des Ambassadeurs, l’escalier de la Reine, la galerie des Glaces, le salon d’Hercule, les cheminées et les lambris des appartements du Roi et de la Reine. Il évoquera le chantier des jardins avec le bosquet de la Colonnade et d’autres bosquets.

In situ study of the impact of inter- and intra-reader variability on region of interest (ROI) analysis in preclinical molecular imaging.

Science.gov (United States)

Habte, Frezghi; Budhiraja, Shradha; Keren, Shay; Doyle, Timothy C; Levin, Craig S; Paik, David S

2013-01-01

We estimated reader-dependent variability of region of interest (ROI) analysis and evaluated its impact on preclinical quantitative molecular imaging. To estimate reader variability, we used five independent image datasets acquired each using microPET and multispectral fluorescence imaging (MSFI). We also selected ten experienced researchers who utilize molecular imaging in the same environment that they typically perform their own studies. Nine investigators blinded to the data type completed the ROI analysis by drawing ROIs manually that delineate the tumor regions to the best of their knowledge and repeated the measurements three times, non-consecutively. Extracted mean intensities of voxels within each ROI are used to compute the coefficient of variation (CV) and characterize the inter- and intra-reader variability. The impact of variability was assessed through random samples iterated from normal distributions for control and experimental groups on hypothesis testing and computing statistical power by varying subject size, measured difference between groups and CV. The results indicate that inter-reader variability was 22.5% for microPET and 72.2% for MSFI. Additionally, mean intra-reader variability was 10.1% for microPET and 26.4% for MSFI. Repeated statistical testing showed that a total variability of CV variability has been observed mainly due to differences in the ROI placement and geometry drawn between readers, which may adversely affect statistical power and erroneously lead to negative study outcomes.

Land-use change and managed aquifer recharge effects on the hydrogeochemistry of two contrasting atoll island aquifers, Roi-Namur Island, Republic of the Marshall Islands

Science.gov (United States)

Hejazian, Mehrdad; Gurdak, Jason J.; Swarzenski, Peter W.; Odigie, Kingsley; Storlazzi, Curt

2017-01-01

Freshwater resources on low-lying atoll islands are highly vulnerable to climate change and sea-level rise. In addition to rainwater catchment, groundwater in the freshwater lens is a critically important water resource on many atoll islands, especially during drought. Although many atolls have high annual rainfall rates, dense natural vegetation and high evapotranspiration rates can limit recharge to the freshwater lens. Here we evaluate the effects of land-use/land-cover change and managed aquifer recharge on the hydrogeochemistry and supply of groundwater on Roi-Namur Island, Republic of the Marshall Islands. Roi-Namur is an artificially conjoined island that has similar hydrogeology on the Roi and Namur lobes, but has contrasting land-use/land-cover and managed aquifer recharge only on Roi. Vegetation removal and managed aquifer recharge operations have resulted in an estimated 8.6 x 105 m3 of potable groundwater in the freshwater lens on Roi, compared to only 1.6 x 104 m3 on Namur. We use groundwater samples from a suite of 33 vertically nested monitoring wells, statistical testing, and geochemical modeling using PHREEQC to show that the differences in land-use/land-cover and managed aquifer recharge on Roi and Namur have a statistically significant effect on several groundwater-quality parameters and the controlling geochemical processes. Results also indicate a seven-fold reduction in the dissolution of carbonate rock in the freshwater lens and overlying vadose zone of Roi compared to Namur. Mixing of seawater and the freshwater lens is a more dominant hydrogeochemical process on Roi because of the greater recharge and flushing of the aquifer with freshwater as compared to Namur. In contrast, equilibrium processes and dissolution-precipitation non-equilibrium reactions are more dominant on Namur because of the longer residence times relative to the rate of geochemical reactions. Findings from Roi-Namur Island support selective land-use/land-cover change and

Land-use change and managed aquifer recharge effects on the hydrogeochemistry of two contrasting atoll island aquifers, Roi-Namur Island, Republic of the Marshall Islands

International Nuclear Information System (INIS)

Hejazian, Mehrdad; Gurdak, Jason J.; Swarzenski, Peter; Odigie, Kingsley O.; Storlazzi, Curt D.

2017-01-01

Freshwater resources on low-lying atoll islands are highly vulnerable to climate change and sea-level rise. In addition to rainwater catchment, groundwater in the freshwater lens is a critically important water resource on many atoll islands, especially during drought. Although many atolls have high annual rainfall rates, dense natural vegetation and high evapotranspiration rates can limit recharge to the freshwater lens. Here we evaluate the effects of land-use/land-cover change and managed aquifer recharge on the hydrogeochemistry and supply of groundwater on Roi-Namur Island, Republic of the Marshall Islands. Roi-Namur is an artificially conjoined island that has similar hydrogeology on the Roi and Namur lobes, but has contrasting land-use/land-cover and managed aquifer recharge only on Roi. Vegetation removal and managed aquifer recharge operations have resulted in an estimated 8.6 × 10"5 m"3 of potable groundwater in the freshwater lens on Roi, compared to only 1.6 × 10"4 m"3 on Namur. We use groundwater samples from a suite of 33 vertically nested monitoring wells, statistical testing, and geochemical modeling using PHREEQC to show that the differences in land-use/land-cover and managed aquifer recharge on Roi and Namur have a statistically significant effect on several groundwater-quality parameters and the controlling geochemical processes. Results also indicate a six-fold reduction in the dissolution of carbonate rock in the freshwater lens and overlying vadose zone of Roi compared to Namur. Mixing of seawater and the freshwater lens is a more dominant hydrogeochemical process on Roi because of the greater recharge and flushing of the aquifer with freshwater as compared to Namur. In contrast, equilibrium processes and dissolution-precipitation non-equilibrium reactions are more dominant on Namur because of the longer residence times relative to the rate of geochemical reactions. Findings from Roi-Namur Island support selective land

Roi Detection and Vessel Segmentation in Retinal Image

Science.gov (United States)

Sabaz, F.; Atila, U.

2017-11-01

Diabetes disrupts work by affecting the structure of the eye and afterwards leads to loss of vision. Depending on the stage of disease that called diabetic retinopathy, there are sudden loss of vision and blurred vision problems. Automated detection of vessels in retinal images is a useful study to diagnose eye diseases, disease classification and other clinical trials. The shape and structure of the vessels give information about the severity of the disease and the stage of the disease. Automatic and fast detection of vessels allows for a quick diagnosis of the disease and the treatment process to start shortly. ROI detection and vessel extraction methods for retinal image are mentioned in this study. It is shown that the Frangi filter used in image processing can be successfully used in detection and extraction of vessels.

A comparison between the conventional manual ROI method and an automatic algorithm for semiquantitative analysis of SPECT studies

International Nuclear Information System (INIS)

Pagan, L; Novi, B; Guidarelli, G; Tranfaglia, C; Galli, S; Lucchi, G; Fagioli, G

2011-01-01

In this study, the performance of a free software for automatic segmentation of striatal SPECT brain studies (BasGanV2 - www.aimn.it) and a standard manual Region Of Interest (ROI) method were compared. The anthropomorphic Alderson RSD phantom, filled with solutions at different concentration of 123 I-FP-CIT with Caudate-Putamen to Background ratios between 1 and 8.7 and Caudate to Putamen ratios between 1 and 2, was imaged on a Philips-Irix triple head gamma camera. Images were reconstructed using filtered back-projection and processed with both BasGanV2, that provides normalized striatal uptake values on volumetric anatomical ROIs, and a manual method, based on average counts per voxel in ROIs drawn in a three-slice section. Caudate-Putamen/Background and Caudate/Putamen ratios obtained with the two methods were compared with true experimental ratios. Good correlation was found for each method; BasGanV2, however, has higher R index (BasGan R mean = 0.95, p mean = 0.89, p 123 I-FP-CIT SPECT data with, moreover, the advantage of the availability of a control subject's database.

ROI DETECTION AND VESSEL SEGMENTATION IN RETINAL IMAGE

Directory of Open Access Journals (Sweden)

F. Sabaz

2017-11-01

Full Text Available Diabetes disrupts work by affecting the structure of the eye and afterwards leads to loss of vision. Depending on the stage of disease that called diabetic retinopathy, there are sudden loss of vision and blurred vision problems. Automated detection of vessels in retinal images is a useful study to diagnose eye diseases, disease classification and other clinical trials. The shape and structure of the vessels give information about the severity of the disease and the stage of the disease. Automatic and fast detection of vessels allows for a quick diagnosis of the disease and the treatment process to start shortly. ROI detection and vessel extraction methods for retinal image are mentioned in this study. It is shown that the Frangi filter used in image processing can be successfully used in detection and extraction of vessels.

Reinterpretation of ozone data from Base Roi Baudouin

Science.gov (United States)

Kelder, H.; Muller, C.

1994-01-01

The ozone Dobson measurements obtained in Antarctica at the Belgian 'Base Roi Baudouin' (70 deg 26 min S, 24 deg 19 min E) in 1965 and 1966 were retrieved from the KNMI (Royal Netherlands Meteorological Institute) archives in De Bilt. Despite excellent treatment at the time by the meteorologists in charge at the KNMI (Wisse and Meerburg, 1969), a study of the original observers notes was made in order to check possible seasonal ozone phenomena. No systematic anomaly in the first analysis was found; meteorological data from the site together with Brewer-Mast ozone soundings concur that the conditions did not correspond either in 1965 nor 1966 to the current ozone hole (Farman et al., 1985) situation, however, the data yields excellent correlation with stratospheric temperature and shows in 1966 a clear November maximum in opposition to an October value around 344 Dobson units.

Multi-ROI Association and Tracking With Belief Functions: Application to Traffic Sign Recognition

OpenAIRE

Boumediene , Mohammed; Lauffenburger , Jean-Philippe; Daniel , Jérémie; Cudel , Christophe; Ouamri , Abdelaziz

2014-01-01

International audience; —This paper presents an object tracking algorithm using belief functions applied to vision-based traffic sign recognition systems. This algorithm tracks detected sign candidates over time in order to reduce false positives due to data fusion formalization. In the first stage, regions of interest (ROIs) are detected and combined using the transferable belief model semantics. In the second stage, the local pignistic probability algorithm generates the associations maximi...

Cerebral blood flow SPET in transient global amnesia with automated ROI analysis by 3DSRT

Energy Technology Data Exchange (ETDEWEB)

Takeuchi, Ryo [Division of Nuclear Medicine, Nishi-Kobe Medical Center, Kohjidai 5-7-1, 651-2273, Nishi-ku, Kobe-City, Hyogo (Japan); Matsuda, Hiroshi [Department of Radiology, National Center Hospital for Mental, Nervous and Muscular Disorders, National Center of Neurology and Psychiatry, Tokyo (Japan); Yoshioka, Katsunori [Daiichi Radioisotope Laboratories, Ltd., Tokyo (Japan); Yonekura, Yoshiharu [Biomedical Imaging Research Center, University of Fukui, Fukui (Japan)

2004-04-01

The aim of this study was to determine the areas involved in episodes of transient global amnesia (TGA) by calculation of cerebral blood flow (CBF) using 3DSRT, fully automated ROI analysis software which we recently developed. Technetium-99m l,l-ethyl cysteinate dimer single-photon emission tomography ({sup 99m}Tc-ECD SPET) was performed during and after TGA attacks on eight patients (four men and four women; mean study interval, 34 days). The SPET images were anatomically standardized using SPM99 followed by quantification of 318 constant ROIs, grouped into 12 segments (callosomarginal, precentral, central, parietal, angular, temporal, posterior cerebral, pericallosal, lenticular nucleus, thalamus, hippocampus and cerebellum), in each hemisphere to calculate segmental CBF (sCBF) as the area-weighted mean value for each of the respective 12 segments based on the regional CBF in each ROI. Correlation of the intra- and post-episodic sCBF of each of the 12 segments of the eight patients was estimated by scatter-plot graphical analysis and Pearson's correlation test with Fisher's Z-transformation. For the control, {sup 99m}Tc-ECD SPET was performed on eight subjects (three men and five women) and repeated within 1 month; the correlation between the first and second sCBF values of each of the 12 segments was evaluated in the same way as for patients with TGA. Excellent reproducibility between the two sCBF values was found in all 12 segments of the control subjects. However, a significant correlation between intra- and post-episodic sCBF was not shown in the thalamus or angular segments of TGA patients. The present study was preliminary, but at least suggested that thalamus and angular regions are closely involved in the symptoms of TGA. (orig.)

Cerebral blood flow SPET in transient global amnesia with automated ROI analysis by 3DSRT

International Nuclear Information System (INIS)

Takeuchi, Ryo; Matsuda, Hiroshi; Yoshioka, Katsunori; Yonekura, Yoshiharu

2004-01-01

The aim of this study was to determine the areas involved in episodes of transient global amnesia (TGA) by calculation of cerebral blood flow (CBF) using 3DSRT, fully automated ROI analysis software which we recently developed. Technetium-99m l,l-ethyl cysteinate dimer single-photon emission tomography ( 99m Tc-ECD SPET) was performed during and after TGA attacks on eight patients (four men and four women; mean study interval, 34 days). The SPET images were anatomically standardized using SPM99 followed by quantification of 318 constant ROIs, grouped into 12 segments (callosomarginal, precentral, central, parietal, angular, temporal, posterior cerebral, pericallosal, lenticular nucleus, thalamus, hippocampus and cerebellum), in each hemisphere to calculate segmental CBF (sCBF) as the area-weighted mean value for each of the respective 12 segments based on the regional CBF in each ROI. Correlation of the intra- and post-episodic sCBF of each of the 12 segments of the eight patients was estimated by scatter-plot graphical analysis and Pearson's correlation test with Fisher's Z-transformation. For the control, 99m Tc-ECD SPET was performed on eight subjects (three men and five women) and repeated within 1 month; the correlation between the first and second sCBF values of each of the 12 segments was evaluated in the same way as for patients with TGA. Excellent reproducibility between the two sCBF values was found in all 12 segments of the control subjects. However, a significant correlation between intra- and post-episodic sCBF was not shown in the thalamus or angular segments of TGA patients. The present study was preliminary, but at least suggested that thalamus and angular regions are closely involved in the symptoms of TGA. (orig.)

Voxel based statistical analysis method for microPET studies to assess the cerebral glucose metabolism in cat deafness model: comparison to ROI based method

International Nuclear Information System (INIS)

Kim, Jin Su; Lee, Jae Sung; Park, Min Hyun; Lee, Jong Jin; Kang, Hye Jin; Lee, Hyo Jeong; Oh, Seung Ha; Kim, Chong Sun; Jung, June Key; Lee, Myung Chul; Lee, Dong Soo; Lim, Sang Moo

2005-01-01

Imaging research on the brain of sensory-deprived cats using small animal PET scanner has gained interest since the abundant information about the sensory system of ths animal is available and close examination of the brain is possible due to larger size of its brain than mouse or rat. In this study, we have established the procedures for 3D voxel-based statistical analysis (SPM) of FDG PET image of cat brain, and confirmed using ROI based-method. FDG PET scans of 4 normal and 4 deaf cats were acquired for 30 minutes using microPET R4 scanner. Only the brain cortices were extracted using a masking and threshold method to facilitate spatial normalization. After spatial normalization and smoothing, 3D voxel-wise and ROI based t-test were performed to identify the regions with significant different FDG uptake between the normal and deaf cats. In ROI analysis, 26 ROIs were drawn on both hemispheres, and regional mean pixel value in each ROI was normalized to the global mean of the brain. Cat brains were spatially normalized well onto the target brain due to the removal of background activity. When cerebral glucose metabolism of deaf cats were compared to the normal controls after removing the effects of the global count, the glucose metabolism in the auditory cortex, head of caudate nucleus, and thalamus in both hemispheres of the deaf cats was significantly lower than that of the controls (P<0.01). No area showed a significantly increased metabolism in the deaf cats even in higher significance level (P<0.05). ROI analysis also showed significant reduction of glucose metabolism in the same region. This study established and confirmed a method for voxel-based analysis of animal PET data of cat brain, which showed high localization accuracy and specificity and was useful for examining the cerebral glucose metabolism in a cat cortical deafness model

Voxel based statistical analysis method for microPET studies to assess the cerebral glucose metabolism in cat deafness model: comparison to ROI based method

Energy Technology Data Exchange (ETDEWEB)

Kim, Jin Su; Lee, Jae Sung; Park, Min Hyun; Lee, Jong Jin; Kang, Hye Jin; Lee, Hyo Jeong; Oh, Seung Ha; Kim, Chong Sun; Jung, June Key; Lee, Myung Chul; Lee, Dong Soo [Seoul National University College of Medicine, Seoul (Korea, Republic of); Lim, Sang Moo [KIRAMS, Seoul (Korea, Republic of)

2005-07-01

Imaging research on the brain of sensory-deprived cats using small animal PET scanner has gained interest since the abundant information about the sensory system of ths animal is available and close examination of the brain is possible due to larger size of its brain than mouse or rat. In this study, we have established the procedures for 3D voxel-based statistical analysis (SPM) of FDG PET image of cat brain, and confirmed using ROI based-method. FDG PET scans of 4 normal and 4 deaf cats were acquired for 30 minutes using microPET R4 scanner. Only the brain cortices were extracted using a masking and threshold method to facilitate spatial normalization. After spatial normalization and smoothing, 3D voxel-wise and ROI based t-test were performed to identify the regions with significant different FDG uptake between the normal and deaf cats. In ROI analysis, 26 ROIs were drawn on both hemispheres, and regional mean pixel value in each ROI was normalized to the global mean of the brain. Cat brains were spatially normalized well onto the target brain due to the removal of background activity. When cerebral glucose metabolism of deaf cats were compared to the normal controls after removing the effects of the global count, the glucose metabolism in the auditory cortex, head of caudate nucleus, and thalamus in both hemispheres of the deaf cats was significantly lower than that of the controls (P<0.01). No area showed a significantly increased metabolism in the deaf cats even in higher significance level (P<0.05). ROI analysis also showed significant reduction of glucose metabolism in the same region. This study established and confirmed a method for voxel-based analysis of animal PET data of cat brain, which showed high localization accuracy and specificity and was useful for examining the cerebral glucose metabolism in a cat cortical deafness model.

Efficient ConvNet Feature Extraction with Multiple RoI Pooling for Landmark-Based Visual Localization of Autonomous Vehicles

Directory of Open Access Journals (Sweden)

Yi Hou

2017-01-01

Full Text Available Efficient and robust visual localization is important for autonomous vehicles. By achieving impressive localization accuracy under conditions of significant changes, ConvNet landmark-based approach has attracted the attention of people in several research communities including autonomous vehicles. Such an approach relies heavily on the outstanding discrimination power of ConvNet features to match detected landmarks between images. However, a major challenge of this approach is how to extract discriminative ConvNet features efficiently. To address this challenging, inspired by the high efficiency of the region of interest (RoI pooling layer, we propose a Multiple RoI (MRoI pooling technique, an enhancement of RoI, and a simple yet efficient ConvNet feature extraction method. Our idea is to leverage MRoI pooling to exploit multilevel and multiresolution information from multiple convolutional layers and then fuse them to improve the discrimination capacity of the final ConvNet features. The main advantages of our method are (a high computational efficiency for real-time applications; (b GPU memory efficiency for mobile applications; and (c use of pretrained model without fine-tuning or retraining for easy implementation. Experimental results on four datasets have demonstrated not only the above advantages but also the high discriminating power of the extracted ConvNet features with state-of-the-art localization accuracy.

SU-F-J-29: Dosimetric Effect of Image Registration ROI Size and Focus in Automated CBCT Registration for Spine SBRT

Energy Technology Data Exchange (ETDEWEB)

Magnelli, A; Smith, A; Chao, S; Suh, J; Xia, P [The Cleveland Clinic Foundation, Cleveland, OH (United States)

2016-06-15

Purpose: Spinal stereotactic body radiotherapy (SBRT) involves highly conformal dose distributions and steep dose gradients due to the proximity of the spinal cord to the treatment volume. To achieve the planning goals while limiting the spinal cord dose, patients are setup using kV cone-beam CT (kV-CBCT) with 6 degree corrections. The kV-CBCT registration with the reference CT is dependent on a user selected region of interest (ROI). The objective of this work is to determine the dosimetric impact of ROI selection. Methods: Twenty patients were selected for this study. For each patient, the kV-CBCT was registered to the reference CT using three ROIs including: 1) the external body, 2) a large anatomic region, and 3) a small region focused in the target volume. Following each registration, the aligned CBCTs and contours were input to the treatment planning system for dose evaluation. The minimum dose, dose to 99% and 90% of the tumor volume (D99%, D90%), dose to 0.03cc and the dose to 10% of the spinal cord subvolume (V10Gy) were compared to the planned values. Results: The average deviations in the tumor minimum dose were 2.68%±1.7%, 4.6%±4.0%, 14.82%±9.9% for small, large and the external ROIs, respectively. The average deviations in tumor D99% were 1.15%±0.7%, 3.18%±1.7%, 10.0%±6.6%, respectively. The average deviations in tumor D90% were 1.00%±0.96%, 1.14%±1.05%, 3.19%±4.77% respectively. The average deviations in the maximum dose to the spinal cord were 2.80%±2.56%, 7.58%±8.28%, 13.35%±13.14%, respectively. The average deviation in V10Gy to the spinal cord were 1.69%±0.88%, 1.98%±2.79%, 2.71%±5.63%. Conclusion: When using automated registration algorithms for CBCT-Reference alignment, a small target-focused ROI results in the least dosimetric deviation from the plan. It is recommended to focus narrowly on the target volume to keep the spinal cord dose below tolerance.

An alternative to γ histograms for ROI-based quantitative dose comparisons

International Nuclear Information System (INIS)

Dvorak, P

2009-01-01

An alternative to gamma (γ) histograms for ROI-based quantitative comparisons of dose distributions using the γ concept is proposed. The method provides minimum values of dose difference and distance-to-agreement such that a pre-set fraction of the region of interest passes the γ test. Compared to standard γ histograms, the method provides more information in terms of pass rate per γ calculation. This is achieved at negligible additional calculation cost and without loss of accuracy. The presented method is proposed as a useful and complementary alternative to standard γ histograms, increasing both the quantity and quality of information for use in acceptance or rejection decisions. (note)

A method to estimate the fractional fat volume within a ROI of a breast biopsy for WAXS applications: Animal tissue evaluation

International Nuclear Information System (INIS)

Tang, Robert Y.; McDonald, Nancy; Laamanen, Curtis; LeClair, Robert J.

2014-01-01

Purpose: To develop a method to estimate the mean fractional volume of fat (ν ¯ fat ) within a region of interest (ROI) of a tissue sample for wide-angle x-ray scatter (WAXS) applications. A scatter signal from the ROI was obtained and use of ν ¯ fat in a WAXS fat subtraction model provided a way to estimate the differential linear scattering coefficient μ s of the remaining fatless tissue. Methods: The efficacy of the method was tested using animal tissue from a local butcher shop. Formalin fixed samples, 5 mm in diameter 4 mm thick, were prepared. The two main tissue types were fat and meat (fibrous). Pure as well as composite samples consisting of a mixture of the two tissue types were analyzed. For the latter samples, ν fat for the tissue columns of interest were extracted from corresponding pixels in CCD digital x-ray images using a calibration curve. The means ν ¯ fat were then calculated for use in a WAXS fat subtraction model. For the WAXS measurements, the samples were interrogated with a 2.7 mm diameter 50 kV beam and the 6° scattered photons were detected with a CdTe detector subtending a solid angle of 7.75 × 10 −5 sr. Using the scatter spectrum, an estimate of the incident spectrum, and a scatter model, μ s was determined for the tissue in the ROI. For the composite samples, a WAXS fat subtraction model was used to estimate the μ s of the fibrous tissue in the ROI. This signal was compared to μ s of fibrous tissue obtained using a pure fibrous sample. Results: For chicken and beef composites, ν ¯ fat =0.33±0.05 and 0.32 ± 0.05, respectively. The subtractions of these fat components from the WAXS composite signals provided estimates of μ s for chicken and beef fibrous tissue. The differences between the estimates and μ s of fibrous obtained with a pure sample were calculated as a function of the momentum transfer x. A t-test showed that the mean of the differences did not vary from zero in a statistically significant way thereby

Wavelet-based compression with ROI coding support for mobile access to DICOM images over heterogeneous radio networks.

Science.gov (United States)

Maglogiannis, Ilias; Doukas, Charalampos; Kormentzas, George; Pliakas, Thomas

2009-07-01

Most of the commercial medical image viewers do not provide scalability in image compression and/or region of interest (ROI) encoding/decoding. Furthermore, these viewers do not take into consideration the special requirements and needs of a heterogeneous radio setting that is constituted by different access technologies [e.g., general packet radio services (GPRS)/ universal mobile telecommunications system (UMTS), wireless local area network (WLAN), and digital video broadcasting (DVB-H)]. This paper discusses a medical application that contains a viewer for digital imaging and communications in medicine (DICOM) images as a core module. The proposed application enables scalable wavelet-based compression, retrieval, and decompression of DICOM medical images and also supports ROI coding/decoding. Furthermore, the presented application is appropriate for use by mobile devices activating in heterogeneous radio settings. In this context, performance issues regarding the usage of the proposed application in the case of a prototype heterogeneous system setup are also discussed.

Cephalopholis argus fish census and assemblage data from the West Hawaii Roi Removal Project 2010-2012 (NODC Accession 0099263)

Data.gov (United States)

National Oceanic and Atmospheric Administration, Department of Commerce — This project examined the results of the field manipulative experiment that has been set up to test the ecological effects of introduced roi on reef fish...

A method to estimate the fractional fat volume within a ROI of a breast biopsy for WAXS applications: Animal tissue evaluation

Energy Technology Data Exchange (ETDEWEB)

Tang, Robert Y., E-mail: rx-tang@laurentian.ca [Biomolecular Sciences Program, Laurentian University, 935 Ramsey Lake Road, Sudbury, Ontario P3E 2C6 (Canada); McDonald, Nancy, E-mail: mcdnancye@gmail.com; Laamanen, Curtis, E-mail: cx-laamanen@laurentian.ca [Department of Physics, Laurentian University, 935 Ramsey Lake Road, Sudbury, Ontario P3E 2C6 (Canada); LeClair, Robert J., E-mail: rleclair@laurentian.ca [Department of Physics, Laurentian University, 935 Ramsey Lake Road, Sudbury, Ontario P3E 2C6, Canada and Biomolecular Sciences Program, Laurentian University, 935 Ramsey Lake Road, Sudbury, Ontario P3E 2C6 (Canada)

2014-11-01

Purpose: To develop a method to estimate the mean fractional volume of fat (ν{sup ¯}{sub fat}) within a region of interest (ROI) of a tissue sample for wide-angle x-ray scatter (WAXS) applications. A scatter signal from the ROI was obtained and use of ν{sup ¯}{sub fat} in a WAXS fat subtraction model provided a way to estimate the differential linear scattering coefficient μ{sub s} of the remaining fatless tissue. Methods: The efficacy of the method was tested using animal tissue from a local butcher shop. Formalin fixed samples, 5 mm in diameter 4 mm thick, were prepared. The two main tissue types were fat and meat (fibrous). Pure as well as composite samples consisting of a mixture of the two tissue types were analyzed. For the latter samples, ν{sub fat} for the tissue columns of interest were extracted from corresponding pixels in CCD digital x-ray images using a calibration curve. The means ν{sup ¯}{sub fat} were then calculated for use in a WAXS fat subtraction model. For the WAXS measurements, the samples were interrogated with a 2.7 mm diameter 50 kV beam and the 6° scattered photons were detected with a CdTe detector subtending a solid angle of 7.75 × 10{sup −5} sr. Using the scatter spectrum, an estimate of the incident spectrum, and a scatter model, μ{sub s} was determined for the tissue in the ROI. For the composite samples, a WAXS fat subtraction model was used to estimate the μ{sub s} of the fibrous tissue in the ROI. This signal was compared to μ{sub s} of fibrous tissue obtained using a pure fibrous sample. Results: For chicken and beef composites, ν{sup ¯}{sub fat}=0.33±0.05 and 0.32 ± 0.05, respectively. The subtractions of these fat components from the WAXS composite signals provided estimates of μ{sub s} for chicken and beef fibrous tissue. The differences between the estimates and μ{sub s} of fibrous obtained with a pure sample were calculated as a function of the momentum transfer x. A t-test showed that the mean of the

Genomic Analyses Reveal the Influence of Geographic Origin, Migration, and Hybridization on Modern Dog Breed Development

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Heidi G. Parker

2017-04-01

Full Text Available There are nearly 400 modern domestic dog breeds with a unique histories and genetic profiles. To track the genetic signatures of breed development, we have assembled the most diverse dataset of dog breeds, reflecting their extensive phenotypic variation and heritage. Combining genetic distance, migration, and genome-wide haplotype sharing analyses, we uncover geographic patterns of development and independent origins of common traits. Our analyses reveal the hybrid history of breeds and elucidate the effects of immigration, revealing for the first time a suggestion of New World dog within some modern breeds. Finally, we used cladistics and haplotype sharing to show that some common traits have arisen more than once in the history of the dog. These analyses characterize the complexities of breed development, resolving longstanding questions regarding individual breed origination, the effect of migration on geographically distinct breeds, and, by inference, transfer of trait and disease alleles among dog breeds.

Comparative genomics analyses revealed two virulent Listeria monocytogenes strains isolated from ready-to-eat food.

Science.gov (United States)

Lim, Shu Yong; Yap, Kien-Pong; Thong, Kwai Lin

2016-01-01

Listeria monocytogenes is an important foodborne pathogen that causes considerable morbidity in humans with high mortality rates. In this study, we have sequenced the genomes and performed comparative genomics analyses on two strains, LM115 and LM41, isolated from ready-to-eat food in Malaysia. The genome size of LM115 and LM41 was 2,959,041 and 2,963,111 bp, respectively. These two strains shared approximately 90% homologous genes. Comparative genomics and phylogenomic analyses revealed that LM115 and LM41 were more closely related to the reference strains F2365 and EGD-e, respectively. Our virulence profiling indicated a total of 31 virulence genes shared by both analysed strains. These shared genes included those that encode for internalins and L. monocytogenes pathogenicity island 1 (LIPI-1). Both the Malaysian L. monocytogenes strains also harboured several genes associated with stress tolerance to counter the adverse conditions. Seven antibiotic and efflux pump related genes which may confer resistance against lincomycin, erythromycin, fosfomycin, quinolone, tetracycline, and penicillin, and macrolides were identified in the genomes of both strains. Whole genome sequencing and comparative genomics analyses revealed two virulent L. monocytogenes strains isolated from ready-to-eat foods in Malaysia. The identification of strains with pathogenic, persistent, and antibiotic resistant potentials from minimally processed food warrant close attention from both healthcare and food industry.

MEASURES OF EFFICIENCY AND INVESTMENTS RETURN: AN STUDY OF BRAZILIAN ELECTRICITY DISTRIBUTORS WITH DATA ENVELOPMENT ANALYSIS, MALMQUIST INDEX AND ROI

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Valter Saurin

2013-03-01

Full Text Available This paper aims to determine, in a group of companies from the Brazilian electric sector, if there is a relationship between the return on investment (ROI and the concept of efficiency estimated by the method Data Envelopment Analysis (DEA, as well as evaluating the growth of productivity based on Malmquist Index (Fare et al, 1996. The hypothesis is that firms that had return on investment higher during certain period of time are those employed their resources efficiently in getting their outputs (DEA efficient. The input (1 Products (5 DEA model correspond to the operating cost (I, the network length (km, the number of consumers and the market billed high, medium and low voltage, respectively. The sample consisted of 31 companies of Brazilian electricity distribution and timing of the study was from 2007 to 2009. We calculated the Malmquist index (M0, represented by the change in total factor productivity (TFPC, which is composed by the evolution of technical efficiency (EC and the change in the technological frontier (TC of the companies were also determined ROI for each period. We calculated the correlation between the TFPC, TC, EC, score the DEA and the ROI for the period 2007 to 2009. The results showed a positive correlation, although weak, between efficiency change and the indexes mentioned above, rejecting the initial hypothesis

Study of regional cerebral blood flow in obsessive compulsive disorder patients with SPM and ROI method

International Nuclear Information System (INIS)

Li Peiyong; Jiang Xufeng; Zhang Liying; Guo Wanhua; Zhu Chengmo

2002-01-01

Objective: To investigate the alternations in regional cerebral blood flow (rCBF) in obsessive compulsive disorder (OCD) patients using statistical parametric mapping (SPM). Methods: rCBF measurements using 99 Tc m -ethyl cysteinate dimer (ECD) SPECT was performed on 14 OCD patients and 23 age-matched healthy volunteers. The rCBF distribution was compared between these two groups with SPM under the conditions of increased and decreased perfusion, and with regions of interest (ROIs) using cerebral template. P value was set at 0.01 level. Results: SPM analysis showed that rCBF decreased in cerebral areas including bilateral putamen, superior temporal gyrus and precuneus, and right orbital gyrus, superior and middle frontal gyrus, and left temporo-occipital lobule and superior parietal gyrus, and vermis. rCBF was also increased in left inferior frontal gyrus and posterior cingulate gyrus. With ROIs method, rCBF was decreased in right anterior frontal, temporo-parietal lobule and left temporo-occipital lobule. Conclusions: The study supports the viewpoint that rCBF abnormality of fronto-striatal circuits is involved in OCD patients. SPM method is a forceful tool in analyzing cerebral regional characters

Keeping it real--building an ROI model for an ambulatory EMR initiative that the physician practices espouse.

Science.gov (United States)

Mullen, Rńee; Donnelly, John T

2006-01-01

The ambulatory electronic medical record initiative at Magic Valley Regional Medical Center (MVRMC) in South Central Idaho underwent a rigorous product evaluation process that resulted in one of the market-leading EMR products being selected for implementation. MVRMC includes four business entities, including a 213-bed regional hospital and a 19-practice management services organization. Early in the process, the organization viewed buy-in from its physicians as a critical success factor. The physicians had been integral to product selection, and it was equally important for them to trust the economic model for its acquisition-especially because it was likely that they would be asked to put "some skin in the game." To make this initiative economically feasible, MVRMC received a grant from Agency for Healthcare Research and Quality based on the potential impact of the endeavor on healthcare delivery in the region. However, because the functional analysis did not result in the selection of the least expensive product, the AHRQ grant would only help defray the startup expenses, but not ongoing support and maintenance expenses after implementation; these costs would be borne by anticipated increases in the practice's revenue or reduction in its operating expenses. The ROI model would need to explain how each practice, from the single physician specialist to an almost 20-physician family practice, could pay for the desirable outcomes discussed during the selection phase of the project. The physicians, who had participated in technology initiatives in the past, were skeptical that cost-justifying an IT system was realistic, even though they recognized the potential benefits it could have on the quality and consistency of the care. Because some process standardization within and between practices would be needed to use electronic charting effectively, it was important that the ROI model did not outweigh the benefits of an as-yet untested operational workflow that

Single-Cell Analyses of ESCs Reveal Alternative Pluripotent Cell States and Molecular Mechanisms that Control Self-Renewal

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Dmitri Papatsenko

2015-08-01

Full Text Available Analyses of gene expression in single mouse embryonic stem cells (mESCs cultured in serum and LIF revealed the presence of two distinct cell subpopulations with individual gene expression signatures. Comparisons with published data revealed that cells in the first subpopulation are phenotypically similar to cells isolated from the inner cell mass (ICM. In contrast, cells in the second subpopulation appear to be more mature. Pluripotency Gene Regulatory Network (PGRN reconstruction based on single-cell data and published data suggested antagonistic roles for Oct4 and Nanog in the maintenance of pluripotency states. Integrated analyses of published genomic binding (ChIP data strongly supported this observation. Certain target genes alternatively regulated by OCT4 and NANOG, such as Sall4 and Zscan10, feed back into the top hierarchical regulator Oct4. Analyses of such incoherent feedforward loops with feedback (iFFL-FB suggest a dynamic model for the maintenance of mESC pluripotency and self-renewal.

Effect of scatter and attenuation correction in ROI analysis of brain perfusion scintigraphy. Phantom experiment and clinical study in patients with unilateral cerebrovascular disease

Energy Technology Data Exchange (ETDEWEB)

Bai, J. [Keio Univ., Tokyo (Japan). 21st Century Center of Excellence Program; Hashimoto, J.; Kubo, A. [Keio Univ., Tokyo (Japan). Dept. of Radiology; Ogawa, K. [Hosei Univ., Tokyo (Japan). Dept. of Electronic Informatics; Fukunaga, A.; Onozuka, S. [Keio Univ., Tokyo (Japan). Dept. of Neurosurgery

2007-07-01

The aim of this study was to evaluate the effect of scatter and attenuation correction in region of interest (ROI) analysis of brain perfusion single-photon emission tomography (SPECT), and to assess the influence of selecting the reference area on the calculation of lesion-to-reference count ratios. Patients, methods: Data were collected from a brain phantom and ten patients with unilateral internal carotid artery stenosis. A simultaneous emission and transmission scan was performed after injecting {sup 123}I-iodoamphetamine. We reconstructed three SPECT images from common projection data: with scatter correction and nonuniform attenuation correction, with scatter correction and uniform attenuation correction, and with uniform attenuation correction applied to data without scatter correction. Regional count ratios were calculated by using four different reference areas (contralateral intact side, ipsilateral cerebellum, whole brain and hemisphere). Results: Scatter correction improved the accuracy of measuring the count ratios in the phantom experiment. It also yielded marked difference in the count ratio in the clinical study when using the cerebellum, whole brain or hemisphere as the reference. Difference between nonuniform and uniform attenuation correction was not significant in the phantom and clinical studies except when the cerebellar reference was used. Calculation of the lesion-to-normal count ratios referring the same site in the contralateral hemisphere was not dependent on the use of scatter correction or transmission scan-based attenuation correction. Conclusion: Scatter correction was indispensable for accurate measurement in most of the ROI analyses. Nonuniform attenuation correction is not necessary when using the reference area other than the cerebellum. (orig.)

Gender differences in functional connectivities between insular subdivisions and selective pain-related brain structures.

Science.gov (United States)

Dai, Yu-Jie; Zhang, Xin; Yang, Yang; Nan, Hai-Yan; Yu, Ying; Sun, Qian; Yan, Lin-Feng; Hu, Bo; Zhang, Jin; Qiu, Zi-Yu; Gao, Yi; Cui, Guang-Bin; Chen, Bi-Liang; Wang, Wen

2018-03-14

The incidence of pain disorders in women is higher than in men, making gender differences in pain a research focus. The human insular cortex is an important brain hub structure for pain processing and is divided into several subdivisions, serving different functions in pain perception. Here we aimed to examine the gender differences of the functional connectivities (FCs) between the twelve insular subdivisions and selected pain-related brain structures in healthy adults. Twenty-six healthy males and 11 age-matched healthy females were recruited in this cross-sectional study. FCs between the 12 insular subdivisions (as 12 regions of interest (ROIs)) and the whole brain (ROI-whole brain level) or 64 selected pain-related brain regions (64 ROIs, ROI-ROI level) were measured between the males and females. Significant gender differences in the FCs of the insular subdivisions were revealed: (1) The FCs between the dorsal dysgranular insula (dId) and other brain regions were significantly increased in males using two different techniques (ROI-whole brain and ROI-ROI analyses); (2) Based on the ROI-whole brain analysis, the FC increases in 4 FC-pairs were observed in males, including the left dId - the right median cingulate and paracingulate/ right posterior cingulate gyrus/ right precuneus, the left dId - the right median cingulate and paracingulate, the left dId - the left angular as well as the left dId - the left middle frontal gyrus; (3) According to the ROI-ROI analysis, increased FC between the left dId and the right rostral anterior cingulate cortex was investigated in males. In summary, the gender differences in the FCs of the insular subdivisions with pain-related brain regions were revealed in the current study, offering neuroimaging evidence for gender differences in pain processing. ClinicalTrials.gov, NCT02820974 . Registered 28 June 2016.

In situ observation data from the grouper roi (Cephalopholis argus) removal project in West Hawaii from 2010-2011 (NODC Accession 0082197)

Data.gov (United States)

National Oceanic and Atmospheric Administration, Department of Commerce — In situ observations of the introduced predatory grouper roi (Cephalopholis argus) were taken within the coral reef ecosystem of Puako, northwest side of the Island...

Trial sequential analysis reveals insufficient information size and potentially false positive results in many meta-analyses

DEFF Research Database (Denmark)

Brok, J.; Thorlund, K.; Gluud, C.

2008-01-01

in 80% (insufficient information size). TSA(15%) and TSA(LBHIS) found that 95% and 91% had absence of evidence. The remaining nonsignificant meta-analyses had evidence of lack of effect. CONCLUSION: TSA reveals insufficient information size and potentially false positive results in many meta......OBJECTIVES: To evaluate meta-analyses with trial sequential analysis (TSA). TSA adjusts for random error risk and provides the required number of participants (information size) in a meta-analysis. Meta-analyses not reaching information size are analyzed with trial sequential monitoring boundaries...... analogous to interim monitoring boundaries in a single trial. STUDY DESIGN AND SETTING: We applied TSA on meta-analyses performed in Cochrane Neonatal reviews. We calculated information sizes and monitoring boundaries with three different anticipated intervention effects of 30% relative risk reduction (TSA...

Time-Series Analyses of Transcriptomes and Proteomes Reveal Molecular Networks Underlying Oil Accumulation in Canola.

Science.gov (United States)

Wan, Huafang; Cui, Yixin; Ding, Yijuan; Mei, Jiaqin; Dong, Hongli; Zhang, Wenxin; Wu, Shiqi; Liang, Ying; Zhang, Chunyu; Li, Jiana; Xiong, Qing; Qian, Wei

2016-01-01

Understanding the regulation of lipid metabolism is vital for genetic engineering of canola ( Brassica napus L.) to increase oil yield or modify oil composition. We conducted time-series analyses of transcriptomes and proteomes to uncover the molecular networks associated with oil accumulation and dynamic changes in these networks in canola. The expression levels of genes and proteins were measured at 2, 4, 6, and 8 weeks after pollination (WAP). Our results show that the biosynthesis of fatty acids is a dominant cellular process from 2 to 6 WAP, while the degradation mainly happens after 6 WAP. We found that genes in almost every node of fatty acid synthesis pathway were significantly up-regulated during oil accumulation. Moreover, significant expression changes of two genes, acetyl-CoA carboxylase and acyl-ACP desaturase, were detected on both transcriptomic and proteomic levels. We confirmed the temporal expression patterns revealed by the transcriptomic analyses using quantitative real-time PCR experiments. The gene set association analysis show that the biosynthesis of fatty acids and unsaturated fatty acids are the most significant biological processes from 2-4 WAP and 4-6 WAP, respectively, which is consistent with the results of time-series analyses. These results not only provide insight into the mechanisms underlying lipid metabolism, but also reveal novel candidate genes that are worth further investigation for their values in the genetic engineering of canola.

Analysing performance through value creation

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Adrian TRIFAN

2015-12-01

Full Text Available This paper draws a parallel between measuring financial performance in 2 variants: the first one using data offered by accounting, which lays emphasis on maximizing profit, and the second one which aims to create value. The traditional approach to performance is based on some indicators from accounting data: ROI, ROE, EPS. The traditional management, based on analysing the data from accounting, has shown its limits, and a new approach is needed, based on creating value. The evaluation of value based performance tries to avoid the errors due to accounting data, by using other specific indicators: EVA, MVA, TSR, CVA. The main objective is shifted from maximizing the income to maximizing the value created for shareholders. The theoretical part is accompanied by a practical analysis regarding the creation of value and an analysis of the main indicators which evaluate this concept.

Metabolomic Analyses of Leishmania Reveal Multiple Species Differences and Large Differences in Amino Acid Metabolism.

Directory of Open Access Journals (Sweden)

Gareth D Westrop

Full Text Available Comparative genomic analyses of Leishmania species have revealed relatively minor heterogeneity amongst recognised housekeeping genes and yet the species cause distinct infections and pathogenesis in their mammalian hosts. To gain greater information on the biochemical variation between species, and insights into possible metabolic mechanisms underpinning visceral and cutaneous leishmaniasis, we have undertaken in this study a comparative analysis of the metabolomes of promastigotes of L. donovani, L. major and L. mexicana. The analysis revealed 64 metabolites with confirmed identity differing 3-fold or more between the cell extracts of species, with 161 putatively identified metabolites differing similarly. Analysis of the media from cultures revealed an at least 3-fold difference in use or excretion of 43 metabolites of confirmed identity and 87 putatively identified metabolites that differed to a similar extent. Strikingly large differences were detected in their extent of amino acid use and metabolism, especially for tryptophan, aspartate, arginine and proline. Major pathways of tryptophan and arginine catabolism were shown to be to indole-3-lactate and arginic acid, respectively, which were excreted. The data presented provide clear evidence on the value of global metabolomic analyses in detecting species-specific metabolic features, thus application of this technology should be a major contributor to gaining greater understanding of how pathogens are adapted to infecting their hosts.

Baseline Marine Biological Survey ROI-NAMUR Outfall United States Army Kwajalein Atoll, Republic of the Marshall Islands, 1997(NODC Accession 0000630)

Data.gov (United States)

National Oceanic and Atmospheric Administration, Department of Commerce — Roi-Namur is located at the northernmost tip of Kwajalein Atoll, approximately 64 kilometers north of the U.S. Army Kwajalein Atoll(USAKA) central command post on...

Individual-based analyses reveal limited functional overlap in a coral reef fish community.

Science.gov (United States)

Brandl, Simon J; Bellwood, David R

2014-05-01

Detailed knowledge of a species' functional niche is crucial for the study of ecological communities and processes. The extent of niche overlap, functional redundancy and functional complementarity is of particular importance if we are to understand ecosystem processes and their vulnerability to disturbances. Coral reefs are among the most threatened marine systems, and anthropogenic activity is changing the functional composition of reefs. The loss of herbivorous fishes is particularly concerning as the removal of algae is crucial for the growth and survival of corals. Yet, the foraging patterns of the various herbivorous fish species are poorly understood. Using a multidimensional framework, we present novel individual-based analyses of species' realized functional niches, which we apply to a herbivorous coral reef fish community. In calculating niche volumes for 21 species, based on their microhabitat utilization patterns during foraging, and computing functional overlaps, we provide a measurement of functional redundancy or complementarity. Complementarity is the inverse of redundancy and is defined as less than 50% overlap in niche volumes. The analyses reveal extensive complementarity with an average functional overlap of just 15.2%. Furthermore, the analyses divide herbivorous reef fishes into two broad groups. The first group (predominantly surgeonfishes and parrotfishes) comprises species feeding on exposed surfaces and predominantly open reef matrix or sandy substrata, resulting in small niche volumes and extensive complementarity. In contrast, the second group consists of species (predominantly rabbitfishes) that feed over a wider range of microhabitats, penetrating the reef matrix to exploit concealed surfaces of various substratum types. These species show high variation among individuals, leading to large niche volumes, more overlap and less complementarity. These results may have crucial consequences for our understanding of herbivorous processes on

Integrated Marketing Communications (IMC) Variables That Influence Perceived Return on Investment (ROI) in Higher Education: Chief Marketing Officers' Perceptions

Science.gov (United States)

King, Adrienne L.

2013-01-01

This study examines the relationship of the level of Integrated Marketing Communications (IMC) implementation, level of open systems and change in state appropriations on perceived return on investment (ROI) in U.S. public higher education institutions (HEIs). Designed to provide HEI leaders with data to more accurately determine the best IMC…

Du bon maniement de l’argent du roi en Espagne au XVIIIe siècle. Les enseignements d’un procès pour fraude

Directory of Open Access Journals (Sweden)

Anne Dubet

2010-07-01

Full Text Available Pour nombre d’historiens – dont je fais partie – les réformes financières entreprises par les premiers Bourbons d’Espagne au XVIIIe siècle n’affectent pas tant l’organisation fiscale de leurs territoires que leur administration. Avant que de modifier la répartition sociale des contributions, il s’agit de rendre au roi et à ses ministres de confiance la décision en matière de dépenses et de s’assurer de son exécution. Ce projet de contrôle accru du roi sur ses propres deniers se traduit certes...

Comparison of a zero-profile anchored spacer (ROI-C) and the polyetheretherketone (PEEK) cages with an anterior plate in anterior cervical discectomy and fusion for multilevel cervical spondylotic myelopathy.

Science.gov (United States)

Liu, Yijie; Wang, Heng; Li, Xuefeng; Chen, Jie; Sun, Han; Wang, Genlin; Yang, Huilin; Jiang, Weimin

2016-06-01

We aimed to analyze the clinical and radiographic efficacy of a new zero-profile anchored spacer called the ROI-C in anterior discectomy and fusion (ACDF) for multilevel cervical spondylotic myelopathy (MCSM). We retrospectively reviewed the clinical, radiological outcomes and complications of multilevel ACDF with the ROI-C or with the polyetheretherketone (PEEK) cages with an anterior plate. From April 2011 to April 2014, 60 patients with MCSM were operated on using ACDF, with the ROI-C in 28 patients and PEEK cages with an anterior plate in 32 patients. The operative time, intraoperative blood loss, and clinical and radiological results were compared between the ROI-C group and the cage-plate group. The mean follow-up time was 23.8 ± 6.6 months, ranging from 12 to 36 months. At the first month and the last follow-up, the neck disability index (NDI) scores were decreased, and the Japanese Orthopedic Association (JOA) scores were significantly increased, compared with the presurgical measurements in both groups. There were no significant differences in NDI scores or JOA scores between the two groups (P > 0.05), but there were significant differences in the operation time, blood loss and the presence of dysphagia (P PEEK cage with an anterior plate.

Lib-Value: Values, Outcomes, and Return on Investment of Academic Libraries, Phase III: ROI of the Syracuse University Library

Science.gov (United States)

Kingma, Bruce; McClure, Kathleen

2015-01-01

This study measures the return on investment (ROI) of the Syracuse University library. Faculty and students at Syracuse University were surveyed using contingent valuation methodology to measure their willingness to pay in time and money for the services of the academic library. Their travel time and use of the online library was measured to…

Special analyses reveal coke-deposit structure

International Nuclear Information System (INIS)

Albright, L.F.

1988-01-01

A scanning electron microscope (SEM) and an energy dispersive X-ray analyzer (EDAX) have been used to obtain information that clarifies the three mechanisms of coke formation in ethylene furnaces, and to analyze the metal condition at the exit of furnace. The results can be used to examine furnace operations and develop improved ethylene plant practices. In this first of four articles on the analyses of coke and metal samples, the coking mechanisms and coke deposits in a section of tube from an actual ethylene furnace (Furnace A) from a plant on the Texas Gulf Coast are discussed. The second articles in the series will analyze the condition of the tube metal in the same furnace. To show how coke deposition and metal condition dependent on the operating parameters of an ethylene furnace, the third article in the series will show the coke deposition in a Texas Gulf Coast furnace tube (Furnace B) that operated at shorter residence time. The fourth article discusses the metal condition in that furnace. Some recommendations, based on the analyses and findings, are offered in the fourth article that could help extend the life of ethylene furnace tubes, and also improve overall ethylene plant operations

The leap from ROI to SROI: Farther than expected?

Science.gov (United States)

Gargani, John

2017-10-01

Social return on investment (SROI) is a popular method for evaluating the impact that organizations have on society and the environment. It has its roots in finance, where return on investment (ROI) is used to evaluate investments. Over the past ten years, SROI has made the leap from a tool for building private wealth to one that advances the public good. Has it landed us in a better place? To answer the question, I describe the general approach to financial analysis, how it is applied to financial decisions, and how it has been adapted to evaluate impact. I then consider the strengths and weaknesses of SROI, and suggest how, by pushing beyond the constraints of financial analysis, it can give stakeholders voice and provide evidence of success from diverse perspectives. Along the way, I propose a conceptual model for value, a foundational concept in SROI that has been criticized by some as underdeveloped, and I include a technical appendix that identifies potential sources of statistical bias in SROI estimates. I conclude by acknowledging our growing need to incorporate efficiency as one of multiple success criteria and the role that SROI-properly implemented-can play. Copyright © 2017 Elsevier Ltd. All rights reserved.

Genome-wide analyses reveal a role for peptide hormones in planarian germline development.

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James J Collins

Full Text Available Bioactive peptides (i.e., neuropeptides or peptide hormones represent the largest class of cell-cell signaling molecules in metazoans and are potent regulators of neural and physiological function. In vertebrates, peptide hormones play an integral role in endocrine signaling between the brain and the gonads that controls reproductive development, yet few of these molecules have been shown to influence reproductive development in invertebrates. Here, we define a role for peptide hormones in controlling reproductive physiology of the model flatworm, the planarian Schmidtea mediterranea. Based on our observation that defective neuropeptide processing results in defects in reproductive system development, we employed peptidomic and functional genomic approaches to characterize the planarian peptide hormone complement, identifying 51 prohormone genes and validating 142 peptides biochemically. Comprehensive in situ hybridization analyses of prohormone gene expression revealed the unanticipated complexity of the flatworm nervous system and identified a prohormone specifically expressed in the nervous system of sexually reproducing planarians. We show that this member of the neuropeptide Y superfamily is required for the maintenance of mature reproductive organs and differentiated germ cells in the testes. Additionally, comparative analyses of our biochemically validated prohormones with the genomes of the parasitic flatworms Schistosoma mansoni and Schistosoma japonicum identified new schistosome prohormones and validated half of all predicted peptide-encoding genes in these parasites. These studies describe the peptide hormone complement of a flatworm on a genome-wide scale and reveal a previously uncharacterized role for peptide hormones in flatworm reproduction. Furthermore, they suggest new opportunities for using planarians as free-living models for understanding the reproductive biology of flatworm parasites.

Comparative Genomics and Transcriptomics Analyses Reveal Divergent Lifestyle Features of Nematode Endoparasitic Fungus Hirsutella minnesotensis

Science.gov (United States)

Lai, Yiling; Liu, Keke; Zhang, Xinyu; Zhang, Xiaoling; Li, Kuan; Wang, Niuniu; Shu, Chi; Wu, Yunpeng; Wang, Chengshu; Bushley, Kathryn E.; Xiang, Meichun; Liu, Xingzhong

2014-01-01

Hirsutella minnesotensis [Ophiocordycipitaceae (Hypocreales, Ascomycota)] is a dominant endoparasitic fungus by using conidia that adhere to and penetrate the secondary stage juveniles of soybean cyst nematode. Its genome was de novo sequenced and compared with five entomopathogenic fungi in the Hypocreales and three nematode-trapping fungi in the Orbiliales (Ascomycota). The genome of H. minnesotensis is 51.4 Mb and encodes 12,702 genes enriched with transposable elements up to 32%. Phylogenomic analysis revealed that H. minnesotensis was diverged from entomopathogenic fungi in Hypocreales. Genome of H. minnesotensis is similar to those of entomopathogenic fungi to have fewer genes encoding lectins for adhesion and glycoside hydrolases for cellulose degradation, but is different from those of nematode-trapping fungi to possess more genes for protein degradation, signal transduction, and secondary metabolism. Those results indicate that H. minnesotensis has evolved different mechanism for nematode endoparasitism compared with nematode-trapping fungi. Transcriptomics analyses for the time-scale parasitism revealed the upregulations of lectins, secreted proteases and the genes for biosynthesis of secondary metabolites that could be putatively involved in host surface adhesion, cuticle degradation, and host manipulation. Genome and transcriptome analyses provided comprehensive understanding of the evolution and lifestyle of nematode endoparasitism. PMID:25359922

Phylogeographic analyses of the pampas cat (Leopardus colocola; Carnivora, Felidae) reveal a complex demographic history

Science.gov (United States)

da Silva Santos, Anelisie; Trigo, Tatiane Campos; de Oliveira, Tadeu Gomes; Silveira, Leandro

2018-01-01

Abstract The pampas cat is a small felid that occurs in open habitats throughout much of South America. Previous studies have revealed intriguing patterns of morphological differentiation and genetic structure among its populations, as well as molecular evidence for hybridization with the closely related L. tigrinus. Here we report phylogeographic analyses encompassing most of its distribution (focusing particularly on Brazilian specimens, which had been poorly sampled in previous studies), using a novel dataset comprising 2,143 bp of the mitogenome, along with previously reported mtDNA sequences. Our data revealed strong population strutucture and supported a west-to-east colonization process in this species’ history. We detected two population expansion events, one older (ca. 200 thousand years ago [kya]) in western South America and another more recent (ca. 60-50 kya) in eastern areas, coinciding with the expansion of savanna environments in Brazil. Analyses including L. tigrinus individuals bearing introgressed mtDNA from L. colocola showed a complete lack of shared haplotypes between species, indicating that their hybridization was ancient. Finally, we observed a close relationship between Brazilian/Uruguayan L. colocola haplotypes and those sampled in L. tigrinus, indicating that their hybridization was likely related to the demographic expansion of L. colocola into eastern South America. PMID:29668017

Baseline marine biological survey at Roi-Namur sewage outfall, United States Army Kwajalein Atoll, Republic of the Marshall Islands, 1997 (NODC Accession 0000630)

Data.gov (United States)

National Oceanic and Atmospheric Administration, Department of Commerce — Roi-Namur is located at the northernmost tip of Kwajalein Atoll, approximately 64 kilometers north of the U.S. Army Kwajalein Atoll (USAKA) central command post on...

包装彩盒检测中定位核提取算法%Extraction algorithm of ROI for detecting colored box

Institute of Scientific and Technical Information of China (English)

陈功明; 李锋

2016-01-01

To reduce the complexity of the existing method for automatically extracting region of interest (ROI)and improve the detection efficiency in package printing detection process,an algorithm for automatic extraction of ROI was proposed on account of multi-feature.Based on the input selected rectangular region,by comparing the output parameters like contrast ratio,duty cycle,XY direction confidence interval and the symmetry of the fitting curve of the matching coefficient,the ROI was j udged to be good or not.The feasibility of the scheme was verified using the method of automatically calculative center coordinate error. Simulation analysis demonstrates that the algorithm succeeds in extracting automatic ROI for less than 100 ms,and success rate reaches 99.78% or more,the complexity of the proposed algorithm is much lower than that of the existing ones.The proposed verification method is simple and reliable.%为降低现有包装印刷品检测过程中感兴趣区域(简称定位核)提取方法的复杂度，提高检测效率，提出一种基于多特征的定位核自动提取方案。通过输入选中的矩形区域，输出参数对比度、占空比、XY 方向置信区间的取值范围及匹配系数拟合曲线的对称性，综合判断提取定位核的好坏。提出自动求取中心点坐标误差法对该方案的有效性进行验证。仿真分析结果表明，该方案可在100 ms内自动提取定位核，成功率达到99.78%以上，明显优于已有方案，所提验证方法简单可靠。

Shifting from region of interest (ROI) to voxel-based analysis in human brain mapping

International Nuclear Information System (INIS)

Astrakas, Loukas G.; Argyropoulou, Maria I.

2010-01-01

Current clinical studies involve multidimensional high-resolution images containing an overwhelming amount of structural and functional information. The analysis of such a wealth of information is becoming increasingly difficult yet necessary in order to improve diagnosis, treatment and healthcare. Voxel-wise analysis is a class of modern methods of image processing in the medical field with increased popularity. It has replaced manual region of interest (ROI) analysis and has provided tools to make statistical inferences at voxel level. The introduction of voxel-based analysis software in all modern commercial scanners allows clinical use of these techniques. This review will explain the main principles, advantages and disadvantages behind these methods of image analysis. (orig.)

A Joint Watermarking and ROI Coding Scheme for Annotating Traffic Surveillance Videos

Directory of Open Access Journals (Sweden)

Su Po-Chyi

2010-01-01

Full Text Available We propose a new application of information hiding by employing the digital watermarking techniques to facilitate the data annotation in traffic surveillance videos. There are two parts in the proposed scheme. The first part is the object-based watermarking, in which the information of each vehicle collected by the intelligent transportation system will be conveyed/stored along with the visual data via information hiding. The scheme is integrated with H.264/AVC, which is assumed to be adopted by the surveillance system, to achieve an efficient implementation. The second part is a Region of Interest (ROI rate control mechanism for encoding traffic surveillance videos, which helps to improve the overall performance. The quality of vehicles in the video will be better preserved and a good rate-distortion performance can be attained. Experimental results show that this potential scheme works well in traffic surveillance videos.

Tombes et cimetières éthiopiens : des rois, des saints, des anonymes1

OpenAIRE

Derat, Marie-Laure

2009-01-01

L’histoire des tombes et cimetières éthiopiens, dans la longue durée, en est encore à ses balbutiements. Si les tombes des saints et des rois nous sont un peu mieux connus grâce à des textes témoignant à la fois des enjeux entourant les sépultures de ces personnages hors du commun et des soins apportés à leur inhumation, en revanche, les cimetières ordinaires échappent encore largement à l’enquête, en grande partie parce que le commun des mortels est inhumé dans l’anonymat et dans un grand dé...

Marine biological survey of ROI-NAMUR outfall at the United States Army Kwajalein Atoll, Republic of the Marshall Islands, May 2000 (NODC Accession 0000653)

Data.gov (United States)

National Oceanic and Atmospheric Administration, Department of Commerce — Roi-Namur is located at the northernmost tip of Kwajalein Atoll, approximately 64 kilometers north of the U.S. Army Kwajalein Atoll (USAKA) central command post on...

The Development of Rally Activities to Environmental Conservationfor Social Education Teachers of Mathayom Suksa Education Area Office 27 Roi-Et Province

Directory of Open Access Journals (Sweden)

Phiphop Sinthuphong

2016-09-01

Full Text Available The purposes of this research on the development of rally activities to environmental conservation for social education teachers of Mathayom suksa education area office 27 Roi-et province were ; 1 to study and analyze the place organized rally to environmental conservation, 2 to develop activities rally to environmental conservation for social education teachers 3 and compare knowledge and attitude toward environmental conservation, before and after the activity 4 to study participation in activities rally to environmental conservation after the activities. The samples used in the study and analysis of the event was social Education Teachers of Mathayom Suksa Education Area Office 27 Roi-Et Province were 77 and sample used in the event of 50 people. Social education teachers under the office of the secondary area 27 province. The tools used in this study were manual and brochures of Green activities Car Rally to environmental conservation, knowledge test, attitudes test and participating questionnaire manuals. The statistical analysis of data were percentage, mean, standard deviation and Paired t-test The results showed that there were proper place in activity all 9 points include 1. Wat Burapharam, 2. Pralanchai Swamp, 3.Roi-Et aquarium, 4. Ku Ka Sing ancient park, 5. Ku Phra Kona ancient park, 6. Jasmine rice learning source (land development station , 7. Chi river, 8.Don Swamp and 9. Rai Dakdea and dodo scouts camp. The tool in rally activities environmental conservation had suitability at more level. After participation of rally activities environmental conservation, social education teachers had mean score of knowledge and attitude to environmental conservation at more than before the participation at statistical significant level .05. And the score of knowledge and attitude toward environmental conservation, before and after the organized activities, it was found that, according to the hypothesis .05 and They had participation in

The fast iris image clarity evaluation based on Tenengrad and ROI selection

Science.gov (United States)

Gao, Shuqin; Han, Min; Cheng, Xu

2018-04-01

In iris recognition system, the clarity of iris image is an important factor that influences recognition effect. In the process of recognition, the blurred image may possibly be rejected by the automatic iris recognition system, which will lead to the failure of identification. Therefore it is necessary to evaluate the iris image definition before recognition. Considered the existing evaluation methods on iris image definition, we proposed a fast algorithm to evaluate the definition of iris image in this paper. In our algorithm, firstly ROI (Region of Interest) is extracted based on the reference point which is determined by using the feature of the light spots within the pupil, then Tenengrad operator is used to evaluate the iris image's definition. Experiment results show that, the iris image definition algorithm proposed in this paper could accurately distinguish the iris images of different clarity, and the algorithm has the merit of low computational complexity and more effectiveness.

Mitochondrial DNA analyses reveal low genetic diversity in Culex quinquefasciatus from residential areas in Malaysia.

Science.gov (United States)

Low, V L; Lim, P E; Chen, C D; Lim, Y A L; Tan, T K; Norma-Rashid, Y; Lee, H L; Sofian-Azirun, M

2014-06-01

The present study explored the intraspecific genetic diversity, dispersal patterns and phylogeographic relationships of Culex quinquefasciatus Say (Diptera: Culicidae) in Malaysia using reference data available in GenBank in order to reveal this species' phylogenetic relationships. A statistical parsimony network of 70 taxa aligned as 624 characters of the cytochrome c oxidase subunit I (COI) gene and 685 characters of the cytochrome c oxidase subunit II (COII) gene revealed three haplotypes (A1-A3) and four haplotypes (B1-B4), respectively. The concatenated sequences of both COI and COII genes with a total of 1309 characters revealed seven haplotypes (AB1-AB7). Analysis using tcs indicated that haplotype AB1 was the common ancestor and the most widespread haplotype in Malaysia. The genetic distance based on concatenated sequences of both COI and COII genes ranged from 0.00076 to 0.00229. Sequence alignment of Cx. quinquefasciatus from Malaysia and other countries revealed four haplotypes (AA1-AA4) by the COI gene and nine haplotypes (BB1-BB9) by the COII gene. Phylogenetic analyses demonstrated that Malaysian Cx. quinquefasciatus share the same genetic lineage as East African and Asian Cx. quinquefasciatus. This study has inferred the genetic lineages, dispersal patterns and hypothetical ancestral genotypes of Cx. quinquefasciatus. © 2013 The Royal Entomological Society.

Implementasi CMMI dalam Sebuah Organisasi Pengembang Software untuk Mencapai Return on Investment (ROI yang Diinginkan

Directory of Open Access Journals (Sweden)

Ikrar Adinata Arin

2012-06-01

Full Text Available The main mechanism to achieve a level of maturity in the organization of software developers is always focused, structured and consistent in carrying out work procedures of a quality standard applied. This article offers readers an approach and discourse of using CMMI (Capability Maturity Model Integrated concept thatgives a positive impact on development of organizational business in a software developer. The goals of CMMI are getting the best product quality, increasing productivity, reducing operational costs as well as software development period and increasing customer’s satisfaction. Nevertheless, a leader of the organization shouldalso be able to take important decisions to be consistent with the estimated time of desired return on investment (ROI.

Recovery from optic neuritis: an ROI-based analysis of LGN and visual cortical areas

DEFF Research Database (Denmark)

Korsholm, Kirsten; Madsen, Kristoffer Hougaard; Frederiksen, Jette L

2007-01-01

in the ROIs and compared activation during monocular stimulation of the affected and unaffected eye. In the acute phase the activation of LGN during visual stimulation of the affected eye was significantly reduced (P difference in LGN activation between...... the affected and unaffected eye diminished during recovery, and after 180 days the difference was no longer significant (P = 0.59). The decreased difference during recovery was mainly due to an increase in the fMRI signal when stimulating the affected eye, but included a component of a decreasing fMRI signal...... from LGN when stimulating the unaffected eye. In LOC, V1 and V2 activation during visual stimulation of the affected eye in the acute phase was significantly reduced (P difference diminished with no significant differences left after 180...

Fossil-based comparative analyses reveal ancient marine ancestry erased by extinction in ray-finned fishes.

Science.gov (United States)

Betancur-R, Ricardo; Ortí, Guillermo; Pyron, Robert Alexander

2015-05-01

The marine-freshwater boundary is a major biodiversity gradient and few groups have colonised both systems successfully. Fishes have transitioned between habitats repeatedly, diversifying in rivers, lakes and oceans over evolutionary time. However, their history of habitat colonisation and diversification is unclear based on available fossil and phylogenetic data. We estimate ancestral habitats and diversification and transition rates using a large-scale phylogeny of extant fish taxa and one containing a massive number of extinct species. Extant-only phylogenetic analyses indicate freshwater ancestry, but inclusion of fossils reveal strong evidence of marine ancestry in lineages now restricted to freshwaters. Diversification and colonisation dynamics vary asymmetrically between habitats, as marine lineages colonise and flourish in rivers more frequently than the reverse. Our study highlights the importance of including fossils in comparative analyses, showing that freshwaters have played a role as refuges for ancient fish lineages, a signal erased by extinction in extant-only phylogenies. © 2015 John Wiley & Sons Ltd/CNRS.

La Maison du Roi sous Louis XIV, une troupe d’élite. Étude tactique

OpenAIRE

Chauviré, Frédéric

2009-01-01

La Maison du roi constitue le corps le plus prestigieux de l’armée royale. Mais c’est aussi une troupe d’élite, redoutée sur tous les champs de bataille. Sa supériorité tactique trouve son origine dans la singularité de sa doctrine de combat. Beaucoup plus manœuvrière que les régiments ordinaires, elle s’en distingue également par sa conduite de la charge : choix de l’arme blanche, adoption d’une allure élevée et recherche du choc. Les qualités de cette troupe expliquent que Louis XIV ait vou...

A voxel-based approach to gray matter asymmetries.

Science.gov (United States)

Luders, E; Gaser, C; Jancke, L; Schlaug, G

2004-06-01

Voxel-based morphometry (VBM) was used to analyze gray matter (GM) asymmetries in a large sample (n = 60) of male and female professional musicians with and without absolute pitch (AP). We chose to examine these particular groups because previous studies using traditional region-of-interest (ROI) analyses have shown differences in hemispheric asymmetry related to AP and gender. Voxel-based methods may have advantages over traditional ROI-based methods since the analysis can be performed across the whole brain with minimal user bias. After determining that the VBM method was sufficiently sensitive for the detection of differences in GM asymmetries between groups, we found that male AP musicians were more leftward lateralized in the anterior region of the planum temporale (PT) than male non-AP musicians. This confirmed the results of previous studies using ROI-based methods that showed an association between PT asymmetry and the AP phenotype. We further observed that male non-AP musicians revealed an increased leftward GM asymmetry in the postcentral gyrus compared to female non-AP musicians, again corroborating results of a previously published study using ROI-based methods. By analyzing hemispheric GM differences across our entire sample, we were able to partially confirm findings of previous studies using traditional morphometric techniques, as well as more recent, voxel-based analyses. In addition, we found some unusually pronounced GM asymmetries in our musician sample not previously detected in subjects unselected for musical training. Since we were able to validate gender- and AP-related brain asymmetries previously described using traditional ROI-based morphometric techniques, the results of our analyses support the use of VBM for examinations of GM asymmetries.

Diabetes and Obesity as Independent Risk Factors for Osteoporosis: Updated Results from the ROIS/EMEROS Registry in a Population of Five Thousand Post-Menopausal Women Living in a Region Characterized by Heavy Environmental Pressure.

Science.gov (United States)

Neglia, Cosimo; Argentiero, Alberto; Chitano, Giovanna; Agnello, Nadia; Ciccarese, Roberta; Vigilanza, Antonella; Pantile, Valerio; Argentiero, Domenico; Quarta, Raffaele; Rivezzi, Matteo; Di Tanna, Gian Luca; Di Somma, Carolina; Migliore, Alberto; Iolascon, Giovanni; Gimigliano, Francesca; Distante, Alessandro; Piscitelli, Prisco

2016-11-01

Objectives : We aimed to analyze bone mineralization and the effect of different risk factors for osteoporosis in postmenopausal women. Methods : We found 4909 postmenopausal subjects within ≥10,000 records from the ROIS/EMEROS (Ionian and Salento Osteoporosis Registry/Euro Mediterranean Registry of Osteoporosis) registry, a population study carried out in an area characterized by heavy environmental pressure between Brindisi and Taranto from 2009 to 2016. All subjects were assessed via phalangeal quantitative ultrasound (QUS) to evaluate their bone mineralization (assessed via amplitude dependent speed of sound (AD-SoS)) and the association between demineralization and the presence of other conditions or risk factors. Results : Mean age was 64 ± 9.5 years and mean body mass index (BMI) was 28.7 ± 3.5 kg/m². Pearson correlation analyses revealed a negative association between bone mineralization (AD-SoS) and BMI ( p osteoporosis (adjusted for age, physical activity, and the use of drugs known to increase the risk of fractures) in subjects with diabetes and obesity: 1.39 (confidence interval (CI): 1.05-1.83) and 1.46 (CI: 1.20-1.78), respectively. A statistically significant linear trend of higher ORs of osteoporosis was found for increasing values of BMI. Conclusions : Our study confirmed the high impact of obesity and type 1 and type 2 diabetes on osteoporosis.

MRI Texture Analysis Reveals Deep Gray Nuclei Damage in Amyotrophic Lateral Sclerosis.

Science.gov (United States)

de Albuquerque, Milena; Anjos, Lara G V; Maia Tavares de Andrade, Helen; de Oliveira, Márcia S; Castellano, Gabriela; Junqueira Ribeiro de Rezende, Thiago; Nucci, Anamarli; França Junior, Marcondes Cavalcante

2016-01-01

Amyotrophic Lateral Sclerosis (ALS) is characterized by extensive corticospinal damage, but extrapyramidal involvement is suggested in pathological studies. Texture analysis (TA) is an image processing technique that evaluates the distribution of gray levels between pixels in a given region of interest (ROI). It provides quantitative data and has been employed in several neurodegenerative disorders. Here, we used TA to investigate possible deep gray nuclei (DGN) abnormalities in a cohort of ALS patients. Thirty-two ALS patients and 32 healthy controls underwent MRI in a 3T scanner. The T1 volumetric sequence was used for DGN segmentation and extraction of 11 texture parameters using the MaZda software. Statistical analyses were performed using the Mann-Whitney non-parametric test, with a significance level set at α = 0.025 (FDR-corrected) for TA. Patients had significantly higher values for the parameter correlation (CO) in both thalami and in the right caudate nucleus compared to healthy controls. Also, the parameter Inverse Difference Moment or Homogeneity (IDM) presented significantly smaller values in the ALS group in both thalami. TA of T1 weighted images revealed DGN alterations in patients with ALS, namely in the thalami and caudate nuclei. Copyright © 2015 by the American Society of Neuroimaging.

Integrated analyses resolve conflicts over squamate reptile phylogeny and reveal unexpected placements for fossil taxa.

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Tod W Reeder

Full Text Available Squamate reptiles (lizards and snakes are a pivotal group whose relationships have become increasingly controversial. Squamates include >9000 species, making them the second largest group of terrestrial vertebrates. They are important medicinally and as model systems for ecological and evolutionary research. However, studies of squamate biology are hindered by uncertainty over their relationships, and some consider squamate phylogeny unresolved, given recent conflicts between molecular and morphological results. To resolve these conflicts, we expand existing morphological and molecular datasets for squamates (691 morphological characters and 46 genes, for 161 living and 49 fossil taxa, including a new set of 81 morphological characters and adding two genes from published studies and perform integrated analyses. Our results resolve higher-level relationships as indicated by molecular analyses, and reveal hidden morphological support for the molecular hypothesis (but not vice-versa. Furthermore, we find that integrating molecular, morphological, and paleontological data leads to surprising placements for two major fossil clades (Mosasauria and Polyglyphanodontia. These results further demonstrate the importance of combining fossil and molecular information, and the potential problems of estimating the placement of fossil taxa from morphological data alone. Thus, our results caution against estimating fossil relationships without considering relevant molecular data, and against placing fossils into molecular trees (e.g. for dating analyses without considering the possible impact of molecular data on their placement.

Integrated analyses resolve conflicts over squamate reptile phylogeny and reveal unexpected placements for fossil taxa.

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Reeder, Tod W; Townsend, Ted M; Mulcahy, Daniel G; Noonan, Brice P; Wood, Perry L; Sites, Jack W; Wiens, John J

2015-01-01

Squamate reptiles (lizards and snakes) are a pivotal group whose relationships have become increasingly controversial. Squamates include >9000 species, making them the second largest group of terrestrial vertebrates. They are important medicinally and as model systems for ecological and evolutionary research. However, studies of squamate biology are hindered by uncertainty over their relationships, and some consider squamate phylogeny unresolved, given recent conflicts between molecular and morphological results. To resolve these conflicts, we expand existing morphological and molecular datasets for squamates (691 morphological characters and 46 genes, for 161 living and 49 fossil taxa, including a new set of 81 morphological characters and adding two genes from published studies) and perform integrated analyses. Our results resolve higher-level relationships as indicated by molecular analyses, and reveal hidden morphological support for the molecular hypothesis (but not vice-versa). Furthermore, we find that integrating molecular, morphological, and paleontological data leads to surprising placements for two major fossil clades (Mosasauria and Polyglyphanodontia). These results further demonstrate the importance of combining fossil and molecular information, and the potential problems of estimating the placement of fossil taxa from morphological data alone. Thus, our results caution against estimating fossil relationships without considering relevant molecular data, and against placing fossils into molecular trees (e.g. for dating analyses) without considering the possible impact of molecular data on their placement.

Integrated Analyses Resolve Conflicts over Squamate Reptile Phylogeny and Reveal Unexpected Placements for Fossil Taxa

Science.gov (United States)

Reeder, Tod W.; Townsend, Ted M.; Mulcahy, Daniel G.; Noonan, Brice P.; Wood, Perry L.; Sites, Jack W.; Wiens, John J.

2015-01-01

Squamate reptiles (lizards and snakes) are a pivotal group whose relationships have become increasingly controversial. Squamates include >9000 species, making them the second largest group of terrestrial vertebrates. They are important medicinally and as model systems for ecological and evolutionary research. However, studies of squamate biology are hindered by uncertainty over their relationships, and some consider squamate phylogeny unresolved, given recent conflicts between molecular and morphological results. To resolve these conflicts, we expand existing morphological and molecular datasets for squamates (691 morphological characters and 46 genes, for 161 living and 49 fossil taxa, including a new set of 81 morphological characters and adding two genes from published studies) and perform integrated analyses. Our results resolve higher-level relationships as indicated by molecular analyses, and reveal hidden morphological support for the molecular hypothesis (but not vice-versa). Furthermore, we find that integrating molecular, morphological, and paleontological data leads to surprising placements for two major fossil clades (Mosasauria and Polyglyphanodontia). These results further demonstrate the importance of combining fossil and molecular information, and the potential problems of estimating the placement of fossil taxa from morphological data alone. Thus, our results caution against estimating fossil relationships without considering relevant molecular data, and against placing fossils into molecular trees (e.g. for dating analyses) without considering the possible impact of molecular data on their placement. PMID:25803280

Evaluation of bone involvement in patients with Gaucher disease: a semi-quantitative magnetic resonance imaging method (using ROI estimation of bone lesion) as an alternative method to semi-quantitative methods used so far.

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Komninaka, Veroniki; Kolomodi, Dionysia; Christoulas, Dimitrios; Marinakis, Theodoros; Papatheodorou, Athanasios; Repa, Konstantina; Voskaridou, Ersi; Revenas, Konstantinos; Terpos, Evangelos

2015-10-01

The aim of this study was to evaluate bone involvement in patients with Gaucher disease (GD) and to propose a novel semi-quantitative magnetic resonance imaging (MRI) staging. MRI of the lumbar spine, femur, and tibia was performed in 24 patients with GD and 24 healthy controls. We also measured circulating levels of C-C motif ligand-3 (CCL-3) chemokine, C-telopeptide of collagen type-1 (CTX), and tartrate-resistant acid phosphatase isoform type-b (TRACP-5b). We used the following staging based on MRI data: stage I: region of interest (ROI) 1/2 of normal values and bone infiltration up to 30%; stage II: ROI 1/3 of normal values and bone infiltration from 30 to 60%; stage III: ROI 1/4 of normal values and bone infiltration from 60% to 80%; and stage IV: detection of epiphyseal infiltration, osteonecrosis and deformity regardless of the ROI's values. All but two patients had abnormal MRI findings: 9 (37.5%), 6 (25%), 3 (12.5%), and 4 (16.7%) had stages I-IV, respectively. Patients with GD had elevated chitotriosidase, serum TRACP-5b, and CCL-3 levels (P < 0.001). We propose an easily reproducible semi-quantitative scoring system and confirm that patients with GD have abnormal MRI bone findings and enhanced osteoclast activity possibly due to elevated CCL-3. © 2015 John Wiley & Sons A/S. Published by John Wiley & Sons Ltd.

