Mechanistic Insights on Human Phosphoglucomutase Revealed by Transition Path Sampling and Molecular Dynamics Calculations.

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Brás, Natércia F; Fernandes, Pedro A; Ramos, Maria J; Schwartz, Steven D

2018-02-06

Human α-phosphoglucomutase 1 (α-PGM) catalyzes the isomerization of glucose-1-phosphate into glucose-6-phosphate (G6P) through two sequential phosphoryl transfer steps with a glucose-1,6-bisphosphate (G16P) intermediate. Given that the release of G6P in the gluconeogenesis raises the glucose output levels, α-PGM represents a tempting pharmacological target for type 2 diabetes. Here, we provide the first theoretical study of the catalytic mechanism of human α-PGM. We performed transition-path sampling simulations to unveil the atomic details of the two catalytic chemical steps, which could be key for developing transition state (TS) analogue molecules with inhibitory properties. Our calculations revealed that both steps proceed through a concerted S N 2-like mechanism, with a loose metaphosphate-like TS. Even though experimental data suggests that the two steps are identical, we observed noticeable differences: 1) the transition state ensemble has a well-defined TS region and a late TS for the second step, and 2) larger coordinated protein motions are required to reach the TS of the second step. We have identified key residues (Arg23, Ser117, His118, Lys389), and the Mg 2+ ion that contribute in different ways to the reaction coordinate. Accelerated molecular dynamics simulations suggest that the G16P intermediate may reorient without leaving the enzymatic binding pocket, through significant conformational rearrangements of the G16P and of specific loop regions of the human α-PGM. © 2018 Wiley-VCH Verlag GmbH & Co. KGaA, Weinheim.

A method for the estimation of the significance of cross-correlations in unevenly sampled red-noise time series

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Max-Moerbeck, W.; Richards, J. L.; Hovatta, T.; Pavlidou, V.; Pearson, T. J.; Readhead, A. C. S.

2014-11-01

We present a practical implementation of a Monte Carlo method to estimate the significance of cross-correlations in unevenly sampled time series of data, whose statistical properties are modelled with a simple power-law power spectral density. This implementation builds on published methods; we introduce a number of improvements in the normalization of the cross-correlation function estimate and a bootstrap method for estimating the significance of the cross-correlations. A closely related matter is the estimation of a model for the light curves, which is critical for the significance estimates. We present a graphical and quantitative demonstration that uses simulations to show how common it is to get high cross-correlations for unrelated light curves with steep power spectral densities. This demonstration highlights the dangers of interpreting them as signs of a physical connection. We show that by using interpolation and the Hanning sampling window function we are able to reduce the effects of red-noise leakage and to recover steep simple power-law power spectral densities. We also introduce the use of a Neyman construction for the estimation of the errors in the power-law index of the power spectral density. This method provides a consistent way to estimate the significance of cross-correlations in unevenly sampled time series of data.

Transgenic zebrafish reveal tissue-specific differences in estrogen signaling in response to environmental water samples.

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Gorelick, Daniel A; Iwanowicz, Luke R; Hung, Alice L; Blazer, Vicki S; Halpern, Marnie E

2014-04-01

Environmental endocrine disruptors (EEDs) are exogenous chemicals that mimic endogenous hormones such as estrogens. Previous studies using a zebrafish transgenic reporter demonstrated that the EEDs bisphenol A and genistein preferentially activate estrogen receptors (ERs) in the larval heart compared with the liver. However, it was not known whether the transgenic zebrafish reporter was sensitive enough to detect estrogens from environmental samples, whether environmental estrogens would exhibit tissue-specific effects similar to those of BPA and genistein, or why some compounds preferentially target receptors in the heart. We tested surface water samples using a transgenic zebrafish reporter with tandem estrogen response elements driving green fluorescent protein expression (5xERE:GFP). Reporter activation was colocalized with tissue-specific expression of ER genes by RNA in situ hybridization. We observed selective patterns of ER activation in transgenic fish exposed to river water samples from the Mid-Atlantic United States, with several samples preferentially activating receptors in embryonic and larval heart valves. We discovered that tissue specificity in ER activation was due to differences in the expression of ER subtypes. ERα was expressed in developing heart valves but not in the liver, whereas ERβ2 had the opposite profile. Accordingly, subtype-specific ER agonists activated the reporter in either the heart valves or the liver. The use of 5xERE:GFP transgenic zebrafish revealed an unexpected tissue-specific difference in the response to environmentally relevant estrogenic compounds. Exposure to estrogenic EEDs in utero was associated with adverse health effects, with the potentially unanticipated consequence of targeting developing heart valves.

Fecal steroid hormones reveal reproductive state in female blue whales sampled in the Gulf of California, Mexico.

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Valenzuela-Molina, Marcia; Atkinson, Shannon; Mashburn, Kendall; Gendron, Diane; Brownell, Robert L

2018-05-15

Steroid hormone assessment using non-invasive sample collection techniques can reveal the reproductive status of aquatic mammals and the physiological mechanisms by which they respond to changes in their environment. A portion of the eastern North Pacific blue whale (Balaenoptera musculus) population that seasonally visits the Gulf of California, Mexico has been monitored using photo-identified individuals for over 30 years. The whales use the area in winter-early spring for nursing their calves and feeding and it therefore is well suited for fecal sample collection. Using radioimmunoassays in 25 fecal samples collected between 2009 and 2012 to determine reproductive state and stress, we validated three steroid hormones (progesterone, corticosterone and cortisol) in adult female blue whales. Females that were categorized as pregnant had higher mean fecal progesterone metabolite concentrations (1292.6 ± 415.6 ng·g -1 ) than resting and lactating females (14.0 ± 3.7 ng·g -1 ; 23.0 ± 5.4 ng·g -1 , respectively). Females classified as pregnant also had higher concentrations of corticosterone metabolites (37.5 ± 9.9 ng·g -1 ) than resting and lactating females (17.4 ± 2.0 ng·g -1 ; 16.8 ± 2.8 ng·g -1 , respectively). In contrast, cortisol metabolite concentrations showed high variability between groups and no significant relationship to reproductive state. We successfully determined preliminary baseline parameters of key steroid hormones by reproductive state in adult female blue whales. The presence of pregnant or with luteal activity and known lactating females confirms that the Gulf of California is an important winter-spring area for the reproductive phase of these blue whales. The baseline corticosterone levels we are developing will be useful for assessing the impact of the increasing coastal development and whale-watching activities on the whales in the Gulf of California. Copyright © 2018 Elsevier Inc. All

Significant increase in cultivation of Gardnerella vaginalis, Alloscardovia omnicolens, Actinotignum schaalii, and Actinomyces spp. in urine samples with total laboratory automation.

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Klein, Sabrina; Nurjadi, Dennis; Horner, Susanne; Heeg, Klaus; Zimmermann, Stefan; Burckhardt, Irene

2018-04-13

While total laboratory automation (TLA) is well established in laboratory medicine, only a few microbiological laboratories are using TLA systems. Especially in terms of speed and accuracy, working with TLA is expected to be superior to conventional microbiology. We compared in total 35,564 microbiological urine cultures with and without incubation and processing with BD Kiestra TLA for a 6-month period each retrospectively. Sixteen thousand three hundred thirty-eight urine samples were analyzed in the pre-TLA period and 19,226 with TLA. Sixty-two percent (n = 10,101/16338) of the cultures processed without TLA and 68% (n = 13,102/19226) of the cultures processed with TLA showed growth. There were significantly more samples with two or more species per sample and with low numbers of colony forming units (CFU) after incubation with TLA. Regarding the type of bacteria, there were comparable amounts of Enterobacteriaceae in the samples, slightly less non-fermenting Gram-negative bacteria, but significantly more Gram-positive cocci, and Gram-positive rods. Especially Alloscardivia omnicolens, Gardnerella vaginalis, Actinomyces spp., and Actinotignum schaalii were significantly more abundant in the samples incubated and processed with TLA. The time to report was significantly lower in the TLA processed samples by 1.5 h. We provide the first report in Europe of a large number of urine samples processed with TLA. TLA showed enhanced growth of non-classical and rarely cultured bacteria from urine samples. Our findings suggest that previously underestimated bacteria may be relevant pathogens for urinary tract infections. Further studies are needed to confirm our findings.

The significance of sampling time in therapeutic drug monitoring of clozapine

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Jakobsen, M I; Larsen, J R; Svensson, C K

2017-01-01

OBJECTIVE: Therapeutic drug monitoring (TDM) of clozapine is standardized to 12-h postdose samplings. In clinical settings, sampling time often deviates from this time point, although the importance of the deviation is unknown. To this end, serum concentrations (s-) of clozapine and its metabolite...... N-desmethyl-clozapine (norclozapine) were measured at 12 ± 1 and 2 h postdose. METHOD: Forty-six patients with a diagnosis of schizophrenia, and on stable clozapine treatment, were enrolled for hourly, venous blood sampling at 10-14 h postdose. RESULTS: Minor changes in median percentage values were...

Predator-guided sampling reveals biotic structure in the bathypelagic.

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Benoit-Bird, Kelly J; Southall, Brandon L; Moline, Mark A

2016-02-24

We targeted a habitat used differentially by deep-diving, air-breathing predators to empirically sample their prey's distributions off southern California. Fine-scale measurements of the spatial variability of potential prey animals from the surface to 1,200 m were obtained using conventional fisheries echosounders aboard a surface ship and uniquely integrated into a deep-diving autonomous vehicle. Significant spatial variability in the size, composition, total biomass, and spatial organization of biota was evident over all spatial scales examined and was consistent with the general distribution patterns of foraging Cuvier's beaked whales (Ziphius cavirostris) observed in separate studies. Striking differences found in prey characteristics between regions at depth, however, did not reflect differences observed in surface layers. These differences in deep pelagic structure horizontally and relative to surface structure, absent clear physical differences, change our long-held views of this habitat as uniform. The revelation that animals deep in the water column are so spatially heterogeneous at scales from 10 m to 50 km critically affects our understanding of the processes driving predator-prey interactions, energy transfer, biogeochemical cycling, and other ecological processes in the deep sea, and the connections between the productive surface mixed layer and the deep-water column. © 2016 The Author(s).

Hypothesis Tests for Bernoulli Experiments: Ordering the Sample Space by Bayes Factors and Using Adaptive Significance Levels for Decisions

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Carlos A. de B. Pereira

2017-12-01

Full Text Available The main objective of this paper is to find the relation between the adaptive significance level presented here and the sample size. We statisticians know of the inconsistency, or paradox, in the current classical tests of significance that are based on p-value statistics that are compared to the canonical significance levels (10%, 5%, and 1%: “Raise the sample to reject the null hypothesis” is the recommendation of some ill-advised scientists! This paper will show that it is possible to eliminate this problem of significance tests. We present here the beginning of a larger research project. The intention is to extend its use to more complex applications such as survival analysis, reliability tests, and other areas. The main tools used here are the Bayes factor and the extended Neyman–Pearson Lemma.

Delineating sampling procedures: Pedagogical significance of analysing sampling descriptions and their justifications in TESL experimental research reports

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Jason Miin-Hwa Lim

2011-04-01

Full Text Available Teaching second language learners how to write research reports constitutes a crucial component in programmes on English for Specific Purposes (ESP in institutions of higher learning. One of the rhetorical segments in research reports that merit attention has to do with the descriptions and justifications of sampling procedures. This genre-based study looks into sampling delineations in the Method-related sections of research articles on the teaching of English as a second language (TESL written by expert writers and published in eight reputed international refereed journals. Using Swales’s (1990 & 2004 framework, I conducted a quantitative analysis of the rhetorical steps and a qualitative investigation into the language resources employed in delineating sampling procedures. This investigation has considerable relevance to ESP students and instructors as it has yielded pertinent findings on how samples can be appropriately described to meet the expectations of dissertation examiners, reviewers, and supervisors. The findings of this study have furnished insights into how supervisors and instructors can possibly teach novice writers ways of using specific linguistic mechanisms to lucidly describe and convincingly justify the sampling procedures in the Method sections of experimental research reports.

Denaturing gradient gel electrophoresis and barcoded pyrosequencing reveal unprecedented archaeal diversity in mangrove sediment and rhizosphere samples.

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Pires, Ana C C; Cleary, Daniel F R; Almeida, Adelaide; Cunha, Angela; Dealtry, Simone; Mendonça-Hagler, Leda C S; Smalla, Kornelia; Gomes, Newton C M

2012-08-01

Mangroves are complex ecosystems that regulate nutrient and sediment fluxes to the open sea. The importance of bacteria and fungi in regulating nutrient cycles has led to an interest in their diversity and composition in mangroves. However, very few studies have assessed Archaea in mangroves, and virtually nothing is known about whether mangrove rhizospheres affect archaeal diversity and composition. Here, we studied the diversity and composition of Archaea in mangrove bulk sediment and the rhizospheres of two mangrove trees, Rhizophora mangle and Laguncularia racemosa, using denaturing gradient gel electrophoresis (DGGE) and pyrosequencing of archaeal 16S rRNA genes with a nested-amplification approach. DGGE profiles revealed significant structural differences between bulk sediment and rhizosphere samples, suggesting that roots of both mangrove species influence the sediment archaeal community. Nearly all of the detected sequences obtained with pyrosequencing were identified as Archaea, but most were unclassified at the level of phylum or below. Archaeal richness was, furthermore, the highest in the L. racemosa rhizosphere, intermediate in bulk sediment, and the lowest in the R. mangle rhizosphere. This study shows that rhizosphere microhabitats of R. mangle and L. racemosa, common plants in subtropical mangroves located in Rio de Janeiro, Brazil, hosted distinct archaeal assemblages.

Comparing identified and statistically significant lipids and polar metabolites in 15-year old serum and dried blood spot samples for longitudinal studies: Comparing lipids and metabolites in serum and DBS samples

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Kyle, Jennifer E. [Earth and Biological Sciences Directorate, Pacific Northwest National Laboratory, Richland WA USA; Casey, Cameron P. [Earth and Biological Sciences Directorate, Pacific Northwest National Laboratory, Richland WA USA; Stratton, Kelly G. [National Security Directorate, Pacific Northwest National Laboratory, Richland WA USA; Zink, Erika M. [Earth and Biological Sciences Directorate, Pacific Northwest National Laboratory, Richland WA USA; Kim, Young-Mo [Earth and Biological Sciences Directorate, Pacific Northwest National Laboratory, Richland WA USA; Zheng, Xueyun [Earth and Biological Sciences Directorate, Pacific Northwest National Laboratory, Richland WA USA; Monroe, Matthew E. [Earth and Biological Sciences Directorate, Pacific Northwest National Laboratory, Richland WA USA; Weitz, Karl K. [Earth and Biological Sciences Directorate, Pacific Northwest National Laboratory, Richland WA USA; Bloodsworth, Kent J. [Earth and Biological Sciences Directorate, Pacific Northwest National Laboratory, Richland WA USA; Orton, Daniel J. [Earth and Biological Sciences Directorate, Pacific Northwest National Laboratory, Richland WA USA; Ibrahim, Yehia M. [Earth and Biological Sciences Directorate, Pacific Northwest National Laboratory, Richland WA USA; Moore, Ronald J. [Earth and Biological Sciences Directorate, Pacific Northwest National Laboratory, Richland WA USA; Lee, Christine G. [Department of Medicine, Bone and Mineral Unit, Oregon Health and Science University, Portland OR USA; Research Service, Portland Veterans Affairs Medical Center, Portland OR USA; Pedersen, Catherine [Department of Medicine, Bone and Mineral Unit, Oregon Health and Science University, Portland OR USA; Orwoll, Eric [Department of Medicine, Bone and Mineral Unit, Oregon Health and Science University, Portland OR USA; Smith, Richard D. [Earth and Biological Sciences Directorate, Pacific Northwest National Laboratory, Richland WA USA; Burnum-Johnson, Kristin E. [Earth and Biological Sciences Directorate, Pacific Northwest National Laboratory, Richland WA USA; Baker, Erin S. [Earth and Biological Sciences Directorate, Pacific Northwest National Laboratory, Richland WA USA

2017-02-05

The use of dried blood spots (DBS) has many advantages over traditional plasma and serum samples such as smaller blood volume required, storage at room temperature, and ability for sampling in remote locations. However, understanding the robustness of different analytes in DBS samples is essential, especially in older samples collected for longitudinal studies. Here we analyzed DBS samples collected in 2000-2001 and stored at room temperature and compared them to matched serum samples stored at -80°C to determine if they could be effectively used as specific time points in a longitudinal study following metabolic disease. Four hundred small molecules were identified in both the serum and DBS samples using gas chromatograph-mass spectrometry (GC-MS), liquid chromatography-MS (LC-MS) and LC-ion mobility spectrometry-MS (LC-IMS-MS). The identified polar metabolites overlapped well between the sample types, though only one statistically significant polar metabolite in a case-control study was conserved, indicating degradation occurs in the DBS samples affecting quantitation. Differences in the lipid identifications indicated that some oxidation occurs in the DBS samples. However, thirty-six statistically significant lipids correlated in both sample types indicating that lipid quantitation was more stable across the sample types.

DNA entropy reveals a significant difference in complexity between housekeeping and tissue specific gene promoters.

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Thomas, David; Finan, Chris; Newport, Melanie J; Jones, Susan

2015-10-01

The complexity of DNA can be quantified using estimates of entropy. Variation in DNA complexity is expected between the promoters of genes with different transcriptional mechanisms; namely housekeeping (HK) and tissue specific (TS). The former are transcribed constitutively to maintain general cellular functions, and the latter are transcribed in restricted tissue and cells types for specific molecular events. It is known that promoter features in the human genome are related to tissue specificity, but this has been difficult to quantify on a genomic scale. If entropy effectively quantifies DNA complexity, calculating the entropies of HK and TS gene promoters as profiles may reveal significant differences. Entropy profiles were calculated for a total dataset of 12,003 human gene promoters and for 501 housekeeping (HK) and 587 tissue specific (TS) human gene promoters. The mean profiles show the TS promoters have a significantly lower entropy (pentropy distributions for the 3 datasets show that promoter entropies could be used to identify novel HK genes. Functional features comprise DNA sequence patterns that are non-random and hence they have lower entropies. The lower entropy of TS gene promoters can be explained by a higher density of positive and negative regulatory elements, required for genes with complex spatial and temporary expression. Copyright © 2015 Elsevier Ltd. All rights reserved.

Sample normalization methods in quantitative metabolomics.

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Wu, Yiman; Li, Liang

2016-01-22

To reveal metabolomic changes caused by a biological event in quantitative metabolomics, it is critical to use an analytical tool that can perform accurate and precise quantification to examine the true concentration differences of individual metabolites found in different samples. A number of steps are involved in metabolomic analysis including pre-analytical work (e.g., sample collection and storage), analytical work (e.g., sample analysis) and data analysis (e.g., feature extraction and quantification). Each one of them can influence the quantitative results significantly and thus should be performed with great care. Among them, the total sample amount or concentration of metabolites can be significantly different from one sample to another. Thus, it is critical to reduce or eliminate the effect of total sample amount variation on quantification of individual metabolites. In this review, we describe the importance of sample normalization in the analytical workflow with a focus on mass spectrometry (MS)-based platforms, discuss a number of methods recently reported in the literature and comment on their applicability in real world metabolomics applications. Sample normalization has been sometimes ignored in metabolomics, partially due to the lack of a convenient means of performing sample normalization. We show that several methods are now available and sample normalization should be performed in quantitative metabolomics where the analyzed samples have significant variations in total sample amounts. Copyright © 2015 Elsevier B.V. All rights reserved.

No significant association of the 5' end of neuregulin 1 and schizophrenia in a large Danish sample

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Ingason, Andrés; Søeby, Karen; Timm, Sally

2006-01-01

schizophrenia patients. We found that the at-risk haplotype initially reported in the Icelandic population was not found in significant excess (or = 1.4, p = 0.12). The haplotype structure in the Danish sample was similar to that of other reported in other Caucasian populations and highly different from...

Multielemental analysis of samples from patients with dermatological pathologies using synchrotron radiation

International Nuclear Information System (INIS)

Soares, J.C.A.C.R.; Canellas, C.G.L.; Anjos, M.J.; Lopes, R.T.

2014-01-01

Using synchrotron radiation total X-ray fluorescence (SRTXRF) technique, the concentrations of trace elements were measured in four skin lesions: seborrheic keratosis, fibroepithelial polyp, cherry angioma and dermatosis papulosa nigra. The concentrations of P, S, K, Ca, Fe, Cu, Zn and Rb were evaluated in 62 pairs of lesions and healthy samples, each one having been collected from the same patient. The results revealed significant differences of P, Ca, K, Fe and Cu levels as well as a common trend in their variations between lesion and control samples among the skin diseases. This study revealed a powerful tool that can be useful for skin disorders research. The measurements were conducted at Brazilian National Synchrotron Light Laboratory (LNLS). - Highlights: • Concentrations of trace elements were measured and compared in four skin lesions. • The results revealed significant differences of P, Ca, K, Fe and Cu levels. • This study revealed a powerful tool that can be useful for skin disorders research

Moonrise: Sampling the South Pole-Aitken Basin to Address Problems of Solar System Significance

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Zeigler, R. A.; Jolliff, B. L.; Korotev, R. L.; Shearer, C. K.

2016-01-01

A mission to land in the giant South Pole-Aitken (SPA) Basin on the Moon's southern farside and return a sample to Earth for analysis is a high priority for Solar System Science. Such a sample would be used to determine the age of the SPA impact; the chronology of the basin, including the ages of basins and large impacts within SPA, with implications for early Solar System dynamics and the magmatic history of the Moon; the age and composition of volcanic rocks within SPA; the origin of the thorium signature of SPA with implications for the origin of exposed materials and thermal evolution of the Moon; and possibly the magnetization that forms a strong anomaly especially evident in the northern parts of the SPA basin. It is well known from studies of the Apollo regolith that rock fragments found in the regolith form a representative collection of many different rock types delivered to the site by the impact process (Fig. 1). Such samples are well documented to contain a broad suite of materials that reflect both the local major rock formations, as well as some exotic materials from far distant sources. Within the SPA basin, modeling of the impact ejection process indicates that regolith would be dominated by SPA substrate, formed at the time of the SPA basin-forming impact and for the most part moved around by subsequent impacts. Consistent with GRAIL data, the SPA impact likely formed a vast melt body tens of km thick that took perhaps several million years to cool, but that nonetheless represents barely an instant in geologic time that should be readily apparent through integrated geochronologic studies involving multiple chronometers. It is anticipated that a statistically significant number of age determinations would yield not only the age of SPA but also the age of several prominent nearby basins and large craters within SPA. This chronology would provide a contrast to the Imbrium-dominated chronology of the nearside Apollo samples and an independent test of

Amygdala subnuclei connectivity in response to violence reveals unique influences of individual differences in psychopathic traits in a nonforensic sample.

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Yoder, Keith J; Porges, Eric C; Decety, Jean

2015-04-01

Atypical amygdala function and connectivity have reliably been associated with psychopathy. However, the amygdala is not a unitary structure. To examine how psychopathic traits in a nonforensic sample are linked to amygdala response to violence, this study used probabilistic tractography to classify amygdala subnuclei based on anatomical projections to and from amygdala subnuclei in a group of 43 male participants. The segmentation identified the basolateral complex (BLA; lateral, basal, and accessory basal subnuclei) and the central subnucleus (CE), which were used as seeds in a functional connectivity analysis to identify differences in neuronal coupling specific to observed violence. While a full amygdala seed showed significant connectivity only to right middle occipital gyrus, subnuclei seeds revealed unique connectivity patterns. BLA showed enhanced coupling with anterior cingulate and prefrontal regions, while CE showed increased connectivity with the brainstem, but reduced connectivity with superior parietal and precentral gyrus. Further, psychopathic personality factors were related to specific patterns of connectivity. Fearless Dominance scores on the psychopathic personality inventory predicted increased coupling between the BLA seed and sensory integration cortices, and increased connectivity between the CE seed and posterior insula. Conversely, Self-Centered Impulsivity scores were negatively correlated with coupling between BLA and ventrolateral prefrontal cortex, and Coldheartedness scores predicted increased functional connectivity between BLA and dorsal anterior cingulate cortex. Taken together, these findings demonstrate how subnuclei segmentations reveal important functional connectivity differences that are otherwise inaccessible. Such an approach yields a better understanding of amygdala dysfunction in psychopathy. © 2014 Wiley Periodicals, Inc.

A Next-Generation Sequencing Data Analysis Pipeline for Detecting Unknown Pathogens from Mixed Clinical Samples and Revealing Their Genetic Diversity.

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Yu-Nong Gong

Full Text Available Forty-two cytopathic effect (CPE-positive isolates were collected from 2008 to 2012. All isolates could not be identified for known viral pathogens by routine diagnostic assays. They were pooled into 8 groups of 5-6 isolates to reduce the sequencing cost. Next-generation sequencing (NGS was conducted for each group of mixed samples, and the proposed data analysis pipeline was used to identify viral pathogens in these mixed samples. Polymerase chain reaction (PCR or enzyme-linked immunosorbent assay (ELISA was individually conducted for each of these 42 isolates depending on the predicted viral types in each group. Two isolates remained unknown after these tests. Moreover, iteration mapping was implemented for each of these 2 isolates, and predicted human parechovirus (HPeV in both. In summary, our NGS pipeline detected the following viruses among the 42 isolates: 29 human rhinoviruses (HRVs, 10 HPeVs, 1 human adenovirus (HAdV, 1 echovirus and 1 rotavirus. We then focused on the 10 identified Taiwanese HPeVs because of their reported clinical significance over HRVs. Their genomes were assembled and their genetic diversity was explored. One novel 6-bp deletion was found in one HPeV-1 virus. In terms of nucleotide heterogeneity, 64 genetic variants were detected from these HPeVs using the mapped NGS reads. Most importantly, a recombination event was found between our HPeV-3 and a known HPeV-4 strain in the database. Similar event was detected in the other HPeV-3 strains in the same clade of the phylogenetic tree. These findings demonstrated that the proposed NGS data analysis pipeline identified unknown viruses from the mixed clinical samples, revealed their genetic identity and variants, and characterized their genetic features in terms of viral evolution.

The origin of water in the primitive Moon as revealed by the lunar highlands samples

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Barnes, Jessica J.; Tartèse, Romain; Anand, Mahesh; McCubbin, Francis M.; Franchi, Ian A.; Starkey, Natalie A.; Russell, Sara S.

2014-03-01

The recent discoveries of hydrogen (H) bearing species on the lunar surface and in samples derived from the lunar interior have necessitated a paradigm shift in our understanding of the water inventory of the Moon, which was previously considered to be a ‘bone-dry’ planetary body. Most sample-based studies have focused on assessing the water contents of the younger mare basalts and pyroclastic glasses, which are partial-melting products of the lunar mantle. In contrast, little attention has been paid to the inventory and source(s) of water in the lunar highlands rocks which are some of the oldest and most pristine materials available for laboratory investigations, and that have the potential to reveal the original history of water in the Earth-Moon system. Here, we report in-situ measurements of hydroxyl (OH) content and H isotopic composition of the mineral apatite from four lunar highlands samples (two norites, a troctolite, and a granite clast) collected during the Apollo missions. Apart from troctolite in which the measured OH contents in apatite are close to our analytical detection limit and its H isotopic composition appears to be severely compromised by secondary processes, we have measured up to ˜2200 ppm OH in the granite clast with a weighted average δD of ˜ -105±130‰, and up to ˜3400 ppm OH in the two norites (77215 and 78235) with weighted average δD values of -281±49‰ and -27±98‰, respectively. The apatites in the granite clast and the norites are characterised by higher OH contents than have been reported so far for highlands samples, and have H isotopic compositions similar to those of terrestrial materials and some carbonaceous chondrites, providing one of the strongest pieces of evidence yet for a common origin for water in the Earth-Moon system. In addition, the presence of water, of terrestrial affinity, in some samples of the earliest-formed lunar crust suggests that either primordial terrestrial water survived the aftermath

Survey of French spine surgeons reveals significant variability in spine trauma practices in 2013.

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Lonjon, G; Grelat, M; Dhenin, A; Dauzac, C; Lonjon, N; Kepler, C K; Vaccaro, A R

2015-02-01

In France, attempts to define common ground during spine surgery meetings have revealed significant variability in clinical practices across different schools of surgery and the two specialities involved in spine surgery, namely, neurosurgery and orthopaedic surgery. To objectively characterise this variability by performing a survey based on a fictitious spine trauma case. Our working hypothesis was that significant variability existed in trauma practices and that this variability was related to a lack of strong scientific evidence in spine trauma care. We performed a cross-sectional survey based on a clinical vignette describing a 31-year-old male with an L1 burst fracture and neurologic symptoms (numbness). Surgeons received the vignette and a 14-item questionnaire on the management of this patient. For each question, surgeons had to choose among five possible answers. Differences in answers across surgeons were assessed using the Index of Qualitative Variability (IQV), in which 0 indicates no variability and 1 maximal variability. Surgeons also received a questionnaire about their demographics and surgical experience. Of 405 invited spine surgeons, 200 responded to the survey. Five questions had an IQV greater than 0.9, seven an IQV between 0.5 and 0.9, and two an IQV lower than 0.5. Variability was greatest about the need for MRI (IQV=0.93), degree of urgency (IQV=0.93), need for fusion (IQV=0.92), need for post-operative bracing (IQV=0.91), and routine removal of instrumentation (IQV=0.94). Variability was lowest for questions about the need for surgery (IQV=0.42) and use of the posterior approach (IQV=0.36). Answers were influenced by surgeon specialty, age, experience level, and type of centre. Clinical practice regarding spine trauma varies widely in France. Little published evidence is available on which to base recommendations that would diminish this variability. Copyright © 2015. Published by Elsevier Masson SAS.

Untargeted metabolomic profiling plasma samples of patients with lung cancer for searching significant metabolites by HPLC-MS method

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Dementeva, N.; Ivanova, K.; Kokova, D.; Kurzina, I.; Ponomaryova, A.; Kzhyshkowska, J.

2017-09-01

Lung cancer is one of the most common types of cancer leading to death. Consequently, the search and the identification of the metabolites associated with the risk of developing cancer are very valuable. For the purpose, untargeted metabolic profiling of the plasma samples collected from the patients with lung cancer (n = 100) and the control group (n = 100) was conducted. After sample preparation, the plasma samples were analyzed using LC-MS method. Biostatistics methods were applied to pre-process the data for elicitation of dominating metabolites which responded to the difference between the case and the control groups. At least seven significant metabolites were evaluated and annotated. The most part of identified metabolites are connected with lipid metabolism and their combination could be useful for follow-up studies of lung cancer pathogenesis.