Development of intelligent surveillance system (ISS) in region of interest (ROI) using Kalman filter and camshift on Raspberry Pi 2

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Park, Junghun; Hong, Kicheon

2017-06-01

Due to the improvement of the picture quality of closed-circuit television (CCTV), the demand for CCTV has increased rapidly and its market size has also increased. The current system structure of CCTV transfers compressed images without analysis received from CCTV to a control center. The compressed images are suitable for the evidence required for a criminal arrest, but they cannot prevent crime in real time, which has been considered a limitation. Thus, the present paper proposes a system implementation that can prevent crimes by applying a situation awareness system at the back end of the CCTV cameras for image acquisition to prevent crimes efficiently. In the system implemented in the present paper, the region of interest (ROI) is set virtually within the image data when a barrier, such as fence, cannot be installed in actual sites and unauthorized intruders are tracked constantly through data analysis and recognized in the ROI via the developed algorithm. Additionally, a searchlight or alarm sound is activated to prevent crime in real time and the urgent information is transferred to the control center. The system was implemented in the Raspberry Pi 2 board to be run in real time. The experiment results showed that the recognition success rate was 85% or higher and the track accuracy was 90% or higher. By utilizing the system, crime prevention can be achieved by implementing a social safety network.

Comparative proteomic analyses reveal that FlbA down-regulates gliT expression and SOD activity in Aspergillus fumigatus.

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Shin, Kwang-Soo; Park, Hee-Soo; Kim, Young-Hwan; Yu, Jae-Hyuk

2013-07-11

FlbA is a regulator of G-protein signaling protein that plays a central role in attenuating heterotrimeric G-protein mediated vegetative growth signaling in Aspergillus. The deletion of flbA (∆flbA) in the opportunistic human pathogen Aspergillus fumigatus results in accelerated cell death and autolysis in submerged culture. To further investigate the effects of ∆flbA on intracellular protein levels we carried out 2-D proteome analyses of 2-day old submerged cultures of ∆flbA and wild type (WT) strains and observed 160 differentially expressed proteins. Via nano-LC-ESI-MS/MS analyses, we revealed the identity of 10 and 2 proteins exhibiting high and low level accumulation, respectively, in ∆flbA strain. Notably, the GliT protein is accumulated at about 1800-fold higher levels in ∆flbA than WT. Moreover, GliT is secreted at high levels from ∆flbA strain, whereas Sod1 (superoxide dismutase) is secreted at a higher level in WT. Northern blot analyses reveal that ∆flbA results in elevated accumulation of gliT mRNA. Consequently, ∆flbA strain exhibits enhanced tolerance to gliotoxin toxicity. Finally, ∆flbA strain displayed enhanced SOD activity and elevated resistance to menadione and paraquat. In summary, FlbA-mediated signaling control negatively affects cellular responses associated with detoxification of reactive oxygen species and of exogenous gliotoxin in A. fumigatus. Regulator of G protein Signaling (RGS) proteins play crucial roles in fundamental biological processes in filamentous fungi. FlbA is the first studied filamentous fungal RGS protein, yet much remains to be understood about its roles in the opportunistic human pathogen Aspergillus fumigatus. In the present study, we examined the effects of the deletion of flbA using comprehensive analyses of the intra- and extracellular proteomes of A. fumigatus wild type and the flbA deletion mutant. Via MS analyses, we identified 10 proteins exhibiting high level accumulation in the flbA deletion

Diabetes and Obesity as Independent Risk Factors for Osteoporosis: Updated Results from the ROIS/EMEROS Registry in a Population of Five Thousand Post-Menopausal Women Living in a Region Characterized by Heavy Environmental Pressure

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Cosimo Neglia

2016-11-01

Full Text Available Objectives: We aimed to analyze bone mineralization and the effect of different risk factors for osteoporosis in postmenopausal women. Methods: We found 4909 postmenopausal subjects within ≥10,000 records from the ROIS/EMEROS (Ionian and Salento Osteoporosis Registry/Euro Mediterranean Registry of Osteoporosis registry, a population study carried out in an area characterized by heavy environmental pressure between Brindisi and Taranto from 2009 to 2016. All subjects were assessed via phalangeal quantitative ultrasound (QUS to evaluate their bone mineralization (assessed via amplitude dependent speed of sound (AD-SoS and the association between demineralization and the presence of other conditions or risk factors. Results: Mean age was 64 ± 9.5 years and mean body mass index (BMI was 28.7 ± 3.5 kg/m2. Pearson correlation analyses revealed a negative association between bone mineralization (AD-SoS and BMI (p < 0.001. By using multivariate logistic regression analysis, we observed significant values of odds ratios (ORs of osteoporosis (adjusted for age, physical activity, and the use of drugs known to increase the risk of fractures in subjects with diabetes and obesity: 1.39 (confidence interval (CI: 1.05–1.83 and 1.46 (CI: 1.20–1.78, respectively. A statistically significant linear trend of higher ORs of osteoporosis was found for increasing values of BMI. Conclusions: Our study confirmed the high impact of obesity and type 1 and type 2 diabetes on osteoporosis.

Functional assays and metagenomic analyses reveals differences between the microbial communities inhabiting the soil horizons of a Norway spruce plantation.

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Stéphane Uroz

Full Text Available In temperate ecosystems, acidic forest soils are among the most nutrient-poor terrestrial environments. In this context, the long-term differentiation of the forest soils into horizons may impact the assembly and the functions of the soil microbial communities. To gain a more comprehensive understanding of the ecology and functional potentials of these microbial communities, a suite of analyses including comparative metagenomics was applied on independent soil samples from a spruce plantation (Breuil-Chenue, France. The objectives were to assess whether the decreasing nutrient bioavailability and pH variations that naturally occurs between the organic and mineral horizons affects the soil microbial functional biodiversity. The 14 Gbp of pyrosequencing and Illumina sequences generated in this study revealed complex microbial communities dominated by bacteria. Detailed analyses showed that the organic soil horizon was significantly enriched in sequences related to Bacteria, Chordata, Arthropoda and Ascomycota. On the contrary the mineral horizon was significantly enriched in sequences related to Archaea. Our analyses also highlighted that the microbial communities inhabiting the two soil horizons differed significantly in their functional potentials according to functional assays and MG-RAST analyses, suggesting a functional specialisation of these microbial communities. Consistent with this specialisation, our shotgun metagenomic approach revealed a significant increase in the relative abundance of sequences related glycoside hydrolases in the organic horizon compared to the mineral horizon that was significantly enriched in glycoside transferases. This functional stratification according to the soil horizon was also confirmed by a significant correlation between the functional assays performed in this study and the functional metagenomic analyses. Together, our results suggest that the soil stratification and particularly the soil resource

Bias in tensor based morphometry Stat-ROI measures may result in unrealistic power estimates.

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Thompson, Wesley K; Holland, Dominic

2011-07-01

A series of reports have recently appeared using tensor based morphometry statistically-defined regions of interest, Stat-ROIs, to quantify longitudinal atrophy in structural MRIs from the Alzheimer's Disease Neuroimaging Initiative (ADNI). This commentary focuses on one of these reports, Hua et al. (2010), but the issues raised here are relevant to the others as well. Specifically, we point out a temporal pattern of atrophy in subjects with Alzheimer's disease and mild cognitive impairment whereby the majority of atrophy in two years occurs within the first 6 months, resulting in overall elevated estimated rates of change. Using publicly-available ADNI data, this temporal pattern is also found in a group of identically-processed healthy controls, strongly suggesting that methodological bias is corrupting the measures. The resulting bias seriously impacts the validity of conclusions reached using these measures; for example, sample size estimates reported by Hua et al. (2010) may be underestimated by a factor of five to sixteen. Copyright © 2011 Elsevier Inc. All rights reserved.

[Buffon, the director of 'Jardin du Roi' in the 1700s].

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Jeune, Bernard; Petersen, Hans Christian

2008-01-01

Buffon and Linné were the two greatest naturalists of the 1700s. As they were both born in 1707, their 300 anniversaries were therefore celebrated in France and Sweden. At the celebration meeting at the University of Bourgogne in Dijon - The Buffon Legacy - September 3-6, 2007, we presented the following paper: "Buffon and the longevity of species". In the present paper the life and work of Buffon is introduced on the basis of recent literature, including Jacques Roger's famous biography. Among non-biologists Buffon has nearly been forgotten, even though in the 1700s he was considered to be at the same level as the most famous French thinkers of the Enlightenment - Montesquieu, Voltaire, Rousseau and Diderot. His largest contributions were the publication of his comprehensive "Histoire naturelle" and his long and significant leadership of "Jardin du Roi", which he built up to become one of the best scientific institutions of Europe. Buffon's scientific contributions wereas overshadowed by those of Linné, as it was his classification system, which became dominant all overn Europe. Buffon's student Lamarck and later Darwin contributed by pushing Buffon in oblivion of history, even though Darwin valued him highly. However, in recent decades Buffon is experiencing a renaissance in connection with the increasing interest in biological anthropology, biogeography, ethology, and ecology, as well as on account of his modern species concept.

Investigating the Impact uf E-Learning as an Alternative for Business Education in Pharmaceutical Industry in Romania by Roi Methodology

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Petruţa Blaga

2014-08-01

Full Text Available The capability of organizations to accumulate and apply new knowledge is a key factor in order to achieve the new competitive standards. A continuous changing diversity, to which the need of adaptation to the changes of external environment is added, speeds up the rate of development and business education. The new information and communication technologies speed up the rate of change and increase the need of education that is subject to a higher information flow. The achievements of information technology, along with changes within society, determine the creation of new paradigms for business education and training. Under these circumstances, e-learning has become one of the main educational forms of human resources in business. This research aims to measure the impact of some initiatives within human resources on an organization, market leader within pharmaceutical field, namely measuring the efficiency of business education programs concerning human resources through e-learning. Under these circumstances, the carried-out research aims to put into practice the theoretical frame of ROI (Return on Investment methodology of evaluating the business education programs concerning human resources in five stages, suggested by J. J. Phillips. The research validates theoretical data of the surveyed model and it is based on the analysis of the data gathering process within the ROI Methodology. This work shows only aspects related to the measuring of the participants` reaction towards the e-learning business education program, respectively

Procès inquisitorial contra el castellà d'Amposta Fra Pedro Roiç de Moros a la cúria pontificia del papa Benet XIII (I414-1418

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Alanyà i Roig, Josep

2002-06-01

Full Text Available The Arxiu de la Corona d'Aragó in Barcelona houses the original commital proceedings instituted by a court of cardinals set up by pope Benedict XIII in the year 1414 and teh trial itself of the lord of Amposta, Fra Pedro Roiç de Moros, knight of the Order of St. John of Jerusalem, who had been charged with indictable offences—concubinage, robbery, housing apostates, oath breaking and counterfeiting money, mismanagement of the Castlery's assets, excesses against his vassals, wasteful use of assets, dereliction and property abandonment— of which he was found guilty, and thereafter sentenced to losing the dignity of his lordship. Roiç de Moros appealed to the Council of Constance as well as to pope Martin V. It would be to no avail. Roiç de Moros paid a very high price for choosing to support count Jaume d'Urgell and deciding to oppose Ferran dAntequera and the policies of pope Benedict XIII. The follow up and analysis of the court´s records are very interesting for their human variety and interesting informations about fortresses, houses, barns, treaures and services there were in different locations of the Castlery of Amposta, such as Batea, Gandesa, Miravet, Ulldecona, Ascó and other towns and villages along the Ribera d´Ebre. The whole criminal prosecution bears a very peculiar historic interest mainly because the protagonists, the court procedures, and their causes are the link between the Interregnum in the Aragonese Crown and the fìnal days of the Western Schism.

A l'Arxiu de la Corona d'Aragó de Barcelona es conserva el procés original instruït per un tribunal de cardenals creat pel papa Benet XIII l'any 1414 per jutjar el Castella d'Amposta, l'hospitaler Fra Pedro Roiç de Moros, acusat de crims greus —concubinat, bandositats, recepció d’apòstates, perjuri i fabricació de moneda falsa, mala administració dels bens de la Castellania, comissió d'excessos contra els seus vassalls, dilapidado de bens i abando

Reliability evaluation of I-123 ADAM SPECT imaging using SPM software and AAL ROI methods

Energy Technology Data Exchange (ETDEWEB)

Yang, Bang-Hung [Department of Biomedical Imaging and Radiological Sciences, National Yang-Ming University, Taipei, Taiwan (China); Department of Nuclear Medicine, Taipei Veterans General Hospital, Taiwan (China); Tsai, Sung-Yi [Department of Biomedical Imaging and Radiological Sciences, National Yang-Ming University, Taipei, Taiwan (China); Department of Imaging Medical, St.Martin De Porres Hospital, Chia-Yi, Taiwan (China); Wang, Shyh-Jen [Department of Biomedical Imaging and Radiological Sciences, National Yang-Ming University, Taipei, Taiwan (China); Department of Nuclear Medicine, Taipei Veterans General Hospital, Taiwan (China); Su, Tung-Ping; Chou, Yuan-Hwa [Department of Psychiatry, Taipei Veterans General Hospital, Taipei, Taiwan (China); Chen, Chia-Chieh [Institute of Nuclear Energy Research, Longtan, Taiwan (China); Chen, Jyh-Cheng, E-mail: jcchen@ym.edu.tw [Department of Biomedical Imaging and Radiological Sciences, National Yang-Ming University, Taipei, Taiwan (China)

2011-08-21

The level of serotonin was regulated by serotonin transporter (SERT), which is a decisive protein in regulation of serotonin neurotransmission system. Many psychiatric disorders and therapies were also related to concentration of cerebral serotonin. I-123 ADAM was the novel radiopharmaceutical to image SERT in brain. The aim of this study was to measure reliability of SERT densities of healthy volunteers by automated anatomical labeling (AAL) method. Furthermore, we also used statistic parametric mapping (SPM) on a voxel by voxel analysis to find difference of cortex between test and retest of I-123 ADAM single photon emission computed tomography (SPECT) images. Twenty-one healthy volunteers were scanned twice with SPECT at 4 h after intravenous administration of 185 MBq of {sup 123}I-ADAM. The image matrix size was 128x128 and pixel size was 3.9 mm. All images were obtained through filtered back-projection (FBP) reconstruction algorithm. Region of interest (ROI) definition was performed based on the AAL brain template in PMOD version 2.95 software package. ROI demarcations were placed on midbrain, pons, striatum, and cerebellum. All images were spatially normalized to the SPECT MNI (Montreal Neurological Institute) templates supplied with SPM2. And each image was transformed into standard stereotactic space, which was matched to the Talairach and Tournoux atlas. Then differences across scans were statistically estimated on a voxel by voxel analysis using paired t-test (population main effect: 2 cond's, 1 scan/cond.), which was applied to compare concentration of SERT between the test and retest cerebral scans. The average of specific uptake ratio (SUR: target/cerebellum-1) of {sup 123}I-ADAM binding to SERT in midbrain was 1.78{+-}0.27, pons was 1.21{+-}0.53, and striatum was 0.79{+-}0.13. The cronbach's {alpha} of intra-class correlation coefficient (ICC) was 0.92. Besides, there was also no significant statistical finding in cerebral area using SPM2

Molecular analyses reveal high species diversity of trematodes in a sub-Arctic lake

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Soldánová, Miroslava; Georgieva, Simona; Roháčováa, Jana; Knudsen, Rune; Kuhn, Jesper A.; Henriksen, Eirik H.; Siwertsson, Anna; Shaw, Jenny C.; Kuris, Armand M.; Amundsen, Per-Arne; Scholz, Tomáš; Lafferty, Kevin D.; Kostadinova, Aneta

2017-01-01

To identify trematode diversity and life-cycles in the sub-Arctic Lake Takvatn, Norway, we characterised 120 trematode isolates from mollusc first intermediate hosts, metacercariae from second intermediate host fishes and invertebrates, and adults from fish and invertebrate definitive hosts, using molecular techniques. Phylogenies based on nuclear and/or mtDNA revealed high species richness (24 species or species-level genetic lineages), and uncovered trematode diversity (16 putative new species) from five families typical in lake ecosystems (Allocreadiidae, Diplostomidae, Plagiorchiidae, Schistosomatidae and Strigeidae). Sampling potential invertebrate hosts allowed matching of sequence data for different stages, thus achieving molecular elucidation of trematode life-cycles and exploration of host-parasite interactions. Phylogenetic analyses also helped identify three major mollusc intermediate hosts (Radix balthica, Pisidium casertanum and Sphaerium sp.) in the lake. Our findings increase the known trematode diversity at the sub-Arctic Lake Takvatn, showing that digenean diversity is high in this otherwise depauperate sub-Arctic freshwater ecosystem, and indicating that sub-Arctic and Arctic ecosystems may be characterised by unique trematode assemblages.

Genetic Diversity among Rhizobium leguminosarum bv. Trifolii Strains Revealed by Allozyme and Restriction Fragment Length Polymorphism Analyses

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Demezas, David H.; Reardon, Terry B.; Watson, John M.; Gibson, Alan H.

1991-01-01

Allozyme electrophoresis and restriction fragment length polymorphism (RFLP) analyses were used to examine the genetic diversity of a collection of 18 Rhizobium leguminosarum bv. trifolii, 1 R. leguminosarum bv. viciae, and 2 R. meliloti strains. Allozyme analysis at 28 loci revealed 16 electrophoretic types. The mean genetic distance between electrophoretic types of R. leguminosarum and R. meliloti was 0.83. Within R. leguminosarum, the single strain of bv. viciae differed at an average of 0.65 from strains of bv. trifolii, while electrophoretic types of bv. trifolii differed at a range of 0.23 to 0.62. Analysis of RFLPs around two chromosomal DNA probes also delineated 16 unique RFLP patterns and yielded genetic diversity similar to that revealed by the allozyme data. Analysis of RFLPs around three Sym (symbiotic) plasmid-derived probes demonstrated that the Sym plasmids reflect genetic divergence similar to that of their bacterial hosts. The large genetic distances between many strains precluded reliable estimates of their genetic relationships. PMID:16348600

« Les rois de Ségou » : De l'épopée à la série télévisée | Tamari ...

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Les Rois de Ségou (“The Kings of Segu”) is a television series from Mali directed by ... Together with another film released at about the same time, Samanyana Basi (“Basi from ... dialogues are laden with adages, thus approximating the characteristics of bardic speech. ... EMAIL FREE FULL TEXT EMAIL FREE FULL TEXT

Using Soil Conservation Strategies in the Development of Learning Activities for the Students of Roi - Et College of Agriculture and Technology

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Jariya Kanchanwong

2017-06-01

Full Text Available The purposes of this research were 1 to study nutrient content in soil samples taken from Roi - Et College of Agriculture and Technology Campus, 2 to study the social factors, economic factors and technological factors the effect on soil conservation of Roi - Et College of Agriculture and Technology students, 3 the development of soil conservation activities Learning package efficiency of 80/80, 4 to Study and to compare the knowledge, attitudes and skills regarding soil conservation of students of Roi - Et College of Agriculture and Technology. The student activities package of learning soil conservation was enrolled by 40 people in its club. These people were selected by purposive sampling. The instruments were used in this research as follows; 1 scientific analysis, 2 social questionnaire on economic and technological factors affecting soil conservation, 3 test of knowledge about soil conservation, 4 test of attitudes about soil conservation, 5 test of skill about soil conservation. The experimental research was designed to use students as key informants. The statistics analysis was used in the research as follows: frequency, percentage, average, standard deviation, test results, assumptions which included a dependent t-test statistical at the significance level of 0.05. The results of the study were as follows: 1 The study found that the amount of soil nutrient content (N: P: K around cultivated plants in an area of converted agriculture land have the significance: Soil checks collected in plots from soil containing morning glory, chrysanthemums, marigolds, corn and cassava, and had neutral pH. 2 The results of the analysis determing the factors that affected the conservation of soil found economic factors were at a high level Social factors and technology factors were moderate thus leading the approach that has come to create of learning activities package in soil conservation. 3 The results showed that the efficiency of the manual was 83

Semi-automatic ROI placement system for analysis of brain PET images based on elastic model. Application to diagnosis of Alzheimer's disease

International Nuclear Information System (INIS)

Ohyama, Masashi; Mishina, Masahiro; Kitamura, Shin; Katayama, Yasuo; Senda, Michio; Tanizaki, Naoki; Ishii, Kenji

2000-01-01

PET with 18F-fluorodeoxyglucose (FDG) is a useful technique to image cerebral glucose metabolism and to detect patients with Alzheimer's disease in the early stage, in which characteristic temporoparietal hypometabolism is visualized. We have developed a new system, in which the standard brain ROI atlas made of networks of segments is elastically transformed to match the subject brain images, so that standard ROIs defined on the segments are placed on the individual brain images and are used to measure radioactivity over each brain region. We applied this methods to Alzheimer's disease. This method was applied to the images of 10 normal subjects (ages 55 +/- 12) and 21 patients clinically diagnosed as Alzheimer's disease (age 61 +/- 10). The FDG uptake reflecting glucose metabolism was evaluated with SUV, i.e. decay corrected radioactivity divided by injected dose per body weight in (Bq/ml)/(Bq/g). The system worked all right in every subject including those with extensive hypometabolism. Alzheimer patients showed markedly lower in the parietal cortex (4.0-4.1). When the threshold value of FDG uptake in the parietal lobe was set as 5 (Bq/ml)/(Bq/g), we could discriminate the patients with Alzheimer's disease from the normal subjects. The sensitivity was 86% and the specificity was 90%. This system can assist diagnosis of FDG images and may be useful for treating data of a large number of subjects; e.g. when PET is applied to health screening. (author)

Comparative analyses reveal different consequences of two oxidative stress inducers, gamma irradiation and potassium tellurite, in the extremophile Deinococcus radiodurans

International Nuclear Information System (INIS)

Narasimha, Anaganti; Basu, Bhakti; Apte, Shree Kumar

2014-01-01

Proteomic and mass spectrometric analyses revealed differential responses of D. radiodurans to two oxidative stressors. While both elicited oxidative stress alleviation response, major divergence was observed at the level of DNA repair, metabolic pathways and protein homeostasis. Response to gamma irradiation was focused on DNA repair and ROS scavenging but supported metabolism as well as protein homeostasis. Tellurite, induced oxidative stress alleviation but decreased reducing affected and adversely affected metabolism and protein homeostasis

Grey-matter volume as a potential feature for the classification of Alzheimer's disease and mild cognitive impairment: an exploratory study.

Science.gov (United States)

Guo, Yane; Zhang, Zengqiang; Zhou, Bo; Wang, Pan; Yao, Hongxiang; Yuan, Minshao; An, Ningyu; Dai, Haitao; Wang, Luning; Zhang, Xi; Liu, Yong

2014-06-01

Specific patterns of brain atrophy may be helpful in the diagnosis of Alzheimer's disease (AD). In the present study, we set out to evaluate the utility of grey-matter volume in the classification of AD and amnestic mild cognitive impairment (aMCI) compared to normal control (NC) individuals. Voxel-based morphometric analyses were performed on structural MRIs from 35 AD patients, 27 aMCI patients, and 27 NC participants. A two-sample two-tailed t-test was computed between the NC and AD groups to create a map of abnormal grey matter in AD. The brain areas with significant differences were extracted as regions of interest (ROIs), and the grey-matter volumes in the ROIs of the aMCI patients were included to evaluate the patterns of change across different disease severities. Next, correlation analyses between the grey-matter volumes in the ROIs and all clinical variables were performed in aMCI and AD patients to determine whether they varied with disease progression. The results revealed significantly decreased grey matter in the bilateral hippocampus/parahippocampus, the bilateral superior/middle temporal gyri, and the right precuneus in AD patients. The grey-matter volumes were positively correlated with clinical variables. Finally, we performed exploratory linear discriminative analyses to assess the classifying capacity of grey-matter volumes in the bilateral hippocampus and parahippocampus among AD, aMCI, and NC. Leave-one-out cross-validation analyses demonstrated that grey-matter volumes in hippocampus and parahippocampus accurately distinguished AD from NC. These findings indicate that grey-matter volumes are useful in the classification of AD.

Development of Guidelines for Mentoring Internal Supervision for the Schools under Roi-Et Office of Primary Education Service Area 2

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Natchana Sahunil

2017-06-01

Full Text Available The research aimed to 1 study the factors and indicators of mentoring internal supervision for schools, 2 study the current state and the desirable state of mentoring internal supervision for schools, and 3 study the guidelines on the operation of mentoring internal supervision for the schools under Roi-Et Office of Primary Education Service Area 2. The research was divided into 3 phases. In phase 1 the informants comprised 5 certified experts. In phase 2 the sample comprised 488 government teachers under Roi-Et Office of Primary Education Service Area 2, btained through multi-stage random sampling. In phase 3 the informants comprised school directors, school deputy directors and supervisor teachers under Roi-Et Office of Primary Education Service Area 2, totally 9 persons. The research instruments onsisted of 1 a questionnaire having the discrimination from 0.34 to 0.79 and the total reliability of 0.87, 2 a structured interview form, and 3 a suitability and feasibility assessment form for the guidelines on the operation of mentoring internal supervision. The analysis of data employed percentage, the mean and standard deviation. The results are as follows: 1. There are 4 factors of the guidelines on mentoring internal supervision for schools. They are: preparation of mentoring supervision, with 12 indicators ; management of mentoring supervision, with 12 indicators ; operation of mentoring supervision, with 14 indicators ; and evaluation of mentoring supervision, with 10 indicators, all of which had been evaluated by the experts as, on the whole, very suitable. 2. The current state of the mentoring internal supervision for schools, on the whole and factor by factor, was in the moderate level in every factor. Meanwhile, the desirable state of mentoring internal supervision for schools, on the whole, was in the high level. When considered factor by factor, the factor with the highest mean is management of mentoring supervision. The factor with

Global terrestrial water storage connectivity revealed using complex climate network analyses

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Sun, A. Y.; Chen, J.; Donges, J.

2015-07-01

Terrestrial water storage (TWS) exerts a key control in global water, energy, and biogeochemical cycles. Although certain causal relationship exists between precipitation and TWS, the latter quantity also reflects impacts of anthropogenic activities. Thus, quantification of the spatial patterns of TWS will not only help to understand feedbacks between climate dynamics and the hydrologic cycle, but also provide new insights and model calibration constraints for improving the current land surface models. This work is the first attempt to quantify the spatial connectivity of TWS using the complex network theory, which has received broad attention in the climate modeling community in recent years. Complex networks of TWS anomalies are built using two global TWS data sets, a remote sensing product that is obtained from the Gravity Recovery and Climate Experiment (GRACE) satellite mission, and a model-generated data set from the global land data assimilation system's NOAH model (GLDAS-NOAH). Both data sets have 1° × 1° grid resolutions and cover most global land areas except for permafrost regions. TWS networks are built by first quantifying pairwise correlation among all valid TWS anomaly time series, and then applying a cutoff threshold derived from the edge-density function to retain only the most important features in the network. Basinwise network connectivity maps are used to illuminate connectivity of individual river basins with other regions. The constructed network degree centrality maps show the TWS anomaly hotspots around the globe and the patterns are consistent with recent GRACE studies. Parallel analyses of networks constructed using the two data sets reveal that the GLDAS-NOAH model captures many of the spatial patterns shown by GRACE, although significant discrepancies exist in some regions. Thus, our results provide further measures for constraining the current land surface models, especially in data sparse regions.

Combining region- and network-level brain-behavior relationships in a structural equation model.

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Bolt, Taylor; Prince, Emily B; Nomi, Jason S; Messinger, Daniel; Llabre, Maria M; Uddin, Lucina Q

2018-01-15

Brain-behavior associations in fMRI studies are typically restricted to a single level of analysis: either a circumscribed brain region-of-interest (ROI) or a larger network of brain regions. However, this common practice may not always account for the interdependencies among ROIs of the same network or potentially unique information at the ROI-level, respectively. To account for both sources of information, we combined measurement and structural components of structural equation modeling (SEM) approaches to empirically derive networks from ROI activity, and to assess the association of both individual ROIs and their respective whole-brain activation networks with task performance using three large task-fMRI datasets and two separate brain parcellation schemes. The results for working memory and relational tasks revealed that well-known ROI-performance associations are either non-significant or reversed when accounting for the ROI's common association with its corresponding network, and that the network as a whole is instead robustly associated with task performance. The results for the arithmetic task revealed that in certain cases, an ROI can be robustly associated with task performance, even when accounting for its associated network. The SEM framework described in this study provides researchers additional flexibility in testing brain-behavior relationships, as well as a principled way to combine ROI- and network-levels of analysis. Copyright © 2017 Elsevier Inc. All rights reserved.

IntroductionLa parole des rois à la fin du Moyen Âge : les voies d’une enquête

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Stéphane PÉQUIGNOT

2007-10-01

Full Text Available El artículo sugiere algunas propuestas para una investigación general sobre el hablar de los reyes a finales de la Edad Media. Basándose en un estado de la cuestión para el caso de la Corona de Aragón, se indaga la inscripción del hablar de los reyes en distintas temporalidades imbricadas entre sí. La transcripción de las palabras resulta de un proceso complejo, la « fábrica de la palabra », cuyos mecanismos y huellas son objeto de estudio. Por otra parte, las representaciones del hablar de los reyes hacen a menudo referencia a unos modelos traídos del pasado, a veces se dirigen a un público futuro, mientras testimonian también su necesaria adaptación a las circunstancias de cada momento. Estos « actas reales de palabra », así como los « estilos expresivos » que contribuyen a forjar, se examinan en la secunda parte del artículo. Finalmente, el tiempo dedicado o dejado a las palabras reales participa de las evoluciones a largo plazo de las relaciones a lo escrito, de los regímenes políticos y de su forma de legitimación ; constituye un modo de comunicación político importante, un recurso y, también, una toma de riesgo para el poder y la autoridad monarquica.L’article invite à une enquête générale sur la parole des rois à la fin du Moyen Âge et en esquisse plusieurs voies possibles. À l’aide d’un état de la question sur la couronne d’Aragon, c’est l’inscription de la parole des rois dans différentes temporalités imbriquées qui est visée. Sa transcription même résulte d’un processus complexe, la « fabrique de la parole », dont mécanismes et traces sont examinés. D’autre part, les représentations de la parole des rois renvoient souvent à des modèles du passé, visent parfois un public futur tout en témoignant aussi d’une nécessaire adaptation aux circonstances présentes. Ces « actes royaux de parole » et les « styles expressifs » qu’ils contribuent à consolider

Career satisfaction and work-life balance of specialist orthodontists within the UK/ROI.

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Al-Junaid, S M; Hodges, S J; Petrie, A; Cunningham, S J

2017-07-07

Objectives To investigate factors affecting career satisfaction and work-life balance in specialist orthodontists in the UK/ROI.Design and setting Prospective questionnaire-based study.Subjects and methods The questionnaire was sent to specialist orthodontists who were members of the British Orthodontic Society.Results Orthodontists reported high levels of career satisfaction (median score 90/100). Career satisfaction was significantly higher in those who exhibited: i) satisfaction with working hours; ii) satisfaction with the level of control over their working day; iii) ability to manage unexpected home events; and iv) confidence in how readily they managed patient expectations. The work-life balance score was lower than the career satisfaction score but the median score was 75/100. Work-life balance scores were significantly affected by the same four factors, but additionally were higher in those who worked part-time.Conclusions Orthodontists in this study were highly satisfied with their career and the majority responded that they would choose orthodontics again. Work-life balance scores were lower than career satisfaction scores but still relatively high. It is important for the profession to consider ways of maintaining, or improving, career satisfaction and work-life balance; including maintaining flexibility of working hours and ensuring that all clinicians have ready access to appropriate training courses throughout their careers (for example, management of patient expectations).

Conserved regulators of nucleolar size revealed by global phenotypic analyses.

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Neumüller, Ralph A; Gross, Thomas; Samsonova, Anastasia A; Vinayagam, Arunachalam; Buckner, Michael; Founk, Karen; Hu, Yanhui; Sharifpoor, Sara; Rosebrock, Adam P; Andrews, Brenda; Winston, Fred; Perrimon, Norbert

2013-08-20

Regulation of cell growth is a fundamental process in development and disease that integrates a vast array of extra- and intracellular information. A central player in this process is RNA polymerase I (Pol I), which transcribes ribosomal RNA (rRNA) genes in the nucleolus. Rapidly growing cancer cells are characterized by increased Pol I-mediated transcription and, consequently, nucleolar hypertrophy. To map the genetic network underlying the regulation of nucleolar size and of Pol I-mediated transcription, we performed comparative, genome-wide loss-of-function analyses of nucleolar size in Saccharomyces cerevisiae and Drosophila melanogaster coupled with mass spectrometry-based analyses of the ribosomal DNA (rDNA) promoter. With this approach, we identified a set of conserved and nonconserved molecular complexes that control nucleolar size. Furthermore, we characterized a direct role of the histone information regulator (HIR) complex in repressing rRNA transcription in yeast. Our study provides a full-genome, cross-species analysis of a nuclear subcompartment and shows that this approach can identify conserved molecular modules.

Conserved Regulators of Nucleolar Size Revealed by Global Phenotypic Analyses

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Neumüller, Ralph A.; Gross, Thomas; Samsonova, Anastasia A.; Vinayagam, Arunachalam; Buckner, Michael; Founk, Karen; Hu, Yanhui; Sharifpoor, Sara; Rosebrock, Adam P.; Andrews, Brenda; Winston, Fred; Perrimon, Norbert

2014-01-01

Regulation of cell growth is a fundamental process in development and disease that integrates a vast array of extra- and intracellular information. A central player in this process is RNA polymerase I (Pol I), which transcribes ribosomal RNA (rRNA) genes in the nucleolus. Rapidly growing cancer cells are characterized by increased Pol I–mediated transcription and, consequently, nucleolar hypertrophy. To map the genetic network underlying the regulation of nucleolar size and of Pol I–mediated transcription, we performed comparative, genome-wide loss-of-function analyses of nucleolar size in Saccharomyces cerevisiae and Drosophila melanogaster coupled with mass spectrometry–based analyses of the ribosomal DNA (rDNA) promoter. With this approach, we identified a set of conserved and nonconserved molecular complexes that control nucleolar size. Furthermore, we characterized a direct role of the histone information regulator (HIR) complex in repressing rRNA transcription in yeast. Our study provides a full-genome, cross-species analysis of a nuclear subcompartment and shows that this approach can identify conserved molecular modules. PMID:23962978

Mitochondrial dysfunction, oxidative stress and apoptosis revealed by proteomic and transcriptomic analyses of the striata in two mouse models of Parkinson’s disease

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Chin, Mark H.; Qian, Weijun; Wang, Haixing; Petyuk, Vladislav A.; Bloom, Joshua S.; Sforza, Daniel M.; Lacan, Goran; Liu, Dahai; Khan, Arshad H.; Cantor, Rita M.; Bigelow, Diana J.; Melega, William P.; Camp, David G.; Smith, Richard D.; Smith, Desmond J.

2008-02-10

The molecular mechanisms underlying the changes in the nigrostriatal pathway in Parkinson disease (PD) are not completely understood. Here we use mass spectrometry and microarrays to study the proteomic and transcriptomic changes in the striatum of two mouse models of PD, induced by the distinct neurotoxins 1-methyl-4-phenyl-1,2,3,6-tetrahydropyridine (MPTP) and methamphetamine (METH). Proteomic analyses resulted in the identification and relative quantification of 912 proteins with two or more unique peptides and 85 proteins with significant abundance changes following neurotoxin treatment. Similarly, microarray analyses revealed 181 genes with significant changes in mRNA following neurotoxin treatment. The combined protein and gene list provides a clearer picture of the potential mechanisms underlying neurodegeneration observed in PD. Functional analysis of this combined list revealed a number of significant categories, including mitochondrial dysfunction, oxidative stress response and apoptosis. Additionally, codon usage and miRNAs may play an important role in translational control in the striatum. These results constitute one of the largest datasets integrating protein and transcript changes for these neurotoxin models with many similar endpoint phenotypes but distinct mechanisms.

Total Mini-Mental State Examination score and regional cerebral blood flow using Z score imaging and automated ROI analysis software in subjects with memory impairment

International Nuclear Information System (INIS)

Ikeda, Eiji; Shiozaki, Kazumasa; Takahashi, Nobukazu; Togo, Takashi; Odawara, Toshinari; Oka, Takashi; Inoue, Tomio; Hirayasu, Yoshio

2008-01-01

The Mini-Mental State Examination (MMSE) is considered a useful supplementary method to diagnose dementia and evaluate the severity of cognitive disturbance. However, the region of the cerebrum that correlates with the MMSE score is not clear. Recently, a new method was developed to analyze regional cerebral blood flow (rCBF) using a Z score imaging system (eZIS). This system shows changes of rCBF when compared with a normal database. In addition, a three-dimensional stereotaxic region of interest (ROI) template (3DSRT), fully automated ROI analysis software was developed. The objective of this study was to investigate the correlation between rCBF changes and total MMSE score using these new methods. The association between total MMSE score and rCBF changes was investigated in 24 patients (mean age±standard deviation (SD) 71.5±9.2 years; 6 men and 18 women) with memory impairment using eZIS and 3DSRT. Step-wise multiple regression analysis was used for multivariate analysis, with the total MMSE score as the dependent variable and rCBF change in 24 areas as the independent variable. Total MMSE score was significantly correlated only with the reduction of left hippocampal perfusion but not with right (P<0.01). Total MMSE score is an important indicator of left hippocampal function. (author)

Effects of Land-Use Change and Managed Aquifer Recharge on Geochemical Reactions with Implications for Groundwater Quantity and Quality in Atoll Island Aquifers, Roi-Namur, Republic of the Marshall Islands

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Hejazian, M.; Swarzenski, P. W.; Gurdak, J. J.; Odigie, K. O.; Storlazzi, C. D.

2015-12-01

This study compares the hydrogeochemistry of two contrasting atoll groundwater systems in Roi-Namur, Republic of the Marshall Islands. Roi-Namur houses a U.S. Department of Defense military installation and presents an ideal study location where a human impacted aquifer is co-located next to a natural aquifer as part of two artificially conjoined atoll islands. The hydrogeology and geochemistry of carbonate atoll aquifers has been well studied, particularly because of its small, well-defined hydrologic system that allows for relatively precise modeling. However, it is unknown how changes in land-use/land cover and managed aquifer recharge (MAR) alters natural geochemical processes in atoll aquifers. A better understanding of this has implications on groundwater quantity and quality, carbonate dissolution, and best aquifer management practices in the context of rising sea level and saltwater intrusion. Roi has been heavily modified to house military and civilian operations; here, lack of vegetation and managed recharge has increased the volume of potable groundwater and affected the geochemical processes in the freshwater lens and saltwater transition zone. Namur is heavily vegetated and the hydrogeology is indicative of a natural atoll island. A suite of monitoring wells were sampled across both island settings for major ions, nutrients, trace elements, DOC/DIC, δ13C and δ18O/2H isotopes. By modeling geochemical reactions using a conservative mixing approach, we measure deviations from expected reactions and compare the two contrasting settings using derived geochemical profiles through a wide salinity spectrum. Results indicate that groundwater on Namur is more heavily depleted in δ13C and has greater dissolved inorganic carbon, suggesting higher microbial oxidation and greater dissolution within the carbonate aquifer. This suggests MAR and reduction of vegetation makes the groundwater supply on atoll islands more resilient to sea level rise.

Le roi et la parole dans quelques recueils d’exempla castillans des XIIIe et XIVe siècles

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Olivier Biaggini

2007-05-01

Full Text Available Aquí se examina el hablar del rey tal como lo ponen en escena los relatos ejemplares de Calila e Dimna, Sendebar, Castigos de Sancho IV y El conde Lucanor de don Juan Manuel. Un recorrido previo por el discurso alfonsí (Espéculo y Segunda partida permite precisar los planteamientos de la cuestión mostrando que la palabra regia vale menos por su enunciado que por su enunciación, sometida a unas reglas estrictas. Ahora bien, regular la palabra sirve para definir las condiciones de su poder. De modo muy diverso, las colecciones de exempla representan el hablar del rey en situaciones que subrayan su prestigio o que indican a la inversa la necesidad de controlar sus efectos nefastos. En todo caso, contribuye directamente a la construcción de modelos políticos que, si bien se aplican ante todo a la realeza (Calila, Sendebar, Castigos, pueden en cierta medida ajustarse también a la nobleza (Conde Lucanor.On examine ici la parole du roi telle que la mettent en scène les récits exemplaires du Calila e Dimna, du Sendebar, des Castigos de Sanche IV et du Conde Lucanor de Don Juan Manuel. Un détour par le discours juridique alphonsin (Espéculo et Segunda partida permet de préciser les enjeux de cette question en montrant que la parole royale vaut moins par son énoncé que par son énonciation, soumise à des contraintes strictes. Or, réguler la parole sert à définir les conditions de son pouvoir. De façon très variée, les recueils d’exempla représentent la parole du roi dans des situations qui soulignent son prestige ou, inversement, pointent la nécessité d’en contrôler les effets néfastes. Dans tous les cas, elle contribue directement à la construction de modèles politiques qui, s’ils s’appliquent avant tout à la royauté (Calila, Sendebar, Castigos, sont aussi en partie transposables à la noblesse (Conde Lucanor.

Structural analyses of Legionella LepB reveal a new GAP fold that catalytically mimics eukaryotic RasGAP.

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Yu, Qin; Hu, Liyan; Yao, Qing; Zhu, Yongqun; Dong, Na; Wang, Da-Cheng; Shao, Feng

2013-06-01

Rab GTPases are emerging targets of diverse bacterial pathogens. Here, we perform biochemical and structural analyses of LepB, a Rab GTPase-activating protein (GAP) effector from Legionella pneumophila. We map LepB GAP domain to residues 313-618 and show that the GAP domain is Rab1 specific with a catalytic activity higher than the canonical eukaryotic TBC GAP and the newly identified VirA/EspG family of bacterial RabGAP effectors. Exhaustive mutation analyses identify Arg444 as the arginine finger, but no catalytically essential glutamine residues. Crystal structures of LepB313-618 alone and the GAP domain of Legionella drancourtii LepB in complex with Rab1-GDP-AlF3 support the catalytic role of Arg444, and also further reveal a 3D architecture and a GTPase-binding mode distinct from all known GAPs. Glu449, structurally equivalent to TBC RabGAP glutamine finger in apo-LepB, undergoes a drastic movement upon Rab1 binding, which induces Rab1 Gln70 side-chain flipping towards GDP-AlF3 through a strong ionic interaction. This conformationally rearranged Gln70 acts as the catalytic cis-glutamine, therefore uncovering an unexpected RasGAP-like catalytic mechanism for LepB. Our studies highlight an extraordinary structural and catalytic diversity of RabGAPs, particularly those from bacterial pathogens.

Multiple spectroscopic analyses reveal the fate and metabolism of sulfamide herbicide triafamone in agricultural environments

International Nuclear Information System (INIS)

Wang, Mengcen; Qian, Yuan; Liu, Xiaoyu; Wei, Peng; Deng, Man; Wang, Lei; Wu, Huiming; Zhu, Guonian

2017-01-01

Triafamone, a sulfamide herbicide, has been extensively utilized for weed control in rice paddies in Asia. However, its fate and transformation in the environment have not been established. Through a rice paddy microcosm-based simulation trial combined with multiple spectroscopic analyses, we isolated and identified three novel metabolites of triafamone, including hydroxyl triafamone (HTA), hydroxyl triafamone glycoside (HTAG), and oxazolidinedione triafamone (OTA). When triafamone was applied to rice paddies at a concentration of 34.2 g active ingredient/ha, this was predominantly distributed in the paddy soil and water, and then rapidly dissipated in accordance with the first-order rate model, with half-lives of 4.3–11.0 days. As the main transformation pathway, triafamone was assimilated by the rice plants and was detoxified into HTAG, whereas the rest was reduced into HTA with subsequent formation of OTA. At the senescence stage, brown rice had incurred triafamone at a concentration of 0.0016 mg/kg, but the hazard quotient was <1, suggesting that long-term consumption of the triafamone-containing brown rice is relatively safe. The findings of the present study indicate that triafamone is actively metabolized in the agricultural environment, and elucidation of the link between environmental exposure to these triazine or oxazolidinedione moieties that contain metabolites and their potential impacts is warranted. - Highlights: • Multiple spectroscopic analyses were applied to investigate agrochemicals transformation in environment. • Three novel compounds were isolated and identified as triafamone metabolites. • The fate and transformation pathway of triafamone in rice paddy were revealed. • Long-term consumption of the triafamone-containing brown rice is relatively safe. • Elucidation of environmental impacts by exposure to these triazine or oxazolidinedione metabolites is warranted. - Triafamone rapidly dissipates in agricultural environments

A localization algorithm of adaptively determining the ROI of the reference circle in image

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Xu, Zeen; Zhang, Jun; Zhang, Daimeng; Liu, Xiaomao; Tian, Jinwen

2018-03-01

Aiming at solving the problem of accurately positioning the detection probes underwater, this paper proposed a method based on computer vision which can effectively solve this problem. The theory of this method is that: First, because the shape information of the heat tube is similar to a circle in the image, we can find a circle which physical location is well known in the image, we set this circle as the reference circle. Second, we calculate the pixel offset between the reference circle and the probes in the picture, and adjust the steering gear through the offset. As a result, we can accurately measure the physical distance between the probes and the under test heat tubes, then we can know the precise location of the probes underwater. However, how to choose reference circle in image is a difficult problem. In this paper, we propose an algorithm that can adaptively confirm the area of reference circle. In this area, there will be only one circle, and the circle is the reference circle. The test results show that the accuracy of the algorithm of extracting the reference circle in the whole picture without using ROI (region of interest) of the reference circle is only 58.76% and the proposed algorithm is 95.88%. The experimental results indicate that the proposed algorithm can effectively improve the efficiency of the tubes detection.

Normalized STEAM-based diffusion tensor imaging provides a robust assessment of muscle tears in football players: preliminary results of a new approach to evaluate muscle injuries.

Science.gov (United States)

Giraudo, Chiara; Motyka, Stanislav; Weber, Michael; Karner, Manuela; Resinger, Christoph; Feiweier, Thorsten; Trattnig, Siegfried; Bogner, Wolfgang

2018-02-08

To assess acute muscle tears in professional football players by diffusion tensor imaging (DTI) and evaluate the impact of normalization of data. Eight football players with acute lower limb muscle tears were examined. DTI metrics of the injured muscle and corresponding healthy contralateral muscle and of ROIs drawn in muscle tears (ROI tear ) in the corresponding healthy contralateral muscle (ROI hc_t ) in a healthy area ipsilateral to the injury (ROI hi ) and in a corresponding contralateral area (ROI hc_i ) were compared. The same comparison was performed for ratios of the injured (ROI tear /ROI hi ) and contralateral sides (ROI hc_t /ROI hc_i ). ANOVA, Bonferroni-corrected post-hoc and Student's t-tests were used. Analyses of the entire muscle did not show any differences (p>0.05 each) except for axial diffusivity (AD; p=0.048). ROI tear showed higher mean diffusivity (MD) and AD than ROI hc_t (ptear than in ROI hi and ROI hc_t (ptear than in any other ROI (pmuscle tears in athletes especially after normalization to healthy muscle tissue. • STEAM-based DTI allows the investigation of muscle tears affecting professional football players. • Fractional anisotropy and mean diffusivity differ between injured and healthy muscle areas. • Only normalized data show differences of fibre tracking metrics in muscle tears. • The normalization of DTI-metrics enables a more robust characterization of muscle tears.

MRI-derived Restriction Spectrum Imaging Cellularity Index is Associated with High Grade Prostate Cancer on Radical Prostatectomy Specimens

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Michael Andre Liss

2015-02-01

Full Text Available Objectives: We evaluate a novel magnetic resonance imaging (MRI technique to improve detection of aggressive prostate cancer. Methods: We performed a retrospective analysis of presurgical prostate MRI scans using an advanced diffusion weighted imaging technique called Restriction Spectrum Imaging (RSI, which can be presented as a normalized z-score statistic (RSI z-score. Scans were acquired prior to radical prostatectomy. Prostatectomy specimens were processed using whole mount sectioning and regions of interest (ROIs were drawn around individual prostate cancer (PCa tumors. Corresponding ROIs were drawn on the MRI imaging and paired with ROIs in regions with no pathology. RSI z-score and conventional apparent diffusion coefficient (ADC values were recorded for each ROI. Paired t-test, ANOVA and logistic regression analyses were performed.Results: We evaluated 28 patients with 64 regions of interest (28 benign and 36 PCa. The mean difference in RSI z-score (PCa ROI – Benign ROI was 2.17 (SE = 0.11; p <0.001 and in ADC was 551 mm2/sec (SE = 80 mm2/sec; paired t-test, p <0.001. The differences in the means among all groups (benign, primary Gleason 3 and primary Gleason 4 was significant for both RSI z-score (F3,64 = 97.7, p <0.001 and ADC (F3,64 = 13.9, p <0.001. A t-test was performed on only PCa tumor ROIs (n=36 to determine prostate cancer aggressiveness (Gleason 3 vs. Gleason 4 revealing that RSI z-score was still significant (p = 0.03, whereas, ADC values were no longer significant (p = 0.08. In multivariable analysis adjusting for age and race, RSI z-score was associated with PCa aggressiveness (OR 10.3, 95%CI: 1.4-78.0, p=0.02 while ADC trended to significance (p=0.07. Conclusions: The RSI derived normalized cellularity index (RSI z-score is associated with aggressive prostate cancer as determined by pathologic Gleason scores. Further utilization of RSI techniques may serve to enhance standardized reporting systems.

Patterns and processes of Mycobacterium bovis evolution revealed by phylogenomic analyses

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Mycobacterium bovis is an important animal pathogen worldwide that parasitizes wild and domesticated vertebrate livestock as well as humans. A comparison of the five M. bovis complete genomes from UK, South Korea, Brazil and USA revealed four novel large-scale structural variations of at least 2,000...

Integrated in silico Analyses of Regulatory and Metabolic Networks of Synechococcus sp. PCC 7002 Reveal Relationships between Gene Centrality and Essentiality

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Hyun-Seob Song

2015-03-01

Full Text Available Cyanobacteria dynamically relay environmental inputs to intracellular adaptations through a coordinated adjustment of photosynthetic efficiency and carbon processing rates. The output of such adaptations is reflected through changes in transcriptional patterns and metabolic flux distributions that ultimately define growth strategy. To address interrelationships between metabolism and regulation, we performed integrative analyses of metabolic and gene co-expression networks in a model cyanobacterium, Synechococcus sp. PCC 7002. Centrality analyses using the gene co-expression network identified a set of key genes, which were defined here as “topologically important.” Parallel in silico gene knock-out simulations, using the genome-scale metabolic network, classified what we termed as “functionally important” genes, deletion of which affected growth or metabolism. A strong positive correlation was observed between topologically and functionally important genes. Functionally important genes exhibited variable levels of topological centrality; however, the majority of topologically central genes were found to be functionally essential for growth. Subsequent functional enrichment analysis revealed that both functionally and topologically important genes in Synechococcus sp. PCC 7002 are predominantly associated with translation and energy metabolism, two cellular processes critical for growth. This research demonstrates how synergistic network-level analyses can be used for reconciliation of metabolic and gene expression data to uncover fundamental biological principles.

Gross alpha/beta analyses in water by liquid scintillation counting

International Nuclear Information System (INIS)

Wong, C.T.; Lawrence Livermore National Laboratory, CA; Soliman, V.M.; Perera, S.K.

2005-01-01

The standard procedure for analyzing gross alpha and gross beta in water is evaporation of the sample and radioactivity determination of the resultant solids by proportional counting. This technique lacks precision, and lacks sensitivity for samples with high total dissolved solids. Additionally, the analytical results are dependent on the choice of radionuclide calibration standard and the sample matrix. Direct analysis by liquid scintillation counting has the advantages of high counting efficiencies and minimal sample preparation time. However, due to the small sample aliquants used for analysis, long count times are necessary to reach required detection limits. The procedure proposed consists of evaporating a sample aliquant to dryness, dissolving the resultant solids in a small volume of dilute acid, followed by liquid scintillation counting to determine radioactivity. This procedure can handle sample aliquants containing up to 500 mg of dissolved solids. Various acids, scintillation cocktail mixtures, instrument discriminator settings, and regions of interest (ROI) were evaluated to determine optimum counting conditions. Precision is improved and matrix effects are reduced as compared to proportional counting. Tests indicate that this is a viable alternative to proportional counting for gross alpha and gross beta analyses of water samples. (author)

Revealing climate modes in steric sea levels: lessons learned from satellite geodesy, objective analyses and ocean reanalyses

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Pfeffer, J.; Tregoning, P.; Purcell, A. P.

2017-12-01

Due to increased greenhouse gases emissions, the oceans are accumulating heat. In response to the ocean circulation and atmospheric forcing, the heat is irregularly redistributed within the oceans, causing sea level to rise at variable rates in space and time. These rates of steric expansion are extremely difficult to assess because of the sparsity of in-situ hydrographic observations available within the course of the 20th century. We compare here three methods to reconstruct the steric sea levels over the past 13, 25 and 58 years based on satellite geodesy, objective analyses and ocean reanalyses. The interannual to decadal variability of each dataset is explored with a model merging six climate indices representative of the natural variability of the ocean and climate system. Consistent regional patterns are identified for the Pacific Decadal Oscillation (PDO) and El Niño Southern Oscillation (ENSO) in all datasets at all timescales. Despite the short time coverage (13 years), the combination of satellite geodetic data (altimetry and GRACE) also reveals significant steric responses to the North Pacific Gyre Oscillation (NPGO), Indian Dipole (IOD) and Indian ocean basinwide (IOBM) mode. The richer information content in the ocean reanalyses allows us to recover the regional fingerprints of the PDO, ENSO, NPGO, IOD and IOBM, but also of the Atlantic Multidecadal Oscillation (AMO) acting over longer time scales (40 to 60 years). Therefore, ocean reanalyses, coupled with climate mode analyses, constitute innovative and promising tools to investigate the mechanisms triggering the variability of sea level rise over the past decades.

Schizophrenia and Category-Selectivity in the Brain: Normal for Faces but Abnormal for Houses

Directory of Open Access Journals (Sweden)

Lisa Kronbichler

2018-02-01

Full Text Available Face processing is regularly found to be impaired in schizophrenia (SZ, thus suggesting that social malfunctioning might be caused by dysfunctional face processing. Most studies focused on emotional face processes, whereas non-emotional face processing received less attention. While current reports on abnormal face processing in SZ are mixed, examinations of non-emotional face processing compared to adequate control stimuli may clarify whether SZ is characterized by a face-processing deficit. Patients with SZ (n = 28 and healthy controls (n = 30 engaged in an fMRI scan where images of non-emotional faces and houses were presented. A simple inverted-picture detection task warranted the participants’ attention. Region of interest (ROI analyses were conducted on face-sensitive regions including the fusiform face area, the occipital face area, and the superior temporal sulcus. Scene-sensitivity was assessed in the parahippocampal place area (PPA and served as control condition. Patients did not show aberrant face-related neural processes in face-sensitive regions. This finding was also evident when analyses were done on individually defined ROIs or on in-house-localizer ROIs. Patients revealed a decreased specificity toward house stimuli as reflected in decreased neural response toward houses in the PPA. Again, this result was supported by supplementary analyses. Neural activation toward neutral faces was not found to be impaired in SZ, therefore speaking against an overall face-processing deficit. Aberrant activation in scene-sensitive PPA is also found in assessments of memory processes in SZ. It is up to future studies to show how impairments in PPA relate to functional outcome in SZ.

Genome-wide Comparative Analyses Reveal the Dynamic Evolution of Nucleotide-Binding Leucine-Rich Repeat Gene Family among Solanaceae Plants

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Eunyoung Seo

2016-08-01

Full Text Available Plants have evolved an elaborate innate immune system against invading pathogens. Within this system, intracellular nucleotide-binding leucine-rich repeat (NLR immune receptors are known play critical roles in effector-triggered immunity (ETI plant defense. We performed genome-wide identification and classification of NLR-coding sequences from the genomes of pepper, tomato, and potato using fixed criteria. We then compared genomic duplication and evolution features. We identified intact 267, 443, and 755 NLR-encoding genes in tomato, potato, and pepper genomes, respectively. Phylogenetic analyses and classification of Solanaceae NLRs revealed that the majority of NLR super family members fell into 14 subgroups, including a TIR-NLR (TNL subgroup and 13 non-TNL subgroups. Specific subgroups have expanded in each genome, with the expansion in pepper showing subgroup-specific physical clusters. Comparative analysis of duplications showed distinct duplication patterns within pepper and among Solanaceae plants suggesting subgroup- or species-specific gene duplication events after speciation, resulting in divergent evolution. Taken together, genome-wide analyses of NLR family members provide insights into their evolutionary history in Solanaceae. These findings also provide important foundational knowledge for understanding NLR evolution and will empower broader characterization of disease resistance genes to be used for crop breeding.

Bibliometric Analyses Reveal Patterns of Collaboration between ASMS Members

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Palmblad, Magnus; van Eck, Nees Jan

2018-03-01

We have explored the collaborative network of the current American Society for Mass Spectrometry (ASMS) membership using bibliometric methods. The analysis shows that 4249 members are connected in a single, large, co-authorship graph, including the majority of the most published authors in the field of mass spectrometry. The map reveals topographical differences between university groups and national laboratories, and that the co-authors with the strongest links have long worked together at the same location. We have collected and summarized information on the geographical distribution of members, showing a high coverage of active researchers in North America and Western Europe. Looking at research fields, we could also identify a number of new or `hot' topics among ASMS members. Interactive versions of the maps are available on-line at https://goo.gl/UBNFMQ (collaborative network) and https://goo.gl/WV25vm (research topics). [Figure not available: see fulltext.

Iron homeostasis in Arabidopsis thaliana: transcriptomic analyses reveal novel FIT-regulated genes, iron deficiency marker genes and functional gene networks.

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Mai, Hans-Jörg; Pateyron, Stéphanie; Bauer, Petra

2016-10-03

FIT (FER-LIKE IRON DEFICIENCY-INDUCED TRANSCRIPTION FACTOR) is the central regulator of iron uptake in Arabidopsis thaliana roots. We performed transcriptome analyses of six day-old seedlings and roots of six week-old plants using wild type, a fit knock-out mutant and a FIT over-expression line grown under iron-sufficient or iron-deficient conditions. We compared genes regulated in a FIT-dependent manner depending on the developmental stage of the plants. We assembled a high likelihood dataset which we used to perform co-expression and functional analysis of the most stably iron deficiency-induced genes. 448 genes were found FIT-regulated. Out of these, 34 genes were robustly FIT-regulated in root and seedling samples and included 13 novel FIT-dependent genes. Three hundred thirty-one genes showed differential regulation in response to the presence and absence of FIT only in the root samples, while this was the case for 83 genes in the seedling samples. We assembled a virtual dataset of iron-regulated genes based on a total of 14 transcriptomic analyses of iron-deficient and iron-sufficient wild-type plants to pinpoint the best marker genes for iron deficiency and analyzed this dataset in depth. Co-expression analysis of this dataset revealed 13 distinct regulons part of which predominantly contained functionally related genes. We could enlarge the list of FIT-dependent genes and discriminate between genes that are robustly FIT-regulated in roots and seedlings or only in one of those. FIT-regulated genes were mostly induced, few of them were repressed by FIT. With the analysis of a virtual dataset we could filter out and pinpoint new candidates among the most reliable marker genes for iron deficiency. Moreover, co-expression and functional analysis of this virtual dataset revealed iron deficiency-induced and functionally distinct regulons.

Selection of optimum ROI for dual radionuclide analysis of 55Fe-63Ni and 63Ni-60Co

International Nuclear Information System (INIS)

Priya, S.; Prabhath Ravi, K.; Yadav, R.K.B.; Rao, D.D.; Gopalakrishnan, R.K.

2016-01-01

Dual label counting in liquid scintillation counting (LSC) enables simultaneous activity determination of two radionuclides. Dual counting procedure for 3 H and 14 C has been well established. There are several other nuclides like 63 Ni (E β- =67keV), 55 Fe (6 keV X-ray and auger electron) which are often chemically separated using detailed procedures with high decontamination factors (DF) and quantified using LSC. Despite the laborious separations, traces of these nuclides in the chemically separated fractions can mutually make their quantification difficult due to overlap of counts from both radionuclides in the spectrum, which gets further complicated in presence of traces of 60 Co. For dual label counting technique, it is essential to establish the discriminator setting at which there will be spillover of counts from both radionuclides in the two counting regions required for the inclusion method. The objective of the current work is to establish two counting ROI's for dual counting of (i) 63 Ni- 55 Fe and (ii) 63 Ni- 60 Co in a TDCR based LSC system

Coastal groundwater exchange on a small Pacific atoll island: Roi Namur, Republic of the Marshall Islands

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Oberle, Ferdinand K. J.; Swarzenski, Peter W.; Storlazzi, Curt

2017-04-01

Atoll islands, most of which only average 1-2 meters above today's sea level, provide a tremendous natural laboratory in which to study and better understand the intensifying impacts of high rates of sea-level rise on tropical reef-lined islands globally due to their unique geologic structure and limited water supply. Groundwater resources of atolls are typically minimal due to the low elevation and small surface area of the islands and are also subject to recurring droughts, and more frequent, storm-driven seawater overwash events. Although groundwater is the principal means of freshwater storage on atoll islands and is a major factor in determining the overall sustainability of island communities, hydrological data on how an aquifer will response to changes in sea-level rise or storm-driven overwash remain limited. We here present high-resolution time series hydrogeological and geochemical data to determine the role of the atoll's carbonate geology, land use, and atmospheric and oceanographic forcing in driving coastal groundwater exchange on the island of Roi Namur on Kwajalein Atoll in the Republic of the Marshall Islands. This information can provide new estimates on the recovery and resilience of coastal groundwater resources on such islands to expected climate change-driven perturbations.

Optimization of Region-of-Interest Sampling Strategies for Hepatic MRI Proton Density Fat Fraction Quantification

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Hong, Cheng William; Wolfson, Tanya; Sy, Ethan Z.; Schlein, Alexandra N.; Hooker, Jonathan C.; Dehkordy, Soudabeh Fazeli; Hamilton, Gavin; Reeder, Scott B.; Loomba, Rohit; Sirlin, Claude B.

2017-01-01

BACKGROUND Clinical trials utilizing proton density fat fraction (PDFF) as an imaging biomarker for hepatic steatosis have used a laborious region-of-interest (ROI) sampling strategy of placing an ROI in each hepatic segment. PURPOSE To identify a strategy with the fewest ROIs that consistently achieves close agreement with the nine-ROI strategy. STUDY TYPE Retrospective secondary analysis of prospectively acquired clinical research data. POPULATION A total of 391 adults (173 men, 218 women) with known or suspected NAFLD. FIELD STRENGTH/SEQUENCE Confounder-corrected chemical-shift-encoded 3T MRI using a 2D multiecho gradientrecalled echo technique. ASSESSMENT An ROI was placed in each hepatic segment. Mean nine-ROI PDFF and segmental PDFF standard deviation were computed. Segmental and lobar PDFF were compared. PDFF was estimated using every combinatorial subset of ROIs and compared to the nine-ROI average. STATISTICAL TESTING Mean nine-ROI PDFF and segmental PDFF standard deviation were summarized descriptively. Segmental PDFF was compared using a one-way analysis of variance, and lobar PDFF was compared using a paired t-test and a Bland–Altman analysis. The PDFF estimated by every subset of ROIs was informally compared to the nine-ROI average using median intraclass correlation coefficients (ICCs) and Bland–Altman analyses. RESULTS The study population’s mean whole-liver PDFF was 10.1±8.9% (range: 1.1–44.1%). Although there was no significant difference in average segmental (P=0.452) or lobar (P=0.154) PDFF, left and right lobe PDFF differed by at least 1.5 percentage points in 25.1% (98/391) of patients. Any strategy with ≥ 4 ROIs had ICC >0.995. 115 of 126 four-ROI strategies (91%) had limits of agreement (LOA) 0.995, and 2/36 (6%) of two-ROI strategies and 46/84 (55%) of three-ROI strategies had LOA <1.5%. DATA CONCLUSION Four-ROI sampling strategies with two ROIs in the left and right lobes achieve close agreement with nine-ROI PDFF. Level of

Optimization of region-of-interest sampling strategies for hepatic MRI proton density fat fraction quantification.

Science.gov (United States)

Hong, Cheng William; Wolfson, Tanya; Sy, Ethan Z; Schlein, Alexandra N; Hooker, Jonathan C; Fazeli Dehkordy, Soudabeh; Hamilton, Gavin; Reeder, Scott B; Loomba, Rohit; Sirlin, Claude B

2018-04-01

Clinical trials utilizing proton density fat fraction (PDFF) as an imaging biomarker for hepatic steatosis have used a laborious region-of-interest (ROI) sampling strategy of placing an ROI in each hepatic segment. To identify a strategy with the fewest ROIs that consistently achieves close agreement with the nine-ROI strategy. Retrospective secondary analysis of prospectively acquired clinical research data. A total of 391 adults (173 men, 218 women) with known or suspected NAFLD. Confounder-corrected chemical-shift-encoded 3T MRI using a 2D multiecho gradient-recalled echo technique. An ROI was placed in each hepatic segment. Mean nine-ROI PDFF and segmental PDFF standard deviation were computed. Segmental and lobar PDFF were compared. PDFF was estimated using every combinatorial subset of ROIs and compared to the nine-ROI average. Mean nine-ROI PDFF and segmental PDFF standard deviation were summarized descriptively. Segmental PDFF was compared using a one-way analysis of variance, and lobar PDFF was compared using a paired t-test and a Bland-Altman analysis. The PDFF estimated by every subset of ROIs was informally compared to the nine-ROI average using median intraclass correlation coefficients (ICCs) and Bland-Altman analyses. The study population's mean whole-liver PDFF was 10.1 ± 8.9% (range: 1.1-44.1%). Although there was no significant difference in average segmental (P = 0.452) or lobar (P = 0.154) PDFF, left and right lobe PDFF differed by at least 1.5 percentage points in 25.1% (98/391) of patients. Any strategy with ≥4 ROIs had ICC >0.995. 115 of 126 four-ROI strategies (91%) had limits of agreement (LOA) 0.995, and 2/36 (6%) of two-ROI strategies and 46/84 (55%) of three-ROI strategies had LOA <1.5%. Four-ROI sampling strategies with two ROIs in the left and right lobes achieve close agreement with nine-ROI PDFF. 3 Technical Efficacy: Stage 2 J. Magn. Reson. Imaging 2018;47:988-994. © 2017 International Society for Magnetic Resonance

Interspecies introgressive hybridization in spiny frogs Quasipaa (Family Dicroglossidae) revealed by analyses on multiple mitochondrial and nuclear genes.

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Zhang, Qi-Peng; Hu, Wen-Fang; Zhou, Ting-Ting; Kong, Shen-Shen; Liu, Zhi-Fang; Zheng, Rong-Quan

2018-01-01

Introgression may lead to discordant patterns of variation among loci and traits. For example, previous phylogeographic studies on the genus Quasipaa detected signs of genetic introgression from genetically and morphologically divergent Quasipaa shini or Quasipaa spinosa . In this study, we used mitochondrial and nuclear DNA sequence data to verify the widespread introgressive hybridization in the closely related species of the genus Quasipaa , evaluate the level of genetic diversity, and reveal the formation mechanism of introgressive hybridization. In Longsheng, Guangxi Province, signs of asymmetrical nuclear introgression were detected between Quasipaa boulengeri and Q. shini . Unidirectional mitochondrial introgression was revealed from Q. spinosa to Q. shini . By contrast, bidirectional mitochondrial gene introgression was detected between Q. spinosa and Q. shini in Lushan, Jiangxi Province. Our study also detected ancient hybridizations between a female Q. spinosa and a male Q. jiulongensis in Zhejiang Province. Analyses on mitochondrial and nuclear genes verified three candidate cryptic species in Q. spinosa , and a cryptic species may also exist in Q. boulengeri . However, no evidence of introgressive hybridization was found between Q. spinosa and Q. boulengeri . Quasipaa exilispinosa from all the sampling localities appeared to be deeply divergent from other communities. Our results suggest widespread introgressive hybridization in closely related species of Quasipaa and provide a fundamental basis for illumination of the forming mechanism of introgressive hybridization, classification of species, and biodiversity assessment in Quasipaa .

Comprehensive analyses of imprinted differentially methylated regions reveal epigenetic and genetic characteristics in hepatoblastoma

International Nuclear Information System (INIS)

Rumbajan, Janette Mareska; Aoki, Shigehisa; Kohashi, Kenichi; Oda, Yoshinao; Hata, Kenichiro; Saji, Tsutomu; Taguchi, Tomoaki; Tajiri, Tatsuro; Soejima, Hidenobu; Joh, Keiichiro; Maeda, Toshiyuki; Souzaki, Ryota; Mitsui, Kazumasa; Higashimoto, Ken; Nakabayashi, Kazuhiko; Yatsuki, Hitomi; Nishioka, Kenichi; Harada, Ryoko

2013-01-01

Aberrant methylation at imprinted differentially methylated regions (DMRs) in human 11p15.5 has been reported in many tumors including hepatoblastoma. However, the methylation status of imprinted DMRs in imprinted loci scattered through the human genome has not been analyzed yet in any tumors. The methylation statuses of 33 imprinted DMRs were analyzed in 12 hepatoblastomas and adjacent normal liver tissue by MALDI-TOF MS and pyrosequencing. Uniparental disomy (UPD) and copy number abnormalities were investigated with DNA polymorphisms. Among 33 DMRs analyzed, 18 showed aberrant methylation in at least 1 tumor. There was large deviation in the incidence of aberrant methylation among the DMRs. KvDMR1 and IGF2-DMR0 were the most frequently hypomethylated DMRs. INPP5Fv2-DMR and RB1-DMR were hypermethylated with high frequencies. Hypomethylation was observed at certain DMRs not only in tumors but also in a small number of adjacent histologically normal liver tissue, whereas hypermethylation was observed only in tumor samples. The methylation levels of long interspersed nuclear element-1 (LINE-1) did not show large differences between tumor tissue and normal liver controls. Chromosomal abnormalities were also found in some tumors. 11p15.5 and 20q13.3 loci showed the frequent occurrence of both genetic and epigenetic alterations. Our analyses revealed tumor-specific aberrant hypermethylation at some imprinted DMRs in 12 hepatoblastomas with additional suggestion for the possibility of hypomethylation prior to tumor development. Some loci showed both genetic and epigenetic alterations with high frequencies. These findings will aid in understanding the development of hepatoblastoma

Three genetic stocks of frigate tuna Auxis thazard thazard (Lacepede, 1800) along the Indian coast revealed from sequence analyses of mitochondrial DNA D-loop region

Digital Repository Service at National Institute of Oceanography (India)

GirishKumar; Kunal, S.P.; Menezes, M.R.; Meena, R.M.

revealed from sequence analyses of mitochondrial DNA D-loop region Name of authors: 1. Girish Kumar* Biological Oceanography Division (BOD) National Institute of Oceanography (NIO) Dona Paula, Goa 403004, India. Email: girishkumar....nio@gmail.com Tel: +919766548060 2. Swaraj Priyaranjan Kunal Biological Oceanography Division (BOD) National Institute of Oceanography (NIO) Dona Paula, Goa 403004, India. Email: swar.mbt@gmail.com 3. Maria Rosalia Menezes Biological Oceanography...

Genome and metagenome enabled analyses reveal new insight into the global biogeography and potential urea utilization in marine Thaumarchaeota.

Science.gov (United States)

Ahlgren, N.; Parada, A. E.; Fuhrman, J. A.

2016-02-01

Marine Thaumarchaea are an abundant, important group of marine microbial communities as they fix carbon, oxidize ammonium, and thus contribute to key N and C cycles in the oceans. From an enrichment culture, we have sequenced the complete genome of a new Thaumarchaeota strain, SPOT01. Analysis of this genome and other Thaumarchaeal genomes contributes new insight into its role in N cycling and clarifies the broader biogeography of marine Thaumarchaeal genera. Phylogenomics of Thaumarchaeota genomes reveal coherent separation into clusters roughly equivalent to the genus level, and SPOT01 represents a new genus of marine Thaumarchaea. Competitive fragment recruitment of globally distributed metagenomes from TARA, Ocean Sampling Day, and those generated from a station off California shows that the SPOT01 genus is often the most abundant genus, especially where total Thaumarchaea are most abundant in the overall community. The SPOT01 genome contains urease genes allowing it to use an alternative form of N. Genomic and metagenomic analysis also reveal that among planktonic genomes and populations, the urease genes in general are more frequently found in members of the SPOT01 genus and another genus dominant in deep waters, thus we predict these two genera contribute most significantly to urea utilization among marine Thaumarchaea. Recruitment also revealed broader biogeographic and ecological patterns of the putative genera. The SPOT01 genus was most abundant at colder temperatures (45 degrees). The genus containing Nitrosopumilus maritimus had the highest temperature range, and the genus containing Candidatus Nitrosopelagicus brevis was typically most abundant at intermediate temperatures and intermediate latitudes ( 35-45 degrees). Together these genome and metagenome enabled analyses provide significant new insight into the ecology and biogeochemical contributions of marine archaea.

Return on Investment of a Work-Family Intervention: Evidence From the Work, Family, and Health Network.

Science.gov (United States)

Barbosa, Carolina; Bray, Jeremy W; Dowd, William N; Mills, Michael J; Moen, Phyllis; Wipfli, Brad; Olson, Ryan; Kelly, Erin L

2015-09-01

To estimate the return on investment (ROI) of a workplace initiative to reduce work-family conflict in a group-randomized 18-month field experiment in an information technology firm in the United States. Intervention resources were micro-costed; benefits included medical costs, productivity (presenteeism), and turnover. Regression models were used to estimate the ROI, and cluster-robust bootstrap was used to calculate its confidence interval. For each participant, model-adjusted costs of the intervention were $690 and company savings were $1850 (2011 prices). The ROI was 1.68 (95% confidence interval, -8.85 to 9.47) and was robust in sensitivity analyses. The positive ROI indicates that employers' investment in an intervention to reduce work-family conflict can enhance their business. Although this was the first study to present a confidence interval for the ROI, results are comparable with the literature.

Proteomic and physiological analyses reveal the role of exogenous spermidine on cucumber roots in response to Ca(NO3)2 stress.

Science.gov (United States)

Du, Jing; Guo, Shirong; Sun, Jin; Shu, Sheng

2018-05-01

The mechanism of exogenous Spd-induced Ca(NO 3 ) 2 stress tolerance in cucumber was studied by proteomics and physiological analyses. Protein-protein interaction network revealed 13 key proteins involved in Spd-induced Ca(NO 3 ) 2 stress resistance. Ca(NO 3 ) 2 stress is one of the major reasons for secondary salinization that limits cucumber plant development in greenhouse. The conferred protective role of exogenous Spd on cucumber in response to Ca(NO 3 ) 2 stress cues involves changes at the cellular and physiological levels. To investigate the molecular foundation of exogenous Spd in Ca(NO 3 ) 2 stress tolerance, a proteomic approach was performed in our work. After a 9 days period of Ca(NO 3 ) 2 stress and/or exogenous Spd, 71 differential protein spots were confidently identified. The resulting proteins were enriched in seven different categories of biological processes, including protein metabolism, carbohydrate and energy metabolism, ROS homeostasis and stress defense, cell wall related, transcription, others and unknown. Protein metabolism (31.2%), carbohydrate and energy metabolism (15.6%), ROS homeostasis and stress defense (32.5%) were the three largest functional categories in cucumber root and most of them were significantly increased by exogenous Spd. The Spd-responsive protein interaction network revealed 13 key proteins, whose accumulation changes could be critical for Spd-induced resistance; all 13 proteins were upregulated by Spd at transcriptional and protein levels in response to Ca(NO 3 ) 2 stress. Furthermore, accumulation of antioxidant enzymes, non-enzymatic antioxidant and polyamines, along with reduction of H 2 O 2 and MDA, were detected after exogenous Spd application during Ca(NO 3 ) 2 stress. The results of these proteomic and physiological analyses in cucumber root may facilitate a better understanding of the underlying mechanism of Ca(NO 3 ) 2 stress tolerance mediated by exogenous Spd.

Influence of hilar deposition in the evaluation of the alveolar epithelial permeability on 99mTc-DTPA aerosol inhaled scintigraphy

International Nuclear Information System (INIS)

Ogi, Shigeyuki; Uchiyama, Mayuki; Fukuda, Kunihiko; Urashima, Mitsuyoshi; Gotoh, Eisuke; Fukumitsu, Nobuyoshi

2009-01-01

We investigated whether hilar radioaerosol deposition affects the clearance rate of technetium-99m-labeled diethylenetriaminepentaacetic acid ( 99m Tc-DTPA) from peripheral alveolar regions. A total of 38 patients underwent 99m Tc-DTPA inhalation lung scintigraphy. Six region of interest (ROI) patterns were adopted: ROI 1 was outlined around the entire hemithorax, and ROIs 2-6 were outlined around the hemithorax but excluded square ROIs of different size in the hilar region. Half-times (T 1/2 ) were calculated with time-activity curves using one-compartment and two-compartment analyses. The T 1/2 of ROIs 1-5 were plotted against the T 1/2 of ROI 6, and regression lines were obtained with the least-squares method. The absolute values of the differences between surveyed values and regression line were calculated. The Wilcoxon test for trend and a single linear regression model were used to determine statistical significance. There were significant reductions in the absolute values of the differences between surveyed values and regression line from ROIs 1-5 by one-component analysis and the fast component of two-compartment analysis (P 99m Tc-DTPA from the alveoli in damaged lungs. The hilar region should be excluded from ROIs when alveolar epithelial permeability is evaluated. (author)

Cerebro-cerebellar resting state functional connectivity in children and adolescents with autism spectrum disorder

Science.gov (United States)

Khan, Amanda J.; Nair, Aarti; Keown, Christopher L.; Datko, Michael C.; Lincoln, Alan J.; Müller, Ralph-Axel

2017-01-01

Background The cerebellum plays important roles in both sensorimotor and supramodal cognitive functions. Cellular, volumetric, and functional abnormalities of the cerebellum have been found in autism spectrum disorders (ASD), but no comprehensive investigation of cerebro-cerebellar connectivity in ASD is available. Methods We used resting-state functional connectivity MRI in 56 children and adolescents (28 ASD, 28 typically developing [TD]) aged 8–17 years. Partial and total correlation analyses were performed for unilateral regions of interest (ROIs), distinguished in two broad domains as sensorimotor (premotor/primary motor, somatosensory, superior temporal, occipital) and supramodal (prefrontal, posterior parietal, and inferior and middle temporal). Results There were three main findings: (i) Total correlation analyses showed predominant cerebro-cerebellar functional overconnectivity in the ASD group; (ii) partial correlation analyses that emphasized domain-specificity (sensorimotor vs. supramodal) indicated a pattern of robustly increased connectivity in the ASD group (compared to the TD group) for sensorimotor ROIs, but predominantly reduced connectivity for supramodal ROIs; (iii) this atypical pattern of connectivity was supported by significantly increased non-canonical connections (between sensorimotor cerebral and supramodal cerebellar ROIs, and vice versa) in the ASD group. Conclusions Our findings indicate that sensorimotor intrinsic functional connectivity is atypically increased in ASD, at the expense of connectivity supporting cerebellar participation in supramodal cognition. PMID:25959247

Comparative Analyses of Nonpathogenic, Opportunistic, and Totally Pathogenic Mycobacteria Reveal Genomic and Biochemical Variabilities and Highlight the Survival Attributes of Mycobacterium tuberculosis

Science.gov (United States)

Singh, Yadvir; Kohli, Sakshi; Ahmad, Javeed; Ehtesham, Nasreen Z.; Tyagi, Anil K.

2014-01-01

ABSTRACT Mycobacterial evolution involves various processes, such as genome reduction, gene cooption, and critical gene acquisition. Our comparative genome size analysis of 44 mycobacterial genomes revealed that the nonpathogenic (NP) genomes were bigger than those of opportunistic (OP) or totally pathogenic (TP) mycobacteria, with the TP genomes being smaller yet variable in size—their genomic plasticity reflected their ability to evolve and survive under various environmental conditions. From the 44 mycobacterial species, 13 species, representing TP, OP, and NP, were selected for genomic-relatedness analyses. Analysis of homologous protein-coding genes shared between Mycobacterium indicus pranii (NP), Mycobacterium intracellulare ATCC 13950 (OP), and Mycobacterium tuberculosis H37Rv (TP) revealed that 4,995 (i.e., ~95%) M. indicaus pranii proteins have homology with M. intracellulare, whereas the homologies among M. indicus pranii, M. intracellulare ATCC 13950, and M. tuberculosis H37Rv were significantly lower. A total of 4,153 (~79%) M. indicus pranii proteins and 4,093 (~79%) M. intracellulare ATCC 13950 proteins exhibited homology with the M. tuberculosis H37Rv proteome, while 3,301 (~82%) and 3,295 (~82%) M. tuberculosis H37Rv proteins showed homology with M. indicus pranii and M. intracellulare ATCC 13950 proteomes, respectively. Comparative metabolic pathway analyses of TP/OP/NP mycobacteria showed enzymatic plasticity between M. indicus pranii (NP) and M. intracellulare ATCC 13950 (OP), Mycobacterium avium 104 (OP), and M. tuberculosis H37Rv (TP). Mycobacterium tuberculosis seems to have acquired novel alternate pathways with possible roles in metabolism, host-pathogen interactions, virulence, and intracellular survival, and by implication some of these could be potential drug targets. PMID:25370496

Bliss and Loewe interaction analyses of clinically relevant drug combinations in human colon cancer cell lines reveal complex patterns of synergy and antagonism.

Science.gov (United States)

Kashif, Muhammad; Andersson, Claes; Mansoori, Sharmineh; Larsson, Rolf; Nygren, Peter; Gustafsson, Mats G

2017-11-28

We analyzed survival effects for 15 different pairs of clinically relevant anti-cancer drugs in three iso-genic pairs of human colorectal cancer carcinoma cell lines, by applying for the first time our novel software (R package) called COMBIA. In our experiments iso-genic pairs of cell lines were used, differing only with respect to a single clinically important KRAS or BRAF mutation. Frequently, concentration dependent but mutation independent joint Bliss and Loewe synergy/antagonism was found statistically significant. Four combinations were found synergistic/antagonistic specifically to the parental (harboring KRAS or BRAF mutation) cell line of the corresponding iso-genic cell lines pair. COMBIA offers considerable improvements over established software for synergy analysis such as MacSynergy™ II as it includes both Bliss (independence) and Loewe (additivity) analyses, together with a tailored non-parametric statistical analysis employing heteroscedasticity, controlled resampling, and global (omnibus) testing. In many cases Loewe analyses found significant synergistic as well as antagonistic effects in a cell line at different concentrations of a tested drug combination. By contrast, Bliss analysis found only one type of significant effect per cell line. In conclusion, the integrated Bliss and Loewe interaction analysis based on non-parametric statistics may provide more robust interaction analyses and reveal complex patterns of synergy and antagonism.

A framework supporting the development of a Grid portal for analysis based on ROI.

Science.gov (United States)

Ichikawa, K; Date, S; Kaishima, T; Shimojo, S

2005-01-01

In our research on brain function analysis, users require two different simultaneous types of processing: interactive processing to a specific part of data and high-performance batch processing to an entire dataset. The difference between these two types of processing is in whether or not the analysis is for data in the region of interest (ROI). In this study, we propose a Grid portal that has a mechanism to freely assign computing resources to the users on a Grid environment according to the users' two different types of processing requirements. We constructed a Grid portal which integrates interactive processing and batch processing by the following two mechanisms. First, a job steering mechanism controls job execution based on user-tagged priority among organizations with heterogeneous computing resources. Interactive jobs are processed in preference to batch jobs by this mechanism. Second, a priority-based result delivery mechanism that administrates a rank of data significance. The portal ensures a turn-around time of interactive processing by the priority-based job controlling mechanism, and provides the users with quality of services (QoS) for interactive processing. The users can access the analysis results of interactive jobs in preference to the analysis results of batch jobs. The Grid portal has also achieved high-performance computation of MEG analysis with batch processing on the Grid environment. The priority-based job controlling mechanism has been realized to freely assign computing resources to the users' requirements. Furthermore the achievement of high-performance computation contributes greatly to the overall progress of brain science. The portal has thus made it possible for the users to flexibly include the large computational power in what they want to analyze.

Un inventaire phytosociologique des dunes à la côte méditerranéenne française entre carnon et le grau du roi (département de l’hérault)

NARCIS (Netherlands)

Hekking, W.H.A.

1959-01-01

Dans la région des dunes et des bas-fonds située à une distance de 3.6 à 5.3 kilomètres de Carnon au Grau du Roi, entre l’Etang de Mauguio et la Mer méditerranéenne et dans le département de l’Hérault on peut constater deux suites progressives des associations phytosociologiques : A) LA VÉGÉ TATION

ATHENA/INTRA analyses for ITER, NSSR-2

International Nuclear Information System (INIS)

Shen, Kecheng; Eriksson, John; Sjoeberg, A.

1999-02-01

The present report is a summary report including thermal-hydraulic analyses made at Studsvik Eco and Safety AB for the ITER NSSR-2 safety documentation. The objective of the analyses was to reveal the safety characteristics of various heat transfer systems at specified operating conditions and to indicate the conditions for which there were obvious risks of jeopardising the structural integrity of the coolant systems. In the latter case also some analyses were made to indicate conceivable mitigating measures for maintaining the integrity.The analyses were primarily concerned with the First Wall and Divertor heat transfer systems. Several enveloping transients were analysed with associated specific flow and heat load boundary conditions. The analyses were performed with the ATHENA and INTRA codes

ATHENA/INTRA analyses for ITER, NSSR-2

Energy Technology Data Exchange (ETDEWEB)

Shen, Kecheng; Eriksson, John; Sjoeberg, A

1999-02-01

The present report is a summary report including thermal-hydraulic analyses made at Studsvik Eco and Safety AB for the ITER NSSR-2 safety documentation. The objective of the analyses was to reveal the safety characteristics of various heat transfer systems at specified operating conditions and to indicate the conditions for which there were obvious risks of jeopardising the structural integrity of the coolant systems. In the latter case also some analyses were made to indicate conceivable mitigating measures for maintaining the integrity.The analyses were primarily concerned with the First Wall and Divertor heat transfer systems. Several enveloping transients were analysed with associated specific flow and heat load boundary conditions. The analyses were performed with the ATHENA and INTRA codes 8 refs, 14 figs, 15 tabs

Underestimation of species richness in neotropical frogs revealed by mtDNA analyses.

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Antoine Fouquet

2007-10-01

Full Text Available Amphibians are rapidly vanishing. At the same time, it is most likely that the number of amphibian species is highly underestimated. Recent DNA barcoding work has attempted to define a threshold between intra- and inter-specific genetic distances to help identify candidate species. In groups with high extinction rates and poorly known species boundaries, like amphibians, such tools may provide a way to rapidly evaluate species richness.Here we analyse published and new 16S rDNA sequences from 60 frog species of Amazonia-Guianas to obtain a minimum estimate of the number of undescribed species in this region. We combined isolation by distance, phylogenetic analyses, and comparison of molecular distances to evaluate threshold values for the identification of candidate species among these frogs.In most cases, geographically distant populations belong to genetically highly distinct lineages that could be considered as candidate new species. This was not universal among the taxa studied and thus widespread species of Neotropical frogs really do exist, contrary to previous assumptions. Moreover, the many instances of paraphyly and the wide overlap between distributions of inter- and intra-specific distances reinforce the hypothesis that many cryptic species remain to be described. In our data set, pairwise genetic distances below 0.02 are strongly correlated with geographical distances. This correlation remains statistically significant until genetic distance is 0.05, with no such relation thereafter. This suggests that for higher distances allopatric and sympatric cryptic species prevail. Based on our analyses, we propose a more inclusive pairwise genetic distance of 0.03 between taxa to target lineages that could correspond to candidate species.Using this approach, we identify 129 candidate species, two-fold greater than the 60 species included in the current study. This leads to estimates of around 170 to 460 frog taxa unrecognized in Amazonia

Metabarcoding and metabolome analyses of copepod grazing reveal feeding preference and linkage to metabolite classes in dynamic microbial plankton communities.

Science.gov (United States)

Ray, Jessica L; Althammer, Julia; Skaar, Katrine S; Simonelli, Paolo; Larsen, Aud; Stoecker, Diane; Sazhin, Andrey; Ijaz, Umer Z; Quince, Christopher; Nejstgaard, Jens C; Frischer, Marc; Pohnert, Georg; Troedsson, Christofer

2016-11-01

In order to characterize copepod feeding in relation to microbial plankton community dynamics, we combined metabarcoding and metabolome analyses during a 22-day seawater mesocosm experiment. Nutrient amendment of mesocosms promoted the development of haptophyte (Phaeocystis pouchetii)- and diatom (Skeletonema marinoi)-dominated plankton communities in mesocosms, in which Calanus sp. copepods were incubated for 24 h in flow-through chambers to allow access to prey particles (<500 μm). Copepods and mesocosm water sampled six times spanning the experiment were analysed using metabarcoding, while intracellular metabolite profiles of mesocosm plankton communities were generated for all experimental days. Taxon-specific metabarcoding ratios (ratio of consumed prey to available prey in the surrounding seawater) revealed diverse and dynamic copepod feeding selection, with positive selection on large diatoms, heterotrophic nanoflagellates and fungi, while smaller phytoplankton, including P. pouchetii, were passively consumed or even negatively selected according to our indicator. Our analysis of the relationship between Calanus grazing ratios and intracellular metabolite profiles indicates the importance of carbohydrates and lipids in plankton succession and copepod-prey interactions. This molecular characterization of Calanus sp. grazing therefore provides new evidence for selective feeding in mixed plankton assemblages and corroborates previous findings that copepod grazing may be coupled to the developmental and metabolic stage of the entire prey community rather than to individual prey abundances. © 2016 John Wiley & Sons Ltd.

Decoding the Traumatic Memory among Women with PTSD: Implications for Neurocircuitry Models of PTSD and Real-Time fMRI Neurofeedback.

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Josh M Cisler

Full Text Available Posttraumatic Stress Disorder (PTSD is characterized by intrusive recall of the traumatic memory. While numerous studies have investigated the neural processing mechanisms engaged during trauma memory recall in PTSD, these analyses have only focused on group-level contrasts that reveal little about the predictive validity of the identified brain regions. By contrast, a multivariate pattern analysis (MVPA approach towards identifying the neural mechanisms engaged during trauma memory recall would entail testing whether a multivariate set of brain regions is reliably predictive of (i.e., discriminates whether an individual is engaging in trauma or non-trauma memory recall. Here, we use a MVPA approach to test 1 whether trauma memory vs neutral memory recall can be predicted reliably using a multivariate set of brain regions among women with PTSD related to assaultive violence exposure (N=16, 2 the methodological parameters (e.g., spatial smoothing, number of memory recall repetitions, etc. that optimize classification accuracy and reproducibility of the feature weight spatial maps, and 3 the correspondence between brain regions that discriminate trauma memory recall and the brain regions predicted by neurocircuitry models of PTSD. Cross-validation classification accuracy was significantly above chance for all methodological permutations tested; mean accuracy across participants was 76% for the methodological parameters selected as optimal for both efficiency and accuracy. Classification accuracy was significantly better for a voxel-wise approach relative to voxels within restricted regions-of-interest (ROIs; classification accuracy did not differ when using PTSD-related ROIs compared to randomly generated ROIs. ROI-based analyses suggested the reliable involvement of the left hippocampus in discriminating memory recall across participants and that the contribution of the left amygdala to the decision function was dependent upon PTSD symptom

The future of oil and bioethanol in Brazil

International Nuclear Information System (INIS)

Moreira, Jose R.; Pacca, Sergio A.; Parente, Virginia

2014-01-01

This work compares the return on investments (ROI) of oil versus biofuels in Brazil. Although several renewable energy sources might displace oil, the country's forte is sugarcane biofuels. In our analysis we carry out simplified benefit–cost analyses of producing oil fields, pre-salt oil fields (without and with enhanced oil recovery), a business as the usual ethanol scenario, and a high ethanol scenario. Excluding the ROI from existing oil fields, which is the highest, when the discount rate is 4% or more, the ROI of the high ethanol scenario is greater than that of the ROI of pre-salt oil. Considering a US$40/t CO 2 tax, the high ethanol scenario's ROI is greater than the pre-salt oil's ROI if a discount rate of 2% or more is adopted. Moreover, the high ethanol scenario throughput up to 2070 compares to 97% of the pre-salt oil reserve without EOR, and demands 78% of its investment. Pre-salt oil production declines beyond 2042 when the country might become a net oil importer. In contrast, ethanol production reaches 2.1 million boe per day, and another 0.9 million boe of fossil demand is displaced through bioelectricity, yielding a total of 3 million boe (62% of the country's oil demand). - Highlights: • Cost-benefit analyses of pre-salt and biofuels in Brazil. • Hubbert model applied to pre-salt oil reserves. • Sustainable energy scenarios. • Carbon mitigation accounting based on biofuel scenarios. • Enhanced oil recovery effect on pre-salt oil reserves

Spiral scan long object reconstruction through PI line reconstruction

International Nuclear Information System (INIS)

Tam, K C; Hu, J; Sourbelle, K

2004-01-01

The response of a point object in a cone beam (CB) spiral scan is analysed. Based on the result, a reconstruction algorithm for long object imaging in spiral scan cone beam CT is developed. A region-of-interest (ROI) of the long object is scanned with a detector smaller than the ROI, and a portion of it can be reconstructed without contamination from overlaying materials. The top and bottom surfaces of the ROI are defined by two sets of PI lines near the two ends of the spiral path. With this novel definition of the top and bottom ROI surfaces and through the use of projective geometry, it is straightforward to partition the cone beam image into regions corresponding to projections of the ROI, the overlaying objects or both. This also simplifies computation at source positions near the spiral ends, and makes it possible to reduce radiation exposure near the spiral ends substantially through simple hardware collimation. Simulation results to validate the algorithm are presented

Mitochondrial DNA analyses revealed low genetic diversity in the endangered Indian wild ass Equus hemionus khur.

Science.gov (United States)

Khaire, Devendra; Atkulwar, Ashwin; Farah, Sameera; Baig, Mumtaz

2017-09-01

The Indian wild ass Equus hemionus khur, belonging to ass-like equid branch, inhabits the dry and arid desert of the Little Rann of Kutch, Gujarat. The E. h. khur is the sole survivor of Asiatic wild ass species/subspecies in South Asia. To provide first ever insights into the genetic diversity, phylogeny, and demography of the endangered Indian wild ass, we sampled 52 free-ranging individuals from the Little Rann of Kutch by using a non-invasive methodology. The sequencing of 230 bp in cytochrome b (Cyt b) and displacement loop (D-loop) region revealed that current ∼4000 extant population of Indian wild ass harbours low genetic diversity. Phylogenetic analyses confirmed that E. h. khur, E. h. onager, and E. h. kulan belong to a single strict monophyletic clade. Therefore, we suggest the delimitation of the five E. hemionus subspecies in vogue to a single species E. hemionus. The application of molecular clock confirmed that the Asiatic wild ass had undergone diversification 0.65 Million years ago. Demographic measurements assessed using a Bayesian skyline plot demonstrated decline in the maternal effective population size of the Indian wild ass during different periods; these periods coincided with the origin and rise of the Indus civilization in the northwest of the Indian subcontinent during the Neolithic. In conclusion, maintaining high genetic diversity in the existing isolated population of 4000 Indian wild asses inhabiting the wild ass sanctuary is important compared with subspecies preservation alone.

Regulatory complexity revealed by integrated cytological and RNA-seq analyses of meiotic substages in mouse spermatocytes.

Science.gov (United States)

Ball, Robyn L; Fujiwara, Yasuhiro; Sun, Fengyun; Hu, Jianjun; Hibbs, Matthew A; Handel, Mary Ann; Carter, Gregory W

2016-08-12

The continuous and non-synchronous nature of postnatal male germ-cell development has impeded stage-specific resolution of molecular events of mammalian meiotic prophase in the testis. Here the juvenile onset of spermatogenesis in mice is analyzed by combining cytological and transcriptomic data in a novel computational analysis that allows decomposition of the transcriptional programs of spermatogonia and meiotic prophase substages. Germ cells from testes of individual mice were obtained at two-day intervals from 8 to 18 days post-partum (dpp), prepared as surface-spread chromatin and immunolabeled for meiotic stage-specific protein markers (STRA8, SYCP3, phosphorylated H2AFX, and HISTH1T). Eight stages were discriminated cytologically by combinatorial antibody labeling, and RNA-seq was performed on the same samples. Independent principal component analyses of cytological and transcriptomic data yielded similar patterns for both data types, providing strong evidence for substage-specific gene expression signatures. A novel permutation-based maximum covariance analysis (PMCA) was developed to map co-expressed transcripts to one or more of the eight meiotic prophase substages, thereby linking distinct molecular programs to cytologically defined cell states. Expression of meiosis-specific genes is not substage-limited, suggesting regulation of substage transitions at other levels. This integrated analysis provides a general method for resolving complex cell populations. Here it revealed not only features of meiotic substage-specific gene expression, but also a network of substage-specific transcription factors and relationships to potential target genes.

"Textural analysis of multiparametric MRI detects transition zone prostate cancer".

Science.gov (United States)

Sidhu, Harbir S; Benigno, Salvatore; Ganeshan, Balaji; Dikaios, Nikos; Johnston, Edward W; Allen, Clare; Kirkham, Alex; Groves, Ashley M; Ahmed, Hashim U; Emberton, Mark; Taylor, Stuart A; Halligan, Steve; Punwani, Shonit

2017-06-01

To evaluate multiparametric-MRI (mpMRI) derived histogram textural-analysis parameters for detection of transition zone (TZ) prostatic tumour. Sixty-seven consecutive men with suspected prostate cancer underwent 1.5T mpMRI prior to template-mapping-biopsy (TPM). Twenty-six men had 'significant' TZ tumour. Two radiologists in consensus matched TPM to the single axial slice best depicting tumour, or largest TZ diameter for those with benign histology, to define single-slice whole TZ-regions-of-interest (ROIs). Textural-parameter differences between single-slice whole TZ-ROI containing significant tumour versus benign/insignificant tumour were analysed using Mann Whitney U test. Diagnostic accuracy was assessed by receiver operating characteristic area under curve (ROC-AUC) analysis cross-validated with leave-one-out (LOO) analysis. ADC kurtosis was significantly lower (p Textural features of the whole prostate TZ can discriminate significant prostatic cancer through reduced kurtosis of the ADC-histogram where significant tumour is included in TZ-ROI and reduced T1 entropy independent of tumour inclusion. • MR textural features of prostate transition zone may discriminate significant prostatic cancer. • Transition zone (TZ) containing significant tumour demonstrates a less peaked ADC histogram. • TZ containing significant tumour reveals higher post-contrast T1-weighted homogeneity. • The utility of MR texture analysis in prostate cancer merits further investigation.

Phenotype specific analyses reveal distinct regulatory mechanism for chronically activated p53.

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Kristina Kirschner

2015-03-01

Full Text Available The downstream functions of the DNA binding tumor suppressor p53 vary depending on the cellular context, and persistent p53 activation has recently been implicated in tumor suppression and senescence. However, genome-wide information about p53-target gene regulation has been derived mostly from acute genotoxic conditions. Using ChIP-seq and expression data, we have found distinct p53 binding profiles between acutely activated (through DNA damage and chronically activated (in senescent or pro-apoptotic conditions p53. Compared to the classical 'acute' p53 binding profile, 'chronic' p53 peaks were closely associated with CpG-islands. Furthermore, the chronic CpG-island binding of p53 conferred distinct expression patterns between senescent and pro-apoptotic conditions. Using the p53 targets seen in the chronic conditions together with external high-throughput datasets, we have built p53 networks that revealed extensive self-regulatory 'p53 hubs' where p53 and many p53 targets can physically interact with each other. Integrating these results with public clinical datasets identified the cancer-associated lipogenic enzyme, SCD, which we found to be directly repressed by p53 through the CpG-island promoter, providing a mechanistic link between p53 and the 'lipogenic phenotype', a hallmark of cancer. Our data reveal distinct phenotype associations of chronic p53 targets that underlie specific gene regulatory mechanisms.

Big data analyses reveal patterns and drivers of the movements of southern elephant seals

KAUST Repository

Rodrí guez, J. P.; Ferná ndez-Gracia, Juan; Thums, Michele; Hindell, Mark A.; Sequeira, Ana M. M.; Meekan, Mark G.; Costa, Daniel P.; Guinet, Christophe; Harcourt, R.; McMahon, Clive R.; Muelbert, Monica; Duarte, Carlos M.; Eguí luz, V. M.

2017-01-01

The growing number of large databases of animal tracking provides an opportunity for analyses of movement patterns at the scales of populations and even species. We used analytical approaches, developed to cope with

Big data analyses reveal patterns and drivers of the movements of southern elephant seals

KAUST Repository

Rodríguez, Jorge P.

2017-03-02

The growing number of large databases of animal tracking provides an opportunity for analyses of movement patterns at the scales of populations and even species. We used analytical approaches, developed to cope with

Comparative physiological, metabolomic, and transcriptomic analyses reveal mechanisms of improved abiotic stress resistance in bermudagrass [Cynodon dactylon (L). Pers.] by exogenous melatonin

Science.gov (United States)

Shi, Haitao; Jiang, Chuan; Ye, Tiantian; Tan, Dun-xian; Reiter, Russel J.; Zhang, Heng; Liu, Renyi; Chan, Zhulong

2015-01-01

Melatonin (N-acetyl-5-methoxytryptamine), a well-known animal hormone, is also involved in plant development and abiotic stress responses. In this study, it is shown that exogenous application of melatonin conferred improved salt, drought, and cold stress resistances in bermudagrass. Moreover, exogenous melatonin treatment alleviated reactive oxygen species (ROS) burst and cell damage induced by abiotic stress; this involved activation of several antioxidants. Additionally, melatonin-pre-treated plants exhibited higher concentrations of 54 metabolites, including amino acids, organic acids, sugars, and sugar alcohols, than non-treated plants under abiotic stress conditions. Genome-wide transcriptomic profiling identified 3933 transcripts (2361 up-regulated and 1572 down-regulated) that were differentially expressed in melatonin-treated plants versus controls. Pathway and gene ontology (GO) term enrichment analyses revealed that genes involved in nitrogen metabolism, major carbohydrate metabolism, tricarboxylic acid (TCA)/org transformation, transport, hormone metabolism, metal handling, redox, and secondary metabolism were over-represented after melatonin pre-treatment. Taken together, this study provides the first evidence of the protective roles of exogenous melatonin in the bermudagrass response to abiotic stresses, partially via activation of antioxidants and modulation of metabolic homeostasis. Notably, metabolic and transcriptomic analyses showed that the underlying mechanisms of melatonin could involve major reorientation of photorespiratory and carbohydrate and nitrogen metabolism. PMID:25225478

Integrative functional analyses using rainbow trout selected for tolerance to plant diets reveal nutrigenomic signatures for soy utilization without the concurrence of enteritis.

Directory of Open Access Journals (Sweden)

Jason Abernathy

Full Text Available Finding suitable alternative protein sources for diets of carnivorous fish species remains a major concern for sustainable aquaculture. Through genetic selection, we created a strain of rainbow trout that outperforms parental lines in utilizing an all-plant protein diet and does not develop enteritis in the distal intestine, as is typical with salmonids on long-term plant protein-based feeds. By incorporating this strain into functional analyses, we set out to determine which genes are critical to plant protein utilization in the absence of gut inflammation. After a 12-week feeding trial with our selected strain and a control trout strain fed either a fishmeal-based diet or an all-plant protein diet, high-throughput RNA sequencing was completed on both liver and muscle tissues. Differential gene expression analyses, weighted correlation network analyses and further functional characterization were performed. A strain-by-diet design revealed differential expression ranging from a few dozen to over one thousand genes among the various comparisons and tissues. Major gene ontology groups identified between comparisons included those encompassing central, intermediary and foreign molecule metabolism, associated biosynthetic pathways as well as immunity. A systems approach indicated that genes involved in purine metabolism were highly perturbed. Systems analysis among the tissues tested further suggests the interplay between selection for growth, dietary utilization and protein tolerance may also have implications for nonspecific immunity. By combining data from differential gene expression and co-expression networks using selected trout, along with ontology and pathway analyses, a set of 63 candidate genes for plant diet tolerance was found. Risk loci in human inflammatory bowel diseases were also found in our datasets, indicating rainbow trout selected for plant-diet tolerance may have added utility as a potential biomedical model.

RNA-seq analyses reveal insights into the function of respiratory nitrate reductase of the diazotroph Herbaspirillum seropedicae.

Science.gov (United States)

Bonato, Paloma; Batista, Marcelo B; Camilios-Neto, Doumit; Pankievicz, Vânia C S; Tadra-Sfeir, Michelle Z; Monteiro, Rose Adele; Pedrosa, Fabio O; Souza, Emanuel M; Chubatsu, Leda S; Wassem, Roseli; Rigo, Liu Un

2016-09-01

Herbaspirillum seropedicae is a nitrogen-fixing β-proteobacterium that associates with roots of gramineous plants. In silico analyses revealed that H. seropedicae genome has genes encoding a putative respiratory (NAR) and an assimilatory nitrate reductase (NAS). To date, little is known about nitrate metabolism in H. seropedicae, and, as this bacterium cannot respire nitrate, the function of NAR remains unknown. This study aimed to investigate the function of NAR in H. seropedicae and how it metabolizes nitrate in a low aerated-condition. RNA-seq transcriptional profiling in the presence of nitrate allowed us to pinpoint genes important for nitrate metabolism in H. seropedicae, including nitrate transporters and regulatory proteins. Additionally, both RNA-seq data and physiological characterization of a mutant in the catalytic subunit of NAR (narG mutant) showed that NAR is not required for nitrate assimilation but is required for: (i) production of high levels of nitrite, (ii) production of NO and (iii) dissipation of redox power, which in turn lead to an increase in carbon consumption. In addition, wheat plants showed an increase in shoot dry weight only when inoculated with H. seropedicae wild type, but not with the narG mutant, suggesting that NAR is important to H. seropedicae-wheat interaction. © 2016 Society for Applied Microbiology and John Wiley & Sons Ltd.

DNA sequence analyses reveal abundant diversity, endemism and evidence for Asian origin of the porcini mushrooms.

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Bang Feng

Full Text Available The wild gourmet mushroom Boletus edulis and its close allies are of significant ecological and economic importance. They are found throughout the Northern Hemisphere, but despite their ubiquity there are still many unresolved issues with regard to the taxonomy, systematics and biogeography of this group of mushrooms. Most phylogenetic studies of Boletus so far have characterized samples from North America and Europe and little information is available on samples from other areas, including the ecologically and geographically diverse regions of China. Here we analyzed DNA sequence variation in three gene markers from samples of these mushrooms from across China and compared our findings with those from other representative regions. Our results revealed fifteen novel phylogenetic species (about one-third of the known species and a newly identified lineage represented by Boletus sp. HKAS71346 from tropical Asia. The phylogenetic analyses support eastern Asia as the center of diversity for the porcini sensu stricto clade. Within this clade, B. edulis is the only known holarctic species. The majority of the other phylogenetic species are geographically restricted in their distributions. Furthermore, molecular dating and geological evidence suggest that this group of mushrooms originated during the Eocene in eastern Asia, followed by dispersal to and subsequent speciation in other parts of Asia, Europe, and the Americas from the middle Miocene through the early Pliocene. In contrast to the ancient dispersal of porcini in the strict sense in the Northern Hemisphere, the occurrence of B. reticulatus and B. edulis sensu lato in the Southern Hemisphere was probably due to recent human-mediated introductions.

DNA Sequence Analyses Reveal Abundant Diversity, Endemism and Evidence for Asian Origin of the Porcini Mushrooms

Science.gov (United States)

Feng, Bang; Xu, Jianping; Wu, Gang; Zeng, Nian-Kai; Li, Yan-Chun; Tolgor, Bau; Kost, Gerhard W.; Yang, Zhu L.

2012-01-01

The wild gourmet mushroom Boletus edulis and its close allies are of significant ecological and economic importance. They are found throughout the Northern Hemisphere, but despite their ubiquity there are still many unresolved issues with regard to the taxonomy, systematics and biogeography of this group of mushrooms. Most phylogenetic studies of Boletus so far have characterized samples from North America and Europe and little information is available on samples from other areas, including the ecologically and geographically diverse regions of China. Here we analyzed DNA sequence variation in three gene markers from samples of these mushrooms from across China and compared our findings with those from other representative regions. Our results revealed fifteen novel phylogenetic species (about one-third of the known species) and a newly identified lineage represented by Boletus sp. HKAS71346 from tropical Asia. The phylogenetic analyses support eastern Asia as the center of diversity for the porcini sensu stricto clade. Within this clade, B. edulis is the only known holarctic species. The majority of the other phylogenetic species are geographically restricted in their distributions. Furthermore, molecular dating and geological evidence suggest that this group of mushrooms originated during the Eocene in eastern Asia, followed by dispersal to and subsequent speciation in other parts of Asia, Europe, and the Americas from the middle Miocene through the early Pliocene. In contrast to the ancient dispersal of porcini in the strict sense in the Northern Hemisphere, the occurrence of B. reticulatus and B. edulis sensu lato in the Southern Hemisphere was probably due to recent human-mediated introductions. PMID:22629418

Hydrogeology and geochemistry of the freshwater lens on Roi Namur atoll, the Republic of the Marshall Islands

Science.gov (United States)

Swarzenski, P. W.

2015-12-01

More than 90% of the world's ~400 larger atoll islands are located in the Pacific and Indian Oceans and are inhabited by ~ 3/4 million people. As ground elevations of these atolls rarely exceed a few meters above mean sea level, atoll communities must rely precariously on finite resources, including fresh water and land. When demand for water exceeds precipitation rates, fresh groundwater may provide an additional, albeit also limited resource. The shape and size of this freshwater lens is controlled by precipitation, infiltration, discharge, and groundwater pumping, as well as hydrogeologic characteristics of the aquifer, and climate. Small atoll islands like Roi Namur on Kwajalein perhaps best illustrate the strong interdependence of the islet's depositional history and geochemical transformations that occur within the shallow aquifer and its host rock. This study utilized electrical resistivity tomography (ERT) to define the position of the freshwater lens above underlying seawater and to examine scales of freshwater /saltwater mixing. Time series Rn-222 measurements were used to evaluate groundwater discharge rates to the coastal waters, and a suite of groundwater geochemical tracers, including select nutrients, trace elements, and water isotopes, were used to develop a better understanding of how the fresh water lens will likely to respond to external perturbations, such as managed recharge, and the inevitability of future marine over wash events that will be become more frequent and severe under expected sea level rise.

The 'revealed preferences' theory: Assumptions and conjectures

International Nuclear Information System (INIS)

Green, C.H.

1983-01-01

Being kind of intuitive psychology the 'Revealed-Preferences'- theory based approaches towards determining the acceptable risks are a useful method for the generation of hypotheses. In view of the fact that reliability engineering develops faster than methods for the determination of reliability aims the Revealed-Preferences approach is a necessary preliminary help. Some of the assumptions on which the 'Revealed-Preferences' theory is based will be identified and analysed and afterwards compared with experimentally obtained results. (orig./DG) [de

Cerebro-cerebellar Resting-State Functional Connectivity in Children and Adolescents with Autism Spectrum Disorder.

Science.gov (United States)

Khan, Amanda J; Nair, Aarti; Keown, Christopher L; Datko, Michael C; Lincoln, Alan J; Müller, Ralph-Axel

2015-11-01

The cerebellum plays important roles in sensori-motor and supramodal cognitive functions. Cellular, volumetric, and functional abnormalities of the cerebellum have been found in autism spectrum disorders (ASD), but no comprehensive investigation of cerebro-cerebellar connectivity in ASD is available. We used resting-state functional connectivity magnetic resonance imaging in 56 children and adolescents (28 subjects with ASD, 28 typically developing subjects) 8-17 years old. Partial and total correlation analyses were performed for unilateral regions of interest (ROIs), distinguished in two broad domains as sensori-motor (premotor/primary motor, somatosensory, superior temporal, and occipital) and supramodal (prefrontal, posterior parietal, and inferior and middle temporal). There were three main findings: 1) Total correlation analyses showed predominant cerebro-cerebellar functional overconnectivity in the ASD group; 2) partial correlation analyses that emphasized domain specificity (sensori-motor vs. supramodal) indicated a pattern of robustly increased connectivity in the ASD group (compared with the typically developing group) for sensori-motor ROIs but predominantly reduced connectivity for supramodal ROIs; and 3) this atypical pattern of connectivity was supported by significantly increased noncanonical connections (between sensori-motor cerebral and supramodal cerebellar ROIs and vice versa) in the ASD group. Our findings indicate that sensori-motor intrinsic functional connectivity is atypically increased in ASD, at the expense of connectivity supporting cerebellar participation in supramodal cognition. Copyright © 2015 Society of Biological Psychiatry. Published by Elsevier Inc. All rights reserved.

Integrative analyses of human reprogramming reveal dynamic nature of induced pluripotency

Science.gov (United States)

Cacchiarelli, Davide; Trapnell, Cole; Ziller, Michael J.; Soumillon, Magali; Cesana, Marcella; Karnik, Rahul; Donaghey, Julie; Smith, Zachary D.; Ratanasirintrawoot, Sutheera; Zhang, Xiaolan; Ho Sui, Shannan J.; Wu, Zhaoting; Akopian, Veronika; Gifford, Casey A.; Doench, John; Rinn, John L.; Daley, George Q.; Meissner, Alexander; Lander, Eric S.; Mikkelsen, Tarjei S.

2015-01-01

Summary Induced pluripotency is a promising avenue for disease modeling and therapy, but the molecular principles underlying this process, particularly in human cells, remain poorly understood due to donor-to-donor variability and intercellular heterogeneity. Here we constructed and characterized a clonal, inducible human reprogramming system that provides a reliable source of cells at any stage of the process. This system enabled integrative transcriptional and epigenomic analysis across the human reprogramming timeline at high resolution. We observed distinct waves of gene network activation, including the ordered reactivation of broad developmental regulators followed by early embryonic patterning genes and culminating in the emergence of a signature reminiscent of pre-implantation stages. Moreover, complementary functional analyses allowed us to identify and validate novel regulators of the reprogramming process. Altogether, this study sheds light on the molecular underpinnings of induced pluripotency in human cells and provides a robust cell platform for further studies. PMID:26186193

Combined metabonomic and quantitative real-time PCR analyses reveal systems metabolic changes in Jurkat T-cells treated with HIV-1 Tat protein.

Science.gov (United States)

Liao, Wenting; Tan, Guangguo; Zhu, Zhenyu; Chen, Qiuli; Lou, Ziyang; Dong, Xin; Zhang, Wei; Pan, Wei; Chai, Yifeng

2012-11-02

HIV-1 Tat protein is released by infected cells and can affect bystander uninfected T cells and induce numerous biological responses which contribute to its pathogenesis. To elucidate the complex pathogenic mechanism, we conducted a comprehensive investigation on Tat protein-related extracellular and intracellular metabolic changes in Jurkat T-cells using combined gas chromatography-mass spectrometry (GC-MS), reversed-phase liquid chromatography-mass spectrometry (RPLC-MS) and a hydrophilic interaction liquid chromatography-mass spectrometry (HILIC-MS)-based metabonomics approach. Quantitative real-time PCR (qRT-PCR) analyses were further employed to measure expressions of several relevant enzymes together with perturbed metabolic pathways. Combined metabonomic and qRT-PCR analyses revealed that HIV-1 Tat caused significant and comprehensive metabolic changes, as represented by significant changes of 37 metabolites and 10 relevant enzymes in HIV-1 Tat-treated cells. Using MetaboAnalyst 2.0, it was found that 11 pathways (Impact-value >0.10) among the regulated pathways were acutely perturbed, including sphingolipid metabolism, glycine, serine and threonine metabolism, pyruvate metabolism, inositol phosphate metabolism, arginine and proline metabolism, citrate cycle, phenylalanine metabolism, tryptophan metabolism, pentose phosphate pathway, glycerophospholipid metabolism, glycolysis or gluconeogenesis. These results provide metabolic evidence of the complex pathogenic mechanism of HIV-1 Tat protein as a "viral toxin", and would help obligate Tat protein as "an important target" for therapeutic intervention and vaccine development.

Comparative physiological, metabolomic, and transcriptomic analyses reveal mechanisms of improved abiotic stress resistance in bermudagrass [Cynodon dactylon (L). Pers.] by exogenous melatonin.

Science.gov (United States)

Shi, Haitao; Jiang, Chuan; Ye, Tiantian; Tan, Dun-Xian; Reiter, Russel J; Zhang, Heng; Liu, Renyi; Chan, Zhulong

2015-02-01

Melatonin (N-acetyl-5-methoxytryptamine), a well-known animal hormone, is also involved in plant development and abiotic stress responses. In this study, it is shown that exogenous application of melatonin conferred improved salt, drought, and cold stress resistances in bermudagrass. Moreover, exogenous melatonin treatment alleviated reactive oxygen species (ROS) burst and cell damage induced by abiotic stress; this involved activation of several antioxidants. Additionally, melatonin-pre-treated plants exhibited higher concentrations of 54 metabolites, including amino acids, organic acids, sugars, and sugar alcohols, than non-treated plants under abiotic stress conditions. Genome-wide transcriptomic profiling identified 3933 transcripts (2361 up-regulated and 1572 down-regulated) that were differentially expressed in melatonin-treated plants versus controls. Pathway and gene ontology (GO) term enrichment analyses revealed that genes involved in nitrogen metabolism, major carbohydrate metabolism, tricarboxylic acid (TCA)/org transformation, transport, hormone metabolism, metal handling, redox, and secondary metabolism were over-represented after melatonin pre-treatment. Taken together, this study provides the first evidence of the protective roles of exogenous melatonin in the bermudagrass response to abiotic stresses, partially via activation of antioxidants and modulation of metabolic homeostasis. Notably, metabolic and transcriptomic analyses showed that the underlying mechanisms of melatonin could involve major reorientation of photorespiratory and carbohydrate and nitrogen metabolism. © The Author 2014. Published by Oxford University Press on behalf of the Society for Experimental Biology.

Comparative analyses of population-scale phenomic data in electronic medical records reveal race-specific disease networks

Science.gov (United States)

Glicksberg, Benjamin S.; Li, Li; Badgeley, Marcus A.; Shameer, Khader; Kosoy, Roman; Beckmann, Noam D.; Pho, Nam; Hakenberg, Jörg; Ma, Meng; Ayers, Kristin L.; Hoffman, Gabriel E.; Dan Li, Shuyu; Schadt, Eric E.; Patel, Chirag J.; Chen, Rong; Dudley, Joel T.

2016-01-01

Motivation: Underrepresentation of racial groups represents an important challenge and major gap in phenomics research. Most of the current human phenomics research is based primarily on European populations; hence it is an important challenge to expand it to consider other population groups. One approach is to utilize data from EMR databases that contain patient data from diverse demographics and ancestries. The implications of this racial underrepresentation of data can be profound regarding effects on the healthcare delivery and actionability. To the best of our knowledge, our work is the first attempt to perform comparative, population-scale analyses of disease networks across three different populations, namely Caucasian (EA), African American (AA) and Hispanic/Latino (HL). Results: We compared susceptibility profiles and temporal connectivity patterns for 1988 diseases and 37 282 disease pairs represented in a clinical population of 1 025 573 patients. Accordingly, we revealed appreciable differences in disease susceptibility, temporal patterns, network structure and underlying disease connections between EA, AA and HL populations. We found 2158 significantly comorbid diseases for the EA cohort, 3265 for AA and 672 for HL. We further outlined key disease pair associations unique to each population as well as categorical enrichments of these pairs. Finally, we identified 51 key ‘hub’ diseases that are the focal points in the race-centric networks and of particular clinical importance. Incorporating race-specific disease comorbidity patterns will produce a more accurate and complete picture of the disease landscape overall and could support more precise understanding of disease relationships and patient management towards improved clinical outcomes. Contacts: rong.chen@mssm.edu or joel.dudley@mssm.edu Supplementary information: Supplementary data are available at Bioinformatics online. PMID:27307606

Financial analysis of technology acquisition using fractionated lasers as a model.

Science.gov (United States)

Jutkowitz, Eric; Carniol, Paul J; Carniol, Alan R

2010-08-01

Ablative fractional lasers are among the most advanced and costly devices on the market. Yet, there is a dearth of published literature on the cost and potential return on investment (ROI) of such devices. The objective of this study was to provide a methodological framework for physicians to evaluate ROI. To facilitate this analysis, we conducted a case study on the potential ROI of eight ablative fractional lasers. In the base case analysis, a 5-year lease and a 3-year lease were assumed as the purchase option with a $0 down payment and 3-month payment deferral. In addition to lease payments, service contracts, labor cost, and disposables were included in the total cost estimate. Revenue was estimated as price per procedure multiplied by total number of procedures in a year. Sensitivity analyses were performed to account for variability in model assumptions. Based on the assumptions of the model, all lasers had higher ROI under the 5-year lease agreement compared with that for the 3-year lease agreement. When comparing results between lasers, those with lower operating and purchase cost delivered a higher ROI. Sensitivity analysis indicates the model is most sensitive to purchase method. If physicians opt to purchase the device rather than lease, they can significantly enhance ROI. ROI analysis is an important tool for physicians who are considering making an expensive device acquisition. However, physicians should not rely solely on ROI and must also consider the clinical benefits of a laser. (c) Thieme Medical Publishers.

Exploratory Metabolomic Analyses Reveal Compounds Correlated with Lutein Concentration in Frontal Cortex, Hippocampus, and Occipital Cortex of Human Infant Brain.

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Jacqueline C Lieblein-Boff

Full Text Available Lutein is a dietary carotenoid well known for its role as an antioxidant in the macula, and recent reports implicate a role for lutein in cognitive function. Lutein is the dominant carotenoid in both pediatric and geriatric brain tissue. In addition, cognitive function in older adults correlated with macular and postmortem brain lutein concentrations. Furthermore, lutein was found to preferentially accumulate in the infant brain in comparison to other carotenoids that are predominant in diet. While lutein is consistently related to cognitive function, the mechanisms by which lutein may influence cognition are not clear. In an effort to identify potential mechanisms through which lutein might influence neurodevelopment, an exploratory study relating metabolite signatures and lutein was completed. Post-mortem metabolomic analyses were performed on human infant brain tissues in three regions important for learning and memory: the frontal cortex, hippocampus, and occipital cortex. Metabolomic profiles were compared to lutein concentration, and correlations were identified and reported here. A total of 1276 correlations were carried out across all brain regions. Of 427 metabolites analyzed, 257 were metabolites of known identity. Unidentified metabolite correlations (510 were excluded. In addition, moderate correlations with xenobiotic relationships (2 or those driven by single outliers (3 were excluded from further study. Lutein concentrations correlated with lipid pathway metabolites, energy pathway metabolites, brain osmolytes, amino acid neurotransmitters, and the antioxidant homocarnosine. These correlations were often brain region-specific. Revealing relationships between lutein and metabolic pathways may help identify potential candidates on which to complete further analyses and may shed light on important roles of lutein in the human brain during development.

A study on the characteristics of retrospective optimal interpolation using an Observing System Simulation Experiment

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Kim, Shin-Woo; Noh, Nam-Kyu; Lim, Gyu-Ho

2013-04-01

This study presents the introduction of retrospective optimal interpolation (ROI) and its application with Weather Research and Forecasting model (WRF). Song et al. (2009) suggested ROI method which is an optimal interpolation (OI) that gradually assimilates observations over the analysis window for variance-minimum estimate of an atmospheric state at the initial time of the analysis window. The assimilation window of ROI algorithm is gradually increased, similar with that of the quasi-static variational assimilation (QSVA; Pires et al., 1996). Unlike QSVA method, however, ROI method assimilates the data at post analysis time using perturbation method (Verlaan and Heemink, 1997) without adjoint model. Song and Lim (2011) improved this method by incorporating eigen-decomposition and covariance inflation. The computational costs for ROI can be reduced due to the eigen-decomposition of background error covariance which can concentrate ROI analyses on the error variances of governing eigenmodes by transforming the control variables into eigenspace. A total energy norm is used for the normalization of each control variables. In this study, ROI method is applied to WRF model with Observing System Simulation Experiment (OSSE) to validate the algorithm and to investigate the capability. Horizontal wind, pressure, potential temperature, and water vapor mixing ratio are used for control variables and observations. Firstly, 1-profile assimilation experiment is performed. Subsequently, OSSE's are performed using the virtual observing system which consists of synop, ship, and sonde data. The difference between forecast errors with assimilation and without assimilation is obviously increased as time passed, which means the improvement of forecast error with the assimilation by ROI. The characteristics and strength/weakness of ROI method are also investigated by conducting the experiments with 3D-Var (3-dimensional variational) method and 4D-Var (4-dimensional variational) method

Comparative Genome Analyses of Serratia marcescens FS14 Reveals Its High Antagonistic Potential

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Li, Pengpeng; Kwok, Amy H. Y.; Jiang, Jingwei; Ran, Tingting; Xu, Dongqing; Wang, Weiwu; Leung, Frederick C.

2015-01-01

S. marcescens FS14 was isolated from an Atractylodes macrocephala Koidz plant that was infected by Fusarium oxysporum and showed symptoms of root rot. With the completion of the genome sequence of FS14, the first comprehensive comparative-genomic analysis of the Serratia genus was performed. Pan-genome and COG analyses showed that the majority of the conserved core genes are involved in basic cellular functions, while genomic factors such as prophages contribute considerably to genome diversity. Additionally, a Type I restriction-modification system, a Type III secretion system and tellurium resistance genes are found in only some Serratia species. Comparative analysis further identified that S. marcescens FS14 possesses multiple mechanisms for antagonism against other microorganisms, including the production of prodigiosin, bacteriocins, and multi-antibiotic resistant determinants as well as chitinases. The presence of two evolutionarily distinct Type VI secretion systems (T6SSs) in FS14 may provide further competitive advantages for FS14 against other microbes. To our knowledge, this is the first report of comparative analysis on T6SSs in the genus, which identifies four types of T6SSs in Serratia spp.. Competition bioassays of FS14 against the vital plant pathogenic bacterium Ralstonia solanacearum and fungi Fusarium oxysporum and Sclerotinia sclerotiorum were performed to support our genomic analyses, in which FS14 demonstrated high antagonistic activities against both bacterial and fungal phytopathogens. PMID:25856195

Comparative genome analyses of Serratia marcescens FS14 reveals its high antagonistic potential.

Science.gov (United States)

Li, Pengpeng; Kwok, Amy H Y; Jiang, Jingwei; Ran, Tingting; Xu, Dongqing; Wang, Weiwu; Leung, Frederick C

2015-01-01

S. marcescens FS14 was isolated from an Atractylodes macrocephala Koidz plant that was infected by Fusarium oxysporum and showed symptoms of root rot. With the completion of the genome sequence of FS14, the first comprehensive comparative-genomic analysis of the Serratia genus was performed. Pan-genome and COG analyses showed that the majority of the conserved core genes are involved in basic cellular functions, while genomic factors such as prophages contribute considerably to genome diversity. Additionally, a Type I restriction-modification system, a Type III secretion system and tellurium resistance genes are found in only some Serratia species. Comparative analysis further identified that S. marcescens FS14 possesses multiple mechanisms for antagonism against other microorganisms, including the production of prodigiosin, bacteriocins, and multi-antibiotic resistant determinants as well as chitinases. The presence of two evolutionarily distinct Type VI secretion systems (T6SSs) in FS14 may provide further competitive advantages for FS14 against other microbes. To our knowledge, this is the first report of comparative analysis on T6SSs in the genus, which identifies four types of T6SSs in Serratia spp.. Competition bioassays of FS14 against the vital plant pathogenic bacterium Ralstonia solanacearum and fungi Fusarium oxysporum and Sclerotinia sclerotiorum were performed to support our genomic analyses, in which FS14 demonstrated high antagonistic activities against both bacterial and fungal phytopathogens.

Optimization of Region of Interest Drawing for Quantitative Analysis: Differentiation Between Benign and Malignant Breast Lesions on Contrast-Enhanced Sonography.

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Nakata, Norio; Ohta, Tomoyuki; Nishioka, Makiko; Takeyama, Hiroshi; Toriumi, Yasuo; Kato, Kumiko; Nogi, Hiroko; Kamio, Makiko; Fukuda, Kunihiko

2015-11-01

This study was performed to evaluate the diagnostic utility of quantitative analysis of benign and malignant breast lesions using contrast-enhanced sonography. Contrast-enhanced sonography using the perflubutane-based contrast agent Sonazoid (Daiichi Sankyo, Tokyo, Japan) was performed in 94 pathologically proven palpable breast mass lesions, which could be depicted with B-mode sonography. Quantitative analyses using the time-intensity curve on contrast-enhanced sonography were performed in 5 region of interest (ROI) types (manually traced ROI and circular ROIs of 5, 10, 15, and 20 mm in diameter). The peak signal intensity, initial slope, time to peak, positive enhancement integral, and wash-out ratio were investigated in each ROI. There were significant differences between benign and malignant lesions in the time to peak (P benign and malignant lesions in the time to peak (P benign and malignant breast lesions. © 2015 by the American Institute of Ultrasound in Medicine.

Maintenance of water uptake and reduced water loss contribute to water stress tolerance of Spiraea alba Du Roi and Spiraea tomentosa L.

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Stanton, Kelly M; Mickelbart, Michael V

2014-01-01

Two primarily eastern US native shrubs, Spiraea alba Du Roi and Spiraea tomentosa L., are typically found growing in wet areas, often with standing water. Both species have potential for use in the landscape, but little is known of their environmental requirements, including their adaptation to water stress. Two geographic accessions of each species were evaluated for their response to water stress under greenhouse conditions. Above-ground biomass, water relations and gas exchange were measured in well-watered and water stress treatments. In both species, water stress resulted in reduced growth, transpiration and pre-dawn water potential. However, both species also exhibited the ability to osmotically adjust to lower soil water content, resulting in maintained midday leaf turgor potential in all accessions. Net CO2 assimilation was reduced only in one accession of S. alba, primarily due to large reductions in stomatal conductance. S. tomentosa lost a larger proportion of leaves than S. alba in response to water stress. The primary water stress tolerance strategies of S. alba and S. tomentosa appear to be the maintenance of water uptake and reduced water loss.

Spatial genetic analyses reveal cryptic population structure and migration patterns in a continuously harvested grey wolf (Canis lupus population in north-eastern Europe.

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Maris Hindrikson

Full Text Available Spatial genetics is a relatively new field in wildlife and conservation biology that is becoming an essential tool for unravelling the complexities of animal population processes, and for designing effective strategies for conservation and management. Conceptual and methodological developments in this field are therefore critical. Here we present two novel methodological approaches that further the analytical possibilities of STRUCTURE and DResD. Using these approaches we analyse structure and migrations in a grey wolf (Canislupus population in north-eastern Europe. We genotyped 16 microsatellite loci in 166 individuals sampled from the wolf population in Estonia and Latvia that has been under strong and continuous hunting pressure for decades. Our analysis demonstrated that this relatively small wolf population is represented by four genetic groups. We also used a novel methodological approach that uses linear interpolation to statistically test the spatial separation of genetic groups. The new method, which is capable of using program STRUCTURE output, can be applied widely in population genetics to reveal both core areas and areas of low significance for genetic groups. We also used a recently developed spatially explicit individual-based method DResD, and applied it for the first time to microsatellite data, revealing a migration corridor and barriers, and several contact zones.

Post-genomic analyses of fungal lignocellulosic biomass degradation reveal the unexpected potential of the plant pathogen Ustilago maydis

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Couturier Marie

2012-02-01

Full Text Available Abstract Background Filamentous fungi are potent biomass degraders due to their ability to thrive in ligno(hemicellulose-rich environments. During the last decade, fungal genome sequencing initiatives have yielded abundant information on the genes that are putatively involved in lignocellulose degradation. At present, additional experimental studies are essential to provide insights into the fungal secreted enzymatic pools involved in lignocellulose degradation. Results In this study, we performed a wide analysis of 20 filamentous fungi for which genomic data are available to investigate their biomass-hydrolysis potential. A comparison of fungal genomes and secretomes using enzyme activity profiling revealed discrepancies in carbohydrate active enzymes (CAZymes sets dedicated to plant cell wall. Investigation of the contribution made by each secretome to the saccharification of wheat straw demonstrated that most of them individually supplemented the industrial Trichoderma reesei CL847 enzymatic cocktail. Unexpectedly, the most striking effect was obtained with the phytopathogen Ustilago maydis that improved the release of total sugars by 57% and of glucose by 22%. Proteomic analyses of the best-performing secretomes indicated a specific enzymatic mechanism of U. maydis that is likely to involve oxido-reductases and hemicellulases. Conclusion This study provides insight into the lignocellulose-degradation mechanisms by filamentous fungi and allows for the identification of a number of enzymes that are potentially useful to further improve the industrial lignocellulose bioconversion process.

Analyses in zebrafish embryos reveal that nanotoxicity profiles are dependent on surface-functionalization controlled penetrance of biological membranes.

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Paatero, Ilkka; Casals, Eudald; Niemi, Rasmus; Özliseli, Ezgi; Rosenholm, Jessica M; Sahlgren, Cecilia

2017-08-21

Mesoporous silica nanoparticles (MSNs) are extensively explored as drug delivery systems, but in depth understanding of design-toxicity relationships is still scarce. We used zebrafish (Danio rerio) embryos to study toxicity profiles of differently surface functionalized MSNs. Embryos with the chorion membrane intact, or dechoroniated embryos, were incubated or microinjected with amino (NH 2 -MSNs), polyethyleneimine (PEI-MSNs), succinic acid (SUCC-MSNs) or polyethyleneglycol (PEG-MSNs) functionalized MSNs. Toxicity was assessed by viability and cardiovascular function. NH 2 -MSNs, SUCC-MSNs and PEG-MSNs were well tolerated, 50 µg/ml PEI-MSNs induced 100% lethality 48 hours post fertilization (hpf). Dechoroniated embryos were more sensitive and 10 µg/ml PEI-MSNs reduced viability to 5% at 96hpf. Sensitivity to PEG- and SUCC-, but not NH 2 -MSNs, was also enhanced. Typically cardiovascular toxicity was evident prior to lethality. Confocal microscopy revealed that PEI-MSNs penetrated into the embryos whereas PEG-, NH2- and SUCC-MSNs remained aggregated on the skin surface. Direct exposure of inner organs by microinjecting NH 2 -MSNs and PEI-MSNs demonstrated that the particles displayed similar toxicity indicating that functionalization affects the toxicity profile by influencing penetrance through biological barriers. The data emphasize the need for careful analyses of toxicity mechanisms in relevant models and constitute an important knowledge step towards the development of safer and sustainable nanotherapies.

Transcriptomic analyses reveal novel genes with sexually dimorphic expression in the zebrafish gonad and brain.

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Rajini Sreenivasan

Full Text Available BACKGROUND: Our knowledge on zebrafish reproduction is very limited. We generated a gonad-derived cDNA microarray from zebrafish and used it to analyze large-scale gene expression profiles in adult gonads and other organs. METHODOLOGY/PRINCIPAL FINDINGS: We have identified 116638 gonad-derived zebrafish expressed sequence tags (ESTs, 21% of which were isolated in our lab. Following in silico normalization, we constructed a gonad-derived microarray comprising 6370 unique, full-length cDNAs from differentiating and adult gonads. Labeled targets from adult gonad, brain, kidney and 'rest-of-body' from both sexes were hybridized onto the microarray. Our analyses revealed 1366, 881 and 656 differentially expressed transcripts (34.7% novel that showed highest expression in ovary, testis and both gonads respectively. Hierarchical clustering showed correlation of the two gonadal transcriptomes and their similarities to those of the brains. In addition, we have identified 276 genes showing sexually dimorphic expression both between the brains and between the gonads. By in situ hybridization, we showed that the gonadal transcripts with the strongest array signal intensities were germline-expressed. We found that five members of the GTP-binding septin gene family, from which only one member (septin 4 has previously been implicated in reproduction in mice, were all strongly expressed in the gonads. CONCLUSIONS/SIGNIFICANCE: We have generated a gonad-derived zebrafish cDNA microarray and demonstrated its usefulness in identifying genes with sexually dimorphic co-expression in both the gonads and the brains. We have also provided the first evidence of large-scale differential gene expression between female and male brains of a teleost. Our microarray would be useful for studying gonad development, differentiation and function not only in zebrafish but also in related teleosts via cross-species hybridizations. Since several genes have been shown to play similar

MRI texture analysis (MRTA) of T2-weighted images in Crohn's disease may provide information on histological and MRI disease activity in patients undergoing ileal resection

Energy Technology Data Exchange (ETDEWEB)

Makanyanga, Jesica; Bhatnagar, Gauraang; Halligan, Steve; Taylor, Stuart A. [University College London and University College London Hospitals NIHR Biomedical Research Centre, Center for Medical Imaging, London (United Kingdom); Ganeshan, Balaji; Groves, Ashley; Miles, Ken [University College London, University College Hospital, Institute of Nuclear Medicine, London (United Kingdom); Rodriguez-Justo, Manuel [University College London, Department of Research Pathology, University College London Cancer Institute, London (United Kingdom)

2017-02-15

To associate MRI textural analysis (MRTA) with MRI and histological Crohn's disease (CD) activity. Sixteen patients (mean age 39.5 years, 9 male) undergoing MR enterography before ileal resection were retrospectively analysed. Thirty-six small (≤3 mm) ROIs were placed on T2-weighted images and location-matched histological acute inflammatory scores (AIS) measured. MRI activity (mural thickness, T2 signal, T1 enhancement) (CDA) was scored in large ROIs. MRTA features (mean, standard deviation, mean of positive pixels (MPP), entropy, kurtosis, skewness) were extracted using a filtration histogram technique. Spatial scale filtration (SSF) ranged from 2 to 5 mm. Regression (linear/logistic) tested associations between MRTA and AIS (small ROIs), and CDA/constituent parameters (large ROIs). Skewness (SSF = 2 mm) was associated with AIS [regression coefficient (rc) 4.27, p = 0.02]. Of 120 large ROI analyses (for each MRI, MRTA feature and SSF), 15 were significant. Entropy (SSF = 2, 3 mm) and kurtosis (SSF = 3 mm) were associated with CDA (rc 0.9, 1.0, -0.45, p = 0.006-0.01). Entropy and mean (SSF = 2-4 mm) were associated with T2 signal [odds ratio (OR) 2.32-3.16, p = 0.02-0.004], [OR 1.22-1.28, p = 0.03-0.04]. MPP (SSF = 2 mm) was associated with mural thickness (OR 0.91, p = 0.04). Kurtosis (SSF = 3 mm), standard deviation (SSF = 5 mm) were associated with decreased T1 enhancement (OR 0.59, 0.42, p = 0.004, 0.007). MRTA features may be associated with CD activity. (orig.)

Comparative genome analyses of Serratia marcescens FS14 reveals its high antagonistic potential.

Directory of Open Access Journals (Sweden)

Pengpeng Li

Full Text Available S. marcescens FS14 was isolated from an Atractylodes macrocephala Koidz plant that was infected by Fusarium oxysporum and showed symptoms of root rot. With the completion of the genome sequence of FS14, the first comprehensive comparative-genomic analysis of the Serratia genus was performed. Pan-genome and COG analyses showed that the majority of the conserved core genes are involved in basic cellular functions, while genomic factors such as prophages contribute considerably to genome diversity. Additionally, a Type I restriction-modification system, a Type III secretion system and tellurium resistance genes are found in only some Serratia species. Comparative analysis further identified that S. marcescens FS14 possesses multiple mechanisms for antagonism against other microorganisms, including the production of prodigiosin, bacteriocins, and multi-antibiotic resistant determinants as well as chitinases. The presence of two evolutionarily distinct Type VI secretion systems (T6SSs in FS14 may provide further competitive advantages for FS14 against other microbes. To our knowledge, this is the first report of comparative analysis on T6SSs in the genus, which identifies four types of T6SSs in Serratia spp.. Competition bioassays of FS14 against the vital plant pathogenic bacterium Ralstonia solanacearum and fungi Fusarium oxysporum and Sclerotinia sclerotiorum were performed to support our genomic analyses, in which FS14 demonstrated high antagonistic activities against both bacterial and fungal phytopathogens.

MRI evaluation of cerebral perfusion changes in patients with MELAS syndrome

International Nuclear Information System (INIS)

Xie Sheng; Qi Zhaoyue; Xiao Jiangxi; Jiang Xuexiang; Yang Yanling

2008-01-01

Objective: To detect the changes of cerebral perfusion in patients with MELAS syndrome by using MR perfusion technique. Methods: Thirteen patients with MELAS syndrome and 13 controls with normal neurological conditions were scanned with the sequence of flow-sensitive alternating inversion recovery exempting separate T 1 measurement (FAIREST). Their rCBF values were obtained in regions of bilateral basilar nuclei and thalami, as well as bilateral temporal lobes and occipital lobes. Regression analysis was carried out to determine the effect of location and side on the measurement of rCBF in controls. One-way ANOVA was conducted to compare rCBF values among the control group, the lesion ROIs and normal ROIs of the MELAS syndrome group. Results: The values of rCBF were 0.83 ± 0.23, 1.17± 0.30, 0.93 ± 0.28, and 1.11 ± 0.25 for the left basilar ganglia, thalamus, temporal lobe, and occipital lobe respectively, while they were 0.77 ± 0.15, 1.03 ± 0.34, 1.06 ± 0.23, and 1.09 ± 0.23 for the right basilar ganglia, thalamus, temporal lobe, and occipital lobe respectively. Regression analysis revealed no effect of location and side on the rCBF (P>0.05). The rCBF value for control group was 1.00 + 0. 28, while it was 1.01 ± 0.31 for the normal ROIs and 1.95 ± 0.43 for the lesion ROIs in the MELAS syndrome group (F=54.99, P<0.01). The rCBF of the lesion ROIs in the MELAS syndrome group was significantly higher than the normal ROIs and the control group. Conclusion: CBF maps can reveal changes of cerebral blood flow in patients with ictal MELAS, which suggests increased perfusion in the stroke-like lesions. (authors)

Concurrent growth rate and transcript analyses reveal essential gene stringency in Escherichia coli.

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Shan Goh

Full Text Available BACKGROUND: Genes essential for bacterial growth are of particular scientific interest. Many putative essential genes have been identified or predicted in several species, however, little is known about gene expression requirement stringency, which may be an important aspect of bacterial physiology and likely a determining factor in drug target development. METHODOLOGY/PRINCIPAL FINDINGS: Working from the premise that essential genes differ in absolute requirement for growth, we describe silencing of putative essential genes in E. coli to obtain a titration of declining growth rates and transcript levels by using antisense peptide nucleic acids (PNA and expressed antisense RNA. The relationship between mRNA decline and growth rate decline reflects the degree of essentiality, or stringency, of an essential gene, which is here defined by the minimum transcript level for a 50% reduction in growth rate (MTL(50. When applied to four growth essential genes, both RNA silencing methods resulted in MTL(50 values that reveal acpP as the most stringently required of the four genes examined, with ftsZ the next most stringently required. The established antibacterial targets murA and fabI were less stringently required. CONCLUSIONS: RNA silencing can reveal stringent requirements for gene expression with respect to growth. This method may be used to validate existing essential genes and to quantify drug target requirement.

Short- and long-term reliability of language fMRI.

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Nettekoven, Charlotte; Reck, Nicola; Goldbrunner, Roland; Grefkes, Christian; Weiß Lucas, Carolin

2018-08-01

When using functional magnetic resonance imaging (fMRI) for mapping important language functions, a high test-retest reliability is mandatory, both in basic scientific research and for clinical applications. We, therefore, systematically tested the short- and long-term reliability of fMRI in a group of healthy subjects using a picture naming task and a sparse-sampling fMRI protocol. We hypothesized that test-retest reliability might be higher for (i) speech-related motor areas than for other language areas and for (ii) the short as compared to the long intersession interval. 16 right-handed subjects (mean age: 29 years) participated in three sessions separated by 2-6 (session 1 and 2, short-term) and 21-34 days (session 1 and 3, long-term). Subjects were asked to perform the same overt picture naming task in each fMRI session (50 black-white images per session). Reliability was tested using the following measures: (i) Euclidean distances (ED) between local activation maxima and Centers of Gravity (CoGs), (ii) overlap volumes and (iii) voxel-wise intraclass correlation coefficients (ICCs). Analyses were performed for three regions of interest which were chosen based on whole-brain group data: primary motor cortex (M1), superior temporal gyrus (STG) and inferior frontal gyrus (IFG). Our results revealed that the activation centers were highly reliable, independent of the time interval, ROI or hemisphere with significantly smaller ED for the local activation maxima (6.45 ± 1.36 mm) as compared to the CoGs (8.03 ± 2.01 mm). In contrast, the extent of activation revealed rather low reliability values with overlaps ranging from 24% (IFG) to 56% (STG). Here, the left hemisphere showed significantly higher overlap volumes than the right hemisphere. Although mean ICCs ranged between poor (ICC0.75) were found for all ROIs. Voxel-wise reliability of the different ROIs was influenced by the intersession interval. Taken together, we could show that, despite of

Comparative analyses of population-scale phenomic data in electronic medical records reveal race-specific disease networks.

Science.gov (United States)

Glicksberg, Benjamin S; Li, Li; Badgeley, Marcus A; Shameer, Khader; Kosoy, Roman; Beckmann, Noam D; Pho, Nam; Hakenberg, Jörg; Ma, Meng; Ayers, Kristin L; Hoffman, Gabriel E; Dan Li, Shuyu; Schadt, Eric E; Patel, Chirag J; Chen, Rong; Dudley, Joel T

2016-06-15

Underrepresentation of racial groups represents an important challenge and major gap in phenomics research. Most of the current human phenomics research is based primarily on European populations; hence it is an important challenge to expand it to consider other population groups. One approach is to utilize data from EMR databases that contain patient data from diverse demographics and ancestries. The implications of this racial underrepresentation of data can be profound regarding effects on the healthcare delivery and actionability. To the best of our knowledge, our work is the first attempt to perform comparative, population-scale analyses of disease networks across three different populations, namely Caucasian (EA), African American (AA) and Hispanic/Latino (HL). We compared susceptibility profiles and temporal connectivity patterns for 1988 diseases and 37 282 disease pairs represented in a clinical population of 1 025 573 patients. Accordingly, we revealed appreciable differences in disease susceptibility, temporal patterns, network structure and underlying disease connections between EA, AA and HL populations. We found 2158 significantly comorbid diseases for the EA cohort, 3265 for AA and 672 for HL. We further outlined key disease pair associations unique to each population as well as categorical enrichments of these pairs. Finally, we identified 51 key 'hub' diseases that are the focal points in the race-centric networks and of particular clinical importance. Incorporating race-specific disease comorbidity patterns will produce a more accurate and complete picture of the disease landscape overall and could support more precise understanding of disease relationships and patient management towards improved clinical outcomes. rong.chen@mssm.edu or joel.dudley@mssm.edu Supplementary data are available at Bioinformatics online. © The Author 2016. Published by Oxford University Press.

Combined Metabonomic and Quantitative RT-PCR Analyses Revealed Metabolic Reprogramming Associated with Fusarium graminearum Resistance in Transgenic Arabidopsis thaliana

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Fangfang Chen

2018-01-01

Full Text Available Fusarium head blight disease resulting from Fusarium graminearum (FG infection causes huge losses in global production of cereals and development of FG-resistant plants is urgently needed. To understand biochemistry mechanisms for FG resistance, here, we have systematically investigated the plant metabolomic phenotypes associated with FG resistance for transgenic Arabidopsis thaliana expressing a class-I chitinase (Chi, a Fusarium-specific recombinant antibody gene (CWP2 and fused Chi-CWP2. Plant disease indices, mycotoxin levels, metabonomic characteristics, and expression levels of several key genes were measured together with their correlations. We found that A. thaliana expressing Chi-CWP2 showed higher FG resistance with much lower disease indices and mycotoxin levels than the wild-type and the plants expressing Chi or CWP2 alone. The combined metabonomic and quantitative RT-PCR analyses revealed that such FG-resistance was closely associated with the promoted biosynthesis of secondary metabolites (phenylpropanoids, alkanoids and organic osmolytes (proline, betaine, glucose, myo-inositol together with enhanced TCA cycle and GABA shunt. These suggest that the concurrently enhanced biosyntheses of the shikimate-mediated secondary metabolites and organic osmolytes be an important strategy for A. thaliana to develop and improve FG resistance. These findings provide essential biochemical information related to FG resistance which is important for developing FG-resistant cereals.

Dynamic PET reconstruction using temporal patch-based low rank penalty for ROI-based brain kinetic analysis

International Nuclear Information System (INIS)

Kim, Kyungsang; Ye, Jong Chul; Son, Young Don; Cho, Zang Hee; Bresler, Yoram; Ra, Jong Beom

2015-01-01

Dynamic positron emission tomography (PET) is widely used to measure changes in the bio-distribution of radiopharmaceuticals within particular organs of interest over time. However, to retain sufficient temporal resolution, the number of photon counts in each time frame must be limited. Therefore, conventional reconstruction algorithms such as the ordered subset expectation maximization (OSEM) produce noisy reconstruction images, thus degrading the quality of the extracted time activity curves (TACs). To address this issue, many advanced reconstruction algorithms have been developed using various spatio-temporal regularizations. In this paper, we extend earlier results and develop a novel temporal regularization, which exploits the self-similarity of patches that are collected in dynamic images. The main contribution of this paper is to demonstrate that the correlation of patches can be exploited using a low-rank constraint that is insensitive to global intensity variations. The resulting optimization framework is, however, non-Lipschitz and non-convex due to the Poisson log-likelihood and low-rank penalty terms. Direct application of the conventional Poisson image deconvolution by an augmented Lagrangian (PIDAL) algorithm is, however, problematic due to its large memory requirements, which prevents its parallelization. Thus, we propose a novel optimization framework using the concave-convex procedure (CCCP) by exploiting the Legendre–Fenchel transform, which is computationally efficient and parallelizable. In computer simulation and a real in vivo experiment using a high-resolution research tomograph (HRRT) scanner, we confirm that the proposed algorithm can improve image quality while also extracting more accurate region of interests (ROI) based kinetic parameters. Furthermore, we show that the total reconstruction time for HRRT PET is significantly accelerated using our GPU implementation, which makes the algorithm very practical in clinical environments

Automatic feature learning using multichannel ROI based on deep structured algorithms for computerized lung cancer diagnosis.

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Sun, Wenqing; Zheng, Bin; Qian, Wei

2017-10-01

This study aimed to analyze the ability of extracting automatically generated features using deep structured algorithms in lung nodule CT image diagnosis, and compare its performance with traditional computer aided diagnosis (CADx) systems using hand-crafted features. All of the 1018 cases were acquired from Lung Image Database Consortium (LIDC) public lung cancer database. The nodules were segmented according to four radiologists' markings, and 13,668 samples were generated by rotating every slice of nodule images. Three multichannel ROI based deep structured algorithms were designed and implemented in this study: convolutional neural network (CNN), deep belief network (DBN), and stacked denoising autoencoder (SDAE). For the comparison purpose, we also implemented a CADx system using hand-crafted features including density features, texture features and morphological features. The performance of every scheme was evaluated by using a 10-fold cross-validation method and an assessment index of the area under the receiver operating characteristic curve (AUC). The observed highest area under the curve (AUC) was 0.899±0.018 achieved by CNN, which was significantly higher than traditional CADx with the AUC=0.848±0.026. The results from DBN was also slightly higher than CADx, while SDAE was slightly lower. By visualizing the automatic generated features, we found some meaningful detectors like curvy stroke detectors from deep structured schemes. The study results showed the deep structured algorithms with automatically generated features can achieve desirable performance in lung nodule diagnosis. With well-tuned parameters and large enough dataset, the deep learning algorithms can have better performance than current popular CADx. We believe the deep learning algorithms with similar data preprocessing procedure can be used in other medical image analysis areas as well. Copyright © 2017. Published by Elsevier Ltd.

Brain-wide slowing of spontaneous alpha rhythms in mild cognitive impairment

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Pilar eGarcés

2013-12-01

Full Text Available The neurophysiological changes associated with Alzheimer’s Disease (AD and Mild Cognitive Impairment (MCI include an increase in low frequency activity, as measured with electroencephalography or magnetoencephalography (MEG. A relevant property of spectral measures is the alpha peak, which corresponds to the dominant alpha rhythm. Here we studied the spatial distribution of MEG resting state alpha peak frequency and amplitude values in a sample of 27 MCI patients and 24 age-matched healthy controls. Power spectra were reconstructed in source space with linearly constrained minimum variance beamformer. Then, 88 Regions of Interest (ROIs were defined and an alpha peak per ROI and subject was identified. Statistical analyses were performed at every ROI, accounting for age, sex and educational level. Peak frequency was significantly decreased (p< 0.05 in MCIs in many posterior ROIs. The average peak frequency over all ROIs was 9.68±0.71 Hz for controls and 9.05±0.90 Hz for MCIs and the average normalized amplitude was (2.57±0.59•10-2 for controls and (2.70±0.49•10-2 for MCIs. Age and gender were also found to play a role in the alpha peak, since its frequency was higher in females than in males in posterior ROIs and correlated negatively with age in frontal ROIs. Furthermore, we examined the dependence of peak parameters with hippocampal volume, which is a commonly used marker of early structural AD-related damage. Peak frequency was positively correlated with hippocampal volume in many posterior ROIs. Overall, these findings indicate a pathological alpha slowing in MCI.

Core microbial functional activities in ocean environments revealed by global metagenomic profiling analyses.

KAUST Repository

Ferreira, Ari J S

2014-06-12

Metagenomics-based functional profiling analysis is an effective means of gaining deeper insight into the composition of marine microbial populations and developing a better understanding of the interplay between the functional genome content of microbial communities and abiotic factors. Here we present a comprehensive analysis of 24 datasets covering surface and depth-related environments at 11 sites around the world\\'s oceans. The complete datasets comprises approximately 12 million sequences, totaling 5,358 Mb. Based on profiling patterns of Clusters of Orthologous Groups (COGs) of proteins, a core set of reference photic and aphotic depth-related COGs, and a collection of COGs that are associated with extreme oxygen limitation were defined. Their inferred functions were utilized as indicators to characterize the distribution of light- and oxygen-related biological activities in marine environments. The results reveal that, while light level in the water column is a major determinant of phenotypic adaptation in marine microorganisms, oxygen concentration in the aphotic zone has a significant impact only in extremely hypoxic waters. Phylogenetic profiling of the reference photic/aphotic gene sets revealed a greater variety of source organisms in the aphotic zone, although the majority of individual photic and aphotic depth-related COGs are assigned to the same taxa across the different sites. This increase in phylogenetic and functional diversity of the core aphotic related COGs most probably reflects selection for the utilization of a broad range of alternate energy sources in the absence of light.

Core microbial functional activities in ocean environments revealed by global metagenomic profiling analyses.

KAUST Repository

Ferreira, Ari J S; Siam, Rania; Setubal, Joã o C; Moustafa, Ahmed; Sayed, Ahmed; Chambergo, Felipe S; Dawe, Adam S; Ghazy, Mohamed A; Sharaf, Hazem; Ouf, Amged; Alam, Intikhab; Abdel-Haleem, Alyaa M; Lehvä slaiho, Heikki; Ramadan, Eman; Antunes, André ; Stingl, Ulrich; Archer, John A.C.; Jankovic, Boris R; Sogin, Mitchell; Bajic, Vladimir B.; El-Dorry, Hamza

2014-01-01

Metagenomics-based functional profiling analysis is an effective means of gaining deeper insight into the composition of marine microbial populations and developing a better understanding of the interplay between the functional genome content of microbial communities and abiotic factors. Here we present a comprehensive analysis of 24 datasets covering surface and depth-related environments at 11 sites around the world's oceans. The complete datasets comprises approximately 12 million sequences, totaling 5,358 Mb. Based on profiling patterns of Clusters of Orthologous Groups (COGs) of proteins, a core set of reference photic and aphotic depth-related COGs, and a collection of COGs that are associated with extreme oxygen limitation were defined. Their inferred functions were utilized as indicators to characterize the distribution of light- and oxygen-related biological activities in marine environments. The results reveal that, while light level in the water column is a major determinant of phenotypic adaptation in marine microorganisms, oxygen concentration in the aphotic zone has a significant impact only in extremely hypoxic waters. Phylogenetic profiling of the reference photic/aphotic gene sets revealed a greater variety of source organisms in the aphotic zone, although the majority of individual photic and aphotic depth-related COGs are assigned to the same taxa across the different sites. This increase in phylogenetic and functional diversity of the core aphotic related COGs most probably reflects selection for the utilization of a broad range of alternate energy sources in the absence of light.

Core microbial functional activities in ocean environments revealed by global metagenomic profiling analyses.

Directory of Open Access Journals (Sweden)

Ari J S Ferreira

Full Text Available Metagenomics-based functional profiling analysis is an effective means of gaining deeper insight into the composition of marine microbial populations and developing a better understanding of the interplay between the functional genome content of microbial communities and abiotic factors. Here we present a comprehensive analysis of 24 datasets covering surface and depth-related environments at 11 sites around the world's oceans. The complete datasets comprises approximately 12 million sequences, totaling 5,358 Mb. Based on profiling patterns of Clusters of Orthologous Groups (COGs of proteins, a core set of reference photic and aphotic depth-related COGs, and a collection of COGs that are associated with extreme oxygen limitation were defined. Their inferred functions were utilized as indicators to characterize the distribution of light- and oxygen-related biological activities in marine environments. The results reveal that, while light level in the water column is a major determinant of phenotypic adaptation in marine microorganisms, oxygen concentration in the aphotic zone has a significant impact only in extremely hypoxic waters. Phylogenetic profiling of the reference photic/aphotic gene sets revealed a greater variety of source organisms in the aphotic zone, although the majority of individual photic and aphotic depth-related COGs are assigned to the same taxa across the different sites. This increase in phylogenetic and functional diversity of the core aphotic related COGs most probably reflects selection for the utilization of a broad range of alternate energy sources in the absence of light.