Assessment of Psychopathic Traits in an Incarcerated Adolescent Sample: A Methodological Comparison

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Fink, Brandi C.; Tant, Adam S.; Tremba, Katherine; Kiehl, Kent A.

2012-01-01

Analyses of convergent validity and group assignment using self-report, caregiver-report and interview-based measures of adolescent psychopathy were conducted in a sample of 160 incarcerated adolescents. Results reveal significant convergent validity between caregiver-report measures of adolescent psychopathy, significant convergent validity…

Direct sampling during multiple sediment density flows reveals dynamic sediment transport and depositional environment in Monterey submarine canyon

Science.gov (United States)

Maier, K. L.; Gales, J. A.; Paull, C. K.; Gwiazda, R.; Rosenberger, K. J.; McGann, M.; Lundsten, E. M.; Anderson, K.; Talling, P.; Xu, J.; Parsons, D. R.; Barry, J.; Simmons, S.; Clare, M. A.; Carvajal, C.; Wolfson-Schwehr, M.; Sumner, E.; Cartigny, M.

2017-12-01

Sediment density flows were directly sampled with a coupled sediment trap-ADCP-instrument mooring array to evaluate the character and frequency of turbidity current events through Monterey Canyon, offshore California. This novel experiment aimed to provide links between globally significant sediment density flow processes and their resulting deposits. Eight to ten Anderson sediment traps were repeatedly deployed at 10 to 300 meters above the seafloor on six moorings anchored at 290 to 1850 meters water depth in the Monterey Canyon axial channel during 6-month deployments (October 2015 - April 2017). Anderson sediment traps include a funnel and intervalometer (discs released at set time intervals) above a meter-long tube, which preserves fine-scale stratigraphy and chronology. Photographs, multi-sensor logs, CT scans, and grain size analyses reveal layers from multiple sediment density flow events that carried sediment ranging from fine sand to granules. More sediment accumulation from sediment density flows, and from between flows, occurred in the upper canyon ( 300 - 800 m water depth) compared to the lower canyon ( 1300 - 1850 m water depth). Sediment accumulated in the traps during sediment density flows is sandy and becomes finer down-canyon. In the lower canyon where sediment directly sampled from density flows are clearly distinguished within the trap tubes, sands have sharp basal contacts, normal grading, and muddy tops that exhibit late-stage pulses. In at least two of the sediment density flows, the simultaneous low velocity and high backscatter measured by the ADCPs suggest that the trap only captured the collapsing end of a sediment density flow event. In the upper canyon, accumulation between sediment density flow events is twice as fast compared to the lower canyon; it is characterized by sub-cm-scale layers in muddy sediment that appear to have accumulated with daily to sub-daily frequency, likely related to known internal tidal dynamics also measured

The prevalence, diagnostic significance and demographic characteristics of Schneiderian first-rank symptoms in an epidemiological sample of first-episode psychoses.

LENUS (Irish Health Repository)

Ihara, Kazushige

2009-01-01

The diagnostic significance of first-rank symptoms (FRSs) remains uncertain. Ethnic differences in FRSs may account for high rates of schizophrenia in minority groups. This study aims to examine the prevalence of FRSs in an epidemiological sample of first-episode psychoses stratified by relevant demographic variables. SAMPLING AND METHOD: We identified everyone aged 16-64 presenting with their first psychosis over 2 years in 3 UK centres.

Analysis of sequences from field samples reveals the presence of the recently described pepper vein yellows virus (genus Polerovirus) in six additional countries.

Science.gov (United States)

Knierim, Dennis; Tsai, Wen-Shi; Kenyon, Lawrence

2013-06-01

Polerovirus infection was detected by reverse transcription polymerase chain reaction (RT-PCR) in 29 pepper plants (Capsicum spp.) and one black nightshade plant (Solanum nigrum) sample collected from fields in India, Indonesia, Mali, Philippines, Thailand and Taiwan. At least two representative samples for each country were selected to generate a general polerovirus RT-PCR product of 1.4 kb length for sequencing. Sequence analysis of the partial genome sequences revealed the presence of pepper vein yellows virus (PeVYV) in all 13 samples. A 1990 Australian herbarium sample of pepper described by serological means as infected with capsicum yellows virus (CYV) was identified by sequence analysis of a partial CP sequence as probably infected with a potato leaf roll virus (PLRV) isolate.

Clinically significant fatigue: prevalence and associated factors in an international sample of adults with multiple sclerosis recruited via the internet.

Directory of Open Access Journals (Sweden)

Tracey J Weiland

Full Text Available Fatigue contributes a significant burden of disease for people with multiple sclerosis (PwMS. Modifiable lifestyle factors have been recognized as having a role in a range of morbidity outcomes in PwMS. There is significant potential to prevent and treat fatigue in PwMS by addressing modifiable risk factors.To explore the associations between clinically significant fatigue and demographic factors, clinical factors (health-related quality of life, disability and relapse rate and modifiable lifestyle, disease-modifying drugs (DMD and supplement use in a large international sample of PwMS.PwMS were recruited to the study via Web 2.0 platforms and completed a comprehensive survey measuring demographic, lifestyle and clinical characteristics, including health-related quality of life, disability, and relapse rate.Of 2469 participants with confirmed MS, 2138 (86.6% completed a validated measure of clinically significant fatigue, the Fatigue Severity Scale. Participants were predominantly female from English speaking countries, with relatively high levels of education, and due to recruitment methods may have been highly pro-active about engaging in lifestyle management and self-help. Approximately two thirds of our sample (1402/2138; 65.6% (95% CI 63.7-67.7 screened positive for clinically significant fatigue. Bivariate associations were present between clinically significant fatigue and several demographic, clinical, lifestyle, and medication variables. After controlling for level of disability and a range of stable socio-demographic variables, we found increased odds of fatigue associated with obesity, DMD use, poor diet, and reduced odds of fatigue with exercise, fish consumption, moderate alcohol use, and supplementation with vitamin D and flaxseed oil.This study supports strong and significant associations between clinically significant fatigue and modifiable lifestyle factors. Longitudinal follow-up of this sample may help clarify the contribution

Whole blood transcriptional profiling reveals significant down-regulation of human leukocyte antigen class I and II genes in essential thrombocythemia, polycythemia vera and myelofibrosis

DEFF Research Database (Denmark)

Skov, Vibe; Riley, Caroline Hasselbalch; Thomassen, Mads

2013-01-01

Gene expression profiling studies in the Philadelphia-negative chronic myeloproliferative neoplasms have revealed significant deregulation of several immune and inflammation genes that might be of importance for clonal evolution due to defective tumor immune surveillance. Other mechanisms might b...

Engagement in activities revealing the body and psychosocial adjustment in adults with a trans-tibial prosthesis.

Science.gov (United States)

Donovan-Hall, M K; Yardley, L; Watts, R J

2002-04-01

The purpose of this study was to examine the effects of the appearance of a prosthesis on social behaviour, social discomfort and psychological well-being in eleven amputees taking delivery of a prosthesis with a silicone cover. Two new scales were developed: the 'Engagement in everyday activities involving revealing the body' (EEARB); and the 'Discomfort-Engagement in everyday activities involving revealing the body' (Discomfort-EEARB) scales. The psychometric properties of these scales were determined using a sample of 101 able-bodied adults. The Hospital Anxiety and Depression Scale and the Rosenberg Self-Esteem Scale were also used to measure psychological well-being in the amputee sample. The EEARB and Discomfort-EEARB proved to have good reliability and validity. Comparison of amputees' scores prior to receiving the silicone cosmesis with those of the able-bodied adults revealed significant behavioural limitations and social discomfort, associated with low self-esteem, anxiety and depression. There was a significant increase in amputees' scores three months afier taking delivery of their prosthesis, indicating that amputees reported engaging in more activities which involved revealing their body, and that they would feel more comfortable in situations which involved revealing the body. As the amputee sample available was small and self-selected, it is not possible to generalise these findings to the amputee population as a whole. However, since there is little previous research investigating the effects of the appearance of the prosthesis, these findings demonstrate the need for further research in this area.

Trace metal depositional patterns from an open pit mining activity as revealed by archived avian gizzard contents

Energy Technology Data Exchange (ETDEWEB)

Bendell, L.I., E-mail: bendell@sfu.ca

2011-02-15

Archived samples of blue grouse (Dendragapus obscurus) gizzard contents, inclusive of grit, collected yearly between 1959 and 1970 were analyzed for cadmium, lead, zinc, and copper content. Approximately halfway through the 12-year sampling period, an open-pit copper mine began activities, then ceased operations 2 years later. Thus the archived samples provided a unique opportunity to determine if avian gizzard contents, inclusive of grit, could reveal patterns in the anthropogenic deposition of trace metals associated with mining activities. Gizzard concentrations of cadmium and copper strongly coincided with the onset of opening and the closing of the pit mining activity. Gizzard zinc and lead demonstrated significant among year variation; however, maximum concentrations did not correlate to mining activity. The archived gizzard contents did provide a useful tool for documenting trends in metal depositional patterns related to an anthropogenic activity. Further, blue grouse ingesting grit particles during the time of active mining activity would have been exposed to toxicologically significant levels of cadmium. Gizzard lead concentrations were also of toxicological significance but not related to mining activity. This type of 'pulse' toxic metal exposure as a consequence of open-pit mining activity would not necessarily have been revealed through a 'snap-shot' of soil, plant or avian tissue trace metal analysis post-mining activity. - Research Highlights: {yields} Archived gizzard samples reveals mining history. {yields} Grit ingestion exposes grouse to cadmium and lead. {yields} Grit selection includes particles enriched in cadmium. {yields} Cadmium enriched particles are of toxicological significance.

Sequence tagging reveals unexpected modifications in toxicoproteomics

Science.gov (United States)

Dasari, Surendra; Chambers, Matthew C.; Codreanu, Simona G.; Liebler, Daniel C.; Collins, Ben C.; Pennington, Stephen R.; Gallagher, William M.; Tabb, David L.

2010-01-01

Toxicoproteomic samples are rich in posttranslational modifications (PTMs) of proteins. Identifying these modifications via standard database searching can incur significant performance penalties. Here we describe the latest developments in TagRecon, an algorithm that leverages inferred sequence tags to identify modified peptides in toxicoproteomic data sets. TagRecon identifies known modifications more effectively than the MyriMatch database search engine. TagRecon outperformed state of the art software in recognizing unanticipated modifications from LTQ, Orbitrap, and QTOF data sets. We developed user-friendly software for detecting persistent mass shifts from samples. We follow a three-step strategy for detecting unanticipated PTMs in samples. First, we identify the proteins present in the sample with a standard database search. Next, identified proteins are interrogated for unexpected PTMs with a sequence tag-based search. Finally, additional evidence is gathered for the detected mass shifts with a refinement search. Application of this technology on toxicoproteomic data sets revealed unintended cross-reactions between proteins and sample processing reagents. Twenty five proteins in rat liver showed signs of oxidative stress when exposed to potentially toxic drugs. These results demonstrate the value of mining toxicoproteomic data sets for modifications. PMID:21214251

Tritium inventory differences: I. Sampling and U-getter pump holdup

International Nuclear Information System (INIS)

Ellefson, R.E.; Gill, J.T.

1986-01-01

Inventory differences (ID) in tritium material balance accounts (MBA) can occur with unmeasured transfers from the process or unmeasured holdup in the system. Small but cumulatively significant quantities of tritium can leave the MBA by normal capillary sampling of process gas operation. A predictor model for estimating the quantity of tritium leaving the MBA by sampling has been developed and implemented. The model calculates the gas transferred per sample; using the tritium concentration in the process and the number of samples, a quantity of tritium transferred is predicted. Verification of the model is made by PVT measurement of process transfer from multiple samplings. Comparison of predicted sample transfers with IDs from several MBA's reveals that sampling typically represents 50% of unmeasured transfers for regularly sampled processes

77 FR 34121 - Culturally Significant Objects Imported for Exhibition Determinations: “Revealing the African...

Science.gov (United States)

2012-06-08

... exhibition ``Revealing the African Presence in Renaissance Europe'' imported from abroad for temporary... exhibit objects at The Walters Art Museum, Baltimore, MD, from on or about October 14, 2012, until on or about January 21, 2013; at the Princeton University Art Museum, Princeton, NJ, from on or about February...

Pathophysiological Significance of Dermatan Sulfate Proteoglycans Revealed by Human Genetic Disorders

Directory of Open Access Journals (Sweden)

Shuji Mizumoto

2017-03-01

Full Text Available The indispensable roles of dermatan sulfate-proteoglycans (DS-PGs have been demonstrated in various biological events including construction of the extracellular matrix and cell signaling through interactions with collagen and transforming growth factor-β, respectively. Defects in the core proteins of DS-PGs such as decorin and biglycan cause congenital stromal dystrophy of the cornea, spondyloepimetaphyseal dysplasia, and Meester-Loeys syndrome. Furthermore, mutations in human genes encoding the glycosyltransferases, epimerases, and sulfotransferases responsible for the biosynthesis of DS chains cause connective tissue disorders including Ehlers-Danlos syndrome and spondyloepimetaphyseal dysplasia with joint laxity characterized by skin hyperextensibility, joint hypermobility, and tissue fragility, and by severe skeletal disorders such as kyphoscoliosis, short trunk, dislocation, and joint laxity. Glycobiological approaches revealed that mutations in DS-biosynthetic enzymes cause reductions in enzymatic activities and in the amount of synthesized DS and also disrupt the formation of collagen bundles. This review focused on the growing number of glycobiological studies on recently reported genetic diseases caused by defects in the biosynthesis of DS and DS-PGs.

Metabolic fingerprinting of high-fat plasma samples processed by centrifugation- and filtration-based protein precipitation delineates significant differences in metabolite information coverage.

Science.gov (United States)

Barri, Thaer; Holmer-Jensen, Jens; Hermansen, Kjeld; Dragsted, Lars O

2012-03-09

Metabolomics and metabolic fingerprinting are being extensively employed for improved understanding of biological changes induced by endogenous or exogenous factors. Blood serum or plasma samples are often employed for metabolomics studies. Plasma protein precipitation (PPP) is currently performed in most laboratories before LC-MS analysis. However, the impact of fat content in plasma samples on metabolite coverage has not previously been investigated. Here, we have studied whether PPP procedures influence coverage of plasma metabolites from high-fat plasma samples. An optimized UPLC-QTOF/MS metabolic fingerprinting approach and multivariate modeling (PCA and OPLS-DA) were utilized for finding characteristic metabolite changes induced by two PPP procedures; centrifugation and filtration. We used 12-h fasting samples and postprandial samples collected at 2h after a standardized high-fat protein-rich meal in obese non-diabetic subjects recruited in a dietary intervention. The two PPP procedures as well as external and internal standards (ISs) were used to track errors in response normalization and quantification. Remarkably and sometimes uniquely, the fPPP, but not the cPPP approach, recovered not only high molecular weight (HMW) lipophilic metabolites, but also small molecular weight (SMW) relatively polar metabolites. Characteristic SMW markers of postprandial samples were aromatic and branched-chain amino acids that were elevated (p<0.001) as a consequence of the protein challenge. In contrast, some HMW lipophilic species, e.g. acylcarnitines, were moderately lower (p<0.001) in postprandial samples. LysoPCs were largely unaffected. In conclusion, the fPPP procedure is recommended for processing high-fat plasma samples in metabolomics studies. While method improvements presented here were clear, use of several ISs revealed substantial challenges to untargeted metabolomics due to large and variable matrix effects. Copyright © 2012 Elsevier B.V. All rights reserved.

Increased taxon sampling reveals thousands of hidden orthologs in flatworms

Science.gov (United States)

2017-01-01

Gains and losses shape the gene complement of animal lineages and are a fundamental aspect of genomic evolution. Acquiring a comprehensive view of the evolution of gene repertoires is limited by the intrinsic limitations of common sequence similarity searches and available databases. Thus, a subset of the gene complement of an organism consists of hidden orthologs, i.e., those with no apparent homology to sequenced animal lineages—mistakenly considered new genes—but actually representing rapidly evolving orthologs or undetected paralogs. Here, we describe Leapfrog, a simple automated BLAST pipeline that leverages increased taxon sampling to overcome long evolutionary distances and identify putative hidden orthologs in large transcriptomic databases by transitive homology. As a case study, we used 35 transcriptomes of 29 flatworm lineages to recover 3427 putative hidden orthologs, some unidentified by OrthoFinder and HaMStR, two common orthogroup inference algorithms. Unexpectedly, we do not observe a correlation between the number of putative hidden orthologs in a lineage and its “average” evolutionary rate. Hidden orthologs do not show unusual sequence composition biases that might account for systematic errors in sequence similarity searches. Instead, gene duplication with divergence of one paralog and weak positive selection appear to underlie hidden orthology in Platyhelminthes. By using Leapfrog, we identify key centrosome-related genes and homeodomain classes previously reported as absent in free-living flatworms, e.g., planarians. Altogether, our findings demonstrate that hidden orthologs comprise a significant proportion of the gene repertoire in flatworms, qualifying the impact of gene losses and gains in gene complement evolution. PMID:28400424

The significance of sense of coherence for the perceptions of task characteristics and stress during interruptions amongst a sample of public health nurses in Hong Kong: implications for nursing management.

Science.gov (United States)

Shiu, A T

1998-08-01

The study aimed to investigate the significance of sense of coherence (SOC) for the perceptions of task characteristics and for stress perceptions during interruptions of public health nurses (PHNs) with children in Hong Kong. The research design employed the experience sampling method. Convenience sampling was used to recruit 20 subjects. During stage one of the study a watch was worn that gave a signal at six random times each day for seven days to complete an experience sampling diary. PHNs on average responded to 34 signals (80%) to complete the diaries which collected data on work and family juggling, task characteristics, and their effects on mood states. At stage two respondents completed the SOC scale which measured confidence in life as comprehensible, manageable, and meaningful. Two major findings provide the focus for this paper. First, results indicate that there was positive correlation between SOC and perceived task characteristics. Second, results reveal that when interruptions occurred, PHNs with high SOC had higher positive affect and lower negative affect than PHNs with low SOC. These results suggest that SOC as a salutogenic model helps PHNs to cope with the family and work juggling as well as the occupational stress. Implications for nursing management on strengthening SOC of PHNs are discussed.

Effect of postmortem sampling technique on the clinical significance of autopsy blood cultures.

Science.gov (United States)

Hove, M; Pencil, S D

1998-02-01

Our objective was to investigate the value of postmortem autopsy blood cultures performed with an iodine-subclavian technique relative to the classical method of atrial heat searing and antemortem blood cultures. The study consisted of a prospective autopsy series with each case serving as its own control relative to subsequent testing, and a retrospective survey of patients coming to autopsy who had both autopsy blood cultures and premortem blood cultures. A busy academic autopsy service (600 cases per year) at University of Texas Medical Branch Hospitals, Galveston, Texas, served as the setting for this work. The incidence of non-clinically relevant (false-positive) culture results were compared using different methods for collecting blood samples in a prospective series of 38 adult autopsy specimens. One hundred eleven adult autopsy specimens in which both postmortem and antemortem blood cultures were obtained were studied retrospectively. For both studies, positive culture results were scored as either clinically relevant or false positives based on analysis of the autopsy findings and the clinical summary. The rate of false-positive culture results obtained by an iodine-subclavian technique from blood drawn soon after death were statistically significantly lower (13%) than using the classical method of obtaining blood through the atrium after heat searing at the time of the autopsy (34%) in the same set of autopsy subjects. When autopsy results were compared with subjects' antemortem blood culture results, there was no significant difference in the rate of non-clinically relevant culture results in a paired retrospective series of antemortem blood cultures and postmortem blood cultures using the iodine-subclavian postmortem method (11.7% v 13.5%). The results indicate that autopsy blood cultures obtained using the iodine-subclavian technique have reliability equivalent to that of antemortem blood cultures.

Sample preparation of Medicago sativa L. hay for chemical analysis ...

African Journals Online (AJOL)

The objective of this study was to quantify the effect of the grinding procedure on the moisture and crude protein concentration of a ground Medicago sativa L. hay sample for quality grading. An additional aim was to investigate the accuracy of electronic moisture testers (EMT). Variance of analyses revealed significant ...

Nutritional significance of a winter-flowering succulent for opportunistic avian nectarivores

CSIR Research Space (South Africa)

Symes, CT

2010-01-01

Full Text Available the enriched crassulacean acid metabolism (CAM) isotopic signature of nectar ()12.6 ± 0.5&). This relatively small contribution of A. marlothii nectar to assimilated carbon in whole blood contrasted with that of exhaled CO2 in Afri- can Red-eyed Bulbuls... Pycnonotus nigricans and Cape White-eyes Zosterops capensis. In both these species, the d13C of breath samples was significantly enriched compared with blood and feathers, and closely resembled that of the nectar, revealing combustion of ingested nectar...

A genome scan revealed significant associations of growth traits with a major QTL and GHR2 in tilapia

Science.gov (United States)

Liu, Feng; Sun, Fei; Xia, Jun Hong; Li, Jian; Fu, Gui Hong; Lin, Grace; Tu, Rong Jian; Wan, Zi Yi; Quek, Delia; Yue, Gen Hua

2014-01-01

Growth is an important trait in animal breeding. However, the genetic effects underpinning fish growth variability are still poorly understood. QTL mapping and analysis of candidate genes are effective methods to address this issue. We conducted a genome-wide QTL analysis for growth in tilapia. A total of 10, 7 and 8 significant QTLs were identified for body weight, total length and standard length at 140 dph, respectively. The majority of these QTLs were sex-specific. One major QTL for growth traits was identified in the sex-determining locus in LG1, explaining 71.7%, 67.2% and 64.9% of the phenotypic variation (PV) of body weight, total length and standard length, respectively. In addition, a candidate gene GHR2 in a QTL was significantly associated with body weight, explaining 13.1% of PV. Real-time qPCR revealed that different genotypes at the GHR2 locus influenced the IGF-1 expression level. The markers located in the major QTL for growth traits could be used in marker-assisted selection of tilapia. The associations between GHR2 variants and growth traits suggest that the GHR2 gene should be an important gene that explains the difference in growth among tilapia species. PMID:25435025

The radioactivity of meat samples between 1977 and 1982

International Nuclear Information System (INIS)

Zalabai, Bela

1983-01-01

90 Sr and 137 Cs from atmospheric nuclear explosions can get into the organizations of domestic animals via fodder. Radiological tests of meat samples revealed a load maximum last time in 1976. The regular tests of pork and beef samples between 1977 and 1982 in Hungary showed no significant differences in their radiocesium contents. The change of strontium activity in bones, however, lasts longer than that of cesium. According to the measurements, the strontium activity in swine bones was almost one order lower than that in cattle bones. (Sz.J.)

Evaluation of common methods for sampling invertebrate pollinator assemblages: net sampling out-perform pan traps.

Science.gov (United States)

Popic, Tony J; Davila, Yvonne C; Wardle, Glenda M

2013-01-01

Methods for sampling ecological assemblages strive to be efficient, repeatable, and representative. Unknowingly, common methods may be limited in terms of revealing species function and so of less value for comparative studies. The global decline in pollination services has stimulated surveys of flower-visiting invertebrates, using pan traps and net sampling. We explore the relative merits of these two methods in terms of species discovery, quantifying abundance, function, and composition, and responses of species to changing floral resources. Using a spatially-nested design we sampled across a 5000 km(2) area of arid grasslands, including 432 hours of net sampling and 1296 pan trap-days, between June 2010 and July 2011. Net sampling yielded 22% more species and 30% higher abundance than pan traps, and better reflected the spatio-temporal variation of floral resources. Species composition differed significantly between methods; from 436 total species, 25% were sampled by both methods, 50% only by nets, and the remaining 25% only by pans. Apart from being less comprehensive, if pan traps do not sample flower-visitors, the link to pollination is questionable. By contrast, net sampling functionally linked species to pollination through behavioural observations of flower-visitation interaction frequency. Netted specimens are also necessary for evidence of pollen transport. Benefits of net-based sampling outweighed minor differences in overall sampling effort. As pan traps and net sampling methods are not equivalent for sampling invertebrate-flower interactions, we recommend net sampling of invertebrate pollinator assemblages, especially if datasets are intended to document declines in pollination and guide measures to retain this important ecosystem service.

Comparison of Different Sample Preparation Protocols Reveals Lysis Buffer-Specific Extraction Biases in Gram-Negative Bacteria and Human Cells.

Science.gov (United States)

Glatter, Timo; Ahrné, Erik; Schmidt, Alexander

2015-11-06

We evaluated different in-solution and FASP-based sample preparation strategies for absolute protein quantification. Label-free quantification (LFQ) was employed to compare different sample preparation strategies in the bacterium Pseudomonas aeruginosa and human embryonic kidney cells (HEK), and organismal-specific differences in general performance and enrichment of specific protein classes were noted. The original FASP protocol globally enriched for most proteins in the bacterial sample, whereas the sodium deoxycholate in-solution strategy was more efficient with HEK cells. Although detergents were found to be highly suited for global proteome analysis, higher intensities were obtained for high-abundant nucleic acid-associated protein complexes, like the ribosome and histone proteins, using guanidine hydrochloride. Importantly, we show for the first time that the observable total proteome mass of a sample strongly depends on the sample preparation protocol, with some protocols resulting in a significant underestimation of protein mass due to incomplete protein extraction of biased protein groups. Furthermore, we demonstrate that some of the observed abundance biases can be overcome by incorporating a nuclease treatment step or, alternatively, a correction factor for complementary sample preparation approaches.

A Review of New and Developing Technology to Significantly Improve Mars Sample-Return Missions

Science.gov (United States)

Carsey, F.; Brophy, J.; Gilmore, M.; Rodgers, D.; Wilcox, B.

2000-07-01

A JPL development activity was initiated in FY 1999 for the purpose of examining and evaluating technologies that could materially improve future (i.e., beyond the 2005 launch) Mars sample return missions. The scope of the technology review was comprehensive and end-to-end; the goal was to improve mass, cost, risk, and scientific return. A specific objective was to assess approaches to sample return with only one Earth launch. While the objective of the study was specifically for sample-return, in-situ missions can also benefit from using many of the technologies examined.

Extensive monitoring through multiple blood samples in professional soccer players

DEFF Research Database (Denmark)

Heisterberg, Mette F; Fahrenkrug, Jan; Krustrup, Peter

2013-01-01

of the season. Leucocytes decreased with increased physical training. Lymphocytes decreased at the end of the season. VO2max decreased towards the end of the season whereas no significant changes were observed in the IE2 test.The regular blood samples from elite soccer players reveal significant changes......ABSTRACT: The aim of this study was to make a comprehensive gathering of consecutive detailed blood samples from professional soccer players, and to analyze different blood parameters in relation to seasonal changes in training and match exposure.Blood samples were collected five times during a six...... months period and analyzed for 37 variables in 27 professional soccer players from the best Danish league. Additionally, players were tested for body composition, VO2max and physical performance by the Yo-Yo intermittent endurance sub-max test (IE2).Multiple variations in blood parameters occurred during...

Understanding the Sampling Distribution and Its Use in Testing Statistical Significance.

Science.gov (United States)

Breunig, Nancy A.

Despite the increasing criticism of statistical significance testing by researchers, particularly in the publication of the 1994 American Psychological Association's style manual, statistical significance test results are still popular in journal articles. For this reason, it remains important to understand the logic of inferential statistics. A…

Different continuous cropping spans significantly affect microbial community membership and structure in a vanilla-grown soil as revealed by deep pyrosequencing.

Science.gov (United States)

Xiong, Wu; Zhao, Qingyun; Zhao, Jun; Xun, Weibing; Li, Rong; Zhang, Ruifu; Wu, Huasong; Shen, Qirong

2015-07-01

In the present study, soil bacterial and fungal communities across vanilla continuous cropping time-series fields were assessed through deep pyrosequencing of 16S ribosomal RNA (rRNA) genes and internal transcribed spacer (ITS) regions. The results demonstrated that the long-term monoculture of vanilla significantly altered soil microbial communities. Soil fungal diversity index increased with consecutive cropping years, whereas soil bacterial diversity was relatively stable. Bray-Curtis dissimilarity cluster and UniFrac-weighted principal coordinate analysis (PCoA) revealed that monoculture time was the major determinant for fungal community structure, but not for bacterial community structure. The relative abundances (RAs) of the Firmicutes, Actinobacteria, Bacteroidetes, and Basidiomycota phyla were depleted along the years of vanilla monoculture. Pearson correlations at the phyla level demonstrated that Actinobacteria, Armatimonadetes, Bacteroidetes, Verrucomicrobia, and Firmicutes had significant negative correlations with vanilla disease index (DI), while no significant correlation for fungal phyla was observed. In addition, the amount of the pathogen Fusarium oxysporum accumulated with increasing years and was significantly positively correlated with vanilla DI. By contrast, the abundance of beneficial bacteria, including Bradyrhizobium and Bacillus, significantly decreased over time. In sum, soil weakness and vanilla stem wilt disease after long-term continuous cropping can be attributed to the alteration of the soil microbial community membership and structure, i.e., the reduction of the beneficial microbes and the accumulation of the fungal pathogen.

Significant relationship between lifetime alcohol use disorders and suicide attempts in an Australian schizophrenia sample.

Science.gov (United States)

McLean, Duncan; Gladman, Beverley; Mowry, Bryan

2012-02-01

Suicide and attempted suicide are common in individuals with schizophrenia, and evidence exists for a link between substance use disorders and suicidality in this disorder. However, alcohol has not been consistently implicated. We examined the relationship between substance use disorders and suicide attempts in schizophrenia. We recruited a schizophrenia sample in Australia (n = 821) for genetic analyses. We analysed demographic and clinical variables, including substance use disorders, and their relationship to suicide attempts using generalised equation modelling. A significant association was identified between lifetime alcohol abuse/dependence and suicide attempts (OR = 1.66; 95% CI, 1.23 to 2.24; p = 0.001) after adjustment for potential confounders, but not between cannabis abuse/dependence and suicide attempts, nor between other illicit drug abuse/dependence and suicide attempts. Polysubstance abuse/dependence was also not implicated. These results suggest that the presence of alcohol abuse/dependence may be a risk factor for suicide attempts in individuals with schizophrenia, independent of comorbid substance abuse/dependence.

Significance evaluation in factor graphs

DEFF Research Database (Denmark)

Madsen, Tobias; Hobolth, Asger; Jensen, Jens Ledet

2017-01-01

in genomics and the multiple-testing issues accompanying them, accurate significance evaluation is of great importance. We here address the problem of evaluating statistical significance of observations from factor graph models. Results Two novel numerical approximations for evaluation of statistical...... significance are presented. First a method using importance sampling. Second a saddlepoint approximation based method. We develop algorithms to efficiently compute the approximations and compare them to naive sampling and the normal approximation. The individual merits of the methods are analysed both from....... Conclusions The applicability of saddlepoint approximation and importance sampling is demonstrated on known models in the factor graph framework. Using the two methods we can substantially improve computational cost without compromising accuracy. This contribution allows analyses of large datasets...

Evaluation of common methods for sampling invertebrate pollinator assemblages: net sampling out-perform pan traps.

Directory of Open Access Journals (Sweden)

Tony J Popic

Full Text Available Methods for sampling ecological assemblages strive to be efficient, repeatable, and representative. Unknowingly, common methods may be limited in terms of revealing species function and so of less value for comparative studies. The global decline in pollination services has stimulated surveys of flower-visiting invertebrates, using pan traps and net sampling. We explore the relative merits of these two methods in terms of species discovery, quantifying abundance, function, and composition, and responses of species to changing floral resources. Using a spatially-nested design we sampled across a 5000 km(2 area of arid grasslands, including 432 hours of net sampling and 1296 pan trap-days, between June 2010 and July 2011. Net sampling yielded 22% more species and 30% higher abundance than pan traps, and better reflected the spatio-temporal variation of floral resources. Species composition differed significantly between methods; from 436 total species, 25% were sampled by both methods, 50% only by nets, and the remaining 25% only by pans. Apart from being less comprehensive, if pan traps do not sample flower-visitors, the link to pollination is questionable. By contrast, net sampling functionally linked species to pollination through behavioural observations of flower-visitation interaction frequency. Netted specimens are also necessary for evidence of pollen transport. Benefits of net-based sampling outweighed minor differences in overall sampling effort. As pan traps and net sampling methods are not equivalent for sampling invertebrate-flower interactions, we recommend net sampling of invertebrate pollinator assemblages, especially if datasets are intended to document declines in pollination and guide measures to retain this important ecosystem service.

78 FR 55772 - Culturally Significant Object Imported for Exhibition Determinations: “Beauty Revealed: Images of...

Science.gov (United States)

2013-09-11

..., 1965 (79 Stat. 985; 22 U.S.C. 2459), Executive Order 12047 of March 27, 1978, the Foreign Affairs...). The mailing address is U.S. Department of State, SA-5, L/PD, Fifth Floor (Suite 5H03), Washington, DC... Determinations: ``Beauty Revealed: Images of Women in Qing Dynasty Chinese Painting'' SUMMARY: Notice is hereby...

SubID, a non-median dichotomization tool for heterogeneous populations, reveals the pan-cancer significance of INPP4B and its regulation by EVI1 in AML.

Directory of Open Access Journals (Sweden)

Irakli Dzneladze

Full Text Available Our previous studies demonstrated that INPP4B, a member of the PI3K/Akt signaling pathway, is overexpressed in a subset of AML patients and is associated with lower response to chemotherapy and shorter survival. INPP4B expression analysis in AML revealed a right skewed frequency distribution with 25% of patients expressing significantly higher levels than the majority. The 75% low/25% high cut-off revealed the prognostic power of INPP4B expression status in AML, which would not have been apparent with a standard median cut-off approach. Our identification of a clinically relevant non-median cut-off for INPP4B indicated a need for a generalizable non-median dichotomization approach to optimally study clinically relevant genes. To address this need, we developed Subgroup Identifier (SubID, a tool which examines the relationship between a continuous variable (e.g. gene expression, and a test parameter (e.g. CoxPH or Fisher's exact P values. In our study, Fisher's exact SubID was used to reveal EVI1 as a transcriptional regulator of INPP4B in AML; a finding which was validated in vitro. Next, we used CoxPH SubID to conduct a pan-cancer analysis of INPP4B's prognostic significance. Our analysis revealed that INPP4Blow is associated with shorter survival in kidney clear cell, liver hepatocellular, and bladder urothelial carcinomas. Conversely, INPP4Blow was shown to be associated with increased survival in pancreatic adenocarcinoma in three independent datasets. Overall, our study describes the development and application of a novel subgroup identification tool used to identify prognostically significant rare subgroups based upon gene expression, and for investigating the association between a gene with skewed frequency distribution and potentially important upstream and downstream genes that relate to the index gene.

SubID, a non-median dichotomization tool for heterogeneous populations, reveals the pan-cancer significance of INPP4B and its regulation by EVI1 in AML.

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Dzneladze, Irakli; Woolley, John F; Rossell, Carla; Han, Youqi; Rashid, Ayesha; Jain, Michael; Reimand, Jüri; Minden, Mark D; Salmena, Leonardo

2018-01-01

Our previous studies demonstrated that INPP4B, a member of the PI3K/Akt signaling pathway, is overexpressed in a subset of AML patients and is associated with lower response to chemotherapy and shorter survival. INPP4B expression analysis in AML revealed a right skewed frequency distribution with 25% of patients expressing significantly higher levels than the majority. The 75% low/25% high cut-off revealed the prognostic power of INPP4B expression status in AML, which would not have been apparent with a standard median cut-off approach. Our identification of a clinically relevant non-median cut-off for INPP4B indicated a need for a generalizable non-median dichotomization approach to optimally study clinically relevant genes. To address this need, we developed Subgroup Identifier (SubID), a tool which examines the relationship between a continuous variable (e.g. gene expression), and a test parameter (e.g. CoxPH or Fisher's exact P values). In our study, Fisher's exact SubID was used to reveal EVI1 as a transcriptional regulator of INPP4B in AML; a finding which was validated in vitro. Next, we used CoxPH SubID to conduct a pan-cancer analysis of INPP4B's prognostic significance. Our analysis revealed that INPP4Blow is associated with shorter survival in kidney clear cell, liver hepatocellular, and bladder urothelial carcinomas. Conversely, INPP4Blow was shown to be associated with increased survival in pancreatic adenocarcinoma in three independent datasets. Overall, our study describes the development and application of a novel subgroup identification tool used to identify prognostically significant rare subgroups based upon gene expression, and for investigating the association between a gene with skewed frequency distribution and potentially important upstream and downstream genes that relate to the index gene.

Melatonin Distribution Reveals Clues to Its Biological Significance in Basal Metazoans

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Roopin, Modi; Levy, Oren

2012-01-01

Although nearly ubiquitous in nature, the precise biological significance of endogenous melatonin is poorly understood in phylogenetically basal taxa. In the present work, we describe insights into the functional role of melatonin at the most “basal” level of metazoan evolution. Hitherto unknown morphological determinants of melatonin distribution were evaluated in Nematostella vectensis by detecting melatonin immunoreactivity and examining the spatial gene expression patterns of putative melatonin biosynthetic and receptor elements that are located at opposing ends of the melatonin signaling pathway. Immuno-melatonin profiling indicated an elaborate interaction with reproductive tissues, reinforcing previous conjectures of a melatonin-responsive component in anthozoan reproduction. In situ hybridization (ISH) to putative melatonin receptor elements highlighted the possibility that the bioregulatory effects of melatonin in anthozoan reproduction may be mediated by interactions with membrane receptors, as in higher vertebrates. Another intriguing finding of the present study pertains to the prevalence of melatonin in centralized nervous structures. This pattern may be of great significance given that it 1) identifies an ancestral association between melatonin and key neuronal components and 2) potentially implies that certain effects of melatonin in basal species may be spread widely by regionalized nerve centers. PMID:23300630

Statistical sampling strategies

International Nuclear Information System (INIS)

Andres, T.H.

1987-01-01

Systems assessment codes use mathematical models to simulate natural and engineered systems. Probabilistic systems assessment codes carry out multiple simulations to reveal the uncertainty in values of output variables due to uncertainty in the values of the model parameters. In this paper, methods are described for sampling sets of parameter values to be used in a probabilistic systems assessment code. Three Monte Carlo parameter selection methods are discussed: simple random sampling, Latin hypercube sampling, and sampling using two-level orthogonal arrays. Three post-selection transformations are also described: truncation, importance transformation, and discretization. Advantages and disadvantages of each method are summarized

Expression of the cytoskeleton regulatory protein Mena in human gastric carcinoma and its prognostic significance.

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Xu, Lihua; Tan, Huo; Liu, Ruiming; Huang, Qungai; Zhang, Nana; Li, Xi; Wang, Jiani

2017-11-01

The cytoskeleton regulatory protein Mena is reportedly overexpressed in breast cancer; however, data regarding its expression level and clinical significance in gastric carcinoma (GC) is limited. The aim of the present study was to investigate Mena expression levels and prognostic significance in GC. Mena mRNA expression level was determined by reverse transcription-quantitative polymerase chain reaction in 10 paired GC and adjacent normal tissues. The Mena protein expression level was analyzed in paraffin-embedded GC samples and adjacent normal tissues by immunohistochemistry. Statistical analyses were also performed to evaluate the clinicopathological significance of Mena. The results revealed that the mRNA expression level of Mena was significantly higher in G Ct issues compared with in adjacent normal tissues from10 paired samples. In the paraffin-embedded tissue samples, the protein expression level of Mena was higher in G Ct issues compared with in adjacent normal tissues. Compared with adjacent normal tissues, Mena overexpression was observed in 52.83% (56/106) of patients. The overexpression of Mena was significantly associated with the T stage (P=0.033), tumor-node-metastasis (TNM) stage (PMena expression level was an independent prognostic factor for overall survival time. In conclusion, Mena wasoverexpressed in G C tissues and significantly associated with the T stage, TNM stage and overall survival time. Mena may therefore be suitable as a prognostic indicator for patients with GC.

Prevalence and clinical significance of mediator complex subunit 12 mutations in 362 Han Chinese samples with uterine leiomyoma.

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Wu, Juan; Zou, Yang; Luo, Yong; Guo, Jiu-Bai; Liu, Fa-Ying; Zhou, Jiang-Yan; Zhang, Zi-Yu; Wan, Lei; Huang, Ou-Ping

2017-07-01

Uterine leiomyomas (ULs) are the most common gynecological benign tumors originating from the myometrium. Prevalent mutations in the mediator complex subunit 12 (MED12) gene have been identified in ULs, and functional evidence has revealed that these mutations may promote the development of ULs. However, whether MED12 mutations are associated with certain clinical characteristics in ULs remains largely unknown. In the present study, the potential mutations of MED12 and its paralogous gene, mediator complex subunit 12-like (MED12L), were screened in 362 UL tumors from Han Chinese patients. A total of 158 out of 362 UL tumors (43.6%) were identified as harboring MED12 somatic mutations, and the majority of these mutations were restricted to the 44th residue. MED12 mutations were also observed in 2 out of 145 (1.4%) adjacent control myometrium. Furthermore, the mutation spectrum of MED12 in the concurrent leiomyomas was noticeably different. Correlation analysis of MED12 mutations with the available clinical features indicated that patients with mutated MED12 tended to have smaller cervical diameters. By contrast, no MED12L mutation was identified in the present samples. In summary, the present study demonstrated the presence of prevalent MED12 somatic mutations in UL samples, and the MED12 mutation was associated with smaller cervical diameters. The low mutation frequency of MED12 in adjacent control myometrium indicated that MED12 mutation may be an early event in the pathogenesis of ULs. Furthermore, MED12 mutation status in concurrent tumors from multiple leiomyomas supported several prior observations that the majority of these tumors arose independently.

The challenging measurement of protein in complex biomass-derived samples

DEFF Research Database (Denmark)

Haven, M.O.; Jørgensen, H.

2014-01-01

and fast protein measurement on this type of samples was the ninhydrin assay. This method has also been used widely for this purpose, but with two different methods for protein hydrolysis prior to the assay - alkaline or acidic hydrolysis. In samples containing glucose or ethanol, there was significant...... that the presence of cellulose, lignin and glucose (above 50 g/kg) could significantly affect the results of the assay. Comparison of analyses performed with the ninhydrin assay and with a CN analyser revealed that there was good agreement between these two analytical methods, but care has to be taken when applying...... the ninhydrin assay. If used correctly, the ninhydrin assay can be used as a fast method to evaluate the adsorption of cellulases to lignin....

Stable isotope analysis of precipitation samples obtained via crowdsourcing reveals the spatiotemporal evolution of Superstorm Sandy.

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Stephen P Good

Full Text Available Extra-tropical cyclones, such as 2012 Superstorm Sandy, pose a significant climatic threat to the northeastern United Sates, yet prediction of hydrologic and thermodynamic processes within such systems is complicated by their interaction with mid-latitude water patterns as they move poleward. Fortunately, the evolution of these systems is also recorded in the stable isotope ratios of storm-associated precipitation and water vapor, and isotopic analysis provides constraints on difficult-to-observe cyclone dynamics. During Superstorm Sandy, a unique crowdsourced approach enabled 685 precipitation samples to be obtained for oxygen and hydrogen isotopic analysis, constituting the largest isotopic sampling of a synoptic-scale system to date. Isotopically, these waters span an enormous range of values (> 21‰ for δ(18O, > 160‰ for δ(2H and exhibit strong spatiotemporal structure. Low isotope ratios occurred predominantly in the west and south quadrants of the storm, indicating robust isotopic distillation that tracked the intensity of the storm's warm core. Elevated values of deuterium-excess (> 25‰ were found primarily in the New England region after Sandy made landfall. Isotope mass balance calculations and Lagrangian back-trajectory analysis suggest that these samples reflect the moistening of dry continental air entrained from a mid-latitude trough. These results demonstrate the power of rapid-response isotope monitoring to elucidate the structure and dynamics of water cycling within synoptic-scale systems and improve our understanding of storm evolution, hydroclimatological impacts, and paleo-storm proxies.

Stable isotope analysis of precipitation samples obtained via crowdsourcing reveals the spatiotemporal evolution of Superstorm Sandy.

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Good, Stephen P; Mallia, Derek V; Lin, John C; Bowen, Gabriel J

2014-01-01

Extra-tropical cyclones, such as 2012 Superstorm Sandy, pose a significant climatic threat to the northeastern United Sates, yet prediction of hydrologic and thermodynamic processes within such systems is complicated by their interaction with mid-latitude water patterns as they move poleward. Fortunately, the evolution of these systems is also recorded in the stable isotope ratios of storm-associated precipitation and water vapor, and isotopic analysis provides constraints on difficult-to-observe cyclone dynamics. During Superstorm Sandy, a unique crowdsourced approach enabled 685 precipitation samples to be obtained for oxygen and hydrogen isotopic analysis, constituting the largest isotopic sampling of a synoptic-scale system to date. Isotopically, these waters span an enormous range of values (> 21‰ for δ(18)O, > 160‰ for δ(2)H) and exhibit strong spatiotemporal structure. Low isotope ratios occurred predominantly in the west and south quadrants of the storm, indicating robust isotopic distillation that tracked the intensity of the storm's warm core. Elevated values of deuterium-excess (> 25‰) were found primarily in the New England region after Sandy made landfall. Isotope mass balance calculations and Lagrangian back-trajectory analysis suggest that these samples reflect the moistening of dry continental air entrained from a mid-latitude trough. These results demonstrate the power of rapid-response isotope monitoring to elucidate the structure and dynamics of water cycling within synoptic-scale systems and improve our understanding of storm evolution, hydroclimatological impacts, and paleo-storm proxies.

Evolution of concentration-discharge relations revealed by high frequency diurnal sampling of stream water during spring snowmelt

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Olshansky, Y.; White, A. M.; Thompson, M.; Moravec, B. G.; McIntosh, J. C.; Chorover, J.

2017-12-01

Concentration discharge (C-Q) relations contain potentially important information on critical zone (CZ) processes including: weathering reactions, water flow paths and nutrient export. To examine the C-Q relations in a small (3.3 km2) headwater catchment - La Jara Creek located in the Jemez River Basin Critical Zone Observatory, daily, diurnal stream water samples were collected during spring snow melt 2017, from two flumes located in outlets of the La Jara Creek and a high elevation zero order basin within this catchment. Previous studies from this site (McIntosh et al., 2017) suggested that high frequency sampling was needed to improve our interpretation of C-Q relations. The dense sampling covered two ascending and two descending limbs of the snowmelt hydrograph, from March 1 to May 15, 2017. While Na showed inverse correlation (dilution) with discharge, most other solutes (K, Mg, Fe, Al, dissolved organic carbon) exhibited positive (concentration) or chemostatic trends (Ca, Mn, Si, dissolved inorganic carbon and dissolved nitrogen). Hysteresis in the C-Q relation was most pronounced for bio-cycled cations (K, Mg) and for Fe, which exhibited concentration during the first ascending limb followed by a chemostatic trend. A pulsed increase in Si concentration immediately after the first ascending limb in both flumes suggests mixing of deep groundwater with surface water. A continual increase in Ge/Si concentrations followed by a rapid decrease after the second rising limb may suggest a fast transition between soil water to ground water dominating the stream flow. Fourier transform infrared spectroscopy of selected samples across the hydrograph demonstrated pronounced changes in dissolved organic matter molecular composition with the advancement of the spring snow melt. X-ray micro-spectroscopy of colloidal material isolated from the collected water samples indicated a significant role for organic matter in the transport of inorganic colloids. Analyses of high

Improved orientation sampling for indexing diffraction patterns of polycrystalline materials

DEFF Research Database (Denmark)

Larsen, Peter Mahler; Schmidt, Søren

2017-01-01

to that of optimally distributing points on a four‐dimensional sphere. In doing so, the number of orientation samples needed to achieve a desired indexing accuracy is significantly reduced. Orientation sets at a range of sizes are generated in this way for all Laue groups and are made available online for easy use.......Orientation mapping is a widely used technique for revealing the microstructure of a polycrystalline sample. The crystalline orientation at each point in the sample is determined by analysis of the diffraction pattern, a process known as pattern indexing. A recent development in pattern indexing...... in the presence of noise, it has very high computational requirements. In this article, the computational burden is reduced by developing a method for nearly optimal sampling of orientations. By using the quaternion representation of orientations, it is shown that the optimal sampling problem is equivalent...

Random sampling of evolution time space and Fourier transform processing

International Nuclear Information System (INIS)

Kazimierczuk, Krzysztof; Zawadzka, Anna; Kozminski, Wiktor; Zhukov, Igor

2006-01-01

Application of Fourier Transform for processing 3D NMR spectra with random sampling of evolution time space is presented. The 2D FT is calculated for pairs of frequencies, instead of conventional sequence of one-dimensional transforms. Signal to noise ratios and linewidths for different random distributions were investigated by simulations and experiments. The experimental examples include 3D HNCA, HNCACB and 15 N-edited NOESY-HSQC spectra of 13 C 15 N labeled ubiquitin sample. Obtained results revealed general applicability of proposed method and the significant improvement of resolution in comparison with conventional spectra recorded in the same time

Molecular detection and ecological significance of the cyanobacterial genera Geitlerinema and Leptolyngbya in black band disease of corals.

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Myers, Jamie L; Sekar, Raju; Richardson, Laurie L

2007-08-01

Black band disease (BBD) is a pathogenic, sulfide-rich microbial mat dominated by filamentous cyanobacteria that infect corals worldwide. We isolated cyanobacteria from BBD into culture, confirmed their presence in the BBD community by using denaturing gradient gel electrophoresis (DGGE), and demonstrated their ecological significance in terms of physiological sulfide tolerance and photosynthesis-versus-irradiance values. Twenty-nine BBD samples were collected from nine host coral species, four of which have not previously been investigated, from reefs of the Florida Keys, the Bahamas, St. Croix, and the Philippines. From these samples, seven cyanobacteria were isolated into culture. Cloning and sequencing of the 16S rRNA gene using universal primers indicated that four isolates were related to the genus Geitlerinema and three to the genus Leptolyngbya. DGGE results, obtained using Cyanobacteria-specific 16S rRNA primers, revealed that the most common BBD cyanobacterial sequence, detected in 26 BBD field samples, was related to that of an Oscillatoria sp. The next most common sequence, 99% similar to that of the Geitlerinema BBD isolate, was present in three samples. One Leptolyngbya- and one Phormidium-related sequence were also found. Laboratory experiments using isolates of BBD Geitlerinema and Leptolyngbya revealed that they could carry out sulfide-resistant oxygenic photosynthesis, a relatively rare characteristic among cyanobacteria, and that they are adapted to the sulfide-rich, low-light BBD environment. The presence of the cyanotoxin microcystin in these cultures and in BBD suggests a role in BBD pathogenicity. Our results confirm the presence of Geitlerinema in the BBD microbial community and its ecological significance, which have been challenged, and provide evidence of a second ecologically significant BBD cyanobacterium, Leptolyngbya.

DNA damage focus analysis in blood samples of minipigs reveals acute partial body irradiation.

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Andreas Lamkowski

Full Text Available Radiation accidents frequently involve acute high dose partial body irradiation leading to victims with radiation sickness and cutaneous radiation syndrome that implements radiation-induced cell death. Cells that are not lethally hit seek to repair ionizing radiation (IR induced damage, albeit at the expense of an increased risk of mutation and tumor formation due to misrepair of IR-induced DNA double strand breaks (DSBs. The response to DNA damage includes phosphorylation of histone H2AX in the vicinity of DSBs, creating foci in the nucleus whose enumeration can serve as a radiation biodosimeter. Here, we investigated γH2AX and DNA repair foci in peripheral blood lymphocytes of Göttingen minipigs that experienced acute partial body irradiation (PBI with 49 Gy (± 6% Co-60 γ-rays of the upper lumbar region. Blood samples taken 4, 24 and 168 hours post PBI were subjected to γ-H2AX, 53BP1 and MRE11 focus enumeration. Peripheral blood lymphocytes (PBL of 49 Gy partial body irradiated minipigs were found to display 1-8 DNA damage foci/cell. These PBL values significantly deceed the high foci numbers observed in keratinocyte nuclei of the directly γ-irradiated minipig skin regions, indicating a limited resident time of PBL in the exposed tissue volume. Nonetheless, PBL samples obtained 4 h post IR in average contained 2.2% of cells displaying a pan-γH2AX signal, suggesting that these received a higher IR dose. Moreover, dispersion analysis indicated partial body irradiation for all 13 minipigs at 4 h post IR. While dose reconstruction using γH2AX DNA repair foci in lymphocytes after in vivo PBI represents a challenge, the DNA damage focus assay may serve as a rapid, first line indicator of radiation exposure. The occurrence of PBLs with pan-γH2AX staining and of cells with relatively high foci numbers that skew a Poisson distribution may be taken as indicator of acute high dose partial body irradiation, particularly when samples are available

Scrupulosity in Islam: a comparison of highly religious Turkish and Canadian samples.

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Inozu, Mujgan; Clark, David A; Karanci, A Nuray

2012-03-01

Scrupulosity is a form of obsessive-compulsive disorder (OCD) characterized by a tendency to have persistent doubts about God, sin, and the adequacy of one's religious behaviors and devotion. To date, no published studies have compared scrupulosity in high- and low-religious Muslim and Christian samples. In the present study religious school students as well as high- and low-religious university students in Turkey and Canada were compared on the Penn Inventory of Scrupulosity (PIOS), Obsessive Beliefs Questionnaire (OBQ-44), and symptom measures of obssesionality and negative affect. Between-group comparisons revealed that the highly religious Turkish sample scored significantly higher than the highly religious Canadian students on the PIOS Fear of God but not the Fear of Sin subscale. Separate multiple regression analyses revealed that the Clark-Beck Obsessive Compulsive Inventory (CBOCI) Obsessions subscale, OBQ-44 Importance and Control of Thoughts subscale, and guilt were significant unique predictors of PIOS scrupulosity. These findings suggest that subtle differences exist in how scrupulosity is manifested in Islamic and Christian believers. Copyright © 2011. Published by Elsevier Ltd.

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

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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

Population Screening Using Sewage Reveals Pan-Resistant Bacteria in Hospital and Community Samples.

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Meir-Gruber, Lital; Manor, Yossi; Gefen-Halevi, Shiraz; Hindiyeh, Musa Y; Mileguir, Fernando; Azar, Roberto; Smollan, Gill; Belausov, Natasha; Rahav, Galia; Shamiss, Ari; Mendelson, Ella; Keller, Nathan

2016-01-01

The presence of pan-resistant bacteria worldwide possesses a threat to global health. It is difficult to evaluate the extent of carriage of resistant bacteria in the population. Sewage sampling is a possible way to monitor populations. We evaluated the presence of pan-resistant bacteria in Israeli sewage collected from all over Israel, by modifying the pour plate method for heterotrophic plate count technique using commercial selective agar plates. This method enables convenient and fast sewage sampling and detection. We found that sewage in Israel contains multiple pan-resistant bacteria including carbapenemase resistant Enterobacteriacae carrying blaKPC and blaNDM-1, MRSA and VRE. blaKPC carrying Klebsiella pneumonia and Enterobacter cloacae were the most common Enterobacteriacae drug resistant bacteria found in the sewage locations we sampled. Klebsiella pneumonia, Enterobacter spp., Escherichia coli and Citrobacter spp. were the 4 main CRE isolated from Israeli sewage and also from clinical samples in our clinical microbiology laboratory. Hospitals and Community sewage had similar percentage of positive samplings for blaKPC and blaNDM-1. VRE was found to be more abundant in sewage in Israel than MRSA but there were more locations positive for MRSA and VRE bacteria in Hospital sewage than in the Community. Therefore, our upgrade of the pour plate method for heterotrophic plate count technique using commercial selective agar plates can be a useful tool for routine screening and monitoring of the population for pan-resistant bacteria using sewage.

Large Sample Neutron Activation Analysis of Heterogeneous Samples

International Nuclear Information System (INIS)

Stamatelatos, I.E.; Vasilopoulou, T.; Tzika, F.

2018-01-01

A Large Sample Neutron Activation Analysis (LSNAA) technique was developed for non-destructive analysis of heterogeneous bulk samples. The technique incorporated collimated scanning and combining experimental measurements and Monte Carlo simulations for the identification of inhomogeneities in large volume samples and the correction of their effect on the interpretation of gamma-spectrometry data. Corrections were applied for the effect of neutron self-shielding, gamma-ray attenuation, geometrical factor and heterogeneous activity distribution within the sample. A benchmark experiment was performed to investigate the effect of heterogeneity on the accuracy of LSNAA. Moreover, a ceramic vase was analyzed as a whole demonstrating the feasibility of the technique. The LSNAA results were compared against results obtained by INAA and a satisfactory agreement between the two methods was observed. This study showed that LSNAA is a technique capable to perform accurate non-destructive, multi-elemental compositional analysis of heterogeneous objects. It also revealed the great potential of the technique for the analysis of precious objects and artefacts that need to be preserved intact and cannot be damaged for sampling purposes. (author)

The history of nursing in the home: revealing the significance of place in the expression of moral agency.

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Peter, Elizabeth

2002-06-01

The history of nursing in the home: revealing the significance of place in the expression of moral agency The relationship between place and moral agency in home care nursing is explored in this paper. The notion of place is argued to have relevance to moral agency beyond moral context. This argument is theoretically located in feminist ethics and human geography and is supported through an examination of historical documents (1900-33) that describe the experiences and insights of American home care/private duty nurses or that are related to nursing ethics. Specifically, the role of place in inhibiting and enhancing care, justice, good relationships, and power in the practice of private duty nurses is explored. Several implications for current nursing ethics come out of this analysis. (i) The moral agency of nurses is highly nuanced. It is not only structured by nurses' relationships to patients and health professionals, i.e. moral context, it is also structured by the place of nursing care. (ii) Place has the potential to limit and enhance the power of nurses. (iii) Some aspects of nursing's conception of the good, such as what constitutes a good nurse-patient relationship, are historically and geographically relative.

Trace metal depositional patterns from an open pit mining activity as revealed by archived avian gizzard contents.

Science.gov (United States)

Bendell, L I

2011-02-15

Archived samples of blue grouse (Dendragapus obscurus) gizzard contents, inclusive of grit, collected yearly between 1959 and 1970 were analyzed for cadmium, lead, zinc, and copper content. Approximately halfway through the 12-year sampling period, an open-pit copper mine began activities, then ceased operations 2 years later. Thus the archived samples provided a unique opportunity to determine if avian gizzard contents, inclusive of grit, could reveal patterns in the anthropogenic deposition of trace metals associated with mining activities. Gizzard concentrations of cadmium and copper strongly coincided with the onset of opening and the closing of the pit mining activity. Gizzard zinc and lead demonstrated significant among year variation; however, maximum concentrations did not correlate to mining activity. The archived gizzard contents did provide a useful tool for documenting trends in metal depositional patterns related to an anthropogenic activity. Further, blue grouse ingesting grit particles during the time of active mining activity would have been exposed to toxicologically significant levels of cadmium. Gizzard lead concentrations were also of toxicological significance but not related to mining activity. This type of "pulse" toxic metal exposure as a consequence of open-pit mining activity would not necessarily have been revealed through a "snap-shot" of soil, plant or avian tissue trace metal analysis post-mining activity. Copyright © 2010 Elsevier B.V. All rights reserved.

Molecular Detection and Ecological Significance of the Cyanobacterial Genera Geitlerinema and Leptolyngbya in Black Band Disease of Corals▿ †

Science.gov (United States)

Myers, Jamie L.; Sekar, Raju; Richardson, Laurie L.