Deciphering the Cryptic Genome: Genome-wide Analyses of the Rice Pathogen Fusarium fujikuroi Reveal Complex Regulation of Secondary Metabolism and Novel Metabolites

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Studt, Lena; Niehaus, Eva-Maria; Espino, Jose J.; Huß, Kathleen; Michielse, Caroline B.; Albermann, Sabine; Wagner, Dominik; Bergner, Sonja V.; Connolly, Lanelle R.; Fischer, Andreas; Reuter, Gunter; Kleigrewe, Karin; Bald, Till; Wingfield, Brenda D.; Ophir, Ron; Freeman, Stanley; Hippler, Michael; Smith, Kristina M.; Brown, Daren W.; Proctor, Robert H.; Münsterkötter, Martin; Freitag, Michael; Humpf, Hans-Ulrich; Güldener, Ulrich; Tudzynski, Bettina

2013-01-01

The fungus Fusarium fujikuroi causes “bakanae” disease of rice due to its ability to produce gibberellins (GAs), but it is also known for producing harmful mycotoxins. However, the genetic capacity for the whole arsenal of natural compounds and their role in the fungus' interaction with rice remained unknown. Here, we present a high-quality genome sequence of F. fujikuroi that was assembled into 12 scaffolds corresponding to the 12 chromosomes described for the fungus. We used the genome sequence along with ChIP-seq, transcriptome, proteome, and HPLC-FTMS-based metabolome analyses to identify the potential secondary metabolite biosynthetic gene clusters and to examine their regulation in response to nitrogen availability and plant signals. The results indicate that expression of most but not all gene clusters correlate with proteome and ChIP-seq data. Comparison of the F. fujikuroi genome to those of six other fusaria revealed that only a small number of gene clusters are conserved among these species, thus providing new insights into the divergence of secondary metabolism in the genus Fusarium. Noteworthy, GA biosynthetic genes are present in some related species, but GA biosynthesis is limited to F. fujikuroi, suggesting that this provides a selective advantage during infection of the preferred host plant rice. Among the genome sequences analyzed, one cluster that includes a polyketide synthase gene (PKS19) and another that includes a non-ribosomal peptide synthetase gene (NRPS31) are unique to F. fujikuroi. The metabolites derived from these clusters were identified by HPLC-FTMS-based analyses of engineered F. fujikuroi strains overexpressing cluster genes. In planta expression studies suggest a specific role for the PKS19-derived product during rice infection. Thus, our results indicate that combined comparative genomics and genome-wide experimental analyses identified novel genes and secondary metabolites that contribute to the evolutionary success of F

Gender Classification Based on Eye Movements: A Processing Effect During Passive Face Viewing.

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Sammaknejad, Negar; Pouretemad, Hamidreza; Eslahchi, Changiz; Salahirad, Alireza; Alinejad, Ashkan

2017-01-01

Studies have revealed superior face recognition skills in females, partially due to their different eye movement strategies when encoding faces. In the current study, we utilized these slight but important differences and proposed a model that estimates the gender of the viewers and classifies them into two subgroups, males and females. An eye tracker recorded participant's eye movements while they viewed images of faces. Regions of interest (ROIs) were defined for each face. Results showed that the gender dissimilarity in eye movements was not due to differences in frequency of fixations in the ROI s per se. Instead, it was caused by dissimilarity in saccade paths between the ROIs. The difference enhanced when saccades were towards the eyes. Females showed significant increase in transitions from other ROI s to the eyes. Consequently, the extraction of temporal transient information of saccade paths through a transition probability matrix, similar to a first order Markov chain model, significantly improved the accuracy of the gender classification results.

Diet and stable isotope analyses reveal the feeding ecology of the orangeback squid Sthenoteuthis pteropus (Steenstrup 1855 (Mollusca, Ommastrephidae in the eastern tropical Atlantic.

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Véronique Merten

Full Text Available In the eastern tropical Atlantic, the orangeback flying squid Sthenoteuthis pteropus (Steenstrup 1855 (Cephalopoda, Ommastrephidae is a dominant species of the epipelagic nekton community. This carnivore squid has a short lifespan and is one of the fastest-growing squids. In this study, we characterise the role of S. pteropus in the pelagic food web of the eastern tropical Atlantic by investigating its diet and the dynamics of its feeding habits throughout its ontogeny and migration. During three expeditions in the eastern tropical Atlantic in 2015, 129 specimens were caught by hand jigging. Stomach content analyses (via visual identification and DNA barcoding were combined with stable isotope data (∂15N and ∂13C of muscle tissue to describe diet, feeding habits and trophic ecology of S. pteropus. Additionally, stable isotope analyses of incremental samples along the squid's gladius-the chitinous spiniform structure supporting the muscles and organs-were carried out to explore possible diet shifts through ontogeny and migration. Our results show that S. pteropus preys mainly on myctophid fishes (e.g. Myctophum asperum, Myctophum nitidulum, Vinciguerria spp., but also on other teleost species, cephalopods (e.g. Enoploteuthidae, Bolitinidae, Ommastrephidae, crustaceans and possibly on gelatinous zooplankton as well. The squid shows a highly opportunistic feeding behaviour that includes cannibalism. Our study indicates that the trophic position of S. pteropus may increase by approximately one trophic level from a mantle length of 15 cm to 47 cm. The reconstructed isotope-based feeding chronologies of the gladii revealed high intra- and inter-individual variability in the squid's trophic position and foraging area. These findings are not revealed by diet or muscle tissue stable isotope analysis. This suggests a variable and complex life history involving individual variation and migration. The role of S. pteropus in transferring energy and

Diet and stable isotope analyses reveal the feeding ecology of the orangeback squid Sthenoteuthis pteropus (Steenstrup 1855) (Mollusca, Ommastrephidae) in the eastern tropical Atlantic.

Science.gov (United States)

Merten, Véronique; Christiansen, Bernd; Javidpour, Jamileh; Piatkowski, Uwe; Puebla, Oscar; Gasca, Rebeca; Hoving, Henk-Jan T

2017-01-01

In the eastern tropical Atlantic, the orangeback flying squid Sthenoteuthis pteropus (Steenstrup 1855) (Cephalopoda, Ommastrephidae) is a dominant species of the epipelagic nekton community. This carnivore squid has a short lifespan and is one of the fastest-growing squids. In this study, we characterise the role of S. pteropus in the pelagic food web of the eastern tropical Atlantic by investigating its diet and the dynamics of its feeding habits throughout its ontogeny and migration. During three expeditions in the eastern tropical Atlantic in 2015, 129 specimens were caught by hand jigging. Stomach content analyses (via visual identification and DNA barcoding) were combined with stable isotope data (∂15N and ∂13C) of muscle tissue to describe diet, feeding habits and trophic ecology of S. pteropus. Additionally, stable isotope analyses of incremental samples along the squid's gladius-the chitinous spiniform structure supporting the muscles and organs-were carried out to explore possible diet shifts through ontogeny and migration. Our results show that S. pteropus preys mainly on myctophid fishes (e.g. Myctophum asperum, Myctophum nitidulum, Vinciguerria spp.), but also on other teleost species, cephalopods (e.g. Enoploteuthidae, Bolitinidae, Ommastrephidae), crustaceans and possibly on gelatinous zooplankton as well. The squid shows a highly opportunistic feeding behaviour that includes cannibalism. Our study indicates that the trophic position of S. pteropus may increase by approximately one trophic level from a mantle length of 15 cm to 47 cm. The reconstructed isotope-based feeding chronologies of the gladii revealed high intra- and inter-individual variability in the squid's trophic position and foraging area. These findings are not revealed by diet or muscle tissue stable isotope analysis. This suggests a variable and complex life history involving individual variation and migration. The role of S. pteropus in transferring energy and nutrients from

More consistently altered connectivity patterns for cerebellum and medial temporal lobes than for amygdala and striatum in schizophrenia

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Henning ePeters

2016-02-01

Full Text Available Background: Brain architecture can be divided into a cortico-thalamic system and modulatory ‘subcortical-cerebellar’ systems containing key structures such as striatum, medial temporal lobes (MTLs, amygdala, and cerebellum. Subcortical-cerebellar systems are known to be altered in schizophrenia. In particular, intrinsic functional brain connectivity (iFC between these systems has been consistently demonstrated in patients. While altered connectivity is known for each subcortical-cerebellar system separately, it is unknown whether subcortical-cerebellar systems’ connectivity patterns with the cortico-thalamic system are comparably altered across systems, i.e., if separate subcortical-cerebellar systems’ connectivity patterns are consistent across patients. Methods: To investigate this question, 18 patients with schizophrenia (3 unmedicated, 15 medicated with atypical antipsychotics and 18 healthy controls were assessed by resting-state functional magnetic resonance imaging (fMRI. Independent component analysis of fMRI data revealed cortical intrinsic brain networks (NWs with time courses representing proxies for cortico-thalamic system activity. Subcortical-cerebellar systems’ activity was represented by fMRI-based time courses of selected regions-of-interest (ROIs (i.e., striatum, MTL, amygdala, cerebellum. Correlation analysis among ROI- and NWs-time courses yielded individual connectivity matrices (i.e. connectivity between NW and ROIs (allROIs-NW, separateROI-NW, only NWs (NWs-NWs, and only ROIs (allROIs-allROIs as main outcome measures, which were classified by support-vector-machine-based leave-one-out cross-validation. Differences in classification accuracy were statistically evaluated for consistency across subjects and systems. Results: Correlation matrices based on allROIs-NWs yielded 91% classification accuracy, which was significantly superior to allROIs-allROIs and NWs-NWs (56% and 74%, respectively. Considering separate

Decoding of visual activity patterns from fMRI responses using multivariate pattern analyses and convolutional neural network.

Science.gov (United States)

Zafar, Raheel; Kamel, Nidal; Naufal, Mohamad; Malik, Aamir Saeed; Dass, Sarat C; Ahmad, Rana Fayyaz; Abdullah, Jafri M; Reza, Faruque

2017-01-01

Decoding of human brain activity has always been a primary goal in neuroscience especially with functional magnetic resonance imaging (fMRI) data. In recent years, Convolutional neural network (CNN) has become a popular method for the extraction of features due to its higher accuracy, however it needs a lot of computation and training data. In this study, an algorithm is developed using Multivariate pattern analysis (MVPA) and modified CNN to decode the behavior of brain for different images with limited data set. Selection of significant features is an important part of fMRI data analysis, since it reduces the computational burden and improves the prediction performance; significant features are selected using t-test. MVPA uses machine learning algorithms to classify different brain states and helps in prediction during the task. General linear model (GLM) is used to find the unknown parameters of every individual voxel and the classification is done using multi-class support vector machine (SVM). MVPA-CNN based proposed algorithm is compared with region of interest (ROI) based method and MVPA based estimated values. The proposed method showed better overall accuracy (68.6%) compared to ROI (61.88%) and estimation values (64.17%).

Genome size analyses of Pucciniales reveal the largest fungal genomes.

Science.gov (United States)

Tavares, Sílvia; Ramos, Ana Paula; Pires, Ana Sofia; Azinheira, Helena G; Caldeirinha, Patrícia; Link, Tobias; Abranches, Rita; Silva, Maria do Céu; Voegele, Ralf T; Loureiro, João; Talhinhas, Pedro

2014-01-01

Rust fungi (Basidiomycota, Pucciniales) are biotrophic plant pathogens which exhibit diverse complexities in their life cycles and host ranges. The completion of genome sequencing of a few rust fungi has revealed the occurrence of large genomes. Sequencing efforts for other rust fungi have been hampered by uncertainty concerning their genome sizes. Flow cytometry was recently applied to estimate the genome size of a few rust fungi, and confirmed the occurrence of large genomes in this order (averaging 225.3 Mbp, while the average for Basidiomycota was 49.9 Mbp and was 37.7 Mbp for all fungi). In this work, we have used an innovative and simple approach to simultaneously isolate nuclei from the rust and its host plant in order to estimate the genome size of 30 rust species by flow cytometry. Genome sizes varied over 10-fold, from 70 to 893 Mbp, with an average genome size value of 380.2 Mbp. Compared to the genome sizes of over 1800 fungi, Gymnosporangium confusum possesses the largest fungal genome ever reported (893.2 Mbp). Moreover, even the smallest rust genome determined in this study is larger than the vast majority of fungal genomes (94%). The average genome size of the Pucciniales is now of 305.5 Mbp, while the average Basidiomycota genome size has shifted to 70.4 Mbp and the average for all fungi reached 44.2 Mbp. Despite the fact that no correlation could be drawn between the genome sizes, the phylogenomics or the life cycle of rust fungi, it is interesting to note that rusts with Fabaceae hosts present genomes clearly larger than those with Poaceae hosts. Although this study comprises only a small fraction of the more than 7000 rust species described, it seems already evident that the Pucciniales represent a group where genome size expansion could be a common characteristic. This is in sharp contrast to sister taxa, placing this order in a relevant position in fungal genomics research.

Validation of corrections for errors in collimation during measurement of gastric emptying of nuclide-labeled meals

Energy Technology Data Exchange (ETDEWEB)

Van Deventer, G.; Thomson, J.; Graham, L.S.; Thomasson, D.; Meyer, J.H.

1983-03-01

The study was undertaken to validate phantom-derived corrections for errors in collimation due to septal penetration or scatter, which vary with the size of the gastric region of interest (ROI). Six volunteers received 495 ml of 20% glucose labeled with both In-113m DTPA and Tc-99m DTPA. Gastric emptying of each nuclide was monitored by gamma camera as well as by periodic removal and reinstillation of the meal through a gastric tube. Serial aspirates from the gastric tube confirmed parallel emptying of In-113m and Tc-99m, but analyses of gamma-camera data yielded parallel emptying only when adequate corrections were made for errors in collimation. Analyses of ratios of gastric counts from anterior to posterior, as well as analyses of peak-to-scatter ratios, revealed only small, insignificant anteroposterior movement of the tracers within the stomach during emptying. Accordingly, there was no significant improvement in the camera data when corrections were made for attenuation with intragastric depth.

A simple derivation and analysis of a helical cone beam tomographic algorithm for long object imaging via a novel definition of region of interest

International Nuclear Information System (INIS)

Hu Jicun; Tam, Kwok; Johnson, Roger H

2004-01-01

We derive and analyse a simple algorithm first proposed by Kudo et al (2001 Proc. 2001 Meeting on Fully 3D Image Reconstruction in Radiology and Nuclear Medicine (Pacific Grove, CA) pp 7-10) for long object imaging from truncated helical cone beam data via a novel definition of region of interest (ROI). Our approach is based on the theory of short object imaging by Kudo et al (1998 Phys. Med. Biol. 43 2885-909). One of the key findings in their work is that filtering of the truncated projection can be divided into two parts: one, finite in the axial direction, results from ramp filtering the data within the Tam window. The other, infinite in the z direction, results from unbounded filtering of ray sums over PI lines only. We show that for an ROI defined by PI lines emanating from the initial and final source positions on a helical segment, the boundary data which would otherwise contaminate the reconstruction of the ROI can be completely excluded. This novel definition of the ROI leads to a simple algorithm for long object imaging. The overscan of the algorithm is analytically calculated and it is the same as that of the zero boundary method. The reconstructed ROI can be divided into two regions: one is minimally contaminated by the portion outside the ROI, while the other is reconstructed free of contamination. We validate the algorithm with a 3D Shepp-Logan phantom and a disc phantom

Multiparametric voxel-based analyses of standardized uptake values and apparent diffusion coefficients of soft-tissue tumours with a positron emission tomography/magnetic resonance system: Preliminary results

Energy Technology Data Exchange (ETDEWEB)

Sagiyama, Koji; Kamei, Ryotaro; Honda, Hiroshi [Kyushu University, Department of Clinical Radiology, Graduate School of Medical Sciences, Fukuoka (Japan); Watanabe, Yuji; Kawanami, Satoshi [Kyushu University, Department of Molecular Imaging and Diagnosis, Graduate School of Medical Sciences, Fukuoka (Japan); Hong, Sungtak [Philips Electronics Japan, Healthcare, Tokyo (Japan); Matsumoto, Yoshihiro [Kyushu University, Departmant of Orthopaedic Surgery, Graduate School of Medical Sciences, Fukuoka (Japan)

2017-12-15

To investigate the usefulness of voxel-based analysis of standardized uptake values (SUVs) and apparent diffusion coefficients (ADCs) for evaluating soft-tissue tumour malignancy with a PET/MR system. Thirty-five subjects with either ten low/intermediate-grade tumours or 25 high-grade tumours were prospectively enrolled. Zoomed diffusion-weighted and fluorodeoxyglucose ({sup 18}FDG)-PET images were acquired along with fat-suppressed T2-weighted images (FST2WIs). Regions of interest (ROIs) were drawn on FST2WIs including the tumour in all slices. ROIs were pasted onto PET and ADC-maps to measure SUVs and ADCs within tumour ROIs. Tumour volume, SUVmax, ADCminimum, the heterogeneity and the correlation coefficients of SUV and ADC were recorded. The parameters of high- and low/intermediate-grade groups were compared, and receiver operating characteristic (ROC) analysis was also performed. The mean correlation coefficient for SUV and ADC in high-grade sarcomas was lower than that of low/intermediate-grade tumours (-0.41 ± 0.25 vs. -0.08 ± 0.34, P < 0.01). Other parameters did not differ significantly. ROC analysis demonstrated that correlation coefficient showed the best diagnostic performance for differentiating the two groups (AUC 0.79, sensitivity 96.0%, specificity 60%, accuracy 85.7%). SUV and ADC determined via PET/MR may be useful for differentiating between high-grade and low/intermediate-grade soft tissue tumours. (orig.)

Brain cortical thickness in male adolescents with serious substance use and conduct problems.

Science.gov (United States)

Chumachenko, Serhiy Y; Sakai, Joseph T; Dalwani, Manish S; Mikulich-Gilbertson, Susan K; Dunn, Robin; Tanabe, Jody; Young, Susan; McWilliams, Shannon K; Banich, Marie T; Crowley, Thomas J

2015-01-01

Adolescents with substance use disorder (SUD) and conduct problems exhibit high levels of impulsivity and poor self-control. Limited work to date tests for brain cortical thickness differences in these youths. To investigate differences in cortical thickness between adolescents with substance use and conduct problems and controls. We recruited 25 male adolescents with SUD, and 19 male adolescent controls, and completed structural 3T magnetic resonance brain imaging. Using the surface-based morphometry software FreeSurfer, we completed region-of-interest (ROI) analyses for group cortical thickness differences in left, and separately right, inferior frontal gyrus (IFG), orbitofrontal cortex (OFC) and insula. Using FreeSurfer, we completed whole-cerebrum analyses of group differences in cortical thickness. Versus controls, the SUD group showed no cortical thickness differences in ROI analyses. Controlling for age and IQ, no regions with cortical thickness differences were found using whole-cerebrum analyses (though secondary analyses co-varying IQ and whole-cerebrum cortical thickness yielded a between-group cortical thickness difference in the left posterior cingulate/precuneus). Secondary findings showed that the SUD group, relative to controls, demonstrated significantly less right > left asymmetry in IFG, had weaker insular-to-whole-cerebrum cortical thickness correlations, and showed a positive association between conduct disorder symptom count and cortical thickness in a superior temporal gyrus cluster. Functional group differences may reflect a more nuanced cortical morphometric difference than ROI cortical thickness. Further investigation of morphometric differences is needed. If replicable findings can be established, they may aid in developing improved diagnostic or more targeted treatment approaches.

Transcriptome and membrane fatty acid analyses reveal different strategies for responding to permeating and non-permeating solutes in the bacterium Sphingomonas wittichii

Directory of Open Access Journals (Sweden)

Johnson David R

2011-11-01

opposite effect and decreased after perturbation with PEG8000. Conclusions A combination of growth assays, transcriptome profiling, and membrane fatty acid analyses revealed that permeating and non-permeating solutes trigger different adaptive responses in strain RW1, suggesting these solutes affect cells in fundamentally different ways. Future work is now needed that connects these responses with the responses observed in more realistic scenarios of soil desiccation.

Ancient ancestry of KFDV and AHFV revealed by complete genome analyses of viruses isolated from ticks and mammalian hosts.

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Kimberly A Dodd

2011-10-01

Full Text Available BACKGROUND: Alkhurma hemorrhagic fever virus (AHFV and Kyasanur forest disease virus (KFDV cause significant human disease and mortality in Saudi Arabia and India, respectively. Despite their distinct geographic ranges, AHFV and KFDV share a remarkably high sequence identity. Given its emergence decades after KFDV, AHFV has since been considered a variant of KFDV and thought to have arisen from an introduction of KFDV to Saudi Arabia from India. To gain a better understanding of the evolutionary history of AHFV and KFDV, we analyzed the full length genomes of 16 AHFV and 3 KFDV isolates. METHODOLOGY/PRINCIPAL FINDINGS: Viral genomes were sequenced and compared to two AHFV sequences available in GenBank. Sequence analyses revealed higher genetic diversity within AHFVs isolated from ticks than human AHFV isolates. A Bayesian coalescent phylogenetic analysis demonstrated an ancient divergence of AHFV and KFDV of approximately 700 years ago. CONCLUSIONS/SIGNIFICANCE: The high sequence diversity within tick populations and the presence of competent tick vectors in the surrounding regions, coupled with the recent identification of AHFV in Egypt, indicate possible viral range expansion or a larger geographic range than previously thought. The divergence of AHFV from KFDV nearly 700 years ago suggests other AHFV/KFDV-like viruses might exist in the regions between Saudi Arabia and India. Given the human morbidity and mortality associated with these viruses, these results emphasize the importance of more focused study of these significant public health threats.

Integrative analyses reveal novel strategies in HPV11,-16 and-45 early infection

DEFF Research Database (Denmark)

Kaczkowski, Bogumil; Rossing, Maria; Andersen, Ditte

2012-01-01

of genes not previously implicated in HPV biology, such as the PSG family and ANKRD1, and of genes implicated in the biology of other viruses, e. g. MX1, IFI44 and DDX60. Carcinogenesis-related genes, e. g. ABL2, MGLL and CYR61, were upregulated by high-risk HPV16 and -45. The integrative analysis revealed...... the suppression of DNA repair by HPV11 and -16, and downregulation of cytoskeleton genes by all HPV types. Various signalling pathways were affected by the HPVs: IL-2 by HPV11; JAK-STAT by HPV16; and TGF-beta, NOTCH and tyrosine kinase signalling by HPV45. This study uncovered novel strategies employed by HPV...... to establish infection and promote uncontrolled growth....

Detecting high spatial variability of ice shelf basal mass balance, Roi Baudouin Ice Shelf, Antarctica

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S. Berger

2017-11-01

Full Text Available Ice shelves control the dynamic mass loss of ice sheets through buttressing and their integrity depends on the spatial variability of their basal mass balance (BMB, i.e. the difference between refreezing and melting. Here, we present an improved technique – based on satellite observations – to capture the small-scale variability in the BMB of ice shelves. As a case study, we apply the methodology to the Roi Baudouin Ice Shelf, Dronning Maud Land, East Antarctica, and derive its yearly averaged BMB at 10 m horizontal gridding. We use mass conservation in a Lagrangian framework based on high-resolution surface velocities, atmospheric-model surface mass balance and hydrostatic ice-thickness fields (derived from TanDEM-X surface elevation. Spatial derivatives are implemented using the total-variation differentiation, which preserves abrupt changes in flow velocities and their spatial gradients. Such changes may reflect a dynamic response to localized basal melting and should be included in the mass budget. Our BMB field exhibits much spatial detail and ranges from −14.7 to 8.6 m a−1 ice equivalent. Highest melt rates are found close to the grounding line where the pressure melting point is high, and the ice shelf slope is steep. The BMB field agrees well with on-site measurements from phase-sensitive radar, although independent radar profiling indicates unresolved spatial variations in firn density. We show that an elliptical surface depression (10 m deep and with an extent of 0.7 km × 1.3 km lowers by 0.5 to 1.4 m a−1, which we tentatively attribute to a transient adaptation to hydrostatic equilibrium. We find evidence for elevated melting beneath ice shelf channels (with melting being concentrated on the channel's flanks. However, farther downstream from the grounding line, the majority of ice shelf channels advect passively (i.e. no melting nor refreezing toward the ice shelf front. Although the absolute, satellite

The effect of the benzodiazepine antagonist flumazenil on regional cerebral blood flow in human volunteers

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Wolf, J; Friberg, L; Jensen, J

1990-01-01

computerized tomography, SPECT, immediately before, and 5 and 35 min after intravenous injection of flumazenil 1.0 mg or placebo. In addition, mean arterial blood pressures or PaCO2, rCBF were analysed for changes in various regions of interest (RoI). No alterations were found either in the global CBF or in r......CBF in RoI after flumazenil injection. The results showed that a clinically active dose of flumazenil did not directly affect the cerebral circulation in the normal brain and indicated absence of significant intrinsic activity of the drug....

Differential spectral power alteration following acupuncture at different designated places revealed by magnetoencephalography

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You, Youbo; Bai, Lijun; Dai, Ruwei; Xue, Ting; Zhong, Chongguang; Liu, Zhenyu; Wang, Hu; Feng, Yuanyuan; Wei, Wenjuan; Tian, Jie

2012-03-01

As an ancient therapeutic technique in Traditional Chinese Medicine, acupuncture has been used increasingly in modern society to treat a range of clinical conditions as an alternative and complementary therapy. However, acupoint specificity, lying at the core of acupuncture, still faces many controversies. Considering previous neuroimaging studies on acupuncture have mainly employed functional magnetic resonance imaging, which only measures the secondary effect of neural activity on cerebral metabolism and hemodynamics, in the current study, we adopted an electrophysiological measurement technique named magnetoencephalography (MEG) to measure the direct neural activity. 28 healthy college students were recruited in this study. We filtered MEG data into 5 consecutive frequency bands (delta, theta, alpha, beta and gamma band) and grouped 140 sensors into 10 main brain regions (left/right frontal, central, temporal, parietal and occipital regions). Fast Fourier Transformation (FFT) based spectral analysis approach was further performed to explore the differential band-limited power change patterns of acupuncture at Stomach Meridian 36 (ST36) using a nearby nonacupoint (NAP) as control condition. Significantly increased delta power and decreased alpha as well as beta power in bilateral frontal ROIs were observed following stimulation at ST36. Compared with ST36, decreased alpha power in left and right central, right parietal as well as right temporal ROIs were detected in NAP group. Our research results may provide additional evidence for acupoint specificity.

Recovery of resting brain connectivity ensuing mild traumatic brain injury

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Rose Dawn Bharath

2015-09-01

Full Text Available Brains reveal amplified plasticity as they recover from an injury. We aimed to define time dependent plasticity changes in patients recovering from mild traumatic brain injury (mTBI. 25 subjects with mild head injury were longitudinally evaluated within 36 hours, 3 and 6 months using resting state functional connectivity (RSFC. Region of interest (ROI based connectivity differences over time within the patient group and in comparison with a healthy control group were analyzed at p<0.005. We found 33 distinct ROI pairs that revealed significant changes in their connectivity strength with time. Within three months, the majority of the ROI pairs had decreased connectivity in mTBI population, which increased and became comparable to healthy controls at 6 months. Initial imaging within 36 hours of injury revealed hyper connectivity predominantly involving the salience network and default mode network, which reduced at 3 months when lingual, inferior frontal and fronto-parietal networks revealed hyper connectivity. At six months all the evaluated networks revealed hyper connectivity and became comparable to the healthy controls. Our findings in a fairly homogenous group of patients with mTBI evaluated during the 6 month window of recovery defines time varying brain connectivity changes as the brain recovers from an injury. A majority of these changes were seen in the frontal and parietal lobes between 3-6 months after injury. Hyper connectivity of several networks supported normal recovery in the first six months and it remains to be seen in future studies whether this can predict an early and efficient recovery of brain function.

Correlation between computer-aided dynamic gadolinium-enhanced MRI assessment of inflammation and semi-quantitative synovitis and bone marrow oedema scores of the wrist in patients with rheumatoid arthritis--a cohort study

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Boesen, Mikael; Kubassova, Olga; Bouert, Rasmus

2012-01-01

Objective. To test the correlation between assessment of inflammation using dynamic contrast-enhanced MRI (DCE-MRI) analysed by a novel computer-aided approach and semi-quantitative scores of synovitis and bone marrow oedema (BME) using the OMERACT-RA MRI Scoring (RAMRIS) system, in the wrist...... extended region of interest (ROI) placed around the wrist joint (semi-automated approach) and (iii) within a small ROI placed in the area with most visual enhancement (semi-automated approach). Time spent on each procedure was noted. Spearman's rank correlation test was applied to assess the correlation...... between RAMRIS and the computer-generated dynamic parameters. Results. RAMRIS synovitis (range 2-9), BME (range 0-39) and the dynamic parameters reflecting the number of enhancing voxels were significantly correlated, especially when an extended ROI around the wrist was used (¿¿=¿0.74; P¿...

Analyses of Catharanthus roseus and Arabidopsis thaliana WRKY transcription factors reveal involvement in jasmonate signaling.

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Schluttenhofer, Craig; Pattanaik, Sitakanta; Patra, Barunava; Yuan, Ling

2014-06-20

To combat infection to biotic stress plants elicit the biosynthesis of numerous natural products, many of which are valuable pharmaceutical compounds. Jasmonate is a central regulator of defense response to pathogens and accumulation of specialized metabolites. Catharanthus roseus produces a large number of terpenoid indole alkaloids (TIAs) and is an excellent model for understanding the regulation of this class of valuable compounds. Recent work illustrates a possible role for the Catharanthus WRKY transcription factors (TFs) in regulating TIA biosynthesis. In Arabidopsis and other plants, the WRKY TF family is also shown to play important role in controlling tolerance to biotic and abiotic stresses, as well as secondary metabolism. Here, we describe the WRKY TF families in response to jasmonate in Arabidopsis and Catharanthus. Publically available Arabidopsis microarrays revealed at least 30% (22 of 72) of WRKY TFs respond to jasmonate treatments. Microarray analysis identified at least six jasmonate responsive Arabidopsis WRKY genes (AtWRKY7, AtWRKY20, AtWRKY26, AtWRKY45, AtWRKY48, and AtWRKY72) that have not been previously reported. The Catharanthus WRKY TF family is comprised of at least 48 members. Phylogenetic clustering reveals 11 group I, 32 group II, and 5 group III WRKY TFs. Furthermore, we found that at least 25% (12 of 48) were jasmonate responsive, and 75% (9 of 12) of the jasmonate responsive CrWRKYs are orthologs of AtWRKYs known to be regulated by jasmonate. Overall, the CrWRKY family, ascertained from transcriptome sequences, contains approximately 75% of the number of WRKYs found in other sequenced asterid species (pepper, tomato, potato, and bladderwort). Microarray and transcriptomic data indicate that expression of WRKY TFs in Arabidopsis and Catharanthus are under tight spatio-temporal and developmental control, and potentially have a significant role in jasmonate signaling. Profiling of CrWRKY expression in response to jasmonate treatment

Increased spatial granularity of left brain activation and unique age/gender signatures: a 4D frequency domain approach to cerebral lateralization at rest.

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Agcaoglu, O; Miller, R; Mayer, A R; Hugdahl, K; Calhoun, V D

2016-12-01

Cerebral lateralization is a well-studied topic. However, most of the research to date in functional magnetic resonance imaging (fMRI) has been carried out on hemodynamic fluctuations of voxels, networks, or regions of interest (ROIs). For example, cerebral differences can be revealed by comparing the temporal activation of an ROI in one hemisphere with the corresponding homotopic region in the other hemisphere. While this approach can reveal significant information about cerebral organization, it does not provide information about the full spatiotemporal organization of the hemispheres. The cerebral differences revealed in literature suggest that hemispheres have different spatiotemporal organization in the resting state. In this study, we evaluate cerebral lateralization in the 4D spatiotemporal frequency domain to compare the hemispheres in the context of general activation patterns at different spatial and temporal scales. We use a gender-balanced resting fMRI dataset comprising over 600 healthy subjects ranging in age from 12 to 71, that have previously been studied with a network specific voxel-wise and global analysis of lateralization (Agcaoglu, et al. NeuroImage, 2014). Our analysis elucidates significant differences in the spatiotemporal organization of brain activity between hemispheres, and generally more spatiotemporal fluctuation in the left hemisphere especially in the high spatial frequency bands, and more power in the right hemisphere in the low and middle spatial frequencies. Importantly, the identified effects are not visible in the context of a typical assessment of voxelwise, regional, or even global laterality, thus our study highlights the value of 4D spatiotemporal frequency domain analyses as a complementary and powerful tool for studying brain function.

Common and distinct structural features of schizophrenia and bipolar disorder: The European Network on Psychosis, Affective disorders and Cognitive Trajectory (ENPACT) study

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Crespo-Facorro, Benedicto; Nenadic, Igor; Benedetti, Francesco; Gaser, Christian; Sauer, Heinrich; Roiz-Santiañez, Roberto; Poletti, Sara; Marinelli, Veronica; Bellani, Marcella; Perlini, Cinzia; Ruggeri, Mirella; Altamura, A. Carlo; Diwadkar, Vaibhav A.; Brambilla, Paolo

2017-01-01

Introduction Although schizophrenia (SCZ) and bipolar disorder (BD) share elements of pathology, their neural underpinnings are still under investigation. Here, structural Magnetic Resonance Imaging (MRI) data collected from a large sample of BD and SCZ patients and healthy controls (HC) were analyzed in terms of gray matter volume (GMV) using both voxel based morphometry (VBM) and a region of interest (ROI) approach. Methods The analysis was conducted on two datasets, Dataset1 (802 subjects: 243 SCZ, 176 BD, 383 HC) and Dataset2, a homogeneous subset of Dataset1 (301 subjects: 107 HC, 85 BD and 109 SCZ). General Linear Model analyses were performed 1) at the voxel-level in the whole brain (VBM study), 2) at the regional level in the anatomical regions emerged from the VBM study (ROI study). The GMV comparison across groups was integrated with the analysis of GMV correlates of different clinical dimensions. Results The VBM results of Dataset1 showed 1) in BD compared to HC, GMV deficits in right cingulate, superior temporal and calcarine cortices, 2) in SCZ compared to HC, GMV deficits in widespread cortical and subcortical areas, 3) in SCZ compared to BD, GMV deficits in insula and thalamus (p<0.05, cluster family wise error corrected). The regions showing GMV deficits in the BD group were mostly included in the SCZ ones. The ROI analyses confirmed the VBM results at the regional level in most of the clusters from the SCZ vs. HC comparison (p<0.05, Bonferroni corrected). The VBM and ROI analyses of Dataset2 provided further evidence for the enhanced GMV deficits characterizing SCZ. Based on the clinical-neuroanatomical analyses, we cannot exclude possible confounding effects due to 1) age of onset and medication in BD patients, 2) symptoms severity in SCZ patients. Conclusion Our study reported both shared and specific neuroanatomical characteristics between the two disorders, suggesting more severe and generalized GMV deficits in SCZ, with a specific role for

Common and distinct structural features of schizophrenia and bipolar disorder: The European Network on Psychosis, Affective disorders and Cognitive Trajectory (ENPACT study.

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Eleonora Maggioni

Full Text Available Although schizophrenia (SCZ and bipolar disorder (BD share elements of pathology, their neural underpinnings are still under investigation. Here, structural Magnetic Resonance Imaging (MRI data collected from a large sample of BD and SCZ patients and healthy controls (HC were analyzed in terms of gray matter volume (GMV using both voxel based morphometry (VBM and a region of interest (ROI approach.The analysis was conducted on two datasets, Dataset1 (802 subjects: 243 SCZ, 176 BD, 383 HC and Dataset2, a homogeneous subset of Dataset1 (301 subjects: 107 HC, 85 BD and 109 SCZ. General Linear Model analyses were performed 1 at the voxel-level in the whole brain (VBM study, 2 at the regional level in the anatomical regions emerged from the VBM study (ROI study. The GMV comparison across groups was integrated with the analysis of GMV correlates of different clinical dimensions.The VBM results of Dataset1 showed 1 in BD compared to HC, GMV deficits in right cingulate, superior temporal and calcarine cortices, 2 in SCZ compared to HC, GMV deficits in widespread cortical and subcortical areas, 3 in SCZ compared to BD, GMV deficits in insula and thalamus (p<0.05, cluster family wise error corrected. The regions showing GMV deficits in the BD group were mostly included in the SCZ ones. The ROI analyses confirmed the VBM results at the regional level in most of the clusters from the SCZ vs. HC comparison (p<0.05, Bonferroni corrected. The VBM and ROI analyses of Dataset2 provided further evidence for the enhanced GMV deficits characterizing SCZ. Based on the clinical-neuroanatomical analyses, we cannot exclude possible confounding effects due to 1 age of onset and medication in BD patients, 2 symptoms severity in SCZ patients.Our study reported both shared and specific neuroanatomical characteristics between the two disorders, suggesting more severe and generalized GMV deficits in SCZ, with a specific role for insula and thalamus.

Transcriptome, expression, and activity analyses reveal a vital heat shock protein 70 in the stress response of stony coral Pocillopora damicornis.

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Zhang, Yidan; Zhou, Zhi; Wang, Lingui; Huang, Bo

2018-02-12

Coral bleaching occurs worldwide with increasing frequencies and intensities, which is caused by the stress response of stony coral to environmental change, especially increased sea surface temperature. In the present study, transcriptome, expression, and activity analyses were employed to illustrate the underlying molecular mechanisms of heat shock protein 70 (HSP70) in the stress response of coral to environmental changes. The domain analyses of assembled transcripts revealed 30 HSP70 gene contigs in stony coral Pocillopora damicornis. One crucial HSP70 (PdHSP70) was observed, whose expressions were induced by both elevated temperature and ammonium after expression difference analysis. The complete complementary DNA (cDNA) sequence of PdHSP70 was identified, which encoded a polypeptide of 650 amino acids with a molecular weight of 71.93 kDa. The deduced amino acid sequence of PdHSP70 contained a HSP70 domain (from Pro8 to Gly616), and it shared the highest similarity (95%) with HSP70 from Stylophora pistillata. The expression level of PdHSP70 gene increased significantly at 12 h, and returned to the initial level at 24 h after the stress of high temperature (32 °C). The cDNA fragment encoding the mature peptide of PdHSP70 was recombined and expressed in the prokaryotic expression system. The ATPase activity of recombinant PdHSP70 protein was determined, and it did not change significantly in a wide range of temperature from 25 to 40 °C. These results collectively suggested that PdHSP70 was a vital heat shock protein 70 in the stony coral P. damicornis, whose mRNA expression could be induced by diverse environmental stress and whose activity could remain stable under heat stress. PdHSP70 might be involved in the regulation of the bleaching owing to heat stress in the stony coral P. damicornis.

Possible Factors Promoting Car Evacuation in the 2011 Tohoku Tsunami Revealed by Analysing a Large-Scale Questionnaire Survey in Kesennuma City

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Fumiyasu Makinoshima

2017-11-01

Full Text Available Excessive car evacuation can cause severe traffic jams that can lead to large numbers of casualties during tsunami disasters. Investigating the possible factors that lead to unnecessary car evacuation can ensure smoother tsunami evacuations and mitigate casualty damages in future tsunami events. In this study, we quantitatively investigated the possible factors that promote car evacuation, including both necessary and unnecessary usages, by statistically analysing a large amount of data on actual tsunami evacuation behaviours surveyed in Kesennuma, where devastating damage occurred during the 2011 Tohoku Tsunami. A straightforward statistical analysis revealed a high percentage of car evacuations (approx. 50%; however, this fraction includes a high number of unnecessary usage events that were distinguished based on mode choice reasons. In addition, a binary logistic regression was conducted to quantitatively evaluate the effects of several factors and to identify the dominant factor that affected evacuation mode choice. The regression results suggested that the evacuation distance was the dominant factor for choosing car evacuation relative to other factors, such as age and sex. The cross-validation test of the regression model demonstrated that the considered factors were useful for decision making and the prediction of evacuation mode choice in the target area.

Comparative genome analyses reveal distinct structure in the saltwater crocodile MHC.

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Weerachai Jaratlerdsiri

Full Text Available The major histocompatibility complex (MHC is a dynamic genome region with an essential role in the adaptive immunity of vertebrates, especially antigen presentation. The MHC is generally divided into subregions (classes I, II and III containing genes of similar function across species, but with different gene number and organisation. Crocodylia (crocodilians are widely distributed and represent an evolutionary distinct group among higher vertebrates, but the genomic organisation of MHC within this lineage has been largely unexplored. Here, we studied the MHC region of the saltwater crocodile (Crocodylus porosus and compared it with that of other taxa. We characterised genomic clusters encompassing MHC class I and class II genes in the saltwater crocodile based on sequencing of bacterial artificial chromosomes. Six gene clusters spanning ∼452 kb were identified to contain nine MHC class I genes, six MHC class II genes, three TAP genes, and a TRIM gene. These MHC class I and class II genes were in separate scaffold regions and were greater in length (2-6 times longer than their counterparts in well-studied fowl B loci, suggesting that the compaction of avian MHC occurred after the crocodilian-avian split. Comparative analyses between the saltwater crocodile MHC and that from the alligator and gharial showed large syntenic areas (>80% identity with similar gene order. Comparisons with other vertebrates showed that the saltwater crocodile had MHC class I genes located along with TAP, consistent with birds studied. Linkage between MHC class I and TRIM39 observed in the saltwater crocodile resembled MHC in eutherians compared, but absent in avian MHC, suggesting that the saltwater crocodile MHC appears to have gene organisation intermediate between these two lineages. These observations suggest that the structure of the saltwater crocodile MHC, and other crocodilians, can help determine the MHC that was present in the ancestors of archosaurs.

An evolutionary computation approach to examine functional brain plasticity

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Arnab eRoy

2016-04-01

Full Text Available One common research goal in systems neurosciences is to understand how the functional relationship between a pair of regions of interest (ROIs evolves over time. Examining neural connectivity in this way is well-suited for the study of developmental processes, learning, and even in recovery or treatment designs in response to injury. For most fMRI based studies, the strength of the functional relationship between two ROIs is defined as the correlation between the average signal representing each region. The drawback to this approach is that much information is lost due to averaging heterogeneous voxels, and therefore, the functional relationship between a ROI-pair that evolve at a spatial scale much finer than the ROIs remain undetected. To address this shortcoming, we introduce a novel evolutionary computation (EC based voxel-level procedure to examine functional plasticity between an investigator defined ROI-pair by simultaneously using subject-specific BOLD-fMRI data collected from two sessions seperated by finite duration of time. This data-driven procedure detects a sub-region composed of spatially connected voxels from each ROI (a so-called sub-regional-pair such that the pair shows a significant gain/loss of functional relationship strength across the two time points. The procedure is recursive and iteratively finds all statistically significant sub-regional-pairs within the ROIs. Using this approach, we examine functional plasticity between the default mode network (DMN and the executive control network (ECN during recovery from traumatic brain injury (TBI; the study includes 14 TBI and 12 healthy control subjects. We demonstrate that the EC based procedure is able to detect functional plasticity where a traditional averaging based approach fails. The subject-specific plasticity estimates obtained using the EC-procedure are highly consistent across multiple runs. Group-level analyses using these plasticity estimates showed an increase in

Real-time single-molecule co-immunoprecipitation analyses reveal cancer-specific Ras signalling dynamics

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Lee, Hong-Won; Kyung, Taeyoon; Yoo, Janghyun; Kim, Tackhoon; Chung, Chaeuk; Ryu, Ji Young; Lee, Hanki; Park, Kihyun; Lee, Sangkyu; Jones, Walton D.; Lim, Dae-Sik; Hyeon, Changbong; Do Heo, Won; Yoon, Tae-Young

2013-01-01

Co-immunoprecipitation (co-IP) has become a standard technique, but its protein-band output provides only static, qualitative information about protein–protein interactions. Here we demonstrate a real-time single-molecule co-IP technique that generates real-time videos of individual protein–protein interactions as they occur in unpurified cell extracts. By analysing single Ras–Raf interactions with a 50-ms time resolution, we have observed transient intermediates of the protein–protein interaction and determined all the essential kinetic rates. Using this technique, we have quantified the active fraction of native Ras proteins in xenograft tumours, normal tissue and cancer cell lines. We demonstrate that the oncogenic Ras mutations selectively increase the active-Ras fraction by one order of magnitude, without affecting total Ras levels or single-molecule signalling kinetics. Our approach allows us to probe the previously hidden, dynamic aspects of weak protein–protein interactions. It also suggests a path forward towards precision molecular diagnostics at the protein–protein interaction level. PMID:23422673

Complex analyses of inverted repeats in mitochondrial genomes revealed their importance and variability.

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Cechová, Jana; Lýsek, Jirí; Bartas, Martin; Brázda, Václav

2018-04-01

The NCBI database contains mitochondrial DNA (mtDNA) genomes from numerous species. We investigated the presence and locations of inverted repeat sequences (IRs) in these mtDNA sequences, which are known to be important for regulating nuclear genomes. IRs were identified in mtDNA in all species. IR lengths and frequencies correlate with evolutionary age and the greatest variability was detected in subgroups of plants and fungi and the lowest variability in mammals. IR presence is non-random and evolutionary favoured. The frequency of IRs generally decreased with IR length, but not for IRs 24 or 30 bp long, which are 1.5 times more abundant. IRs are enriched in sequences from the replication origin, followed by D-loop, stem-loop and miscellaneous sequences, pointing to the importance of IRs in regulatory regions of mitochondrial DNA. Data were produced using Palindrome analyser, freely available on the web at http://bioinformatics.ibp.cz. vaclav@ibp.cz. Supplementary data are available at Bioinformatics online.

Physiological and Proteomics Analyses Reveal Low-Phosphorus Stress Affected the Regulation of Photosynthesis in Soybean.

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Chu, Shanshan; Li, Hongyan; Zhang, Xiangqian; Yu, Kaiye; Chao, Maoni; Han, Suoyi; Zhang, Dan

2018-06-06

Previous studies have revealed a significant genetic relationship between phosphorus (P)-efficiency and photosynthesis-related traits in soybean. In this study, we used proteome profiling in combination with expression analysis, biochemical investigations, and leaf ultrastructural analysis to identify the underlying physiological and molecular responses. The expression analysis and ultrastructural analysis showed that the photosynthesis key genes were decreased at transcript levels and the leaf mesophyll and chloroplast were severely damaged after low-P stress. Approximately 55 protein spots showed changes under low-P condition by mass spectrometry, of which 17 were involved in various photosynthetic processes. Further analysis revealed the depression of photosynthesis caused by low-P stress mainly involves the regulation of leaf structure, adenosine triphosphate (ATP) synthesis, absorption and transportation of CO₂, photosynthetic electron transport, production of assimilatory power, and levels of enzymes related to the Calvin cycle. In summary, our findings indicated that the existence of a stringent relationship between P supply and the genomic control of photosynthesis in soybean. As an important strategy to protect soybean photosynthesis, P could maintain the stability of cell structure, up-regulate the enzymes’ activities, recover the process of photosystem II (PSII), and induce the expression of low-P responsive genes and proteins.

Similarities and differences between stakeholders' opinions on using Health Technology Assessment (HTA) information across five European countries: results from the EQUIPT survey.

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Vokó, Zoltan; Cheung, Kei Long; Józwiak-Hagymásy, Judit; Wolfenstetter, Silke; Jones, Teresa; Muñoz, Celia; Evers, Silvia M A A; Hiligsmann, Mickaël; de Vries, Hein; Pokhrel, Subhash

2016-05-26

The European-study on Quantifying Utility of Investment in Protection from Tobacco (EQUIPT) project aimed to study transferability of economic evidence by co-creating the Tobacco Return On Investment (ROI) tool, previously developed in the United Kingdom, for four sample countries (Germany, Hungary, Spain and the Netherlands). The EQUIPT tool provides policymakers and stakeholders with customized information about the economic and wider returns on the investment in evidence-based tobacco control, including smoking cessation interventions. A Stakeholder Interview Survey was developed to engage with the stakeholders in early phases of the development and country adaptation of the ROI tool. The survey assessed stakeholders' information needs, awareness about underlying principles used in economic analyses, opinion about the importance, effectiveness and cost-effectiveness of tobacco control interventions, and willingness to use a Health Technology Assessment (HTA) tool such as the ROI tool. A cross sectional study using a mixed method approach was conducted among participating stakeholders in the sample countries and the United Kingdom. The individual questionnaire contained open-ended questions as well as single choice and 7- or 3-point Likert-scale questions. The results corresponding to the priority and needs assessment and to the awareness of stakeholders about underlying principles used in economic analysis are analysed by country and stakeholder categories. Stakeholders considered it important that the decisions on the investments in tobacco control interventions should be supported by scientific evidence, including prevalence of smoking, cost of smoking, quality of life, mortality due to smoking, and effectiveness, cost-effectiveness and budget impact of smoking cessation interventions. The proposed ROI tool was required to provide this granularity of information. The majority of the stakeholders were aware of the general principles of economic analyses used in

Dynamic gadolinium-enhanced magnetic resonance imaging allows accurate assessment of the synovial inflammatory activity in rheumatoid arthritis knee joints: a comparison with synovial histology

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Axelsen, Mette Bjørndal; Stoltenberg, M.; Poggenborg, R.

2012-01-01

, the average grade of histological synovial inflammation was determined from four biopsies obtained during surgery. A preoperative series of T(1)-weighted dynamic fast low-angle shot (FLASH) MR images was obtained. Parameters characterizing contrast uptake dynamics, including the initial rate of enhancement...... capsule of the knee joint (Precise ROI). Intra- and interreader agreement was assessed using the intra-class correlation coefficient (ICC). Results: The IRE from the Quick ROI and the Precise ROI revealed high correlations to the grade of histological inflammation (Spearman's correlation coefficient (rho......) = 0.70, p = 0.001 and rho = 0.74, p = 0.001, respectively). Intraand inter-reader ICCs were very high (0.93-1.00). No Whole slice parameters were correlated to histology. Conclusion: DCE-MRI provides fast and accurate assessment of synovial inflammation in RA patients. Manual outlining of the joint...

Asymmetry of the structural brain connectome in healthy older adults.

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Leonardo eBonilha

2014-01-01

Full Text Available Background: It is now possible to map neural connections in vivo across the whole brain (i.e., the brain connectome. This is a promising development in neuroscience since many health and disease processes are believed to arise from the architecture of neural networks.Objective: To describe the normal range of hemispheric asymmetry in structural connectivity in healthy older adults.Methods: We obtained high-resolution structural magnetic resonance images (MRI from 17 healthy older adults. For each subject, the brain connectome was reconstructed by parcelating the probabilistic map of gray matter into anatomically defined regions of interested (ROIs. White matter fiber tractography was reconstructed from diffusion tensor imaging and streamlines connecting gray matter ROIs were computed. Asymmetry indices were calculated regarding ROI connectivity (representing the sum of connectivity weight of each cortical ROI and for regional white matter links. All asymmetry measures were compared to a normal distribution with mean=0 through one sample t-tests.Results: Leftward cortical ROI asymmetry was observed in medial temporal, dorsolateral frontal and occipital regions. Rightward cortical ROI asymmetry was observed in middle temporal and orbito-frontal regions. Link-wise asymmetry revealed stronger connections in the left hemisphere between the medial temporal, anterior and posterior peri-Sylvian and occipito-temporal regions. Rightward link asymmetry was observed in lateral temporal, parietal and dorsolateral frontal connections.Conclusions: We postulate that asymmetry of specific connections may be related to functional hemispheric organization. This study may provide reference for future studies evaluating the architecture of the connectome in health and disease processes in senior individuals.

Grey matter volumes in treatment naïve vs. chronically treated children with attention deficit/hyperactivity disorder: a combined approach.

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Villemonteix, Thomas; De Brito, Stéphane A; Kavec, Martin; Balériaux, Danielle; Metens, Thierry; Slama, Hichem; Baijot, Simon; Mary, Alison; Peigneux, Philippe; Massat, Isabelle

2015-08-01

Psychostimulants are the first-line treatment in attention deficit/hyperactivity disorder (ADHD), but their effects on brain development remain poorly understood. In particular, previous structural magnetic resonance imaging (sMRI) studies only investigated treatment effects on grey matter (GM) volumes in selected regions of interest (ROIs). In this study, voxel-based morphometry (VBM) was used to assess medication-related GM volume differences across the entire brain. Automated tracing measurements of selected ROIs were also obtained. Three groups (77 participants aged 7-to-13 year old) underwent MRI scans and were compared: never-medicated children with ADHD (n=33), medicated (methylphenidate) children with ADHD (n=20) and typically developing children (TD; n=24). Optimised VBM was used to investigate regional GM volumes, controlling for age and gender. Automated tracing procedures were also used to assess the average volume of the caudate nucleus, the amygdala and the nucleus accumbens. When compared to both medicated children with ADHD and TD children, never-medicated children with ADHD exhibited decreased GM volume in the insula and in the middle temporal gyrus. When compared to TD children, medicated children with ADHD had decreased GM volume in the middle frontal gyrus and in the precentral gyrus. Finally, ROI analyses revealed a significant association between duration of treatment and GM volume of the left nucleus accumbens in medicated children with ADHD. In conclusion, this study documents potential methylphenidate-related GM volume normalization and deviation in previously unexplored brain structures, and reports a positive association between treatment history and GM volume in the nucleus accumbens, a key region for reward-processing. Copyright © 2015 Elsevier B.V. and ECNP. All rights reserved.

White matter correlates of impaired attention control in major depressive disorder and healthy volunteers.

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Rizk, Mina M; Rubin-Falcone, Harry; Keilp, John; Miller, Jeffrey M; Sublette, M Elizabeth; Burke, Ainsley; Oquendo, Maria A; Kamal, Ahmed M; Abdelhameed, Mohamed A; Mann, J John

2017-11-01

Major depressive disorder (MDD) is associated with impaired attention control and alterations in frontal-subcortical connectivity. We hypothesized that attention control as assessed by Stroop task interference depends on white matter integrity in fronto-cingulate regions and assessed this relationship using diffusion tensor imaging (DTI) in MDD and healthy volunteers (HV). DTI images and Stroop task were acquired in 29 unmedicated MDD patients and 16 HVs, aged 18-65 years. The relationship between Stroop interference and fractional anisotropy (FA) was examined using region-of-interest (ROI) and tract-based spatial statistics (TBSS) analyses. ROI analysis revealed that Stroop interference correlated positively with FA in left caudal anterior cingulate cortex (cACC) in HVs (r = 0.62, p = 0.01), but not in MDD (r = -0.05, p= 0.79) even after controlling for depression severity. The left cACC was among 4 ROIs in fronto-cingulate network where FA was lower in MDD relative to HVs (F (1,41) = 8.87, p = 0.005). Additionally, TBSS showed the same group interaction of differences and correlations, although only at a statistical trend level. The modest sample size limits the generalizability of the findings. Structural connectivity of white matter network of cACC correlated with magnitude of Stroop interference in HVs, but not MDD. The cACC-frontal network, sub-serving attention control, may be disrupted in MDD. Less cognitive control may include enhanced effects of salience in HVs, or less effective response inhibition in MDD. Further studies of salience and inhibition components of executive function may better elucidate the relationship between brain white matter changes and executive dysfunction in MDD. Copyright © 2017 Elsevier B.V. All rights reserved.

Language processing of auditory cortex revealed by functional magnetic resonance imaging in presbycusis patients.

Science.gov (United States)

Chen, Xianming; Wang, Maoxin; Deng, Yihong; Liang, Yonghui; Li, Jianzhong; Chen, Shiyan

2016-01-01

Contralateral temporal lobe activation decreases with aging, regardless of hearing status, with elderly individuals showing reduced right ear advantage. Aging and hearing loss possibly lead to presbycusis speech discrimination decline. To evaluate presbycusis patients' auditory cortex activation under verbal stimulation. Thirty-six patients were enrolled: 10 presbycusis patients (mean age = 64 years, range = 60-70), 10 in the healthy aged group (mean age = 66 years, range = 60-70), and 16 young healthy volunteers (mean age = 25 years, range = 23-28). These three groups underwent simultaneous 1 kHz and 90 dB single-syllable word stimuli and (blood-oxygen-level-dependent functional magnetic resonance imaging) BOLD fMRI examinations. The main activation regions were superior temporal and middle temporal gyrus. For all aged subjects, the right region of interest (ROI) activation volume was decreased compared with the young group. With left ear stimulation, bilateral ROI activation intensity held. With right ear stimulation, the aged group's activation intensity was higher. Using monaural stimulation in the young group, contralateral temporal lobe activation volume and intensity were higher vs ipsilateral, while they were lower in the aged and presbycusis groups. On left and right ear auditory tasks, the young group showed right ear advantage, while the aged and presbycusis groups showed reduced right ear advantage.

Reticulate evolution: frequent introgressive hybridization among chinese hares (genus lepus revealed by analyses of multiple mitochondrial and nuclear DNA loci

Directory of Open Access Journals (Sweden)

Wu Shi-Fang

2011-07-01

Full Text Available Abstract Background Interspecific hybridization may lead to the introgression of genes and genomes across species barriers and contribute to a reticulate evolutionary pattern and thus taxonomic uncertainties. Since several previous studies have demonstrated that introgressive hybridization has occurred among some species within Lepus, therefore it is possible that introgressive hybridization events also occur among Chinese Lepus species and contribute to the current taxonomic confusion. Results Data from four mtDNA genes, from 116 individuals, and one nuclear gene, from 119 individuals, provides the first evidence of frequent introgression events via historical and recent interspecific hybridizations among six Chinese Lepus species. Remarkably, the mtDNA of L. mandshuricus was completely replaced by mtDNA from L. timidus and L. sinensis. Analysis of the nuclear DNA sequence revealed a high proportion of heterozygous genotypes containing alleles from two divergent clades and that several haplotypes were shared among species, suggesting repeated and recent introgression. Furthermore, results from the present analyses suggest that Chinese hares belong to eight species. Conclusion This study provides a framework for understanding the patterns of speciation and the taxonomy of this clade. The existence of morphological intermediates and atypical mitochondrial gene genealogies resulting from frequent hybridization events likely contribute to the current taxonomic confusion of Chinese hares. The present study also demonstrated that nuclear gene sequence could offer a powerful complementary data set with mtDNA in tracing a complete evolutionary history of recently diverged species.

Infra-Red Gas Analysers of Liquid Crystal Type for Environmental Monitoring

Directory of Open Access Journals (Sweden)

V. I. Nazarov

2004-01-01

Full Text Available The paper reveals an opportunity to use infra-red gas analysers on the basis of the developed dichroic liquid crystal cells for investigation of absorption bands of various gases in the near infrared spectral region.

Complete mitochondrial genome sequences of three bats species and whole genome mitochondrial analyses reveal patterns of codon bias and lend support to a basal split in Chiroptera.

Science.gov (United States)

Meganathan, P R; Pagan, Heidi J T; McCulloch, Eve S; Stevens, Richard D; Ray, David A

2012-01-15

Order Chiroptera is a unique group of mammals whose members have attained self-powered flight as their main mode of locomotion. Much speculation persists regarding bat evolution; however, lack of sufficient molecular data hampers evolutionary and conservation studies. Of ~1200 species, complete mitochondrial genome sequences are available for only eleven. Additional sequences should be generated if we are to resolve many questions concerning these fascinating mammals. Herein, we describe the complete mitochondrial genomes of three bats: Corynorhinus rafinesquii, Lasiurus borealis and Artibeus lituratus. We also compare the currently available mitochondrial genomes and analyze codon usage in Chiroptera. C. rafinesquii, L. borealis and A. lituratus mitochondrial genomes are 16438 bp, 17048 bp and 16709 bp, respectively. Genome organization and gene arrangements are similar to other bats. Phylogenetic analyses using complete mitochondrial genome sequences support previously established phylogenetic relationships and suggest utility in future studies focusing on the evolutionary aspects of these species. Comprehensive analyses of available bat mitochondrial genomes reveal distinct nucleotide patterns and synonymous codon preferences corresponding to different chiropteran families. These patterns suggest that mutational and selection forces are acting to different extents within Chiroptera and shape their mitochondrial genomes. Copyright © 2011 Elsevier B.V. All rights reserved.

Lexical factors and cerebral regions influencing verbal fluency performance in MCI.

Science.gov (United States)

Clark, D G; Wadley, V G; Kapur, P; DeRamus, T P; Singletary, B; Nicholas, A P; Blanton, P D; Lokken, K; Deshpande, H; Marson, D; Deutsch, G

2014-02-01

To evaluate assumptions regarding semantic (noun), verb, and letter fluency in mild cognitive impairment (MCI) and Alzheimer disease (AD) using novel techniques for measuring word similarity in fluency lists and a region of interest (ROI) analysis of gray matter correlates. Fifty-eight individuals with normal cognition (NC, n=25), MCI (n=23), or AD (n=10) underwent neuropsychological tests, including 10 verbal fluency tasks (three letter tasks [F, A, S], six noun categories [animals, water creatures, fruits and vegetables, tools, vehicles, boats], and verbs). All pairs of words generated by each participant on each task were compared in terms of semantic (meaning), orthographic (spelling), and phonemic (pronunciation) similarity. We used mixed-effects logistic regression to determine which lexical factors were predictive of word adjacency within the lists. Associations between each fluency raw score and gray matter volumes in sixteen ROIs were identified by means of multiple linear regression. We evaluated causal models for both types of analyses to specify the contributions of diagnosis and various mediator variables to the outcomes of word adjacency and fluency raw score. Semantic similarity between words emerged as the strongest predictor of word adjacency for all fluency tasks, including the letter fluency tasks. Semantic similarity mediated the effect of cognitive impairment on word adjacency only for three fluency tasks employing a biological cue. Orthographic similarity was predictive of word adjacency for the A and S tasks, while phonemic similarity was predictive only for the S task and one semantic task (vehicles). The ROI analysis revealed different patterns of correlations among the various fluency tasks, with the most common associations in the right lower temporal and bilateral dorsal frontal regions. Following correction with gray matter volumes from the opposite hemisphere, significant associations persisted for animals, vehicles, and a composite

Energy Technology Investments: Maximizing Efficiency Through a Maritime Energy Portfolio Interface and Decision Aid

Science.gov (United States)

2012-02-09

Investment (ROI) and Break Even Point ( BEP ). These metrics are essential for determining whether an initiative would be worth pursuing. Balanced...is Unlimited Energy Decision Framework Identify Inefficiencies 2. Perform Analyses 3. Examine Technology Candidates 1. Improve Energy...Unlimited Energy Decision Framework Identify Inefficiencies 2. Perform Analyses 3. Examine Technology Candidates 1. Improve Energy Efficiency 4

Micro-CT and FE-SEM enamel analyses of calcium-based agent application after bleaching.

Science.gov (United States)

Gomes, Mauricio Neves; Rodrigues, Flávia Pires; Silikas, Nick; Francci, Carlos Eduardo

2018-03-01

The objective of the present study is to evaluate the effects of casein phosphopeptide-amorphous calcium phosphate (CPP-ACP) on bleached enamel. A bleaching agent (35% hydrogen peroxide) was applied, 4 × 8 min on premolar teeth (n = 8). A CPP-ACP paste was applied for 7 days. Prior and post-treatment, microtomography images were obtained and 3D regions of interest (ROIs) were selected, from outer enamel, extending to 110.2-μm depth. CT parameters of structure: thickness (St.Th), separation (St.Sp), and fragmentation index (Fr.I.) were calculated for each (ROI). Data was submitted to paired t tests at a 95% confidence level. The samples were evaluated at 3000 to 100,000 magnification. Quantitative analysis of enamel mineral content was also determined by SEM EDX. There was a significant increase in structure thickness and calcium content. The phosphorus content increased after bleaching. There was also a decreased separation and fragmentation index on the outer enamel to a depth of 56.2 μm (p spaces between the hydroxyapatite crystals appeared around the enamel prisms, 7 days after the CPP-ACP application. The application of a CPP-ACP provides a compact structure on the enamel's outer surface, for 7 days, due to calcium deposition. CT parameters seem to be a useful tool for mineralizing and remineralizing future studies. CPP-ACP neutralizes any adverse effects on enamel surface when applied during a week after bleaching and minimizes any side effects of the bleaching treatment due to a more compact structure.

Comparative metagenomic and metatranscriptomic analyses of microbial communities in acid mine drainage.

Science.gov (United States)

Chen, Lin-xing; Hu, Min; Huang, Li-nan; Hua, Zheng-shuang; Kuang, Jia-liang; Li, Sheng-jin; Shu, Wen-sheng

2015-07-01

The microbial communities in acid mine drainage have been extensively studied to reveal their roles in acid generation and adaption to this environment. Lacking, however, are integrated community- and organism-wide comparative gene transcriptional analyses that could reveal the response and adaptation mechanisms of these extraordinary microorganisms to different environmental conditions. In this study, comparative metagenomics and metatranscriptomics were performed on microbial assemblages collected from four geochemically distinct acid mine drainage (AMD) sites. Taxonomic analysis uncovered unexpectedly high microbial biodiversity of these extremely acidophilic communities, and the abundant taxa of Acidithiobacillus, Leptospirillum and Acidiphilium exhibited high transcriptional activities. Community-wide comparative analyses clearly showed that the AMD microorganisms adapted to the different environmental conditions via regulating the expression of genes involved in multiple in situ functional activities, including low-pH adaptation, carbon, nitrogen and phosphate assimilation, energy generation, environmental stress resistance, and other functions. Organism-wide comparative analyses of the active taxa revealed environment-dependent gene transcriptional profiles, especially the distinct strategies used by Acidithiobacillus ferrivorans and Leptospirillum ferrodiazotrophum in nutrients assimilation and energy generation for survival under different conditions. Overall, these findings demonstrate that the gene transcriptional profiles of AMD microorganisms are closely related to the site physiochemical characteristics, providing clues into the microbial response and adaptation mechanisms in the oligotrophic, extremely acidic environments.

High overlap of CNVs and selection signatures revealed by varLD analyses of taurine and zebu cattle

Science.gov (United States)

Selection Signatures (SS) assessed through analysis of genomic data are being widely studied to discover population specific regions selected via artificial or natural selection. Different methodologies have been proposed for these analyses, each having specific limitations as to the age of the sele...

Family-based Association Analyses of Imputed Genotypes Reveal Genome-Wide Significant Association of Alzheimer’s disease with OSBPL6, PTPRG and PDCL3

Science.gov (United States)

Herold, Christine; Hooli, Basavaraj V.; Mullin, Kristina; Liu, Tian; Roehr, Johannes T; Mattheisen, Manuel; Parrado, Antonio R.; Bertram, Lars; Lange, Christoph; Tanzi, Rudolph E.

2015-01-01

The genetic basis of Alzheimer's disease (AD) is complex and heterogeneous. Over 200 highly penetrant pathogenic variants in the genes APP, PSEN1 and PSEN2 cause a subset of early-onset familial Alzheimer's disease (EOFAD). On the other hand, susceptibility to late-onset forms of AD (LOAD) is indisputably associated to the ε4 allele in the gene APOE, and more recently to variants in more than two-dozen additional genes identified in the large-scale genome-wide association studies (GWAS) and meta-analyses reports. Taken together however, although the heritability in AD is estimated to be as high as 80%, a large proportion of the underlying genetic factors still remain to be elucidated. In this study we performed a systematic family-based genome-wide association and meta-analysis on close to 15 million imputed variants from three large collections of AD families (~3,500 subjects from 1,070 families). Using a multivariate phenotype combining affection status and onset age, meta-analysis of the association results revealed three single nucleotide polymorphisms (SNPs) that achieved genome-wide significance for association with AD risk: rs7609954 in the gene PTPRG (P-value = 3.98·10−08), rs1347297 in the gene OSBPL6 (P-value = 4.53·10−08), and rs1513625 near PDCL3 (P-value = 4.28·10−08). In addition, rs72953347 in OSBPL6 (P-value = 6.36·10−07) and two SNPs in the gene CDKAL1 showed marginally significant association with LOAD (rs10456232, P-value: 4.76·10−07; rs62400067, P-value: 3.54·10−07). In summary, family-based GWAS meta-analysis of imputed SNPs revealed novel genomic variants in (or near) PTPRG, OSBPL6, and PDCL3 that influence risk for AD with genome-wide significance. PMID:26830138

Improving the safety of a body composition analyser based on the PGNAA method

Energy Technology Data Exchange (ETDEWEB)

Miri-Hakimabad, Hashem; Izadi-Najafabadi, Reza; Vejdani-Noghreiyan, Alireza; Panjeh, Hamed [FUM Radiation Detection And Measurement Laboratory, Ferdowsi University of Mashhad (Iran, Islamic Republic of)

2007-12-15

The {sup 252}Cf radioisotope and {sup 241}Am-Be are intense neutron emitters that are readily encapsulated in compact, portable and sealed sources. Some features such as high flux of neutron emission and reliable neutron spectrum of these sources make them suitable for the prompt gamma neutron activation analysis (PGNAA) method. The PGNAA method can be used in medicine for neutron radiography and body chemical composition analysis. {sup 252}Cf and {sup 241}Am-Be sources generate not only neutrons but also are intense gamma emitters. Furthermore, the sample in medical treatments is a human body, so it may be exposed to the bombardments of these gamma-rays. Moreover, accumulations of these high-rate gamma-rays in the detector volume cause simultaneous pulses that can be piled up and distort the spectra in the region of interest (ROI). In order to remove these disadvantages in a practical way without being concerned about losing the thermal neutron flux, a gamma-ray filter made of Pb must be employed. The paper suggests a relatively safe body chemical composition analyser (BCCA) machine that uses a spherical Pb shield, enclosing the neutron source. Gamma-ray shielding effects and the optimum radius of the spherical Pb shield have been investigated, using the MCNP-4C code, and compared with the unfiltered case, the bare source. Finally, experimental results demonstrate that an optimised gamma-ray shield for the neutron source in a BCCA can reduce effectively the risk of exposure to the {sup 252}Cf and {sup 241}Am-Be sources.

Combined metabolomic and correlation networks analyses reveal fumarase insufficiency altered amino acid metabolism.

Science.gov (United States)

Hou, Entai; Li, Xian; Liu, Zerong; Zhang, Fuchang; Tian, Zhongmin

2018-04-01

Fumarase catalyzes the interconversion of fumarate and l-malate in the tricarboxylic acid cycle. Fumarase insufficiencies were associated with increased levels of fumarate, decreased levels of malate and exacerbated salt-induced hypertension. To gain insights into the metabolism profiles induced by fumarase insufficiency and identify key regulatory metabolites, we applied a GC-MS based metabolomics platform coupled with a network approach to analyze fumarase insufficient human umbilical vein endothelial cells (HUVEC) and negative controls. A total of 24 altered metabolites involved in seven metabolic pathways were identified as significantly altered, and enriched for the biological module of amino acids metabolism. In addition, Pearson correlation network analysis revealed that fumaric acid, l-malic acid, l-aspartic acid, glycine and l-glutamic acid were hub metabolites according to Pagerank based on their three centrality indices. Alanine aminotransferase and glutamate dehydrogenase activities increased significantly in fumarase deficiency HUVEC. These results confirmed that fumarase insufficiency altered amino acid metabolism. The combination of metabolomics and network methods would provide another perspective on expounding the molecular mechanism at metabolomics level. Copyright © 2017 John Wiley & Sons, Ltd.

Subcomponents and Connectivity of the Inferior Fronto-Occipital Fasciculus Revealed by Diffusion Spectrum Imaging Fiber Tracking

OpenAIRE

Wu, Yupeng; Sun, Dandan; Wang, Yong; Wang, Yibao

2016-01-01

The definitive structure and functional role of the inferior fronto-occipital fasciculus (IFOF) are still controversial. In this study, we aimed to investigate the connectivity, asymmetry, and segmentation patterns of this bundle. High angular diffusion spectrum imaging (DSI) analysis was performed on 10 healthy adults and a 90-subject DSI template (NTU-90 Atlas). In addition, a new tractography approach based on the anatomic subregions and two regions of interest (ROI) was evaluated for the ...

dātu ša šarri. La « loi du roi »dans la Babylonie achéménide et séleucide dātu ša šarri, The “Law of the King” in Achaemenid and Seleucid Babylonia

Directory of Open Access Journals (Sweden)

Sophie Démare-Lafont

2009-06-01

Full Text Available Cet article examine le champ sémantique de l’expression dātu ša šarri, « loi du roi », formée sur un terme d’origine vieux-perse (data. La dizaine d’occurrences d’époques achéménide et séleucide montre que la « loi du roi »désigne un mode d’élaboration de la norme issu de la pratique judiciaire du souverain, progressivement compilée pour former un corps de règles invoquées dans les contrats. Ce procédé de création de la loi et de fabrication des recueils législatifs rappelle celui du rescrit romain.This article investigates the meaning of the formula dātu ša šarri, “law of the king”, using the akkadian dātu based on the old Persian word dāta. The ten Achaemenid and Seleucid occurrences of this formula suggest a process of creation of legal rules comparable to the Roman rescript: the legal standard dātu ša šarri derives from the judicial practice of the king, whose decisions were progressively compiled in order to create a body of regulations which were invoked in contracts.

Expression and phylogenetic analyses reveal paralogous lineages of putatively classical and non-classical MHC-I genes in three sparrow species (Passer).

Science.gov (United States)

Drews, Anna; Strandh, Maria; Råberg, Lars; Westerdahl, Helena

2017-06-26

The Major Histocompatibility Complex (MHC) plays a central role in immunity and has been given considerable attention by evolutionary ecologists due to its associations with fitness-related traits. Songbirds have unusually high numbers of MHC class I (MHC-I) genes, but it is not known whether all are expressed and equally important for immune function. Classical MHC-I genes are highly expressed, polymorphic and present peptides to T-cells whereas non-classical MHC-I genes have lower expression, are more monomorphic and do not present peptides to T-cells. To get a better understanding of the highly duplicated MHC genes in songbirds, we studied gene expression in a phylogenetic framework in three species of sparrows (house sparrow, tree sparrow and Spanish sparrow), using high-throughput sequencing. We hypothesize that sparrows could have classical and non-classical genes, as previously indicated though never tested using gene expression. The phylogenetic analyses reveal two distinct types of MHC-I alleles among the three sparrow species, one with high and one with low level of polymorphism, thus resembling classical and non-classical genes, respectively. All individuals had both types of alleles, but there was copy number variation both within and among the sparrow species. However, the number of highly polymorphic alleles that were expressed did not vary between species, suggesting that the structural genomic variation is counterbalanced by conserved gene expression. Overall, 50% of the MHC-I alleles were expressed in sparrows. Expression of the highly polymorphic alleles was very variable, whereas the alleles with low polymorphism had uniformly low expression. Interestingly, within an individual only one or two alleles from the polymorphic genes were highly expressed, indicating that only a single copy of these is highly expressed. Taken together, the phylogenetic reconstruction and the analyses of expression suggest that sparrows have both classical and non

Lactococcus lactis Diversity in Undefined Mixed Dairy Starter Cultures as Revealed by Comparative Genome Analyses and Targeted Amplicon Sequencing of epsD.

Science.gov (United States)

Frantzen, Cyril A; Kleppen, Hans Petter; Holo, Helge

2018-02-01

Undefined mesophilic mixed (DL) starter cultures are used in the production of continental cheeses and contain unknown strain mixtures of Lactococcus lactis and leuconostocs. The choice of starter culture affects the taste, aroma, and quality of the final product. To gain insight into the diversity of Lactococcus lactis strains in starter cultures, we whole-genome sequenced 95 isolates from three different starter cultures. Pan-genomic analyses, which included 30 publically available complete genomes, grouped the strains into 21 L. lactis subsp . lactis and 28 L. lactis subsp. cremoris lineages. Only one of the 95 isolates grouped with previously sequenced strains, and the three starter cultures showed no overlap in lineage distributions. The culture diversity was assessed by targeted amplicon sequencing using purR , a core gene, and epsD , present in 93 of the 95 starter culture isolates but absent in most of the reference strains. This enabled an unprecedented discrimination of starter culture Lactococcus lactis and revealed substantial differences between the three starter cultures and compositional shifts during the cultivation of cultures in milk. IMPORTANCE In contemporary cheese production, standardized frozen seed stock starter cultures are used to ensure production stability, reproducibility, and quality control of the product. The dairy industry experiences significant disruptions of cheese production due to phage attacks, and one commonly used countermeasure to phage attack is to employ a starter rotation strategy, in which two or more starters with minimal overlap in phage sensitivity are used alternately. A culture-independent analysis of the lactococcal diversity in complex undefined starter cultures revealed large differences between the three starter cultures and temporal shifts in lactococcal composition during the production of bulk starters. A better understanding of the lactococcal diversity in starter cultures will enable the development of

Post-facta Analyses of Fukushima Accident and Lessons Learned

Energy Technology Data Exchange (ETDEWEB)

Tanabe, Fumiya [Sociotechnical Systems Safety Research Institute, Ichige (Japan)

2014-08-15

Independent analyses have been performed of the core melt behavior of the Unit 1, Unit 2 and Unit 3 reactors of Fukushima Daiichi Nuclear Power Station on 11-15 March 2011. The analyses are based on a phenomenological methodology with measured data investigation and a simple physical model calculation. Estimated are time variation of core water level, core material temperature and hydrogen generation rate. The analyses have revealed characteristics of accident process of each reactor. In the case of Unit 2 reactor, the calculated result suggests little hydrogen generation because of no steam generation in the core for zirconium-steam reaction during fuel damage process. It could be the reason of no hydrogen explosion in the Unit 2 reactor building. Analyses have been performed also on the core material behavior in another chaotic period of 19-31 March 2011, and it resulted in a re-melt hypothesis that core material in each reactor should have melted again due to shortage of cooling water. The hypothesis is consistent with many observed features of radioactive materials dispersion into the environment.

Return on investment of public health interventions: a systematic review.

Science.gov (United States)

Masters, Rebecca; Anwar, Elspeth; Collins, Brendan; Cookson, Richard; Capewell, Simon

2017-08-01

Public sector austerity measures in many high-income countries mean that public health budgets are reducing year on year. To help inform the potential impact of these proposed disinvestments in public health, we set out to determine the return on investment (ROI) from a range of existing public health interventions. We conducted systematic searches on all relevant databases (including MEDLINE; EMBASE; CINAHL; AMED; PubMed, Cochrane and Scopus) to identify studies that calculated a ROI or cost-benefit ratio (CBR) for public health interventions in high-income countries. We identified 2957 titles, and included 52 studies. The median ROI for public health interventions was 14.3 to 1, and median CBR was 8.3. The median ROI for all 29 local public health interventions was 4.1 to 1, and median CBR was 10.3. Even larger benefits were reported in 28 studies analysing nationwide public health interventions; the median ROI was 27.2, and median CBR was 17.5. This systematic review suggests that local and national public health interventions are highly cost-saving. Cuts to public health budgets in high income countries therefore represent a false economy, and are likely to generate billions of pounds of additional costs to health services and the wider economy. Published by the BMJ Publishing Group Limited. For permission to use (where not already granted under a licence) please go to http://www.bmj.com/company/products-services/rights-and-licensing/.

Chemical analyses of wasp-associated streptomyces bacteria reveal a prolific potential for natural products discovery

DEFF Research Database (Denmark)

Poulsen, Michael; Oh, Dong-Chan; Clardy, Jon

2011-01-01

and solitary Hymenoptera. Here we test this possibility by examining two species of solitary mud dauber wasps, Sceliphron caementarium and Chalybion californicum. We performed enrichment isolations from 33 wasps and obtained more than 200 isolates of Streptomyces Actinobacteria. Chemical analyses of 15...... and antibacterial activity. The prevalence and anti-microbial properties of Actinobacteria associated with these two solitary wasp species suggest the potential role of these Streptomyces as antibiotic-producing symbionts, potentially helping defend their wasp hosts from pathogenic microbes. Finding...... phylogenetically diverse and chemically prolific Actinobacteria from solitary wasps suggests that insect-associated Actinobacteria can provide a valuable source of novel natural products of pharmaceutical interest....