2007-01-01

Black band disease (BBD) is a pathogenic, sulfide-rich microbial mat dominated by filamentous cyanobacteria that infect corals worldwide. We isolated cyanobacteria from BBD into culture, confirmed their presence in the BBD community by using denaturing gradient gel electrophoresis (DGGE), and demonstrated their ecological significance in terms of physiological sulfide tolerance and photosynthesis-versus-irradiance values. Twenty-nine BBD samples were collected from nine host coral species, four of which have not previously been investigated, from reefs of the Florida Keys, the Bahamas, St. Croix, and the Philippines. From these samples, seven cyanobacteria were isolated into culture. Cloning and sequencing of the 16S rRNA gene using universal primers indicated that four isolates were related to the genus Geitlerinema and three to the genus Leptolyngbya. DGGE results, obtained using Cyanobacteria-specific 16S rRNA primers, revealed that the most common BBD cyanobacterial sequence, detected in 26 BBD field samples, was related to that of an Oscillatoria sp. The next most common sequence, 99% similar to that of the Geitlerinema BBD isolate, was present in three samples. One Leptolyngbya- and one Phormidium-related sequence were also found. Laboratory experiments using isolates of BBD Geitlerinema and Leptolyngbya revealed that they could carry out sulfide-resistant oxygenic photosynthesis, a relatively rare characteristic among cyanobacteria, and that they are adapted to the sulfide-rich, low-light BBD environment. The presence of the cyanotoxin microcystin in these cultures and in BBD suggests a role in BBD pathogenicity. Our results confirm the presence of Geitlerinema in the BBD microbial community and its ecological significance, which have been challenged, and provide evidence of a second ecologically significant BBD cyanobacterium, Leptolyngbya. PMID:17601818

The distinctive gastric fluid proteome in gastric cancer reveals a multi-biomarker diagnostic profile

Directory of Open Access Journals (Sweden)

Eng Alvin KH

2008-10-01

Full Text Available Abstract Background Overall gastric cancer survival remains poor mainly because there are no reliable methods for identifying highly curable early stage disease. Multi-protein profiling of gastric fluids, obtained from the anatomic site of pathology, could reveal diagnostic proteomic fingerprints. Methods Protein profiles were generated from gastric fluid samples of 19 gastric cancer and 36 benign gastritides patients undergoing elective, clinically-indicated gastroscopy using surface-enhanced laser desorption/ionization time-of-flight mass spectrometry on multiple ProteinChip arrays. Proteomic features were compared by significance analysis of microarray algorithm and two-way hierarchical clustering. A second blinded sample set (24 gastric cancers and 29 clinically benign gastritides was used for validation. Results By significance analysyis of microarray, 60 proteomic features were up-regulated and 46 were down-regulated in gastric cancer samples (p Conclusion This simple and reproducible multimarker proteomic assay could supplement clinical gastroscopic evaluation of symptomatic patients to enhance diagnostic accuracy for gastric cancer and pre-malignant lesions.

Stable isotope probing reveals the importance of Comamonas and Pseudomonadaceae in RDX degradation in samples from a Navy detonation site.

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Jayamani, Indumathy; Cupples, Alison M

2015-07-01

This study investigated the microorganisms involved in hexahydro-1,3,5-trinitro-1,3,5-triazine (RDX) degradation from a detonation area at a Navy base. Using Illumina sequencing, microbial communities were compared between the initial sample, samples following RDX degradation, and controls not amended with RDX to determine which phylotypes increased in abundance following RDX degradation. The effect of glucose on these communities was also examined. In addition, stable isotope probing (SIP) using labeled ((13)C3, (15)N3-ring) RDX was performed. Illumina sequencing revealed that several phylotypes were more abundant following RDX degradation compared to the initial soil and the no-RDX controls. For the glucose-amended samples, this trend was strong for an unclassified Pseudomonadaceae phylotype and for Comamonas. Without glucose, Acinetobacter exhibited the greatest increase following RDX degradation compared to the initial soil and no-RDX controls. Rhodococcus, a known RDX degrader, also increased in abundance following RDX degradation. For the SIP study, unclassified Pseudomonadaceae was the most abundant phylotype in the heavy fractions in both the presence and absence of glucose. In the glucose-amended heavy fractions, the 16S ribosomal RNA (rRNA) genes of Comamonas and Anaeromxyobacter were also present. Without glucose, the heavy fractions also contained the 16S rRNA genes of Azohydromonas and Rhodococcus. However, all four phylotypes were present at a much lower level compared to unclassified Pseudomonadaceae. Overall, these data indicate that unclassified Pseudomonadaceae was primarily responsible for label uptake in both treatments. This study indicates, for the first time, the importance of Comamonas for RDX removal.

Non-destructive sampling of ancient insect DNA

DEFF Research Database (Denmark)

Thomsen, Philip Francis; Elias, Scott; Gilbert, Tom

2009-01-01

BACKGROUND: A major challenge for ancient DNA (aDNA) studies on insect remains is that sampling procedures involve at least partial destruction of the specimens. A recent extraction protocol reveals the possibility of obtaining DNA from past insect remains without causing visual morphological...... of 77-204 base pairs (-bp) in size using species-specific and general insect primers. CONCLUSION/SIGNIFICANCE: The applied non-destructive DNA extraction method shows promising potential on insect museum specimens of historical age as far back as AD 1820, but less so on the ancient permafrost......-preserved insect fossil remains tested, where DNA was obtained from samples up to ca. 26,000 years old. The non-frozen sediment DNA approach appears to have great potential for recording the former presence of insect taxa not normally preserved as macrofossils and opens new frontiers in research on ancient...

Religiosity, health and happiness: significant relations in adolescents from Qatar.

Science.gov (United States)

Abdel-Khalek, Ahmed M

2014-11-01

Several studies have revealed positive associations between religiosity, health and happiness. However, the vast majority of these studies were carried out on native English-speaking participants. The objective of this study was to estimate the relations between religiosity, health and happiness among a sample (N = 372) of Qatari adolescents (M age = 15.2). The students responded to five self-rating scales to assess religiosity, mental health, physical health, happiness and satisfaction with life. Boys obtained a higher mean score on mental health than did their female counterparts. All the correlations between the rating scales were significant and positive. Principal component analysis disclosed one component and labelled 'Religiosity, health and happiness' in both sexes. The multiple stepwise regression indicated that the predictors of religiosity were the self-ratings of satisfaction with life and happiness in boys, whereas the predictors among girls were satisfaction with life and physical health. On the basis of the responses of the present sample, it was concluded that those who consider themselves as religious were more happy, satisfied with their life and healthy. © The Author(s) 2013.

Bovine teat microbiome analysis revealed reduced alpha diversity and significant changes in taxonomic profiles in quarters with a history of mastitis

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Helene eFalentin

2016-04-01

Full Text Available Mastitis is a mammary gland inflammatory disease often due to bacterial infections. Like many other infections, it used to be considered as a host-pathogen interaction driven by host and bacterial determinants. Until now, the involvement of the bovine mammary gland microbiota in the host-pathogen interaction has been poorly investigated, and mainly during the infectious episode. In this study, the bovine teat microbiome was investigated in 31 quarters corresponding to 27 animals, which were all free of inflammation at sampling time but which had different histories regarding mastitis: from no episode of mastitis on all the previous lactations (Healthy quarter, Hq to one or several clinical mastitis events (Mastitic quarter, Mq. Several quarters whose status was unclear (possible history of subclinical mastitis were classified as NDq. Total bacterial DNA was extracted from foremilk samples and swab samples of the teat canal. Taxonomic profiles were determined by pyrosequencing on 16s amplicons of the V3-4 region. Hq quarters showed a higher diversity compared to Mq ones (Shannon index: ~8 and 6, respectively. Clustering of the quarters based on their bacterial composition made it possible to separate Mq and Hq quarters into two separate clusters (C1 and C2, respectively. Discriminant analysis of taxonomic profiles between these clusters revealed several differences and allowed the identification of taxonomic markers in relation to mastitis history. C2 quarters were associated with a higher proportion of the Clostridia class (including genera such as Ruminococcus, Oscillospira, Roseburia, Dorea, etc., the Bacteroidetes phylum (Prevotella, Bacteroides, Paludibacter, etc., and the Bifidobacteriales order (Bifidobacterium, whereas C1 quarters showed a higher proportion of the Bacilli class (Staphylococcus and Chlamydiia class. These results indicate that microbiota is altered in udders which have already developed mastitis, even far from the

Dynamic metabolome profiling reveals significant metabolic changes during grain development of bread wheat (Triticum aestivum L.).

Science.gov (United States)

Zhen, Shoumin; Dong, Kun; Deng, Xiong; Zhou, Jiaxing; Xu, Xuexin; Han, Caixia; Zhang, Wenying; Xu, Yanhao; Wang, Zhimin; Yan, Yueming

2016-08-01

Metabolites in wheat grains greatly influence nutritional values. Wheat provides proteins, minerals, B-group vitamins and dietary fiber to humans. These metabolites are important to human health. However, the metabolome of the grain during the development of bread wheat has not been studied so far. In this work the first dynamic metabolome of the developing grain of the elite Chinese bread wheat cultivar Zhongmai 175 was analyzed, using non-targeted gas chromatography/mass spectrometry (GC/MS) for metabolite profiling. In total, 74 metabolites were identified over the grain developmental stages. Metabolite-metabolite correlation analysis revealed that the metabolism of amino acids, carbohydrates, organic acids, amines and lipids was interrelated. An integrated metabolic map revealed a distinct regulatory profile. The results provide information that can be used by metabolic engineers and molecular breeders to improve wheat grain quality. The present metabolome approach identified dynamic changes in metabolite levels, and correlations among such levels, in developing seeds. The comprehensive metabolic map may be useful when breeding programs seek to improve grain quality. The work highlights the utility of GC/MS-based metabolomics, in conjunction with univariate and multivariate data analysis, when it is sought to understand metabolic changes in developing seeds. © 2015 Society of Chemical Industry. © 2015 Society of Chemical Industry.

Eating Disorders Among a Community-based Sample of Chilean Female Adolescents

Science.gov (United States)

Granillo, M. Teresa; Grogan-Kaylor, Andrew; Delva, Jorge; Castillo, Marcela

2010-01-01

The purpose of this study was to explore the prevalence and correlates of eating disorders among a community-based sample of female Chilean adolescents. Data were collected through structured interviews with 420 female adolescents residing in Santiago, Chile. Approximately 4% of the sample reported ever being diagnosed with an eating disorder. Multivariate logistic regression analyses revealed that those with higher symptoms of anxiety and who had tried cigarettes were significantly more likely to have been diagnosed with an eating disorder. Findings indicate that Chilean female adolescents are at risk of eating disorders and that eating disorders, albeit maladaptive, may be a means to cope with negative affect, specifically anxiety. PMID:22121329

Ceres Revealed in a Grain of Salt

Science.gov (United States)

Zolensky, M. E.; Bodnar, R. J.; Fries, M.; Chan, Q. H.-S.; Kebukawa, Y.; Mikouchi, T.; Hagiya, K.; Komatsu, M.; Ohsumi, K.; Steele, A.

2016-01-01

Introduction: Zag and Monahans (1998) are H chondrite regolith breccias containing 4.5 giga-year-old halite crystals which contain abundant inclusions of aqueous fluids, solids and organics. These all originated on a cryo-volcanically-active C class asteroid, probably 1 Ceres; the halite was transported to the regolith of the H chondrite parent asteroid, potentially 6 Hebe. Detailed analysis of these solids will thus potentially reveal the mineralogy of Ceres. Mineralogy of solids in the Monahans Halite Solid grains are present in the halites, which were entrained within the mother brines during eruption, including material from the interior and surface of the erupting body. The solids include abundant, widely variable organics that could not have been significantly heated (which would have resulted in the loss of fluids from the halite). Our analyses by Raman microprobe, SEM/EDX, synchrotron X-ray diffraction, UPLC-FD/QToF-MS, C-XANES and TEM reveal that these trapped grains include macromolecular carbon (MMC) similar in structure to CV3 chondrite matrix carbon, aliphatic carbon compounds, olivine (Fo99-59), high- and low-Ca pyroxene, feldspars, phyllosilicates, magnetite, sulfides, metal, lepidocrocite, carbonates, diamond, apatite and zeolites. Conclusions: The halite in Monahans and Zag derive from a water and carbon-rich object that was cryo-volcanically active in the early solar system, probably Ceres. The Dawn spacecraft found that Ceres includes C chondrite materials. Our samples include both protolith and aqueously-altered samples of the body, permitting understanding of alteration conditions. Whatever the halite parent body, it was rich in a wide variety of organics and warm, liquid water at the solar system's dawn.

Meta-Analysis Reveals Significant Association of the 3'-UTR VNTR in SLC6A3 with Alcohol Dependence.

Science.gov (United States)

Ma, Yunlong; Fan, Rongli; Li, Ming D

2016-07-01

Although many studies have analyzed the association of 3'-untranslated region variable-number tandem repeat (VNTR) polymorphism in SLC6A3 with alcohol dependence (AD), the results remain controversial. This study aimed to determine whether this variant indeed has any genetic effect on AD by integrating 17 reported studies with 5,929 participants included. The A9-dominant genetic model that considers A9-repeat and non-A9 repeat as 2 genotypes and compared their frequencies in alcoholics with that in controls was adopted. Considering the potential influence of ethnicity, differences in diagnostic criteria of AD, and alcoholic subgroups, stratified meta-analyses were conducted. There existed no evidence for the presence of heterogeneity among the studied samples, indicating the results under the fixed-effects model are acceptable. We found a significant association of VNTR A9 genotypes with AD in all ethnic populations (pooled odds ratio [OR] 1.12; 95% confidence interval [CI] 1.00, 1.25; p = 0.045) and the Caucasian population (pooled OR 1.15; 95% CI 1.01, 1.31; p = 0.036). We also found VNTR A9 genotypes to be significantly associated with alcoholism as defined by the DSM-IV criteria (pooled OR 1.18; 95% CI 1.03, 1.36; p = 0.02). Further, we found a significant association between VNTR A9 genotypes and alcoholism associated with alcohol withdrawal seizure or delirium tremens (pooled OR 1.55; 95% CI 1.24, 1.92; p = 1.0 × 10(-4) ). In all these meta-analyses, no evidence of publication bias was detected. We concluded that the VNTR polymorphism has an important role in the etiology of AD, and individuals with at least 1 A9 allele are more likely to be dependent on alcohol than persons carrying the non-A9 allele. Copyright © 2016 by the Research Society on Alcoholism.

Urine Proteomics Revealed a Significant Correlation Between Urine-Fibronectin Abundance and Estimated-GFR Decline in Patients with Bardet-Biedl Syndrome

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Marianna Caterino

2018-03-01

Full Text Available Background:/Aims: Renal disease is a common cause of morbidity in patients with Bardet-Biedl syndrome (BBS, however the severity of kidney dysfunction is highly variable. To date, there is little information on the pathogenesis, the risk and predictor factors for poor renal outcome in this setting. The present study aims to analyze the spectrum of urinary proteins in BBS patients, in order to potentially identify 1 disease-specific proteomic profiles that may differentiate the patients from normal subjects; 2 urinary markers of renal dysfunction. Methods: Fourteen individuals (7 males and 7 females with a clinical diagnosis of BBS have been selected in this study. A pool of 10 aged-matched males and 10 aged-matched females have been used as controls for proteomic analysis. The glomerular filtration rate (eGFR has been estimated using the CKD-EPI formula. Variability of eGFR has been retrospectively assessed calculating average annual eGFR decline (ΔeGFR in a mean follow-up period of 4 years (3-7. Results: 42 proteins were significantly over- or under-represented in BBS patients compared with controls; the majority of these proteins are involved in fibrosis, cell adhesion and extracellular matrix organization. Statistic studies revealed a significant correlation between urine fibronectin (u-FN (r2=0.28; p<0.05, CD44 antigen (r2 =0.35; p<0.03 and lysosomal alfa glucosidase ( r20.27; p<0.05 abundance with the eGFR. In addition, u-FN (r2 =0.2389; p<0.05 was significantly correlated with ΔeGFR. Conclusion: The present study demonstrates that urine proteome of BBS patients differs from that of normal subjects; in addition, kidney dysfunction correlated with urine abundance of known markers of renal fibrosis.

Independent component analysis reveals new and biologically significant structures in micro array data

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Veerla Srinivas

2006-06-01

Full Text Available Abstract Background An alternative to standard approaches to uncover biologically meaningful structures in micro array data is to treat the data as a blind source separation (BSS problem. BSS attempts to separate a mixture of signals into their different sources and refers to the problem of recovering signals from several observed linear mixtures. In the context of micro array data, "sources" may correspond to specific cellular responses or to co-regulated genes. Results We applied independent component analysis (ICA to three different microarray data sets; two tumor data sets and one time series experiment. To obtain reliable components we used iterated ICA to estimate component centrotypes. We found that many of the low ranking components indeed may show a strong biological coherence and hence be of biological significance. Generally ICA achieved a higher resolution when compared with results based on correlated expression and a larger number of gene clusters with significantly enriched for gene ontology (GO categories. In addition, components characteristic for molecular subtypes and for tumors with specific chromosomal translocations were identified. ICA also identified more than one gene clusters significant for the same GO categories and hence disclosed a higher level of biological heterogeneity, even within coherent groups of genes. Conclusion Although the ICA approach primarily detects hidden variables, these surfaced as highly correlated genes in time series data and in one instance in the tumor data. This further strengthens the biological relevance of latent variables detected by ICA.

Metabolomics reveals dose effects of low-dose chronic exposure to uranium in rats: identification of candidate biomarkers in urine samples.

Science.gov (United States)

Grison, Stéphane; Favé, Gaëlle; Maillot, Matthieu; Manens, Line; Delissen, Olivia; Blanchardon, Éric; Dublineau, Isabelle; Aigueperse, Jocelyne; Bohand, Sandra; Martin, Jean-Charles; Souidi, Maâmar

2016-01-01

Data are sparse about the potential health risks of chronic low-dose contamination of humans by uranium (natural or anthropogenic) in drinking water. Previous studies report some molecular imbalances but no clinical signs due to uranium intake. In a proof-of-principle study, we reported that metabolomics is an appropriate method for addressing this chronic low-dose exposure in a rat model (uranium dose: 40 mg L -1 ; duration: 9 months, n = 10). In the present study, our aim was to investigate the dose-effect pattern and identify additional potential biomarkers in urine samples. Compared to our previous protocol, we doubled the number of rats per group (n = 20), added additional sampling time points (3 and 6 months) and included several lower doses of natural uranium (doses used: 40, 1.5, 0.15 and 0.015 mg L -1 ). LC-MS metabolomics was performed on urine samples and statistical analyses were made with SIMCA-P+ and R packages. The data confirmed our previous results and showed that discrimination was both dose and time related. Uranium exposure was revealed in rats contaminated for 9 months at a dose as low as 0.15 mg L -1 . Eleven features, including the confidently identified N1-methylnicotinamide, N1-methyl-2-pyridone-5-carboxamide and 4-hydroxyphenylacetylglycine, discriminated control from contaminated rats with a specificity and a sensitivity ranging from 83 to 96 %, when combined into a composite score. These findings show promise for the elucidation of underlying radiotoxicologic mechanisms and the design of a diagnostic test to assess exposure in urine, in a dose range experimentally estimated to be above a threshold between 0.015 and 0.15 mg L -1 .

Laboratory simulation reveals significant impacts of ocean acidification on microbial community composition and host-pathogen interactions between the blood clam and Vibrio harveyi.

Science.gov (United States)

Zha, Shanjie; Liu, Saixi; Su, Wenhao; Shi, Wei; Xiao, Guoqiang; Yan, Maocang; Liu, Guangxu

2017-12-01

It has been suggested that climate change may promote the outbreaks of diseases in the sea through altering the host susceptibility, the pathogen virulence, and the host-pathogen interaction. However, the impacts of ocean acidification (OA) on the pathogen components of bacterial community and the host-pathogen interaction of marine bivalves are still poorly understood. Therefore, 16S rRNA high-throughput sequencing and host-pathogen interaction analysis between blood clam (Tegillarca granosa) and Vibrio harveyi were conducted in the present study to gain a better understanding of the ecological impacts of ocean acidification. The results obtained revealed a significant impact of ocean acidification on the composition of microbial community at laboratory scale. Notably, the abundance of Vibrio, a major group of pathogens to many marine organisms, was significantly increased under ocean acidification condition. In addition, the survival rate and haemolytic activity of V. harveyi were significantly higher in the presence of haemolymph of OA treated T. granosa, indicating a compromised immunity of the clam and enhanced virulence of V. harveyi under future ocean acidification scenarios. Conclusively, the results obtained in this study suggest that future ocean acidification may increase the risk of Vibrio pathogen infection for marine bivalve species, such as blood clams. Copyright © 2017 Elsevier Ltd. All rights reserved.

Pre-storage centrifugation conditions have significant impact on measured microRNA levels in biobanked EDTA plasma samples

DEFF Research Database (Denmark)

Binderup, Helle Glud; Houlind, Kim; Madsen, Jonna Skov

2016-01-01

in platelets this may partly be explained by residual platelets in the plasma samples used. When collecting fresh plasma samples, it is possible to produce cell-free/platelet-poor plasma by centrifugation. In this study, we systematically investigated whether biobanked EDTA plasma samples could be processed...... to be suitable for miRNA analysis. Materials and methods: Blood samples were collected from ten healthy volunteers and centrifuged to produce platelet-poor-plasma (PPP) and standard biobank plasma. After one week at -80 °C the biobanked EDTA plasma was re-centrifuged by different steps to remove residual...... platelets. Using RT-qPCR the levels of 14 miRNAs in the different plasma preparations were compared to that of PPP. Results: We were able to remove residual platelets from biobanked EDTA plasma by re-centrifugation of the thawed samples. Nevertheless, for most of the investigated miRNAs, the miRNA level...

TRU waste-sampling program

International Nuclear Information System (INIS)

Warren, J.L.; Zerwekh, A.

1985-08-01

As part of a TRU waste-sampling program, Los Alamos National Laboratory retrieved and examined 44 drums of 238 Pu- and 239 Pu-contaminated waste. The drums ranged in age from 8 months to 9 years. The majority of drums were tested for pressure, and gas samples withdrawn from the drums were analyzed by a mass spectrometer. Real-time radiography and visual examination were used to determine both void volumes and waste content. Drum walls were measured for deterioration, and selected drum contents were reassayed for comparison with original assays and WIPP criteria. Each drum tested at atmospheric pressure. Mass spectrometry revealed no problem with 239 Pu-contaminated waste, but three 8-month-old drums of 238 Pu-contaminated waste contained a potentially hazardous gas mixture. Void volumes fell within the 81 to 97% range. Measurements of drum walls showed no significant corrosion or deterioration. All reassayed contents were within WIPP waste acceptance criteria. Five of the drums opened and examined (15%) could not be certified as packaged. Three contained free liquids, one had corrosive materials, and one had too much unstabilized particulate. Eleven drums had the wrong (or not the most appropriate) waste code. In many cases, disposal volumes had been inefficiently used. 2 refs., 23 figs., 7 tabs

Characterization of Fasciola samples by ITS of rDNA sequences revealed the existence of Fasciola hepatica and Fasciola gigantica in Yunnan Province, China.

Science.gov (United States)

Shu, Fan-Fan; Lv, Rui-Qing; Zhang, Yi-Fang; Duan, Gang; Wu, Ding-Yu; Li, Bi-Feng; Yang, Jian-Fa; Zou, Feng-Cai

2012-08-01

On mainland China, liver flukes of Fasciola spp. (Digenea: Fasciolidae) can cause serious acute and chronic morbidity in numerous species of mammals such as sheep, goats, cattle, and humans. The objective of the present study was to examine the taxonomic identity of Fasciola species in Yunnan province by sequences of the first and second internal transcribed spacers (ITS-1 and ITS-2) of nuclear ribosomal DNA (rDNA). The ITS rDNA was amplified from 10 samples representing Fasciola species in cattle from 2 geographical locations in Yunnan Province, by polymerase chain reaction (PCR), and the products were sequenced directly. The lengths of the ITS-1 and ITS-2 sequences were 422 and 361-362 base pairs, respectively, for all samples sequenced. Using ITS sequences, 2 Fasciola species were revealed, namely Fasciola hepatica and Fasciola gigantica. This is the first demonstration of F. gigantica in cattle in Yunnan Province, China using a molecular approach; our findings have implications for studying the population genetic characterization of the Chinese Fasciola species and for the prevention and control of Fasciola spp. in this province.

Analyses and Comparison of Bulk and Coil Surface Samples from the DWPF Slurry Mix Evaporator

International Nuclear Information System (INIS)

Hay, M.; Nash, C.; Stone, M.

2012-01-01

Sludge samples from the DWPF Slurry Mix Evaporator (SME) heating coil frame and coil surface were characterized to identify differences that might help identify heat transfer fouling materials. The SME steam coils have seen increased fouling leading to lower boil-up rates. Samples of the sludge were taken from the coil frame somewhat distant from the coil (bulk tank material) and from the coil surface (coil surface sample). The results of the analysis indicate the composition of the two SME samples are very similar with the exception that the coil surface sample shows ∼5-10X higher mercury concentration than the bulk tank sample. Elemental analyses and x-ray diffraction results did not indicate notable differences between the two samples. The ICP-MS and Cs-137 data indicate no significant differences in the radionuclide composition of the two SME samples. Semi-volatile organic analysis revealed numerous organic molecules, these likely result from antifoaming additives. The compositions of the two SME samples also match well with the analyzed composition of the SME batch with the exception of significantly higher silicon, lithium, and boron content in the batch sample indicating the coil samples are deficient in frit relative to the SME batch composition.

Do women's voices provide cues of the likelihood of ovulation? The importance of sampling regime.

Directory of Open Access Journals (Sweden)

Julia Fischer

Full Text Available The human voice provides a rich source of information about individual attributes such as body size, developmental stability and emotional state. Moreover, there is evidence that female voice characteristics change across the menstrual cycle. A previous study reported that women speak with higher fundamental frequency (F0 in the high-fertility compared to the low-fertility phase. To gain further insights into the mechanisms underlying this variation in perceived attractiveness and the relationship between vocal quality and the timing of ovulation, we combined hormone measurements and acoustic analyses, to characterize voice changes on a day-to-day basis throughout the menstrual cycle. Voice characteristics were measured from free speech as well as sustained vowels. In addition, we asked men to rate vocal attractiveness from selected samples. The free speech samples revealed marginally significant variation in F0 with an increase prior to and a distinct drop during ovulation. Overall variation throughout the cycle, however, precluded unequivocal identification of the period with the highest conception risk. The analysis of vowel samples revealed a significant increase in degree of unvoiceness and noise-to-harmonic ratio during menstruation, possibly related to an increase in tissue water content. Neither estrogen nor progestogen levels predicted the observed changes in acoustic characteristics. The perceptual experiments revealed a preference by males for voice samples recorded during the pre-ovulatory period compared to other periods in the cycle. While overall we confirm earlier findings in that women speak with a higher and more variable fundamental frequency just prior to ovulation, the present study highlights the importance of taking the full range of variation into account before drawing conclusions about the value of these cues for the detection of ovulation.

Laser ablation: Laser parameters: Frequency, pulse length, power, and beam charter play significant roles with regard to sampling complex samples for ICP/MS analysis

International Nuclear Information System (INIS)

Smith, M.R.; Alexander, M.L.; Hartman, J.S.; Koppenaal, D.W.

1996-01-01

Inductively coupled plasma mass spectrometry is used to investigate the influence of laser parameters with regard to sampling complex matrices ranging from relatively homogenous glasses to multi-phase sludge/slurry materials including radioactive Hanford tank waste. The resulting plume composition caused by the pulsed laser is evaluated as a function of wavelength, pulse energy, pulse length, focus, and beam power profiles. The author's studies indicate that these parameters play varying and often synergistic roles regarding quantitative results. (In a companion paper, particle transport and size distribution studies are presented.) The work described here will illustrate other laser parameters such as focusing and consequently power density and beam power profiles which are shown to influence precision and accuracy. Representative sampling by the LA approach is largely dependent on the sample's optical properties as well as laser parameters. Experimental results indicate that optimal laser parameters; short wavelength (UV), relatively low power (300 mJ), low-to-sub ns pulse lengths, and laser beams with reasonable power distributions (i.e., Gaussian or top-hat beam profiles) provide superior precision and accuracy. Remote LA-ICP/MS analyses of radioactive sludges are used to illustrate these optimal conditions laser ablation sampling

DNA Sampling Hook

Data.gov (United States)

National Oceanic and Atmospheric Administration, Department of Commerce — The DNA Sampling Hook is a significant improvement on a method of obtaining a tissue sample from a live fish in situ from an aquatic environment. A tissue sample...

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

Directory of Open Access Journals (Sweden)

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.

Major ions in spitsbergen snow samples

International Nuclear Information System (INIS)

Semb, A.; Braekkan, R.; Joranger, E.

1984-01-01

Chemical analysis of Spitsbergen snow cores sampled in spring 1983, reveals a spatial pattern consistent with orographic deposition of major anthropogenic pollutants with air movements from southeast towards northwest. The highest concentrations of pollutant species were found at an altitude of 700 metres above sea level, and are higher than for any other recorded snow samples from the Arctic

Structure in nascent carbon nanotubes revealed by spatially resolved Raman spectroscopy

Energy Technology Data Exchange (ETDEWEB)

Landois, Périne [CEA, IRAMIS, SPAM, Laboratoire Francis Perrin (CNRS URA 2453), 91191 Gif-sur-Yvette (France); Laboratoire de Physique des Solides, UMR CNRS 8502, Université Paris Sud 11, 91405 Orsay (France); Pinault, Mathieu [CEA, IRAMIS, SPAM, Laboratoire Francis Perrin (CNRS URA 2453), 91191 Gif-sur-Yvette (France); Huard, Mickaël [Laboratoire de Physique des Solides, UMR CNRS 8502, Université Paris Sud 11, 91405 Orsay (France); Reita, Valérie [Univ. Grenoble Alpes, Inst NEEL, F-38042 Grenoble (France); CNRS, Inst NEEL, F-38042 Grenoble (France); Rouzière, Stéphan; Launois, Pascale [Laboratoire de Physique des Solides, UMR CNRS 8502, Université Paris Sud 11, 91405 Orsay (France); Mayne-L' Hermite, Martine [CEA, IRAMIS, SPAM, Laboratoire Francis Perrin (CNRS URA 2453), 91191 Gif-sur-Yvette (France); Bendiab, Nedjma, E-mail: nedjma.bendiab@grenoble.cnrs.fr [Univ. Grenoble Alpes, Inst NEEL, F-38042 Grenoble (France); CNRS, Inst NEEL, F-38042 Grenoble (France)

2014-10-01

The understanding of carbon nanotube (CNT) growth is crucial for the control of their production. In particular, the identification of structural changes of carbon possibly occurring near the catalyst particle in the very early stages of their formation is of high interest. In this study, samples of nascent CNT obtained during nucleation step and samples of vertically aligned CNT obtained during growth step are analysed by combined spatially resolved Raman spectroscopy and X-ray diffraction measurements. Spatially resolved Raman spectroscopy reveals that iron-based phases and carbon phases are co-localized at the same position, and indicates that sp{sup 2} carbon nucleates preferentially on iron-based particles during this nucleation step. Depth scan Raman spectroscopy analysis, performed on nascent CNT, highlights that carbon structural organisation is significantly changing from defective graphene layers surrounding the iron-based particles at their base up to multi-walled nanotube structures in the upper part of iron-based particles. - Highlights: • Spatial co-localization of iron and carbon structures in nascent carbon nanotubes • Imaging local carbon structure changes along catalyst particles by Raman spectroscopy. • In nascent nanotubes, significant structural changes occur along catalyst particle.

'Neknomination': Predictors in a sample of UK university students.

Science.gov (United States)

Moss, Antony C; Spada, Marcantonio M; Harkin, Jamila; Albery, Ian P; Rycroft, Nicola; Nikčević, Ana V

2015-06-01

To identify prevalence and predictors of participation in the online drinking game 'neknomination' amongst university students. A convenience sample of 145 university students participated in a study about drinking behaviours, completing a questionnaire about their participation in neknomination, the Alcohol Use Disorders Identification Test, and the Resistance to Peer Influence Scale. Out of 145 students sampled, 54% took part in neknomination in the previous month. Mann-Whitney U tests revealed significantly higher scores on the Alcohol Use Disorders Identification Test, and significantly lower scores on the Resistance to Peer Influence Scale, for those who had participated in neknomination. A significant correlation was also shown between specific peer pressure to neknominate, and engagement in neknomination. A logistic regression analysis indicated that scores on the Alcohol Use Disorders Identification Test, but not the Resistance to Peer Influence Scale, predicted classification as an individual who participated in neknomination. We found that over half of respondents had participated in a neknomination game in the past month, with almost all male respondents having done so. Participation in neknomination was strongly associated with general hazardous drinking behaviour but not with resistance to peer influence. Further research is needed to understand the role of engagement with social media in drinking games and risky drinking.

Physiological and Pathological Impact of Blood Sampling by Retro-Bulbar Sinus Puncture and Facial Vein Phlebotomy in Laboratory Mice

DEFF Research Database (Denmark)

Teilmann, Anne Charlotte; Nygaard Madsen, Andreas; Holst, Birgitte

2014-01-01

weight following blood sampling, but the body weight loss was higher in mice subjected to facial vein phlebotomy. The food consumption was not significantly different between the two groups. At gross necropsy, subcutaneous hematomas were found in both groups and the histopathological analyses revealed...

Comprehensive behavioral analysis of the Cdkl5 knockout mice revealed significant enhancement in anxiety- and fear-related behaviors and impairment in both acquisition and long-term retention of spatial reference memory.

Science.gov (United States)

Okuda, Kosuke; Takao, Keizo; Watanabe, Aya; Miyakawa, Tsuyoshi; Mizuguchi, Masashi; Tanaka, Teruyuki

2018-01-01

Mutations in the Cyclin-dependent kinase-like 5 (CDKL5) gene cause severe neurodevelopmental disorders. Recently we have generated Cdkl5 KO mice by targeting exon 2 on the C57BL/6N background, and demonstrated postsynaptic overaccumulation of GluN2B-containing N-methyl-D-aspartate (NMDA) receptors in the hippocampus. In the current study, we subjected the Cdkl5 KO mice to a battery of comprehensive behavioral tests, aiming to reveal the effects of loss of CDKL5 in a whole perspective of motor, emotional, social, and cognition/memory functions, and to identify its undetermined roles. The neurological screen, rotarod, hot plate, prepulse inhibition, light/dark transition, open field, elevated plus maze, Porsolt forced swim, tail suspension, one-chamber and three-chamber social interaction, 24-h home cage monitoring, contextual and cued fear conditioning, Barnes maze, and T-maze tests were applied on adult Cdkl5 -/Y and +/Y mice. Cdkl5 -/Y mice showed a mild alteration in the gait. Analyses of emotional behaviors revealed significantly enhanced anxiety-like behaviors of Cdkl5 -/Y mice. Depressive-like behaviors and social interaction of Cdkl5 -/Y mice were uniquely altered. The contextual and cued fear conditioning of Cdkl5 -/Y mice were comparable to control mice; however, Cdkl5 -/Y mice showed a significantly increased freezing time and a significantly decreased distance traveled during the pretone period in the altered context. Both acquisition and long-term retention of spatial reference memory were significantly impaired. The morphometric analysis of hippocampal CA1 pyramidal neurons revealed impaired dendritic arborization and immature spine development in Cdkl5 -/Y mice. These results indicate that CDKL5 plays significant roles in regulating emotional behaviors especially on anxiety- and fear-related responses, and in both acquisition and long-term retention of spatial reference memory, which suggests that focus and special attention should be paid to the

Comprehensive behavioral analysis of the Cdkl5 knockout mice revealed significant enhancement in anxiety- and fear-related behaviors and impairment in both acquisition and long-term retention of spatial reference memory.

Directory of Open Access Journals (Sweden)

Kosuke Okuda

Full Text Available Mutations in the Cyclin-dependent kinase-like 5 (CDKL5 gene cause severe neurodevelopmental disorders. Recently we have generated Cdkl5 KO mice by targeting exon 2 on the C57BL/6N background, and demonstrated postsynaptic overaccumulation of GluN2B-containing N-methyl-D-aspartate (NMDA receptors in the hippocampus. In the current study, we subjected the Cdkl5 KO mice to a battery of comprehensive behavioral tests, aiming to reveal the effects of loss of CDKL5 in a whole perspective of motor, emotional, social, and cognition/memory functions, and to identify its undetermined roles. The neurological screen, rotarod, hot plate, prepulse inhibition, light/dark transition, open field, elevated plus maze, Porsolt forced swim, tail suspension, one-chamber and three-chamber social interaction, 24-h home cage monitoring, contextual and cued fear conditioning, Barnes maze, and T-maze tests were applied on adult Cdkl5 -/Y and +/Y mice. Cdkl5 -/Y mice showed a mild alteration in the gait. Analyses of emotional behaviors revealed significantly enhanced anxiety-like behaviors of Cdkl5 -/Y mice. Depressive-like behaviors and social interaction of Cdkl5 -/Y mice were uniquely altered. The contextual and cued fear conditioning of Cdkl5 -/Y mice were comparable to control mice; however, Cdkl5 -/Y mice showed a significantly increased freezing time and a significantly decreased distance traveled during the pretone period in the altered context. Both acquisition and long-term retention of spatial reference memory were significantly impaired. The morphometric analysis of hippocampal CA1 pyramidal neurons revealed impaired dendritic arborization and immature spine development in Cdkl5 -/Y mice. These results indicate that CDKL5 plays significant roles in regulating emotional behaviors especially on anxiety- and fear-related responses, and in both acquisition and long-term retention of spatial reference memory, which suggests that focus and special attention should be

Comprehensive behavioral analysis of the Cdkl5 knockout mice revealed significant enhancement in anxiety- and fear-related behaviors and impairment in both acquisition and long-term retention of spatial reference memory

Science.gov (United States)

Okuda, Kosuke; Takao, Keizo; Watanabe, Aya; Miyakawa, Tsuyoshi; Mizuguchi, Masashi

2018-01-01

Mutations in the Cyclin-dependent kinase-like 5 (CDKL5) gene cause severe neurodevelopmental disorders. Recently we have generated Cdkl5 KO mice by targeting exon 2 on the C57BL/6N background, and demonstrated postsynaptic overaccumulation of GluN2B-containing N-methyl-D-aspartate (NMDA) receptors in the hippocampus. In the current study, we subjected the Cdkl5 KO mice to a battery of comprehensive behavioral tests, aiming to reveal the effects of loss of CDKL5 in a whole perspective of motor, emotional, social, and cognition/memory functions, and to identify its undetermined roles. The neurological screen, rotarod, hot plate, prepulse inhibition, light/dark transition, open field, elevated plus maze, Porsolt forced swim, tail suspension, one-chamber and three-chamber social interaction, 24-h home cage monitoring, contextual and cued fear conditioning, Barnes maze, and T-maze tests were applied on adult Cdkl5 -/Y and +/Y mice. Cdkl5 -/Y mice showed a mild alteration in the gait. Analyses of emotional behaviors revealed significantly enhanced anxiety-like behaviors of Cdkl5 -/Y mice. Depressive-like behaviors and social interaction of Cdkl5 -/Y mice were uniquely altered. The contextual and cued fear conditioning of Cdkl5 -/Y mice were comparable to control mice; however, Cdkl5 -/Y mice showed a significantly increased freezing time and a significantly decreased distance traveled during the pretone period in the altered context. Both acquisition and long-term retention of spatial reference memory were significantly impaired. The morphometric analysis of hippocampal CA1 pyramidal neurons revealed impaired dendritic arborization and immature spine development in Cdkl5 -/Y mice. These results indicate that CDKL5 plays significant roles in regulating emotional behaviors especially on anxiety- and fear-related responses, and in both acquisition and long-term retention of spatial reference memory, which suggests that focus and special attention should be paid to the

Psychometric properties of the Thought-Action Fusion Scale in a Turkish sample.

Science.gov (United States)

Yorulmaz, Orçun; Yilmaz, A Esin; Gençöz, Tülin

2004-10-01

The aim of the present study was to reveal the cross-cultural utility of the Thought-Action Fusion Scale (TAFS; J. Anxiety Disord. 10 (1996) 379). Thought-action fusion (TAF) refers to the tendency to overvalue the significance and the consequences of thoughts. Two hundred and fifty one undergraduate Turkish students participated in the current study. The reliability and validity analyses of the Turkish version of the scale indicated that the TAFS had adequate psychometric properties in a Turkish sample. Consistent with the original TAF, the Turkish version of TAFS revealed two subscales as TAF-Likelihood and TAF-Morality. Reliability analysis showed that TAF Scale and its factors had adequate internal consistencies and split-half reliability coefficients. Confirming the expectations, TAFS scores were found to be significantly and positively correlated with obsessive-compulsive symptoms, responsibility, and guilt measures. Moreover, it was found that people with high obsessive-compulsive symptoms had higher TAFS scores than those with low symptoms.

Energy landscape of all-atom protein-protein interactions revealed by multiscale enhanced sampling.

Directory of Open Access Journals (Sweden)

Kei Moritsugu

2014-10-01

Full Text Available Protein-protein interactions are regulated by a subtle balance of complicated atomic interactions and solvation at the interface. To understand such an elusive phenomenon, it is necessary to thoroughly survey the large configurational space from the stable complex structure to the dissociated states using the all-atom model in explicit solvent and to delineate the energy landscape of protein-protein interactions. In this study, we carried out a multiscale enhanced sampling (MSES simulation of the formation of a barnase-barstar complex, which is a protein complex characterized by an extraordinary tight and fast binding, to determine the energy landscape of atomistic protein-protein interactions. The MSES adopts a multicopy and multiscale scheme to enable for the enhanced sampling of the all-atom model of large proteins including explicit solvent. During the 100-ns MSES simulation of the barnase-barstar system, we observed the association-dissociation processes of the atomistic protein complex in solution several times, which contained not only the native complex structure but also fully non-native configurations. The sampled distributions suggest that a large variety of non-native states went downhill to the stable complex structure, like a fast folding on a funnel-like potential. This funnel landscape is attributed to dominant configurations in the early stage of the association process characterized by near-native orientations, which will accelerate the native inter-molecular interactions. These configurations are guided mostly by the shape complementarity between barnase and barstar, and lead to the fast formation of the final complex structure along the downhill energy landscape.

Quality Control Samples for the Radiological Determination of Tritium in Urine Samples

International Nuclear Information System (INIS)

Ost'pezuk, P.; Froning, M.; Laumen, S.; Richert, I.; Hill, P.

2004-01-01

The radioactive decay product of tritium is a low energy beta that cannot penetrate the outer dead layer of human skin. Therefore , the main hazard associated with tritium is internal exposure. In addition, due to the relatively long half life and short biological half life, tritium must be ingested in large amounts to pose a significant health risk. On the other hand, the internal exposure should be kept as low as practical. For incorporation monitoring of professional radiation workers the quality control is of utmost importance. In the Research Centre Juelich GmbH (FZJ) a considerable fraction of monitoring by excretion analysis relates to the isotope Tritium. Usually an aliquot of an urine sample is mixed with a liquid scintillator and measured in a liquid scintillation counter. Quality control samples in the form of three kind of internal reference samples (blank, reference samples with low activity and reference sample with elevated activity) were prepared from a mixed, Tritium (free) urine samples. 1 ml of these samples were pipetted into a liquid scintillation vial. In the part of theses vials a known amounts of Tritium were added. All these samples were stored at 20 degrees. Based on long term use of all these reference samples it was possible to construct appropriate control charts with the upper and lower alarm limits. Daily use of these reference samples decrease significantly the risk for false results in original urine with no significant increase of the determination time. (Author) 2 refs

A comparison of two common sample preparation techniques for lipid and fatty acid analysis in three different coral morphotypes reveals quantitative and qualitative differences.

Science.gov (United States)

Conlan, Jessica A; Rocker, Melissa M; Francis, David S

2017-01-01

Lipids are involved in a host of biochemical and physiological processes in corals. Therefore, changes in lipid composition reflect changes in the ecology, nutrition, and health of corals. As such, accurate lipid extraction, quantification, and identification is critical to obtain comprehensive insight into a coral's condition. However, discrepancies exist in sample preparation methodology globally, and it is currently unknown whether these techniques generate analogous results. This study compared the two most common sample preparation techniques for lipid analysis in corals: (1) tissue isolation by air-spraying and (2) crushing the coral in toto . Samples derived from each preparation technique were subsequently analysed to quantify lipids and their constituent classes and fatty acids in four common, scleractinian coral species representing three distinct morphotypes ( Acropora millepora , Montipora crassotuberculata , Porites cylindrica , and Pocillopora damicornis ). Results revealed substantial amounts of organic material, including lipids, retained in the skeletons of all species following air-spraying, causing a marked underestimation of total lipid concentration using this method. Moreover, lipid class and fatty acid compositions between the denuded skeleton and sprayed tissue were substantially different. In particular, the majority of the total triacylglycerol and total fatty acid concentrations were retained in the skeleton (55-69% and 56-64%, respectively). As such, the isolated, sprayed tissue cannot serve as a reliable proxy for lipid quantification or identification in the coral holobiont. The in toto crushing method is therefore recommended for coral sample preparation prior to lipid analysis to capture the lipid profile of the entire holobiont, permitting accurate diagnoses of coral condition.

A comparison of two common sample preparation techniques for lipid and fatty acid analysis in three different coral morphotypes reveals quantitative and qualitative differences

Directory of Open Access Journals (Sweden)

Jessica A. Conlan

2017-08-01

Full Text Available Lipids are involved in a host of biochemical and physiological processes in corals. Therefore, changes in lipid composition reflect changes in the ecology, nutrition, and health of corals. As such, accurate lipid extraction, quantification, and identification is critical to obtain comprehensive insight into a coral’s condition. However, discrepancies exist in sample preparation methodology globally, and it is currently unknown whether these techniques generate analogous results. This study compared the two most common sample preparation techniques for lipid analysis in corals: (1 tissue isolation by air-spraying and (2 crushing the coral in toto. Samples derived from each preparation technique were subsequently analysed to quantify lipids and their constituent classes and fatty acids in four common, scleractinian coral species representing three distinct morphotypes (Acropora millepora, Montipora crassotuberculata, Porites cylindrica, and Pocillopora damicornis. Results revealed substantial amounts of organic material, including lipids, retained in the skeletons of all species following air-spraying, causing a marked underestimation of total lipid concentration using this method. Moreover, lipid class and fatty acid compositions between the denuded skeleton and sprayed tissue were substantially different. In particular, the majority of the total triacylglycerol and total fatty acid concentrations were retained in the skeleton (55–69% and 56–64%, respectively. As such, the isolated, sprayed tissue cannot serve as a reliable proxy for lipid quantification or identification in the coral holobiont. The in toto crushing method is therefore recommended for coral sample preparation prior to lipid analysis to capture the lipid profile of the entire holobiont, permitting accurate diagnoses of coral condition.

The effects of parameter estimation on minimizing the in-control average sample size for the double sampling X bar chart

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Michael B.C. Khoo

2013-11-01

Full Text Available The double sampling (DS X bar chart, one of the most widely-used charting methods, is superior for detecting small and moderate shifts in the process mean. In a right skewed run length distribution, the median run length (MRL provides a more credible representation of the central tendency than the average run length (ARL, as the mean is greater than the median. In this paper, therefore, MRL is used as the performance criterion instead of the traditional ARL. Generally, the performance of the DS X bar chart is investigated under the assumption of known process parameters. In practice, these parameters are usually estimated from an in-control reference Phase-I dataset. Since the performance of the DS X bar chart is significantly affected by estimation errors, we study the effects of parameter estimation on the MRL-based DS X bar chart when the in-control average sample size is minimised. This study reveals that more than 80 samples are required for the MRL-based DS X bar chart with estimated parameters to perform more favourably than the corresponding chart with known parameters.

Comparison at the peptide level with post-translational modification consideration reveals more differences between two unenriched samples.

Science.gov (United States)

Yin, Jianrui; Shao, Chen; Jia, Lulu; Gao, Youhe

2014-06-30

In shotgun strategies, peptide sequences are first identified from tandem mass (MS/MS) spectra, and the existence and abundance of the proteins are then inferred from the peptide information. However, the protein inference step can produce errors and a loss of information. To identify the information that is lost using the traditional approaches, this study compared the proteomic data of two leukemia cell lines (Jurkat and K562) at the peptide level with consideration of post-translational modifications (PTMs). The raw files from the two cell lines were searched against the decoy IPI-human database version 3.68, which contains forward and reverse sequences. Then the observed modification name in the results was matched with the modification classification on the Unimod website by a manual search. Only the peptides with 'post-translational' modifications were compared between the two cell lines. After searching the database with consideration of PTMs, a total of 44046 non-redundant peptides were identified in both the Jurkat and K562 cell lines. Of these peptides, even without specific PTM enrichment, 11.43% of them (with at least two spectra in one cell line) existed in different PTM forms between the two cell lines, and 1.73% of the peptides were modified in both cell lines, but with different modifications or possibly on different sites. Comparing proteomic data at the peptide level with consideration of PTMs can reveal more differences between two unenriched samples. Copyright © 2014 John Wiley & Sons, Ltd.

Statistical Analysis Of Tank 19F Floor Sample Results

International Nuclear Information System (INIS)

Harris, S.

2010-01-01

Representative sampling has been completed for characterization of the residual material on the floor of Tank 19F as per the statistical sampling plan developed by Harris and Shine. Samples from eight locations have been obtained from the tank floor and two of the samples were archived as a contingency. Six samples, referred to in this report as the current scrape samples, have been submitted to and analyzed by SRNL. This report contains the statistical analysis of the floor sample analytical results to determine if further data are needed to reduce uncertainty. Included are comparisons with the prior Mantis samples results to determine if they can be pooled with the current scrape samples to estimate the upper 95% confidence limits (UCL95%) for concentration. Statistical analysis revealed that the Mantis and current scrape sample results are not compatible. Therefore, the Mantis sample results were not used to support the quantification of analytes in the residual material. Significant spatial variability among the current scrape sample results was not found. Constituent concentrations were similar between the North and South hemispheres as well as between the inner and outer regions of the tank floor. The current scrape sample results from all six samples fall within their 3-sigma limits. In view of the results from numerous statistical tests, the data were pooled from all six current scrape samples. As such, an adequate sample size was provided for quantification of the residual material on the floor of Tank 19F. The uncertainty is quantified in this report by an UCL95% on each analyte concentration. The uncertainty in analyte concentration was calculated as a function of the number of samples, the average, and the standard deviation of the analytical results. The UCL95% was based entirely on the six current scrape sample results (each averaged across three analytical determinations).

Influence of sampling depth and post-sampling analysis time on the ...

African Journals Online (AJOL)

Bacteriological analysis was carried out for samples taken at water depth and at 1, 6, 12 and 24 hours post-sampling. It was observed that the total and faecal coliform bacteria were significantly higher in the 3 m water depth samples than in the surface water samples (ANOVA, F = 59.41, 26.751, 9.82 (T.C); 46.41, 26.81, ...

Sieve-based device for MALDI sample preparation. I. Influence of sample deposition conditions in oligonucleotide analysis to achieve significant increases in both sensitivity and resolution.

Science.gov (United States)

Molin, Laura; Cristoni, Simone; Crotti, Sara; Bernardi, Luigi Rossi; Seraglia, Roberta; Traldi, Pietro

2008-11-01

Spraying of oligonucleotide-matrix solutions through a stainless steel (ss) sieve (38 microm, 450 mesh) leads to the formation, on the matrix-assisted laser desorption/ionization (MALDI) sample holder, of uniformly distributed microcrystals, well separated from each other. When the resulting sample holder surface is irradiated by laser, abundant molecular species form, with a clear increase in both intensity and resolution with respect to values obtained by 'Dried Droplet', 'Double Layer', and 'Sandwich' deposition methods. In addition, unlike the usual situation, the sample is perfectly homogeneous, and identical spectra are obtained by irradiating different areas. On one hand, the data indicate that this method is highly effective for oligonucleotide MALDI analysis, and on the other, that it can be validly employed for fully automated MALDI procedures.

Algorithm for computing significance levels using the Kolmogorov-Smirnov statistic and valid for both large and small samples

Energy Technology Data Exchange (ETDEWEB)

Kurtz, S.E.; Fields, D.E.

1983-10-01

The KSTEST code presented here is designed to perform the Kolmogorov-Smirnov one-sample test. The code may be used as a stand-alone program or the principal subroutines may be excerpted and used to service other programs. The Kolmogorov-Smirnov one-sample test is a nonparametric goodness-of-fit test. A number of codes to perform this test are in existence, but they suffer from the inability to provide meaningful results in the case of small sample sizes (number of values less than or equal to 80). The KSTEST code overcomes this inadequacy by using two distinct algorithms. If the sample size is greater than 80, an asymptotic series developed by Smirnov is evaluated. If the sample size is 80 or less, a table of values generated by Birnbaum is referenced. Valid results can be obtained from KSTEST when the sample contains from 3 to 300 data points. The program was developed on a Digital Equipment Corporation PDP-10 computer using the FORTRAN-10 language. The code size is approximately 450 card images and the typical CPU execution time is 0.19 s.

[Addictive, criminal and psychopathological profile of a sample of women in prison].

Science.gov (United States)

Villagrá Lanza, Patricia; González Menéndez, Ana; Fernández García, Paula; Casares, Ma José; Martín Martín, José Luis; Rodríguez Lamelas, Filomena

2011-01-01

This study examines the addictive, criminal and psychopathological profile of a sample of 59 women incarcerated in the Villabona prison in Asturias (a region in northern Spain). The instruments administered were the EuropASI, the SCL-90-R and a semi-structured interview. Results showed that the profile is a young, single women with family dependents serving an average of 5 years' imprisonment. Of the total sample, 64.4% met criteria for a substance abuse disorder. We found a statistically significant relationship between the variables use-nonuse and type of crime: women who used substances had committed the most crimes against property and against the socioeconomic order. As regards psychopathology, 44.06% of the sample fulfilled the requirements for clinical case according to Derogatis' (1994) criteria. The results of the SCL-90-R showed that the predominant psychological disorders were, in the following order, depression, somatization, obsessive-compulsive disorder and paranoid ideation. Moreover, in the group of female users, 47.4% had dual pathology. Our results revealed a statistically significant relationship between clinical case and substance use. Finally, statistically significant differences were found between the user and nonuser groups in the EuropASI severity profile. Highest scores were found for the medical, psychiatric and family areas in the user group.

Expression status and clinical significance of lncRNA APPAT in the progression of atherosclerosis

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Fanming Meng

2018-01-01

Full Text Available Background Long non-coding RNAs (lncRNAs have been reported to modulate cardiovascular diseases, and expression dynamics of lncRNAs in the bloodstream were proposed to be potential biomarkers for clinical diagnosis. However, few cardiovascular diseases-related circulating lncRNAs were identified and their prediction power has not been investigated in depth. Here we report a new circulating lncRNA, atherosclerotic plaque pathogenesis associated transcript (APPAT, and evaluated its role and predicting ability in atherosclerotic development. Methods APPAT was analyzed and screened by high-throughput sequencing, and then detected in vitro and in vivo. Immunofluorescence-fluorescence in situ hybridization (IF-FISH was utilized to explore distribution and subcellular location of APPAT. The expressing alteration of APPAT in samples of healthy and pathological coronary artery was explored further. We also assessed the level of circulating APPAT in blood samples from healthy individuals, and patients with angina pectoris (AP or myocardial infarction (MI. Additionally, we predicted and validated microRNA targets of APPAT, then showed the expression level of a candidate target which was primarily measured in human VSMCs cell line, coronary artery, and blood samples. Lastly, we examined the potential indicating ability of APPAT for the risk of AP or MI. Results APPAT showed significant reduction in ox-LDL treated human VSMCs in vitro. It enriched in contractile VSMCs of artery tunica media and mainly existed in cytoplasm. Significant down-regulation of APPAT was found in coronary artery samples with severe stenosis. More importantly, we observed decreased expression of APPAT in blood samples accompanying disease progression. ROC and correlation analyses further verified the relatively high predicting ability of APPAT. We also observed the predicted miRNA exhibited opposite expression direction to that of APPAT. Conclusions This study revealed that

IAEA Sampling Plan

Energy Technology Data Exchange (ETDEWEB)

Geist, William H. [Los Alamos National Lab. (LANL), Los Alamos, NM (United States)

2017-09-15

The objectives for this presentation are to describe the method that the IAEA uses to determine a sampling plan for nuclear material measurements; describe the terms detection probability and significant quantity; list the three nuclear materials measurement types; describe the sampling method applied to an item facility; and describe multiple method sampling.

Significant Locus and Metabolic Genetic Correlations Revealed in Genome-Wide Association Study of Anorexia Nervosa.

Science.gov (United States)

Duncan, Laramie; Yilmaz, Zeynep; Gaspar, Helena; Walters, Raymond; Goldstein, Jackie; Anttila, Verneri; Bulik-Sullivan, Brendan; Ripke, Stephan; Thornton, Laura; Hinney, Anke; Daly, Mark; Sullivan, Patrick F; Zeggini, Eleftheria; Breen, Gerome; Bulik, Cynthia M

2017-09-01

The authors conducted a genome-wide association study of anorexia nervosa and calculated genetic correlations with a series of psychiatric, educational, and metabolic phenotypes. Following uniform quality control and imputation procedures using the 1000 Genomes Project (phase 3) in 12 case-control cohorts comprising 3,495 anorexia nervosa cases and 10,982 controls, the authors performed standard association analysis followed by a meta-analysis across cohorts. Linkage disequilibrium score regression was used to calculate genome-wide common variant heritability (single-nucleotide polymorphism [SNP]-based heritability [h 2 SNP ]), partitioned heritability, and genetic correlations (r g ) between anorexia nervosa and 159 other phenotypes. Results were obtained for 10,641,224 SNPs and insertion-deletion variants with minor allele frequencies >1% and imputation quality scores >0.6. The h 2 SNP of anorexia nervosa was 0.20 (SE=0.02), suggesting that a substantial fraction of the twin-based heritability arises from common genetic variation. The authors identified one genome-wide significant locus on chromosome 12 (rs4622308) in a region harboring a previously reported type 1 diabetes and autoimmune disorder locus. Significant positive genetic correlations were observed between anorexia nervosa and schizophrenia, neuroticism, educational attainment, and high-density lipoprotein cholesterol, and significant negative genetic correlations were observed between anorexia nervosa and body mass index, insulin, glucose, and lipid phenotypes. Anorexia nervosa is a complex heritable phenotype for which this study has uncovered the first genome-wide significant locus. Anorexia nervosa also has large and significant genetic correlations with both psychiatric phenotypes and metabolic traits. The study results encourage a reconceptualization of this frequently lethal disorder as one with both psychiatric and metabolic etiology.

Influence of Sampling Practices on the Appearance of DNA Image Histograms of Prostate Cells in FNAB Samples

Directory of Open Access Journals (Sweden)

Abdelbaset Buhmeida

1999-01-01

Full Text Available Twenty‐one fine needle aspiration biopsies (FNAB of the prostate, diagnostically classified as definitely malignant, were studied. The Papanicolaou or H&E stained samples were destained and then stained for DNA with the Feulgen reaction. DNA cytometry was applied after different sampling rules. The histograms varied according to the sampling rule applied. Because free cells between cell groups were easier to measure than cells in the cell groups, two sampling rules were tested in all samples: (i cells in the cell groups were measured, and (ii free cells between cell groups were measured. Abnormal histograms were more common after the sampling rule based on free cells, suggesting that abnormal patterns are best revealed through the free cells in these samples. The conclusions were independent of the applied histogram interpretation method.

Rare human papillomavirus 16 E6 variants reveal significant oncogenic potential

Directory of Open Access Journals (Sweden)

Tommasino Massimo

2011-06-01

Full Text Available Abstract The aim of this study was to determine whether low prevalence human papillomavirus (HPV 16 E6 variants differ from high prevalence types in their functional abilities. We evaluated functions relevant to carcinogenesis for the rarely-detected European variants R8Q, R10G and R48W as compared to the commonly detected L83V. Human immortalized keratinocytes (NIKS stably transduced with the E6 variants were used in most functional assays. Low and high prevalence E6 variants displayed similar abilities in abrogation of growth arrest and inhibition of p53 elevation induced by actinomycin D. Differences were detected in the abilities to dysregulate stratification and differentiation of NIKS in organotypic raft cultures, modulate detachment induced apoptosis (anoikis and hyperactivate Wnt signaling. No distinctive phenotype could be assigned to include all rare variants. Like L83V, raft cultures derived from variants R10G and R48W similarly induced hyperplasia and aberrantly expressed keratin 5 in the suprabasal compartment with significantly lower expression of keratin 10. Unlike L83V, both variants, and particularly R48W, induced increased levels of anoikis upon suspension in semisolid medium. R8Q induced a unique phenotype characterized by thin organotypic raft cultures, low expression of keratin 10, and high expression of keratins 5 and 14 throughout all raft layers. Interestingly, in a reporter based assay R8Q exhibited a higher ability to augment TCF/β-catenin transcription. The data suggests that differences in E6 variant prevalence in cervical carcinoma may not be related to the carcinogenic potential of the E6 protein.

Discovering the Significance of Scientific Design Practice

DEFF Research Database (Denmark)

Pries-Heje, Jan; Baskerville, Richard

2016-01-01

This paper discusses and defines the achievement of significance in design science research. We review the values and processes of old-science and how this mode of science attacks the complexity of scientific knowledge production through analysis. We then explain how new-science attacks...... the complexity of scientific knowledge production through synthesis. The work argues that significance of the new-science contribution in design science can be obfuscated when wrapped in old-science. This understanding helps reveal how new-science, such as design science research, constitutes its significance...