Combined genomic and structural analyses of a cultured magnetotactic bacterium reveals its niche adaptation to a dynamic environment

Directory of Open Access Journals (Sweden)

Ana Carolina Vieira Araujo

2016-10-01

Full Text Available Abstract Background Magnetotactic bacteria (MTB are a unique group of prokaryotes that have a potentially high impact on global geochemical cycling of significant primary elements because of their metabolic plasticity and the ability to biomineralize iron-rich magnetic particles called magnetosomes. Understanding the genetic composition of the few cultivated MTB along with the unique morphological features of this group of bacteria may provide an important framework for discerning their potential biogeochemical roles in natural environments. Results Genomic and ultrastructural analyses were combined to characterize the cultivated magnetotactic coccus Magnetofaba australis strain IT-1. Cells of this species synthesize a single chain of elongated, cuboctahedral magnetite (Fe3O4 magnetosomes that cause them to align along magnetic field lines while they swim being propelled by two bundles of flagella at velocities up to 300 μm s−1. High-speed microscopy imaging showed the cells move in a straight line rather than in the helical trajectory described for other magnetotactic cocci. Specific genes within the genome of Mf. australis strain IT-1 suggest the strain is capable of nitrogen fixation, sulfur reduction and oxidation, synthesis of intracellular polyphosphate granules and transporting iron with low and high affinity. Mf. australis strain IT-1 and Magnetococcus marinus strain MC-1 are closely related phylogenetically although similarity values between their homologous proteins are not very high. Conclusion Mf. australis strain IT-1 inhabits a constantly changing environment and its complete genome sequence reveals a great metabolic plasticity to deal with these changes. Aside from its chemoautotrophic and chemoheterotrophic metabolism, genomic data indicate the cells are capable of nitrogen fixation, possess high and low affinity iron transporters, and might be capable of reducing and oxidizing a number of sulfur compounds. The relatively

Temporal Fluctuation in North East Baltic Sea Region Cattle Population Revealed by Mitochondrial and Y-Chromosomal DNA Analyses

Science.gov (United States)

Niemi, Marianna; Bläuer, Auli; Iso-Touru, Terhi; Harjula, Janne; Nyström Edmark, Veronica; Rannamäe, Eve; Lõugas, Lembi; Sajantila, Antti; Lidén, Kerstin; Taavitsainen, Jussi-Pekka

2015-01-01

Background Ancient DNA analysis offers a way to detect changes in populations over time. To date, most studies of ancient cattle have focused on their domestication in prehistory, while only a limited number of studies have analysed later periods. Conversely, the genetic structure of modern cattle populations is well known given the undertaking of several molecular and population genetic studies. Results Bones and teeth from ancient cattle populations from the North-East Baltic Sea region dated to the Prehistoric (Late Bronze and Iron Age, 5 samples), Medieval (14), and Post-Medieval (26) periods were investigated by sequencing 667 base pairs (bp) from the mitochondrial DNA (mtDNA) and 155 bp of intron 19 in the Y-chromosomal UTY gene. Comparison of maternal (mtDNA haplotypes) genetic diversity in ancient cattle (45 samples) with modern cattle populations in Europe and Asia (2094 samples) revealed 30 ancient mtDNA haplotypes, 24 of which were shared with modern breeds, while 6 were unique to the ancient samples. Of seven Y-chromosomal sequences determined from ancient samples, six were Y2 and one Y1 haplotype. Combined data including Swedish samples from the same periods (64 samples) was compared with the occurrence of Y-chromosomal haplotypes in modern cattle (1614 samples). Conclusions The diversity of haplogroups was highest in the Prehistoric samples, where many haplotypes were unique. The Medieval and Post-Medieval samples also show a high diversity with new haplotypes. Some of these haplotypes have become frequent in modern breeds in the Nordic Countries and North-Western Russia while other haplotypes have remained in only a few local breeds or seem to have been lost. A temporal shift in Y-chromosomal haplotypes from Y2 to Y1 was detected that corresponds with the appearance of new mtDNA haplotypes in the Medieval and Post-Medieval period. This suggests a replacement of the Prehistoric mtDNA and Y chromosomal haplotypes by new types of cattle. PMID:25992976

Systems Analyses Reveal Shared and Diverse Attributes of Oct4 Regulation in Pluripotent Cells

DEFF Research Database (Denmark)

Ding, Li; Paszkowski-Rogacz, Maciej; Winzi, Maria

2015-01-01

We combine a genome-scale RNAi screen in mouse epiblast stem cells (EpiSCs) with genetic interaction, protein localization, and "protein-level dependency" studies-a systematic technique that uncovers post-transcriptional regulation-to delineate the network of factors that control the expression...... of Oct4, a key regulator of pluripotency. Our data signify that there are similarities, but also fundamental differences in Oct4 regulation in EpiSCs versus embryonic stem cells (ESCs). Through multiparametric data analyses, we predict that Tox4 is associating with the Paf1C complex, which maintains cell...... identity in both cell types, and validate that this protein-protein interaction exists in ESCs and EpiSCs. We also identify numerous knockdowns that increase Oct4 expression in EpiSCs, indicating that, in stark contrast to ESCs, Oct4 is under active repressive control in EpiSCs. These studies provide...

The genetic diversity of genus Bacillus and the related genera revealed by 16S rRNA gene sequences and ardra analyses isolated from geothermal regions of turkey

Directory of Open Access Journals (Sweden)

Arzu Coleri Cihan

2012-03-01

Full Text Available Previously isolated 115 endospore-forming bacilli were basically grouped according to their temperature requirements for growth: the thermophiles (74%, the facultative thermophiles (14% and the mesophiles (12%. These isolates were taken into 16S rRNA gene sequence analyses, and they were clustered among the 7 genera: Anoxybacillus, Aeribacillus, Bacillus, Brevibacillus, Geobacillus, Paenibacillus, and Thermoactinomycetes. Of these bacilli, only the thirty two isolates belonging to genera Bacillus (16, Brevibacillus (13, Paenibacillus (1 and Thermoactinomycetes (2 were selected and presented in this paper. The comparative sequence analyses revealed that the similarity values were ranged as 91.4-100 %, 91.8- 99.2 %, 92.6- 99.8 % and 90.7 - 99.8 % between the isolates and the related type strains from these four genera, respectively. Twenty nine of them were found to be related with the validly published type strains. The most abundant species was B. thermoruber with 9 isolates followed by B. pumilus (6, B. lichenformis (3, B. subtilis (3, B. agri (3, B. smithii (2, T. vulgaris (2 and finally P. barengoltzii (1. In addition, isolates of A391a, B51a and D295 were proposed as novel species as their 16S rRNA gene sequences displayed similarities ≤ 97% to their closely related type strains. The AluI-, HaeIII- and TaqI-ARDRA results were in congruence with the 16S rRNA gene sequence analyses. The ARDRA results allowed us to differentiate these isolates, and their discriminative restriction fragments were able to be determined. Some of their phenotypic characters and their amylase, chitinase and protease production were also studied and biotechnologically valuable enzyme producing isolates were introduced in order to use in further studies.

Combining tract- and atlas-based analysis reveals microstructural abnormalities in early Tourette syndrome children.

Science.gov (United States)

Wen, Hongwei; Liu, Yue; Wang, Jieqiong; Rekik, Islem; Zhang, Jishui; Zhang, Yue; Tian, Hongwei; Peng, Yun; He, Huiguang

2016-05-01

Tourette syndrome (TS) is a neurological disorder that causes uncontrolled repetitive motor and vocal tics in children. Examining the neural basis of TS churned out different research studies that advanced our understanding of the brain pathways involved in its development. Particularly, growing evidence points to abnormalities within the fronto-striato-thalamic pathways. In this study, we combined Tract-Based Spatial Statistics (TBSS) and Atlas-based regions of interest (ROI) analysis approach, to investigate the microstructural diffusion changes in both deep and superficial white matter (SWM) in TS children. We then characterized the altered microstructure of white matter in 27 TS children in comparison with 27 age- and gender-matched healthy controls. We found that fractional anisotropy (FA) decreases and radial diffusivity (RD) increases in deep white matter (DWM) tracts in cortico-striato-thalamo-cortical (CSTC) circuit as well as SWM. Furthermore, we found that lower FA values and higher RD values in white matter regions are correlated with more severe tics, but not tics duration. Besides, we also found both axial diffusivity and mean diffusivity increase using Atlas-based ROI analysis. Our work may suggest that microstructural diffusion changes in white matter is not only restricted to the gray matter of CSTC circuit but also affects SWM within the primary motor and somatosensory cortex, commissural and association fibers. Hum Brain Mapp 37:1903-1919, 2016. © 2016 Wiley Periodicals, Inc. © 2016 Wiley Periodicals, Inc.

Phylogenomic analyses data of the avian phylogenomics project

DEFF Research Database (Denmark)

Jarvis, Erich D; Mirarab, Siavash; Aberer, Andre J

2015-01-01

BACKGROUND: Determining the evolutionary relationships among the major lineages of extant birds has been one of the biggest challenges in systematic biology. To address this challenge, we assembled or collected the genomes of 48 avian species spanning most orders of birds, including all Neognathae...... and two of the five Palaeognathae orders. We used these genomes to construct a genome-scale avian phylogenetic tree and perform comparative genomic analyses. FINDINGS: Here we present the datasets associated with the phylogenomic analyses, which include sequence alignment files consisting of nucleotides......ML algorithm or when using statistical binning with the coalescence-based MP-EST algorithm (which we refer to as MP-EST*). Other data sets, such as the coding sequence of some exons, revealed other properties of genome evolution, namely convergence. CONCLUSIONS: The Avian Phylogenomics Project is the largest...

Comparing the decline in coronary heart disease and stroke mortality in neighbouring countries with different healthcare systems.

LENUS (Irish Health Repository)

Bennett, K

2013-06-04

OBJECTIVE: To examine age and gender specific trends in coronary heart disease (CHD) and stroke mortality in two neighbouring countries, the Republic of Ireland (ROI) and Northern Ireland (NI). DESIGN: Epidemiological study of time trends in CHD and stroke mortality. SETTING\\/PATIENTS: The populations of the ROI and NI, 1985-2010. INTERVENTIONS: None. MAIN OUTCOME MEASURES: Directly age standardised CHD and stroke mortality rates were calculated and analysed using joinpoint regression to identify years where the slope of the linear trend changed significantly. This was performed separately for specific age groups (25-54, 55-64, 65-74 and 75-84 years) and by gender. Annual percentage change (APC) and 95% CIs are presented. RESULTS: There was a striking similarity between the two countries, with percentage change between 1985 and 1989 and between 2006 and 2010 of 67% and 69% in CHD mortality, and 64% and 62% in stroke mortality for the ROI and NI, respectively. However, joinpoint analysis identified differences in the pace of change between the two countries. There was an accelerated pace of decline (negative APC) in mortality for both CHD and stroke in both countries from the mid-1990s (APC ROI -8% (95% CI -9.5 to 6.5) and NI -6.6% (-6.9 to -6.3)), but the accelerated decrease started later for CHD mortality in the ROI. In recent years, a levelling off in CHD mortality was observed in the 25-54 year age group in NI and in stroke mortality for men and women in the ROI. CONCLUSIONS: While differences in the pace of change in mortality were observed at different time points, similar, substantial decreases in CHD and stroke mortality were achieved between 1985 and 1989 and between 2006 and 2010 in the ROI and NI despite important differences in health service structures. There is evidence of a levelling in mortality rates in some groups in recent years.

Comparative live-cell imaging analyses of SPA-2, BUD-6 and BNI-1 in Neurospora crassa reveal novel features of the filamentous fungal polarisome.

Directory of Open Access Journals (Sweden)

Alexander Lichius

Full Text Available A key multiprotein complex involved in regulating the actin cytoskeleton and secretory machinery required for polarized growth in fungi, is the polarisome. Recognized core constituents in budding yeast are the proteins Spa2, Pea2, Aip3/Bud6, and the key effector Bni1. Multicellular fungi display a more complex polarized morphogenesis than yeasts, suggesting that the filamentous fungal polarisome might fulfill additional functions. In this study, we compared the subcellular organization and dynamics of the putative polarisome components BUD-6 and BNI-1 with those of the bona fide polarisome marker SPA-2 at various developmental stages of Neurospora crassa. All three proteins exhibited a yeast-like polarisome configuration during polarized germ tube growth, cell fusion, septal pore plugging and tip repolarization. However, the localization patterns of all three proteins showed spatiotemporally distinct characteristics during the establishment of new polar axes, septum formation and cytokinesis, and maintained hyphal tip growth. Most notably, in vegetative hyphal tips BUD-6 accumulated as a subapical cloud excluded from the Spitzenkörper (Spk, whereas BNI-1 and SPA-2 partially colocalized with the Spk and the tip apex. Novel roles during septal plugging and cytokinesis, connected to the reinitiation of tip growth upon physical injury and conidial maturation, were identified for BUD-6 and BNI-1, respectively. Phenotypic analyses of gene deletion mutants revealed additional functions for BUD-6 and BNI-1 in cell fusion regulation, and the maintenance of Spk integrity. Considered together, our findings reveal novel polarisome-independent functions of BUD-6 and BNI-1 in Neurospora, but also suggest that all three proteins cooperate at plugged septal pores, and their complex arrangement within the apical dome of mature hypha might represent a novel aspect of filamentous fungal polarisome architecture.

Perception of co-speech gestures in aphasic patients: a visual exploration study during the observation of dyadic conversations.

Science.gov (United States)

Preisig, Basil C; Eggenberger, Noëmi; Zito, Giuseppe; Vanbellingen, Tim; Schumacher, Rahel; Hopfner, Simone; Nyffeler, Thomas; Gutbrod, Klemens; Annoni, Jean-Marie; Bohlhalter, Stephan; Müri, René M

2015-03-01

Co-speech gestures are part of nonverbal communication during conversations. They either support the verbal message or provide the interlocutor with additional information. Furthermore, they prompt as nonverbal cues the cooperative process of turn taking. In the present study, we investigated the influence of co-speech gestures on the perception of dyadic dialogue in aphasic patients. In particular, we analysed the impact of co-speech gestures on gaze direction (towards speaker or listener) and fixation of body parts. We hypothesized that aphasic patients, who are restricted in verbal comprehension, adapt their visual exploration strategies. Sixteen aphasic patients and 23 healthy control subjects participated in the study. Visual exploration behaviour was measured by means of a contact-free infrared eye-tracker while subjects were watching videos depicting spontaneous dialogues between two individuals. Cumulative fixation duration and mean fixation duration were calculated for the factors co-speech gesture (present and absent), gaze direction (to the speaker or to the listener), and region of interest (ROI), including hands, face, and body. Both aphasic patients and healthy controls mainly fixated the speaker's face. We found a significant co-speech gesture × ROI interaction, indicating that the presence of a co-speech gesture encouraged subjects to look at the speaker. Further, there was a significant gaze direction × ROI × group interaction revealing that aphasic patients showed reduced cumulative fixation duration on the speaker's face compared to healthy controls. Co-speech gestures guide the observer's attention towards the speaker, the source of semantic input. It is discussed whether an underlying semantic processing deficit or a deficit to integrate audio-visual information may cause aphasic patients to explore less the speaker's face. Copyright © 2014 Elsevier Ltd. All rights reserved.

Financial return-on-investment of ophthalmic interventions: a new paradigm.

Science.gov (United States)

Brown, Melissa M; Brown, Gary C; Lieske, Heidi B; Lieske, P Alexander

2014-05-01

Although the patient value gain (improvement in quality-of-life and/or length-of-life) has been highlighted in Value-based Medicine cost-utility analyses, the financial value gain associated with healthcare interventions has received less emphasis. It is important for professional healthcare providers to realize their interventions often confer a large financial return-on-investment (ROI) to society. The societal costs associated with vitreoretinal and other ophthalmic interventions include: direct ophthalmic medical costs expended (hospital, physician, drug, diagnostic testing and so forth), direct medical costs saved (decreased costs for depression, injury, skilled nursing facility, nursing home and others), direct nonmedical costs saved (decreased costs for caregivers, transportation, residence costs, moving costs, and others), and indirect medical costs saved (improving employment incidence and wages). The financial ROI for direct ophthalmic medical costs expended for ranibizumab therapy for neovascular age-related macular degeneration is 450%, whereas that for cataract surgery is 4500% and for medical open-angle glaucoma therapy is 4000%. Many costs gained add to the Gross Domestic Product and increase the wealth of the nation. Many vitreoretinal and other ophthalmologic interventions confer considerable patient value, but also result in a large financial ROI to society. This financial ROI increases the wealth of the nation.

A Local Region of Interest Imaging Method for Electrical Impedance Tomography with Internal Electrodes

Directory of Open Access Journals (Sweden)

Hyeuknam Kwon

2013-01-01

Full Text Available Electrical Impedance Tomography (EIT is a very attractive functional imaging method despite the low sensitivity and resolution. The use of internal electrodes with the conventional reconstruction algorithms was not enough to enhance image resolution and accuracy in the region of interest (ROI. We propose a local ROI imaging method with internal electrodes developed from careful analysis of the sensitivity matrix that is designed to reduce the sensitivity of the voxels outside the local region and optimize the sensitivity of the voxel inside the local region. We perform numerical simulations and physical measurements to demonstrate the localized EIT imaging method. In preliminary results with multiple objects we show the benefits of using an internal electrode and the improved resolution due to the local ROI image reconstruction method. The sensitivity is further increased by allowing the surface electrodes to be unevenly spaced with a higher density of surface electrodes near the ROI. Also, we analyse how much the image quality is improved using several performance parameters for comparison. While these have not yet been studied in depth, it convincingly shows an improvement in local sensitivity in images obtained with an internal electrode in comparison to a standard reconstruction method.

Can T1 w/T2 w ratio be used as a myelin-specific measure in subcortical structures? Comparisons between FSE-based T1 w/T2 w ratios, GRASE-based T1 w/T2 w ratios and multi-echo GRASE-based myelin water fractions.

Science.gov (United States)

Uddin, Md Nasir; Figley, Teresa D; Marrie, Ruth Ann; Figley, Chase R

2018-03-01

Given the growing popularity of T 1 -weighted/T 2 -weighted (T 1 w/T 2 w) ratio measurements, the objective of the current study was to evaluate the concordance between T 1 w/T 2 w ratios obtained using conventional fast spin echo (FSE) versus combined gradient and spin echo (GRASE) sequences for T 2 w image acquisition, and to compare the resulting T 1 w/T 2 w ratios with histologically validated myelin water fraction (MWF) measurements in several subcortical brain structures. In order to compare these measurements across a relatively wide range of myelin concentrations, whole-brain T 1 w magnetization prepared rapid acquisition gradient echo (MPRAGE), T 2 w FSE and three-dimensional multi-echo GRASE data were acquired from 10 participants with multiple sclerosis at 3 T. Then, after high-dimensional, non-linear warping, region of interest (ROI) analyses were performed to compare T 1 w/T 2 w ratios and MWF estimates (across participants and brain regions) in 11 bilateral white matter (WM) and four bilateral subcortical grey matter (SGM) structures extracted from the JHU_MNI_SS 'Eve' atlas. Although the GRASE sequence systematically underestimated T 1 w/T 2 w values compared to the FSE sequence (revealed by Bland-Altman and mountain plots), linear regressions across participants and ROIs revealed consistently high correlations between the two methods (r 2 = 0.62 for all ROIs, r 2 = 0.62 for WM structures and r 2 = 0.73 for SGM structures). However, correlations between either FSE-based or GRASE-based T 1 w/T 2 w ratios and MWFs were extremely low in WM structures (FSE-based, r 2 = 0.000020; GRASE-based, r 2 = 0.0014), low across all ROIs (FSE-based, r 2 = 0.053; GRASE-based, r 2 = 0.029) and moderate in SGM structures (FSE-based, r 2 = 0.20; GRASE-based, r 2 = 0.17). Overall, our findings indicated a high degree of correlation (but not equivalence) between FSE-based and GRASE-based T 1 w/T 2 w ratios, and low correlations between T 1 w/T 2 w ratios and MWFs. This

Aspergillus fumigatus Copper Export Machinery and Reactive Oxygen Intermediate Defense Counter Host Copper-Mediated Oxidative Antimicrobial Offense

Directory of Open Access Journals (Sweden)

Philipp Wiemann

2017-05-01

Full Text Available The Fenton-chemistry-generating properties of copper ions are considered a potent phagolysosome defense against pathogenic microbes, yet our understanding of underlying host/microbe dynamics remains unclear. We address this issue in invasive aspergillosis and demonstrate that host and fungal responses inextricably connect copper and reactive oxygen intermediate (ROI mechanisms. Loss of the copper-binding transcription factor AceA yields an Aspergillus fumigatus strain displaying increased sensitivity to copper and ROI in vitro, increased intracellular copper concentrations, decreased survival in challenge with murine alveolar macrophages (AMΦs, and reduced virulence in a non-neutropenic murine model. ΔaceA survival is remediated by dampening of host ROI (chemically or genetically or enhancement of copper-exporting activity (CrpA in A. fumigatus. Our study exposes a complex host/microbe multifactorial interplay that highlights the importance of host immune status and reveals key targetable A. fumigatus counter-defenses.

Auditory middle latency responses differ in right- and left-handed subjects: an evaluation through topographic brain mapping.

Science.gov (United States)

Mohebbi, Mehrnaz; Mahmoudian, Saeid; Alborzi, Marzieh Sharifian; Najafi-Koopaie, Mojtaba; Farahani, Ehsan Darestani; Farhadi, Mohammad

2014-09-01

To investigate the association of handedness with auditory middle latency responses (AMLRs) using topographic brain mapping by comparing amplitudes and latencies in frontocentral and hemispheric regions of interest (ROIs). The study included 44 healthy subjects with normal hearing (22 left handed and 22 right handed). AMLRs were recorded from 29 scalp electrodes in response to binaural 4-kHz tone bursts. Frontocentral ROI comparisons revealed that Pa and Pb amplitudes were significantly larger in the left-handed than the right-handed group. Topographic brain maps showed different distributions in AMLR components between the two groups. In hemispheric comparisons, Pa amplitude differed significantly across groups. A left-hemisphere emphasis of Pa was found in the right-handed group but not in the left-handed group. This study provides evidence that handedness is associated with AMLR components in frontocentral and hemispheric ROI. Handedness should be considered an essential factor in the clinical or experimental use of AMLRs.

Momentum-based morphometric analysis with application to Parkinson's disease

Science.gov (United States)

Chen, Jingyun; Khan, Ali R.; McKeown, Martin J.; Beg, Mirza F.

2011-03-01

We apply the initial momentum shape representation of diffeomorphic metric mapping from a template region of interest (ROI) to a given ROI as a morphometic marker in Parkinson's disease. We used a three-step segmentation-registrationmomentum process to derive feature vectors from ROIs in a group of 42 subjects consisting of 19 Parkinson's Disease (PD) subjects and 23 normal control (NC) subjects. Significant group differences between PD and NC subjects were detected in four basal ganglia structures including the caudate, putamen, thalamus and globus pallidus. The magnitude of regionally significant between-group differences detected ranged between 34-75%. Visualization of the different structural deformation pattern between-groups revealed that some parts of basal ganglia structure actually hypertrophy, presumably as a compensatory response to more widespread atrophy. Our results of both hypertrophy and atrophy in the same structures further demonstrate the importance of morphological measures as opposed to overall volume in the assessment of neurodegenerative disease.

A review of bioinformatic methods for forensic DNA analyses.

Science.gov (United States)

Liu, Yao-Yuan; Harbison, SallyAnn

2018-03-01

Short tandem repeats, single nucleotide polymorphisms, and whole mitochondrial analyses are three classes of markers which will play an important role in the future of forensic DNA typing. The arrival of massively parallel sequencing platforms in forensic science reveals new information such as insights into the complexity and variability of the markers that were previously unseen, along with amounts of data too immense for analyses by manual means. Along with the sequencing chemistries employed, bioinformatic methods are required to process and interpret this new and extensive data. As more is learnt about the use of these new technologies for forensic applications, development and standardization of efficient, favourable tools for each stage of data processing is being carried out, and faster, more accurate methods that improve on the original approaches have been developed. As forensic laboratories search for the optimal pipeline of tools, sequencer manufacturers have incorporated pipelines into sequencer software to make analyses convenient. This review explores the current state of bioinformatic methods and tools used for the analyses of forensic markers sequenced on the massively parallel sequencing (MPS) platforms currently most widely used. Copyright © 2017 Elsevier B.V. All rights reserved.

Extratemporal abnormalities of brain parenchyma in young adults with temporal lobe epilepsy: A diffusion tensor imaging study

International Nuclear Information System (INIS)

Yin, X.-Y.; Qiu, S.-J.; Liu, Z.-Y.; Wang, H.-Z.; Xiong, W.-F.; Li, S.-S.; Wang, Y.

2014-01-01

Aim: To examine extratemporal abnormalities of the cerebral parenchyma in young adult temporal lobe epilepsy (TLE) patients using diffusion tensor imaging (DTI). Materials and methods: The study comprised 20 adults with unilateral TLE and 20 controls. The fractional anisotropy (FA), apparent diffusion coefficient (ADC), parallel eigenvalue (λ ∥ ), and perpendicular eigenvalue (λ ⊥ ) were calculated in the regions of interest (ROIs) using a 3 T MRI system. ROIs included the anterior/posterior limb of the internal capsule (AIC/PIC), external capsule (EC), head of caudate nucleus (HCN), lenticular nucleus (LN), thalamus (TL), and genu/body/splenium of the corpus callosum (GCC/BCC/SCC). Results: Compared to controls, TLE patients showed lower FA in all ROIs; higher ADC in bilateral ECs, HCNs, TLs, and BCC; lower λ ∥ in the ipsilateral LN and bilateral AICs, TL, and GCC; and higher λ ⊥ in all ROIs except the bilateral PICs. In TLE patients, the ipsilateral TL had decreased FA compared with the contralateral TL. Pearson correlation analysis revealed a negative correlation between the ADC of the GCC and the age at onset of epilepsy; the λ ∥ of the ipsilateral PIC and age at onset of epilepsy; the λ ⊥ of the contralateral AIC and duration of epilepsy, respectively; and a positive correlation between the ADC of the GCC and the duration of epilepsy and the λ ⊥ of the GCC and the duration of epilepsy, respectively. Conclusion: The study revealed bilateral extratemporal abnormalities in young adult TLE patients compared with controls. In addition, TLE patients with younger age at onset or longer duration of epilepsy may have more serious extratemporal changes

Defining the most probable location of the parahippocampal place area using cortex-based alignment and cross-validation.

Science.gov (United States)

Weiner, Kevin S; Barnett, Michael A; Witthoft, Nathan; Golarai, Golijeh; Stigliani, Anthony; Kay, Kendrick N; Gomez, Jesse; Natu, Vaidehi S; Amunts, Katrin; Zilles, Karl; Grill-Spector, Kalanit

2018-04-15

The parahippocampal place area (PPA) is a widely studied high-level visual region in the human brain involved in place and scene processing. The goal of the present study was to identify the most probable location of place-selective voxels in medial ventral temporal cortex. To achieve this goal, we first used cortex-based alignment (CBA) to create a probabilistic place-selective region of interest (ROI) from one group of 12 participants. We then tested how well this ROI could predict place selectivity in each hemisphere within a new group of 12 participants. Our results reveal that a probabilistic ROI (pROI) generated from one group of 12 participants accurately predicts the location and functional selectivity in individual brains from a new group of 12 participants, despite between subject variability in the exact location of place-selective voxels relative to the folding of parahippocampal cortex. Additionally, the prediction accuracy of our pROI is significantly higher than that achieved by volume-based Talairach alignment. Comparing the location of the pROI of the PPA relative to published data from over 500 participants, including data from the Human Connectome Project, shows a striking convergence of the predicted location of the PPA and the cortical location of voxels exhibiting the highest place selectivity across studies using various methods and stimuli. Specifically, the most predictive anatomical location of voxels exhibiting the highest place selectivity in medial ventral temporal cortex is the junction of the collateral and anterior lingual sulci. Methodologically, we make this pROI freely available (vpnl.stanford.edu/PlaceSelectivity), which provides a means to accurately identify a functional region from anatomical MRI data when fMRI data are not available (for example, in patient populations). Theoretically, we consider different anatomical and functional factors that may contribute to the consistent anatomical location of place selectivity

SU-E-T-497: Semi-Automated in Vivo Radiochromic Film Dosimetry Using a Novel Image Processing Algorithm

International Nuclear Information System (INIS)

Reyhan, M; Yue, N

2014-01-01

Purpose: To validate an automated image processing algorithm designed to detect the center of radiochromic film used for in vivo film dosimetry against the current gold standard of manual selection. Methods: An image processing algorithm was developed to automatically select the region of interest (ROI) in *.tiff images that contain multiple pieces of radiochromic film (0.5x1.3cm 2 ). After a user has linked a calibration file to the processing algorithm and selected a *.tiff file for processing, an ROI is automatically detected for all films by a combination of thresholding and erosion, which removes edges and any additional markings for orientation. Calibration is applied to the mean pixel values from the ROIs and a *.tiff image is output displaying the original image with an overlay of the ROIs and the measured doses. Validation of the algorithm was determined by comparing in vivo dose determined using the current gold standard (manually drawn ROIs) versus automated ROIs for n=420 scanned films. Bland-Altman analysis, paired t-test, and linear regression were performed to demonstrate agreement between the processes. Results: The measured doses ranged from 0.2-886.6cGy. Bland-Altman analysis of the two techniques (automatic minus manual) revealed a bias of -0.28cGy and a 95% confidence interval of (5.5cGy,-6.1cGy). These values demonstrate excellent agreement between the two techniques. Paired t-test results showed no statistical differences between the two techniques, p=0.98. Linear regression with a forced zero intercept demonstrated that Automatic=0.997*Manual, with a Pearson correlation coefficient of 0.999. The minimal differences between the two techniques may be explained by the fact that the hand drawn ROIs were not identical to the automatically selected ones. The average processing time was 6.7seconds in Matlab on an IntelCore2Duo processor. Conclusion: An automated image processing algorithm has been developed and validated, which will help minimize

Analysing Access Control Specifications

DEFF Research Database (Denmark)

Probst, Christian W.; Hansen, René Rydhof

2009-01-01

When prosecuting crimes, the main question to answer is often who had a motive and the possibility to commit the crime. When investigating cyber crimes, the question of possibility is often hard to answer, as in a networked system almost any location can be accessed from almost anywhere. The most...... common tool to answer this question, analysis of log files, faces the problem that the amount of logged data may be overwhelming. This problems gets even worse in the case of insider attacks, where the attacker’s actions usually will be logged as permissible, standard actions—if they are logged at all....... Recent events have revealed intimate knowledge of surveillance and control systems on the side of the attacker, making it often impossible to deduce the identity of an inside attacker from logged data. In this work we present an approach that analyses the access control configuration to identify the set...

Cerebral perfusion in homogeneity in normal volunteers

International Nuclear Information System (INIS)

Gruenwald, S.M.; Larcos, G.

1998-01-01

Full text: In the interpretation of cerebral perfusion scans, it is important to know the normal variation in perfusion which may occur between the cerebral hemispheres. For this reason 24 normal volunteers with no neurological or psychiatric history, and who were on no medications, had 99m Tc-HMPAO brain SPECT studies using a single headed gamma camera computer system. Oblique, coronal and sagittal images were reviewed separately by two experienced observers and any differences were resolved by consensus. Semi-quantitation was performed by summing two adjacent oblique slices and drawing right and left mirror image ROIs corresponding to the mid section level of anterior and posterior frontal lobes, anterior and posterior parietal lobes, temporal lobes and cerebellum. From the mean counts per pixel, right: left ROI ratios and ROI: cerebellar ratios were calculated. On qualitative review 6/24 subjects had mild asymmetry in tracer distribution between right and left cerebral lobes. Semi-quantitation revealed a 5-10% difference in counts between right and left ROIs in 12/24 subjects and an additional three subjects had 10-20% difference in counts between right and left temporal lobes. This study demonstrates the presence of mild asymmetry of cerebral perfusion in a significant minority of normal subjects

Test-retest reliability of prefrontal transcranial Direct Current Stimulation (tDCS) effects on functional MRI connectivity in healthy subjects.

Science.gov (United States)

Wörsching, Jana; Padberg, Frank; Helbich, Konstantin; Hasan, Alkomiet; Koch, Lena; Goerigk, Stephan; Stoecklein, Sophia; Ertl-Wagner, Birgit; Keeser, Daniel

2017-07-15

Transcranial Direct Current Stimulation (tDCS) of the prefrontal cortex (PFC) can be used for probing functional brain connectivity and meets general interest as novel therapeutic intervention in psychiatric and neurological disorders. Along with a more extensive use, it is important to understand the interplay between neural systems and stimulation protocols requiring basic methodological work. Here, we examined the test-retest (TRT) characteristics of tDCS-induced modulations in resting-state functional-connectivity MRI (RS fcMRI). Twenty healthy subjects received 20minutes of either active or sham tDCS of the dorsolateral PFC (2mA, anode over F3 and cathode over F4, international 10-20 system), preceded and ensued by a RS fcMRI (10minutes each). All subject underwent three tDCS sessions with one-week intervals in between. Effects of tDCS on RS fcMRI were determined at an individual as well as at a group level using both ROI-based and independent-component analyses (ICA). To evaluate the TRT reliability of individual active-tDCS and sham effects on RS fcMRI, voxel-wise intra-class correlation coefficients (ICC) of post-tDCS maps between testing sessions were calculated. For both approaches, results revealed low reliability of RS fcMRI after active tDCS (ICC (2,1) = -0.09 - 0.16). Reliability of RS fcMRI (baselines only) was low to moderate for ROI-derived (ICC (2,1) = 0.13 - 0.50) and low for ICA-derived connectivity (ICC (2,1) = 0.19 - 0.34). Thus, for ROI-based analyses, the distribution of voxel-wise ICC was shifted to lower TRT reliability after active, but not after sham tDCS, for which the distribution was similar to baseline. The intra-individual variation observed here resembles variability of tDCS effects in motor regions and may be one reason why in this study robust tDCS effects at a group level were missing. The data can be used for appropriately designing large scale studies investigating methodological issues such as sources of variability and

Een kwantitatieve analyse van Nederlandse bijdragen aan internationaal arbeids- en organisatiepsychologisch onderzoek

NARCIS (Netherlands)

de Dreu, C.K.W.

2010-01-01

The author reports a quantitative analysis of the absolute and relative numbers of publications in six high-ranking journals on work and organisational psychology, (co-)authored by scientists with a Dutch, German, or British affiliation. In contrast to Germany and Great Britain, analyses reveal a

Allochthonous Addition of Meteoritic Organics to the Lunar Regolith

Science.gov (United States)

Thomas-Keprta, K. L.; Clemett, S.; Ross, D. K.; Le, L.; Rahman, Z.; McKay, D. S.; Gibson, E. K.; Gonzalez, C.

2013-01-01

Preparation of lunar samples 74220,861 was discussed in detail in [3, 4]. Our analysis sequence was as follows: optical microscopy, UV fluorescence imaging, -Raman, FESEM-EDX imaging and mapping, FETEMEDX imaging and mapping of a Focused Ion Beam (FIB) extracted section, and NanoSIMs analysis. We observed fluffytextured C-rich regions of interest (ROI) on three different volcanic glass beads. Each ROI was several m2 in size and fluoresced when exposed to UV. Using FESEM/EDX, the largest ROI measured 36 m and was located on an edge of a plateau located on the uppermost surface of the bead. The ROI was covered on one edge by a siliceous filament emanating from the plateau surface indicating it was attached to the bead while on the Moon. EDX mapping of the ROI shows it is composed primarily of heterogeneously distributed C. Embedded with the carbonaceous phase are localized concentrations of Si, Fe, Al and Ti indicating the presence of glass and/or minerals grains. -Raman showed strong D- and G-bands and their associated second order bands; intensity and location of these bands indicates the carbonaceous matter is structurally disorganized. A TEM thin section was extracted from the surface of a glass bead using FIB microscopy. High resolution TEM imaging and selected area electron diffraction demonstrate the carbonaceous layer to be amorphous; it lacked any long or short range order characteristic of micro- or nanocrystalline graphite. Additionally TEM imaging also revealed the presence of submicron mineral grains, typically < 50 nm in size, dispersed within the carbonaceous layer. NanoSIMs data will be presented and discussed at the meeting. Given the noted similarities between the carbonaceous matter present on 74220 glass beads and meteoritic kerogen, we suggest the allochthonous addition of meteoritic organics as the most probable source for the C-rich ROIs.

Comprehensive genetic analyses reveal evolutionary distinction of a mouse (Zapus hudsonius preblei) proposed for delisting from the US Endangered Species Act.

Science.gov (United States)

King, Tim L; Switzer, John F; Morrison, Cheryl L; Eackles, Michael S; Young, Colleen C; Lubinski, Barbara A; Cryan, Paul

2006-12-01

Zapus hudsonius preblei, listed as threatened under the US Endangered Species Act (ESA), is one of 12 recognized subspecies of meadow jumping mice found in North America. Recent morphometric and phylogenetic comparisons among Z. h. preblei and neighbouring conspecifics questioned the taxonomic status of selected subspecies, resulting in a proposal to delist the Z. h. preblei from the ESA. We present additional analyses of the phylogeographic structure within Z. hudsonius that calls into question previously published data (and conclusions) and confirms the original taxonomic designations. A survey of 21 microsatellite DNA loci and 1380 base pairs from two mitochondrial DNA (mtDNA) regions (control region and cytochrome b) revealed that each Z. hudsonius subspecies is genetically distinct. These data do not support the null hypothesis of a homogeneous gene pool among the five subspecies found within the southwestern portion of the species' range. The magnitude of the observed differentiation was considerable and supported by significant findings for nearly every statistical comparison made, regardless of the genome or the taxa under consideration. Structuring of nuclear multilocus genotypes and subspecies-specific mtDNA haplotypes corresponded directly with the disjunct distributions of the subspecies investigated. Given the level of correspondence between the observed genetic population structure and previously proposed taxonomic classification of subspecies (based on the geographic separation and surveys of morphological variation), we conclude that the nominal subspecies surveyed in this study do not warrant synonymy, as has been proposed for Z. h. preblei, Z. h. campestris, and Z. h. intermedius.

''Textural analysis of multiparametric MRI detects transition zone prostate cancer''

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Sidhu, Harbir S.; Johnston, Edward W.; Taylor, Stuart A.; Halligan, Steve [Centre for Medical Imaging, University College London, London (United Kingdom); University College London Hospitals NHS Foundation Trust, London (United Kingdom); Benigno, Salvatore; Dikaios, Nikos [Centre for Medical Imaging, University College London, London (United Kingdom); Ganeshan, Balaji [Institute of Nuclear Medicine, University College London, University College Hospital, London (United Kingdom); Allen, Clare; Kirkham, Alex [University College London Hospitals NHS Foundation Trust, London (United Kingdom); Groves, Ashley M. [University College London Hospitals NHS Foundation Trust, London (United Kingdom); Institute of Nuclear Medicine, University College London, University College Hospital, London (United Kingdom); Ahmed, Hashim U.; Emberton, Mark [University College London Hospitals NHS Foundation Trust, London (United Kingdom); University College London, Research Department of Urology, London (United Kingdom); Punwani, Shonit [Centre for Medical Imaging, University College London, London (United Kingdom); University College London Hospitals NHS Foundation Trust, London (United Kingdom); Centre for Medical Imaging, University College London and University College London Hospitals NIHR Biomedical Research Centre, London (United Kingdom)

2017-06-15

To evaluate multiparametric-MRI (mpMRI) derived histogram textural-analysis parameters for detection of transition zone (TZ) prostatic tumour. Sixty-seven consecutive men with suspected prostate cancer underwent 1.5T mpMRI prior to template-mapping-biopsy (TPM). Twenty-six men had 'significant' TZ tumour. Two radiologists in consensus matched TPM to the single axial slice best depicting tumour, or largest TZ diameter for those with benign histology, to define single-slice whole TZ-regions-of-interest (ROIs). Textural-parameter differences between single-slice whole TZ-ROI containing significant tumour versus benign/insignificant tumour were analysed using Mann Whitney U test. Diagnostic accuracy was assessed by receiver operating characteristic area under curve (ROC-AUC) analysis cross-validated with leave-one-out (LOO) analysis. ADC kurtosis was significantly lower (p < 0.001) in TZ containing significant tumour with ROC-AUC 0.80 (LOO-AUC 0.78); the difference became non-significant following exclusion of significant tumour from single-slice whole TZ-ROI (p = 0.23). T1-entropy was significantly lower (p = 0.004) in TZ containing significant tumour with ROC-AUC 0.70 (LOO-AUC 0.66) and was unaffected by excluding significant tumour from TZ-ROI (p = 0.004). Combining these parameters yielded ROC-AUC 0.86 (LOO-AUC 0.83). Textural features of the whole prostate TZ can discriminate significant prostatic cancer through reduced kurtosis of the ADC-histogram where significant tumour is included in TZ-ROI and reduced T1 entropy independent of tumour inclusion. (orig.)

Abnormal subcortical nuclei shapes in patients with type 2 diabetes mellitus

Energy Technology Data Exchange (ETDEWEB)

Chen, Ji; Wang, Xiaoyang; Li, Hui; Yang, Yanqiu; Lu, Jingjing; Chen, Ziqian [Fuzhou General Hospital, Department of Medical Imaging, Fuzhou, Fujian (China); Zhang, Junxiang [Bengbu Medical College, Department of Medical Imaging, Bengbu, Anhui (China); Liu, Xuebing [Fuzhou General Hospital, Department of Medical Imaging, Fuzhou, Fujian (China); The Second Affiliated Hospital of Nanjing Medical University, Department of Medical Imaging, Nanjing, Jiangsu (China); Xu, Xiangjin [Fuzhou General Hospital, Department of Endocrinology, Fuzhou, Fujian (China); Cao, Bo [The Second Affiliated Hospital of Nanjing Medical University, Department of Medical Imaging, Nanjing, Jiangsu (China)

2017-10-15

Type 2 diabetes mellitus (T2DM) increases the risk of brain atrophy and dementia. We aimed to elucidate deep grey matter (GM) structural abnormalities and their relationships with T2DM cognitive deficits by combining region of interest (ROI)-based volumetry, voxel-based morphometry (VBM) and shape analysis. We recruited 23 T2DM patients and 24 age-matched healthy controls to undergo T1-weighted structural MRI scanning. Images were analysed using the three aforementioned methods to obtain deep GM structural shapes and volumes. Biochemical and cognitive assessments were made and were correlated with the resulting metrics. Shape analysis revealed that T2DM is associated with focal atrophy in the bilateral caudate head and dorso-medial part of the thalamus. ROI-based volumetry only detected thalamic volume reduction in T2DM when compared to the controls. No significant between-group differences were found by VBM. Furthermore, a worse performance of cognitive processing speed correlated with more severe GM atrophy in the bilateral dorso-medial part of the thalamus. Also, the GM volume in the bilateral dorso-medial part of the thalamus changed negatively with HbA{sub 1c}. Shape analysis is sensitive in identifying T2DM deep GM structural abnormalities and their relationships with cognitive impairments, which may greatly assist in clarifying the neural substrate of T2DM cognitive dysfunction. (orig.)

FDG-PET findings in the Wernicke-Korsakoff syndrome.

Science.gov (United States)

Reed, Laurence J; Lasserson, Dan; Marsden, Paul; Stanhope, Nicola; Stevens, Tom; Bello, Fernando; Kingsley, Derek; Colchester, Alan; Kopelman, Michael D

2003-01-01

This study reports FDG-PET findings in Wernicke-Korsakoff patients. Twelve patients suffering amnesia arising from the Korsakoff syndrome were compared with 10 control subjects without alcohol-related disability. Subjects received [18F]-fluorodeoxyglucose (FDG-PET) imaging as well as neuropsychological assessment and high-resolution MR imaging with volumetric analysis. Volumetric MRI analysis had revealed thalamic and mamillary body atrophy in the patient group as well as frontal lobe atrophy with relative sparing of medial temporal lobe structures. Differences in regional metabolism were identified using complementary region of interest (ROI) and statistical parametric mapping (SPM) approaches employing either absolute methods or a reference region approach to increase statistical power. In general, we found relative hypermetabolism in white matter and hypometabolism in subcortical grey matter in Korsakoff patients. When FDG uptake ratios were examined with occipital lobe metabolism as covariate reference region, Korsakoff patients showed widespread bilateral white matter hypermetabolism on both SPM and ROI analysis. When white matter metabolism was the reference covariate; Korsakoff patients showed relative hypometabolism in the diencephalic grey matter, consistent with their known underlying neuropathology, and medial temporal and retrosplenial hypometabolism, interpreted as secondary metabolic effects within the diencephalic-limbic memory circuits. There was also evidence of a variable degree of more general frontotemporal neocortical hypometabolism on some, but not all, analyses.

Abnormal subcortical nuclei shapes in patients with type 2 diabetes mellitus

International Nuclear Information System (INIS)

Chen, Ji; Wang, Xiaoyang; Li, Hui; Yang, Yanqiu; Lu, Jingjing; Chen, Ziqian; Zhang, Junxiang; Liu, Xuebing; Xu, Xiangjin; Cao, Bo

2017-01-01

Type 2 diabetes mellitus (T2DM) increases the risk of brain atrophy and dementia. We aimed to elucidate deep grey matter (GM) structural abnormalities and their relationships with T2DM cognitive deficits by combining region of interest (ROI)-based volumetry, voxel-based morphometry (VBM) and shape analysis. We recruited 23 T2DM patients and 24 age-matched healthy controls to undergo T1-weighted structural MRI scanning. Images were analysed using the three aforementioned methods to obtain deep GM structural shapes and volumes. Biochemical and cognitive assessments were made and were correlated with the resulting metrics. Shape analysis revealed that T2DM is associated with focal atrophy in the bilateral caudate head and dorso-medial part of the thalamus. ROI-based volumetry only detected thalamic volume reduction in T2DM when compared to the controls. No significant between-group differences were found by VBM. Furthermore, a worse performance of cognitive processing speed correlated with more severe GM atrophy in the bilateral dorso-medial part of the thalamus. Also, the GM volume in the bilateral dorso-medial part of the thalamus changed negatively with HbA_1_c. Shape analysis is sensitive in identifying T2DM deep GM structural abnormalities and their relationships with cognitive impairments, which may greatly assist in clarifying the neural substrate of T2DM cognitive dysfunction. (orig.)

Quantitative DNA methylation analyses reveal stage dependent DNA methylation and association to clinico-pathological factors in breast tumors

International Nuclear Information System (INIS)

Klajic, Jovana; Tost, Jörg; Kristensen, Vessela N; Fleischer, Thomas; Dejeux, Emelyne; Edvardsen, Hege; Warnberg, Fredrik; Bukholm, Ida; Lønning, Per Eystein; Solvang, Hiroko; Børresen-Dale, Anne-Lise

2013-01-01

Aberrant DNA methylation of regulatory genes has frequently been found in human breast cancers and correlated to clinical outcome. In the present study we investigate stage specific changes in the DNA methylation patterns in order to identify valuable markers to understand how these changes affect breast cancer progression. Quantitative DNA methylation analyses of 12 candidate genes ABCB1, BRCCA1, CDKN2A, ESR1, GSTP1, IGF2, MGMT, HMLH1, PPP2R2B, PTEN, RASSF1A and FOXC1 was performed by pyrosequencing a series of 238 breast cancer tissue samples from DCIS to invasive tumors stage I to IV. Significant differences in methylation levels between the DCIS and invasive stage II tumors were observed for six genes RASSF1A, CDKN2A, MGMT, ABCB1, GSTP1 and FOXC1. RASSF1A, ABCB1 and GSTP1 showed significantly higher methylation levels in late stage compared to the early stage breast carcinoma. Z-score analysis revealed significantly lower methylation levels in DCIS and stage I tumors compared with stage II, III and IV tumors. Methylation levels of PTEN, PPP2R2B, FOXC1, ABCB1 and BRCA1 were lower in tumors harboring TP53 mutations then in tumors with wild type TP53. Z-score analysis showed that TP53 mutated tumors had significantly lower overall methylation levels compared to tumors with wild type TP53. Methylation levels of RASSF1A, PPP2R2B, GSTP1 and FOXC1 were higher in ER positive vs. ER negative tumors and methylation levels of PTEN and CDKN2A were higher in HER2 positive vs. HER2 negative tumors. Z-score analysis also showed that HER2 positive tumors had significantly higher z-scores of methylation compared to the HER2 negative tumors. Univariate survival analysis identifies methylation status of PPP2R2B as significant predictor of overall survival and breast cancer specific survival. In the present study we report that the level of aberrant DNA methylation is higher in late stage compared with early stage of invasive breast cancers and DCIS for genes mentioned above

Harsh corporal punishment is associated with increased T2 relaxation time in dopamine-rich regions.

Science.gov (United States)

Sheu, Yi-Shin; Polcari, Ann; Anderson, Carl M; Teicher, Martin H

2010-11-01

Harsh corporal punishment (HCP) was defined as frequent parental administration of corporal punishment (CP) for discipline, with occasional use of objects such as straps, or paddles. CP is linked to increased risk for depression and substance abuse. We examine whether long-term exposure to HCP acts as sub-traumatic stressor that contributes to brain alterations, particularly in dopaminergic pathways, which may mediate their increased vulnerability to drug and alcohol abuse. Nineteen young adults who experienced early HCP but no other forms of maltreatment and twenty-three comparable controls were studied. T2 relaxation time (T2-RT) measurements were performed with an echo planar imaging TE stepping technique and T2 maps were calculated and analyzed voxel-by-voxel to locate regional T2-RT differences between groups. Previous studies indicated that T2-RT provides an indirect index of resting cerebral blood volume. Region of interest (ROI) analyses were also conducted in caudate, putamen, nucleus accumbens, anterior cingulate cortex, dorsolateral prefrontal cortex, thalamus, globus pallidus and cerebellar hemispheres. Voxel-based relaxometry showed that HCP was associated with increased T2-RT in right caudate and putamen. ROI analyses also revealed increased T2-RT in dorsolateral prefrontal cortex, substantia nigra, thalamus and accumbens but not globus pallidus or cerebellum. There were significant associations between T2-RT measures in dopamine target regions and use of drugs and alcohol, and memory performance. Alteration in the paramagnetic or hemodynamic properties of dopaminergic cell body and projection regions were observed in subjects with HCP, and these findings may relate to their increased risk for drug and alcohol abuse. Copyright 2010 Elsevier Inc. All rights reserved.

Genome-based comparative analyses of Antarctic and temperate species of Paenibacillus.

Directory of Open Access Journals (Sweden)

Melissa Dsouza

Full Text Available Antarctic soils represent a unique environment characterised by extremes of temperature, salinity, elevated UV radiation, low nutrient and low water content. Despite the harshness of this environment, members of 15 bacterial phyla have been identified in soils of the Ross Sea Region (RSR. However, the survival mechanisms and ecological roles of these phyla are largely unknown. The aim of this study was to investigate whether strains of Paenibacillus darwinianus owe their resilience to substantial genomic changes. For this, genome-based comparative analyses were performed on three P. darwinianus strains, isolated from gamma-irradiated RSR soils, together with nine temperate, soil-dwelling Paenibacillus spp. The genome of each strain was sequenced to over 1,000-fold coverage, then assembled into contigs totalling approximately 3 Mbp per genome. Based on the occurrence of essential, single-copy genes, genome completeness was estimated at approximately 88%. Genome analysis revealed between 3,043-3,091 protein-coding sequences (CDSs, primarily associated with two-component systems, sigma factors, transporters, sporulation and genes induced by cold-shock, oxidative and osmotic stresses. These comparative analyses provide an insight into the metabolic potential of P. darwinianus, revealing potential adaptive mechanisms for survival in Antarctic soils. However, a large proportion of these mechanisms were also identified in temperate Paenibacillus spp., suggesting that these mechanisms are beneficial for growth and survival in a range of soil environments. These analyses have also revealed that the P. darwinianus genomes contain significantly fewer CDSs and have a lower paralogous content. Notwithstanding the incompleteness of the assemblies, the large differences in genome sizes, determined by the number of genes in paralogous clusters and the CDS content, are indicative of genome content scaling. Finally, these sequences are a resource for further

Molecular analyses reveal two geographic and genetic lineages for tapeworms, Taenia solium and Taenia saginata, from Ecuador using mitochondrial DNA.

Science.gov (United States)

Solano, Danilo; Navarro, Juan Carlos; León-Reyes, Antonio; Benítez-Ortiz, Washington; Rodríguez-Hidalgo, Richar

2016-12-01

Tapeworms Taenia solium and Taenia saginata are the causative agents of taeniasis/cysticercosis. These are diseases with high medical and veterinary importance due to their impact on public health and rural economy in tropical countries. The re-emergence of T. solium as a result of human migration, the economic burden affecting livestock industry, and the large variability of symptoms in several human cysticercosis, encourage studies on genetic diversity, and the identification of these parasites with molecular phylogenetic tools. Samples collected from the Ecuadorian provinces: Loja, Guayas, Manabí, Tungurahua (South), and Imbabura, Pichincha (North) from 2000 to 2012 were performed under Maximum Parsimony analyses and haplotype networks using partial sequences of mitochondrial DNA, cytochrome oxidase subunit I (COI) and NADH subunit I (NDI), from Genbank and own sequences of Taenia solium and Taenia saginata from Ecuador. Both species have shown reciprocal monophyly, which confirms its molecular taxonomic identity. The COI and NDI genes results suggest phylogenetic structure for both parasite species from south and north of Ecuador. In T. solium, both genes gene revealed greater geographic structure, whereas in T. saginata, the variability for both genes was low. In conclusion, COI haplotype networks of T. solium suggest two geographical events in the introduction of this species in Ecuador (African and Asian lineages) and occurring sympatric, probably through the most common routes of maritime trade between the XV-XIX centuries. Moreover, the evidence of two NDI geographical lineages in T. solium from the north (province of Imbabura) and the south (province of Loja) of Ecuador derivate from a common Indian ancestor open new approaches for studies on genetic populations and eco-epidemiology. Copyright © 2016 Elsevier Inc. All rights reserved.

Proteomic analyses reveal the key roles of BrlA and AbaA in biogenesis of gliotoxin in Aspergillus fumigatus

Energy Technology Data Exchange (ETDEWEB)

Shin, Kwang-Soo, E-mail: shinks@dju.kr [Division of Life Science, Daejeon University, Daejeon, 300-716 (Korea, Republic of); Kim, Young Hwan [Biomedical Omics Team, Korea Basic Science Institute (KBSI), Ohcang, 368-883 (Korea, Republic of); Graduate School of Analytical Science and Technology, Chungnam National University, Daejeon, 305-764 (Korea, Republic of); Department of Bio-Analytical Science, University of Science and Technology, Daejeon, 305-333 (Korea, Republic of); Yu, Jae-Hyuk, E-mail: jyu1@wisc.edu [Departments of Bacteriology and Genetics, The University of Wisconsin–Madison, Madison, WI, 53706 (United States)

2015-07-31

The opportunistic human pathogenic fungus Aspergillus fumigatus primarily reproduces by forming a large number of asexual spores (conidia). Sequential activation of the central regulators BrlA, AbaA and WetA is necessary for the fungus to undergo asexual development. In this study, to address the presumed roles of these key developmental regulators during proliferation of the fungus, we analyzed and compared the proteomes of vegetative cells of wild type (WT) and individual mutant strains. Approximately 1300 protein spots were detectable from 2-D electrophoresis gels. Among these, 13 proteins exhibiting significantly altered accumulation levels were further identified by ESI-MS/MS. Markedly, we found that the GliM and GliT proteins associated with gliotoxin (GT) biosynthesis and self-protection of the fungus from GT were significantly down-regulated in the ΔabaA and ΔbrlA mutants. Moreover, mRNA levels of other GT biosynthetic genes including gliM, gliP, gliT, and gliZ were significantly reduced in both mutant strains, and no and low levels of GT were detectable in the ΔbrlA and ΔabaA mutant strains, respectively. As GliT is required for the protection of the fungus from GT, growth of the ΔbrlA mutant with reduced levels of GliT was severely impaired by exogenous GT. Our studies demonstrate that AbaA and BrlA positively regulate expression of the GT biosynthetic gene cluster in actively growing vegetative cells, and likely bridge morphological and chemical development during the life-cycle of A. fumigatus. - Highlights: • Proteome analyses of WT and mutants reveal 13 differentially expressed proteins. • The GliT and GliM proteins are significantly down-regulated by ΔabaA and ΔbrlA. • Expression of other gliotoxin biosynthetic genes is lowered by ΔabaA and ΔbrlA. • Growth of ΔbrlA strain lacking GliT is completely inhibited by exogenous gliotoxin. • BrlA and AbaA play key roles in biogenesis of gliotoxin in Aspergillus fumigatus.

Proteomic analyses reveal the key roles of BrlA and AbaA in biogenesis of gliotoxin in Aspergillus fumigatus

International Nuclear Information System (INIS)

Shin, Kwang-Soo; Kim, Young Hwan; Yu, Jae-Hyuk

2015-01-01

The opportunistic human pathogenic fungus Aspergillus fumigatus primarily reproduces by forming a large number of asexual spores (conidia). Sequential activation of the central regulators BrlA, AbaA and WetA is necessary for the fungus to undergo asexual development. In this study, to address the presumed roles of these key developmental regulators during proliferation of the fungus, we analyzed and compared the proteomes of vegetative cells of wild type (WT) and individual mutant strains. Approximately 1300 protein spots were detectable from 2-D electrophoresis gels. Among these, 13 proteins exhibiting significantly altered accumulation levels were further identified by ESI-MS/MS. Markedly, we found that the GliM and GliT proteins associated with gliotoxin (GT) biosynthesis and self-protection of the fungus from GT were significantly down-regulated in the ΔabaA and ΔbrlA mutants. Moreover, mRNA levels of other GT biosynthetic genes including gliM, gliP, gliT, and gliZ were significantly reduced in both mutant strains, and no and low levels of GT were detectable in the ΔbrlA and ΔabaA mutant strains, respectively. As GliT is required for the protection of the fungus from GT, growth of the ΔbrlA mutant with reduced levels of GliT was severely impaired by exogenous GT. Our studies demonstrate that AbaA and BrlA positively regulate expression of the GT biosynthetic gene cluster in actively growing vegetative cells, and likely bridge morphological and chemical development during the life-cycle of A. fumigatus. - Highlights: • Proteome analyses of WT and mutants reveal 13 differentially expressed proteins. • The GliT and GliM proteins are significantly down-regulated by ΔabaA and ΔbrlA. • Expression of other gliotoxin biosynthetic genes is lowered by ΔabaA and ΔbrlA. • Growth of ΔbrlA strain lacking GliT is completely inhibited by exogenous gliotoxin. • BrlA and AbaA play key roles in biogenesis of gliotoxin in Aspergillus fumigatus

Serial MR Spectroscopy Reveals a Direct Metabolic Effect of Cediranib in Glioblastoma

Science.gov (United States)

Kim, Heisoog; Catana, Ciprian; Ratai, Eva-Maria; Andronesi, Ovidiu C.; Jennings, D.; Batchelor, Tracy T.; Jain, Rakesh K.; Sorensen, A. Gregory

2011-01-01

Proton magnetic resonance spectroscopy (1H-MRS) is increasingly used in clinical studies of brain tumor to provide information about tissue metabolic profiles. In this study, we evaluated changes in the levels of metabolites predominant in recurrent glioblastoma (rGBM), to characterize the response of rGBM to anti-angiogenic therapy. We examined thirty-one rGBM patients treated with daily doses of cediranib, acquiring serial chemical shift imaging data at specific time points during the treatment regimen. We defined spectra from three regions of interest (ROIs)—enhancing tumor (ET), peritumoral tissue (PT), and normal tissue on the contralateral side (cNT)—in post-contrast T1-weighted images, and normalized the concentrations of N-acetylaspartate (NAA) and choline (Cho) in each ROI to the concentration of creatine in cNT (norCre). We analyzed the ratios of these normalized metabolites (i.e., NAA/Cho, NAA/norCre, and Cho/norCre) by averaging all patients and categorizing two different survival groups. Relative to pre-treatment values, NAA/Cho in ET was unchanged through day 28. However, after day 28, NAA/Cho significantly increased in relation to a significant increase in NAA/norCre and a decrease in Cho/norCre; interestingly, the observed trend was reversed after day 56, consistent with the clinical course of GBM recurrence. Notably, ROC analysis indicated that NAA/Cho in tumor shows a high prediction to 6-month overall survival. These metabolic changes in these rGBM patients strongly suggest a direct metabolic effect of cediranib, and might also reflect an anti-tumor response to anti-angiogenic treatment during the first two months of treatment. Further study is needed to confirm these findings. PMID:21507932

Diplomatie de Léopold II face aux puissances coloniales en Afrique. Contribution à l'histoire diplomatique du Congo

OpenAIRE

Baenda Fimbo, Zacharie

2011-01-01

Cet article essaie d'analyser les stratégies diplomatiques du roi Léopold II face aux grandes puissances de l'époque lors du partage du continent africains. Ces stratégies lui ont permis de gagner la Congo au centre de l'Afrique. Peer reviewed

Whole Genome Analyses of a Well-Differentiated Liposarcoma Reveals Novel SYT1 and DDR2 Rearrangements

Science.gov (United States)

Egan, Jan B.; Barrett, Michael T.; Champion, Mia D.; Middha, Sumit; Lenkiewicz, Elizabeth; Evers, Lisa; Francis, Princy; Schmidt, Jessica; Shi, Chang-Xin; Van Wier, Scott; Badar, Sandra; Ahmann, Gregory; Kortuem, K. Martin; Boczek, Nicole J.; Fonseca, Rafael; Craig, David W.; Carpten, John D.; Borad, Mitesh J.; Stewart, A. Keith

2014-01-01

Liposarcoma is the most common soft tissue sarcoma, but little is known about the genomic basis of this disease. Given the low cell content of this tumor type, we utilized flow cytometry to isolate the diploid normal and aneuploid tumor populations from a well-differentiated liposarcoma prior to array comparative genomic hybridization and whole genome sequencing. This work revealed massive highly focal amplifications throughout the aneuploid tumor genome including MDM2, a gene that has previously been found to be amplified in well-differentiated liposarcoma. Structural analysis revealed massive rearrangement of chromosome 12 and 11 gene fusions, some of which may be part of double minute chromosomes commonly present in well-differentiated liposarcoma. We identified a hotspot of genomic instability localized to a region of chromosome 12 that includes a highly conserved, putative L1 retrotransposon element, LOC100507498 which resides within a gene cluster (NAV3, SYT1, PAWR) where 6 of the 11 fusion events occurred. Interestingly, a potential gene fusion was also identified in amplified DDR2, which is a potential therapeutic target of kinase inhibitors such as dastinib, that are not routinely used in the treatment of patients with liposarcoma. Furthermore, 7 somatic, damaging single nucleotide variants have also been identified, including D125N in the PTPRQ protein. In conclusion, this work is the first to report the entire genome of a well-differentiated liposarcoma with novel chromosomal rearrangements associated with amplification of therapeutically targetable genes such as MDM2 and DDR2. PMID:24505276

Whole genome analyses of a well-differentiated liposarcoma reveals novel SYT1 and DDR2 rearrangements.

Directory of Open Access Journals (Sweden)

Jan B Egan

Full Text Available Liposarcoma is the most common soft tissue sarcoma, but little is known about the genomic basis of this disease. Given the low cell content of this tumor type, we utilized flow cytometry to isolate the diploid normal and aneuploid tumor populations from a well-differentiated liposarcoma prior to array comparative genomic hybridization and whole genome sequencing. This work revealed massive highly focal amplifications throughout the aneuploid tumor genome including MDM2, a gene that has previously been found to be amplified in well-differentiated liposarcoma. Structural analysis revealed massive rearrangement of chromosome 12 and 11 gene fusions, some of which may be part of double minute chromosomes commonly present in well-differentiated liposarcoma. We identified a hotspot of genomic instability localized to a region of chromosome 12 that includes a highly conserved, putative L1 retrotransposon element, LOC100507498 which resides within a gene cluster (NAV3, SYT1, PAWR where 6 of the 11 fusion events occurred. Interestingly, a potential gene fusion was also identified in amplified DDR2, which is a potential therapeutic target of kinase inhibitors such as dastinib, that are not routinely used in the treatment of patients with liposarcoma. Furthermore, 7 somatic, damaging single nucleotide variants have also been identified, including D125N in the PTPRQ protein. In conclusion, this work is the first to report the entire genome of a well-differentiated liposarcoma with novel chromosomal rearrangements associated with amplification of therapeutically targetable genes such as MDM2 and DDR2.

Diffusion weighted imaging for differentiating benign from malignant orbital tumors: Diagnostic performance of the apparent diffusion coefficient based on region of interest selection method

Energy Technology Data Exchange (ETDEWEB)

Xu, Xiao Quan; Hu, Hao Hu; Su, Guo Yi; Liu, Hu; Shi, Hai Bin; Wu, Fei Yun [First Affiliated Hospital of Nanjing Medical University, Nanjing (China)

2016-09-15

To evaluate the differences in the apparent diffusion coefficient (ADC) measurements based on three different region of interest (ROI) selection methods, and compare their diagnostic performance in differentiating benign from malignant orbital tumors. Diffusion-weighted imaging data of sixty-four patients with orbital tumors (33 benign and 31 malignant) were retrospectively analyzed. Two readers independently measured the ADC values using three different ROIs selection methods including whole-tumor (WT), single-slice (SS), and reader-defined small sample (RDSS). The differences of ADC values (ADC-ROI{sub WT}, ADC-ROI{sub SS}, and ADC-ROI{sub RDSS}) between benign and malignant group were compared using unpaired t test. Receiver operating characteristic curve was used to determine and compare their diagnostic ability. The ADC measurement time was compared using ANOVA analysis and the measurement reproducibility was assessed using Bland-Altman method and intra-class correlation coefficient (ICC). Malignant group showed significantly lower ADC-ROI{sub WT}, ADC-ROI{sub SS}, and ADC-ROI{sub RDSS} than benign group (all p < 0.05). The areas under the curve showed no significant difference when using ADC-ROI{sub WT}, ADC-ROI{sub SS}, and ADC-ROI{sub RDSS} as differentiating index, respectively (all p > 0.05). The ROI{sub SS} and ROI{sub RDSS} required comparable measurement time (p > 0.05), while significantly shorter than ROI{sub WT} (p < 0.05). The ROI{sub SS} showed the best reproducibility (mean difference ± limits of agreement between two readers were 0.022 [-0.080–0.123] × 10{sup -3} mm{sup 2}/s; ICC, 0.997) among three ROI method. Apparent diffusion coefficient values based on the three different ROI selection methods can help to differentiate benign from malignant orbital tumors. The results of measurement time, reproducibility and diagnostic ability suggest that the ROI{sub SS} method are potentially useful for clinical practice.

Structural Analyses of Avocado sunblotch viroid Reveal Differences in the Folding of Plus and Minus RNA Strands

Directory of Open Access Journals (Sweden)

Clémentine Delan-Forino

2014-01-01

Full Text Available Viroids are small pathogenic circular single-stranded RNAs, present in two complementary sequences, named plus and minus, in infected plant cells. A high degree of complementarities between different regions of the RNAs allows them to adopt complex structures. Since viroids are naked non-coding RNAs, interactions with host factors appear to be closely related to their structural and catalytic characteristics. Avocado sunblotch viroid (ASBVd, a member of the family Avsunviroidae, replicates via a symmetric RNA-dependant rolling-circle process, involving self-cleavage via hammerhead ribozymes. Consequently, it is assumed that ASBVd plus and minus strands adopt similar structures. Moreover, by computer analyses, a quasi-rod-like secondary structure has been predicted. Nevertheless, secondary and tertiary structures of both polarities of ASBVd remain unsolved. In this study, we analyzed the characteristic of each strand of ASBVd through biophysical analyses. We report that ASBVd transcripts of plus and minus polarities exhibit differences in electrophoretic mobility under native conditions and in thermal denaturation profiles. Subsequently, the secondary structures of plus and minus polarities of ASBVd were probed using the RNA-selective 2'-hydroxyl acylation analyzed by primer extension (SHAPE method. The models obtained show that both polarities fold into different structures. Moreover, our results suggest the existence of a kissing-loop interaction within the minus strand that may play a role in in vivo viroid life cycle.

Self-disclosure on Facebook: How much do we really reveal?

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Stephanie Day

Full Text Available This paper investigates the use of the social networking site Facebook to self-disclose and analyses the responses of a small group of Facebook users surveyed about their own willingness to self-disclose. An online survey was used to ask Facebook users about their level of Facebook use, what types of personal information they are willing to reveal and the frequency of these personal revelations. The survey also asked the participants to take a look at their publicly viewable profile and the types of information revealed there. Results indicated that overall, most people tended to be cautious about the types of information they revealed, posted mainly positive statements about themselves and were aware of personal privacy issues.

Groundwater movement on a Low-lying Carbonate Atoll Island and its Response to Climatic and Sea-level Fluctuations: Roi Namur, Republic of the Marshall Islands

Science.gov (United States)

Oberle, F. J.; Swarzenski, P. W.; Storlazzi, C. D.

2017-12-01

Atoll islands, most of which only average 1-2 meters above today's sea level, provide a tremendous natural laboratory in which to study and better understand the intensifying impacts of high rates of sea-level rise on tropical reef-lined islands. These islands are unique and on the frontline of negative societal impacts due to their geologic structure and limited water supply. Groundwater resources on atolls are typically minimal due to the low elevation and small surface area of the islands and are also subject to recurring droughts, and more frequent, storm-driven seawater overwash events. Although groundwater is the principal means of freshwater storage on atoll islands and is a major factor in determining the overall sustainability of island settlements, hydrological data on how an aquifer will response to changes in sea-level rise or storm-driven overwash remain limited. Here we present high-resolution time series hydrogeological and geochemical data from a 16 month study to determine the role of an atoll's carbonate geology, land use, and atmospheric and oceanographic forcing in driving coastal groundwater exchange including submarine groundwater discharge on the island of Roi-Namur on Kwajalein Atoll in the Republic of the Marshall Islands. This information can provide new estimates on the recovery and resilience of coastal groundwater resources on similar islands that are expected to experience climate change-driven perturbations.

Anomalously-dense firn in an ice-shelf channel revealed by wide-angle radar

Science.gov (United States)

Drews, R.; Brown, J.; Matsuoka, K.; Witrant, E.; Philippe, M.; Hubbard, B.; Pattyn, F.

2015-10-01

The thickness of ice shelves, a basic parameter for mass balance estimates, is typically inferred using hydrostatic equilibrium for which knowledge of the depth-averaged density is essential. The densification from snow to ice depends on a number of local factors (e.g. temperature and surface mass balance) causing spatial and temporal variations in density-depth profiles. However, direct measurements of firn density are sparse, requiring substantial logistical effort. Here, we infer density from radio-wave propagation speed using ground-based wide-angle radar datasets (10 MHz) collected at five sites on Roi Baudouin Ice Shelf (RBIS), Dronning Maud Land, Antarctica. Using a novel algorithm including traveltime inversion and raytracing with a prescribed shape of the depth-density relationship, we show that the depth to internal reflectors, the local ice thickness and depth-averaged densities can reliably be reconstructed. For the particular case of an ice-shelf channel, where ice thickness and surface slope change substantially over a few kilometers, the radar data suggests that firn inside the channel is about 5 % denser than outside the channel. Although this density difference is at the detection limit of the radar, it is consistent with a similar density anomaly reconstructed from optical televiewing, which reveals 10 % denser firn inside compared to outside the channel. The denser firn in the ice-shelf channel should be accounted for when using the hydrostatic ice thickness for determining basal melt rates. The radar method presented here is robust and can easily be adapted to different radar frequencies and data-acquisition geometries.

The relationship between default mode network connectivity and social functioning in individuals at familial high-risk for schizophrenia.

Science.gov (United States)

Dodell-Feder, David; Delisi, Lynn E; Hooker, Christine I

2014-06-01

Unaffected first-degree relatives of individuals with schizophrenia (i.e., those at familial high-risk [FHR]), demonstrate social dysfunction qualitatively similar though less severe than that of their affected relatives. These social difficulties may be the consequence of genetically conferred disruption to aspects of the default mode network (DMN), such as the dMPFC subsystem, which overlaps with the network of brain regions recruited during social cognitive processes. In the present study, we investigate this possibility, testing DMN connectivity and its relationship to social functioning in FHR using resting-state fMRI. Twenty FHR individuals and 17 controls underwent fMRI during a resting-state scan. Hypothesis-driven functional connectivity analyses examined ROI-to-ROI correlations between the DMN's hubs, and regions of the dMPFC subsystem and MTL subsystem. Connectivity values were examined in relationship to a measure of social functioning and empathy/perspective-taking. Results demonstrate that FHR exhibit reduced connectivity specifically within the dMPFC subsystem of the DMN. Certain ROI-to-ROI correlations predicted aspects of social functioning and empathy/perspective-taking across all participants. Together, the data indicate that disruption to the dMPFC subsystem of the DMN may be associated with familial risk for schizophrenia, and that these intrinsic connections may carry measurable consequences for social functioning. Copyright © 2014 Elsevier B.V. All rights reserved.

The Role of the Amygdala in Facial Trustworthiness Processing: A Systematic Review and Meta-Analyses of fMRI Studies

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Oliveiros, Bárbara

2016-01-01

Background Faces play a key role in signaling social cues such as signals of trustworthiness. Although several studies identify the amygdala as a core brain region in social cognition, quantitative approaches evaluating its role are scarce. Objectives This review aimed to assess the role of the amygdala in the processing of facial trustworthiness, by analyzing its amplitude BOLD response polarity to untrustworthy versus trustworthy facial signals under fMRI tasks through a Meta-analysis of effect sizes (MA). Activation Likelihood Estimation (ALE) analyses were also conducted. Data sources Articles were retrieved from MEDLINE, ScienceDirect and Web-of-Science in January 2016. Following the PRISMA statement guidelines, a systematic review of original research articles in English language using the search string “(face OR facial) AND (trustworthiness OR trustworthy OR untrustworthy OR trustee) AND fMRI” was conducted. Study selection and data extraction The MA concerned amygdala responses to facial trustworthiness for the contrast Untrustworthy vs. trustworthy faces, and included whole-brain and ROI studies. To prevent potential bias, results were considered even when at the single study level they did not survive correction for multiple comparisons or provided non-significant results. ALE considered whole-brain studies, using the same methodology to prevent bias. A summary of the methodological options (design and analysis) described in the articles was finally used to get further insight into the characteristics of the studies and to perform a subgroup analysis. Data were extracted by two authors and checked independently. Data synthesis Twenty fMRI studies were considered for systematic review. An MA of effect sizes with 11 articles (12 studies) showed high heterogeneity between studies [Q(11) = 265.68, p < .0001; I2 = 95.86%, 94.20% to 97.05%, with 95% confidence interval, CI]. Random effects analysis [RE(183) = 0.851, .422 to .969, 95% CI] supported the

Categorizing words using 'frequent frames': what cross-linguistic analyses reveal about distributional acquisition strategies.

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Chemla, Emmanuel; Mintz, Toben H; Bernal, Savita; Christophe, Anne

2009-04-01

Mintz (2003) described a distributional environment called a frame, defined as the co-occurrence of two context words with one intervening target word. Analyses of English child-directed speech showed that words that fell within any frequently occurring frame consistently belonged to the same grammatical category (e.g. noun, verb, adjective, etc.). In this paper, we first generalize this result to French, a language in which the function word system allows patterns that are potentially detrimental to a frame-based analysis procedure. Second, we show that the discontinuity of the chosen environments (i.e. the fact that target words are framed by the context words) is crucial for the mechanism to be efficient. This property might be relevant for any computational approach to grammatical categorization. Finally, we investigate a recursive application of the procedure and observe that the categorization is paradoxically worse when context elements are categories rather than actual lexical items. Item-specificity is thus also a core computational principle for this type of algorithm. Our analysis, along with results from behavioural studies (Gómez, 2002; Gómez and Maye, 2005; Mintz, 2006), provides strong support for frames as a basis for the acquisition of grammatical categories by infants. Discontinuity and item-specificity appear to be crucial features.

A Surface-based Analysis of Language Lateralization and Cortical Asymmetry

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Greve, Douglas N.; Van der Haegen, Lise; Cai, Qing; Stufflebeam, Steven; Sabuncu, Mert R.; Fischl, Bruce; Bysbaert, Marc

2013-01-01

Among brain functions, language is one of the most lateralized. Cortical language areas are also some of the most asymmetrical in the brain. An open question is whether the asymmetry in function is linked to the asymmetry in anatomy. To address this question, we measured anatomical asymmetry in 34 participants shown with fMRI to have language dominance of the left hemisphere (LLD) and 21 participants shown to have atypical right hemisphere dominance (RLD). All participants were healthy and left-handed, and most (80%) were female. Gray matter (GM) volume asymmetry was measured using an automated surface-based technique in both ROIs and exploratory analyses. In the ROI analysis, a significant difference between LLD and RLD was found in the insula. No differences were found in planum temporale (PT), pars opercularis (POp), pars triangularis (PTr), or Heschl’s gyrus (HG). The PT, POp, insula, and HG were all significantly left lateralized in both LLD and RLD participants. Both the positive and negative ROI findings replicate a previous study using manually labeled ROIs in a different cohort [Keller, S. S., Roberts, N., Garcia-Finana, M., Mohammadi, S., Ringelstein, E. B., Knecht, S., et al. Can the language-dominant hemisphere be predicted by brain anatomy? Journal of Cognitive Neuroscience, 23, 2013–2029, 2011]. The exploratory analysis was accomplished using a new surface-based registration that aligns cortical folding patterns across both subject and hemisphere. A small but significant cluster was found in the superior temporal gyrus that overlapped with the PT. A cluster was also found in the ventral occipitotemporal cortex corresponding to the visual word recognition area. The surface-based analysis also makes it possible to disentangle the effects of GM volume, thickness, and surface area while removing the effects of curvature. For both the ROI and exploratory analyses, the difference between LLD and RLD volume laterality was most strongly driven by

Transcriptome-wide analyses indicate mitochondrial responses to particulate air pollution exposure

DEFF Research Database (Denmark)

Winckelmans, Ellen; Nawrot, Tim S.; Tsamou, Maria

2017-01-01

validation cohort (n = 169, 55.6% women). Results: Overrepresentation analyses revealed significant pathways (p-value transport chain (ETC) for medium-term exposure in women. For men, medium-term PM10....... Conclusions: In this exploratory study, we identified mitochondrial genes and pathways associated with particulate air pollution indicating upregulation of energy producing pathways as a potential mechanism to compensate for PM-induced mitochondrial damage....

Pancreatic Adenocarcinoma Therapeutic Targets Revealed by Tumor-Stroma Cross-Talk Analyses in Patient-Derived Xenografts

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Rémy Nicolle

2017-11-01

Full Text Available Preclinical models based on patient-derived xenografts have remarkable specificity in distinguishing transformed human tumor cells from non-transformed murine stromal cells computationally. We obtained 29 pancreatic ductal adenocarcinoma (PDAC xenografts from either resectable or non-resectable patients (surgery and endoscopic ultrasound-guided fine-needle aspirate, respectively. Extensive multiomic profiling revealed two subtypes with distinct clinical outcomes. These subtypes uncovered specific alterations in DNA methylation and transcription as well as in signaling pathways involved in tumor-stromal cross-talk. The analysis of these pathways indicates therapeutic opportunities for targeting both compartments and their interactions. In particular, we show that inhibiting NPC1L1 with Ezetimibe, a clinically available drug, might be an efficient approach for treating pancreatic cancers. These findings uncover the complex and diverse interplay between PDAC tumors and the stroma and demonstrate the pivotal role of xenografts for drug discovery and relevance to PDAC.

Diagnosis of angiomyolipoma using computed tomography-region of interest ≤-10 HU or 4 adjacent pixels ≤-10 HU are recommended as the diagnostic thresholds

International Nuclear Information System (INIS)

Simpson, E.; Patel, U.