The Relationship between Racial Identity and Perceived Significance of the Election of President Barack Obama among African American Mothers.

Science.gov (United States)

Franco, Marisa; Smith-Bynum, Mia

2016-01-01

African American women's racial identity is a major determinant for how they interpret the world around them, yet there is little research examining how specific aspects of racial identity are linked with attitudes about an event that has been highly significant for African-Americans: the election of President Barack Obama. The current study examined the relationship between African American mothers' racial identity and their perceived significance of the election of President Barack Obama as an indicator of reduced systemic and actual racism for African Americans, using a sample of 110 African American mothers residing in a Northeastern metropolitan area. Results revealed that racial centrality and assimilation positively predicted perceived significance of President Obama's election for diminishing racism. Implications and future directions are discussed.

A simulative comparison of respondent driven sampling with incentivized snowball sampling--the "strudel effect".

Science.gov (United States)

Gyarmathy, V Anna; Johnston, Lisa G; Caplinskiene, Irma; Caplinskas, Saulius; Latkin, Carl A

2014-02-01

Respondent driven sampling (RDS) and incentivized snowball sampling (ISS) are two sampling methods that are commonly used to reach people who inject drugs (PWID). We generated a set of simulated RDS samples on an actual sociometric ISS sample of PWID in Vilnius, Lithuania ("original sample") to assess if the simulated RDS estimates were statistically significantly different from the original ISS sample prevalences for HIV (9.8%), Hepatitis A (43.6%), Hepatitis B (Anti-HBc 43.9% and HBsAg 3.4%), Hepatitis C (87.5%), syphilis (6.8%) and Chlamydia (8.8%) infections and for selected behavioral risk characteristics. The original sample consisted of a large component of 249 people (83% of the sample) and 13 smaller components with 1-12 individuals. Generally, as long as all seeds were recruited from the large component of the original sample, the simulation samples simply recreated the large component. There were no significant differences between the large component and the entire original sample for the characteristics of interest. Altogether 99.2% of 360 simulation sample point estimates were within the confidence interval of the original prevalence values for the characteristics of interest. When population characteristics are reflected in large network components that dominate the population, RDS and ISS may produce samples that have statistically non-different prevalence values, even though some isolated network components may be under-sampled and/or statistically significantly different from the main groups. This so-called "strudel effect" is discussed in the paper. Copyright © 2013 Elsevier Ireland Ltd. All rights reserved.

[Mastitis revealing Churg-Strauss syndrome].

Science.gov (United States)

Dannepond, C; Le Fourn, E; de Muret, A; Ouldamer, L; Carmier, D; Machet, L

2014-01-01

Churg-Strauss syndrome often involves the skin, and this may sometimes reveal the disease. A 25-year-old woman was referred to a gynaecologist for inflammation of the right breast with breast discharge. Cytological analysis of the liquid showed numerous inflammatory cells, particularly polymorphonuclear eosinophils and neutrophils. Ultrasound examination of the breast was consistent with galactophoritis. CRP was normal, and hypereosinophilia was seen. The patient was subsequently referred to a dermatology unit. Skin examination revealed inflammation of the entire breast, which was painful, warm and erythematous; the border was oedematous with blisters. Necrotic lesions were also present on the thumbs and knees. Skin biopsy of the breast showed a dermal infiltrate with abundant infiltrate of polymorphonuclear eosinophils, including patchy necrosis and intraepidermal vesicles. Histological examination of a biopsy sample from a thumb revealed eosinophilic granuloma and leukocytoclastic vasculitis. The patient was also presenting asthma, pulmonary infiltrates and mononeuropathy at L3, consistent with Churg-Strauss syndrome. Breast involvement in Churg-Strauss syndrome is very rare (only one other case has been reported). This is the first case in which the breast condition revealed the disease. Cutaneous involvement of the breast is, however, also compatible with Wells' cellulitis. The lesions quickly disappeared with 1mg/kg/d oral prednisolone. Copyright © 2013 Elsevier Masson SAS. All rights reserved.

Random Sampling of Squamate Reptiles in Spanish Natural Reserves Reveals the Presence of Novel Adenoviruses in Lacertids (Family Lacertidae) and Worm Lizards (Amphisbaenia).

Science.gov (United States)

Szirovicza, Leonóra; López, Pilar; Kopena, Renáta; Benkő, Mária; Martín, José; Pénzes, Judit J

2016-01-01

Here, we report the results of a large-scale PCR survey on the prevalence and diversity of adenoviruses (AdVs) in samples collected randomly from free-living reptiles. On the territories of the Guadarrama Mountains National Park in Central Spain and of the Chafarinas Islands in North Africa, cloacal swabs were taken from 318 specimens of eight native species representing five squamate reptilian families. The healthy-looking animals had been captured temporarily for physiological and ethological examinations, after which they were released. We found 22 AdV-positive samples in representatives of three species, all from Central Spain. Sequence analysis of the PCR products revealed the existence of three hitherto unknown AdVs in 11 Carpetane rock lizards (Iberolacerta cyreni), nine Iberian worm lizards (Blanus cinereus), and two Iberian green lizards (Lacerta schreiberi), respectively. Phylogeny inference showed every novel putative virus to be a member of the genus Atadenovirus. This is the very first description of the occurrence of AdVs in amphisbaenian and lacertid hosts. Unlike all squamate atadenoviruses examined previously, two of the novel putative AdVs had A+T rich DNA, a feature generally deemed to mirror previous host switch events. Our results shed new light on the diversity and evolution of atadenoviruses.

Random Sampling of Squamate Reptiles in Spanish Natural Reserves Reveals the Presence of Novel Adenoviruses in Lacertids (Family Lacertidae and Worm Lizards (Amphisbaenia.

Directory of Open Access Journals (Sweden)

Leonóra Szirovicza

Full Text Available Here, we report the results of a large-scale PCR survey on the prevalence and diversity of adenoviruses (AdVs in samples collected randomly from free-living reptiles. On the territories of the Guadarrama Mountains National Park in Central Spain and of the Chafarinas Islands in North Africa, cloacal swabs were taken from 318 specimens of eight native species representing five squamate reptilian families. The healthy-looking animals had been captured temporarily for physiological and ethological examinations, after which they were released. We found 22 AdV-positive samples in representatives of three species, all from Central Spain. Sequence analysis of the PCR products revealed the existence of three hitherto unknown AdVs in 11 Carpetane rock lizards (Iberolacerta cyreni, nine Iberian worm lizards (Blanus cinereus, and two Iberian green lizards (Lacerta schreiberi, respectively. Phylogeny inference showed every novel putative virus to be a member of the genus Atadenovirus. This is the very first description of the occurrence of AdVs in amphisbaenian and lacertid hosts. Unlike all squamate atadenoviruses examined previously, two of the novel putative AdVs had A+T rich DNA, a feature generally deemed to mirror previous host switch events. Our results shed new light on the diversity and evolution of atadenoviruses.

1H NMR-based metabolic profiling reveals inherent biological variation in yeast and nematode model systems

International Nuclear Information System (INIS)

Szeto, Samuel S. W.; Reinke, Stacey N.; Lemire, Bernard D.

2011-01-01

The application of metabolomics to human and animal model systems is poised to provide great insight into our understanding of disease etiology and the metabolic changes that are associated with these conditions. However, metabolomic studies have also revealed that there is significant, inherent biological variation in human samples and even in samples from animal model systems where the animals are housed under carefully controlled conditions. This inherent biological variability is an important consideration for all metabolomics analyses. In this study, we examined the biological variation in 1 H NMR-based metabolic profiling of two model systems, the yeast Saccharomyces cerevisiae and the nematode Caenorhabditis elegans. Using relative standard deviations (RSD) as a measure of variability, our results reveal that both model systems have significant amounts of biological variation. The C. elegans metabolome possesses greater metabolic variance with average RSD values of 29 and 39%, depending on the food source that was used. The S. cerevisiae exometabolome RSD values ranged from 8% to 12% for the four strains examined. We also determined whether biological variation occurs between pairs of phenotypically identical yeast strains. Multivariate statistical analysis allowed us to discriminate between pair members based on their metabolic phenotypes. Our results highlight the variability of the metabolome that exists even for less complex model systems cultured under defined conditions. We also highlight the efficacy of metabolic profiling for defining these subtle metabolic alterations.

Random sampling of the Central European bat fauna reveals the existence of numerous hitherto unknown adenoviruses.

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Vidovszky, Márton; Kohl, Claudia; Boldogh, Sándor; Görföl, Tamás; Wibbelt, Gudrun; Kurth, Andreas; Harrach, Balázs

2015-12-01

From over 1250 extant species of the order Chiroptera, 25 and 28 are known to occur in Germany and Hungary, respectively. Close to 350 samples originating from 28 bat species (17 from Germany, 27 from Hungary) were screened for the presence of adenoviruses (AdVs) using a nested PCR that targets the DNA polymerase gene of AdVs. An additional PCR was designed and applied to amplify a fragment from the gene encoding the IVa2 protein of mastadenoviruses. All German samples originated from organs of bats found moribund or dead. The Hungarian samples were excrements collected from colonies of known bat species, throat or rectal swab samples, taken from live individuals that had been captured for faunistic surveys and migration studies, as well as internal organs of dead specimens. Overall, 51 samples (14.73%) were found positive. We detected 28 seemingly novel and six previously described bat AdVs by sequencing the PCR products. The positivity rate was the highest among the guano samples of bat colonies. In phylogeny reconstructions, the AdVs detected in bats clustered roughly, but not perfectly, according to the hosts' families (Vespertilionidae, Rhinolophidae, Hipposideridae, Phyllostomidae and Pteropodidae). In a few cases, identical sequences were derived from animals of closely related species. On the other hand, some bat species proved to harbour more than one type of AdV. The high prevalence of infection and the large number of chiropteran species worldwide make us hypothesise that hundreds of different yet unknown AdV types might circulate in bats.

Types of non-probabilistic sampling used in marketing research. „Snowball” sampling

OpenAIRE

Manuela Rozalia Gabor

2007-01-01

A significant way of investigating a firm’s market is the statistical sampling. The sampling typology provides a non / probabilistic models of gathering information and this paper describes thorough information related to network sampling, named “snowball” sampling. This type of sampling enables the survey of occurrence forms concerning the decision power within an organisation and of the interpersonal relation network governing a certain collectivity, a certain consumer panel. The snowball s...

Information sampling behavior with explicit sampling costs

Science.gov (United States)

Juni, Mordechai Z.; Gureckis, Todd M.; Maloney, Laurence T.

2015-01-01

The decision to gather information should take into account both the value of information and its accrual costs in time, energy and money. Here we explore how people balance the monetary costs and benefits of gathering additional information in a perceptual-motor estimation task. Participants were rewarded for touching a hidden circular target on a touch-screen display. The target’s center coincided with the mean of a circular Gaussian distribution from which participants could sample repeatedly. Each “cue” — sampled one at a time — was plotted as a dot on the display. Participants had to repeatedly decide, after sampling each cue, whether to stop sampling and attempt to touch the hidden target or continue sampling. Each additional cue increased the participants’ probability of successfully touching the hidden target but reduced their potential reward. Two experimental conditions differed in the initial reward associated with touching the hidden target and the fixed cost per cue. For each condition we computed the optimal number of cues that participants should sample, before taking action, to maximize expected gain. Contrary to recent claims that people gather less information than they objectively should before taking action, we found that participants over-sampled in one experimental condition, and did not significantly under- or over-sample in the other. Additionally, while the ideal observer model ignores the current sample dispersion, we found that participants used it to decide whether to stop sampling and take action or continue sampling, a possible consequence of imperfect learning of the underlying population dispersion across trials. PMID:27429991

Environmental sampling of Ceratonia siliqua (carob) trees in Spain reveals the presence of the rare Cryptococcus gattii genotype AFLP7/VGIV.

Science.gov (United States)

Linares, Carlos; Colom, María Francisca; Torreblanca, Marina; Esteban, Violeta; Romera, Álvaro; Hagen, Ferry

2015-01-01

Cryptococcus gattii is a pathogenic basidiomycetous yeast that is emerging in temperate climate zones worldwide. C. gattii has repetitively been isolated from numerous tree species. Ongoing environmental sampling and molecular characterization is essential to understand the presence of this primary pathogenic microorganism in the Mediterranean environment. To report the first isolation of the rare C. gattii genotype AFLP7/VGIV from the environment in Europe. Samples were collected from woody debris of carob trees (Ceratonia siliqua) and olive trees (Olea europaea) in El Perelló, Tarragona, Spain. Cryptococcus species were further characterized by using URA5-RFLP, MALDI-TOF, AFLP and MLST. The antifungal susceptibility profile to amphotericin B, 5-fluorocytosine, fluconazole, itraconazole, posaconazole and voriconazole was determined using Sensititre Yeast One and E-test. Cultures from one carob tree revealed the presence of ten Cryptococcus-like colonies. One colony was identified as C. gattii, and subsequent molecular characterization showed that it was an α mating-type that belonged to the rare genotype AFLP7/VGIV. Antifungal susceptibility testing showed values within the range of sensitivity described for other isolates of the same genotype and within the epidemiological cutoff values for this species. The isolation of the rare C. gattii genotype AFLP7/VGIV in Spain is the first report in the European environment, implying the possible presence in other regions of the Mediterranean area, and underlines that clinicians must be aware for C. gattii infections in healthy individuals. Copyright © 2014 Revista Iberoamericana de Micología. Published by Elsevier Espana. All rights reserved.

Metal and Isotope Analysis of Bird Feathers in a Contaminated Estuary Reveals Bioaccumulation, Biomagnification, and Potential Toxic Effects.

Science.gov (United States)

Einoder, L D; MacLeod, C K; Coughanowr, C

2018-07-01

The Derwent estuary, in south east Tasmania, is highly contaminated with heavy metals, mainly due to past industrial pollution. This study sought to determine the extent of contamination, bioaccumulation, and biomagnification in the resident bird community and therefore to infer the potential for adverse effects in birds. Thirteen metals were measured from breast feathers (n = 51 individuals) of eight sympatric species of aquatic bird. Stable carbon (δ 13 C) and nitrogen (δ 15 N) isotopes were used to identify dietary sources of contaminants, trophic level, and potential biomagnification through food chains. Generalised linear models revealed that metal burdens were often poorly correlated with δ 13 C, indicating their uptake from a range of freshwater, brackish, and marine carbon sources-not surprising due to widespread contamination across the tidal estuary. Feather mercury increased significantly with trophic level (inferred from δ 15 N). White-bellied Sea-eagle Haliaeetus leucogaster samples contained 240 times more mercury than feral Goose Anser cygnoides. Feather arsenic and copper concentrations were significantly higher in birds feeding lower in the food chain. For several piscivorous species, both chick and adults were sampled revealing significantly higher feather mercury, zinc, and selenium in adults. Feathers from birds found dead along the banks of the estuary had significantly higher lead loads than from live birds, and numerous individuals had levels of mercury, zinc, and lead above toxic thresholds reported in other studies. These results highlight the need to include biota from higher trophic levels in contaminant monitoring programs to understand fully the fate and broader implications of contaminants in the environment.

Isotope analytics for the evaluation of the feeding influence on the isotope ratio in beef samples

International Nuclear Information System (INIS)

Herwig, Nadine

2010-01-01

Information about the origin of food and associated production systems has a high significance for food control. An extremely promising approach to obtain such information is the determination of isotope ratios of different elements. In this study the correlation of the isotope ratios C-13/C-12, N-15/N-14, Mg-25/Mg-24, and Sr-87/Sr-86 in bovine samples (milk and urine) and the corresponding isotope ratios in feed was investigated. It was shown that in the bovine samples all four isotope ratios correlate with the isotope composition of the feed. The isotope ratios of strontium and magnesium have the advantage that they directly reflect the isotope ratios of the ingested feed since there is no isotope fractionation in the bovine organism which is in contrast to the case of carbon and nitrogen isotope ratios. From the present feeding study it is evident, that a feed change leads to a significant change in the delta C-13 values in milk and urine within 10 days already. For the deltaN-15 values the feed change was only visible in the bovine urine after 49 days. Investigations of cows from two different regions (Berlin/Germany and Goestling/Austria) kept at different feeding regimes revealed no differences in the N-15/N-14 and Mg-26/Mg-24 isotope ratios. The strongest correlation between the isotope ratio of the bovine samples and the kind of ingested feed was observed for the carbon isotope ratio. With this ratio even smallest differences in the feed composition were traceable in the bovine samples. Since different regions usually coincide with different feeding regimes, carbon isotope ratios can be used to distinguish bovine samples from different regions if the delta C-13 values of the ingested feed are different. Furthermore, the determination of strontium isotope ratios revealed significant differences between bovine and feed samples of Berlin and Goestling due to the different geologic realities. Hence the carbon and strontium isotope ratios allow the best

A comparison of passive and active acoustic sampling for a bat community impacted by White-nose syndrome

Science.gov (United States)

Coleman, Laci S.; Ford, W. Mark; Dobony, Christopher A.; Britzke, Eric R.

2014-01-01

In the summers of 2011 and 2012, we compared passive and active acoustic sampling for bats at 31 sites at Fort Drum Military Installation, New York. We defined active sampling as acoustic sampling that occurred in 30-min intervals between the hours of sunset and 0200 with a user present to manipulate the directionality of the microphone. We defined passive sampling as acoustic sampling that occurred over a 12-h period (1900–0700 hours) without a user present and with the microphone set in a predetermined direction. We detected seven of the nine possible species at Fort Drum, including the federally endangered Indiana bat Myotis sodalis, the proposed-for-listing northern bat M. septentrionalis, the little brown bat M. lucifugus, and the big brown bat Eptesicus fuscus, which are impacted by white-nose syndrome (WNS); and the eastern red bat Lasiurus borealis, the hoary bat L. cinereus, and the silver-haired bat Lasionycteris noctivagans, which are not known to be impacted by WNS. We did not detect two additional WNS-impacted species known to historically occur in the area: the eastern small-footed bat Myotis leibii and the tri-colored bat Perimyotis subflavus. Single-season occupancy models revealed lower detection probabilities of all detected species using active sampling versus passive sampling. Additionally, overall detection probabilities declined in detected WNS-impacted species between years. A paired t-test of simultaneous sampling on 21 occasions revealed that overall recorded foraging activity per hour was greater using active than passive sampling for big brown bats and greater using passive than active sampling for little brown bats. There was no significant difference in recorded activity between methods for other WNS-impacted species, presumably because these species have been so reduced in number that their “apparency” on the landscape is lower. Finally, a cost analysis of standard passive and active sampling protocols revealed that passive

Gene expression analysis of skin grafts and cultured keratinocytes using synthetic RNA normalization reveals insights into differentiation and growth control.

Science.gov (United States)

Katayama, Shintaro; Skoog, Tiina; Jouhilahti, Eeva-Mari; Siitonen, H Annika; Nuutila, Kristo; Tervaniemi, Mari H; Vuola, Jyrki; Johnsson, Anna; Lönnerberg, Peter; Linnarsson, Sten; Elomaa, Outi; Kankuri, Esko; Kere, Juha

2015-06-25

Keratinocytes (KCs) are the most frequent cells in the epidermis, and they are often isolated and cultured in vitro to study the molecular biology of the skin. Cultured primary cells and various immortalized cells have been frequently used as skin models but their comparability to intact skin has been questioned. Moreover, when analyzing KC transcriptomes, fluctuation of polyA+ RNA content during the KCs' lifecycle has been omitted. We performed STRT RNA sequencing on 10 ng samples of total RNA from three different sample types: i) epidermal tissue (split-thickness skin grafts), ii) cultured primary KCs, and iii) HaCaT cell line. We observed significant variation in cellular polyA+ RNA content between tissue and cell culture samples of KCs. The use of synthetic RNAs and SAMstrt in normalization enabled comparison of gene expression levels in the highly heterogenous samples and facilitated discovery of differences between the tissue samples and cultured cells. The transcriptome analysis sensitively revealed genes involved in KC differentiation in skin grafts and cell cycle regulation related genes in cultured KCs and emphasized the fluctuation of transcription factors and non-coding RNAs associated to sample types. The epidermal keratinocytes derived from tissue and cell culture samples showed highly different polyA+ RNA contents. The use of SAMstrt and synthetic RNA based normalization allowed the comparison between tissue and cell culture samples and thus proved to be valuable tools for RNA-seq analysis with translational approach. Transciptomics revealed clear difference both between tissue and cell culture samples and between primary KCs and immortalized HaCaT cells.

Direct analysis by time-of-flight secondary ion mass spectrometry reveals action of bacterial laccase-mediator systems on both hardwood and softwood samples.

Science.gov (United States)

Goacher, Robyn E; Braham, Erick J; Michienzi, Courtney L; Flick, Robert M; Yakunin, Alexander F; Master, Emma R

2017-12-29

The modification and degradation of lignin play a vital role in carbon cycling as well as production of biofuels and bioproducts. The possibility of using bacterial laccases for the oxidation of lignin offers a route to utilize existing industrial protein expression techniques. However, bacterial laccases are most frequently studied on small model compounds that do not capture the complexity of lignocellulosic materials. This work studied the action of laccases from Bacillus subtilis and Salmonella typhimurium (EC 1.10.3.2) on ground wood samples from yellow birch (Betula alleghaniensis) and red spruce (Picea rubens). The ability of bacterial laccases to modify wood can be facilitated by small molecule mediators. Herein, 2,2'-azino-bis(3-ethylbenzothiazoline-6-sulphonic acid) (ABTS), gallic acid and sinapic acid mediators were tested. Direct analysis of the wood samples was achieved by time-of-flight secondary ion mass spectrometry (ToF-SIMS), a surface sensitive mass spectrometry technique that has characteristic peaks for H, G and S lignin. The action of the bacterial laccases on both wood samples was demonstrated and revealed a strong mediator influence. The ABTS mediator led to delignification, evident in an overall increase of polysaccharide peaks in the residual solid, along with equal loss of G and S-lignin peaks. The gallic acid mediator demonstrated minimal laccase activity. Meanwhile, the sinapic acid mediator altered the S/G peak ratio consistent with mediator attaching to the wood solids. The current investigation demonstrates the action of bacterial laccase-mediator systems directly on woody materials, and the potential of using ToF-SIMS to uncover the fundamental and applied role of bacterial enzymes in lignocellulose conversion. © 2017 Scandinavian Plant Physiology Society.

Approach-Induced Biases in Human Information Sampling.

Directory of Open Access Journals (Sweden)

Laurence T Hunt

2016-11-01

Full Text Available Information sampling is often biased towards seeking evidence that confirms one's prior beliefs. Despite such biases being a pervasive feature of human behavior, their underlying causes remain unclear. Many accounts of these biases appeal to limitations of human hypothesis testing and cognition, de facto evoking notions of bounded rationality, but neglect more basic aspects of behavioral control. Here, we investigated a potential role for Pavlovian approach in biasing which information humans will choose to sample. We collected a large novel dataset from 32,445 human subjects, making over 3 million decisions, who played a gambling task designed to measure the latent causes and extent of information-sampling biases. We identified three novel approach-related biases, formalized by comparing subject behavior to a dynamic programming model of optimal information gathering. These biases reflected the amount of information sampled ("positive evidence approach", the selection of which information to sample ("sampling the favorite", and the interaction between information sampling and subsequent choices ("rejecting unsampled options". The prevalence of all three biases was related to a Pavlovian approach-avoid parameter quantified within an entirely independent economic decision task. Our large dataset also revealed that individual differences in the amount of information gathered are a stable trait across multiple gameplays and can be related to demographic measures, including age and educational attainment. As well as revealing limitations in cognitive processing, our findings suggest information sampling biases reflect the expression of primitive, yet potentially ecologically adaptive, behavioral repertoires. One such behavior is sampling from options that will eventually be chosen, even when other sources of information are more pertinent for guiding future action.

STATISTICAL ANALYSIS OF TANK 18F FLOOR SAMPLE RESULTS

Energy Technology Data Exchange (ETDEWEB)

Harris, S.

2010-09-02

Representative sampling has been completed for characterization of the residual material on the floor of Tank 18F as per the statistical sampling plan developed by Shine [1]. Samples from eight locations have been obtained from the tank floor and two of the samples were archived as a contingency. Six samples, referred to in this report as the current scrape samples, have been submitted to and analyzed by SRNL [2]. This report contains the statistical analysis of the floor sample analytical results to determine if further data are needed to reduce uncertainty. Included are comparisons with the prior Mantis samples results [3] to determine if they can be pooled with the current scrape samples to estimate the upper 95% confidence limits (UCL{sub 95%}) for concentration. Statistical analysis revealed that the Mantis and current scrape sample results are not compatible. Therefore, the Mantis sample results were not used to support the quantification of analytes in the residual material. Significant spatial variability among the current sample results was not found. Constituent concentrations were similar between the North and South hemispheres as well as between the inner and outer regions of the tank floor. The current scrape sample results from all six samples fall within their 3-sigma limits. In view of the results from numerous statistical tests, the data were pooled from all six current scrape samples. As such, an adequate sample size was provided for quantification of the residual material on the floor of Tank 18F. The uncertainty is quantified in this report by an upper 95% confidence limit (UCL{sub 95%}) on each analyte concentration. The uncertainty in analyte concentration was calculated as a function of the number of samples, the average, and the standard deviation of the analytical results. The UCL{sub 95%} was based entirely on the six current scrape sample results (each averaged across three analytical determinations).

The presence and prognostic significance of human papillomavirus in squamous cell carcinoma of the larynx.

Science.gov (United States)

Erkul, Evren; Yilmaz, Ismail; Narli, Gizem; Babayigit, Mustafa Alparslan; Gungor, Atila; Demirel, Dilaver

2017-07-01

The aim of the present study was to evaluate the role of HPV in laryngeal squamous cell carcinoma and correlate it with patients' clinicopathological data. In total, 78 laryngeal squamous cell carcinoma patients enrolled in this study. The presence of genotype-specific HPV DNA was evaluated using Genotyping Assay in formalin-fixed paraffin-embedded tissue which was diagnosed between 2005 and 2015. All samples were also evaluated for p16 immunohistochemical staining. HPV DNA and p16 status were assessed in terms of location, smoking, alcohol consumption, lymph node status, tumor stage, overall survival, disease-free survival, perineural invasion, and vascular invasion retrospectively. Five test samples were excluded from the study due to inadequate deoxyribonucleic acid purity. HPV DNA was detected in 19 of 73 (26.02%) in patients with laryngeal squamous cell carcinoma. Human papilloma virus genotyping revealed double human papilloma virus in one case (types 16 and 59) and HPV 16 in the remaining cases. Although HPV-positive cases showed slightly better 3 years survival than HPV-negative ones, this finding was not statistically significant (overall survival p = 0.417, HPV positive: 92.3%, HPV negative: 81.4%, and disease-free survival p = 0.526, HPV positive: 93.8%, HPV negative: 80.9%). The presence of HPV DNA was not significantly associated with any clinicopathological features (p > 0.05). Among 73 patients, only 4 had an immunohistochemical staining of p16 and these patients were also HPV DNA 16 positive. Although our study results revealed a slightly better survival in patients with HPV DNA positivity for HPV 16 compared to the negative ones, the difference was not statistically significant. However, an increasing rate in especially high-risk-type HPV-16 prevalence in laryngeal squamous cell carcinoma by RT-PCR method was observed compared to our previous study. Although the presence of HPV in laryngeal SCCs seems to be associated with slightly better

Manual versus automated blood sampling

DEFF Research Database (Denmark)

Teilmann, A C; Kalliokoski, Otto; Sørensen, Dorte B

2014-01-01

Facial vein (cheek blood) and caudal vein (tail blood) phlebotomy are two commonly used techniques for obtaining blood samples from laboratory mice, while automated blood sampling through a permanent catheter is a relatively new technique in mice. The present study compared physiological parameters......, glucocorticoid dynamics as well as the behavior of mice sampled repeatedly for 24 h by cheek blood, tail blood or automated blood sampling from the carotid artery. Mice subjected to cheek blood sampling lost significantly more body weight, had elevated levels of plasma corticosterone, excreted more fecal...... corticosterone metabolites, and expressed more anxious behavior than did the mice of the other groups. Plasma corticosterone levels of mice subjected to tail blood sampling were also elevated, although less significantly. Mice subjected to automated blood sampling were less affected with regard to the parameters...

Attenuation of species abundance distributions by sampling

Science.gov (United States)

Shimadzu, Hideyasu; Darnell, Ross

2015-01-01

Quantifying biodiversity aspects such as species presence/ absence, richness and abundance is an important challenge to answer scientific and resource management questions. In practice, biodiversity can only be assessed from biological material taken by surveys, a difficult task given limited time and resources. A type of random sampling, or often called sub-sampling, is a commonly used technique to reduce the amount of time and effort for investigating large quantities of biological samples. However, it is not immediately clear how (sub-)sampling affects the estimate of biodiversity aspects from a quantitative perspective. This paper specifies the effect of (sub-)sampling as attenuation of the species abundance distribution (SAD), and articulates how the sampling bias is induced to the SAD by random sampling. The framework presented also reveals some confusion in previous theoretical studies. PMID:26064626

Spatial Distribution and Sampling Plans for Grapevine Plant Canopy-Inhabiting Scaphoideus titanus (Hemiptera: Cicadellidae) Nymphs.

Science.gov (United States)

Rigamonti, Ivo E; Brambilla, Carla; Colleoni, Emanuele; Jermini, Mauro; Trivellone, Valeria; Baumgärtner, Johann

2016-04-01

The paper deals with the study of the spatial distribution and the design of sampling plans for estimating nymph densities of the grape leafhopper Scaphoideus titanus Ball in vine plant canopies. In a reference vineyard sampled for model parameterization, leaf samples were repeatedly taken according to a multistage, stratified, random sampling procedure, and data were subjected to an ANOVA. There were no significant differences in density neither among the strata within the vineyard nor between the two strata with basal and apical leaves. The significant differences between densities on trunk and productive shoots led to the adoption of two-stage (leaves and plants) and three-stage (leaves, shoots, and plants) sampling plans for trunk shoots- and productive shoots-inhabiting individuals, respectively. The mean crowding to mean relationship used to analyze the nymphs spatial distribution revealed aggregated distributions. In both the enumerative and the sequential enumerative sampling plans, the number of leaves of trunk shoots, and of leaves and shoots of productive shoots, was kept constant while the number of plants varied. In additional vineyards data were collected and used to test the applicability of the distribution model and the sampling plans. The tests confirmed the applicability 1) of the mean crowding to mean regression model on the plant and leaf stages for representing trunk shoot-inhabiting distributions, and on the plant, shoot, and leaf stages for productive shoot-inhabiting nymphs, 2) of the enumerative sampling plan, and 3) of the sequential enumerative sampling plan. In general, sequential enumerative sampling was more cost efficient than enumerative sampling.

Predictors of job satisfaction and absenteeism in two samples of Hong Kong nurses.

Science.gov (United States)

Siu, Oi-Ling

2002-10-01

Stress-related outcomes of job satisfaction and absenteeism among nurses should receive more attention in Hong Kong because absenteeism is costly. Many nurses' complaints are due to organizational change in privatization since the establishment of the Hong Kong Hospital Authority in 1991. Organizational climate is found to be an antecedent of job dissatisfaction and absenteeism in many studies in western societies. To investigate the role of organizational climate and psychological distress on job satisfaction; and the role of climate, distress and job satisfaction on absenteeism in Hong Kong nurses, while controlling for demographic variables. A self-administered questionnaire survey method was used to collect data from two samples of nurses within a 8-month period. They are, respectively, 144 (74 general nurses, 70 psychiatric nurses; 47 males, 97 females) and 114 (85 general nurses, 29 psychiatric nurses; 17 males, 97 females) nurses. Multiple regression analyses revealed that occupational type (psychiatric/general), environment (the physical conditions in the work area) and psychological distress were significant predictors of job satisfaction for sample 1; and well-being (social relations, welfare and health issues) was the only significant predictor of job satisfaction for sample 2. However, age, involvement (the degree of commitment displayed towards employees by the organization), psychological distress and job satisfaction were significant predictors of absenteeism for sample 1; and occupational type, organization (the interaction between the worker and the organization), and involvement were significant predictors of absenteeism for sample 2. The empirical findings provide support for the climate-job satisfaction and climate-absenteeism relationships. Psychological distress could be an antecedent of job satisfaction; and job satisfaction could be an antecedent of absenteeism. Certain climate dimensions should be improved to enhance job satisfaction and

Effects of Blood Sample Collection Pre- and Post- Slaughter, Edta ...

African Journals Online (AJOL)

The samples were immediately subjected to Wet mount (WM), Haemotocrit centrifugation test (HCT) and Thin smear (TS) tests. The results revealed that, of the 100 samples examined, 19 (19%) were positive for the presence of Microfilaria spp while 6(6%) yielded Trypanosome spp. Of the 19 samples detected having ...

Membrane bioreactor wastewater treatment plants reveal diverse yeast and protist communities of potential significance in biofouling.

Science.gov (United States)

Liébana, Raquel; Arregui, Lucía; Belda, Ignacio; Gamella, Luis; Santos, Antonio; Marquina, Domingo; Serrano, Susana

2015-01-01

The yeast community was studied in a municipal full-scale membrane bioreactor wastewater treatment plant (MBR-WWTP). The unexpectedly high diversity of yeasts indicated that the activated sludge formed a suitable environment for them to proliferate, with cellular concentrations of 2.2 ± 0.8 × 10(3) CFU ml(-1). Sixteen species of seven genera were present in the biological reactor, with Ascomycetes being the most prevalent group (93%). Most isolates were able to grow in a synthetic wastewater medium, adhere to polyethylene surfaces, and develop biofilms of variable complexity. The relationship between yeast populations and the protists in the MBR-WWTP was also studied, revealing that some protist species preyed on and ingested yeasts. These results suggest that yeast populations may play a role in the food web of a WWTP and, to some extent, contribute to membrane biofouling in MBR systems.

XRF analysis of mineralised samples

International Nuclear Information System (INIS)

Ahmedali, T.

2002-01-01

Full text: Software now supplied by instrument manufacturers has made it practical and convenient for users to analyse unusual samples routinely. Semiquantitative scanning software can be used for rapid preliminary screening of elements ranging from Carbon to Uranium, prior to assigning mineralised samples to an appropriate quantitative analysis routine. The general quality and precision of analytical results obtained from modern XRF spectrometers can be significantly enhanced by several means: a. Modifications in preliminary sample preparation can result in less contamination from crushing and grinding equipment. Optimised techniques of actual sample preparation can significantly increase precision of results. b. Employment of automatic data recording balances and the use of catch weights during sample preparation reduces technician time as well as weighing errors. * c. Consistency of results can be improved significantly by the use of appropriate stable drift monitors with a statistically significant content of the analyte d. A judicious selection of kV/mA combinations, analysing crystals, primary beam filters, collimators, peak positions, accurate background correction and peak overlap corrections, followed by the use of appropriate matrix correction procedures. e. Preventative maintenance procedures for XRF spectrometers and ancillary equipment, which can also contribute significantly to reducing instrument down times, are described. Examples of various facets of sample processing routines are given from the XRF spectrometer component of a multi-instrument analytical university facility, which provides XRF data to 17 Canadian universities. Copyright (2002) Australian X-ray Analytical Association Inc

Genotyping of Toxoplasma Gondii Isolates from Soil Samples in Tehran, Iran

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M Tavalla

2013-06-01

Full Text Available Background: The protozoan parasite Toxoplasma gondii can infect any warm blooded nucleated cells. One of the ways for human infection is ingestion of oocysts directly from soil or via infected fruits or vegetables. To survey the potential role of T. gondii oocyst in soil samples, the present study was conducted in Tehran City, Iran.Methods: A total of 150 soil samples were collected around rubbish dumps, children's play ground, parks and public places. Oocysts recovery was performed by sodium nitrate flotation method on soil samples. For molecular detection, PCR reaction targeting B1 gene was performed and then, the posi­tive results were confirmed using repetitive 529 bp DNA fragment in other PCR reaction. Finally, the positive samples were genotyped at the SAG2 locus.Results: Toxoplasma DNA was found in 13 soil samples. After genotyping and RFLP analysis in SAG2 locus, nine positive samples were revealed type III, one positive sample was type I whereas three samples revealed mixed infection (type, I & III.Conclusion: The predominant genotype in Tehran soil samples is type III.

Sampling system for a boiling reactor NPP

International Nuclear Information System (INIS)

Zabelin, A.I.; Yakovleva, E.D.; Solov'ev, Yu.A.

1976-01-01

Investigations and pilot running of the nuclear power plant with a VK-50 boiling reactor reveal the necessity of normalizing the design system of water sampling and of mandatory replacement of the needle-type throttle device by a helical one. A method for designing a helical throttle device has been worked out. The quantitative characteristics of depositions of corrosion products along the line of reactor water sampling are presented. Recommendations are given on the organizaton of the sampling system of a nuclear power plant with BWR type reactors

Classical and additional antiphospholipid antibodies in blood samples of ischemic stroke patients and healthy controls.

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Carmel-Neiderman, Narin-Nard; Tanne, David; Goren, Idan; Rotman-Pikielny, Pnina; Levy, Yair

2017-04-01

Classical antiphospholipid antibodies (aPLa) are found in 6-25% of blood samples from stroke patients. The frequency of novel aPLa antibodies in blood samples of CVA patients is not known. Enzyme-linked immunosorbent assays (ELISA) were performed on blood samples from 209 CVA patients (170 samples were obtained during the acute phase and 39 samples were from patients with complete carotid stenosis) and compared to 54 healthy controls. Subjects were tested for the presence of the classical aPL antibodies anticardiolipin (aCL) and anti-beta2-glycoprotein (aβ2gI), in addition to antiphosphatidylethanolamine (aPE), anti-phosphatidylserine (aPS), and Annexin V. All antibodies were tested for both IgM and IgG subclasses. Numeric analysis of the antibody titer levels (μ/ml) revealed a significantly higher subclinical titer by two standard deviations of many aPL autoantibodies among CVA patients (Pv < 0.05). However, according to the kit manufacturer's cutoff value, no positive antibodies were found except a trend toward higher percentage of positive aPS IgG titer in the CVA group compared to controls (6.2 vs. %0; P = 0.077). According to the manufacturer's cutoff, significantly higher levels of positive antibodies were not found among stroke patients. However, the absolute ELISA values of stroke patients were significantly higher. These results suggest that lower cutoff values than those used for APS diagnosis should be used for risk stratification of CVA among healthy individuals.

The large sample size fallacy.

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Lantz, Björn

2013-06-01

Significance in the statistical sense has little to do with significance in the common practical sense. Statistical significance is a necessary but not a sufficient condition for practical significance. Hence, results that are extremely statistically significant may be highly nonsignificant in practice. The degree of practical significance is generally determined by the size of the observed effect, not the p-value. The results of studies based on large samples are often characterized by extreme statistical significance despite small or even trivial effect sizes. Interpreting such results as significant in practice without further analysis is referred to as the large sample size fallacy in this article. The aim of this article is to explore the relevance of the large sample size fallacy in contemporary nursing research. Relatively few nursing articles display explicit measures of observed effect sizes or include a qualitative discussion of observed effect sizes. Statistical significance is often treated as an end in itself. Effect sizes should generally be calculated and presented along with p-values for statistically significant results, and observed effect sizes should be discussed qualitatively through direct and explicit comparisons with the effects in related literature. © 2012 Nordic College of Caring Science.

The perils of straying from protocol: sampling bias and interviewer effects.

Directory of Open Access Journals (Sweden)

Carrie J Ngongo

Full Text Available Fidelity to research protocol is critical. In a contingent valuation study in an informal urban settlement in Nairobi, Kenya, participants responded differently to the three trained interviewers. Interviewer effects were present during the survey pilot, then magnified at the start of the main survey after a seemingly slight adaptation of the survey sampling protocol allowed interviewers to speak with the "closest neighbor" in the event that no one was home at a selected household. This slight degree of interviewer choice led to inferred sampling bias. Multinomial logistic regression and post-estimation tests revealed that the three interviewers' samples differed significantly from one another according to six demographic characteristics. The two female interviewers were 2.8 and 7.7 times less likely to talk with respondents of low socio-economic status than the male interviewer. Systematic error renders it impossible to determine which of the survey responses might be "correct." This experience demonstrates why researchers must take care to strictly follow sampling protocols, consistently train interviewers, and monitor responses by interview to ensure similarity between interviewers' groups and produce unbiased estimates of the parameters of interest.

Hierarchical sampling of multiple strata: an innovative technique in exposure characterization

International Nuclear Information System (INIS)

Ericson, J.E.; Gonzalez, Elisabeth J.

2003-01-01

Sampling of multiple strata, or hierarchical sampling of various exposure sources and activity areas, has been tested and is suggested as a method to sample (or to locate) areas with a high prevalence of elevated blood lead in children. Hierarchical sampling was devised to supplement traditional soil lead sampling of a single stratum, either residential or fixed point source, using a multistep strategy. Blood lead (n=1141) and soil lead (n=378) data collected under the USEPA/UCI Tijuana Lead Project (1996-1999) were analyzed to evaluate the usefulness of sampling soil lead from background sites, schools and parks, point sources, and residences. Results revealed that industrial emissions have been a contributing factor to soil lead contamination in Tijuana. At the regional level, point source soil lead was associated with mean blood lead levels and concurrent high background, and point source soil lead levels were predictive of a high percentage of subjects with blood lead equal to or greater than 10 μg/dL (pe 10). Significant relationships were observed between mean blood lead level and fixed point source soil lead (r=0.93; P 2 =0.72 using a quadratic model) and between residential soil lead and fixed point source soil lead (r=0.90; P 2 =0.86 using a cubic model). This study suggests that point sources alone are not sufficient for predicting the relative risk of exposure to lead in the urban environment. These findings will be useful in defining regions for targeted or universal soil lead sampling by site type. Point sources have been observed to be predictive of mean blood lead at the regional level; however, this relationship alone was not sufficient to predict pe 10. It is concluded that when apparently undisturbed sites reveal high soil lead levels in addition to local point sources, dispersion of lead is widespread and will be associated with a high prevalence of elevated blood lead in children. Multiple strata sampling was shown to be useful in

Ocular-following responses to white noise stimuli in humans reveal a novel nonlinearity that results from temporal sampling.

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Sheliga, Boris M; Quaia, Christian; FitzGibbon, Edmond J; Cumming, Bruce G

2016-01-01

White noise stimuli are frequently used to study the visual processing of broadband images in the laboratory. A common goal is to describe how responses are derived from Fourier components in the image. We investigated this issue by recording the ocular-following responses (OFRs) to white noise stimuli in human subjects. For a given speed we compared OFRs to unfiltered white noise with those to noise filtered with band-pass filters and notch filters. Removing components with low spatial frequency (SF) reduced OFR magnitudes, and the SF associated with the greatest reduction matched the SF that produced the maximal response when presented alone. This reduction declined rapidly with SF, compatible with a winner-take-all operation. Removing higher SF components increased OFR magnitudes. For higher speeds this effect became larger and propagated toward lower SFs. All of these effects were quantitatively well described by a model that combined two factors: (a) an excitatory drive that reflected the OFRs to individual Fourier components and (b) a suppression by higher SF channels where the temporal sampling of the display led to flicker. This nonlinear interaction has an important practical implication: Even with high refresh rates (150 Hz), the temporal sampling introduced by visual displays has a significant impact on visual processing. For instance, we show that this distorts speed tuning curves, shifting the peak to lower speeds. Careful attention to spectral content, in the light of this nonlinearity, is necessary to minimize the resulting artifact when using white noise patterns undergoing apparent motion.

Aerial sampling using drones for measuring trace gases

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Chang, Chih-Chung; Wang, Jia-Lin; Chang, Chih-Yuan; Lin, Ming-Ren; Ou-Yang, Chang-Feng; Pan, Xiang-Xu; Lin, Neng-Huei

2017-04-01

Aerial and ground-level samples were simultaneously collected at the northern tip of Taiwan, Cape Fuguei, which is commonly served as a receptor site to receive air parcels from East Asia, Asian continent, the northwest Pacific Ocean and the island of Taiwan itself. Both aerial and surface samples were analyzed for 106 volatile organic compounds (VOCs) and divided into three categories as follows: 1. the total concentrations of 106 VOC (T-VOC) at 300-m height that are lower than the T-VOC level at the surface (Category A), 2. T-VOC concentrations at 300-m that are higher than those at the surface (Category B), and 3. comparable concentrations (Category C). Ten VOCs were exploited as tracers for a variety of emission sources linking to possible sources and transport routes of airborne pollutants. The first two categories A and B showed significant differences in the observed composition and concentrations of tracers between aerial and ground-level samples, implying that the pollutants at different heights may have resulted from different sources and poor air mixing, despite only a 300-m difference in vertical height. In contrast, Category C showed good vertical mixing, as indicated by the comparable concentrations between the aerial and surface measurements. Since the three categories occurred in specific meteorological conditions (between, prior to, and after cold fronts), respectively, it suggests that varied prevailing meteorology controlled the distribution and transport of airborne pollutants. Unlike sampling commonly performed at the surface, this study uses aerial sampling to demonstrate that layered structures under different meteorological conditions. Sampling aloft in lower boundary layer avoids samples being over-influenced by the close-by surface sources such as traffic to reveal signatures of a broader region.

MYC protein expression is detected in plasma cell myeloma but not in monoclonal gammopathy of undetermined significance (MGUS).

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Xiao, Ruobing; Cerny, Jan; Devitt, Katherine; Dresser, Karen; Nath, Rajneesh; Ramanathan, Muthalagu; Rodig, Scott J; Chen, Benjamin J; Woda, Bruce A; Yu, Hongbo

2014-06-01

It has been recognized that monoclonal gammopathy of undetermined significance (MGUS) precedes a diagnosis of plasma cell myeloma in most patients. Recent gene expression array analysis has revealed that an MYC activation signature is detected in plasma cell myeloma but not in MGUS. In this study, we performed immunohistochemical studies using membrane CD138 and nuclear MYC double staining on bone marrow biopsies from patients who met the diagnostic criteria of plasma cell myeloma or MGUS. Our study demonstrated nuclear MYC expression in CD138-positive plasma cells in 22 of 26 (84%) plasma cell myeloma samples and in none of the 29 bone marrow samples from patients with MGUS. In addition, our data on the follow-up biopsies from plasma cell myeloma patients with high MYC expression demonstrated that evaluation of MYC expression in plasma cells can be useful in detecting residual disease. We also demonstrated that plasma cells gained MYC expression in 5 of 8 patients (62.5%) when progressing from MGUS to plasma cell myeloma. Analysis of additional lymphomas with plasmacytic differentiation, including lymphoplasmacytic lymphoma, marginal zone lymphoma, and plasmablastic lymphoma, reveals that MYC detection can be a useful tool in the diagnosis of plasma cell myeloma.

Detection of Strongylus vulgaris in equine faecal samples by real-time PCR and larval culture - method comparison and occurrence assessment.

Science.gov (United States)

Kaspar, A; Pfister, K; Nielsen, M K; Silaghi, C; Fink, H; Scheuerle, M C

2017-01-11

Strongylus vulgaris has become a rare parasite in Germany during the past 50 years due to the practice of frequent prophylactic anthelmintic therapy. To date, the emerging development of resistance in Cyathostominae and Parascaris spp. to numerous equine anthelmintics has changed deworming management and the frequency of anthelmintic usage. In this regard, reliable detection of parasitic infections, especially of the highly pathogenic S. vulgaris is essential. In the current study, two diagnostic methods for the detection of infections with S. vulgaris were compared and information on the occurrence of this parasite in German horses was gained. For this purpose, faecal samples of 501 horses were screened for S. vulgaris with real-time PCR and an additional larval culture was performed in samples of 278 horses. A subset of 26 horses underwent multiple follow-up examinations with both methods in order to evaluate both the persistence of S. vulgaris infections and the reproducibility of each diagnostic method. The real-time PCR revealed S. vulgaris-DNA in ten of 501 investigated equine samples (1.9%). The larval culture demonstrated larvae of S. vulgaris in three of the 278 samples (1.1%). A direct comparison of the two methods was possible in 321 samples including 43 follow-up examinations with the result of 11 S. vulgaris-positive samples by real-time PCR and 4 S. vulgaris-positive samples by larval culture. The McNemar's test (p-value = 0.016) revealed a significant difference and the kappa values (0.525) showed a moderate agreement between real-time PCR and larval culture. The real-time PCR detected a significantly higher proportion of positives of S. vulgaris compared to larval culture and should thus be considered as a routine diagnostic method for the detection of S. vulgaris in equine samples.

A survey of natural terrestrial and airborne radionuclides in moss samples from the peninsular Thailand.

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Wattanavatee, Komrit; Krmar, Miodrag; Bhongsuwan, Tripob

2017-10-01

The aim of this study was to determine the activity concentrations of natural terrestrial radionuclides ( 238 U, 226 Ra, 232 Th and 40 K) and airborne radionuclides ( 210 Pb, 210 Pb ex and 7 Be) in natural terrestrial mosses. The collected moss samples (46) representing 17 species were collected from 17 sampling localities in the National Parks and Wildlife Sanctuaries of Thailand, situated in the mountainous areas between the northern and the southern ends of peninsular Thailand (∼7-12 °N, 99-102 °E). Activity concentrations of radionuclides in the samples were measured using a low background gamma spectrometer. The results revealed non-uniform spatial distributions of all the radionuclides in the study area. Principal component analysis and cluster analysis revealed two distinct origins for the studied radionuclides, and furthermore, the Pearson correlations were strong within 226 Ra, 232 Th, 238 U and 40 K as well as within 210 Pb and 210 Pb ex , but there was no significant correlation between these two groups. Also 7 Be was uncorrelated to the others, as expected due to different origins of the airborne and terrestrial radionuclides. The radionuclide activities of moss samples varied by moss species, topography, geology, and meteorology of each sampling area. The observed abnormally high concentrations of some radionuclides probably indicate that the concentrations of airborne and terrestrial radionuclides in moss samples were directly related to local geological features of the sampling site, or that high levels of 7 Be were most probably linked with topography and regional NE monsoonal winds from mainland China. Copyright © 2017 Elsevier Ltd. All rights reserved.

Fine-scale genetic structure and cryptic associations reveal evidence of kin-based sociality in the African forest elephant.

Science.gov (United States)

Schuttler, Stephanie G; Philbrick, Jessica A; Jeffery, Kathryn J; Eggert, Lori S

2014-01-01

Spatial patterns of relatedness within animal populations are important in the evolution of mating and social systems, and have the potential to reveal information on species that are difficult to observe in the wild. This study examines the fine-scale genetic structure and connectivity of groups within African forest elephants, Loxodonta cyclotis, which are often difficult to observe due to forest habitat. We tested the hypothesis that genetic similarity will decline with increasing geographic distance, as we expect kin to be in closer proximity, using spatial autocorrelation analyses and Tau K(r) tests. Associations between individuals were investigated through a non-invasive genetic capture-recapture approach using network models, and were predicted to be more extensive than the small groups found in observational studies, similar to fission-fusion sociality found in African savanna (Loxodonta africana) and Asian (Elephas maximus) species. Dung samples were collected in Lopé National Park, Gabon in 2008 and 2010 and genotyped at 10 microsatellite loci, genetically sexed, and sequenced at the mitochondrial DNA control region. We conducted analyses on samples collected at three different temporal scales: a day, within six-day sampling sessions, and within each year. Spatial autocorrelation and Tau K(r) tests revealed genetic structure, but results were weak and inconsistent between sampling sessions. Positive spatial autocorrelation was found in distance classes of 0-5 km, and was strongest for the single day session. Despite weak genetic structure, individuals within groups were significantly more related to each other than to individuals between groups. Social networks revealed some components to have large, extensive groups of up to 22 individuals, and most groups were composed of individuals of the same matriline. Although fine-scale population genetic structure was weak, forest elephants are typically found in groups consisting of kin and based on matrilines

Stability of measures from children's interviews: the effects of time, sample length, and topic.

Science.gov (United States)

Heilmann, John; DeBrock, Lindsay; Riley-Tillman, T Chris

2013-08-01

The purpose of this study was to examine the reliability of, and sources of variability in, language measures from interviews collected from young school-age children. Two 10-min interviews were collected from 20 at-risk kindergarten children by an examiner using a standardized set of questions. Test-retest reliability coefficients were calculated for 8 language measures. Generalizability theory (G-theory) analyses were completed to document the variability introduced into the measures from the child, session, sample length, and topic. Significant and strong reliability correlation coefficients were observed for most of the language sample measures. The G-theory analyses revealed that most of the variance in the language measures was attributed to the child. Session, sample length, and topic accounted for negligible amounts of variance in most of the language measures. Measures from interviews were reliable across sessions, and the sample length and topic did not have a substantial impact on the reliability of the language measures. Implications regarding the clinical feasibility of language sample analysis for assessment and progress monitoring are discussed.

Extensive monitoring through multiple blood samples in professional soccer players.

Science.gov (United States)

Heisterberg, Mette F; Fahrenkrug, Jan; Krustrup, Peter; Storskov, Anders; Kjær, Michael; Andersen, Jesper L

2013-05-01

The aim of this study was to make a comprehensive gathering of consecutive detailed blood samples from professional soccer players and to analyze different blood parameters in relation to seasonal changes in training and match exposure. Blood samples were collected 5 times during a 6-month period and analyzed for 37 variables in 27 professional soccer players from the best Danish league. Additionally, the players were tested for body composition, V[Combining Dot Above]O2max and physical performance by the Yo-Yo intermittent endurance submax test (IE2). Multiple variations in blood parameters occurred during the observation period, including a decrease in hemoglobin and an increase in hematocrit as the competitive season progressed. Iron and transferrin were stable, whereas ferritin showed a decrease at the end of the season. The immunoglobulin A (IgA) and IgM increased in the period with basal physical training and at the end of the season. Leucocytes decreased with increased physical training. Lymphocytes decreased at the end of the season. The V[Combining Dot Above]O2max decreased toward the end of the season, whereas no significant changes were observed in the IE2 test. The regular blood samples from elite soccer players reveal significant changes that may be related to changes in training pattern, match exposure, or length of the match season. Especially the end of the preparation season and at the end of the competitive season seem to be time points were the blood-derived values indicate that the players are under excessive physical strain and might be more subjected to a possible overreaching-overtraining conditions. We suggest that regular analyses of blood samples could be an important initiative to optimize training adaptation, training load, and game participation, but sampling has to be regular, and a database has to be built for each individual player.

A simulative comparison of respondent driven sampling with incentivized snowball sampling – the “strudel effect”

Science.gov (United States)

Gyarmathy, V. Anna; Johnston, Lisa G.; Caplinskiene, Irma; Caplinskas, Saulius; Latkin, Carl A.

2014-01-01

Background Respondent driven sampling (RDS) and Incentivized Snowball Sampling (ISS) are two sampling methods that are commonly used to reach people who inject drugs (PWID). Methods We generated a set of simulated RDS samples on an actual sociometric ISS sample of PWID in Vilnius, Lithuania (“original sample”) to assess if the simulated RDS estimates were statistically significantly different from the original ISS sample prevalences for HIV (9.8%), Hepatitis A (43.6%), Hepatitis B (Anti-HBc 43.9% and HBsAg 3.4%), Hepatitis C (87.5%), syphilis (6.8%) and Chlamydia (8.8%) infections and for selected behavioral risk characteristics. Results The original sample consisted of a large component of 249 people (83% of the sample) and 13 smaller components with 1 to 12 individuals. Generally, as long as all seeds were recruited from the large component of the original sample, the simulation samples simply recreated the large component. There were no significant differences between the large component and the entire original sample for the characteristics of interest. Altogether 99.2% of 360 simulation sample point estimates were within the confidence interval of the original prevalence values for the characteristics of interest. Conclusions When population characteristics are reflected in large network components that dominate the population, RDS and ISS may produce samples that have statistically non-different prevalence values, even though some isolated network components may be under-sampled and/or statistically significantly different from the main groups. This so-called “strudel effect” is discussed in the paper. PMID:24360650

SAMPLING IN EXTERNAL AUDIT - THE MONETARY UNIT SAMPLING METHOD

Directory of Open Access Journals (Sweden)

E. Dascalu

2016-12-01

Full Text Available This article approaches the general issue of diminishing the evidence investigation space in audit activities, by means of sampling techniques, given that in the instance of a significant data volume an exhaustive examination of the assessed popula¬tion is not possible and/or effective. The general perspective of the presentation involves dealing with sampling risk, in essence, the risk that a selected sample may not be representative for the overall population, in correlation with the audit risk model and with the component parts of this model (inherent risk, control risk and non detection risk and highlights the inter-conditionings between these two models.

Assessing clinical significance of treatment outcomes using the DASS-21.

Science.gov (United States)

Ronk, Fiona R; Korman, James R; Hooke, Geoffrey R; Page, Andrew C

2013-12-01

Standard clinical significance classifications are based on movement between the "dysfunctional" and "functional" distributions; however, this dichotomy ignores heterogeneity within the "dysfunctional" population. Based on the methodology described by Tingey, Lambert, Burlingame, and Hansen (1996), the present study sought to present a 3-distribution clinical significance model for the 21-item version of the Depression Anxiety Stress Scales (DASS-21; P. F. Lovibond & Lovibond, 1995) using data from a normative sample (n = 2,914), an outpatient sample (n = 1,000), and an inpatient sample (n = 3,964). DASS-21 scores were collected at pre- and post-treatment for both clinical samples, and patients were classified into 1 of 5 categories based on whether they had made a reliable change and whether they had moved into a different functional range. Evidence supported the validity of the 3-distribution model for the DASS-21, since inpatients who were classified as making a clinically significant change showed lower symptom severity, higher perceived quality of life, and higher clinician-rated functioning than those who did not make a clinically significant change. Importantly, results suggest that the new category of recovering is an intermediate point between recovered and making no clinically significant change. Inpatients and outpatients have different treatment goals and therefore use of the concept of clinical significance needs to acknowledge differences in what constitutes a meaningful change. (c) 2013 APA, all rights reserved.

Irrigation Is Significantly Associated with an Increased Prevalence of Listeria monocytogenes in Produce Production Environments in New York State.

Science.gov (United States)

Weller, Daniel; Wiedmann, Martin; Strawn, Laura K

2015-06-01

Environmental (i.e., meteorological and landscape) factors and management practices can affect the prevalence of foodborne pathogens in produce production environments. This study was conducted to determine the prevalence of Listeria monocytogenes, Listeria species (including L. monocytogenes), Salmonella, and Shiga toxin-producing Escherichia coli (STEC) in produce production environments and to identify environmental factors and management practices associated with their isolation. Ten produce farms in New York State were sampled during a 6-week period in 2010, and 124 georeferenced samples (80 terrestrial, 33 water, and 11 fecal) were collected. L. monocytogenes, Listeria spp., Salmonella, and STEC were detected in 16, 44, 4, and 5% of terrestrial samples, 30, 58, 12, and 3% of water samples, and 45, 45, 27, and 9% of fecal samples, respectively. Environmental factors and management practices were evaluated for their association with terrestrial samples positive for L. monocytogenes or other Listeria species by univariate logistic regression; analysis was not conducted for Salmonella or STEC because the number of samples positive for these pathogens was low. Although univariate analysis identified associations between isolation of L. monocytogenes or Listeria spp. from terrestrial samples and various water-related factors (e.g., proximity to wetlands and precipitation), multivariate analysis revealed that only irrigation within 3 days of sample collection was significantly associated with isolation of L. monocytogenes (odds ratio = 39) and Listeria spp. (odds ratio = 5) from terrestrial samples. These findings suggest that intervention at the irrigation level may reduce the risk of produce contamination.

Field Sample Preparation Method Development for Isotope Ratio Mass Spectrometry

International Nuclear Information System (INIS)

Leibman, C.; Weisbrod, K.; Yoshida, T.

2015-01-01

Non-proliferation and International Security (NA-241) established a working group of researchers from Los Alamos National Laboratory (LANL), Pacific Northwest National Laboratory (PNNL) and Savannah River National Laboratory (SRNL) to evaluate the utilization of in-field mass spectrometry for safeguards applications. The survey of commercial off-the-shelf (COTS) mass spectrometers (MS) revealed no instrumentation existed capable of meeting all the potential safeguards requirements for performance, portability, and ease of use. Additionally, fieldable instruments are unlikely to meet the International Target Values (ITVs) for accuracy and precision for isotope ratio measurements achieved with laboratory methods. The major gaps identified for in-field actinide isotope ratio analysis were in the areas of: 1. sample preparation and/or sample introduction, 2. size reduction of mass analyzers and ionization sources, 3. system automation, and 4. decreased system cost. Development work in 2 through 4, numerated above continues, in the private and public sector. LANL is focusing on developing sample preparation/sample introduction methods for use with the different sample types anticipated for safeguard applications. Addressing sample handling and sample preparation methods for MS analysis will enable use of new MS instrumentation as it becomes commercially available. As one example, we have developed a rapid, sample preparation method for dissolution of uranium and plutonium oxides using ammonium bifluoride (ABF). ABF is a significantly safer and faster alternative to digestion with boiling combinations of highly concentrated mineral acids. Actinides digested with ABF yield fluorides, which can then be analyzed directly or chemically converted and separated using established column chromatography techniques as needed prior to isotope analysis. The reagent volumes and the sample processing steps associated with ABF sample digestion lend themselves to automation and field

Effects of Coatings on the High-Cycle Fatigue Life of Threaded Steel Samples

Science.gov (United States)

Eder, M. A.; Haselbach, P. U.; Mishin, O. V.