2006-01-01

AIM: To study and compare the diagnostic accuracy of region of interest (ROI) density measurement and pixel mapping [computed tomography (CT) density of individual pixels] for the diagnosis of renal angiomyolipoma (AML) using CT. MATERIALS AND METHODS: A study group of histologically proven AMLs was compared with a control group of histologically proven renal cell cancers, normal renal parenchyma, and simple renal cysts. The mean tissue density (ROI circle) and a pixel density map were recorded. The diagnostic accuracy of various thresholds of ROI and pixel mapping values were compared using receiver operating characteristic curves. RESULTS: Twenty-two AMLs, 16 renal cell carcinomas (RCCs), 30 simple cysts, and 30 sites of renal parenchyma were evaluated. The mean (±1 SD) density of the AMLs was significantly lower [-15.2(20.8) units] than the three control groups [+36.0(8.1) units, +5.4(3.4) units and +22.2(46.5) units for RCC, renal cyst and parenchyma respectively; p<0.001 (analysis of variance)]. The sensitivities and specificities of the ROI diagnostic thresholds of ≤0 units, ≤-10 units and ≤-20 units were 77 and 97%, 73 and 100% and 50 and 100%, respectively. Using pixel mapping [diagnostic thresholds of either a line of 4 pixels ≤-10 units or a square of 4 pixels ≤-10 units] the sensitivity improves to 86% with a specificity of 97%. CONCLUSION: Although a ROI threshold value of ≤-10 units has a very high specificity (100% in the present study) the sensitivity is modest at only 73%. Pixel mapping is more sensitive for recognizing small clusters of fat. In practice, both methods can be recommended for the analysis of suspected AMLs. ROI density measurement is convenient when analysing large areas of suspected fat and ≤-10 units should be used as the diagnostic threshold. When faced with small lucent areas or indeterminate values after ROI analysis, pixel mapping is recommended using a line of 4 pixels ≤-10 units or a square of 4 pixels ≤-10

Genomic and transcriptomic analyses reveal differential regulation of diverse terpenoid and polyketides secondary metabolites in Hericium erinaceus.

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Chen, Juan; Zeng, Xu; Yang, Yan Long; Xing, Yong Mei; Zhang, Qi; Li, Jia Mei; Ma, Ke; Liu, Hong Wei; Guo, Shun Xing

2017-08-31

The lion's mane mushroom Hericium erinaceus is a famous traditional medicinal fungus credited with anti-dementia activity and a producer of cyathane diterpenoid natural products (erinacines) useful against nervous system diseases. To date, few studies have explored the biosynthesis of these compounds, although their chemical synthesis is known. Here, we report the first genome and tanscriptome sequence of the medicinal fungus H. erinaceus. The size of the genome is 39.35 Mb, containing 9895 gene models. The genome of H. erinaceus reveals diverse enzymes and a large family of cytochrome P450 (CYP) proteins involved in the biosynthesis of terpenoid backbones, diterpenoids, sesquiterpenes and polyketides. Three gene clusters related to terpene biosynthesis and one gene cluster for polyketides biosynthesis (PKS) were predicted. Genes involved in terpenoid biosynthesis were generally upregulated in mycelia, while the PKS gene was upregulated in the fruiting body. Comparative genome analysis of 42 fungal species of Basidiomycota revealed that most edible and medicinal mushroom show many more gene clusters involved in terpenoid and polyketide biosynthesis compared to the pathogenic fungi. None of the gene clusters for terpenoid or polyketide biosynthesis were predicted in the poisonous mushroom Amanita muscaria. Our findings may facilitate future discovery and biosynthesis of bioactive secondary metabolites from H. erinaceus and provide fundamental information for exploring the secondary metabolites in other Basidiomycetes.

Differential co-expression and regulation analyses reveal different mechanisms underlying major depressive disorder and subsyndromal symptomatic depression.

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Xu, Fan; Yang, Jing; Chen, Jin; Wu, Qingyuan; Gong, Wei; Zhang, Jianguo; Shao, Weihua; Mu, Jun; Yang, Deyu; Yang, Yongtao; Li, Zhiwei; Xie, Peng

2015-04-03

Recent depression research has revealed a growing awareness of how to best classify depression into depressive subtypes. Appropriately subtyping depression can lead to identification of subtypes that are more responsive to current pharmacological treatment and aid in separating out depressed patients in which current antidepressants are not particularly effective. Differential co-expression analysis (DCEA) and differential regulation analysis (DRA) were applied to compare the transcriptomic profiles of peripheral blood lymphocytes from patients with two depressive subtypes: major depressive disorder (MDD) and subsyndromal symptomatic depression (SSD). Six differentially regulated genes (DRGs) (FOSL1, SRF, JUN, TFAP4, SOX9, and HLF) and 16 transcription factor-to-target differentially co-expressed gene links or pairs (TF2target DCLs) appear to be the key differential factors in MDD; in contrast, one DRG (PATZ1) and eight TF2target DCLs appear to be the key differential factors in SSD. There was no overlap between the MDD target genes and SSD target genes. Venlafaxine (Efexor™, Effexor™) appears to have a significant effect on the gene expression profile of MDD patients but no significant effect on the gene expression profile of SSD patients. DCEA and DRA revealed no apparent similarities between the differential regulatory processes underlying MDD and SSD. This bioinformatic analysis may provide novel insights that can support future antidepressant R&D efforts.

Precision and accuracy in CT attenuation measurement of vascular wall using region-of-interest supported by differentiation curve

International Nuclear Information System (INIS)

Suzuki, Shigeru; Kidouchi, Takashi; Kuwahara, Sadatoshi; Vembar, Mani; Takei, Ryoji; Yamamoto, Asako

2012-01-01

Objectives: To evaluate the precision and accuracy in CT attenuation measurement of vascular wall using region-of-interest (ROI) supported by differentiation curves. Study design: We used vascular models (actual attenuation value of the wall: 87 HU) with wall thicknesses of 1.5, 1.0, or 0.5 mm, filled with contrast material of 250, 348, or 436 HU. The nine vascular models were scanned with a 64-detector CT. The wall attenuation values were measured using three sizes (diameter: 0.5, 1.0, and 1.5 mm) of ROIs without differentiation curves. Sixteen measurements were repeated for each vascular model by each of two operators. Measurements supported by differentiation curves were also performed. We used analyses of variance with repeated measures for the measured attenuations for each size of the ROI. Results: Without differentiation curves, there were significant differences in the attenuation values of the wall among the three densities of contrast material, and the attenuation values tended to be overestimated more as the contrast material density increased. Operator dependencies were also found in measurements for 0.5- and 1.5-mm thickness models. With differentiation curves, measurements were not possible for 0.5- and 1.0-mm thickness models. Using differentiation curves for 1.5-mm thickness models with a ROI of 1.0- or 1.5-mm diameter, the wall attenuations were not affected by the contrast material densities and were operator independent, measuring between 75 and 103 HU. Conclusions: The use of differentiation curves can improve the precision and accuracy in wall attenuation measurement using a ROI technique, while measurements for walls of ≤1.0 mm thickness are difficult.

Optical coherence tomography to evaluate variance in the extent of carious lesions in depth.

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Park, Kyung-Jin; Schneider, Hartmut; Ziebolz, Dirk; Krause, Felix; Haak, Rainer

2018-05-03

Evaluation of variance in the extent of carious lesions in depth at smooth surfaces within the same ICDAS code group using optical coherence tomography (OCT) in vitro and in vivo. (1) Verification/validation of OCT to assess non-cavitated caries: 13 human molars with ICDAS code 2 at smooth surfaces were imaged using OCT and light microscopy. Regions of interest (ROI) were categorized according to the depth of carious lesions. Agreement between histology and OCT was determined by unweighted Cohen's Kappa and Wilcoxon test. (2) Assessment of 133 smooth surfaces using ICDAS and OCT in vitro, 49 surfaces in vivo. ROI were categorized according to the caries extent (ICDAS: codes 0-4, OCT: scoring based on lesion depth). A frequency distribution of the OCT scores for each ICDAS code was determined. (1) Histology and OCT agreed moderately (κ = 0.54, p ≤ 0.001) with no significant difference between both methods (p = 0.25). The lesions (76.9% (10 of 13)) _were equally scored. (2) In vitro, OCT revealed caries in 42% of ROI clinically assessed as sound. OCT detected dentin-caries in 40% of ROIs visually assessed as enamel-caries. In vivo, large differences between ICDAS and OCT were observed. Carious lesions of ICDAS codes 1 and 2 vary largely in their extent in depth.

Divergent and convergent modes of interaction between wheat and Puccinia graminis f. sp. tritici isolates revealed by the comparative gene co-expression network and genome analyses.

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Rutter, William B; Salcedo, Andres; Akhunova, Alina; He, Fei; Wang, Shichen; Liang, Hanquan; Bowden, Robert L; Akhunov, Eduard

2017-04-12

Two opposing evolutionary constraints exert pressure on plant pathogens: one to diversify virulence factors in order to evade plant defenses, and the other to retain virulence factors critical for maintaining a compatible interaction with the plant host. To better understand how the diversified arsenals of fungal genes promote interaction with the same compatible wheat line, we performed a comparative genomic analysis of two North American isolates of Puccinia graminis f. sp. tritici (Pgt). The patterns of inter-isolate divergence in the secreted candidate effector genes were compared with the levels of conservation and divergence of plant-pathogen gene co-expression networks (GCN) developed for each isolate. Comprative genomic analyses revealed substantial level of interisolate divergence in effector gene complement and sequence divergence. Gene Ontology (GO) analyses of the conserved and unique parts of the isolate-specific GCNs identified a number of conserved host pathways targeted by both isolates. Interestingly, the degree of inter-isolate sub-network conservation varied widely for the different host pathways and was positively associated with the proportion of conserved effector candidates associated with each sub-network. While different Pgt isolates tended to exploit similar wheat pathways for infection, the mode of plant-pathogen interaction varied for different pathways with some pathways being associated with the conserved set of effectors and others being linked with the diverged or isolate-specific effectors. Our data suggest that at the intra-species level pathogen populations likely maintain divergent sets of effectors capable of targeting the same plant host pathways. This functional redundancy may play an important role in the dynamic of the "arms-race" between host and pathogen serving as the basis for diverse virulence strategies and creating conditions where mutations in certain effector groups will not have a major effect on the pathogen

Analysing public relations education through international standards: The Portuguese case

OpenAIRE

Gonçalves, Gisela Marques Pereira; Spínola, Susana de Carvalho; Padamo, Celma

2013-01-01

By using international reports on PR education as a benchmark we analyse the status of PR higher education in Portugal. Despite differences among the study programs, the findings reveal that the standard five courses recommendation by the Commission on Public Relations Education (CPRE) are a part of Portuguese undergraduate curriculum. This includes 12 of the 14 content field guidelines needed to achieve the ideal master's program. Data shows, however, the difficulty of positioning public rel...

Ultrastructural and Molecular Analyses Reveal Enhanced Nucleolar Activity in Medicago truncatula Cells Overexpressing the MtTdp2α Gene

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Macovei, Anca; Faè, Matteo; Biggiogera, Marco; de Sousa Araújo, Susana; Carbonera, Daniela; Balestrazzi, Alma

2018-01-01

The role of tyrosyl-DNA phosphodiesterase 2 (Tdp2) involved in the repair of 5′-end-blocking DNA lesions is still poorly explored in plants. To gain novel insights, Medicago truncatula suspension cultures overexpressing the MtTdp2α gene (Tdp2α-13C and Tdp2α-28 lines, respectively) and a control (CTRL) line carrying the empty vector were investigated. Transmission electron microscopy (TEM) revealed enlarged nucleoli (up to 44% expansion of the area, compared to CTRL), the presence of nucleolar vacuoles, increased frequency of multinucleolate cells (up to 4.3-fold compared to CTRL) and reduced number of ring-shaped nucleoli in Tdp2α-13C and Tdp2α-28 lines. Ultrastructural data suggesting for enhanced nucleolar activity in MtTdp2α-overexpressing lines were integrated with results from bromouridine incorporation. The latter revealed an increase of labeled transcripts in both Tdp2α-13C and Tdp2α-28 cells, within the nucleolus and in the extra-nucleolar region. MtTdp2α-overexpressing cells showed tolerance to etoposide, a selective inhibitor of DNA topoisomerase II, as evidenced by DNA diffusion assay. TEM analysis revealed etoposide-induced rearrangements within the nucleolus, resembling the nucleolar caps observed in animal cells under transcription impairment. Based on these findings it is evident that MtTdp2α-overexpression enhances nucleolar activity in plant cells. PMID:29868059

Ultrastructural and Molecular Analyses Reveal Enhanced Nucleolar Activity in Medicago truncatula Cells Overexpressing the MtTdp2α Gene

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Anca Macovei

2018-05-01

Full Text Available The role of tyrosyl-DNA phosphodiesterase 2 (Tdp2 involved in the repair of 5′-end-blocking DNA lesions is still poorly explored in plants. To gain novel insights, Medicago truncatula suspension cultures overexpressing the MtTdp2α gene (Tdp2α-13C and Tdp2α-28 lines, respectively and a control (CTRL line carrying the empty vector were investigated. Transmission electron microscopy (TEM revealed enlarged nucleoli (up to 44% expansion of the area, compared to CTRL, the presence of nucleolar vacuoles, increased frequency of multinucleolate cells (up to 4.3-fold compared to CTRL and reduced number of ring-shaped nucleoli in Tdp2α-13C and Tdp2α-28 lines. Ultrastructural data suggesting for enhanced nucleolar activity in MtTdp2α-overexpressing lines were integrated with results from bromouridine incorporation. The latter revealed an increase of labeled transcripts in both Tdp2α-13C and Tdp2α-28 cells, within the nucleolus and in the extra-nucleolar region. MtTdp2α-overexpressing cells showed tolerance to etoposide, a selective inhibitor of DNA topoisomerase II, as evidenced by DNA diffusion assay. TEM analysis revealed etoposide-induced rearrangements within the nucleolus, resembling the nucleolar caps observed in animal cells under transcription impairment. Based on these findings it is evident that MtTdp2α-overexpression enhances nucleolar activity in plant cells.

Evaluation of Deformable Image Coregistration in Adaptive Dose Painting by Numbers for Head-and-Neck Cancer

Energy Technology Data Exchange (ETDEWEB)

Olteanu, Luiza A.M., E-mail: AnaMariaLuiza.Olteanu@uzgent.be [Department of Radiotherapy, Ghent University Hospital, De Pintelaan, Ghent (Belgium); Madani, Indira; De Neve, Wilfried; Vercauteren, Tom; De Gersem, Werner [Department of Radiotherapy, Ghent University Hospital, De Pintelaan, Ghent (Belgium)

2012-06-01

Purpose: To assess the accuracy of contour deformation and feasibility of dose summation applying deformable image coregistration in adaptive dose painting by numbers (DPBN) for head and neck cancer. Methods and Materials: Data of 12 head-and-neck-cancer patients treated within a Phase I trial on adaptive {sup 18}F-FDG positron emission tomography (PET)-guided DPBN were used. Each patient had two DPBN treatment plans: the initial plan was based on a pretreatment PET/CT scan; the second adapted plan was based on a PET/CT scan acquired after 8 fractions. The median prescription dose to the dose-painted volume was 30 Gy for both DPBN plans. To obtain deformed contours and dose distributions, pretreatment CT was deformed to per-treatment CT using deformable image coregistration. Deformed contours of regions of interest (ROI{sub def}) were visually inspected and, if necessary, adjusted (ROI{sub def{sub ad}}) and both compared with manually redrawn ROIs (ROI{sub m}) using Jaccard (JI) and overlap indices (OI). Dose summation was done on the ROI{sub m}, ROI{sub def{sub ad}}, or their unions with the ROI{sub def}. Results: Almost all deformed ROIs were adjusted. The largest adjustment was made in patients with substantially regressing tumors: ROI{sub def} = 11.8 {+-} 10.9 cm{sup 3} vs. ROI{sub def{sub ad}} = 5.9 {+-} 7.8 cm{sup 3} vs. ROI{sub m} = 7.7 {+-} 7.2 cm{sup 3} (p = 0.57). The swallowing structures were the most frequently adjusted ROIs with the lowest indices for the upper esophageal sphincter: JI = 0.3 (ROI{sub def}) and 0.4 (ROI{sub def{sub ad}}); OI = 0.5 (both ROIs). The mandible needed the least adjustment with the highest indices: JI = 0.8 (both ROIs), OI = 0.9 (ROI{sub def}), and 1.0 (ROI{sub def{sub ad}}). Summed doses differed non-significantly. There was a trend of higher doses in the targets and lower doses in the spinal cord when doses were summed on unions. Conclusion: Visual inspection and adjustment were necessary for most ROIs. Fast automatic ROI

Evolutionary trajectories of snake genes and genomes revealed by comparative analyses of five-pacer viper

Science.gov (United States)

Yin, Wei; Wang, Zong-ji; Li, Qi-ye; Lian, Jin-ming; Zhou, Yang; Lu, Bing-zheng; Jin, Li-jun; Qiu, Peng-xin; Zhang, Pei; Zhu, Wen-bo; Wen, Bo; Huang, Yi-jun; Lin, Zhi-long; Qiu, Bi-tao; Su, Xing-wen; Yang, Huan-ming; Zhang, Guo-jie; Yan, Guang-mei; Zhou, Qi

2016-01-01

Snakes have numerous features distinctive from other tetrapods and a rich history of genome evolution that is still obscure. Here, we report the high-quality genome of the five-pacer viper, Deinagkistrodon acutus, and comparative analyses with other representative snake and lizard genomes. We map the evolutionary trajectories of transposable elements (TEs), developmental genes and sex chromosomes onto the snake phylogeny. TEs exhibit dynamic lineage-specific expansion, and many viper TEs show brain-specific gene expression along with their nearby genes. We detect signatures of adaptive evolution in olfactory, venom and thermal-sensing genes and also functional degeneration of genes associated with vision and hearing. Lineage-specific relaxation of functional constraints on respective Hox and Tbx limb-patterning genes supports fossil evidence for a successive loss of forelimbs then hindlimbs during snake evolution. Finally, we infer that the ZW sex chromosome pair had undergone at least three recombination suppression events in the ancestor of advanced snakes. These results altogether forge a framework for our deep understanding into snakes' history of molecular evolution. PMID:27708285

Dynamic regulation of GDP binding to G proteins revealed by magnetic field-dependent NMR relaxation analyses.

Science.gov (United States)

Toyama, Yuki; Kano, Hanaho; Mase, Yoko; Yokogawa, Mariko; Osawa, Masanori; Shimada, Ichio

2017-02-22

Heterotrimeric guanine-nucleotide-binding proteins (G proteins) serve as molecular switches in signalling pathways, by coupling the activation of cell surface receptors to intracellular responses. Mutations in the G protein α-subunit (Gα) that accelerate guanosine diphosphate (GDP) dissociation cause hyperactivation of the downstream effector proteins, leading to oncogenesis. However, the structural mechanism of the accelerated GDP dissociation has remained unclear. Here, we use magnetic field-dependent nuclear magnetic resonance relaxation analyses to investigate the structural and dynamic properties of GDP bound Gα on a microsecond timescale. We show that Gα rapidly exchanges between a ground-state conformation, which tightly binds to GDP and an excited conformation with reduced GDP affinity. The oncogenic D150N mutation accelerates GDP dissociation by shifting the equilibrium towards the excited conformation.

Divergent Significance of Bone Mineral Density Changes in Aging Depending on Sites and Sex Revealed through Separate Analyses of Bone Mineral Content and Area

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Yasumoto Matsui

2012-01-01

Full Text Available Bone mineral density (aBMD is equivalent to bone mineral content (BMC divided by area. We rechecked the significance of aBMD changes in aging by examining BMC and area separately. Subjects were 1167 community-dwelling Japanese men and women, aged 40–79 years. ABMDs of femoral neck and lumbar spine were assessed by DXA twice, at 6-year intervals. The change rates of BMC and area, as well as aBMD, were calculated and described separately by the age stratum and by sex. In the femoral neck region, aBMDs were significantly decreased in all age strata by an increase in area as well as BMC loss in the same pattern in both sexes. In the lumbar spine region, aBMDs decreased until the age of 60 in women, caused by the significant BMC decrease accompanying the small area change. Very differently in men, aBMDs increased after their 50s due to BMC increase, accompanied by an area increase. Separate analyses of BMC and area change revealed that the significance of aBMD changes in aging was very divergent among sites and between sexes. This may explain in part the dissociation of aBMD change and bone strength, suggesting that we should be more cautious when interpreting the meaning of aBMD change.

Analysing the Improper Pronunciation of Diphthongs by Iraqi EFL learners

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Mukhalad Malik Almutalabi

2018-04-01

Full Text Available The current study aims at analysing the improper pronunciation of Iraqi EFL learners concerning the pronunciation of diphthongs in words of various syllables. It describes and identifies thoroughly the mispronunciations of such important sounds in English language. The study attempts at analysing such mispronunciations by clarifying and assigning the phonetic deviations of Iraqi EFL learners when they pronounce diphthongs. So the main objective of the study is to analyse the errors committed by Iraqi learners in the pronunciation of diphthongs grouping each error into its specific category. To verify the objective of the paper, 25 Iraqi EFL learners from the department of English at Cihan University/ Slemani are chosen to be the main participants of the study. The test which was conducted in the laboratory of the Department of English contained 10 words comprising various diphthongs. The results clearly revealed that mispronouncing English diphthongs by Iraqi EFL were mostly observed by replacing the required diphthong with another improper one and they also tended to use simple vowels instead of the correct required diphthongs.

Financial relationships in economic analyses of targeted therapies in oncology.

Science.gov (United States)

Valachis, Antonis; Polyzos, Nikolaos P; Nearchou, Andreas; Lind, Pehr; Mauri, Davide

2012-04-20

A potential financial relationship between investigators and pharmaceutical manufacturers has been associated with an increased likelihood of reporting favorable conclusions about a sponsor's proprietary agent in pharmacoeconomic studies. The purpose of this study is to investigate whether there is an association between financial relationships and outcome in economic analyses of new targeted therapies in oncology. We searched PubMed (last update June 2011) for economic analyses of targeted therapies (including monoclonal antibodies, tyrosine-kinase inhibitors, and mammalian target of rapamycin inhibitors) in oncology. The trials were qualitatively rated regarding the cost assessment as favorable, neutral, or unfavorable on the basis of prespecified criteria. Overall, 81 eligible studies were identified. Economic analyses that were funded by pharmaceutical companies were more likely to report favorable qualitative cost estimates (28 [82%] of 34 v 21 [45%] of 47; P = .003). The presence of an author affiliated with manufacturer was not associated with study outcome. Furthermore, if only studies including a conflict of interest statement were included (66 of 81), studies that reported any financial relationship with manufacturers (author affiliation and/or funding and/or other financial relationship) were more likely to report favorable results of targeted therapies compared with studies without financial relationship (32 [71%] of 45 v nine [43%] of 21; P = .025). Our study reveals a potential threat for industry-related bias in economic analyses of targeted therapies in oncology in favor of analyses with financial relationships between authors and manufacturers. A more balanced funding of economic analyses from other sources may allow greater confidence in the interpretation of their results.

Floral reversion mechanism in longan (Dimocarpus longan Lour.) revealed by proteomic and anatomic analyses.

Science.gov (United States)

You, Xiangrong; Wang, Lingxia; Liang, Wenyu; Gai, Yonghong; Wang, Xiaoyan; Chen, Wei

2012-02-02

Two-dimensional gel electrophoresis (2-DE) was used to analyze the proteins related to floral reversion in Dimocarpus longan Lour. Proteins were extracted from buds undergoing the normal process of flowering and from those undergoing floral reversion in three developing stages in D. longan. Differentially expressed proteins were identified from the gels after 2-DE analysis, which were confirmed using matrix-assisted laser desorption/ionization-time of flying-mass spectroscopy and protein database search. A total of 39 proteins, including 18 up-regulated and 21 down-regulated proteins, were classified into different categories, such as energy and substance metabolism, protein translation, secondary metabolism, phytohormone, cytoskeleton structure, regulation, and stress tolerance. Among these, the largest functional class was associated with primary metabolism. Down-regulated proteins were involved in photosynthesis, transcription, and translation, whereas up-regulated proteins were involved in respiration. Decreased flavonoid synthesis and up-regulated GA20ox might be involved in the floral reversion process. Up-regulated 14-3-3 proteins played a role in the regulation of floral reversion in D. longan by responding to abiotic stress. Observations via transmission electron microscopy revealed the ultrastructure changes in shedding buds undergoing floral reversion. Overall, the results provided insights into the molecular basis for the floral reversion mechanism in D. longan. Copyright © 2011 Elsevier B.V. All rights reserved.

« Comment se comporter avec un roi chrétien » : l’ouvrage perdu d’Abū l-Ḥasan ʿAlī Ibn al-Qaṭṭān et les enjeux du cérémonial almohade

Directory of Open Access Journals (Sweden)

Mehdi Ghouirgate

2014-05-01

Full Text Available Cet article propose de revenir sur un document aussi exceptionnel que méconnu. Il s’agit du résumé d’un ouvrage (maqāla, aujourd’hui perdu, intitulé « Comment se comporter avec un roi chrétien », et que l’on trouve dans le dictionnaire bio-bibliographique d’Ibn ʿAbd al-Malik. Cette maqāla fut rédigée, par un homme de lettres au service des Almohades, Abū l-Ḥasan ʿAlī Ibn al-Qaṭṭān (m. 1231. C’est la seule source qui ait consigné des indications sur la conduite que devait adopter le souverain lors d’une cérémonie, en présence d’un prince étranger. À ce titre, on y trouve des renseignements essentiels sur le cérémonial almohade ainsi que sur les dilemmes que devaient résoudre le calife : d’un point de vue idéologique, il ne pouvait souffrir aucun autre pouvoir, mais l’impossibilité de mener des opérations d’envergure sur deux fronts à la fois l’amena à composer avec le roi du León. De même, c’est le seul document à avoir fait état d’une divergence de point de vue entre le calife et les intellectuels organiques du système, les Ṭalaba. Ce différend met en lumière des tensions latentes au sommet entre divers serviteurs de l’État, qui n’avaient pas la même forme de légitimité, ni tout à fait les mêmes intérêts.

Seawater-flooding events and impact on freshwater lenses of low-lying islands: Controlling factors, basic management and mitigation

Science.gov (United States)

Gingerich, Stephen B.; Voss, Clifford I.; Johnson, Adam G.

2017-01-01

An unprecedented set of hydrologic observations was collected after the Dec 2008 seawater-flooding event on Roi-Namur, Kwajalein Atoll, Republic of the Marshall Islands. By two days after the seawater flooding that occurred at the beginning of dry season, the observed salinity of water withdrawn by the island’s main skimming well increased to 100% seawater concentration, but by ten days later already decreased to only 10–20% of seawater fraction. However, the damaging impact on the potability of the groundwater supply (when pumped water had concentrations above 1% seawater fraction) lasted 22 months longer. The data collected make possible analyses of the hydrologic factors that control recovery and management of the groundwater-supply quality on Roi-Namur and on similar low-lying islands.With the observed data as a guide, three-dimensional numerical-model simulation analyses reveal how recovery is controlled by the island’s hydrology. These also allow evaluation of the efficacy of basic water-quality management/mitigation alternatives and elucidate how groundwater withdrawal and timing of the seawater-flooding event affect the length of recovery. Simulations show that, as might be expected, by adding surplus captured rainwater as artificial recharge, the freshwater-lens recovery period (after which potable groundwater may again be produced) can be shortened, with groundwater salinity remaining lower even during the dry season, a period during which no artificial recharge is applied. Simulations also show that the recovery period is not lengthened appreciably by groundwater withdrawals during recovery. Simulations further show that had the flooding event occurred at the start of the wet season, the recovery period would have been about 25% (5.5 months) shorter than actually occurred during the monitored flood that occurred at the dry-season start. Finally, analyses show that artificial recharge improves freshwater-lens water quality, making possible longer

Seawater-flooding events and impact on freshwater lenses of low-lying islands: Controlling factors, basic management and mitigation

Science.gov (United States)

Gingerich, Stephen B.; Voss, Clifford I.; Johnson, Adam G.

2017-08-01

An unprecedented set of hydrologic observations was collected after the Dec 2008 seawater-flooding event on Roi-Namur, Kwajalein Atoll, Republic of the Marshall Islands. By two days after the seawater flooding that occurred at the beginning of dry season, the observed salinity of water withdrawn by the island's main skimming well increased to 100% seawater concentration, but by ten days later already decreased to only 10-20% of seawater fraction. However, the damaging impact on the potability of the groundwater supply (when pumped water had concentrations above 1% seawater fraction) lasted 22 months longer. The data collected make possible analyses of the hydrologic factors that control recovery and management of the groundwater-supply quality on Roi-Namur and on similar low-lying islands. With the observed data as a guide, three-dimensional numerical-model simulation analyses reveal how recovery is controlled by the island's hydrology. These also allow evaluation of the efficacy of basic water-quality management/mitigation alternatives and elucidate how groundwater withdrawal and timing of the seawater-flooding event affect the length of recovery. Simulations show that, as might be expected, by adding surplus captured rainwater as artificial recharge, the freshwater-lens recovery period (after which potable groundwater may again be produced) can be shortened, with groundwater salinity remaining lower even during the dry season, a period during which no artificial recharge is applied. Simulations also show that the recovery period is not lengthened appreciably by groundwater withdrawals during recovery. Simulations further show that had the flooding event occurred at the start of the wet season, the recovery period would have been about 25% (5.5 months) shorter than actually occurred during the monitored flood that occurred at the dry-season start. Finally, analyses show that artificial recharge improves freshwater-lens water quality, making possible longer use of

Extensive expansion of A1 family aspartic proteinases in fungi revealed by evolutionary analyses of 107 complete eukaryotic proteomes

NARCIS (Netherlands)

Revuelta, M.V.; Kan, van J.A.L.; Kay, J.; Have, ten A.

2014-01-01

The A1 family of eukaryotic aspartic proteinases (APs) forms one of the 16 AP families. Although one of the best characterized families, the recent increase in genome sequence data has revealed many fungal AP homologs with novel sequence characteristics. This study was performed to explore the

Advanced exergy-based analyses applied to a system including LNG regasification and electricity generation

Energy Technology Data Exchange (ETDEWEB)

Morosuk, Tatiana; Tsatsaronis, George; Boyano, Alicia; Gantiva, Camilo [Technische Univ. Berlin (Germany)

2012-07-01

Liquefied natural gas (LNG) will contribute more in the future than in the past to the overall energy supply in the world. The paper discusses the application of advanced exergy-based analyses to a recently developed LNG-based cogeneration system. These analyses include advanced exergetic, advanced exergoeconomic, and advanced exergoenvironmental analyses in which thermodynamic inefficiencies (exergy destruction), costs, and environmental impacts have been split into avoidable and unavoidable parts. With the aid of these analyses, the potentials for improving the thermodynamic efficiency and for reducing the overall cost and the overall environmental impact are revealed. The objectives of this paper are to demonstrate (a) the potential for generating electricity while regasifying LNG and (b) some of the capabilities associated with advanced exergy-based methods. The most important subsystems and components are identified, and suggestions for improving them are made. (orig.)

Synthesis, Hirshfeld surface analyses and magnetism of a 1D Mn(II ...

African Journals Online (AJOL)

A new Mn-based complex of {[Mn(L)2(mi)]·H2O}n (1) (HL = p-hydroxy phenylacetic acid; mi = 1,1'-(1,4-butanediyl)bis(imidazole)), has been synthesized and structurally characterized. Single-crystal X-ray analyses reveal that compound 1 has a dinuclear Mn(II) unit linking by four carboxylate groups. The bridging N-donor ...

Abnormal subcortical nuclei shapes in patients with type 2 diabetes mellitus.

Science.gov (United States)

Chen, Ji; Zhang, Junxiang; Liu, Xuebing; Wang, Xiaoyang; Xu, Xiangjin; Li, Hui; Cao, Bo; Yang, Yanqiu; Lu, Jingjing; Chen, Ziqian

2017-10-01

Type 2 diabetes mellitus (T2DM) increases the risk of brain atrophy and dementia. We aimed to elucidate deep grey matter (GM) structural abnormalities and their relationships with T2DM cognitive deficits by combining region of interest (ROI)-based volumetry, voxel-based morphometry (VBM) and shape analysis. We recruited 23 T2DM patients and 24 age-matched healthy controls to undergo T1-weighted structural MRI scanning. Images were analysed using the three aforementioned methods to obtain deep GM structural shapes and volumes. Biochemical and cognitive assessments were made and were correlated with the resulting metrics. Shape analysis revealed that T2DM is associated with focal atrophy in the bilateral caudate head and dorso-medial part of the thalamus. ROI-based volumetry only detected thalamic volume reduction in T2DM when compared to the controls. No significant between-group differences were found by VBM. Furthermore, a worse performance of cognitive processing speed correlated with more severe GM atrophy in the bilateral dorso-medial part of the thalamus. Also, the GM volume in the bilateral dorso-medial part of the thalamus changed negatively with HbA 1c . Shape analysis is sensitive in identifying T2DM deep GM structural abnormalities and their relationships with cognitive impairments, which may greatly assist in clarifying the neural substrate of T2DM cognitive dysfunction. • Type 2 diabetes mellitus is accompanied with brain atrophy and cognitive dysfunction • Deep grey matter structures are essential for multiple cognitive processes • Shape analysis revealed local atrophy in the dorso-medial thalamus and caudatum in patients • Dorso-medial thalamic atrophy correlated to cognitive processing speed slowing and high HbA1c. • Shape analysis has advantages in unraveling neural substrates of diabetic cognitive deficits.

Diagnosis of initial changes in patients suffering from rheumatoid arthritis. A comparison between low-field magnetic resonance imaging, 3-phase bone scintigraphy and conventional X-ray

International Nuclear Information System (INIS)

Hoepfner, S.; Dresel, S.; Weiss, M.; Hahn, K.; Treitl, M.; Krolak, C.; Becker-Gaab, C.; Schattenkirchner, M.

2002-01-01

Besides conventional X-rays, in the diagnostic work up of initial changes in patients suffering from rheumatoid arthritis (RA), 3-phase bone scintigraphy (3P-Sz) is as well established as magnetic resonance imaging (MRI). The aim of this study was to compare the diagnostic value of the newly developed low field MRI with the proven methods X-rays and 3P-Sz. Methods: 65 patients (47f, 18m; 20-86 yrs) were studied on a one day protocol with 3P-Sz (550 MBq Tc-99m DPD), MRI and X-rays of the hands. Images were visually analysed by two blinded nuclear medicine physicians and radiologists and classified as a) RA-typical, b) inflammatory, non-RA-typical and c) non inflammatory changes. All methods were compared to 3P-Sz as golden standard. Results: In comparison to 3P-Sz, low field MRI presents with almost equal sensitivity and specificity in rheumatoid-typical and inflammatory changes. Conventional X-rays revealed in arthritis-typical changes as well as in inflammatory changes a significantly lower sensitivity and also a lower negative predictive value while specificity equals the one of MRI. Quantitative analysis of 3P-Sz using ROI-technique unveiled significantly higher values in patients with rheumatoid arthritis than in those with no inflammatory changes. Conclusion: MRI represents an equally sensitive method in the initial diagnosis of rheumatoid-typical and inflammatory changes in the region of the hands as compared to the 3P-Sz. Besides the basic diagnosis with conventional X-rays, 3P-Sz is still the recommended method of choice to evaluate the whole body when RA is suspected. Additionally, quantitative analysis of the 3P-Sz using the ROI technique in the region of the hands reveals statistically significant results and should therefore be taken into account in the assessment of inflammatory changes. (orig.) [de

Correlating subcortical interhemispheric connectivity and cortical hemispheric dominance in brain tumor patients: A repetitive navigated transcranial magnetic stimulation study.

Science.gov (United States)

Sollmann, Nico; Ille, Sebastian; Tussis, Lorena; Maurer, Stefanie; Hauck, Theresa; Negwer, Chiara; Bauer, Jan S; Ringel, Florian; Meyer, Bernhard; Krieg, Sandro M

2016-02-01

The present study aims to investigate the relationship between transcallosal interhemispheric connectivity (IC) and hemispheric language lateralization by using a novel approach including repetitive navigated transcranial magnetic stimulation (rTMS), hemispheric dominance ratio (HDR) calculation, and rTMS-based diffusion tensor imaging fiber tracking (DTI FT). 31 patients with left-sided perisylvian brain lesions underwent diffusion tensor imaging (DTI) and rTMS language mapping. Cortical language-positive rTMS spots were used to calculate HDRs (HDR: quotient of the left-sided divided by right-sided naming error rates for corresponding left- and right-sided cortical regions) and to create regions of interest (ROIs) for DTI FT. Then, fibers connecting the rTMS-based ROIs of both hemispheres were tracked, and the correlation of IC to HDRs was calculated via Spearman's rank correlation coefficient (rs). Fibers connecting rTMS-based ROIs of both hemispheres were detected in 12 patients (38.7%). Within the patients in which IC was detected, the mean number of subcortical IC fibers ± standard deviation (SD) was 138.0 ± 346.5 (median: 7.5; range: 1-1,217 fibers). Regarding rs for the correlation of HDRs and fiber numbers of patients that showed IC, only moderate correlation was revealed. Our approach might be beneficial and technically feasible for further investigation of the relationship between IC and language lateralization. However, only moderate correlation was revealed in the present study. Copyright © 2015 Elsevier B.V. All rights reserved.

Chemical analyses of wasp-associated streptomyces bacteria reveal a prolific potential for natural products discovery.

Directory of Open Access Journals (Sweden)

Michael Poulsen

2011-02-01

Full Text Available Identifying new sources for small molecule discovery is necessary to help mitigate the continuous emergence of antibiotic-resistance in pathogenic microbes. Recent studies indicate that one potentially rich source of novel natural products is Actinobacterial symbionts associated with social and solitary Hymenoptera. Here we test this possibility by examining two species of solitary mud dauber wasps, Sceliphron caementarium and Chalybion californicum. We performed enrichment isolations from 33 wasps and obtained more than 200 isolates of Streptomyces Actinobacteria. Chemical analyses of 15 of these isolates identified 11 distinct and structurally diverse secondary metabolites, including a novel polyunsaturated and polyoxygenated macrocyclic lactam, which we name sceliphrolactam. By pairing the 15 Streptomyces strains against a collection of fungi and bacteria, we document their antifungal and antibacterial activity. The prevalence and anti-microbial properties of Actinobacteria associated with these two solitary wasp species suggest the potential role of these Streptomyces as antibiotic-producing symbionts, potentially helping defend their wasp hosts from pathogenic microbes. Finding phylogenetically diverse and chemically prolific Actinobacteria from solitary wasps suggests that insect-associated Actinobacteria can provide a valuable source of novel natural products of pharmaceutical interest.

Indian Point 2 steam generator tube rupture analyses

International Nuclear Information System (INIS)

Dayan, A.

1985-01-01

Analyses were conducted with RETRAN-02 to study consequences of steam generator tube rupture (SGTR) events. The Indian Point, Unit 2, power plant (IP2, PWR) was modeled as a two asymmetric loops, consisting of 27 volumes and 37 junctions. The break section was modeled once, conservatively, as a 150% flow area opening at the wall of the steam generator cold leg plenum, and once as a 200% double-ended tube break. Results revealed 60% overprediction of breakflow rates by the traditional conservative model. Two SGTR transients were studied, one with low-pressure reactor trip and one with an earlier reactor trip via over temperature ΔT. The former is more typical to a plant with low reactor average temperature such as IP2. Transient analyses for a single tube break event over 500 seconds indicated continued primary subcooling and no need for steam line pressure relief. In addition, SGTR transients with reactor trip while the pressurizer still contains water were found to favorably reduce depressurization rates. Comparison of the conservative results with independent LOFTRAN predictions showed good agreement

Non-invasive PGAA, PIXE and ToF-ND analyses on Hungarian Bronze Age defensive armour

International Nuclear Information System (INIS)

Marianne Moedlinger; Imre Kovacs; Zoltan Szoekefalvi-Nagy; Ziad El Morr

2014-01-01

Non-invasive, archaeometric analyses on selected Hungarian Bronze Age defensive armour is presented here: three greaves, three helmets two shields as well as one vessel fragment were analysed with PIXE, PGAA and TOF-ND. The detected alloy elemental and phase composition as well as its intergranular or spatial concentration distribution reveals important insights into the alloys used and the manufacturing techniques applied c. 1200-950 BC, and allows to reconstruct the production techniques used during the Late Bronze Age. (author)

Genetic Structuration, Demography and Evolutionary History of Mycobacterium tuberculosis LAM9 Sublineage in the Americas as Two Distinct Subpopulations Revealed by Bayesian Analyses

Science.gov (United States)

Reynaud, Yann; Millet, Julie; Rastogi, Nalin

2015-01-01

Tuberculosis (TB) remains broadly present in the Americas despite intense global efforts for its control and elimination. Starting from a large dataset comprising spoligotyping (n = 21183 isolates) and 12-loci MIRU-VNTRs data (n = 4022 isolates) from a total of 31 countries of the Americas (data extracted from the SITVIT2 database), this study aimed to get an overview of lineages circulating in the Americas. A total of 17119 (80.8%) strains belonged to the Euro-American lineage 4, among which the most predominant genotypic family belonged to the Latin American and Mediterranean (LAM) lineage (n = 6386, 30.1% of strains). By combining classical phylogenetic analyses and Bayesian approaches, this study revealed for the first time a clear genetic structuration of LAM9 sublineage into two subpopulations named LAM9C1 and LAM9C2, with distinct genetic characteristics. LAM9C1 was predominant in Chile, Colombia and USA, while LAM9C2 was predominant in Brazil, Dominican Republic, Guadeloupe and French Guiana. Globally, LAM9C2 was characterized by higher allelic richness as compared to LAM9C1 isolates. Moreover, LAM9C2 sublineage appeared to expand close to twenty times more than LAM9C1 and showed older traces of expansion. Interestingly, a significant proportion of LAM9C2 isolates presented typical signature of ancestral LAM-RDRio MIRU-VNTR type (224226153321). Further studies based on Whole Genome Sequencing of LAM strains will provide the needed resolution to decipher the biogeographical structure and evolutionary history of this successful family. PMID:26517715

Using team cognitive work analysis to reveal healthcare team interactions in a birthing unit.

Science.gov (United States)

Ashoori, Maryam; Burns, Catherine M; d'Entremont, Barbara; Momtahan, Kathryn

2014-01-01

Cognitive work analysis (CWA) as an analytical approach for examining complex sociotechnical systems has shown success in modelling the work of single operators. The CWA approach incorporates social and team interactions, but a more explicit analysis of team aspects can reveal more information for systems design. In this paper, Team CWA is explored to understand teamwork within a birthing unit at a hospital. Team CWA models are derived from theories and models of teamwork and leverage the existing CWA approaches to analyse team interactions. Team CWA is explained and contrasted with prior approaches to CWA. Team CWA does not replace CWA, but supplements traditional CWA to more easily reveal team information. As a result, Team CWA may be a useful approach to enhance CWA in complex environments where effective teamwork is required. This paper looks at ways of analysing cognitive work in healthcare teams. Team Cognitive Work Analysis, when used to supplement traditional Cognitive Work Analysis, revealed more team information than traditional Cognitive Work Analysis. Team Cognitive Work Analysis should be considered when studying teams.

Using team cognitive work analysis to reveal healthcare team interactions in a birthing unit

Science.gov (United States)

Ashoori, Maryam; Burns, Catherine M.; d'Entremont, Barbara; Momtahan, Kathryn

2014-01-01

Cognitive work analysis (CWA) as an analytical approach for examining complex sociotechnical systems has shown success in modelling the work of single operators. The CWA approach incorporates social and team interactions, but a more explicit analysis of team aspects can reveal more information for systems design. In this paper, Team CWA is explored to understand teamwork within a birthing unit at a hospital. Team CWA models are derived from theories and models of teamworkand leverage the existing CWA approaches to analyse team interactions. Team CWA is explained and contrasted with prior approaches to CWA. Team CWA does not replace CWA, but supplements traditional CWA to more easily reveal team information. As a result, Team CWA may be a useful approach to enhance CWA in complex environments where effective teamwork is required. Practitioner Summary: This paper looks at ways of analysing cognitive work in healthcare teams. Team Cognitive Work Analysis, when used to supplement traditional Cognitive Work Analysis, revealed more team information than traditional Cognitive Work Analysis. Team Cognitive Work Analysis should be considered when studying teams PMID:24837514

Optimizing methods for linking cinematic features to fMRI data.

Science.gov (United States)

Kauttonen, Janne; Hlushchuk, Yevhen; Tikka, Pia

2015-04-15

One of the challenges of naturalistic neurosciences using movie-viewing experiments is how to interpret observed brain activations in relation to the multiplicity of time-locked stimulus features. As previous studies have shown less inter-subject synchronization across viewers of random video footage than story-driven films, new methods need to be developed for analysis of less story-driven contents. To optimize the linkage between our fMRI data collected during viewing of a deliberately non-narrative silent film 'At Land' by Maya Deren (1944) and its annotated content, we combined the method of elastic-net regularization with the model-driven linear regression and the well-established data-driven independent component analysis (ICA) and inter-subject correlation (ISC) methods. In the linear regression analysis, both IC and region-of-interest (ROI) time-series were fitted with time-series of a total of 36 binary-valued and one real-valued tactile annotation of film features. The elastic-net regularization and cross-validation were applied in the ordinary least-squares linear regression in order to avoid over-fitting due to the multicollinearity of regressors, the results were compared against both the partial least-squares (PLS) regression and the un-regularized full-model regression. Non-parametric permutation testing scheme was applied to evaluate the statistical significance of regression. We found statistically significant correlation between the annotation model and 9 ICs out of 40 ICs. Regression analysis was also repeated for a large set of cubic ROIs covering the grey matter. Both IC- and ROI-based regression analyses revealed activations in parietal and occipital regions, with additional smaller clusters in the frontal lobe. Furthermore, we found elastic-net based regression more sensitive than PLS and un-regularized regression since it detected a larger number of significant ICs and ROIs. Along with the ISC ranking methods, our regression analysis proved

Evaluation of chronic pulmonary emphysema ultrafast computed tomography

International Nuclear Information System (INIS)

Tsuchida, Fumihiro; Yagyu, Hisanaga; Ohishi, Shuji; Nakamura, Hiroyuki; Matsuoka, Takeshi

2003-01-01

We compared pulmonary ventilation dynamics between 41 patients with pulmonary emphysema and 11 healthy subjects with normal pulmonary function using ultrafast computed tomography (CT). Regions of interest (ROIs) for multislice scanning were selected from the anatomical levels of the carina in the right upper lung field. Several identical slices were selected from the inspiratory and expiratory scans. The average CT values in the ROIs (AvROI) were obtained during the inspiratory phase (inAvROI) and the expiratory phase (exAvROI. The ratio of change from inAvROI to exAvROI ((I-E)/E ratio) was also used for image analysis. Furthermore, possible correlations between the CT image parameters and pulmonary function test parameters were examined. The results showed that the exAvROI and inAvROI values and (I-E)/E ratio were lower in the emphysema group than in the normal pulmonary function group. Among the image data parameters, the exAvROI value correlated most closely with pulmonary function parameters, in particular, with the pulmonary diffusing capacity. These findings suggest that image data parameters of ventilation dynamics may be useful for evaluating the severity of pulmonary emphysema. (author)

Comparative analyses of genetic risk prediction methods reveal ...

Indian Academy of Sciences (India)

2015-03-12

Mar 12, 2015 ... 1National Institute of Biomedical Genomics, Netaji Subhas Sanatorium (T. B. ... 2Institute of Post Graduate Medical Education and Research, J. C. Bose Road, ...... Torres D. M. and Harrison S. A 2008 Diagnosis and therapy of.

Comparative analyses of genetic risk prediction methods reveal ...

Indian Academy of Sciences (India)

0.85. 0.8. 0.95. 0.93. 0.81 rs1227756. 0.5. 0.56. 0.75. 0.55. 0.7. 0.71. 0.58. 0.81. 0.25. 0.5. 0.53. 0.48. 0.64. 0.58. 0.58. 0.8. 0.68. 0.78. 0.48. 0.65. NA. NA. NA. NA rs1501299. 0.64. 0.78. 0.75. 0.83. 0.83. 0.89. 0.83. 0.72. 0.63. 0.73. 0.78. 0.75. 0.84. 0.79. 0.61. 0.78. 0.78. 0.7. 0.73. 0.73. NA. NA. NA. NA rs16944. 0.64. 0.72. 0.68.

The postglacial recolonization of Northern Europe by Rana arvalis as revealed by microsatellite and mitochondrial DNA analyses.

Science.gov (United States)

Knopp, T; Merilä, J

2009-02-01

The postglacial history of the moor frog (Rana arvalis) in Northern Europe was investigated with the aid of eight variable microsatellite loci and a 661 bp sequence of the mitochondrial cytochrome b gene. A division between eastern and western mitochondrial lineages was discovered, supporting two recolonization routes to Fennoscandia since the last glacial maximum. This result was corroborated by the microsatellite data, which revealed a contact zone between the two lineages in Northern Sweden. These findings add to the increasing evidence that an intraspecific genetic biodiversity founded on the existence of eastern and western clades is a common element in Fennoscandian fauna and flora.

A Whole-Tumor Histogram Analysis of Apparent Diffusion Coefficient Maps for Differentiating Thymic Carcinoma from Lymphoma.

Science.gov (United States)

Zhang, Wei; Zhou, Yue; Xu, Xiao-Quan; Kong, Ling-Yan; Xu, Hai; Yu, Tong-Fu; Shi, Hai-Bin; Feng, Qing

2018-01-01

To assess the performance of a whole-tumor histogram analysis of apparent diffusion coefficient (ADC) maps in differentiating thymic carcinoma from lymphoma, and compare it with that of a commonly used hot-spot region-of-interest (ROI)-based ADC measurement. Diffusion weighted imaging data of 15 patients with thymic carcinoma and 13 patients with lymphoma were retrospectively collected and processed with a mono-exponential model. ADC measurements were performed by using a histogram-based and hot-spot-ROI-based approach. In the histogram-based approach, the following parameters were generated: mean ADC (ADC mean ), median ADC (ADC median ), 10th and 90th percentile of ADC (ADC 10 and ADC 90 ), kurtosis, and skewness. The difference in ADCs between thymic carcinoma and lymphoma was compared using a t test. Receiver operating characteristic analyses were conducted to determine and compare the differentiating performance of ADCs. Lymphoma demonstrated significantly lower ADC mean , ADC median , ADC 10 , ADC 90 , and hot-spot-ROI-based mean ADC than those found in thymic carcinoma (all p values histogram analysis of ADC maps can improve the differentiating performance between thymic carcinoma and lymphoma.

Pension Fund Performance in East Asia: A Comparative Study

Directory of Open Access Journals (Sweden)

Zamri Ahmad

2015-06-01

Full Text Available This paper discusses and analyzes asset allocation and performance of the major pension funds in four East Asia countries, namely Malaysia, Singapore, Hong Kong and South Korea. The respective funds for these countries are Employee Provident Fund (EPF, Central Provident Fund (CPF, Mandatory Pension Fund (MPF and National Pension Service (NPS. The impact of some economic crises on the fund performance will also be assessed. Besides looking at the individual countries, a comparison of the performance among all the funds will also be done. From the analyses, it is found that the CPF is the most conservative pension fund as it invested most of its funds in fixed income and the investments were made in the local markets, while MPF is the most aggressive pension fund as most of its funds were invested in equities. Performance of the funds was measured in terms of return on investment (ROI. All funds recorded the lowest ROI during the subprime crisis in 2008. Besides the subprime crisis, these funds were also affected by the Japanese earthquake as lower ROI were also observed in 2011.

Distinct signaling roles of ceramide species in yeast revealed through systematic perturbation and systems biology analyses.

Science.gov (United States)

Montefusco, David J; Chen, Lujia; Matmati, Nabil; Lu, Songjian; Newcomb, Benjamin; Cooper, Gregory F; Hannun, Yusuf A; Lu, Xinghua

2013-10-29

Ceramide, the central molecule of sphingolipid metabolism, is an important bioactive molecule that participates in various cellular regulatory events and that has been implicated in disease. Deciphering ceramide signaling is challenging because multiple ceramide species exist, and many of them may have distinct functions. We applied systems biology and molecular approaches to perturb ceramide metabolism in the yeast Saccharomyces cerevisiae and inferred causal relationships between ceramide species and their potential targets by combining lipidomic, genomic, and transcriptomic analyses. We found that during heat stress, distinct metabolic mechanisms controlled the abundance of different groups of ceramide species and provided experimental support for the importance of the dihydroceramidase Ydc1 in mediating the decrease in dihydroceramides during heat stress. Additionally, distinct groups of ceramide species, with different N-acyl chains and hydroxylations, regulated different sets of functionally related genes, indicating that the structural complexity of these lipids produces functional diversity. The transcriptional modules that we identified provide a resource to begin to dissect the specific functions of ceramides.

Diffusion-weighted imaging of breast lesions: Region-of-interest placement and different ADC parameters influence apparent diffusion coefficient values

Energy Technology Data Exchange (ETDEWEB)

Bickel, Hubert; Pinker, Katja; Polanec, Stephan; Magometschnigg, Heinrich; Wengert, Georg; Spick, Claudio; Helbich, Thomas H.; Baltzer, Pascal [Medical University Vienna, Division of Molecular and Gender Imaging, Department of Biomedical Imaging and Image-Guided Therapy, Vienna (Austria); Bogner, Wolfgang [Medical University Vienna - MR Center of Excellence, Department of Biomedical Imaging and Image-Guided Therapy, Vienna (Austria); Bago-Horvath, Zsuzsanna [Medical University Vienna, Department of Pathology, Vienna (Austria)

2017-05-15

To investigate the influence of region-of-interest (ROI) placement and different apparent diffusion coefficient (ADC) parameters on ADC values, diagnostic performance, reproducibility and measurement time in breast tumours. In this IRB-approved, retrospective study, 149 histopathologically proven breast tumours (109 malignant, 40 benign) in 147 women (mean age 53.2) were investigated. Three radiologists independently measured minimum, mean and maximum ADC, each using three ROI placement approaches:1 - small 2D-ROI, 2 - large 2D-ROI and 3 - 3D-ROI covering the whole lesion. One reader performed all measurements twice. Median ADC values, diagnostic performance, reproducibility, and measurement time were calculated and compared between all combinations of ROI placement approaches and ADC parameters. Median ADC values differed significantly between the ROI placement approaches (p <.001). Minimum ADC showed the best diagnostic performance (AUC.928-.956), followed by mean ADC obtained from 2D ROIs (.926-.94). Minimum and mean ADC showed high intra- (ICC.85-.94) and inter-reader reproducibility (ICC.74-.94). Median measurement time was significantly shorter for the 2D ROIs (p <.001). ROI placement significantly influences ADC values measured in breast tumours. Minimum and mean ADC acquired from 2D-ROIs are useful for the differentiation of benign and malignant breast lesions, and are highly reproducible, with rapid measurement. (orig.)

Less is less: a systematic review of graph use in meta-analyses.

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Schild, Anne H E; Voracek, Martin

2013-09-01

Graphs are an essential part of scientific communication. Complex datasets, of which meta-analyses are textbook examples, benefit the most from visualization. Although a number of graph options for meta-analyses exist, the extent to which these are used was hitherto unclear. A systematic review on graph use in meta-analyses in three disciplines (medicine, psychology, and business) and nine journals was conducted. Interdisciplinary differences, which are mirrored in the respective journals, were revealed, that is, graph use correlates with external factors rather than methodological considerations. There was only limited variation in graph types (with forest plots as the most important representatives), and diagnostic plots were very rare. Although an increase in graph use over time could be observed, it is unlikely that this phenomenon is specific to meta-analyses. There is a gaping discrepancy between available graphic methods and their application in meta-analyses. This may be rooted in a number of factors, namely, (i) insufficient dissemination of new developments, (ii) unsatisfactory implementation in software packages, and (iii) minor attention on graphics in meta-analysis reporting guidelines. Using visualization methods to their full capacity is a further step in using meta-analysis to its full potential. Copyright © 2013 John Wiley & Sons, Ltd.

Comparative Genomics Analyses Reveal Extensive Chromosome Colinearity and Novel Quantitative Trait Loci in Eucalyptus

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Weng, Qijie; Li, Mei; Yu, Xiaoli; Guo, Yong; Wang, Yu; Zhang, Xiaohong; Gan, Siming

2015-01-01

Dense genetic maps, along with quantitative trait loci (QTLs) detected on such maps, are powerful tools for genomics and molecular breeding studies. In the important woody genus Eucalyptus, the recent release of E. grandis genome sequence allows for sequence-based genomic comparison and searching for positional candidate genes within QTL regions. Here, dense genetic maps were constructed for E. urophylla and E. tereticornis using genomic simple sequence repeats (SSR), expressed sequence tag (EST) derived SSR, EST-derived cleaved amplified polymorphic sequence (EST-CAPS), and diversity arrays technology (DArT) markers. The E. urophylla and E. tereticornis maps comprised 700 and 585 markers across 11 linkage groups, totaling at 1,208.2 and 1,241.4 cM in length, respectively. Extensive synteny and colinearity were observed as compared to three earlier DArT-based eucalypt maps (two maps with E. grandis × E. urophylla and one map of E. globulus) and with the E. grandis genome sequence. Fifty-three QTLs for growth (10–56 months of age) and wood density (56 months) were identified in 22 discrete regions on both maps, in which only one colocalizaiton was found between growth and wood density. Novel QTLs were revealed as compared with those previously detected on DArT-based maps for similar ages in Eucalyptus. Eleven to 585 positional candidate genes were obained for a 56-month-old QTL through aligning QTL confidence interval with the E. grandis genome. These results will assist in comparative genomics studies, targeted gene characterization, and marker-assisted selection in Eucalyptus and the related taxa. PMID:26695430

Comparative Genomics Analyses Reveal Extensive Chromosome Colinearity and Novel Quantitative Trait Loci in Eucalyptus.

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Fagen Li

Full Text Available Dense genetic maps, along with quantitative trait loci (QTLs detected on such maps, are powerful tools for genomics and molecular breeding studies. In the important woody genus Eucalyptus, the recent release of E. grandis genome sequence allows for sequence-based genomic comparison and searching for positional candidate genes within QTL regions. Here, dense genetic maps were constructed for E. urophylla and E. tereticornis using genomic simple sequence repeats (SSR, expressed sequence tag (EST derived SSR, EST-derived cleaved amplified polymorphic sequence (EST-CAPS, and diversity arrays technology (DArT markers. The E. urophylla and E. tereticornis maps comprised 700 and 585 markers across 11 linkage groups, totaling at 1,208.2 and 1,241.4 cM in length, respectively. Extensive synteny and colinearity were observed as compared to three earlier DArT-based eucalypt maps (two maps with E. grandis × E. urophylla and one map of E. globulus and with the E. grandis genome sequence. Fifty-three QTLs for growth (10-56 months of age and wood density (56 months were identified in 22 discrete regions on both maps, in which only one colocalizaiton was found between growth and wood density. Novel QTLs were revealed as compared with those previously detected on DArT-based maps for similar ages in Eucalyptus. Eleven to 585 positional candidate genes were obained for a 56-month-old QTL through aligning QTL confidence interval with the E. grandis genome. These results will assist in comparative genomics studies, targeted gene characterization, and marker-assisted selection in Eucalyptus and the related taxa.

Medulloblastoma in China: clinicopathologic analyses of SHH, WNT, and non-SHH/WNT molecular subgroups reveal different therapeutic responses to adjuvant chemotherapy.

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Zhen-Yu Zhang

Full Text Available Medulloblastoma (MB is one of the most common primary central nervous system tumors in children. Data is lacking of a large cohort of medulloblastoma patients in China. Also, our knowledge on the sensitivity of different molecular subgroups of MB to adjuvant radiation therapy (RT or chemotherapy (CHT is still limited. The authors performed a retrospective study of 173 medulloblastoma patients treated at two institutions from 2002 to 2011. Formalin-fixed paraffin embedded (FFPE tissues were available in all the cases and sections were stained to classify histological and molecular subgroups. Univariate and multivariate analyses were used to investigate prognostic factors. Of 173 patients, there were 118 children and 55 adults, 112 males and 61 females. Estimated 5-year overall survival (OS rates for all patients, children and adults were 52%, 48% and 63%, respectively. After multivariate analysis, postoperative primary radiation therapy (RT and chemotherapy (CHT were revealed as favorable prognostic factors influencing OS and EFS. Postoperative primary chemotherapy (CHT was found significantly improving the survival of children (p<0.001 while it was not a significant prognostic factor for adult patients. Moreover, patients in WNT subtype had better OS (p = 0.028 than others (SHH and Non-SHH/WNT subtypes given postoperative adjuvant therapies. Postoperative primary RT was found to be a strong prognostic factor influencing the survival in all histological and molecular subgroups (p<0.001. Postoperative primary CHT was found significantly to influence the survival of classic medulloblastoma (CMB (OS p<0.001, EFS p<0.001, SHH subgroup (OS p = 0.020, EFS p = 0.049 and WNT subgroup (OS p = 0.003, EFS p = 0.016 but not in desmoplastic/nodular medulloblastoma (DMB (OS p = 0.361, EFS p = 0.834 and Non-SHH/WNT subgroup (OS p = 0.127, EFS p = 0.055. Our study showed postoperative primary CHT significantly influence the

Analyses of Mitogenome Sequences Revealed that Asian Citrus Psyllids (Diaphorina citri) from California Were Related to Those from Florida.

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Wu, Fengnian; Kumagai, Luci; Cen, Yijing; Chen, Jianchi; Wallis, Christopher M; Polek, MaryLou; Jiang, Hongyan; Zheng, Zheng; Liang, Guangwen; Deng, Xiaoling

2017-08-31

Asian citrus psyllid (ACP, Diaphorina citri Kuwayama) transmits "Candidatus Liberibacter asiaticus" (CLas), an unculturable alpha-proteobacterium associated with citrus Huanglongbing (HLB). CLas has recently been found in California. Understanding ACP population diversity is necessary for HLB regulatory practices aimed at reducing CLas spread. In this study, two circular ACP mitogenome sequences from California (mt-CApsy, ~15,027 bp) and Florida (mt-FLpsy, ~15,012 bp), USA, were acquired. Each mitogenome contained 13 protein coding genes, 2 ribosomal RNA and 22 transfer RNA genes, and a control region varying in sizes. The Californian mt-CApsy was identical to the Floridian mt-FLpsy, but different from the mitogenome (mt-GDpsy) of Guangdong, China, in 50 single nucleotide polymorphisms (SNPs). Further analyses were performed on sequences in cox1 and trnAsn regions with 100 ACPs, SNPs in nad1-nad4-nad5 locus through PCR with 252 ACP samples. All results showed the presence of a Chinese ACP cluster (CAC) and an American ACP cluster (AAC). We proposed that ACP in California was likely not introduced from China based on our current ACP collection but somewhere in America. However, more studies with ACP samples from around the world are needed. ACP mitogenome sequence analyses will facilitate ACP population research.

Combined Analyses of Chloroplast DNA Haplotypes and Microsatellite Markers Reveal New Insights Into the Origin and Dissemination Route of Cultivated Pears Native to East Asia

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Xiaoyan Yue

2018-05-01

Full Text Available Asian pear plays an important role in the world pear industry, accounting for over 70% of world total production volume. Commercial Asian pear production relies on four major pear cultivar groups, Japanese pear (JP, Chinese white pear (CWP, Chinese sand pear (CSP, and Ussurian pear (UP, but their origins remain controversial. We estimated the genetic diversity levels and structures in a large sample of existing local cultivars to investigate the origins of Asian pears using twenty-five genome-covering nuclear microsatellite (simple sequence repeats, nSSR markers and two non-coding chloroplast DNA (cpDNA regions (trnL-trnF and accD-psaI. High levels of genetic diversity were detected for both nSSRs (HE = 0.744 and cpDNAs (Hd = 0.792. The major variation was found within geographic populations of cultivated pear groups, demonstrating a close relationship among cultivar groups. CSPs showed a greater genetic diversity than CWPs and JPs, and lowest levels of genetic differentiation were detected among them. Phylogeographical analyses indicated that the CSP, CWP, and JP were derived from the same progenitor of Pyrus pyrifolia in China. A dissemination route of cultivated P. pyrifolia estimated by approximate Bayesian computation suggested that cultivated P. pyrifolia from the Middle Yangtze River Valley area contributed the major genetic resources to the cultivars, excluding those of southwestern China. Three major genetic groups of cultivated Pyrus pyrifolia were revealed using nSSRs and a Bayesian statistical inference: (a JPs; (b cultivars from South-Central China northward to northeastern China, covering the main pear production area in China; (c cultivars from southwestern China to southeastern China, including Yunnan, Guizhou, Guangdong, Guangxi, and Fujian Provinces. This reflected the synergistic effects of ecogeographical factors and human selection during cultivar spread and improvement. The analyses indicated that UP cultivars might be

Mitochondrial DNA analyses and ecological niche modeling reveal post-LGM expansion of the Assam macaque (Macaca assamensis) in the foothills of Nepal Himalaya.

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Khanal, Laxman; Chalise, Mukesh K; He, Kai; Acharya, Bipin K; Kawamoto, Yoshi; Jiang, Xuelong

2018-03-01

Genetic diversity of a species is influenced by multiple factors, including the Quaternary glacial-interglacial cycles and geophysical barriers. Such factors are not yet well documented for fauna from the southern border of the Himalayan region. This study used mitochondrial DNA (mtDNA) sequences and ecological niche modeling (ENM) to explore how the late Pleistocene climatic fluctuations and complex geography of the Himalayan region have shaped genetic diversity, population genetic structure, and demographic history of the Nepalese population of Assam macaques (Macaca assamensis) in the Himalayan foothills. A total of 277 fecal samples were collected from 39 wild troops over almost the entire distribution of the species in Nepal. The mtDNA fragment encompassing the complete control region (1121 bp) was recovered from 208 samples, thus defining 54 haplotypes. Results showed low nucleotide diversity (0.0075 ± SD 0.0001) but high haplotype diversity (0.965 ± SD 0.004). The mtDNA sequences revealed a shallow population genetic structure with a moderate but statistically significant effect of isolation by distance. Demographic history analyses using mtDNA sequences suggested a post-pleistocene population expansion. Paleodistribution reconstruction projected that the potential habitat of the Assam macaque was confined to the lower elevations of central Nepal during the Last Glacial Maximum. With the onset of the Holocene climatic optimum, the glacial refugia population experienced eastward range expansion to higher elevations. We conclude that the low genetic diversity and shallow population genetic structure of the Assam macaque population in the Nepal Himalaya region are the consequence of recent demographic and spatial expansion. © 2018 Wiley Periodicals, Inc.

Temporal analyses of Salmonellae in a headwater spring ecosystem reveals the effects of precipitation and runoff events.

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Gaertner, James P; Garres, Tiffany; Becker, Jesse C; Jimenez, Maria L; Forstner, Michael R J; Hahn, Dittmar

2009-03-01

Sediments and water from the spring and slough arm of Spring Lake, the pristine headwaters of the San Marcos River, Texas, were analyzed for Salmonellae by culture and molecular techniques before and after three major precipitation events, each with intermediate dry periods. Polymerase chain reaction (PCR)-assisted analyses of enrichment cultures detected Salmonellae in samples after all three precipitation events, but failed to detect them immediately prior to the rainfall events. Detection among individual locations differed with respect to the precipitation event analyzed, and strains isolated were highly variable with respect to serovars. These results demonstrate that rainwater associated effects, most likely surface runoff, provide an avenue for short-term pollution of aquatic systems with Salmonellae that do not, however, appear to establish for the long-term in water nor sediments.

Integrative analyses of leprosy susceptibility genes indicate a common autoimmune profile.

Science.gov (United States)

Zhang, Deng-Feng; Wang, Dong; Li, Yu-Ye; Yao, Yong-Gang

2016-04-01

Leprosy is an ancient chronic infection in the skin and peripheral nerves caused by Mycobacterium leprae. The development of leprosy depends on genetic background and the immune status of the host. However, there is no systematic view focusing on the biological pathways, interaction networks and overall expression pattern of leprosy-related immune and genetic factors. To identify the hub genes in the center of leprosy genetic network and to provide an insight into immune and genetic factors contributing to leprosy. We retrieved all reported leprosy-related genes and performed integrative analyses covering gene expression profiling, pathway analysis, protein-protein interaction network, and evolutionary analyses. A list of 123 differentially expressed leprosy related genes, which were enriched in activation and regulation of immune response, was obtained in our analyses. Cross-disorder analysis showed that the list of leprosy susceptibility genes was largely shared by typical autoimmune diseases such as lupus erythematosus and arthritis, suggesting that similar pathways might be affected in leprosy and autoimmune diseases. Protein-protein interaction (PPI) and positive selection analyses revealed a co-evolution network of leprosy risk genes. Our analyses showed that leprosy associated genes constituted a co-evolution network and might undergo positive selection driven by M. leprae. We suggested that leprosy may be a kind of autoimmune disease and the development of leprosy is a matter of defect or over-activation of body immunity. Copyright © 2016 Elsevier Ireland Ltd. All rights reserved.

Differential metabolism of Mycoplasma species as revealed by their genomes

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Fabricio B.M. Arraes

2007-01-01

Full Text Available The annotation and comparative analyses of the genomes of Mycoplasma synoviae and Mycoplasma hyopneumonie, as well as of other Mollicutes (a group of bacteria devoid of a rigid cell wall, has set the grounds for a global understanding of their metabolism and infection mechanisms. According to the annotation data, M. synoviae and M. hyopneumoniae are able to perform glycolytic metabolism, but do not possess the enzymatic machinery for citrate and glyoxylate cycles, gluconeogenesis and the pentose phosphate pathway. Both can synthesize ATP by lactic fermentation, but only M. synoviae can convert acetaldehyde to acetate. Also, our genome analysis revealed that M. synoviae and M. hyopneumoniae are not expected to synthesize polysaccharides, but they can take up a variety of carbohydrates via the phosphoenolpyruvate-dependent phosphotransferase system (PEP-PTS. Our data showed that these two organisms are unable to synthesize purine and pyrimidine de novo, since they only possess the sequences which encode salvage pathway enzymes. Comparative analyses of M. synoviae and M. hyopneumoniae with other Mollicutes have revealed differential genes in the former two genomes coding for enzymes that participate in carbohydrate, amino acid and nucleotide metabolism and host-pathogen interaction. The identification of these metabolic pathways will provide a better understanding of the biology and pathogenicity of these organisms.

Proteomic Analyses Reveal the Mechanism of Dunaliella salina Ds-26-16 Gene Enhancing Salt Tolerance in Escherichia coli.

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Yanlong Wang

Full Text Available We previously screened the novel gene Ds-26-16 from a 4 M salt-stressed Dunaliella salina cDNA library and discovered that this gene conferred salt tolerance to broad-spectrum organisms, including E. coli (Escherichia coli, Haematococcus pluvialis and tobacco. To determine the mechanism of this gene conferring salt tolerance, we studied the proteome of E. coli overexpressing the full-length cDNA of Ds-26-16 using the iTRAQ (isobaric tags for relative and absolute quantification approach. A total of 1,610 proteins were identified, which comprised 39.4% of the whole proteome. Of the 559 differential proteins, 259 were up-regulated and 300 were down-regulated. GO (gene ontology and KEGG (Kyoto encyclopedia of genes and genomes enrichment analyses identified 202 major proteins, including those involved in amino acid and organic acid metabolism, energy metabolism, carbon metabolism, ROS (reactive oxygen species scavenging, membrane proteins and ABC (ATP binding cassette transporters, and peptidoglycan synthesis, as well as 5 up-regulated transcription factors. Our iTRAQ data suggest that Ds-26-16 up-regulates the transcription factors in E. coli to enhance salt resistance through osmotic balance, energy metabolism, and oxidative stress protection. Changes in the proteome were also observed in E. coli overexpressing the ORF (open reading frame of Ds-26-16. Furthermore, pH, nitric oxide and glycerol content analyses indicated that Ds-26-16 overexpression increases nitric oxide content but has no effect on glycerol content, thus confirming that enhanced nitric oxide synthesis via lower intercellular pH was one of the mechanisms by which Ds-26-16 confers salt tolerance to E. coli.

A multivariate shape quantification approach for sickle red blood cell in patient-specific microscopy image data

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Xu, Mengjia; Yang, Jinzhu; Zhao, Hong

2017-07-01

The morphological change of red blood cells(RBCs) plays an important role in revealing the biomechanical and biorheological characteristics of RBCs. Aiming to extract the shape indices for the sickle RBCs, an automated ex-vivo RBC shape quantification method is proposed. First, single RBC regions (ROIs) are extracted from raw microscopy image via an automatic hierarchical ROI extraction method. Second, an improved random walk method is used to detect the RBC outline. Finally, three types of RBC shape factors are calculated based on the elliptical fitting RBC contour. Experiments indicate that the proposed method can accurately segment the RBCs from the microscopy images with low contrast and prevent the disturbance of artifacts. Moreover, it can provide an efficient shape quantification means for diverse RBC shapes in a batch manner.

Prey-capture success revealed by echolocation signals in pipistrelle bats (Pipistrellus pygmaeus)

DEFF Research Database (Denmark)

Surlykke, Annemarie; Futtrup, Vibeke; Tougaard, Jakob

2003-01-01

Three Pipistrellus pygmaeus bats were trained to capture prey on the wing while flying in the laboratory. The bats' capture behaviour and capture success were determined and correlated with acoustic analyses of post-buzz echolocation signals. Three acoustic parameters revealed capture success: in...

USE OF BOUNDING ANALYSES TO ESTIMATE THE PREFORMANCE OF A SEISMICALLY ISOLATED STRUCTURE

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Gökhan ÖZDEMİR

2017-03-01

Full Text Available Current design approach for seismic isolated structures is to perform bounding analyses. These analyses provide an envelope for the response of the seismic isolated structure rather than focusing on the actual performance. In this study, the success of bounding analyses to estimate performance of a seismic isolated structure, in which the isolation is provided by means of lead rubber bearings (LRBs, is evaluated in a comparative manner. For this purpose, nonlinear response history analyses were performed under the effect of bidirectional ground motion excitations. In bounding analyses, non-deteriorating hysteretic representations were used to model the hysteretic behavior of LRBs. On the other hand, to estimate the actual performance of both the superstructure and isolator units, deteriorating hysteretic idealizations were employed. The deterioration in strength of LRBs was defined as a function of temperature rise in the lead core. The analyzed structure is an existing seismically isolated hospital building and analytically modeled in accordance with its reported design properties for both isolation units and superstructure. Results obtained from analyses where LRBs are idealized by both deteriorating and non-deteriorating hysteretic representations are used in the comparisons. The response quantities used in the comparisons are maximum isolator displacement, maximum isolator force, maximum absolute floor acceleration, and maximum relative story displacements. In an average sense, bounding analyses is found to provide conservative estimates for the selected response quantities and fulfills its intended purpose. However, it is revealed that there may be individual cases where bounding analyses fails to provide a safe envelope.

Assessing the capital efficiency of healthcare information technologies investments: an econometric perspective.

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Meyer, Rodolphe; Degoulet, Patrice

2008-01-01

To examine the different methods that can be used in the quantification of the added value of information technologies (IT) in the health care sector. This quantification represents a major issue for decision-makers and health care professionals when they have to plan an IT investment. Articles were chosen via Medline, internet and the University of Geneva bibliographic portal. Some of the papers were obtained directly from their authors. We examine the most current methods used to evaluate IT return on investment (ROI) in the general business and in the health care sector, drawing attention on methods traditionally used in macroeconomic studies that could reveal themselves disruptive for IT ROI impact evaluation in hospitals. Financial and accounting methods can provide interesting data on a specific IT project but are usually incomplete for revealing the global IT investment influence. Econometric methods tend to demonstrate the positive impact of health care IT (HIT) on hospital production and productivity. Hospitals having higher levels of IT investment tend to deliver a higher level of clinical quality and show improved hospital cost performances. Information technologies are so intermingled with people and processes that the identification of specific IT benefit remains questionable. Using macroeconomic tools could be the best way to analyze and compute IT ROI in health care. Econometric tools take into account all types investments (inputs) and all the returns (outputs) enabling the precise measurement of IT investments impact, breakeven points, and possible threshold levels, thus providing helpful intelligence to reach the higher levels of IT governance in hospitals.

Osteoprotegerin, pericytes and bone-like vascular calcification are associated with carotid plaque stability.

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Jean-Michel Davaine

Full Text Available BACKGROUND AND PURPOSE: Vascular calcification, recapitulating bone formation, has a profound impact on plaque stability. The aim of the present study was to determine the influence of bone-like vascular calcification (named osteoid metaplasia = OM and of osteoprotegerin on plaque stability. METHODS: Tissue from carotid endarterectomies were analysed for the presence of calcification and signs of vulnerability according to AHA grading system. Osteoprotegerin (OPG, pericytes and endothelial cells were sought using immuno-histochemistry. Symptoms and preoperative imaging findings (CT-scan, MRI and Doppler-scan were analyzed. Human pericytes were cultured to evaluate their ability to secrete OPG and to influence mineralization in the plaque. RESULTS: Seventy-three carotid plaques (49 asymptomatic and 24 symptomatic were harvested. A significantly higher presence of OM (18.4% vs 0%, p<0.01, OPG (10.2% of ROI vs 3.4% of ROI, p<0.05 and pericytes (19% of ROI vs 3.8% of ROI, p<0.05 were noted in asymptomatic compared to symptomatic plaques. Consistently, circulating OPG levels were higher in the plasma of asymptomatic patients (3.2 ng/mL vs 2.5 ng/mL, p = 0.05. In vitro, human vascular pericytes secreted considerable amounts of OPG and underwent osteoblastic differentiation. Pericytes also inhibited the osteoclastic differentiation of CD14+ cells through their secretion of OPG. CONCLUSIONS: OPG (intraplaque an plasmatic and OM are associated with carotid plaque stability. Pericytes may be involved in the secretion of intraplaque OPG and in the formation of OM.

Influence of parameter settings in voxel-based morphometry 8. Using DARTEL and region-of-interest on reproducibility in gray matter volumetry.

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Goto, M; Abe, O; Aoki, S; Hayashi, N; Miyati, T; Takao, H; Matsuda, H; Yamashita, F; Iwatsubo, T; Mori, H; Kunimatsu, A; Ino, K; Yano, K; Ohtomo, K

2015-01-01

To investigate whether reproducibility of gray matter volumetry is influenced by parameter settings for VBM 8 using Diffeomorphic Anatomical Registration Through Exponentiated Lie Algebra (DARTEL) with region-of-interest (ROI) analyses. We prepared three-dimensional T1-weighted magnetic resonance images (3D-T1WIs) of 21 healthy subjects. All subjects were imaged with each of five MRI systems. Voxel-based morphometry 8 (VBM 8) and WFU PickAtlas software were used for gray matter volumetry. The bilateral ROI labels used were those provided as default settings with the software: Frontal Lobe, Hippocampus, Occipital Lobe, Orbital Gyrus, Parietal Lobe, Putamen, and Temporal Lobe. All 3D-T1WIs were segmented to gray matter with six parameters of VBM 8, with each parameter having between three and eight selectable levels. Reproducibility was evaluated as the standard deviation (mm³) of measured values for the five MRI systems. Reproducibility was influenced by 'Bias regularization (BiasR)', 'Bias FWHM', and 'De-noising filter' settings, but not by 'MRF weighting', 'Sampling distance', or 'Warping regularization' settings. Reproducibility in BiasR was influenced by ROI. Superior reproducibility was observed in Frontal Lobe with the BiasR1 setting, and in Hippocampus, Parietal Lobe, and Putamen with the BiasR3*, BiasR1, and BiasR5 settings, respectively. Reproducibility of gray matter volumetry was influenced by parameter settings in VBM 8 using DARTEL and ROI. In multi-center studies, the use of appropriate settings in VBM 8 with DARTEL results in reduced scanner effect.

High-Performance Region-of-Interest Image Error Concealment with Hiding Technique

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Shih-Chang Hsia

2010-01-01

Full Text Available Recently region-of-interest (ROI based image coding is a popular topic. Since ROI area contains much more important information for an image, it must be prevented from error decoding while suffering from channel lost or unexpected attack. This paper presents an efficient error concealment method to recover ROI information with a hiding technique. Based on the progressive transformation, the low-frequency components of ROI are encoded to disperse its information into the high-frequency bank of original image. The capability of protection is carried out with extracting the ROI coefficients from the damaged image without increasing extra information. Simulation results show that the proposed method can efficiently reconstruct the ROI image when ROI bit-stream occurs errors, and the measurement of PSNR result outperforms the conventional error concealment techniques by 2 to 5 dB.

Analyses of soil microbial community compositions and functional genes reveal potential consequences of natural forest succession.

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Cong, Jing; Yang, Yunfeng; Liu, Xueduan; Lu, Hui; Liu, Xiao; Zhou, Jizhong; Li, Diqiang; Yin, Huaqun; Ding, Junjun; Zhang, Yuguang

2015-05-06

The succession of microbial community structure and function is a central ecological topic, as microbes drive the Earth's biogeochemical cycles. To elucidate the response and mechanistic underpinnings of soil microbial community structure and metabolic potential relevant to natural forest succession, we compared soil microbial communities from three adjacent natural forests: a coniferous forest (CF), a mixed broadleaf forest (MBF) and a deciduous broadleaf forest (DBF) on Shennongjia Mountain in central China. In contrary to plant communities, the microbial taxonomic diversity of the DBF was significantly (P the DBF. Furthermore, a network analysis of microbial carbon and nitrogen cycling genes showed the network for the DBF samples was relatively large and tight, revealing strong couplings between microbes. Soil temperature, reflective of climate regimes, was important in shaping microbial communities at both taxonomic and functional gene levels. As a first glimpse of both the taxonomic and functional compositions of soil microbial communities, our results suggest that microbial community structure and function potentials will be altered by future environmental changes, which have implications for forest succession.

Sequence and expression analyses of porcine ISG15 and ISG43 genes.

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Huang, Jiangnan; Zhao, Shuhong; Zhu, Mengjin; Wu, Zhenfang; Yu, Mei

2009-08-01

The coding sequences of porcine interferon-stimulated gene 15 (ISG15) and the interferon-stimulated gene (ISG43) were cloned from swine spleen mRNA. The amino acid sequences deduced from porcine ISG15 and ISG43 genes coding sequence shared 24-75% and 29-83% similarity with ISG15s and ISG43s from other vertebrates, respectively. Structural analyses revealed that porcine ISG15 comprises two ubiquitin homologues motifs (UBQ) domain and a conserved C-terminal LRLRGG conjugating motif. Porcine ISG43 contains an ubiquitin-processing proteases-like domain. Phylogenetic analyses showed that porcine ISG15 and ISG43 were mostly related to rat ISG15 and cattle ISG43, respectively. Using quantitative real-time PCR assay, significant increased expression levels of porcine ISG15 and ISG43 genes were detected in porcine kidney endothelial cells (PK15) cells treated with poly I:C. We also observed the enhanced mRNA expression of three members of dsRNA pattern-recognition receptors (PRR), TLR3, DDX58 and IFIH1, which have been reported to act as critical receptors in inducing the mRNA expression of ISG15 and ISG43 genes. However, we did not detect any induced mRNA expression of IFNalpha and IFNbeta, suggesting that transcriptional activations of ISG15 and ISG43 were mediated through IFN-independent signaling pathway in the poly I:C treated PK15 cells. Association analyses in a Landrace pig population revealed that ISG15 c.347T>C (BstUI) polymorphism and the ISG43 c.953T>G (BccI) polymorphism were significantly associated with hematological parameters and immune-related traits.

Phylogeographic and population genetic analyses reveal multiple species of Boa and independent origins of insular dwarfism.

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Card, Daren C; Schield, Drew R; Adams, Richard H; Corbin, Andrew B; Perry, Blair W; Andrew, Audra L; Pasquesi, Giulia I M; Smith, Eric N; Jezkova, Tereza; Boback, Scott M; Booth, Warren; Castoe, Todd A

2016-09-01

Boa is a Neotropical genus of snakes historically recognized as monotypic despite its expansive distribution. The distinct morphological traits and color patterns exhibited by these snakes, together with the wide diversity of ecosystems they inhabit, collectively suggest that the genus may represent multiple species. Morphological variation within Boa also includes instances of dwarfism observed in multiple offshore island populations. Despite this substantial diversity, the systematics of the genus Boa has received little attention until very recently. In this study we examined the genetic structure and phylogenetic relationships of Boa populations using mitochondrial sequences and genome-wide SNP data obtained from RADseq. We analyzed these data at multiple geographic scales using a combination of phylogenetic inference (including coalescent-based species delimitation) and population genetic analyses. We identified extensive population structure across the range of the genus Boa and multiple lines of evidence for three widely-distributed clades roughly corresponding with the three primary land masses of the Western Hemisphere. We also find both mitochondrial and nuclear support for independent origins and parallel evolution of dwarfism on offshore island clusters in Belize and Cayos Cochinos Menor, Honduras. Copyright © 2016 Elsevier Inc. All rights reserved.

A Multi-Temporal Analyses of Land Surface Temperature Using Landsat-8 Data and Open Source Software: The Case Study of Modena, Italy

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Tommaso Barbieri

2018-05-01

Full Text Available The Urban Heat Island (UHI phenomenon, namely urban areas where the atmospheric temperature is significantly higher than in the surrounding rural areas, is currently a very well-known topic both in the scientific community and in public debates. Growing urbanization is one of the anthropic causes of UHI. The UHI phenomenon has a negative impact on the life quality of the local population (thermal discomfort, summer thermal shock, etc., thus investigations and analyses on this topic are really useful and important for correct and sustainable urban planning; this study is included in this context. A multi-temporal analysis was performed in the municipality of Modena (Italy to identify and estimate the Surface Urban Heat Island (SUHI, strictly correlated to the UHI phenomenon from 2014 to 2017. For this purpose, Landsat-8 satellite images were processed with Quantum Geographic Information System (QGIS to obtain the Land Surface Temperature (LST and the Normalized Difference Vegetation Index (NDVI. For every pixel, LST and NDVI values of three regions of interest (ROI, i.e., Countryside, Suburbs, and City Center were extracted and their correlations were investigated. A maximum variation of 6.4 °C in the LST values between City Center and Countryside was highlighted, confirming the presence of the SUHI phenomenon even in a medium-sized municipality like Modena. The implemented procedure demonstrates that satellite data are suitable for SUHI identification and estimation, therefore it could be a useful tool for public administration for urban planning policies.

Selection of the Best Security Controls for Rapid Development of Enterprise-Level Cyber Security

Science.gov (United States)

2017-03-01

investment (ROI) assessment. This ROI assessment entailed consideration of both the likely/expected security benefits of each candidate security control...the top 10–20 cyber security controls, where ranking was based upon a return on investment (ROI) assessment. This ROI assessment entailed...11  II.  CYBER SECURITY: UNDERLYING PRINCIPLES, FUNDAMENTALS AND BEST PRACTICES .................................................13  A

A multi-institution evaluation of deformable image registration algorithms for automatic organ delineation in adaptive head and neck radiotherapy

International Nuclear Information System (INIS)

Hardcastle, Nicholas; Kumar, Prashant; Oechsner, Markus; Richter, Anne; Song, Shiyu; Myers, Michael; Polat, Bülent; Bzdusek, Karl; Tomé, Wolfgang A; Cannon, Donald M; Brouwer, Charlotte L; Wittendorp, Paul WH; Dogan, Nesrin; Guckenberger, Matthias; Allaire, Stéphane; Mallya, Yogish

2012-01-01

Adaptive Radiotherapy aims to identify anatomical deviations during a radiotherapy course and modify the treatment plan to maintain treatment objectives. This requires regions of interest (ROIs) to be defined using the most recent imaging data. This study investigates the clinical utility of using deformable image registration (DIR) to automatically propagate ROIs. Target (GTV) and organ-at-risk (OAR) ROIs were non-rigidly propagated from a planning CT scan to a per-treatment CT scan for 22 patients. Propagated ROIs were quantitatively compared with expert physician-drawn ROIs on the per-treatment scan using Dice scores and mean slicewise Hausdorff distances, and center of mass distances for GTVs. The propagated ROIs were qualitatively examined by experts and scored based on their clinical utility. Good agreement between the DIR-propagated ROIs and expert-drawn ROIs was observed based on the metrics used. 94% of all ROIs generated using DIR were scored as being clinically useful, requiring minimal or no edits. However, 27% (12/44) of the GTVs required major edits. DIR was successfully used on 22 patients to propagate target and OAR structures for ART with good anatomical agreement for OARs. It is recommended that propagated target structures be thoroughly reviewed by the treating physician

First clinical experience with a multiple region of interest registration and correction method in radiotherapy of head-and-neck cancer patients

International Nuclear Information System (INIS)

Beek, Suzanne van; Kranen, Simon van; Mencarelli, Angelo; Remeijer, Peter; Rasch, Coen; Herk, Marcel van; Sonke, Jan-Jakob

2010-01-01

Purpose: To discuss the first clinical experience with a multiple region of interest (mROI) registration and correction method for high-precision radiotherapy of head-and-neck cancer patients. Materials and methods: 12-13 3D rectangular-shaped ROIs were automatically placed around bony structures on the planning CT scans (n = 50 patients) which were individually registered to subsequent CBCT scans. mROI registration was used to quantify global and local setup errors. The time required to perform the mROI registration was compared with that of a previously used single-ROI method. The number of scans with residual local setup error exceeding 5 mm/5 deg. (warnings) was scored together with the frequency ROIs exceeding these limits for three or more consecutive imaging fractions (systematic errors). Results: In 40% of the CBCT scans, one or more ROI-registrations exceeded the 5 mm/5 deg.. Most warnings were seen in ROI 'hyoid', 31% of the rotation warnings and 14% of the translation warnings. Systematic errors lead to 52 consults of the treating physician. The preparation and registration time was similar for both registration methods. Conclusions: The mROI registration method is easy to use with little extra workload, provides additional information on local setup errors, and helps to select patients for re-planning.

Biochemical and full genome sequence analyses of clinical Vibrio cholerae isolates in Mexico reveals the presence of novel V. cholerae strains.

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Díaz-Quiñonez, José Alberto; Hernández-Monroy, Irma; Montes-Colima, Norma Angélica; Moreno-Pérez, María Asunción; Galicia-Nicolás, Adriana Guadalupe; López-Martínez, Irma; Ruiz-Matus, Cuitláhuac; Kuri-Morales, Pablo; Ortíz-Alcántara, Joanna María; Garcés-Ayala, Fabiola; Ramírez-González, José Ernesto

2016-05-01

The first week of September 2013, the National Epidemiological Surveillance System identified two cases of cholera in Mexico City. The cultures of both samples were confirmed as Vibrio cholerae serogroup O1, serotype Ogawa, biotype El Tor. Initial analyses by PFGE and by PCR-amplification of the virulence genes, suggested that both strains were similar, but different from those previously reported in Mexico. The following week, four more cases were identified in a community in the state of Hidalgo, located 121 km northeast of Mexico City. Thereafter a cholera outbreak started in the region of La Huasteca. Genomic analyses of the four strains obtained in this study confirmed the presence of Pathogenicity Islands VPI-1 and -2, VSP-1 and -2, and of the integrative element SXT. The genomic structure of the 4 isolates was similar to that of V. cholerae strain 2010 EL-1786, identified during the epidemic in Haiti in 2010. Copyright © 2016 Institut Pasteur. Published by Elsevier Masson SAS. All rights reserved.

Neural bases for basic processes in heuristic problem solving: Take solving Sudoku puzzles as an example.

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Qin, Yulin; Xiang, Jie; Wang, Rifeng; Zhou, Haiyan; Li, Kuncheng; Zhong, Ning

2012-12-01

Newell and Simon postulated that the basic steps in human problem-solving involve iteratively applying operators to transform the state of the problem to eventually achieve a goal. To check the neural basis of this framework, the present study focused on the basic processes in human heuristic problem-solving that the participants identified the current problem state and then recalled and applied the corresponding heuristic rules to change the problem state. A new paradigm, solving simplified Sudoku puzzles, was developed for an event-related functional magnetic resonance imaging (fMRI) study in problem solving. Regions of interest (ROIs), including the left prefrontal cortex, the bilateral posterior parietal cortex, the anterior cingulated cortex, the bilateral caudate nuclei, the bilateral fusiform, as well as the bilateral frontal eye fields, were found to be involved in the task. To obtain convergent evidence, in addition to traditional statistical analysis, we used the multivariate voxel classification method to check the accuracy of the predictions for the condition of the task from the blood oxygen level dependent (BOLD) response of the ROIs, using a new classifier developed in this study for fMRI data. To reveal the roles that the ROIs play in problem solving, we developed an ACT-R computational model of the information-processing processes in human problem solving, and tried to predict the BOLD response of the ROIs from the task. Advances in human problem-solving research after Newell and Simon are then briefly discussed. © 2012 The Institute of Psychology, Chinese Academy of Sciences and Blackwell Publishing Asia Pty Ltd.

Automatic Delineation of On-Line Head-And-Neck Computed Tomography Images: Toward On-Line Adaptive Radiotherapy

International Nuclear Information System (INIS)

Zhang Tiezhi; Chi Yuwei; Meldolesi, Elisa; Yan Di

2007-01-01

Purpose: To develop and validate a fully automatic region-of-interest (ROI) delineation method for on-line adaptive radiotherapy. Methods and Materials: On-line adaptive radiotherapy requires a robust and automatic image segmentation method to delineate ROIs in on-line volumetric images. We have implemented an atlas-based image segmentation method to automatically delineate ROIs of head-and-neck helical computed tomography images. A total of 32 daily computed tomography images from 7 head-and-neck patients were delineated using this automatic image segmentation method. Manually drawn contours on the daily images were used as references in the evaluation of automatically delineated ROIs. Two methods were used in quantitative validation: (1) the dice similarity coefficient index, which indicates the overlapping ratio between the manually and automatically delineated ROIs; and (2) the distance transformation, which yields the distances between the manually and automatically delineated ROI surfaces. Results: Automatic segmentation showed agreement with manual contouring. For most ROIs, the dice similarity coefficient indexes were approximately 0.8. Similarly, the distance transformation evaluation results showed that the distances between the manually and automatically delineated ROI surfaces were mostly within 3 mm. The distances between two surfaces had a mean of 1 mm and standard deviation of <2 mm in most ROIs. Conclusion: With atlas-based image segmentation, it is feasible to automatically delineate ROIs on the head-and-neck helical computed tomography images in on-line adaptive treatments

Sequencing, Characterization, and Comparative Analyses of the Plastome of Caragana rosea var. rosea

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Mei Jiang

2018-05-01

Full Text Available To exploit the drought-resistant Caragana species, we performed a comparative study of the plastomes from four species: Caragana rosea, C. microphylla, C. kozlowii, and C. Korshinskii. The complete plastome sequence of the C. rosea was obtained using the next generation DNA sequencing technology. The genome is a circular structure of 133,122 bases and it lacks inverted repeat. It contains 111 unique genes, including 76 protein-coding, 30 tRNA, and four rRNA genes. Repeat analyses obtained 239, 244, 258, and 246 simple sequence repeats in C. rosea, C. microphylla, C. kozlowii, and C. korshinskii, respectively. Analyses of sequence divergence found two intergenic regions: trnI-CAU-ycf2 and trnN-GUU-ycf1, exhibiting a high degree of variations. Phylogenetic analyses showed that the four Caragana species belong to a monophyletic clade. Analyses of Ka/Ks ratios revealed that five genes: rpl16, rpl20, rps11, rps7, and ycf1 and several sites having undergone strong positive selection in the Caragana branch. The results lay the foundation for the development of molecular markers and the understanding of the evolutionary process for drought-resistant characteristics.

Metagenomic analyses reveal the involvement of syntrophic consortia in methanol/electricity conversion in microbial fuel cells.

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Yamamuro, Ayaka; Kouzuma, Atsushi; Abe, Takashi; Watanabe, Kazuya

2014-01-01

Methanol is widely used in industrial processes, and as such, is discharged in large quantities in wastewater. Microbial fuel cells (MFCs) have the potential to recover electric energy from organic pollutants in wastewater; however, the use of MFCs to generate electricity from methanol has not been reported. In the present study, we developed single-chamber MFCs that generated electricity from methanol at the maximum power density of 220 mW m(-2) (based on the projected area of the anode). In order to reveal how microbes generate electricity from methanol, pyrosequencing of 16S rRNA-gene amplicons and Illumina shotgun sequencing of metagenome were conducted. The pyrosequencing detected in abundance Dysgonomonas, Sporomusa, and Desulfovibrio in the electrolyte and anode and cathode biofilms, while Geobacter was detected only in the anode biofilm. Based on known physiological properties of these bacteria, it is considered that Sporomusa converts methanol into acetate, which is then utilized by Geobacter to generate electricity. This speculation is supported by results of shotgun metagenomics of the anode-biofilm microbes, which reconstructed relevant catabolic pathways in these bacteria. These results suggest that methanol is anaerobically catabolized by syntrophic bacterial consortia with electrodes as electron acceptors.

Effects of Hormone Therapy on Brain Volumes Changes of Postmenopausal Women Revealed by Optimally-Discriminative Voxel-Based Morphometry.

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Tianhao Zhang

Full Text Available The Women's Health Initiative Memory Study Magnetic Resonance Imaging (WHIMS-MRI provides an opportunity to evaluate how menopausal hormone therapy (HT affects the structure of older women's brains. Our earlier work based on region of interest (ROI analysis demonstrated potential structural changes underlying adverse effects of HT on cognition. However, the ROI-based analysis is limited in statistical power and precision, and cannot provide fine-grained mapping of whole-brain changes.We aimed to identify local structural differences between HT and placebo groups from WHIMS-MRI in a whole-brain refined level, by using a novel method, named Optimally-Discriminative Voxel-Based Analysis (ODVBA. ODVBA is a recently proposed imaging pattern analysis approach for group comparisons utilizing a spatially adaptive analysis scheme to accurately locate areas of group differences, thereby providing superior sensitivity and specificity to detect the structural brain changes over conventional methods.Women assigned to HT treatments had significant Gray Matter (GM losses compared to the placebo groups in the anterior cingulate and the adjacent medial frontal gyrus, and the orbitofrontal cortex, which persisted after multiple comparison corrections. There were no regions where HT was significantly associated with larger volumes compared to placebo, although a trend of marginal significance was found in the posterior cingulate cortical area. The CEE-Alone and CEE+MPA groups, although compared with different placebo controls, demonstrated similar effects according to the spatial patterns of structural changes.HT had adverse effects on GM volumes and risk for cognitive impairment and dementia in older women. These findings advanced our understanding of the neurobiological underpinnings of HT effects.

Lagrangian Coherent Structure Analysis of Terminal Winds: Three-Dimensionality, Intramodel Variations, and Flight Analyses

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Brent Knutson

2015-01-01

Full Text Available We present a study of three-dimensional Lagrangian coherent structures (LCS near the Hong Kong International Airport and relate to previous developments of two-dimensional (2D LCS analyses. The LCS are contrasted among three independent models and against 2D coherent Doppler light detection and ranging (LIDAR data. Addition of the velocity information perpendicular to the LIDAR scanning cone helps solidify flow structures inferred from previous studies; contrast among models reveals the intramodel variability; and comparison with flight data evaluates the performance among models in terms of Lagrangian analyses. We find that, while the three models and the LIDAR do recover similar features of the windshear experienced by a landing aircraft (along the landing trajectory, their Lagrangian signatures over the entire domain are quite different—a portion of each numerical model captures certain features resembling those LCS extracted from independent 2D LIDAR analyses based on observations.

Histogram analysis of apparent diffusion coefficient maps for assessing thymic epithelial tumours: correlation with world health organization classification and clinical staging.

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Kong, Ling-Yan; Zhang, Wei; Zhou, Yue; Xu, Hai; Shi, Hai-Bin; Feng, Qing; Xu, Xiao-Quan; Yu, Tong-Fu

2018-04-01

To investigate the value of apparent diffusion coefficients (ADCs) histogram analysis for assessing World Health Organization (WHO) pathological classification and Masaoka clinical stages of thymic epithelial tumours. 37 patients with histologically confirmed thymic epithelial tumours were enrolled. ADC measurements were performed using hot-spot ROI (ADC HS-ROI ) and histogram-based approach. ADC histogram parameters included mean ADC (ADC mean ), median ADC (ADC median ), 10 and 90 percentile of ADC (ADC 10 and ADC 90 ), kurtosis and skewness. One-way ANOVA, independent-sample t-test, and receiver operating characteristic were used for statistical analyses. There were significant differences in ADC mean , ADC median , ADC 10 , ADC 90 and ADC HS-ROI among low-risk thymoma (type A, AB, B1; n = 14), high-risk thymoma (type B2, B3; n = 9) and thymic carcinoma (type C, n = 14) groups (all p-values histogram analysis may assist in assessing the WHO pathological classification and Masaoka clinical stages of thymic epithelial tumours. Advances in knowledge: 1. ADC histogram analysis could help to assess WHO pathological classification of thymic epithelial tumours. 2. ADC histogram analysis could help to evaluate Masaoka clinical stages of thymic epithelial tumours. 3. ADC 10 might be a promising imaging biomarker for assessing and characterizing thymic epithelial tumours.

Financial literacy is associated with medial brain region functional connectivity in old age.

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Han, S Duke; Boyle, Patricia A; Yu, Lei; Fleischman, Debra A; Arfanakis, Konstantinos; Leurgans, Sue; Bennett, David A

2014-01-01

Financial literacy refers to the ability to access and utilize financial information in ways that promote better outcomes. In old age, financial literacy has been associated with a wide range of positive characteristics; however, the neural correlates remain unclear. Recent work has suggested greater co-activity between anterior-posterior medial brain regions is associated with better brain functioning. We hypothesized financial literacy would be associated with this pattern. We assessed whole-brain functional connectivity to a posterior cingulate cortex (PCC) seed region of interest (ROI) in 138 participants of the Rush Memory and Aging Project. Results revealed financial literacy was associated with greater functional connectivity between the PCC and three regions: the right ventromedial prefrontal cortex (vmPFC), the left postcentral gyrus, and the right precuneus. Results also revealed financial literacy was associated negatively with functional connectivity between the PCC and left caudate. Post hoc analyses showed the PCC-vmPFC relationship accounted for the most variance in a regression model adjusted for all four significant functional connectivity relationships, demographic factors, and global cognition. These findings provide information on the neural mechanisms associated with financial literacy in old age. Copyright © 2014 Elsevier Ireland Ltd. All rights reserved.

Transcriptomic and Functional Analyses Reveal That PpGLK1 Regulates Chloroplast Development in Peach (Prunus persica

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Min Chen

2018-01-01

Full Text Available Peach is an ideal species for fruit tree research because of its small, fully sequenced genome. Chloroplast development is dependent on the tight cooperation between the nuclear and plastid genomes, and is regulated by GLK transcription factors. In this work, the pigment content was monitored and the chloroplast-to-chromoplast conversion during the fruit ripening was visualized by transmission electron microscopy. Localization and expression analyses showed that PpGLK1 was located in the nucleus and expressed mainly in the leaves and fruit skin. A transcriptome analysis showed that PpGLK1 and its target genes were significantly differentially expressed in ripening peach fruit skin. PpGLK1 silencing affected chlorophyll accumulation in peach leaves and fruits. Overexpression of PpGLK1 rescued the phenotypes of the Arabidopsis Atglk1Atglk2 double mutant and the tomato uniform ripening mutant. The results of a yeast two-hybrid analysis showed that PpGLK1 is autoactivated and that PpGLK1 (301-542 a.a. interacted with PpARF5. Together, our results indicate that PpGLK1 regulates chloroplast development in green tissues in peach. Therefore, it may be a promising target gene for improving the production and quality of peach by genetic engineering and breeding approaches.

Transcriptome-wide mega-analyses reveal joint dysregulation of immunologic genes and transcription regulators in brain and blood in schizophrenia.

Science.gov (United States)

Hess, Jonathan L; Tylee, Daniel S; Barve, Rahul; de Jong, Simone; Ophoff, Roel A; Kumarasinghe, Nishantha; Tooney, Paul; Schall, Ulrich; Gardiner, Erin; Beveridge, Natalie Jane; Scott, Rodney J; Yasawardene, Surangi; Perera, Antionette; Mendis, Jayan; Carr, Vaughan; Kelly, Brian; Cairns, Murray; Tsuang, Ming T; Glatt, Stephen J

2016-10-01

The application of microarray technology in schizophrenia research was heralded as paradigm-shifting, as it allowed for high-throughput assessment of cell and tissue function. This technology was widely adopted, initially in studies of postmortem brain tissue, and later in studies of peripheral blood. The collective body of schizophrenia microarray literature contains apparent inconsistencies between studies, with failures to replicate top hits, in part due to small sample sizes, cohort-specific effects, differences in array types, and other confounders. In an attempt to summarize existing studies of schizophrenia cases and non-related comparison subjects, we performed two mega-analyses of a combined set of microarray data from postmortem prefrontal cortices (n=315) and from ex-vivo blood tissues (n=578). We adjusted regression models per gene to remove non-significant covariates, providing best-estimates of transcripts dysregulated in schizophrenia. We also examined dysregulation of functionally related gene sets and gene co-expression modules, and assessed enrichment of cell types and genetic risk factors. The identities of the most significantly dysregulated genes were largely distinct for each tissue, but the findings indicated common emergent biological functions (e.g. immunity) and regulatory factors (e.g., predicted targets of transcription factors and miRNA species across tissues). Our network-based analyses converged upon similar patterns of heightened innate immune gene expression in both brain and blood in schizophrenia. We also constructed generalizable machine-learning classifiers using the blood-based microarray data. Our study provides an informative atlas for future pathophysiologic and biomarker studies of schizophrenia. Published by Elsevier B.V.

Leveraging Algal Omics to Reveal Potential Targets for Augmenting TAG Accumulation

Energy Technology Data Exchange (ETDEWEB)

Guarnieri, Michael T [National Renewable Energy Laboratory (NREL), Golden, CO (United States); Pienkos, Philip T [National Renewable Energy Laboratory (NREL), Golden, CO (United States); Arora, Neha [Indian Institute of Technology Roorkee; Pruthi, Vikas [Indian Institute of Technology Roorkee; Poluri, Krishna Mohan [Indian Institute of Technology Roorkee

2018-04-18

Ongoing global efforts to commercialize microalgal biofuels have expedited the use of multi-omics techniques to gain insights into lipid biosynthetic pathways. Functional genomics analyses have recently been employed to complement existing sequence-level omics studies, shedding light on the dynamics of lipid synthesis and its interplay with other cellular metabolic pathways, thus revealing possible targets for metabolic engineering. Here, we review the current status of algal omics studies to reveal potential targets to augment TAG accumulation in various microalgae. This review specifically aims to examine and catalog systems level data related to stress-induced TAG accumulation in oleaginous microalgae and inform future metabolic engineering strategies to develop strains with enhanced bioproductivity, which could pave a path for sustainable green energy.

Comparative biochemical analyses of venous blood and peritoneal fluid from horses with colic using a portable analyser and an in-house analyser.

Science.gov (United States)

Saulez, M N; Cebra, C K; Dailey, M

2005-08-20

Fifty-six horses with colic were examined over a period of three months. The concentrations of glucose, lactate, sodium, potassium and chloride, and the pH of samples of blood and peritoneal fluid, were determined with a portable clinical analyser and with an in-house analyser and the results were compared. Compared with the in-house analyser, the portable analyser gave higher pH values for blood and peritoneal fluid with greater variability in the alkaline range, and lower pH values in the acidic range, lower concentrations of glucose in the range below 8.3 mmol/l, and lower concentrations of lactate in venous blood in the range below 5 mmol/l and in peritoneal fluid in the range below 2 mmol/l, with less variability. On average, the portable analyser underestimated the concentrations of lactate and glucose in peritoneal fluid in comparison with the in-house analyser. Its measurements of the concentrations of sodium and chloride in peritoneal fluid had a higher bias and were more variable than the measurements in venous blood, and its measurements of potassium in venous blood and peritoneal fluid had a smaller bias and less variability than the measurements made with the in-house analyser.

Molecular systematics of Indian Alysicarpus (Fabaceae) based on analyses of nuclear ribosomal DNA sequences.

Science.gov (United States)

Gholami, Akram; Subramaniam, Shweta; Geeta, R; Pandey, Arun K

2017-06-01

Alysicarpus Necker ex Desvaux (Fabaceae, Desmodieae) consists of ~30 species that are distributed in tropical and subtropical regions of theworld. In India, the genus is represented by ca. 18 species, ofwhich seven are endemic. Sequences of the nuclear Internal transcribed spacer from38 accessions representing 16 Indian specieswere subjected to phylogenetic analyses. The ITS sequence data strongly support the monophyly of the genus Alysicarpus. Analyses revealed four major well-supported clades within Alysicarpus. Ancestral state reconstructions were done for two morphological characters, namely calyx length in relation to pod (macrocalyx and microcalyx) and pod surface ornamentation (transversely rugose and nonrugose). The present study is the first report on molecular systematics of Indian Alysicarpus.

Landscape genetic analyses reveal fine-scale effects of forest fragmentation in an insular tropical bird.

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Khimoun, Aurélie; Peterman, William; Eraud, Cyril; Faivre, Bruno; Navarro, Nicolas; Garnier, Stéphane

2017-10-01

Within the framework of landscape genetics, resistance surface modelling is particularly relevant to explicitly test competing hypotheses about landscape effects on gene flow. To investigate how fragmentation of tropical forest affects population connectivity in a forest specialist bird species, we optimized resistance surfaces without a priori specification, using least-cost (LCP) or resistance (IBR) distances. We implemented a two-step procedure in order (i) to objectively define the landscape thematic resolution (level of detail in classification scheme to describe landscape variables) and spatial extent (area within the landscape boundaries) and then (ii) to test the relative role of several landscape features (elevation, roads, land cover) in genetic differentiation in the Plumbeous Warbler (Setophaga plumbea). We detected a small-scale reduction of gene flow mainly driven by land cover, with a negative impact of the nonforest matrix on landscape functional connectivity. However, matrix components did not equally constrain gene flow, as their conductivity increased with increasing structural similarity with forest habitat: urban areas and meadows had the highest resistance values whereas agricultural areas had intermediate resistance values. Our results revealed a higher performance of IBR compared to LCP in explaining gene flow, reflecting suboptimal movements across this human-modified landscape, challenging the common use of LCP to design habitat corridors and advocating for a broader use of circuit theory modelling. Finally, our results emphasize the need for an objective definition of landscape scales (landscape extent and thematic resolution) and highlight potential pitfalls associated with parameterization of resistance surfaces. © 2017 John Wiley & Sons Ltd.

Hemoglobin analyses in the Netherlands reveal more than 80 different variants including six novel ones.

Science.gov (United States)

van Zwieten, Rob; Veldthuis, Martijn; Delzenne, Barend; Berghuis, Jeffrey; Groen, Joke; Ait Ichou, Fatima; Clifford, Els; Harteveld, Cornelis L; Stroobants, An K

2014-01-01

More than 20,000 blood samples of individuals living in The Netherlands and suspected of hemolytic anemia or diabetes were analyzed by high resolution cation exchange high performance liquid chromatography (HPLC). Besides common disease-related hemoglobins (Hbs), rare variants were also detected. The variant Hbs were retrospectively analyzed by capillary zone electrophoresis (CZE) and by isoelectric focusing (IEF). For unambiguous identification, the globin genes were sequenced. Most of the 80 Hb variants detected by initial screening on HPLC were also separated by capillary electrophoresis (CE), but a few variants were only detectable with one of these methods. Some variants were unstable, had thalassemic properties or increased oxygen affinity, and some interfered with Hb A2 measurement, detection of sickle cell Hb or Hb A1c quantification. Two of the six novel variants, Hb Enschede (HBA2: c.308G  > A, p.Ser103Asn) and Hb Weesp (HBA1: c.301C > T, p.Leu101Phe), had no clinical consequences. In contrast, two others appeared clinically significant: Hb Ede (HBB: c.53A > T, p.Lys18Met) caused thalassemia and Hb Waterland (HBB: c.428C > T, pAla143Val) was related to mild polycytemia. Hb A2-Venlo (HBD: c.193G > A, p.Gly65Ser) and Hb A2-Rotterdam (HBD: c.38A > C, p.Asn13Thr) interfered with Hb A2 quantification. This survey shows that HPLC analysis followed by globin gene sequencing of rare variants is an effective method to reveal Hb variants.

Analyses of Evolutionary Characteristics of the Hemagglutinin-Esterase Gene of Influenza C Virus during a Period of 68 Years Reveals Evolutionary Patterns Different from Influenza A and B Viruses

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Yuki Furuse

2016-11-01

Full Text Available Infections with the influenza C virus causing respiratory symptoms are common, particularly among children. Since isolation and detection of the virus are rarely performed, compared with influenza A and B viruses, the small number of available sequences of the virus makes it difficult to analyze its evolutionary dynamics. Recently, we reported the full genome sequence of 102 strains of the virus. Here, we exploited the data to elucidate the evolutionary characteristics and phylodynamics of the virus compared with influenza A and B viruses. Along with our data, we obtained public sequence data of the hemagglutinin-esterase gene of the virus; the dataset consists of 218 unique sequences of the virus collected from 14 countries between 1947 and 2014. Informatics analyses revealed that (1 multiple lineages have been circulating globally; (2 there have been weak and infrequent selective bottlenecks; (3 the evolutionary rate is low because of weak positive selection and a low capability to induce mutations; and (4 there is no significant positive selection although a few mutations affecting its antigenicity have been induced. The unique evolutionary dynamics of the influenza C virus must be shaped by multiple factors, including virological, immunological, and epidemiological characteristics.

Conventional and advanced exergetic analyses applied to a combined cycle power plant

International Nuclear Information System (INIS)

Petrakopoulou, Fontina; Tsatsaronis, George; Morosuk, Tatiana; Carassai, Anna

2012-01-01

Conventional exergy-based methods pinpoint components and processes with high irreversibilities. However, they lack certain insight. For a given advanced technological state, there is a minimum level of exergy destruction related to technological and/or economic constraints that is unavoidable. Furthermore, in any thermodynamic system, exergy destruction stems from both component interactions (exogenous) and component inefficiencies (endogenous). To overcome the limitations of the conventional analyses and to increase our knowledge about a plant, advanced exergy-based analyses have been developed. In this paper, a combined cycle power plant is analyzed using both conventional and advanced exergetic analyses. Except for the expander of the gas turbine system and the high-pressure steam turbine, most of the exergy destruction in the plant components is unavoidable. This unavoidable part is constrained by internal technological limitations, i.e. each component’s endogenous exergy destruction. High levels of endogenous exergy destruction show that component interactions do not contribute significantly to the thermodynamic inefficiencies. In addition, these inefficiencies are unavoidable to a large extent. With the advanced analysis, new improvement strategies are revealed that could not otherwise be found. -- Highlights: ► This is the first application of a complete advanced exergetic analysis to a complex power plant. ► In the three-pressure-level combined cycle power plant studied here, the improvement potential of the majority of the components is low, since most of the exergy destruction is unavoidable. ► Component interactions are generally of lower importance for the considered plant. ► Splitting the exogenous exergy destruction reveals one-to-one component interactions and improvement strategies. ► The advanced exergetic analysis is a necessary supplement to the conventional analysis in improving a complex system.

Primary and metastatic ovarian cancer: Characterization by 3.0T diffusion-weighted MRI

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Lindgren, Auni [Kuopio University Hospital, Department of Gynaecology and Obstetrics, Kuopio (Finland); Anttila, Maarit [Kuopio University Hospital, Department of Gynaecology and Obstetrics, Kuopio (Finland); University of Eastern Finland, Institute of Clinical Medicine, School of Medicine, Gynaecology, Kuopio (Finland); Rautiainen, Suvi; Arponen, Otso; Haermae, Kirsi [Kuopio University Hospital, Department of Clinical Radiology, Kuopio (Finland); Kivelae, Annukka; Maekinen, Petri; Ylae-Herttuala, Seppo [University of Eastern Finland, Department of Biotechnology and Molecular Medicine, A.I. Virtanen Institute for Molecular Sciences, Kuopio (Finland); Haemaelaeinen, Kirsi [Kuopio University Hospital, Department of Pathology and Forensic Medicine, Kuopio (Finland); University of Eastern Finland, Institute of Clinical Medicine, School of Medicine, Pathology and Forensic Medicine, Kuopio (Finland); Kosma, Veli-Matti [Kuopio University Hospital, Department of Pathology and Forensic Medicine, Kuopio (Finland); University of Eastern Finland, Institute of Clinical Medicine, School of Medicine, Pathology and Forensic Medicine, Kuopio (Finland); University of Eastern Finland, Cancer Center of Eastern Finland, Kuopio (Finland); Vanninen, Ritva [Kuopio University Hospital, Department of Clinical Radiology, Kuopio (Finland); University of Eastern Finland, Cancer Center of Eastern Finland, Kuopio (Finland); University of Eastern Finland, Institute of Clinical Medicine, School of Medicine, Clinical Radiology, Kuopio (Finland); Sallinen, Hanna [Kuopio University Hospital, Department of Gynaecology and Obstetrics, Kuopio (Finland); University of Eastern Finland, Institute of Clinical Medicine, School of Medicine, Gynaecology, Kuopio (Finland); University of Eastern Finland, Department of Biotechnology and Molecular Medicine, A.I. Virtanen Institute for Molecular Sciences, Kuopio (Finland)

2017-09-15

We aimed to investigate whether apparent diffusion coefficients (ADCs) measured by 3.0T diffusion-weighted magnetic resonance imaging (DWI) associate with histological aggressiveness of ovarian cancer (OC) or predict the clinical outcome. This prospective study enrolled 40 patients with primary OC, treated 2011-2014. DWI was performed prior to surgery. Two observers used whole lesion single plane region of interest (WLsp-ROI) and five small ROIs (S-ROI) to analyze ADCs. Samples from tumours and metastases were collected during surgery. Immunohistochemistry and quantitative reverse transcription polymerase chain reaction (qRT-PCR) were used to measure the expression of vascular endothelial growth factor (VEGF) and its receptors. The interobserver reliability of ADC measurements was excellent for primary tumours ICC 0.912 (WLsp-ROI). Low ADCs significantly associated with poorly differentiated OC (WLsp-ROI P = 0.035). In primary tumours, lower ADCs significantly associated with high Ki-67 (P = 0.001) and low VEGF (P = 0.001) expression. In metastases, lower ADCs (WLsp-ROI) significantly correlated with low VEGF receptors mRNA levels. ADCs had predictive value; 3-year overall survival was poorer in patients with lower ADCs (WLsp-ROI P = 0.023, S-ROI P = 0.038). Reduced ADCs are associated with histological severity and worse outcome in OC. ADCs measured with WLsp-ROI may serve as a prognostic biomarker of OC. (orig.)

Primary and metastatic ovarian cancer: Characterization by 3.0T diffusion-weighted MRI

International Nuclear Information System (INIS)

Lindgren, Auni; Anttila, Maarit; Rautiainen, Suvi; Arponen, Otso; Haermae, Kirsi; Kivelae, Annukka; Maekinen, Petri; Ylae-Herttuala, Seppo; Haemaelaeinen, Kirsi; Kosma, Veli-Matti; Vanninen, Ritva; Sallinen, Hanna

2017-01-01

We aimed to investigate whether apparent diffusion coefficients (ADCs) measured by 3.0T diffusion-weighted magnetic resonance imaging (DWI) associate with histological aggressiveness of ovarian cancer (OC) or predict the clinical outcome. This prospective study enrolled 40 patients with primary OC, treated 2011-2014. DWI was performed prior to surgery. Two observers used whole lesion single plane region of interest (WLsp-ROI) and five small ROIs (S-ROI) to analyze ADCs. Samples from tumours and metastases were collected during surgery. Immunohistochemistry and quantitative reverse transcription polymerase chain reaction (qRT-PCR) were used to measure the expression of vascular endothelial growth factor (VEGF) and its receptors. The interobserver reliability of ADC measurements was excellent for primary tumours ICC 0.912 (WLsp-ROI). Low ADCs significantly associated with poorly differentiated OC (WLsp-ROI P = 0.035). In primary tumours, lower ADCs significantly associated with high Ki-67 (P = 0.001) and low VEGF (P = 0.001) expression. In metastases, lower ADCs (WLsp-ROI) significantly correlated with low VEGF receptors mRNA levels. ADCs had predictive value; 3-year overall survival was poorer in patients with lower ADCs (WLsp-ROI P = 0.023, S-ROI P = 0.038). Reduced ADCs are associated with histological severity and worse outcome in OC. ADCs measured with WLsp-ROI may serve as a prognostic biomarker of OC. (orig.)

Les femmes aux travaux d’aiguille: un topos littéraire?

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Viviane Cunha

2011-11-01

Full Text Available Resumo: O artigo apresenta um estudo do topos da tecedeira/fiandeira no universo das artes visuais e na literatura abordando sobretudo o da literatura grega e o do lirismo medieval. O corpus de análise é constituído da Odisséia no que concerne ao universo clássico, do romance Philomena (Chrétien de Troyes e da epopéia Berte as grans piés (Adenet le Roi no que concerne aos textos medievais. Procura-se assim apresentar essas figuras emblemáticas através da história e numa perspectiva interdisciplinar.Palavras-chave: Literatura comparada; literatura grega; Homero; Odisséia; literatura francesa; Chrétien de Troyes; Philomena; Adenet le Roi; Berte as grans piés; mulher; tecedeira; fiandeira.Résumé: L’article présente une étude du topos de la tisseuse/fileuse dans l’univers des arts visuels et dans la littérature en approchant surtout celui de la poésie grecque et celui du lyrisme medieval. Le corpus d’analyse se constitue de l’Odyssée en ce qui concerne l’univers classique, du roman Philomena (Chrétien de Troyes et de l’épopée Berte as grans piés (Adenet Le Roi en ce qui concerne les textes médiévaux. On cherche ainsi à présenter ces figures emblématiques à travers l’histoire et dans une perspective interdisciplinaire.Mots-clés: Littérature comparée; littérature grecque; Homère; Odyssée; littérature française; Chrétien de Troyes; Philomena; Adenet le Roi; Berte as grans piés; femme; tisseuse; fileuse.Keywords: Comparative literature; Greek literatura; Homer; Odyssey; French literature; Chrétien de Troyes; Philomena; Adenet le Roi; Berte as grans piés; women; weaver; spinner.

Altered relationships between rCBF in different brain regions of never-treated schizophrenics

International Nuclear Information System (INIS)

Sabri, O.; Schreckenberger, M.; Cremerius, U.; Dickmann, C.; Schulz, G.; Zimny, M.; Buell, U.; Erkwoh, R.; Owega, A.; Sass, H.

1997-01-01

Aim of this study was to investigate the relations between regional cerebral blood flow (rCBF) of different brain regions in acute schizophrenia and following neuroleptic treatment. Methods: Twenty-two never-treated, acute schizophrenic patients were examined with HMPAO brain SPECT and assessed psychopathologically, and reexamined following neuroleptic treatment (over 96.8 days) and psychopathological remission. rCBF was determined by region/cerebellar count quotients obtained from 98 irregular regions of interest (ROIs), summed up to 11 ROIs on each hemisphere. In acute schizophrenics, interregional rCBF correlations of each ROI to every other ROI were compared to the interregional correlations following neuroleptic treatment and to those of controls. Results: All significant correlations of rCBF ratios of different brain regions were exclusively positive in controls and patients. In controls, all ROIs of one hemisphere except the mesial temporal ROI correlated significantly to its contralateral ROI. Each hemisphere showed significant frontal-temporal correlations, as well as cortical-subcortical and some cortico-limbic. In contrast, in acute schizophrenics nearly every ROI correlated significantly with every other ROI, without a grouping or relation of the rCBF of certain ROIs as in controls. After neuroleptic treatment and clinical improvement, this diffuse pattern of correlations remained. Conclusions: These results indicate differences in the neuronal interplay between regions in schizophrenic and healthy subjects. In nevertreated schizophrenics, diffuse interregional rCBF correlations can be seen as a sign of change and dysfunction of the systems regulating specificity and diversity of the neuronal functions. Neuroleptic therapy and psychopathologic remission showed no normalizing effect on interregional correlations. (orig.) [de

Biostratigraphic and morphometric analyses of specimens from the calcareous nannofossil genus Tribrachiatus

Science.gov (United States)

Self-Trail, Jean; Seefelt, Ellen L.; Shepherd, Claire L.; Martin, Victoria A.

2017-01-01

Biostratigraphic and morphometric analyses of calcareous nannofossil assemblages from one outcrop and two cored sections of lower Eocene sediments reveal the presence of two new species: Tribrachiatus lunatus sp. nov., and Tribrachiatus absidatus sp. nov. Differences between the new species and Tribrachiatus orthostylus are discussed. The first occurrence of the two new species is just below the calcareous nannofossil Zone NP11/NP12 boundary, close to the Chron 24r/23n boundary, and thus they are globally useful biostratigraphic markers.

Comprehensive logic based analyses of Toll-like receptor 4 signal transduction pathway.

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Mahesh Kumar Padwal

Full Text Available Among the 13 TLRs in the vertebrate systems, only TLR4 utilizes both Myeloid differentiation factor 88 (MyD88 and Toll/Interleukin-1 receptor (TIR-domain-containing adapter interferon-β-inducing Factor (TRIF adaptors to transduce signals triggering host-protective immune responses. Earlier studies on the pathway combined various experimental data in the form of one comprehensive map of TLR signaling. But in the absence of adequate kinetic parameters quantitative mathematical models that reveal emerging systems level properties and dynamic inter-regulation among the kinases/phosphatases of the TLR4 network are not yet available. So, here we used reaction stoichiometry-based and parameter independent logical modeling formalism to build the TLR4 signaling network model that captured the feedback regulations, interdependencies between signaling kinases and phosphatases and the outcome of simulated infections. The analyses of the TLR4 signaling network revealed 360 feedback loops, 157 negative and 203 positive; of which, 334 loops had the phosphatase PP1 as an essential component. The network elements' interdependency (positive or negative dependencies in perturbation conditions such as the phosphatase knockout conditions revealed interdependencies between the dual-specific phosphatases MKP-1 and MKP-3 and the kinases in MAPK modules and the role of PP2A in the auto-regulation of Calmodulin kinase-II. Our simulations under the specific kinase or phosphatase gene-deficiency or inhibition conditions corroborated with several previously reported experimental data. The simulations to mimic Yersinia pestis and E. coli infections identified the key perturbation in the network and potential drug targets. Thus, our analyses of TLR4 signaling highlights the role of phosphatases as key regulatory factors in determining the global interdependencies among the network elements; uncovers novel signaling connections; identifies potential drug targets for

Using wind plant data to increase reliability.

Energy Technology Data Exchange (ETDEWEB)

Peters, Valerie A. (Sandia National Laboratories, Livermore, CA); Ogilvie, Alistair B.; McKenney, Bridget L.

2011-01-01

Operators interested in improving reliability should begin with a focus on the performance of the wind plant as a whole. To then understand the factors which drive individual turbine performance, which together comprise the plant performance, it is necessary to track a number of key indicators. Analysis of these key indicators can reveal the type, frequency, and cause of failures and will also identify their contributions to overall plant performance. The ideal approach to using data to drive good decisions includes first determining which critical decisions can be based on data. When those required decisions are understood, then the analysis required to inform those decisions can be identified, and finally the data to be collected in support of those analyses can be determined. Once equipped with high-quality data and analysis capabilities, the key steps to data-based decision making for reliability improvements are to isolate possible improvements, select the improvements with largest return on investment (ROI), implement the selected improvements, and finally to track their impact.

Dynamic Analyses of Alternative Polyadenylation from RNA-Seq Reveal 3′-UTR Landscape Across 7 Tumor Types

Science.gov (United States)

Xia, Zheng; Donehower, Lawrence A; Cooper, Thomas A.; Neilson, Joel R.; Wheeler, David A.; Wagner, Eric J.; Li, Wei

2015-01-01

Alternative polyadenylation (APA) is a pervasive mechanism in the regulation of most human genes, and its implication in diseases including cancer is only beginning to be appreciated. Since conventional APA profiling has not been widely adopted, global cancer APA studies are very limited. Here we develop a novel bioinformatics algorithm (DaPars) for the de novo identification of dynamic APAs from standard RNA-seq. When applied to 358 TCGA Pan-Cancer tumor/normal pairs across 7 tumor types, DaPars reveals 1,346 genes with recurrent and tumor-specific APAs. Most APA genes (91%) have shorter 3′ UTRs in tumors that can avoid miRNA-mediated repression, including glutaminase (GLS), a key metabolic enzyme for tumor proliferation. Interestingly, selected APA events add strong prognostic power beyond common clinical and molecular variables, suggesting their potential as novel prognostic biomarkers. Finally, our results implicate CstF64, an essential polyadenylation factor, as a master regulator of 3′ UTR shortening across multiple tumor types. PMID:25409906

Metagenomic analyses reveal the involvement of syntrophic consortia in methanol/electricity conversion in microbial fuel cells.

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Ayaka Yamamuro

Full Text Available Methanol is widely used in industrial processes, and as such, is discharged in large quantities in wastewater. Microbial fuel cells (MFCs have the potential to recover electric energy from organic pollutants in wastewater; however, the use of MFCs to generate electricity from methanol has not been reported. In the present study, we developed single-chamber MFCs that generated electricity from methanol at the maximum power density of 220 mW m(-2 (based on the projected area of the anode. In order to reveal how microbes generate electricity from methanol, pyrosequencing of 16S rRNA-gene amplicons and Illumina shotgun sequencing of metagenome were conducted. The pyrosequencing detected in abundance Dysgonomonas, Sporomusa, and Desulfovibrio in the electrolyte and anode and cathode biofilms, while Geobacter was detected only in the anode biofilm. Based on known physiological properties of these bacteria, it is considered that Sporomusa converts methanol into acetate, which is then utilized by Geobacter to generate electricity. This speculation is supported by results of shotgun metagenomics of the anode-biofilm microbes, which reconstructed relevant catabolic pathways in these bacteria. These results suggest that methanol is anaerobically catabolized by syntrophic bacterial consortia with electrodes as electron acceptors.

Correlation between model observer and human observer performance in CT imaging when lesion location is uncertain

Energy Technology Data Exchange (ETDEWEB)

Leng, Shuai; Yu, Lifeng; Zhang, Yi; McCollough, Cynthia H. [Department of Radiology, Mayo Clinic, 200 First Street Southwest, Rochester, Minnesota 55905 (United States); Carter, Rickey [Department of Biostatistics, Mayo Clinic, 200 First Street Southwest, Rochester, Minnesota 55905 (United States); Toledano, Alicia Y. [Biostatistics Consulting, LLC, 10606 Wheatley Street, Kensington, Maryland 20895 (United States)

2013-08-15

Purpose: The purpose of this study was to investigate the correlation between model observer and human observer performance in CT imaging for the task of lesion detection and localization when the lesion location is uncertain.Methods: Two cylindrical rods (3-mm and 5-mm diameters) were placed in a 35 × 26 cm torso-shaped water phantom to simulate lesions with −15 HU contrast at 120 kV. The phantom was scanned 100 times on a 128-slice CT scanner at each of four dose levels (CTDIvol = 5.7, 11.4, 17.1, and 22.8 mGy). Regions of interest (ROIs) around each lesion were extracted to generate images with signal-present, with each ROI containing 128 × 128 pixels. Corresponding ROIs of signal-absent images were generated from images without lesion mimicking rods. The location of the lesion (rod) in each ROI was randomly distributed by moving the ROIs around each lesion. Human observer studies were performed by having three trained observers identify the presence or absence of lesions, indicating the lesion location in each image and scoring confidence for the detection task on a 6-point scale. The same image data were analyzed using a channelized Hotelling model observer (CHO) with Gabor channels. Internal noise was added to the decision variables for the model observer study. Area under the curve (AUC) of ROC and localization ROC (LROC) curves were calculated using a nonparametric approach. The Spearman's rank order correlation between the average performance of the human observers and the model observer performance was calculated for the AUC of both ROC and LROC curves for both the 3- and 5-mm diameter lesions.Results: In both ROC and LROC analyses, AUC values for the model observer agreed well with the average values across the three human observers. The Spearman's rank order correlation values for both ROC and LROC analyses for both the 3- and 5-mm diameter lesions were all 1.0, indicating perfect rank ordering agreement of the figures of merit (AUC

Water deficit mechanisms in perennial shrubs Cerasus humilis leaves revealed by physiological and proteomic analyses.

Science.gov (United States)

Yin, Zepeng; Ren, Jing; Zhou, Lijuan; Sun, Lina; Wang, Jiewan; Liu, Yulong; Song, Xingshun

2016-01-01

Drought (Water deficit, WD) poses a serious threat to extensively economic losses of trees throughout the world. Chinese dwarf cherry ( Cerasus humilis ) is a good perennial plant for studying the physiological and sophisticated molecular network under WD. The aim of this study is to identify the effect of WD on C. humilis through physiological and global proteomics analysis and improve understanding of the WD resistance of plants. Currently, physiological parameters were applied to investigate C. humilis response to WD. Moreover, we used two-dimensional gel electrophoresis (2DE) to identify differentially expressed proteins in C. humilis leaves subjected to WD (24 d). Furthermore, we also examined the correlation between protein and transcript levels. Several physiological parameters, including relative water content and Pn were reduced by WD. In addition, the malondialdehyde (MDA), relative electrolyte leakage (REL), total soluble sugar, and proline were increased in WD-treated C. humilis . Comparative proteomic analysis revealed 46 protein spots (representing 43 unique proteins) differentially expressed in C. humilis leaves under WD. These proteins were mainly involved in photosynthesis, ROS scavenging, carbohydrate metabolism, transcription, protein synthesis, protein processing, and nitrogen and amino acid metabolisms, respectively. WD promoted the CO 2 assimilation by increase light reaction and Calvin cycle, leading to the reprogramming of carbon metabolism. Moreover, the accumulation of osmolytes (i.e., proline and total soluble sugar) and enhancement of ascorbate-glutathione cycle and glutathione peroxidase/glutathione s-transferase pathway in leaves could minimize oxidative damage of membrane and other molecules under WD. Importantly, the regulation role of carbohydrate metabolisms (e. g. glycolysis, pentose phosphate pathways, and TCA) was enhanced. These findings provide key candidate proteins for genetic improvement of perennial plants metabolism under

Bone Regeneration Using N-Methyl-2-pyrrolidone as an Enhancer for Recombinant Human Bone Morphogenetic Protein-2 in a Rabbit Sinus Augmentation Model.

Science.gov (United States)

Lim, Hyun-Chang; Thoma, Daniel S; Yoon, So-Ra; Cha, Jae-Kook; Lee, Jung-Seok; Jung, Ui-Won

2017-01-01

The aim of this study was to determine whether N-methyl-2-pyrrolidone (NMP) can decrease the dose of recombinant human bone morphogenetic protein-2 (rhBMP-2) in sinus augmentation of rabbits. In each of 15 rabbits, 2 sinuses were randomly grafted using 1 of 3 treatment modalities: (i) biphasic calcium phosphate (BCP; control), (ii) rhBMP-2-coated BCP (BMP), or (iii) rhBMP-2-coated BCP soaked in NMP solution (BMP/NMP). The rabbits were sacrificed 2 weeks postoperatively. Histologic and histomorphometric analyses were performed. Bone formation in all groups was predominantly located close to the access window and the lateral walls. Newly formed bone within the total augmented area (NB TA ) was greatest in BMP/NMP (1.94 ± 0.69 mm 2 ), followed by BMP (1.50 ± 0.72 mm 2 ) and BCP (1.28 ± 0.52 mm 2 ) ( P > 0.05). In the center of the augmentation (NB ROI_C ) and the area close to the sinus membrane (NB ROI_M ), BMP/NMP produced the largest area of NB (NB ROI_C : 0.10 ± 0.11 mm 2 ; NB ROI_M : 0.17 ± 0.08 mm 2 ); the corresponding NB values for BCP were 0.05 ± 0.05 mm 2 and 0.08 ± 0.09 mm 2 , respectively ( P > 0.05 for all comparisons). The effect of NMP on bone regeneration was inconsistent between the specimens. Adding NMP as an adjunct to rhBMP-2-coated BCP produced inconsistent effects on bone regeneration, resulting in no significant benefit compared to controls.

The influence of the rs6295 gene polymorphism on serotonin-1A receptor distribution investigated with PET in patients with major depression applying machine learning.

Science.gov (United States)

Kautzky, A; James, G M; Philippe, C; Baldinger-Melich, P; Kraus, C; Kranz, G S; Vanicek, T; Gryglewski, G; Wadsak, W; Mitterhauser, M; Rujescu, D; Kasper, S; Lanzenberger, R

2017-06-13

Major depressive disorder (MDD) is the most common neuropsychiatric disease and despite extensive research, its genetic substrate is still not sufficiently understood. The common polymorphism rs6295 of the serotonin-1A receptor gene (HTR1A) is affecting the transcriptional regulation of the 5-HT 1A receptor and has been closely linked to MDD. Here, we used positron emission tomography (PET) exploiting advances in data mining and statistics by using machine learning in 62 healthy subjects and 19 patients with MDD, which were scanned with PET using the radioligand [carbonyl- 11 C]WAY-100635. All the subjects were genotyped for rs6295 and genotype was grouped in GG vs C allele carriers. Mixed model was applied in a ROI-based (region of interest) approach. ROI binding potential (BP ND ) was divided by dorsal raphe BP ND as a specific measure to highlight rs6295 effects (BP Div ). Mixed model produced an interaction effect of ROI and genotype in the patients' group but no effects in healthy controls. Differences of BP Div was demonstrated in seven ROIs; parahippocampus, hippocampus, fusiform gyrus, gyrus rectus, supplementary motor area, inferior frontal occipital gyrus and lingual gyrus. For classification of genotype, 'RandomForest' and Support Vector Machines were used, however, no model with sufficient predictive capability could be computed. Our results are in line with preclinical data, mouse model knockout studies as well as previous clinical analyses, demonstrating the two-pronged effect of the G allele on 5-HT 1A BP ND for, we believe, the first time. Future endeavors should address epigenetic effects and allosteric heteroreceptor complexes. Replication in larger samples of MDD patients is necessary to substantiate our findings.

Phylogenetic and evolutionary analyses of dengue viruses isolated in Jakarta, Indonesia.

Science.gov (United States)

Lestari, C S Whinie; Yohan, Benediktus; Yunita, Anisa; Meutiawati, Febrina; Hayati, Rahma Fitri; Trimarsanto, Hidayat; Sasmono, R Tedjo

2017-12-01

Dengue has affected Indonesia for the last five decades and become a major health problem in many cities in the country. Jakarta, the capital of Indonesia, reports dengue cases annually, with several outbreaks documented. To gain information on the dynamic and evolutionary history of dengue virus (DENV) in Jakarta, we conducted phylogenetic and evolutionary analyses of DENV isolated in 2009. Three hundred thirty-three dengue-suspected patients were recruited. Our data revealed that dengue predominantly affected young adults, and the majority of cases were due to secondary infection. A total of 171 virus isolates were successfully serotyped. All four DENV serotypes were circulating in the city, and DENV-1 was the predominant serotype. The DENV genotyping of 17 isolates revealed the presence of Genotypes I and IV in DENV-1, while DENV-2 isolates were grouped into the Cosmopolitan genotype. The grouping of isolates into Genotype I and II was seen for DENV-3 and DENV-4, respectively. Evolutionary analysis revealed the relatedness of Jakarta isolates with other isolates from other cities in Indonesia and isolates from imported cases in other countries. We revealed the endemicity of DENV and the role of Jakarta as the potential source of imported dengue cases in other countries. Our study provides genetic information regarding DENV from Jakarta, which will be useful for upstream applications, such as the study of DENV epidemiology and evolution and transmission dynamics.

Qualitative and quantitative image analysis of CT and MR imaging in patients with neuroendocrine liver metastases in comparison to 68Ga-DOTATOC PET

International Nuclear Information System (INIS)

Flechsig, Paul; Zechmann, Christian M.; Schreiweis, Julian; Kratochwil, Clemens; Rath, Daniel; Schwartz, Lawrence H.; Schlemmer, Heinz-Peter; Kauczor, Hans-Ulrich; Haberkorn, Uwe; Giesel, Frederik L.

2015-01-01

Highlights: • Qualitative analysis revealed significantly higher results for spatial lesion detectability of liver metastasis in CE-MRI as compared to DW-imaging (p < 0.05). • Primary visibility of liver metastases was scored equally in CE-MRI and DW-imaging. • Contrast-enhancement ratios in liver metastases reached highest values for DW-imaging (p < 0.05). • Staging of liver metastases in patients with GEP-NETs should rather be performed using a combination of PET and MRI than of PET and CT. • The combination of functional and morphologic native MR-sequences seems to be sufficient for follow-up imaging in clinical routine, especially in post-interventional follow-up. - Abstract: Purpose: To compare lesion conspicuity in patients with liver metastases arising from gastroenteropancreatic neuroendocrine tumors (GEP-NETs) using MRI, PET and CT. Materials and methods: 16 patients with GEP-NETs were evaluated using non-contrast MRI, contrast-enhanced (CE) MRI using Gd-EOB-DTPA and CE- 68 Ga-DOTATOC PET. Quantitative analyses were performed by two blinded readers using ROI-analyses quantifying contrast ratios (CR) between normal liver-tissue and GEP-NET-metastases. Qualitative analyses were performed evaluating primary visibility and spatial detectability of all lesions. Results: 103 of the same liver metastases were detected on all modalities. Qualitatively, lesion conspicuity was superior on CE-MRI imaging compared to non-contrast MR-sequences (T2, DWI, fl2D, fl3D), as well as arterial- and portal-venous phase CT. Concerning detectability of lesions, CE-MRI was superior to all other modalities. The quantitative ROI-analysis demonstrated improved CR for DWI compared to all other non-contrast MR-sequences (p < 0.001). CE-MRI presented with higher CR-values compared to CE- 68 Ga-DOTATOC PET/CT (p < 0.001). Conclusions: Anatomic imaging using non contrast MRI with fl2D-and fl3D-sequences in combination with the molecular imaging modality 68 Ga-DOTATOC PET is

Transcriptome and proteomic analyses reveal multiple differences associated with chloroplast development in the spaceflight-induced wheat albino mutant mta.

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Kui Shi

Full Text Available Chloroplast development is an integral part of plant survival and growth, and occurs in parallel with chlorophyll biosynthesis. However, little is known about the mechanisms underlying chloroplast development in hexaploid wheat. Here, we obtained a spaceflight-induced wheat albino mutant mta. Chloroplast ultra-structural observation showed that chloroplasts of mta exhibit abnormal morphology and distribution compared to wild type. Photosynthetic pigments content was also significantly decreased in mta. Transcriptome and chloroplast proteome profiling of mta and wild type were done to identify differentially expressed genes (DEGs and proteins (DEPs, respectively. In total 4,588 DEGs including 1,980 up- and 2,608 down-regulated, and 48 chloroplast DEPs including 15 up- and 33 down-regulated were identified in mta. Classification of DEGs revealed that most were involved in chloroplast development, chlorophyll biosynthesis, or photosynthesis. Besides, transcription factors such as PIF3, GLK and MYB which might participate in those pathways were also identified. The correlation analysis between DEGs and DEPs revealed that the transcript-to-protein in abundance was functioned into photosynthesis and chloroplast relevant groups. Real time qPCR analysis validated that the expression level of genes encoding photosynthetic proteins was significantly decreased in mta. Together, our results suggest that the molecular mechanism for albino leaf color formation in mta is a thoroughly regulated and complicated process. The combined analysis of transcriptome and proteome afford comprehensive information for further research on chloroplast development mechanism in wheat. And spaceflight provides a potential means for mutagenesis in crop breeding.

Quantifying Shapes: Mathematical Techniques for Analysing Visual Representations of Sound and Music

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Genevieve L. Noyce

2013-12-01

Full Text Available Research on auditory-visual correspondences has a long tradition but innovative experimental paradigms and analytic tools are sparse. In this study, we explore different ways of analysing real-time visual representations of sound and music drawn by both musically-trained and untrained individuals. To that end, participants' drawing responses captured by an electronic graphics tablet were analysed using various regression, clustering, and classification techniques. Results revealed that a Gaussian process (GP regression model with a linear plus squared-exponential covariance function was able to model the data sufficiently, whereas a simpler GP was not a good fit. Spectral clustering analysis was the best of a variety of clustering techniques, though no strong groupings are apparent in these data. This was confirmed by variational Bayes analysis, which only fitted one Gaussian over the dataset. Slight trends in the optimised hyperparameters between musically-trained and untrained individuals allowed for the building of a successful GP classifier that differentiated between these two groups. In conclusion, this set of techniques provides useful mathematical tools for analysing real-time visualisations of sound and can be applied to similar datasets as well.

Automated selection of trabecular bone regions in knee radiographs

International Nuclear Information System (INIS)

Podsiadlo, P.; Wolski, M.; Stachowiak, G. W.

2008-01-01

Osteoarthritic (OA) changes in knee joints can be assessed by analyzing the structure of trabecular bone (TB) in the tibia. This analysis is performed on TB regions selected manually by a human operator on x-ray images. Manual selection is time-consuming, tedious, and expensive. Even if a radiologist expert or highly trained person is available to select regions, high inter- and intraobserver variabilities are still possible. A fully automated image segmentation method was, therefore, developed to select the bone regions for numerical analyses of changes in bone structures. The newly developed method consists of image preprocessing, delineation of cortical bone plates (active shape model), and location of regions of interest (ROI). The method was trained on an independent set of 40 x-ray images. Automatically selected regions were compared to the ''gold standard'' that contains ROIs selected manually by a radiologist expert on 132 x-ray images. All images were acquired from subjects locked in a standardized standing position using a radiography rig. The size of each ROI is 12.8x12.8 mm. The automated method results showed a good agreement with the gold standard [similarity index (SI)=0.83 (medial) and 0.81 (lateral) and the offset=[-1.78, 1.27]x[-0.65,0.26] mm (medial) and [-2.15, 1.59]x[-0.58, 0.52] mm (lateral)]. Bland and Altman plots were constructed for fractal signatures, and changes of fractal dimensions (FD) to region offsets calculated between the gold standard and automatically selected regions were calculated. The plots showed a random scatter and the 95% confidence intervals were (-0.006, 0.008) and (-0.001, 0.011). The changes of FDs to region offsets were less than 0.035. Previous studies showed that differences in FDs between non-OA and OA bone regions were greater than 0.05. ROIs were also selected by a second radiologist and then evaluated. Results indicated that the newly developed method could replace a human operator and produces bone regions

Multicollinearity in spatial genetics: separating the wheat from the chaff using commonality analyses.

Science.gov (United States)

Prunier, J G; Colyn, M; Legendre, X; Nimon, K F; Flamand, M C

2015-01-01

Direct gradient analyses in spatial genetics provide unique opportunities to describe the inherent complexity of genetic variation in wildlife species and are the object of many methodological developments. However, multicollinearity among explanatory variables is a systemic issue in multivariate regression analyses and is likely to cause serious difficulties in properly interpreting results of direct gradient analyses, with the risk of erroneous conclusions, misdirected research and inefficient or counterproductive conservation measures. Using simulated data sets along with linear and logistic regressions on distance matrices, we illustrate how commonality analysis (CA), a detailed variance-partitioning procedure that was recently introduced in the field of ecology, can be used to deal with nonindependence among spatial predictors. By decomposing model fit indices into unique and common (or shared) variance components, CA allows identifying the location and magnitude of multicollinearity, revealing spurious correlations and thus thoroughly improving the interpretation of multivariate regressions. Despite a few inherent limitations, especially in the case of resistance model optimization, this review highlights the great potential of CA to account for complex multicollinearity patterns in spatial genetics and identifies future applications and lines of research. We strongly urge spatial geneticists to systematically investigate commonalities when performing direct gradient analyses. © 2014 John Wiley & Sons Ltd.

Pilot Study of the Use of Hybrid Multidimensional T2-Weighted Imaging-DWI for the Diagnosis of Prostate Cancer and Evaluation of Gleason Score.

Science.gov (United States)

Sadinski, Meredith; Karczmar, Gregory; Peng, Yahui; Wang, Shiyang; Jiang, Yulei; Medved, Milica; Yousuf, Ambereen; Antic, Tatjana; Oto, Aytekin

2016-09-01

The objective of our study was to evaluate the role of a hybrid T2-weighted imaging-DWI sequence for prostate cancer diagnosis and differentiation of aggressive prostate cancer from nonaggressive prostate cancer. Twenty-one patients with prostate cancer who underwent preoperative 3-T MRI and prostatectomy were included in this study. Patients underwent a hybrid T2-weighted imaging-DWI examination consisting of DW images acquired with TEs of 47, 75, and 100 ms and b values of 0 and 750 s/mm(2). The apparent diffusion coefficient (ADC) and T2 were calculated for cancer and normal prostate ROIs at each TE and b value. Changes in ADC and T2 as a function of increasing the TE and b value, respectively, were analyzed. A new metric termed "PQ4" was defined as the percentage of voxels within an ROI that has increasing T2 with increasing b value and has decreasing ADC with increasing TE. ADC values were significantly higher in normal ROIs than in cancer ROIs at all TEs (p T2 was significantly higher in normal ROIs than in cancer ROIs at both b values (p ≤ 0.0002). The mean T2 decreased with increasing b value in cancer ROIs (ΔT2 = -17 ms) and normal ROIs (ΔT2 = -52 ms). PQ4 clearly differentiated normal ROIs from prostate cancer ROIs (p = 0.0004) and showed significant correlation with Gleason score (ρ = 0.508, p T2 to changing TEs and b values, respectively. This approach shows promise for detecting prostate cancer and determining its aggressiveness noninvasively.

Regional cerebral blood flow in fibromyalgia

International Nuclear Information System (INIS)

Kwiatek, R.; Barnden, L.; Rowe, C.; McKinnon, J.; Pile, K.

1998-01-01

Full text: Little is known of the aetiology of fibromyalgia (FM), a condition diagnosed on the basis of widespread chronic pain and multiple tender points. We have used Tc-99m HMPAO SPECT to compare regional cerebral bloodflow (rCBF) in 17 women who fulfill American College of Rheumatology criteria for FM to 22 age, sex and education matched controls. Both Statistical Parametric Mapping (SPM95) and coregistered MRI guided ROI were used for analysis. SPM95 revealed statistically significant hypoperfusion in the pontine tegmentum (p=0.048) and a trend to hypoperfusion in the left putamen (p=0.07). MRI guided ROI placement by an operator blinded to clinical information and the coregistered SPECT images, confirmed significant hypoperfusion of the left thalamus (p<0.0001) and the pontine tegmentum (p=0.001) and revealed trends towards hypoperfusion in the caudate nuclei and right thalamus. These results are consistent with the hypothesis that FM is due to dysfunction of central pain pathways. Spinothalamic neurones are known to be involved in pain perception and there are synapse connections to the thalamus in the gigantocellular part of the medulla and pons

Regional cerebral blood flow in fibromyalgia

Energy Technology Data Exchange (ETDEWEB)

Kwiatek, R.; Barnden, L.; Rowe, C.; McKinnon, J.; Pile, K. [The Queen Elizabeth Hospital , Adelaide, SA (Australia)

1998-06-01

Full text: Little is known of the aetiology of fibromyalgia (FM), a condition diagnosed on the basis of widespread chronic pain and multiple tender points. We have used Tc-99m HMPAO SPECT to compare regional cerebral bloodflow (rCBF) in 17 women who fulfill American College of Rheumatology criteria for FM to 22 age, sex and education matched controls. Both Statistical Parametric Mapping (SPM95) and coregistered MRI guided ROI were used for analysis. SPM95 revealed statistically significant hypoperfusion in the pontine tegmentum (p=0.048) and a trend to hypoperfusion in the left putamen (p=0.07). MRI guided ROI placement by an operator blinded to clinical information and the coregistered SPECT images, confirmed significant hypoperfusion of the left thalamus (p<0.0001) and the pontine tegmentum (p=0.001) and revealed trends towards hypoperfusion in the caudate nuclei and right thalamus. These results are consistent with the hypothesis that FM is due to dysfunction of central pain pathways. Spinothalamic neurones are known to be involved in pain perception and there are synapse connections to the thalamus in the gigantocellular part of the medulla and pons

Comparing brain graphs in which nodes are regions of interest or independent components: A simulation study.

Science.gov (United States)

Yu, Qingbao; Du, Yuhui; Chen, Jiayu; He, Hao; Sui, Jing; Pearlson, Godfrey; Calhoun, Vince D

2017-11-01

A key challenge in building a brain graph using fMRI data is how to define the nodes. Spatial brain components estimated by independent components analysis (ICA) and regions of interest (ROIs) determined by brain atlas are two popular methods to define nodes in brain graphs. It is difficult to evaluate which method is better in real fMRI data. Here we perform a simulation study and evaluate the accuracies of a few graph metrics in graphs with nodes of ICA components, ROIs, or modified ROIs in four simulation scenarios. Graph measures with ICA nodes are more accurate than graphs with ROI nodes in all cases. Graph measures with modified ROI nodes are modulated by artifacts. The correlations of graph metrics across subjects between graphs with ICA nodes and ground truth are higher than the correlations between graphs with ROI nodes and ground truth in scenarios with large overlapped spatial sources. Moreover, moving the location of ROIs would largely decrease the correlations in all scenarios. Evaluating graphs with different nodes is promising in simulated data rather than real data because different scenarios can be simulated and measures of different graphs can be compared with a known ground truth. Since ROIs defined using brain atlas may not correspond well to real functional boundaries, overall findings of this work suggest that it is more appropriate to define nodes using data-driven ICA than ROI approaches in real fMRI data. Copyright © 2017 Elsevier B.V. All rights reserved.

Observer variability of absolute and relative thrombus density measurements in patients with acute ischemic stroke

International Nuclear Information System (INIS)

Santos, Emilie M.M.; Yoo, Albert J.; Beenen, Ludo F.; Majoie, Charles B.; Berkhemer, Olvert A.; Blanken, Mark D. den; Wismans, Carrie; Niessen, Wiro J.; Marquering, Henk A.

2016-01-01

Thrombus density may be a predictor for acute ischemic stroke treatment success. However, only limited data on observer variability for thrombus density measurements exist. This study assesses the variability and bias of four common thrombus density measurement methods by expert and non-expert observers. For 132 consecutive patients with acute ischemic stroke, three experts and two trained observers determined thrombus density by placing three standardized regions of interest (ROIs) in the thrombus and corresponding contralateral arterial segment. Subsequently, absolute and relative thrombus densities were determined using either one or three ROIs. Intraclass correlation coefficient (ICC) was determined, and Bland-Altman analysis was performed to evaluate interobserver and intermethod agreement. Accuracy of the trained observer was evaluated with a reference expert observer using the same statistical analysis. The highest interobserver agreement was obtained for absolute thrombus measurements using three ROIs (ICCs ranging from 0.54 to 0.91). In general, interobserver agreement was lower for relative measurements, and for using one instead of three ROIs. Interobserver agreement of trained non-experts and experts was similar. Accuracy of the trained observer measurements was comparable to the expert interobserver agreement and was better for absolute measurements and with three ROIs. The agreement between the one ROI and three ROI methods was good. Absolute thrombus density measurement has superior interobserver agreement compared to relative density measurement. Interobserver variation is smaller when multiple ROIs are used. Trained non-expert observers can accurately and reproducibly assess absolute thrombus densities using three ROIs. (orig.)

Observer variability of absolute and relative thrombus density measurements in patients with acute ischemic stroke

Energy Technology Data Exchange (ETDEWEB)

Santos, Emilie M.M. [Erasmus MC - University Medical Center Rotterdam, Department of Radiology, P.O. Box 2040, Rotterdam (Netherlands); Department of Radiology, AMC, Amsterdam (Netherlands); Yoo, Albert J. [Texas Stroke Institute, Plano, TX (United States); Beenen, Ludo F.; Majoie, Charles B. [Department of Radiology, AMC, Amsterdam (Netherlands); Berkhemer, Olvert A. [Department of Radiology, AMC, Amsterdam (Netherlands); Department of Neurology, Erasmus MC, Rotterdam (Netherlands); Blanken, Mark D. den; Wismans, Carrie [AMC, Department of Biomedical Engineering and Physics, Amsterdam (Netherlands); Niessen, Wiro J. [Erasmus MC - University Medical Center Rotterdam, Department of Radiology, P.O. Box 2040, Rotterdam (Netherlands); Delft University of Technology, Faculty of Applied Sciences, Delft (Netherlands); Marquering, Henk A. [Department of Radiology, AMC, Amsterdam (Netherlands); AMC, Department of Biomedical Engineering and Physics, Amsterdam (Netherlands); Collaboration: on behalf of the MR CLEAN investigators

2016-02-15

Thrombus density may be a predictor for acute ischemic stroke treatment success. However, only limited data on observer variability for thrombus density measurements exist. This study assesses the variability and bias of four common thrombus density measurement methods by expert and non-expert observers. For 132 consecutive patients with acute ischemic stroke, three experts and two trained observers determined thrombus density by placing three standardized regions of interest (ROIs) in the thrombus and corresponding contralateral arterial segment. Subsequently, absolute and relative thrombus densities were determined using either one or three ROIs. Intraclass correlation coefficient (ICC) was determined, and Bland-Altman analysis was performed to evaluate interobserver and intermethod agreement. Accuracy of the trained observer was evaluated with a reference expert observer using the same statistical analysis. The highest interobserver agreement was obtained for absolute thrombus measurements using three ROIs (ICCs ranging from 0.54 to 0.91). In general, interobserver agreement was lower for relative measurements, and for using one instead of three ROIs. Interobserver agreement of trained non-experts and experts was similar. Accuracy of the trained observer measurements was comparable to the expert interobserver agreement and was better for absolute measurements and with three ROIs. The agreement between the one ROI and three ROI methods was good. Absolute thrombus density measurement has superior interobserver agreement compared to relative density measurement. Interobserver variation is smaller when multiple ROIs are used. Trained non-expert observers can accurately and reproducibly assess absolute thrombus densities using three ROIs. (orig.)

Genome-wide-analyses of Listeria monocytogenes from food-processing plants reveal clonal diversity and date the emergence of persisting sequence types.

Science.gov (United States)

Knudsen, Gitte M; Nielsen, Jesper Boye; Marvig, Rasmus L; Ng, Yin; Worning, Peder; Westh, Henrik; Gram, Lone

2017-08-01

Whole genome sequencing is increasing used in epidemiology, e.g. for tracing outbreaks of food-borne diseases. This requires in-depth understanding of pathogen emergence, persistence and genomic diversity along the food production chain including in food processing plants. We sequenced the genomes of 80 isolates of Listeria monocytogenes sampled from Danish food processing plants over a time-period of 20 years, and analysed the sequences together with 10 public available reference genomes to advance our understanding of interplant and intraplant genomic diversity of L. monocytogenes. Except for three persisting sequence types (ST) based on Multi Locus Sequence Typing being ST7, ST8 and ST121, long-term persistence of clonal groups was limited, and new clones were introduced continuously, potentially from raw materials. No particular gene could be linked to the persistence phenotype. Using time-based phylogenetic analyses of the persistent STs, we estimate the L. monocytogenes evolutionary rate to be 0.18-0.35 single nucleotide polymorphisms/year, suggesting that the persistent STs emerged approximately 100 years ago, which correlates with the onset of industrialization and globalization of the food market. © 2017 Society for Applied Microbiology and John Wiley & Sons Ltd.

Job Demands, Burnout, and Teamwork in Healthcare Professionals Working in a General Hospital that Was Analysed At Two Points in Time

Directory of Open Access Journals (Sweden)

Dragan Mijakoski

2018-04-01

CONCLUSION: Actual longitudinal study revealed significantly higher mean values of emotional exhaustion and depersonalization in 2014 that could be explained by significantly increased job demands between analysed points in time.

Multilocus Sequence Analysis of Nectar Pseudomonads Reveals High Genetic Diversity and Contrasting Recombination Patterns

Science.gov (United States)

Álvarez-Pérez, Sergio; de Vega, Clara; Herrera, Carlos M.

2013-01-01

The genetic and evolutionary relationships among floral nectar-dwelling Pseudomonas ‘sensu stricto’ isolates associated to South African and Mediterranean plants were investigated by multilocus sequence analysis (MLSA) of four core housekeeping genes (rrs, gyrB, rpoB and rpoD). A total of 35 different sequence types were found for the 38 nectar bacterial isolates characterised. Phylogenetic analyses resulted in the identification of three main clades [nectar groups (NGs) 1, 2 and 3] of nectar pseudomonads, which were closely related to five intrageneric groups: Pseudomonas oryzihabitans (NG 1); P. fluorescens, P. lutea and P. syringae (NG 2); and P. rhizosphaerae (NG 3). Linkage disequilibrium analysis pointed to a mostly clonal population structure, even when the analysis was restricted to isolates from the same floristic region or belonging to the same NG. Nevertheless, signatures of recombination were observed for NG 3, which exclusively included isolates retrieved from the floral nectar of insect-pollinated Mediterranean plants. In contrast, the other two NGs comprised both South African and Mediterranean isolates. Analyses relating diversification to floristic region and pollinator type revealed that there has been more unique evolution of the nectar pseudomonads within the Mediterranean region than would be expected by chance. This is the first work analysing the sequence of multiple loci to reveal geno- and ecotypes of nectar bacteria. PMID:24116076

Multilocus sequence analysis of nectar pseudomonads reveals high genetic diversity and contrasting recombination patterns.

Science.gov (United States)

Alvarez-Pérez, Sergio; de Vega, Clara; Herrera, Carlos M

2013-01-01

The genetic and evolutionary relationships among floral nectar-dwelling Pseudomonas 'sensu stricto' isolates associated to South African and Mediterranean plants were investigated by multilocus sequence analysis (MLSA) of four core housekeeping genes (rrs, gyrB, rpoB and rpoD). A total of 35 different sequence types were found for the 38 nectar bacterial isolates characterised. Phylogenetic analyses resulted in the identification of three main clades [nectar groups (NGs) 1, 2 and 3] of nectar pseudomonads, which were closely related to five intrageneric groups: Pseudomonas oryzihabitans (NG 1); P. fluorescens, P. lutea and P. syringae (NG 2); and P. rhizosphaerae (NG 3). Linkage disequilibrium analysis pointed to a mostly clonal population structure, even when the analysis was restricted to isolates from the same floristic region or belonging to the same NG. Nevertheless, signatures of recombination were observed for NG 3, which exclusively included isolates retrieved from the floral nectar of insect-pollinated Mediterranean plants. In contrast, the other two NGs comprised both South African and Mediterranean isolates. Analyses relating diversification to floristic region and pollinator type revealed that there has been more unique evolution of the nectar pseudomonads within the Mediterranean region than would be expected by chance. This is the first work analysing the sequence of multiple loci to reveal geno- and ecotypes of nectar bacteria.

The Effect of Pleistocene Climate Fluctuations on Distribution of European Abalone (Haliotis tuberculata), Revealed by Combined Mitochondrial and Nuclear Marker Analyses.

Science.gov (United States)

Roussel, Valérie; Van Wormhoudt, Alain

2017-04-01

The genetic differentiation among the populations of the European abalone Haliotis tuberculata was investigated using different markers to better understand the evolutionary history and exchanges between populations. Three markers were used: mitochondrial cytochrome oxidase I (COI), the sperm lysin nuclear gene, and eight nuclear microsatellites. These markers present different characteristics concerning mutation rate and inheritance, which provided complementary information about abalone history and gene diversity. Genetic diversity and relationships among subspecies were calculated from a sample of approximately 500 individuals, collected from 17 different locations in the north-eastern Atlantic Ocean, Macaronesia, and Mediterranean Sea. COI marker was used to explore the phylogeny of the species with a network analysis and two phylogenetic methods. The analysis revealed 18 major haplotypes grouped into two distinct clades with a pairwise sequence divergence up to 3.5 %. These clades do not correspond to subspecies but revealed many contacts along Atlantic coast during the Pleistocene interglaciations. The sperm lysin gene analysis separated two different subtaxa: one associated to Macaronesian islands, and the other to all other populations. Moreover, a small population of the northern subtaxon was isolated in the Adriatic Sea-probably before the separation of the two lineages-and evolved independently. Microsatellites were analyzed by different genetics methods, including the Bayesian clustering method and migration patterns analysis. It revealed genetically distinct microsatellite patterns among populations from Mediterranean Sea, Brittany and Normandy, Morocco, and Canary and Balearic islands. Gene flow is asymmetric among the regions; the Azores and the Canary Islands are particularly isolated and have low effective population sizes. Our results support the hypothesis that climate changes since the Pleistocene glaciations have played a major role in the

Molecular Analyses Reveal Inflammatory Mediators in the Solid Component and Cyst Fluid of Human Adamantinomatous Craniopharyngioma.

Science.gov (United States)

Donson, Andrew M; Apps, John; Griesinger, Andrea M; Amani, Vladimir; Witt, Davis A; Anderson, Richard C E; Niazi, Toba N; Grant, Gerald; Souweidane, Mark; Johnston, James M; Jackson, Eric M; Kleinschmidt-DeMasters, Bette K; Handler, Michael H; Tan, Aik-Choon; Gore, Lia; Virasami, Alex; Gonzalez-Meljem, Jose Mario; Jacques, Thomas S; Martinez-Barbera, Juan Pedro; Foreman, Nicholas K; Hankinson, Todd C

2017-09-01

Pediatric adamantinomatous craniopharyngioma (ACP) is a highly solid and cystic tumor, often causing substantial damage to critical neuroendocrine structures such as the hypothalamus, pituitary gland, and optic apparatus. Paracrine signaling mechanisms driving tumor behavior have been hypothesized, with IL-6R overexpression identified as a potential therapeutic target. To identify potential novel therapies, we characterized inflammatory and immunomodulatory factors in ACP cyst fluid and solid tumor components. Cytometric bead analysis revealed a highly pro-inflammatory cytokine pattern in fluid from ACP compared to fluids from another cystic pediatric brain tumor, pilocytic astrocytoma. Cytokines and chemokines with particularly elevated concentrations in ACPs were IL-6, CXCL1 (GRO), CXCL8 (IL-8) and the immunosuppressive cytokine IL-10. These data were concordant with solid tumor compartment transcriptomic data from a larger cohort of ACPs, other pediatric brain tumors and normal brain. The majority of receptors for these cytokines and chemokines were also over-expressed in ACPs. In addition to IL-10, the established immunosuppressive factor IDO-1 was overexpressed by ACPs at the mRNA and protein levels. These data indicate that ACP cyst fluids and solid tumor components are characterized by an inflammatory cytokine and chemokine expression pattern. Further study regarding selective cytokine blockade may inform novel therapeutic interventions. © 2017 American Association of Neuropathologists, Inc. All rights reserved.

The Chlamydomonas Genome Reveals the Evolution of Key Animal and Plant Functions

Energy Technology Data Exchange (ETDEWEB)

Merchant, Sabeeha S

2007-04-09

Chlamydomonas reinhardtii is a unicellular green alga whose lineage diverged from land plants over 1 billion years ago. It is a model system for studying chloroplast-based photosynthesis, as well as the structure, assembly, and function of eukaryotic flagella (cilia), which were inherited from the common ancestor of plants and animals, but lost in land plants. We sequenced the 120-megabase nuclear genome of Chlamydomonas and performed comparative phylogenomic analyses, identifying genes encoding uncharacterized proteins that are likely associated with the function and biogenesis of chloroplasts or eukaryotic flagella. Analyses of the Chlamydomonas genome advance our understanding of the ancestral eukaryotic cell, reveal previously unknown genes associated with photosynthetic and flagellar functions, and establish links between ciliopathy and the composition and function of flagella.

Culture-Independent Analyses Reveal Novel Anaerolineaceae as Abundant Primary Fermenters in Anaerobic Digesters Treating Waste Activated Sludge

Directory of Open Access Journals (Sweden)

Simon J. McIlroy

2017-06-01

Full Text Available Anaerobic digestion for biogas production is reliant on the tightly coupled synergistic activities of complex microbial consortia. Members of the uncultured A6 phylotype, within the phylum Chloroflexi, are among the most abundant genus-level-taxa of mesophilic anaerobic digester systems treating primary and surplus sludge from wastewater treatment plants, yet are known only by their 16S rRNA gene sequence. This study applied metagenomics to obtain a complete circular genome (2.57 Mbp from a representative of the A6 taxon. Preliminary annotation of the genome indicates these organisms to be anaerobic chemoorganoheterotrophs with a fermentative metabolism. Given their observed abundance, they are likely important primary fermenters in digester systems. Application of fluorescence in situ hybridisation probes designed in this study revealed their morphology to be short filaments present within the flocs. The A6 were sometimes co-located with the filamentous Archaea Methanosaeta spp. suggesting potential undetermined synergistic relationships. Based on its genome sequence and morphology we propose the species name Brevefilum fermentans gen. nov. sp. nov.

A new approach to develop computer-aided diagnosis scheme of breast mass classification using deep learning technology.

Science.gov (United States)

Qiu, Yuchen; Yan, Shiju; Gundreddy, Rohith Reddy; Wang, Yunzhi; Cheng, Samuel; Liu, Hong; Zheng, Bin

2017-01-01

To develop and test a deep learning based computer-aided diagnosis (CAD) scheme of mammograms for classifying between malignant and benign masses. An image dataset involving 560 regions of interest (ROIs) extracted from digital mammograms was used. After down-sampling each ROI from 512×512 to 64×64 pixel size, we applied an 8 layer deep learning network that involves 3 pairs of convolution-max-pooling layers for automatic feature extraction and a multiple layer perceptron (MLP) classifier for feature categorization to process ROIs. The 3 pairs of convolution layers contain 20, 10, and 5 feature maps, respectively. Each convolution layer is connected with a max-pooling layer to improve the feature robustness. The output of the sixth layer is fully connected with a MLP classifier, which is composed of one hidden layer and one logistic regression layer. The network then generates a classification score to predict the likelihood of ROI depicting a malignant mass. A four-fold cross validation method was applied to train and test this deep learning network. The results revealed that this CAD scheme yields an area under the receiver operation characteristic curve (AUC) of 0.696±0.044, 0.802±0.037, 0.836±0.036, and 0.822±0.035 for fold 1 to 4 testing datasets, respectively. The overall AUC of the entire dataset is 0.790±0.019. This study demonstrates the feasibility of applying a deep learning based CAD scheme to classify between malignant and benign breast masses without a lesion segmentation, image feature computation and selection process.

Positron emission tomography (PET) imaging of nicotine-induced dopamine release in squirrel monkeys using [18F]Fallypride.

Science.gov (United States)

Naylor, Jennifer E; Hiranita, Takato; Matazel, Katelin S; Zhang, Xuan; Paule, Merle G; Goodwin, Amy K

2017-10-01

Nicotine, the principal psychoactive tobacco constituent, is thought to produce its reinforcing effects via actions within the mesolimbic dopamine (DA) system. The objective of the current study was to examine the effect of nicotine on DA D 2 /D 3 receptor availability in the nonhuman primate brain with the use of the radioligand [ 18 F]fallypride and positron emission tomography (PET). Ten adult male squirrel monkeys were used in the current study. Each subject underwent two PET scans, one with an injection (IV) of saline and subsequently one with an injection of nicotine (0.032mg/kg). The DA D 2 /D 3 antagonist, [ 18 F]fallypride, was delivered IV at the beginning of each scan, and nicotine or saline was delivered at 45min into the scan. Regions of interest (ROI) were drawn on specific brain regions and these were used to quantify standard uptake values (SUVs). The SUV is defined as the average concentration of radioactivity in the ROI x body weight/injected dose. Using the cerebellum as a reference region, SUV ratios (SUV ROI /SUV cerebellum ) were calculated to compare saline and nicotine effects in each ROI. Two-way repeated ANOVA revealed a significant decrease of SUV ratios in both striatal and extrastriatal regions following an injection of nicotine during the PET scans. Like other drugs of abuse, these results indicate that nicotine administration may produce DA release, as suggested by the decrease in [ 18 F]fallypride signal in striatal regions. These findings from a nonhuman primate model provide further evidence that the mesolimbic DA system is affected by the use of products that contain nicotine. Published by Elsevier B.V.

A New Approach to Develop Computer-aided Diagnosis Scheme of Breast Mass Classification Using Deep Learning Technology

Science.gov (United States)

Qiu, Yuchen; Yan, Shiju; Gundreddy, Rohith Reddy; Wang, Yunzhi; Cheng, Samuel; Liu, Hong; Zheng, Bin

2017-01-01

PURPOSE To develop and test a deep learning based computer-aided diagnosis (CAD) scheme of mammograms for classifying between malignant and benign masses. METHODS An image dataset involving 560 regions of interest (ROIs) extracted from digital mammograms was used. After down-sampling each ROI from 512×512 to 64×64 pixel size, we applied an 8 layer deep learning network that involves 3 pairs of convolution-max-pooling layers for automatic feature extraction and a multiple layer perceptron (MLP) classifier for feature categorization to process ROIs. The 3 pairs of convolution layers contain 20, 10, and 5 feature maps, respectively. Each convolution layer is connected with a max-pooling layer to improve the feature robustness. The output of the sixth layer is fully connected with a MLP classifier, which is composed of one hidden layer and one logistic regression layer. The network then generates a classification score to predict the likelihood of ROI depicting a malignant mass. A four-fold cross validation method was applied to train and test this deep learning network. RESULTS The results revealed that this CAD scheme yields an area under the receiver operation characteristic curve (AUC) of 0.696±0.044, 0.802±0.037, 0.836±0.036, and 0.822±0.035 for fold 1 to 4 testing datasets, respectively. The overall AUC of the entire dataset is 0.790±0.019. CONCLUSIONS This study demonstrates the feasibility of applying a deep learning based CAD scheme to classify between malignant and benign breast masses without a lesion segmentation, image feature computation and selection process. PMID:28436410

Genomic Analyses Reveal Demographic History and Temperate Adaptation of the Newly Discovered Honey Bee Subspecies Apis mellifera sinisxinyuan n. ssp.

Science.gov (United States)

Chen, Chao; Liu, Zhiguang; Pan, Qi; Chen, Xiao; Wang, Huihua; Guo, Haikun; Liu, Shidong; Lu, Hongfeng; Tian, Shilin; Li, Ruiqiang; Shi, Wei

2016-05-01

Studying the genetic signatures of climate-driven selection can produce insights into local adaptation and the potential impacts of climate change on populations. The honey bee (Apis mellifera) is an interesting species to study local adaptation because it originated in tropical/subtropical climatic regions and subsequently spread into temperate regions. However, little is known about the genetic basis of its adaptation to temperate climates. Here, we resequenced the whole genomes of ten individual bees from a newly discovered population in temperate China and downloaded resequenced data from 35 individuals from other populations. We found that the new population is an undescribed subspecies in the M-lineage of A. mellifera (Apis mellifera sinisxinyuan). Analyses of population history show that long-term global temperature has strongly influenced the demographic history of A. m. sinisxinyuan and its divergence from other subspecies. Further analyses comparing temperate and tropical populations identified several candidate genes related to fat body and the Hippo signaling pathway that are potentially involved in adaptation to temperate climates. Our results provide insights into the demographic history of the newly discovered A. m. sinisxinyuan, as well as the genetic basis of adaptation of A. mellifera to temperate climates at the genomic level. These findings will facilitate the selective breeding of A. mellifera to improve the survival of overwintering colonies. © The Author 2016. Published by Oxford University Press on behalf of the Society for Molecular Biology and Evolution.

Structural, Bioinformatic, and In Vivo Analyses of Two Treponema pallidum Lipoproteins Reveal a Unique TRAP Transporter

Energy Technology Data Exchange (ETDEWEB)

Deka, Ranjit K.; Brautigam, Chad A.; Goldberg, Martin; Schuck, Peter; Tomchick, Diana R.; Norgard, Michael V. (NIH); (UTSMC)

2012-05-25

Treponema pallidum, the bacterial agent of syphilis, is predicted to encode one tripartite ATP-independent periplasmic transporter (TRAP-T). TRAP-Ts typically employ a periplasmic substrate-binding protein (SBP) to deliver the cognate ligand to the transmembrane symporter. Herein, we demonstrate that the genes encoding the putative TRAP-T components from T. pallidum, tp0957 (the SBP), and tp0958 (the symporter), are in an operon with an uncharacterized third gene, tp0956. We determined the crystal structure of recombinant Tp0956; the protein is trimeric and perforated by a pore. Part of Tp0956 forms an assembly similar to those of 'tetratricopeptide repeat' (TPR) motifs. The crystal structure of recombinant Tp0957 was also determined; like the SBPs of other TRAP-Ts, there are two lobes separated by a cleft. In these other SBPs, the cleft binds a negatively charged ligand. However, the cleft of Tp0957 has a strikingly hydrophobic chemical composition, indicating that its ligand may be substantially different and likely hydrophobic. Analytical ultracentrifugation of the recombinant versions of Tp0956 and Tp0957 established that these proteins associate avidly. This unprecedented interaction was confirmed for the native molecules using in vivo cross-linking experiments. Finally, bioinformatic analyses suggested that this transporter exemplifies a new subfamily of TPATs (TPR-protein-associated TRAP-Ts) that require the action of a TPR-containing accessory protein for the periplasmic transport of a potentially hydrophobic ligand(s).

In vivo evaluation of biofunctionalized implant surfaces with a synthetic peptide (P-15) and its impact on osseointegration. A preclinical animal study.

Science.gov (United States)

Schmitt, Christian M; Koepple, Markus; Moest, Tobias; Neumann, Konrad; Weisel, Tamara; Schlegel, Karl Andreas

2016-11-01

The overall aim of the study was to investigate a biofunctionalized implant surface with electrochemically deposition of hydroxyapatite and the synthetic peptide (P-15) and its effect on osseointegration. Three modified implant types of ANKYLOS ® C/X implants were used; (1) machined implants used as negative control (M, n = 20), (2) implants with the FRIADENT ® plus surface (grit blasted and acid-etched) used as positive control (P, n = 20), and (3) implants with a biomimetic surface consisting of hydroxyapatite and the synthetic 15 aminoacids containing peptide P-15 (BP, n = 40). The implants were randomly inserted in the mandibles of 10 beagle dogs following 4 months after tooth extraction (P1-P4). Three animals were sacrificed 2 and 7 days after implant insertion, respectively, and four animals were sacrificed 6 months post implant insertion. Bone-to-implant contacts (BICs) were analyzed via histomorphometrical analyses at five different region of interests (ROIs); two at the middle part on either side of the implant (ROI 1/4), two at the apical part of the implant at each side (ROI 2/3), and one at the tip of the implant (ROI 5). All implant surfaces showed a high level of osseointegration and osteoconductivity. The cumulative implant survival rate (CSR) was 93.8%, 100% in the M, 85% in the P, and 95% in the BP group. No statistical difference in BICs at ROI 1/4, 2/3, and 5 could be shown between implant types following 2 and 7 days of healing. BIC values increased in all groups over time. After 6 months of healing the BP group showed superiority in BIC in ROI 2/3 (73.2 ± 15.6%) compared to the P (48.3 ± 10.6%) and M group (66.3 ± 30.2%) with a significant difference between BP and P (P = 0.002). It is hypothesized, that the surface biofunctionalization improves peri-implant bone formation and remodeling, leading to an increased bone-to implant contact. However, within the limitations of the study set-up no benefit in the early phase of

Constraints on genome dynamics revealed from gene distribution among the Ralstonia solanacearum species.

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Pierre Lefeuvre

Full Text Available Because it is suspected that gene content may partly explain host adaptation and ecology of pathogenic bacteria, it is important to study factors affecting genome composition and its evolution. While recent genomic advances have revealed extremely large pan-genomes for some bacterial species, it remains difficult to predict to what extent gene pool is accessible within or transferable between populations. As genomes bear imprints of the history of the organisms, gene distribution pattern analyses should provide insights into the forces and factors at play in the shaping and maintaining of bacterial genomes. In this study, we revisited the data obtained from a previous CGH microarrays analysis in order to assess the genomic plasticity of the R. solanacearum species complex. Gene distribution analyses demonstrated the remarkably dispersed genome of R. solanacearum with more than half of the genes being accessory. From the reconstruction of the ancestral genomes compositions, we were able to infer the number of gene gain and loss events along the phylogeny. Analyses of gene movement patterns reveal that factors associated with gene function, genomic localization and ecology delineate gene flow patterns. While the chromosome displayed lower rates of movement, the megaplasmid was clearly associated with hot-spots of gene gain and loss. Gene function was also confirmed to be an essential factor in gene gain and loss dynamics with significant differences in movement patterns between different COG categories. Finally, analyses of gene distribution highlighted possible highways of horizontal gene transfer. Due to sampling and design bias, we can only speculate on factors at play in this gene movement dynamic. Further studies examining precise conditions that favor gene transfer would provide invaluable insights in the fate of bacteria, species delineation and the emergence of successful pathogens.

Comparative sequence analyses of the major quantitative trait locus phosphorus uptake 1 (Pup1) reveal a complex genetic structure.

Science.gov (United States)

Heuer, Sigrid; Lu, Xiaochun; Chin, Joong Hyoun; Tanaka, Juan Pariasca; Kanamori, Hiroyuki; Matsumoto, Takashi; De Leon, Teresa; Ulat, Victor Jun; Ismail, Abdelbagi M; Yano, Masahiro; Wissuwa, Matthias

2009-06-01

The phosphorus uptake 1 (Pup1) locus was identified as a major quantitative trait locus (QTL) for tolerance of phosphorus deficiency in rice. Near-isogenic lines with the Pup1 region from tolerant donor parent Kasalath typically show threefold higher phosphorus uptake and grain yield in phosphorus-deficient field trials than the intolerant parent Nipponbare. In this study, we report the fine mapping of the Pup1 locus to the long arm of chromosome 12 (15.31-15.47 Mb). Genes in the region were initially identified on the basis of the Nipponbare reference genome, but did not reveal any obvious candidate genes related to phosphorus uptake. Kasalath BAC clones were therefore sequenced and revealed a 278-kbp sequence significantly different from the syntenic regions in Nipponbare (145 kb) and in the indica reference genome of 93-11 (742 kbp). Size differences are caused by large insertions or deletions (INDELs), and an exceptionally large number of retrotransposon and transposon-related elements (TEs) present in all three sequences (45%-54%). About 46 kb of the Kasalath sequence did not align with the entire Nipponbare genome, and only three Nipponbare genes (fatty acid alpha-dioxygenase, dirigent protein and aspartic proteinase) are highly conserved in Kasalath. Two Nipponbare genes (expressed proteins) might have evolved by at least three TE integrations in an ancestor gene that is still present in Kasalath. Several predicted Kasalath genes are novel or unknown genes that are mainly located within INDEL regions. Our results highlight the importance of sequencing QTL regions in the respective donor parent, as important genes might not be present in the current reference genomes.

Differential Expression of Proteins Associated with the Hair Follicle Cycle - Proteomics and Bioinformatics Analyses.

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Lei Wang

Full Text Available Hair follicle cycling can be divided into the following three stages: anagen, catagen, and telogen. The molecular signals that orchestrate the follicular transition between phases are still unknown. To better understand the detailed protein networks controlling this process, proteomics and bioinformatics analyses were performed to construct comparative protein profiles of mouse skin at specific time points (0, 8, and 20 days. Ninety-five differentially expressed protein spots were identified by MALDI-TOF/TOF as 44 proteins, which were found to change during hair follicle cycle transition. Proteomics analysis revealed that these changes in protein expression are involved in Ca2+-regulated biological processes, migration, and regulation of signal transduction, among other processes. Subsequently, three proteins were selected to validate the reliability of expression patterns using western blotting. Cluster analysis revealed three expression patterns, and each pattern correlated with specific cell processes that occur during the hair cycle. Furthermore, bioinformatics analysis indicated that the differentially expressed proteins impacted multiple biological networks, after which detailed functional analyses were performed. Taken together, the above data may provide insight into the three stages of mouse hair follicle morphogenesis and provide a solid basis for potential therapeutic molecular targets for this hair disease.

Mutational and structural analyses of Caldanaerobius polysaccharolyticus Man5B reveal novel active site residues for family 5 glycoside hydrolases.

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Takuji Oyama

Full Text Available CpMan5B is a glycoside hydrolase (GH family 5 enzyme exhibiting both β-1,4-mannosidic and β-1,4-glucosidic cleavage activities. To provide insight into the amino acid residues that contribute to catalysis and substrate specificity, we solved the structure of CpMan5B at 1.6 Å resolution. The structure revealed several active site residues (Y12, N92 and R196 in CpMan5B that are not present in the active sites of other structurally resolved GH5 enzymes. Residue R196 in GH5 enzymes is thought to be strictly conserved as a histidine that participates in an electron relay network with the catalytic glutamates, but we show that an arginine fulfills a functionally equivalent role and is found at this position in every enzyme in subfamily GH5_36, which includes CpMan5B. Residue N92 is required for full enzymatic activity and forms a novel bridge over the active site that is absent in other family 5 structures. Our data also reveal a role of Y12 in establishing the substrate preference for CpMan5B. Using these molecular determinants as a probe allowed us to identify Man5D from Caldicellulosiruptor bescii as a mannanase with minor endo-glucanase activity.

Mutational and structural analyses of Caldanaerobius polysaccharolyticus Man5B reveal novel active site residues for family 5 glycoside hydrolases.

Science.gov (United States)

Oyama, Takuji; Schmitz, George E; Dodd, Dylan; Han, Yejun; Burnett, Alanna; Nagasawa, Naoko; Mackie, Roderick I; Nakamura, Haruki; Morikawa, Kosuke; Cann, Isaac

2013-01-01

CpMan5B is a glycoside hydrolase (GH) family 5 enzyme exhibiting both β-1,4-mannosidic and β-1,4-glucosidic cleavage activities. To provide insight into the amino acid residues that contribute to catalysis and substrate specificity, we solved the structure of CpMan5B at 1.6 Å resolution. The structure revealed several active site residues (Y12, N92 and R196) in CpMan5B that are not present in the active sites of other structurally resolved GH5 enzymes. Residue R196 in GH5 enzymes is thought to be strictly conserved as a histidine that participates in an electron relay network with the catalytic glutamates, but we show that an arginine fulfills a functionally equivalent role and is found at this position in every enzyme in subfamily GH5_36, which includes CpMan5B. Residue N92 is required for full enzymatic activity and forms a novel bridge over the active site that is absent in other family 5 structures. Our data also reveal a role of Y12 in establishing the substrate preference for CpMan5B. Using these molecular determinants as a probe allowed us to identify Man5D from Caldicellulosiruptor bescii as a mannanase with minor endo-glucanase activity.

ALBEDO PATTERN RECOGNITION AND TIME-SERIES ANALYSES IN MALAYSIA

Directory of Open Access Journals (Sweden)

S. A. Salleh

2012-07-01

Full Text Available Pattern recognition and time-series analyses will enable one to evaluate and generate predictions of specific phenomena. The albedo pattern and time-series analyses are very much useful especially in relation to climate condition monitoring. This study is conducted to seek for Malaysia albedo pattern changes. The pattern recognition and changes will be useful for variety of environmental and climate monitoring researches such as carbon budgeting and aerosol mapping. The 10 years (2000–2009 MODIS satellite images were used for the analyses and interpretation. These images were being processed using ERDAS Imagine remote sensing software, ArcGIS 9.3, the 6S code for atmospherical calibration and several MODIS tools (MRT, HDF2GIS, Albedo tools. There are several methods for time-series analyses were explored, this paper demonstrates trends and seasonal time-series analyses using converted HDF format MODIS MCD43A3 albedo land product. The results revealed significance changes of albedo percentages over the past 10 years and the pattern with regards to Malaysia's nebulosity index (NI and aerosol optical depth (AOD. There is noticeable trend can be identified with regards to its maximum and minimum value of the albedo. The rise and fall of the line graph show a similar trend with regards to its daily observation. The different can be identified in term of the value or percentage of rises and falls of albedo. Thus, it can be concludes that the temporal behavior of land surface albedo in Malaysia have a uniform behaviours and effects with regards to the local monsoons. However, although the average albedo shows linear trend with nebulosity index, the pattern changes of albedo with respects to the nebulosity index indicates that there are external factors that implicates the albedo values, as the sky conditions and its diffusion plotted does not have uniform trend over the years, especially when the trend of 5 years interval is examined, 2000 shows high

The secondary stress analyses in the fuel pin cladding due to the swelling gradient across the wall thickness

International Nuclear Information System (INIS)

Uwaba, Tomoyuki; Ukai, Shigeharu

2002-01-01

Irradiation deformation analyses of FBR fuel cladding were made by using the finite element method. In these analyses the history of the stress occurred in the cladding was evaluated paying attention to the secondary stress induced by the swelling difference across the wall thickness. It was revealed that the difference of the swelling incubation dose in the direction of the thickness and the irradiation creep deformation play an important role in the history of the secondary stress. The effect of the stress-enhanced swelling was also analyzed in this study

MR-perfusion (MRP) and diffusion-weighted imaging (DWI) in prostate cancer: Quantitative and model-based gadobenate dimeglumine MRP parameters in detection of prostate cancer

Energy Technology Data Exchange (ETDEWEB)

Scherr, M.K., E-mail: michael.scherr@med.uni-muenchen.de [Institute of Clinical Radiology, University of Munich, Munich (Germany); Seitz, M. [Department of Urology, University of Munich, Munich (Germany); Mueller-Lisse, U.G. [Institute of Clinical Radiology, University of Munich, Munich (Germany); Ingrisch, M. [Josef Lissner Laboratory for Biomedical Imaging, Institute of Clinical Radiology, University of Munich, Munich (Germany); Reiser, M.F. [Institute of Clinical Radiology, University of Munich, Munich (Germany); Mueller-Lisse, U.L. [Department of Urology, University of Munich, Munich (Germany)

2010-12-15

Background: Various MR methods, including MR-spectroscopy (MRS), dynamic, contrast-enhanced MRI (DCE-MRI), and diffusion-weighted imaging (DWI) have been applied to improve test quality of standard MRI of the prostate. Purpose: To determine if quantitative, model-based MR-perfusion (MRP) with gadobenate dimeglumine (Gd-BOPTA) discriminates between prostate cancer, benign tissue, and transitional zone (TZ) tissue. Material and methods: 27 patients (age, 65 {+-} 4 years; PSA 11.0 {+-} 6.1 ng/ml) with clinical suspicion of prostate cancer underwent standard MRI, 3D MR-spectroscopy (MRS), and MRP with Gd-BOPTA. Based on results of combined MRI/MRS and subsequent guided prostate biopsy alone (17/27), biopsy and radical prostatectomy (9/27), or sufficient negative follow-up (7/27), maps of model-free, deconvolution-based mean transit time (dMTT) were generated for 29 benign regions (bROIs), 14 cancer regions (cROIs), and 18 regions of transitional zone (tzROIs). Applying a 2-compartment exchange model, quantitative perfusion analysis was performed including as parameters: plasma flow (PF), plasma volume (PV), plasma mean transit time (PMTT), extraction flow (EFL), extraction fraction (EFR), interstitial volume (IV) and interstitial mean transit time (IMTT). Two-sided T-tests (significance level p < 0.05) discriminated bROIs vs. cROIs and cROIs vs. tzROIs, respectively. Results: PMTT discriminated best between bROIs (11.8 {+-} 3.0 s) and cROIs (24.3 {+-} 9.6 s) (p < 0.0001), while PF, PV, PS, EFR, IV, IMTT also differed significantly (p 0.00002-0.0136). Discrimination between cROIs and tzROIs was insignificant for all parameters except PV (14.3 {+-} 2.5 ml vs. 17.6 {+-} 2.6 ml, p < 0.05). Conclusions: Besides MRI, MRS and DWI quantitative, 2-compartment MRP with Gd-BOPTA discriminates between prostate cancer and benign tissue with several parameters. However, distinction of prostate cancer and TZ does not appear to be reliable.

TU-G-BRD-02: Automated Systematic Quality Assurance Program for Radiation Oncology Information System Upgrades

International Nuclear Information System (INIS)

Zhang, B; Yi, B; Eley, J; Mutaf, Y; Rahman, S; D’Souza, W

2015-01-01

Purpose: To: (1) describe an independent, automated, systematic software-based protocol for verifying clinical data accuracy/integrity for mitigation of data corruption/loss risks following radiation oncology information system (ROIS) upgrades; and (2) report on application of this approach in an academic/community practice environment. Methods: We propose a robust approach to perform quality assurance on the ROIS after an upgrade, targeting four data sources: (1) ROIS relational database; (2) ROIS DICOM interface; (3) ROIS treatment machine data configuration; and (4) ROIS-generated clinical reports. We investigated the database schema for differences between pre-/post-upgrade states. Paired DICOM data streams for the same object (such as RT-Plan/Treatment Record) were compared between pre-/post-upgrade states for data corruption. We examined machine configuration and related commissioning data files for changes and corruption. ROIS-generated treatment appointment and treatment parameter reports were compared to ensure patient encounter and treatment plan accuracy. This protocol was supplemented by an end-to-end clinical workflow test to verify essential ROI functionality and integrity of components interfaced during patient care chain of activities. We describe the implementation of this protocol during a Varian ARIA system upgrade at our clinic. Results: We verified 1,638 data tables with 2.4 billion data records. For 222 under-treatment patients, 605 DICOM RT plans and 13,480 DICOM treatment records retrieved from the ROIS DICOM interface were compared, with no differences in fractions, doses delivered, or treatment parameters. We identified 82 new data tables and 78 amended/deleted tables consistent with the upgrade. Reports for 5,073 patient encounters over a 2-week horizon were compared and were identical to those before the upgrade. Content in 12,237 xml machine files was compared, with no differences identified. Conclusion: An independent QA

TU-G-BRD-02: Automated Systematic Quality Assurance Program for Radiation Oncology Information System Upgrades

Energy Technology Data Exchange (ETDEWEB)

Zhang, B; Yi, B; Eley, J; Mutaf, Y; Rahman, S; D’Souza, W [University of Maryland School of Medicine, Baltimore, MD (United States)

2015-06-15

Purpose: To: (1) describe an independent, automated, systematic software-based protocol for verifying clinical data accuracy/integrity for mitigation of data corruption/loss risks following radiation oncology information system (ROIS) upgrades; and (2) report on application of this approach in an academic/community practice environment. Methods: We propose a robust approach to perform quality assurance on the ROIS after an upgrade, targeting four data sources: (1) ROIS relational database; (2) ROIS DICOM interface; (3) ROIS treatment machine data configuration; and (4) ROIS-generated clinical reports. We investigated the database schema for differences between pre-/post-upgrade states. Paired DICOM data streams for the same object (such as RT-Plan/Treatment Record) were compared between pre-/post-upgrade states for data corruption. We examined machine configuration and related commissioning data files for changes and corruption. ROIS-generated treatment appointment and treatment parameter reports were compared to ensure patient encounter and treatment plan accuracy. This protocol was supplemented by an end-to-end clinical workflow test to verify essential ROI functionality and integrity of components interfaced during patient care chain of activities. We describe the implementation of this protocol during a Varian ARIA system upgrade at our clinic. Results: We verified 1,638 data tables with 2.4 billion data records. For 222 under-treatment patients, 605 DICOM RT plans and 13,480 DICOM treatment records retrieved from the ROIS DICOM interface were compared, with no differences in fractions, doses delivered, or treatment parameters. We identified 82 new data tables and 78 amended/deleted tables consistent with the upgrade. Reports for 5,073 patient encounters over a 2-week horizon were compared and were identical to those before the upgrade. Content in 12,237 xml machine files was compared, with no differences identified. Conclusion: An independent QA

An interactive toolkit to extract phenological time series data from digital repeat photography

Science.gov (United States)

Seyednasrollah, B.; Milliman, T. E.; Hufkens, K.; Kosmala, M.; Richardson, A. D.

2017-12-01

Near-surface remote sensing and in situ photography are powerful tools to study how climate change and climate variability influence vegetation phenology and the associated seasonal rhythms of green-up and senescence. The rapidly-growing PhenoCam network has been using in situ digital repeat photography to study phenology in almost 500 locations around the world, with an emphasis on North America. However, extracting time series data from multiple years of half-hourly imagery - while each set of images may contain several regions of interest (ROI's), corresponding to different species or vegetation types - is not always straightforward. Large volumes of data require substantial processing time, and changes (either intentional or accidental) in camera field of view requires adjustment of ROI masks. Here, we introduce and present "DrawROI" as an interactive web-based application for imagery from PhenoCam. DrawROI can also be used offline, as a fully independent toolkit that significantly facilitates extraction of phenological data from any stack of digital repeat photography images. DrawROI provides a responsive environment for phenological scientists to interactively a) delineate ROIs, b) handle field of view (FOV) shifts, and c) extract and export time series data characterizing image color (i.e. red, green and blue channel digital numbers for the defined ROI). The application utilizes artificial intelligence and advanced machine learning techniques and gives user the opportunity to redraw new ROIs every time an FOV shift occurs. DrawROI also offers a quality control flag to indicate noisy data and images with low quality due to presence of foggy weather or snow conditions. The web-based application significantly accelerates the process of creating new ROIs and modifying pre-existing ROI in the PhenoCam database. The offline toolkit is presented as an open source R-package that can be used with similar datasets with time-lapse photography to obtain more data for

Changes in the fractal dimension, feret diameter, and lacunarity of mandibular alveolar bone during initial healing of dental implants.

Science.gov (United States)

Önem, Erinç; Baksı, B Güniz; Sogur, Elif

2012-01-01

To evaluate the combination of fractal dimension (FD), lacunarity, and Feret diameter (FeD) to quantitatively characterize structural changes of mandibular alveolar bone around dental implants during initial healing. Three standard-sized regions of interest (ROIs) (mesial and distal crest and apical area) around implants and three ROIs of the same size in the alveolar bone on the contralateral side were analyzed on digital panoramic images. FD was calculated using the box-counting method, and lacunarity was calculated using the FracLac plugin of Image J software. FeD was measured in the same ROIs. Comparisons of the groups were done with the Dunnett test. Forty-two implants in the posterior mandibles of 21 patients were used for FD measurements. A total of 189 ROIs was segmented into binary images. Mean FD values for mesial, distal, and apical ROIs around implants were 1.26, 1.36, and 1.4, respectively. The mean FD of alveolar bone around premolars/molars was 1.39 for all ROIs. The mean FeD for mesial, distal, and apical ROIs around implants was 7.63, 7.86, and 8.02, respectively, whereas it ranged between 7.88 and 8.13 for premolar teeth. Mean lacunarity values for mesial, distal, and apical ROIs around implants were 0.53, 0.51, and 0.48, respectively. Lacunarity values for ROIs around premolars ranged between 0.45 and 0.50. No significant differences were observed in FD, FeD, or lacunarity measurements between ROIs around implants and around teeth. The satisfactory healing of bone following implant placement may be monitored by calculating FD, lacunarity, and FeD using digital panoramic images. Although preliminary, these values may alert the practitioner to any implants with loss of stability.

Voxel-based morphometry and automated lobar volumetry: The trade-off between spatial scale and statistical correction

Science.gov (United States)

Voormolen, Eduard H.J.; Wei, Corie; Chow, Eva W.C.; Bassett, Anne S.; Mikulis, David J.; Crawley, Adrian P.

2011-01-01

Voxel-based morphometry (VBM) and automated lobar region of interest (ROI) volumetry are comprehensive and fast methods to detect differences in overall brain anatomy on magnetic resonance images. However, VBM and automated lobar ROI volumetry have detected dissimilar gray matter differences within identical image sets in our own experience and in previous reports. To gain more insight into how diverging results arise and to attempt to establish whether one method is superior to the other, we investigated how differences in spatial scale and in the need to statistically correct for multiple spatial comparisons influence the relative sensitivity of either technique to group differences in gray matter volumes. We assessed the performance of both techniques on a small dataset containing simulated gray matter deficits and additionally on a dataset of 22q11-deletion syndrome patients with schizophrenia (22q11DS-SZ) vs. matched controls. VBM was more sensitive to simulated focal deficits compared to automated ROI volumetry, and could detect global cortical deficits equally well. Moreover, theoretical calculations of VBM and ROI detection sensitivities to focal deficits showed that at increasing ROI size, ROI volumetry suffers more from loss in sensitivity than VBM. Furthermore, VBM and automated ROI found corresponding GM deficits in 22q11DS-SZ patients, except in the parietal lobe. Here, automated lobar ROI volumetry found a significant deficit only after a smaller subregion of interest was employed. Thus, sensitivity to focal differences is impaired relatively more by averaging over larger volumes in automated ROI methods than by the correction for multiple comparisons in VBM. These findings indicate that VBM is to be preferred over automated lobar-scale ROI volumetry for assessing gray matter volume differences between groups. PMID:19619660

Analysing E-Services and Mobile Applications with Companied Conjoint Analysis and fMRI Technique

OpenAIRE

Heinonen, Jarmo

2015-01-01

Previous research has shown that neuromarketing and conjoint analysis have been used in many areas of consumer research, and to provide for further understanding of consumer behaviour. Together these two methods may reveal more information about hidden desires, expectations and restrains of consumers’ brain. This paper attempts to examine these two research methods together as a companied analysis. More specifically this study utilizes fMRI and conjoint analysis is a tool for analysing consum...

Fully automated quantification of regional cerebral blood flow with three-dimensional stereotaxic region of interest template. Validation using magnetic resonance imaging. Technical note

Energy Technology Data Exchange (ETDEWEB)

Takeuchi, Ryo; Katayama, Shigenori; Takeda, Naoya; Fujita, Katsuzo [Nishi-Kobe Medical Center (Japan); Yonekura, Yoshiharu [Fukui Medical Univ., Matsuoka (Japan); Konishi, Junji [Kyoto Univ. (Japan). Graduate School of Medicine

2003-03-01

The previously reported three-dimensional stereotaxic region of interest (ROI) template (3DSRT-t) for the analysis of anatomically standardized technetium-99m-L,L-ethyl cysteinate dimer ({sup 99m}Tc-ECD) single photon emission computed tomography (SPECT) images was modified for use in a fully automated regional cerebral blood flow (rCBF) quantification software, 3DSRT, incorporating an anatomical standardization engine transplanted from statistical parametric mapping 99 and ROIs for quantification based on 3DSRT-t. Three-dimensional T{sub 2}-weighted magnetic resonance images of 10 patients with localized infarcted areas were compared with the ROI contour of 3DSRT, and the positions of the central sulcus in the primary sensorimotor area were also estimated. All positions of the 20 lesions were in strict accordance with the ROI delineation of 3DSRT. The central sulcus was identified on at least one side of 210 paired ROIs and in the middle of 192 (91.4%) of these 210 paired ROIs among the 273 paired ROIs of the primary sensorimotor area. The central sulcus was recognized in the middle of more than 71.4% of the ROIs in which the central sulcus was identifiable in the respective 28 slices of the primary sensorimotor area. Fully automated accurate ROI delineation on anatomically standardized images is possible with 3DSRT, which enables objective quantification of rCBF and vascular reserve in only a few minutes using {sup 99m}Tc-ECD SPECT images obtained by the resting and vascular reserve (RVR) method. (author)

Fully automated quantification of regional cerebral blood flow with three-dimensional stereotaxic region of interest template. Validation using magnetic resonance imaging. Technical note

International Nuclear Information System (INIS)

Takeuchi, Ryo; Katayama, Shigenori; Takeda, Naoya; Fujita, Katsuzo; Yonekura, Yoshiharu; Konishi, Junji

2003-01-01

The previously reported three-dimensional stereotaxic region of interest (ROI) template (3DSRT-t) for the analysis of anatomically standardized technetium-99m-L,L-ethyl cysteinate dimer ( 99m Tc-ECD) single photon emission computed tomography (SPECT) images was modified for use in a fully automated regional cerebral blood flow (rCBF) quantification software, 3DSRT, incorporating an anatomical standardization engine transplanted from statistical parametric mapping 99 and ROIs for quantification based on 3DSRT-t. Three-dimensional T 2 -weighted magnetic resonance images of 10 patients with localized infarcted areas were compared with the ROI contour of 3DSRT, and the positions of the central sulcus in the primary sensorimotor area were also estimated. All positions of the 20 lesions were in strict accordance with the ROI delineation of 3DSRT. The central sulcus was identified on at least one side of 210 paired ROIs and in the middle of 192 (91.4%) of these 210 paired ROIs among the 273 paired ROIs of the primary sensorimotor area. The central sulcus was recognized in the middle of more than 71.4% of the ROIs in which the central sulcus was identifiable in the respective 28 slices of the primary sensorimotor area. Fully automated accurate ROI delineation on anatomically standardized images is possible with 3DSRT, which enables objective quantification of rCBF and vascular reserve in only a few minutes using 99m Tc-ECD SPECT images obtained by the resting and vascular reserve (RVR) method. (author)

Cerebral perfusion computerized tomography: influence of reference vessels, regions of interest and interobserver variability

International Nuclear Information System (INIS)

Soustiel, Jean F.; Mor, Nadav; Zaaroor, Menashe; Goldsher, Dorith

2006-01-01

There are still no standardized guidelines for perfusion computerized tomography (PCT) analysis. A total of 61 PCT studies were analyzed using either the anterior cerebral artery (ACA) or the middle cerebral artery (MCA) as the arterial reference, and the superior sagittal sinus (SSS) or the vein of Galen (VG) as the venous reference. The sizes of regions of interest (ROI) were investigated comparing PCT results obtained using a hemispheric ROI combined with vascular pixel elimination with those obtained using five smaller ROIs located over the cortex and basal ganglia. In addition, interobserver variations were explored using a standardized protocol. MCA-based measurements of cerebral blood flow (CBF) and blood volume (CBV) were in accordance with those obtained with the ACA except in 16 patients with ischemic stroke, in whom CBF was overestimated by the ipsilateral MCA. Venous maximal intensity was significantly lower with the VG when compared with the SSS, resulting in overestimation of CBF and CBV. However, in 13.3% of patients the VG ROI yielded higher maximal intensities than the SSS ROI. There was no difference in PCT results between hemispheric ROI and averaged separate ROI when vascular pixel elimination was used. Finally, interobserver variations were as high as 11% for CBF and 12% for CBV. The present results suggest that pathological rather than anatomical considerations should dictate the choice of the arterial ROI. For venous ROI, although SSS seems to be adequate in most instances, deep cerebral veins may occasionally generate higher maximal intensities and should therefore be selected. Importantly, significant user-dependency should be taken into account. (orig.)

Isotropy analyses of the Planck convergence map

Science.gov (United States)

Marques, G. A.; Novaes, C. P.; Bernui, A.; Ferreira, I. S.

2018-01-01

The presence of matter in the path of relic photons causes distortions in the angular pattern of the cosmic microwave background (CMB) temperature fluctuations, modifying their properties in a slight but measurable way. Recently, the Planck Collaboration released the estimated convergence map, an integrated measure of the large-scale matter distribution that produced the weak gravitational lensing (WL) phenomenon observed in Planck CMB data. We perform exhaustive analyses of this convergence map calculating the variance in small and large regions of the sky, but excluding the area masked due to Galactic contaminations, and compare them with the features expected in the set of simulated convergence maps, also released by the Planck Collaboration. Our goal is to search for sky directions or regions where the WL imprints anomalous signatures to the variance estimator revealed through a χ2 analyses at a statistically significant level. In the local analysis of the Planck convergence map, we identified eight patches of the sky in disagreement, in more than 2σ, with what is observed in the average of the simulations. In contrast, in the large regions analysis we found no statistically significant discrepancies, but, interestingly, the regions with the highest χ2 values are surrounding the ecliptic poles. Thus, our results show a good agreement with the features expected by the Λ cold dark matter concordance model, as given by the simulations. Yet, the outliers regions found here could suggest that the data still contain residual contamination, like noise, due to over- or underestimation of systematic effects in the simulation data set.

Analysis of Return on Investment in Different Types of Agile Software Development Project Teams

Directory of Open Access Journals (Sweden)

Goran MILANOV

2012-01-01

Full Text Available This exploratory study of IT project teams in Serbia investigates how the choice of agile methods in different development project teams affects the return-on-investment (ROI. In this paper different types of software project teams are analyzed in order to examine and identify the business-value of using agile methods. In various software development project teams, the ROI of agile methods is yet to be fully explored, while the ROI of traditional methods is well-understood. Since ROI is important indicator of the projects success, in this paper we examine the factors that influence the ROI both from software solution customer point of view, and different agile project teams.

YY1 binding association with sex-biased transcription revealed through X-linked transcript levels and allelic binding analyses.

Science.gov (United States)

Chen, Chih-Yu; Shi, Wenqiang; Balaton, Bradley P; Matthews, Allison M; Li, Yifeng; Arenillas, David J; Mathelier, Anthony; Itoh, Masayoshi; Kawaji, Hideya; Lassmann, Timo; Hayashizaki, Yoshihide; Carninci, Piero; Forrest, Alistair R R; Brown, Carolyn J; Wasserman, Wyeth W

2016-11-18

Sex differences in susceptibility and progression have been reported in numerous diseases. Female cells have two copies of the X chromosome with X-chromosome inactivation imparting mono-allelic gene silencing for dosage compensation. However, a subset of genes, named escapees, escape silencing and are transcribed bi-allelically resulting in sexual dimorphism. Here we conducted in silico analyses of the sexes using human datasets to gain perspectives into such regulation. We identified transcription start sites of escapees (escTSSs) based on higher transcription levels in female cells using FANTOM5 CAGE data. Significant over-representations of YY1 transcription factor binding motif and ChIP-seq peaks around escTSSs highlighted its positive association with escapees. Furthermore, YY1 occupancy is significantly biased towards the inactive X (Xi) at long non-coding RNA loci that are frequent contacts of Xi-specific superloops. Our study suggests a role for YY1 in transcriptional activity on Xi in general through sequence-specific binding, and its involvement at superloop anchors.

Genome sequencing reveals metabolic and cellular interdependence in an amoeba-kinetoplastid symbiosis

Czech Academy of Sciences Publication Activity Database

Tanifuji, G.; Cenci, U.; Moog, D.; Dean, S.; Nakayama, T.; David, Vojtěch; Fiala, Ivan; Curtis, B.A.; Sibbald, S. J.; Onodera, N. T.; Colp, M.; Flegontov, Pavel; Johnson-MacKinnon, J.; McPhee, M.; Inagaki, Y.; Hashimoto, T.; Kelly, S.; Gull, K.; Lukeš, Julius; Archibald, J.M.

2017-01-01

Roč. 7, SEP 15 (2017), č. článku 11688. ISSN 2045-2322 R&D Projects: GA ČR(CZ) GA14-23986S; GA MŠk LL1601 Institutional support: RVO:60077344 Keywords : trypanosoma-brucei reveals * hidden markov model * neoparamoeba-pemaquidensis * gill disease * phylogenetic analyses * ichthyobodo-necator * gene prediction * host control * evolution * proteomics Subject RIV: EB - Genetics ; Molecular Biology OBOR OECD: Biochemistry and molecular biology Impact factor: 4.259, year: 2016

Participation and Business Case Analysis of the Marine for Life Program

National Research Council Canada - National Science Library

Sanders, Shawn G

2007-01-01

.... The ROI analysis found that the M4L Program had a ROI of (154%) in 2004 and (202%) in 2005; however, analysis of ROI does include all costs and omits some of the non-quantifiable benefits of the programs, which may bias the results...

Correlation analyses revealed global microRNA-mRNA expression associations in human peripheral blood mononuclear cells.

Science.gov (United States)

Wang, Lan; Zhu, Jiang; Deng, Fei-Yan; Wu, Long-Fei; Mo, Xing-Bo; Zhu, Xiao-Wei; Xia, Wei; Xie, Fang-Fei; He, Pei; Bing, Peng-Fei; Qiu, Ying-Hua; Lin, Xiang; Lu, Xin; Zhang, Lei; Yi, Neng-Jun; Zhang, Yong-Hong; Lei, Shu-Feng

2018-02-01

MicroRNAs (miRNAs) can regulate gene expression through binding to complementary sites in the 3'-untranslated regions of target mRNAs, which will lead to existence of correlation in expression between miRNA and mRNA. However, the miRNA-mRNA correlation patterns are complex and remain largely unclear yet. To establish the global correlation patterns in human peripheral blood mononuclear cells (PBMCs), multiple miRNA-mRNA correlation analyses and expression quantitative trait locus (eQTL) analysis were conducted in this study. We predicted and achieved 861 miRNA-mRNA pairs (65 miRNAs, 412 mRNAs) using multiple bioinformatics programs, and found global negative miRNA-mRNA correlations in PBMC from all 46 study subjects. Among the 861 pairs of correlations, 19.5% were significant (P correlation network was complex and highlighted key miRNAs/genes in PBMC. Some miRNAs, such as hsa-miR-29a, hsa-miR-148a, regulate a cluster of target genes. Some genes, e.g., TNRC6A, are regulated by multiple miRNAs. The identified genes tend to be enriched in molecular functions of DNA and RNA binding, and biological processes such as protein transport, regulation of translation and chromatin modification. The results provided a global view of the miRNA-mRNA expression correlation profile in human PBMCs, which would facilitate in-depth investigation of biological functions of key miRNAs/mRNAs and better understanding of the pathogenesis underlying PBMC-related diseases.

Microprobe analyses of uranium and thorium in uraninite from the Witwatersrand, South Africa, and Blind River, Ontario, Canada

International Nuclear Information System (INIS)

Grandstaff, D.E.

1981-01-01

Microprobe analyses of uranium and thorium in uraninite grains from the Witwatersrand, South Africa, and Blind River, Ontario, reveal that although individual grains are fairly homogeneous, the assemblage of grains is quite heterogeneous. This heterogeneity appears to favor genetic concepts advocating a detrital, placer origin for the uraninite

18F-FDG PET Reveals Fronto-temporal Dysfunction in Children with Fever-Induced Refractory Epileptic Encephalopathy

International Nuclear Information System (INIS)

Mazzuca, M.; Dulac, O.; Chiron, C.; Jambaque, I.; Hertz-Pannier, L.; Bouilleret, V.; Archambaud, F.; Rodrigo, S.; Dulac, O.; Chiron, C.; Jambaque, I.; Hertz-Pannier, L.; Bouilleret, V.; Archambaud, F.; Rodrigo, S.; Chiron, C.; Hertz-Pannier, L.; Rodrigo, S.; Dulac, O.; Chiron, C.; Caviness, V.

2011-01-01

Fever-induced refractory epileptic encephalopathy in school-age children (FIRES) is a recently described epileptic entity whose etiology remains unknown. Brain abnormalities shown by MRI are usually limited to mesial-temporal structures and do not account for the catastrophic neuro-psychologic findings. Methods: We conducted FIRES studies in 8 patients, aged 6-13 y, using 18 F-FDG PET to disclose eventual neo-cortical dysfunction. Voxel-based analyses of cerebral glucose metabolism were performed using statistical parametric mapping and an age-matched control group. Results: Group analysis revealed a widespread inter-ictal hypo-metabolic network including the temporo-parietal and orbito-frontal cortices bilaterally. The individual analyses in patients identified hypo-metabolic areas corresponding to the predominant electroencephalograph foci and neuro-psychologic deficits involving language, behavior, and memory. Conclusion: Despite clinical heterogeneity, 18 F-FDG PET reveals a common network dysfunction in patients with sequelae due to fever-induced refractory epileptic encephalopathy. (authors)

Maturation of the limbic system revealed by MR FLAIR imaging

Energy Technology Data Exchange (ETDEWEB)

Schneider, Jacques F.; Vergesslich, Klara [University Children' s Hospital UKBB, Department of Paediatric Radiology, Basel (Switzerland)

2007-04-15

Cortical signal intensity (SI) of the limbic system in adults is known to be higher than in neocortical structures, but time-related changes in SI during childhood have not been described. To detect maturation-related SI changes within the limbic system using a fluid-attenuated inversion recovery (FLAIR) MR sequence. Twenty children (10 boys, 10 girls; age 3.5-18 years, mean 11.2 years) with no neurological abnormality and normal MR imaging examination were retrospectively selected. On two coronal FLAIR slices, ten regions of interest (ROI) with a constant area of 10 mm{sup 2} were manually placed in the archeocortex (hippocampus), periarcheocortex (parahippocampal gyrus, subcallosal area, cingulate gyrus) and in the neocortex at the level of the superior frontal gyrus on both sides. Significant SI gradients were observed with a higher intensity in the archeocortex, intermediate intensity in the periarcheocortex and low intensity in the neocortex. Significant higher SI values in hippocampal and parahippocampal structures were detected in children up to 10 years of age. These differences mainly reflected differences in cortical structure and myelination state. Archeocortical structures especially showed significant age-related intensity progression suggesting ongoing organization and/or myelination until early adolescence. (orig.)

Maturation of the limbic system revealed by MR FLAIR imaging

International Nuclear Information System (INIS)

Schneider, Jacques F.; Vergesslich, Klara

2007-01-01

Cortical signal intensity (SI) of the limbic system in adults is known to be higher than in neocortical structures, but time-related changes in SI during childhood have not been described. To detect maturation-related SI changes within the limbic system using a fluid-attenuated inversion recovery (FLAIR) MR sequence. Twenty children (10 boys, 10 girls; age 3.5-18 years, mean 11.2 years) with no neurological abnormality and normal MR imaging examination were retrospectively selected. On two coronal FLAIR slices, ten regions of interest (ROI) with a constant area of 10 mm 2 were manually placed in the archeocortex (hippocampus), periarcheocortex (parahippocampal gyrus, subcallosal area, cingulate gyrus) and in the neocortex at the level of the superior frontal gyrus on both sides. Significant SI gradients were observed with a higher intensity in the archeocortex, intermediate intensity in the periarcheocortex and low intensity in the neocortex. Significant higher SI values in hippocampal and parahippocampal structures were detected in children up to 10 years of age. These differences mainly reflected differences in cortical structure and myelination state. Archeocortical structures especially showed significant age-related intensity progression suggesting ongoing organization and/or myelination until early adolescence. (orig.)

Increased thalamic resting-state connectivity as a core driver of LSD-induced hallucinations.

Science.gov (United States)

Müller, F; Lenz, C; Dolder, P; Lang, U; Schmidt, A; Liechti, M; Borgwardt, S

2017-12-01

It has been proposed that the thalamocortical system is an important site of action of hallucinogenic drugs and an essential component of the neural correlates of consciousness. Hallucinogenic drugs such as LSD can be used to induce profoundly altered states of consciousness, and it is thus of interest to test the effects of these drugs on this system. 100 μg LSD was administrated orally to 20 healthy participants prior to fMRI assessment. Whole brain thalamic functional connectivity was measured using ROI-to-ROI and ROI-to-voxel approaches. Correlation analyses were used to explore relationships between thalamic connectivity to regions involved in auditory and visual hallucinations and subjective ratings on auditory and visual drug effects. LSD caused significant alterations in all dimensions of the 5D-ASC scale and significantly increased thalamic functional connectivity to various cortical regions. Furthermore, LSD-induced functional connectivity measures between the thalamus and the right fusiform gyrus and insula correlated significantly with subjective auditory and visual drug effects. Hallucinogenic drug effects might be provoked by facilitations of cortical excitability via thalamocortical interactions. Our findings have implications for the understanding of the mechanism of action of hallucinogenic drugs and provide further insight into the role of the 5-HT 2A -receptor in altered states of consciousness. © 2017 The Authors Acta Psychiatrica Scandinavica Published by John Wiley & Sons Ltd.

Look@NanoSIMS--a tool for the analysis of nanoSIMS data in environmental microbiology.

Science.gov (United States)

Polerecky, Lubos; Adam, Birgit; Milucka, Jana; Musat, Niculina; Vagner, Tomas; Kuypers, Marcel M M

2012-04-01

We describe an open-source freeware programme for high throughput analysis of nanoSIMS (nanometre-scale secondary ion mass spectrometry) data. The programme implements basic data processing and analytical functions, including display and drift-corrected accumulation of scanned planes, interactive and semi-automated definition of regions of interest (ROIs), and export of the ROIs' elemental and isotopic composition in graphical and text-based formats. Additionally, the programme offers new functions that were custom-designed to address the needs of environmental microbiologists. Specifically, it allows manual and automated classification of ROIs based on the information that is derived either from the nanoSIMS dataset itself (e.g. from labelling achieved by halogen in situ hybridization) or is provided externally (e.g. as a fluorescence in situ hybridization image). Moreover, by implementing post-processing routines coupled to built-in statistical tools, the programme allows rapid synthesis and comparative analysis of results from many different datasets. After validation of the programme, we illustrate how these new processing and analytical functions increase flexibility, efficiency and depth of the nanoSIMS data analysis. Through its custom-made and open-source design, the programme provides an efficient, reliable and easily expandable tool that can help a growing community of environmental microbiologists and researchers from other disciplines process and analyse their nanoSIMS data. © 2012 Society for Applied Microbiology and Blackwell Publishing Ltd.

A motion correction algorithm for an image realignment programme useful for sequential radionuclide renography

International Nuclear Information System (INIS)

De Agostini, A.; Moretti, R.; Belletti, S.; Maira, G.; Magri, G.C.; Bestagno, M.

1992-01-01

The correction of organ movements in sequential radionuclide renography was done using an iterative algorithm that, by means of a set of rectangular regions of interest (ROIs), did not require any anatomical marker or manual elaboration of frames. The realignment programme here proposed is quite independent of the spatial and temporal distribution of activity and analyses the rotational movement in a simplified but reliable way. The position of the object inside a frame is evaluated by choosing the best ROI in a set of ROIs shifted 1 pixel around the central one. Statistical tests have to be fulfilled by the algorithm in order to activate the realignment procedure. Validation of the algorithm was done for different acquisition set-ups and organ movements. Results, summarized in Table 1, show that in about 90% of the stimulated experiments the algorithm is able to correct the movements of the object with a maximum error less of equal to 1 pixel limit. The usefulness of the realignment programme was demonstrated with sequential radionuclide renography as a typical clinical application. The algorithm-corrected curves of a 1-year-old patient were completely different from those obtained without a motion correction procedure. The algorithm may be applicable also to other types of scintigraphic examinations, besides functional imaging in which the realignment of frames of the dynamic sequence was an intrinsic demand. (orig.)

Molecular cytogenetic analyses of Epinephelus bruneus and Epinephelus moara (Perciformes, Epinephelidae

Directory of Open Access Journals (Sweden)

Minglan Guo

2014-06-01

Full Text Available Genus Epinephelus (Perciformes, Epinephelidae, commonly known as groupers, are usually difficult in species identification for the lack and/or change of morphological specialization. In this study, molecular cytogenetic analyses were firstly performed to identify the closely related species Epinephelus bruneus and E. moara in this genus. The species-specific differences of both fish species showed in karyotype, chromosomal distribution of nucleolar organizer regions (NORs and localization of 18S rDNA. The heterochromatin (interstitial C-bands and distribution pattern of telomere (TTAGGGn in E. bruneus revealed the chromosomal rearrangements and different karyotypic evolutionary characteristics compared to those in E. moara. The cytogenetic data suggested that the lineages of E. bruneus and E. moara were recently derived within the genus Epinephelus, and E. moara exhibited more plesiomorphic features than E. bruneus. All results confirmed that E. moara, which has long been considered a synonym of E. bruneus, is a distinct species in the family Epinephelidae. In addition, molecular cytogenetic analyses are useful in species differentiation and phylogenetic reconstruction in groupers.

A Formal Model to Analyse the Firewall Configuration Errors

Directory of Open Access Journals (Sweden)

T. T. Myo

2015-01-01

Full Text Available The firewall is widely known as a brandmauer (security-edge gateway. To provide the demanded security, the firewall has to be appropriately adjusted, i.e. be configured. Unfortunately, when configuring, even the skilled administrators may make mistakes, which result in decreasing level of a network security and network infiltration undesirable packages.The network can be exposed to various threats and attacks. One of the mechanisms used to ensure network security is the firewall.The firewall is a network component, which, using a security policy, controls packages passing through the borders of a secured network. The security policy represents the set of rules.Package filters work in the mode without inspection of a state: they investigate packages as the independent objects. Rules take the following form: (condition, action. The firewall analyses the entering traffic, based on the IP address of the sender and recipient, the port number of the sender and recipient, and the used protocol. When the package meets rule conditions, the action specified in the rule is carried out. It can be: allow, deny.The aim of this article is to develop tools to analyse a firewall configuration with inspection of states. The input data are the file with the set of rules. It is required to submit the analysis of a security policy in an informative graphic form as well as to reveal discrepancy available in rules. The article presents a security policy visualization algorithm and a program, which shows how the firewall rules act on all possible packages. To represent a result in an intelligible form a concept of the equivalence region is introduced.Our task is the program to display results of rules action on the packages in a convenient graphic form as well as to reveal contradictions between the rules. One of problems is the large number of measurements. As it was noted above, the following parameters are specified in the rule: Source IP address, appointment IP

Nomadic lifestyle of Lactobacillus plantarum revealed by comparative genomics of 54 strains isolated from different habitats.

Science.gov (United States)

Martino, Maria Elena; Bayjanov, Jumamurat R; Caffrey, Brian E; Wels, Michiel; Joncour, Pauline; Hughes, Sandrine; Gillet, Benjamin; Kleerebezem, Michiel; van Hijum, Sacha A F T; Leulier, François

2016-12-01

The ability of bacteria to adapt to diverse environmental conditions is well-known. The process of bacterial adaptation to a niche has been linked to large changes in the genome content, showing that many bacterial genomes reflect the constraints imposed by their habitat. However, some highly versatile bacteria are found in diverse habitats that almost share nothing in common. Lactobacillus plantarum is a lactic acid bacterium that is found in a large variety of habitat. With the aim of unravelling the link between evolution and ecological versatility of L. plantarum, we analysed the genomes of 54 L. plantarum strains isolated from different environments. Comparative genome analysis identified a high level of genomic diversity and plasticity among the strains analysed. Phylogenomic and functional divergence studies coupled with gene-trait matching analyses revealed a mixed distribution of the strains, which was uncoupled from their environmental origin. Our findings revealed the absence of specific genomic signatures marking adaptations of L. plantarum towards the diverse habitats it is associated with. This suggests fundamentally similar trends of genome evolution in L. plantarum, which occur in a manner that is apparently uncoupled from ecological constraint and reflects the nomadic lifestyle of this species. © 2016 The Authors. Environmental Microbiology published by Society for Applied Microbiology and John Wiley & Sons Ltd.

Distribution-analytical techniques in the study of AD/HD: Delta plot analyses reveal deficits in response inhibition that are eliminated by methylphenidate treatment

NARCIS (Netherlands)

Ridderinkhof, K.R.; Scheres, A.; Oosterlaan, J.; Sergeant, J.A.

2005-01-01

The authors highlight the utility of distribution-analytical techniques in the study of individual differences and clinical disorders. Cognitive deficits associated with attention-deficit/hyperactivity disorder (AD/HD) were examined by using delta-plot analyses of performance data (reaction time and

Trophic structure of mesopelagic fishes in the Gulf of Mexico revealed by gut content and stable isotope analyses

Science.gov (United States)

McClain-Counts, Jennifer P.; Demopoulos, Amanda W.J.; Ross, Steve W.

2017-01-01

Mesopelagic fishes represent an important component of the marine food web due to their global distributions, high abundances and ability to transport organic material throughout a large part of the water column. This study combined stable isotope (SIAs) and gut content analyses (GCAs) to characterize the trophic structure of mesopelagic fishes in the North-Central Gulf of Mexico. Additionally, this study examined whether mesopelagic fishes utilized chemosynthetic energy from cold seeps. Specimens were collected (9–25 August 2007) over three deep (>1,000 m) cold seeps at discrete depths (surface to 1,503 m) over the diurnal cycle. GCA classified 31 species (five families) of mesopelagic fishes into five feeding guilds: piscivores, large crustacean consumers, copepod consumers, generalists and mixed zooplanktivores. However, these guilds were less clearly defined based on stable isotope mixing model (MixSIAR) results, suggesting diets may be more mixed over longer time periods (weeks–months) and across co-occurring species. Copepods were likely important for the majority of mesopelagic fishes, consistent with GCA (this study) and previous literature. MixSIAR results also identified non-crustacean prey items, including salps and pteropods, as potentially important prey items for mesopelagic fishes, including those fishes not analysed in GCA (Sternoptyx spp. and Melamphaidae). Salps and other soft-bodied species are often missed in GCAs. Mesopelagic fishes had δ13C results consistent with particulate organic matter serving as the baseline organic carbon source, fueling up to three trophic levels. Fishes that undergo diel vertical migration were depleted in 15N relative to weak migrators, consistent with depth-specific isotope trends in sources and consumers, and assimilation of 15N-depleted organic matter in surface waters. Linear correlations between fish size and δ15N values suggested ontogenetic changes in fish diets for several species. While there was

Tomographic local 2D analyses of the WISExSuperCOSMOS all-sky galaxy catalogue

Science.gov (United States)

Novaes, C. P.; Bernui, A.; Xavier, H. S.; Marques, G. A.

2018-05-01

The recent progress in obtaining larger and deeper galaxy catalogues is of fundamental importance for cosmological studies, especially to robustly measure the large scale density fluctuations in the Universe. The present work uses the Minkowski Functionals (MF) to probe the galaxy density field from the WISExSuperCOSMOS (WSC) all-sky catalogue by performing tomographic local analyses in five redshift shells (of thickness δz = 0.05) in the total range of 0.10 methodology reveals 1 - 3 regions of the GNC maps in each redshift shell with an uncommon behaviour (extreme regions), i.e., p-value < 1.4%. Indeed, the resulting MF curves show signatures that suggest the uncommon behaviour to be associated with the presence of over- or under-densities there, but contamination due to residual foregrounds is not discarded. Additionally, even though our analyses indicate a good agreement among data and simulations, we identify 1 highly extreme region, seemingly associated to a large clustered distribution of galaxies. Our results confirm the usefulness of the MF to analyse GNC maps from photometric galaxy datasets.

Linking brain-wide multivoxel activation patterns to behaviour: Examples from language and math

Science.gov (United States)

Raizada, Rajeev D.S.; Tsao, Feng-Ming; Liu, Huei-Mei; Holloway, Ian D.; Ansari, Daniel; Kuhl, Patricia K.

2010-01-01

A key goal of cognitive neuroscience is to find simple and direct connections between brain and behaviour. However, fMRI analysis typically involves choices between many possible options, with each choice potentially biasing any brain–behaviour correlations that emerge. Standard methods of fMRI analysis assess each voxel individually, but then face the problem of selection bias when combining those voxels into a region-of-interest, or ROI. Multivariate pattern-based fMRI analysis methods use classifiers to analyse multiple voxels together, but can also introduce selection bias via data-reduction steps as feature selection of voxels, pre-selecting activated regions, or principal components analysis. We show here that strong brain–behaviour links can be revealed without any voxel selection or data reduction, using just plain linear regression as a classifier applied to the whole brain at once, i.e. treating each entire brain volume as a single multi-voxel pattern. The brain–behaviour correlations emerged despite the fact that the classifier was not provided with any information at all about subjects' behaviour, but instead was given only the neural data and its condition-labels. Surprisingly, more powerful classifiers such as a linear SVM and regularised logistic regression produce very similar results. We discuss some possible reasons why the very simple brain-wide linear regression model is able to find correlations with behaviour that are as strong as those obtained on the one hand from a specific ROI and on the other hand from more complex classifiers. In a manner which is unencumbered by arbitrary choices, our approach offers a method for investigating connections between brain and behaviour which is simple, rigorous and direct. PMID:20132896

Fronto-limbic dysfunction in response to facial emotion in borderline personality disorder: an event-related fMRI study.

Science.gov (United States)

Minzenberg, Michael J; Fan, Jin; New, Antonia S; Tang, Cheuk Y; Siever, Larry J

2007-08-15

Clinical hallmarks of borderline personality disorder (BPD) include social and emotional dysregulation. We tested a model of fronto-limbic dysfunction in facial emotion processing in BPD. Groups of 12 unmedicated adults with BPD by DSM-IV and 12 demographically-matched healthy controls (HC) viewed facial expressions (Conditions) of neutral emotion, fear and anger, and made gender discriminations during rapid event-related functional magnetic resonance imaging (fMRI). Analysis of variance of Region of Interest signal change revealed a statistically significant effect of the Group-by-Region-by-Condition interaction. This was due to the BPD group exhibiting a significantly larger magnitude of deactivation (relative to HC) in the bilateral rostral/subgenual anterior cingulate cortex (ACC) to fear and in the left ACC to fear minus neutral; and significantly greater activation in the right amygdala to fear minus neutral. There were no significant between-group differences in ROI signal change in response to anger. In voxel-wise analyses constrained within these ROIs, the BPD group exhibited significant changes in the fear minus neutral contrast, with relatively less activation in the bilateral rostral/subgenual ACC, and greater activation in the right amygdala. In the anger minus neutral contrast this pattern was reversed, with the BPD group showing greater activation in the bilateral rostral/subgenual ACC and less activation in the bilateral amygdala. We conclude that adults with BPD exhibit changes in fronto-limbic activity in the processing of fear stimuli, with exaggerated amygdala response and impaired emotion-modulation of ACC activity. The neural substrates underlying processing of anger may also be altered. These changes may represent an expression of the volumetric and serotonergic deficits observed in these brain areas in BPD.

Microscopic and Spectroscopic Analyses of Chlorhexidine Tolerance in Delftia acidovorans Biofilms

Science.gov (United States)

Rema, Tara; Lawrence, John R.; Dynes, James J.; Hitchcock, Adam P.

2014-01-01

The physicochemical responses of Delftia acidovorans biofilms exposed to the commonly used antimicrobial chlorhexidine (CHX) were examined in this study. A CHX-sensitive mutant (MIC, 1.0 μg ml−1) was derived from a CHX-tolerant (MIC, 15.0 μg ml−1) D. acidovorans parent strain using transposon mutagenesis. D. acidovorans mutant (MT51) and wild-type (WT15) strain biofilms were cultivated in flow cells and then treated with CHX at sub-MIC and inhibitory concentrations and examined by confocal laser scanning microscopy (CLSM), scanning transmission X-ray microscopy (STXM), and infrared (IR) spectroscopy. Specific morphological, structural, and chemical compositional differences between the CHX-treated and -untreated biofilms of both strains were observed. Apart from architectural differences, CLSM revealed a negative effect of CHX on biofilm thickness in the CHX-sensitive MT51 biofilms relative to those of the WT15 strain. STXM analyses showed that the WT15 biofilms contained two morphochemical cell variants, whereas only one type was detected in the MT51 biofilms. The cells in the MT51 biofilms bioaccumulated CHX to a similar extent as one of the cell types found in the WT15 biofilms, whereas the other cell type in the WT15 biofilms did not bioaccumulate CHX. STXM and IR spectral analyses revealed that CHX-sensitive MT51 cells accumulated the highest levels of CHX. Pretreating biofilms with EDTA promoted the accumulation of CHX in all cells. Thus, it is suggested that a subpopulation of cells that do not accumulate CHX appear to be responsible for greater CHX resistance in D. acidovorans WT15 biofilm in conjunction with the possible involvement of bacterial membrane stability. PMID:25022584

Reconstruction for interior region-of-interest inverse geometry computed tomography: preliminary study

Energy Technology Data Exchange (ETDEWEB)

Kim, Dong Su; Kim, Tae Ho; Kim, Kyeong Hyeon; Yoon, Do Kun; Suh, Tae Suk [Dept. of Biomedical Engineering, Research Institute of Biomedical Engineering, College of Medicine, The Catholic University of Korea, Seoul (Korea, Republic of); Kang, Seong Hee [Dept. of Radiation Oncology, Seoul National University Hospital, Seoul (Korea, Republic of); Cho, Min Seok [Dept. of Radiation Oncology, Asan Medical Center, Seoul (Korea, Republic of); Noh, Yu Yoon [Dept. of Radiation Oncology, Eulji University Hospital, Daejeon (Korea, Republic of)

2017-04-15

The inverse geometry computed tomography (IGCT) composed of multiple source and small size detector has several merits such as reduction of scatter effect and large volumetric imaging within one rotation without cone-beam artifact, compared to conventional cone-beam computed tomography (CBCT). By using this multi-source characteristics, we intend to present a selective and multiple interior region-of-interest (ROI) imaging method by using a designed source on-off sequence of IGCT. ROI-IGCT showed comparable image quality and has the capability to provide multi ROI image within a rotation. In this regard, it seems to be useful for diagnostic or image guidance for radiotherapy. ROI-IGCT showed comparable image quality and has the capability to provide multi ROI image within a rotation. Projection of ROI-IGCT is performed by selective irradiation, hence unnecessary imaging dose to non-interest region can be reduced. In this regard, it seems to be useful for diagnostic or image guidance for radiotherapy.

Region of Interest Selection Interface for Wide-Angle Arthroscope

Directory of Open Access Journals (Sweden)

Jung Kyunghwa

2015-01-01

Full Text Available We have proposed a new interface for an wide-angle endoscope for solo surgery. The wide-angle arthroscopic view and magnified region of interest (ROI within the wide view were shown simultaneously. With a camera affixed to surgical instruments, the position of the ROI could be determined by manipulating the surgical instrument. Image features acquired by the A-KAZE approach were used to estimate the change of position of the surgical instrument by tracking the features every time the camera moved. We examined the accuracy of ROI selection using three different images, which were different-sized square arrays and tested phantom experiments. When the number of ROIs was twelve, the success rate was best, and the rate diminished as the size of ROIs decreased. The experimental results showed that the method of using a camera without additional sensors satisfied the appropriate accuracy required for ROI selection, and this interface was helpful in performing surgery with fewer assistants.

Genetic Markers Analyses and Bioinformatic Approaches to Distinguish Between Olive Tree (Olea europaea L.) Cultivars.

Science.gov (United States)

Ben Ayed, Rayda; Ben Hassen, Hanen; Ennouri, Karim; Rebai, Ahmed

2016-12-01

The genetic diversity of 22 olive tree cultivars (Olea europaea L.) sampled from different Mediterranean countries was assessed using 5 SNP markers (FAD2.1; FAD2.3; CALC; SOD and ANTHO3) located in four different genes. The genotyping analysis of the 22 cultivars with 5 SNP loci revealed 11 alleles (average 2.2 per allele). The dendrogram based on cultivar genotypes revealed three clusters consistent with the cultivars classification. Besides, the results obtained with the five SNPs were compared to those obtained with the SSR markers using bioinformatic analyses and by computing a cophenetic correlation coefficient, indicating the usefulness of the UPGMA method for clustering plant genotypes. Based on principal coordinate analysis using a similarity matrix, the first two coordinates, revealed 54.94 % of the total variance. This work provides a more comprehensive explanation of the diversity available in Tunisia olive cultivars, and an important contribution for olive breeding and olive oil authenticity.

Altered Brain Activity in Unipolar Depression Revisited: Meta-analyses of Neuroimaging Studies.

Science.gov (United States)

Müller, Veronika I; Cieslik, Edna C; Serbanescu, Ilinca; Laird, Angela R; Fox, Peter T; Eickhoff, Simon B

2017-01-01

major depressive disorder. For meta-analyses with a minimum of 17 experiments available, separate analyses were performed for increases and decreases. In total, 57 studies with 99 individual neuroimaging experiments comprising in total 1058 patients were included; 34 of them tested cognitive and 65 emotional processing. Overall analyses across cognitive processing experiments (P > .29) and across emotional processing experiments (P > .47) revealed no significant results. Similarly, no convergence was found in analyses investigating positive (all P > .15), negative (all P > .76), or memory (all P > .48) processes. Analyses that restricted inclusion of confounds (eg, medication, comorbidity, age) did not change the results. Inconsistencies exist across individual experiments investigating aberrant brain activity in UD and replication problems across previous neuroimaging meta-analyses. For individual experiments, these inconsistencies may relate to use of uncorrected inference procedures, differences in experimental design and contrasts, or heterogeneous clinical populations; meta-analytically, differences may be attributable to varying inclusion and exclusion criteria or rather liberal statistical inference approaches.