2018-05-01

In this work, high-cycle fatigue is studied for threaded cylindrical high-strength steel samples coated using three different industrial processes: black oxidation, normal-temperature galvanization and high-temperature galvanization. The fatigue performance in air is compared with that of uncoated samples. Microstructural characterization revealed the abundant presence of small cracks in the zinc coating partially penetrating into the steel. This is consistent with the observation of multiple crack initiation sites along the thread in the galvanized samples, which led to crescent type fracture surfaces governed by circumferential growth. In contrast, the black oxidized and uncoated samples exhibited a semicircular segment type fracture surface governed by single-sided growth with a significantly longer fatigue life. Numerical fatigue life prediction based on an extended Paris-law formulation has been conducted on two different fracture cases: 2D axisymmetric multisided crack growth and 3D single-sided crack growth. The results of this upper-bound and lower-bound approach are in good agreement with experimental data and can potentially be used to predict the lifetime of bolted components.

Structure defects in malachite revealed by positron annihilation

International Nuclear Information System (INIS)

Geffroy, B.; Diallo, I.; Paulin, R.

1984-01-01

Positron lifetime is measured between 77 and 400 K in two malachite samples with different mineralogical structures. The complex spectrum found in zoned malachite reveals a microporosity which remains stable in this range of temperature. Besides, above 200 K, equilibrium defects appear. Their formation energy is estimated to be Esub(f) = 0.27 +- 0.02 eV [fr

Structure defects in malachite revealed by positron annihilation

Energy Technology Data Exchange (ETDEWEB)

Geffroy, B; Diallo, I; Paulin, R [Institut National des Sciences et Techniques Nucleaires, CEN/Saclay, 91 - Gif-sur-Yvette (France)

1984-01-01

Positron lifetime is measured between 77 and 400 K in two malachite samples with different mineralogical structures. The complex spectrum found in zoned malachite reveals a microporosity which remains stable in this range of temperature. Besides, above 200 K, equilibrium defects appear. Their formation energy is estimated to be Esub(f) = 0.27 +- 0.02 eV.

The application of x-ray fluorescence spectrometry for multielemental analysis of air particulate samples

International Nuclear Information System (INIS)

Mohamad Rashid Mohamad Yusoff

1986-01-01

The performance of XRF spectrometer as a tool for multielemental analysis of air pollution samples was discussed. The non-destructive couples with multielemental nature of the technique satisfactory sensitivity for most elements were the most important characteristics for its popularity as a method of analysis. Thus, the technique promises a significant reduction in cost and time of analysis. As a result, more extensive and revealing air particulates survey should be possible, with consequent improvements in the discovery and positive identification of particulate pollution sources. (author)

{sup 1}H NMR-based metabolic profiling reveals inherent biological variation in yeast and nematode model systems

Energy Technology Data Exchange (ETDEWEB)

Szeto, Samuel S. W.; Reinke, Stacey N.; Lemire, Bernard D., E-mail: bernard.lemire@ualberta.ca [University of Alberta, Department of Biochemistry, School of Molecular and Systems Medicine (Canada)

2011-04-15

The application of metabolomics to human and animal model systems is poised to provide great insight into our understanding of disease etiology and the metabolic changes that are associated with these conditions. However, metabolomic studies have also revealed that there is significant, inherent biological variation in human samples and even in samples from animal model systems where the animals are housed under carefully controlled conditions. This inherent biological variability is an important consideration for all metabolomics analyses. In this study, we examined the biological variation in {sup 1}H NMR-based metabolic profiling of two model systems, the yeast Saccharomyces cerevisiae and the nematode Caenorhabditis elegans. Using relative standard deviations (RSD) as a measure of variability, our results reveal that both model systems have significant amounts of biological variation. The C. elegans metabolome possesses greater metabolic variance with average RSD values of 29 and 39%, depending on the food source that was used. The S. cerevisiae exometabolome RSD values ranged from 8% to 12% for the four strains examined. We also determined whether biological variation occurs between pairs of phenotypically identical yeast strains. Multivariate statistical analysis allowed us to discriminate between pair members based on their metabolic phenotypes. Our results highlight the variability of the metabolome that exists even for less complex model systems cultured under defined conditions. We also highlight the efficacy of metabolic profiling for defining these subtle metabolic alterations.

An efficient method for sampling the essential subspace of proteins

NARCIS (Netherlands)

Amadei, A; Linssen, A.B M; de Groot, B.L.; van Aalten, D.M.F.; Berendsen, H.J.C.

A method is presented for a more efficient sampling of the configurational space of proteins as compared to conventional sampling techniques such as molecular dynamics. The method is based on the large conformational changes in proteins revealed by the ''essential dynamics'' analysis. A form of

Significance of TP53 Mutation in Wilms Tumors with Diffuse Anaplasia: A Report from the Children’s Oncology Group

Science.gov (United States)

Ooms, Ariadne H.A.G.; Gadd, Samantha; Gerhard, Daniela S.; Smith, Malcolm A.; Guidry Auvil, Jaime M.; Meerzaman, Daoud; Chen, Qing-Rong; Hsu, Chih Hao; Yan, Chunhua; Nguyen, Cu; Hu, Ying; Ma, Yussanne; Zong, Zusheng; Mungall, Andrew J.; Moore, Richard A.; Marra, Marco A.; Huff, Vicki; Dome, Jeffrey S.; Chi, Yueh-Yun; Tian, Jing; Geller, James I.; Mullighan, Charles G.; Ma, Jing; Wheeler, David A.; Hampton, Oliver A.; Walz, Amy L.; van den Heuvel-Eibrink, Marry M.; de Krijger, Ronald R.; Ross, Nicole; Gastier-Foster, Julie M.; Perlman, Elizabeth J.

2016-01-01

Purpose To investigate the role and significance of TP53 mutation in diffusely anaplastic Wilms tumor (DAWT). Experimental Design All DAWTs registered on National Wilms Tumor Study-5 (n=118) with available samples were analyzed for TP53 mutations and copy loss. Integrative genomic analysis was performed on 39 selected DAWTs. Results Following analysis of a single random sample, 57 DAWT (48%) demonstrated TP53 mutations, 13(11%) copy loss without mutation, and 48(41%) lacked both (defined as TP53-wildtype (wt)). Patients with Stage III/IV TP53-wt DAWTs (but not those with Stage I/II disease) had significantly lower relapse and death rates than those with TP53 abnormalities. In-depth analysis of a subset of 39 DAWT showed 7(18%) to be TP53-wt: these demonstrated gene expression evidence of an active p53 pathway. Retrospective pathology review of TP53-wt DAWT revealed no or very low volume of anaplasia in 6/7 tumors. When samples from TP53-wt tumors known to contain anaplasia histologically were available, abnormal p53 protein accumulation was observed by immunohistochemistry. Conclusion These data support the key role of TP53 loss in the development of anaplasia in WT, and support its significant clinical impact in patients with residual anaplastic tumor following surgery. These data also suggest that most DAWTs will show evidence of TP53 mutation when samples selected for the presence of anaplasia are analyzed. This suggests that modifications of the current criteria to also consider volume of anaplasia and documentation of TP53 aberrations may better reflect the risk of relapse and death and enable optimization of therapeutic stratification. PMID:27702824

The one-sample PARAFAC approach reveals molecular size distributions of fluorescent components in dissolved organic matter

DEFF Research Database (Denmark)

Wünsch, Urban; Murphy, Kathleen R.; Stedmon, Colin

2017-01-01

Molecular size plays an important role in dissolved organic matter (DOM) biogeochemistry, but its relationship with the fluorescent fraction of DOM (FDOM) remains poorly resolved. Here high-performance size exclusion chromatography (HPSEC) was coupled to fluorescence emission-excitation (EEM...... but not their spectral properties. Thus, in contrast to absorption measurements, bulk fluorescence is unlikely to reliably indicate the average molecular size of DOM. The one-sample approach enables robust and independent cross-site comparisons without large-scale sampling efforts and introduces new analytical...... opportunities for elucidating the origins and biogeochemical properties of FDOM...

Are individual differences in appetitive and defensive motivation related? A psychophysiological examination in two samples.

Science.gov (United States)

Sarapas, Casey; Katz, Andrea C; Nelson, Brady D; Campbell, Miranda L; Bishop, Jeffrey R; Robison-Andrew, E Jenna; Altman, Sarah E; Gorka, Stephanie M; Shankman, Stewart A

2014-01-01

Appetitive and defensive motivation account for a good deal of variance in personality and mental health, but whether individual differences in these systems are correlated or orthogonal has not been conclusively established. Previous investigations have generally relied on self-report and have yielded conflicting results. We therefore assessed the relation between psychophysiological indices of appetitive and defensive motivation during elicitation of these motivational states: specifically, frontal electroencephalogram asymmetry during reward anticipation and startle response during anticipation of predictable or unpredictable threat of shock. Results in a sample of psychopathology-free community members (n=63), an independent sample of undergraduates with a range of internalising symptoms (n=64), and the combination of these samples (n=127) revealed that differences in responding to the two tasks were not significantly correlated. Average coefficients approached zero in all three samples (community: .04, undergraduate: -.01, combined: .06). Implications of these findings for research on normal and abnormal personality are discussed.

Network Sampling with Memory: A proposal for more efficient sampling from social networks

Science.gov (United States)

Mouw, Ted; Verdery, Ashton M.

2013-01-01

Techniques for sampling from networks have grown into an important area of research across several fields. For sociologists, the possibility of sampling from a network is appealing for two reasons: (1) A network sample can yield substantively interesting data about network structures and social interactions, and (2) it is useful in situations where study populations are difficult or impossible to survey with traditional sampling approaches because of the lack of a sampling frame. Despite its appeal, methodological concerns about the precision and accuracy of network-based sampling methods remain. In particular, recent research has shown that sampling from a network using a random walk based approach such as Respondent Driven Sampling (RDS) can result in high design effects (DE)—the ratio of the sampling variance to the sampling variance of simple random sampling (SRS). A high design effect means that more cases must be collected to achieve the same level of precision as SRS. In this paper we propose an alternative strategy, Network Sampling with Memory (NSM), which collects network data from respondents in order to reduce design effects and, correspondingly, the number of interviews needed to achieve a given level of statistical power. NSM combines a “List” mode, where all individuals on the revealed network list are sampled with the same cumulative probability, with a “Search” mode, which gives priority to bridge nodes connecting the current sample to unexplored parts of the network. We test the relative efficiency of NSM compared to RDS and SRS on 162 school and university networks from Add Health and Facebook that range in size from 110 to 16,278 nodes. The results show that the average design effect for NSM on these 162 networks is 1.16, which is very close to the efficiency of a simple random sample (DE=1), and 98.5% lower than the average DE we observed for RDS. PMID:24159246

Significance of TP53 Mutation in Wilms Tumors with Diffuse Anaplasia: A Report from the Children's Oncology Group.

Science.gov (United States)

Ooms, Ariadne H A G; Gadd, Samantha; Gerhard, Daniela S; Smith, Malcolm A; Guidry Auvil, Jaime M; Meerzaman, Daoud; Chen, Qing-Rong; Hsu, Chih Hao; Yan, Chunhua; Nguyen, Cu; Hu, Ying; Ma, Yussanne; Zong, Zusheng; Mungall, Andrew J; Moore, Richard A; Marra, Marco A; Huff, Vicki; Dome, Jeffrey S; Chi, Yueh-Yun; Tian, Jing; Geller, James I; Mullighan, Charles G; Ma, Jing; Wheeler, David A; Hampton, Oliver A; Walz, Amy L; van den Heuvel-Eibrink, Marry M; de Krijger, Ronald R; Ross, Nicole; Gastier-Foster, Julie M; Perlman, Elizabeth J

2016-11-15

To investigate the role and significance of TP53 mutation in diffusely anaplastic Wilms tumors (DAWTs). All DAWTs registered on National Wilms Tumor Study-5 (n = 118) with available samples were analyzed for TP53 mutations and copy loss. Integrative genomic analysis was performed on 39 selected DAWTs. Following analysis of a single random sample, 57 DAWTs (48%) demonstrated TP53 mutations, 13 (11%) copy loss without mutation, and 48 (41%) lacked both [defined as TP53-wild-type (wt)]. Patients with stage III/IV TP53-wt DAWTs (but not those with stage I/II disease) had significantly lower relapse and death rates than those with TP53 abnormalities. In-depth analysis of a subset of 39 DAWTs showed seven (18%) to be TP53-wt: These demonstrated gene expression evidence of an active p53 pathway. Retrospective pathology review of TP53-wt DAWT revealed no or very low volume of anaplasia in six of seven tumors. When samples from TP53-wt tumors known to contain anaplasia histologically were available, abnormal p53 protein accumulation was observed by immunohistochemistry. These data support the key role of TP53 loss in the development of anaplasia in WT, and support its significant clinical impact in patients with residual anaplastic tumor following surgery. These data also suggest that most DAWTs will show evidence of TP53 mutation when samples selected for the presence of anaplasia are analyzed. This suggests that modifications of the current criteria to also consider volume of anaplasia and documentation of TP53 aberrations may better reflect the risk of relapse and death and enable optimization of therapeutic stratification. Clin Cancer Res; 22(22); 5582-91. ©2016 AACR. ©2016 American Association for Cancer Research.

Comparative Study of the Effect of Sample Pretreatment and Extraction on the Determination of Flavonoids from Lemon (Citrus limon)

Science.gov (United States)

Ledesma-Escobar, Carlos A.; Priego-Capote, Feliciano; Luque de Castro, María D.

2016-01-01

Background Flavonoids have shown to exert multiple beneficial effects on human health, being also appreciated by both food and pharmaceutical industries. Citrus fruits are a key source of flavonoids, thus promoting studies to obtain them. Characteristics of these studies are the discrepancies among sample pretreatments and among extraction methods, and also the scant number of comparative studies developed so far. Objective Evaluate the effect of both the sample pretreatment and the extraction method on the profile of flavonoids isolated from lemon. Results Extracts from fresh, lyophilized and air-dried samples obtained by shaking extraction (SE), ultrasound-assisted extraction (USAE), microwave-assisted extraction (MAE) and superheated liquid extraction (SHLE) were analyzed by LC–QTOF MS/MS, and 32 flavonoids were tentatively identified using MS/MS information. ANOVA applied to the data from fresh and dehydrated samples and from extraction by the different methods revealed that 26 and 32 flavonoids, respectively, were significant (p≤0.01). The pairwise comparison (Tukey HSD; p≤0.01) showed that lyophilized samples are more different from fresh samples than from air-dried samples; also, principal component analysis (PCA) showed a clear discrimination among sample pretreatment strategies and suggested that such differences are mainly created by the abundance of major flavonoids. On the other hand, pairwise comparison of extraction methods revealed that USAE and MAE provided quite similar extracts, being SHLE extracts different from the other two. In this case, PCA showed a clear discrimination among extraction methods, and their position in the scores plot suggests a lower abundance of flavonoids in the extracts from SHLE. In the two PCA the loadings plots revealed a trend to forming groups according to flavonoid aglycones. Conclusions The present study shows clear discrimination caused by both sample pretreatments and extraction methods. Under the studied

Signal improvement in multiphoton microscopy by reflection with simple mirrors near the sample

Science.gov (United States)

Rehberg, Markus; Krombach, Fritz; Pohl, Ulrich; Dietzel, Steffen

2010-03-01

In conventional fluorescence or confocal microscopy, emitted light is generated not only in the focal plane but also above and below. The situation is different in multiphoton-induced fluorescence and multiphoton-induced higher harmonic generation. Here, restriction of signal generation to a single focal point permits that all emitted photons can contribute to image formation if collected, regardless of their path through the specimen. Often, the intensity of the emitted light is rather low in biological specimens. We present a method to significantly increase the fraction of photons collected by an epi (backward) detector by placing a simple mirror, an aluminum-coated coverslip, directly under the sample. Samples investigated include fluorescent test slides, collagen gels, and thin-layered, intact mouse skeletal muscles. Quantitative analysis revealed an intensity increase of second- and third-harmonic generated signal in skeletal muscle of nine- and sevenfold respectively, and of fluorescent signal in test slides of up to twofold. Our approach thus allows significant signal improvement also for situations were a forward detection is impossible, e.g., due to the anatomy of animals in intravital microscopy.

Cloud-based solution to identify statistically significant MS peaks differentiating sample categories.

Science.gov (United States)

Ji, Jun; Ling, Jeffrey; Jiang, Helen; Wen, Qiaojun; Whitin, John C; Tian, Lu; Cohen, Harvey J; Ling, Xuefeng B

2013-03-23

Mass spectrometry (MS) has evolved to become the primary high throughput tool for proteomics based biomarker discovery. Until now, multiple challenges in protein MS data analysis remain: large-scale and complex data set management; MS peak identification, indexing; and high dimensional peak differential analysis with the concurrent statistical tests based false discovery rate (FDR). "Turnkey" solutions are needed for biomarker investigations to rapidly process MS data sets to identify statistically significant peaks for subsequent validation. Here we present an efficient and effective solution, which provides experimental biologists easy access to "cloud" computing capabilities to analyze MS data. The web portal can be accessed at http://transmed.stanford.edu/ssa/. Presented web application supplies large scale MS data online uploading and analysis with a simple user interface. This bioinformatic tool will facilitate the discovery of the potential protein biomarkers using MS.

Characterization of acid-base properties of two gibbsite samples in the context of literature results.

Science.gov (United States)

Adekola, F; Fédoroff, M; Geckeis, H; Kupcik, T; Lefèvre, G; Lützenkirchen, J; Plaschke, M; Preocanin, T; Rabung, T; Schild, D

2011-02-01

Two different gibbsites, one commercial and one synthesized according to a frequently applied recipe, were studied in an interlaboratory attempt to gain insight into the origin of widely differing reports on gibbsite acid-base surface properties. In addition to a thorough characterization of the two solids, several methods relevant to the interfacial charging were applied to the two samples: potentiometric titrations to obtain the "apparent" proton related surface charge density, zeta-potential measurements characterizing the potential at the plane of shear, and Attenuated Total Reflection Infrared Spectroscopy (ATR-IR) to obtain information on the variation of counter-ion adsorption with pH (using nitrate as a probe). Values of the IEP at 9-10 and 11.2-11.3 were found for the commercial and synthesized sample, respectively. The experimental observations revealed huge differences in the charging behavior between the two samples. Such differences also appeared in the titration kinetics. A detailed literature review revealed similar disparity with no apparent systematic trend. While previously the waiting time between additions had been advocated to explain such differences among synthesized samples, our results do not support such a conclusion. Instead, we find that the amount of titrant added in each aliquot appears to have a significant influence on the titration curves. While we can relate a number of observations to others, a number of open questions and contradictions remain. We suggest various processes, which can explain the observed behavior. Copyright © 2010 Elsevier Inc. All rights reserved.

HICOSMO - cosmology with a complete sample of galaxy clusters - I. Data analysis, sample selection and luminosity-mass scaling relation

Science.gov (United States)

Schellenberger, G.; Reiprich, T. H.

2017-08-01

The X-ray regime, where the most massive visible component of galaxy clusters, the intracluster medium, is visible, offers directly measured quantities, like the luminosity, and derived quantities, like the total mass, to characterize these objects. The aim of this project is to analyse a complete sample of galaxy clusters in detail and constrain cosmological parameters, like the matter density, Ωm, or the amplitude of initial density fluctuations, σ8. The purely X-ray flux-limited sample (HIFLUGCS) consists of the 64 X-ray brightest galaxy clusters, which are excellent targets to study the systematic effects, that can bias results. We analysed in total 196 Chandra observations of the 64 HIFLUGCS clusters, with a total exposure time of 7.7 Ms. Here, we present our data analysis procedure (including an automated substructure detection and an energy band optimization for surface brightness profile analysis) that gives individually determined, robust total mass estimates. These masses are tested against dynamical and Planck Sunyaev-Zeldovich (SZ) derived masses of the same clusters, where good overall agreement is found with the dynamical masses. The Planck SZ masses seem to show a mass-dependent bias to our hydrostatic masses; possible biases in this mass-mass comparison are discussed including the Planck selection function. Furthermore, we show the results for the (0.1-2.4) keV luminosity versus mass scaling relation. The overall slope of the sample (1.34) is in agreement with expectations and values from literature. Splitting the sample into galaxy groups and clusters reveals, even after a selection bias correction, that galaxy groups exhibit a significantly steeper slope (1.88) compared to clusters (1.06).

Monolith Chromatography as Sample Preparation Step in Virome Studies of Water Samples.

Science.gov (United States)

Gutiérrez-Aguirre, Ion; Kutnjak, Denis; Rački, Nejc; Rupar, Matevž; Ravnikar, Maja

2018-01-01

Viruses exist in aquatic media and many of them use this media as transmission route. Next-generation sequencing (NGS) technologies have opened new doors in virus research, allowing also to reveal a hidden diversity of viral species in aquatic environments. Not surprisingly, many of the newly discovered viruses are found in environmental fresh and marine waters. One of the problems in virome research can be the low amount of viral nucleic acids present in the sample in contrast to the background ones (host, eukaryotic, prokaryotic, environmental). Therefore, virus enrichment prior to NGS is necessary in many cases. In water samples, an added problem resides in the low concentration of viruses typically present in aquatic media. Different concentration strategies have been used to overcome such limitations. CIM monoliths are a new generation of chromatographic supports that due to their particular structural characteristics are very efficient in concentration and purification of viruses. In this chapter, we describe the use of CIM monolithic chromatography for sample preparation step in NGS studies targeting viruses in fresh or marine water. The step-by-step protocol will include a case study where CIM concentration was used to study the virome of a wastewater sample using NGS.

Detection of Mycoplasma synoviae in clinical samples by VlhA-PCR method

Directory of Open Access Journals (Sweden)

H Ansari

2010-02-01

Full Text Available As one of the major pathogens of avian species, Mycoplasma Synoviae causes significant economic losses to the poultry industry. The main purpose of this study was to detect Mycoplasma Synoviae in clinical samples using the VlhA-PCR method. For serological screening test, 373 serum samples were collected from 25 breeder farms and rapid serum agglutination test conducted which revealed that 143 samples equivalent to 19 breeder farms were positive. For VlhA-PCR assay, 20 of the previously mentioned breeder farms were selected and sterile swab were collected from the palatine cleft, trachea, air sacs and lungs. Three swabs from 3 birds were placed in a test tube containing 1 ml of PBS and transferred to the laboratory for PCR test. Specific primers for VIhA gene were employed in this study. The PCR product from specific primers showed 350-400 bp for all field isolated on electrophoresis gel in 8 farms. VlhA-PCR with high sensitivity could be employed in definitive diagnosis of Mycoplasma Synoviae infection in the laboratory.

Effects of sample size on the second magnetization peak in ...

Indian Academy of Sciences (India)

the sample size decreases – a result that could be interpreted as a size effect in the order– disorder vortex matter phase transition. However, local magnetic measurements trace this effect to metastable disordered vortex states, revealing the same order–disorder transition induction in samples of different size. Keywords.

Functional gene profiling through metaRNAseq approach reveals diet-dependent variation in rumen microbiota of buffalo (Bubalus bubalis).

Science.gov (United States)

Hinsu, Ankit T; Parmar, Nidhi R; Nathani, Neelam M; Pandit, Ramesh J; Patel, Anand B; Patel, Amrutlal K; Joshi, Chaitanya G

2017-04-01

Recent advances in next generation sequencing technology have enabled analysis of complex microbial community from genome to transcriptome level. In the present study, metatranscriptomic approach was applied to elucidate functionally active bacteria and their biological processes in rumen of buffalo (Bubalus bubalis) adapted to different dietary treatments. Buffaloes were adapted to a diet containing 50:50, 75:25 and 100:0 forage to concentrate ratio, each for 6 weeks, before ruminal content sample collection. Metatranscriptomes from rumen fiber adherent and fiber-free active bacteria were sequenced using Ion Torrent PGM platform followed by annotation using MG-RAST server and CAZYmes (Carbohydrate active enzymes) analysis toolkit. In all the samples Bacteroidetes was the most abundant phylum followed by Firmicutes. Functional analysis using KEGG Orthology database revealed Metabolism as the most abundant category at level 1 within which Carbohydrate metabolism was dominating. Diet treatments also exerted significant differences in proportion of enzymes involved in metabolic pathways for VFA production. Carbohydrate Active Enzyme(CAZy) analysis revealed the abundance of genes encoding glycoside hydrolases with the highest representation of GH13 CAZy family in all the samples. The findings provide an overview of the activities occurring in the rumen as well as active bacterial population and the changes occurring through different dietary treatments. Copyright © 2017 Elsevier Ltd. All rights reserved.

Pyrosequencing Reveals Fungal Communities in the Rhizosphere of Xinjiang Jujube

Directory of Open Access Journals (Sweden)

Peng Liu

2015-01-01

Full Text Available Fungi are important soil components as both decomposers and plant symbionts and play a major role in ecological and biogeochemical processes. However, little is known about the richness and structure of fungal communities. DNA sequencing technologies allow for the direct estimation of microbial community diversity, avoiding culture-based biases. We therefore used 454 pyrosequencing to investigate the fungal communities in the rhizosphere of Xinjiang jujube. We obtained no less than 40,488 internal transcribed spacer (ITS rDNA reads, the number of each sample was 6943, 6647, 6584, 6550, 6860, and 6904, and we used bioinformatics and multivariate statistics to analyze the results. The index of diversity showed greater richness in the rhizosphere fungal community of a 3-year-old jujube than in that of an 8-year-old jujube. Most operational taxonomic units belonged to Ascomycota, and taxonomic analyses identified Hypocreales as the dominant fungal order. Our results demonstrated that the fungal orders are present in different proportions in different sampling areas. Redundancy analysis (RDA revealed a significant correlation between soil properties and the abundance of fungal phyla. Our results indicated lower fungal diversity in the rhizosphere of Xinjiang jujube than that reported in other studies, and we hope our findings provide a reference for future research.

Effect of Sample Storage Temperature and Time Delay on Blood Gases, Bicarbonate and pH in Human Arterial Blood Samples.

Science.gov (United States)

Mohammadhoseini, Elham; Safavi, Enayat; Seifi, Sepideh; Seifirad, Soroush; Firoozbakhsh, Shahram; Peiman, Soheil

2015-03-01

Results of arterial blood gas analysis can be biased by pre-analytical factors, such as time interval before analysis, temperature during storage and syringe type. To investigate the effects of samples storage temperature and time delay on blood gases, bicarbonate and PH results in human arterial blood samples. 2.5 mL arterial blood samples were drawn from 45 patients via an indwelling Intraarterial catheter. Each sample was divided into five equal samples and stored in multipurpose tuberculin plastic syringes. Blood gas analysis was performed on one of five samples as soon as possible. Four other samples were divided into two groups stored at 22°C and 0°C. Blood gas analyses were repeated at 30 and 60 minutes after sampling. PaO2 of the samples stored at 0°C was increased significantly after 60 minutes (P = 0.007). The PaCO2 of the samples kept for 30 and 60 minutes at 22°C was significantly higher than primary result (P = 0.04, P samples stored at 22°C, pH decreased significantly after 30 and 60 minutes (P = 0.017, P = 0.001). There were no significant differences in other results of samples stored at 0°C or 22°C after 30 or 60 minutes. In samples stored in plastic syringes, overestimation of PaO2 levels should be noted if samples cooled before analysis. In samples stored in plastic syringes, it is not necessary to store samples in iced water when analysis delayed up to one hour.

Research-Grade 3D Virtual Astromaterials Samples: Novel Visualization of NASA's Apollo Lunar Samples and Antarctic Meteorite Samples to Benefit Curation, Research, and Education

Science.gov (United States)

Blumenfeld, E. H.; Evans, C. A.; Oshel, E. R.; Liddle, D. A.; Beaulieu, K. R.; Zeigler, R. A.; Righter, K.; Hanna, R. D.; Ketcham, R. A.

2017-01-01

NASA's vast and growing collections of astromaterials are both scientifically and culturally significant, requiring unique preservation strategies that need to be recurrently updated to contemporary technological capabilities and increasing accessibility demands. New technologies have made it possible to advance documentation and visualization practices that can enhance conservation and curation protocols for NASA's Astromaterials Collections. Our interdisciplinary team has developed a method to create 3D Virtual Astromaterials Samples (VAS) of the existing collections of Apollo Lunar Samples and Antarctic Meteorites. Research-grade 3D VAS will virtually put these samples in the hands of researchers and educators worldwide, increasing accessibility and visibility of these significant collections. With new sample return missions on the horizon, it is of primary importance to develop advanced curation standards for documentation and visualization methodologies.

Effect of measurement error budgets and hybrid metrology on qualification metrology sampling

Science.gov (United States)

Sendelbach, Matthew; Sarig, Niv; Wakamoto, Koichi; Kim, Hyang Kyun (Helen); Isbester, Paul; Asano, Masafumi; Matsuki, Kazuto; Osorio, Carmen; Archie, Chas

2014-10-01

Until now, metrologists had no statistics-based method to determine the sampling needed for an experiment before the start that accuracy experiment. We show a solution to this problem called inverse total measurement uncertainty (TMU) analysis, by presenting statistically based equations that allow the user to estimate the needed sampling after providing appropriate inputs, allowing him to make important "risk versus reward" sampling, cost, and equipment decisions. Application examples using experimental data from scatterometry and critical dimension scanning electron microscope tools are used first to demonstrate how the inverse TMU analysis methodology can be used to make intelligent sampling decisions and then to reveal why low sampling can lead to unstable and misleading results. One model is developed that can help experimenters minimize sampling costs. A second cost model reveals the inadequacy of some current sampling practices-and the enormous costs associated with sampling that provides reasonable levels of certainty in the result. We introduce the strategies on how to manage and mitigate these costs and begin the discussion on how fabs are able to manufacture devices using minimal reference sampling when qualifying metrology steps. Finally, the relationship between inverse TMU analysis and hybrid metrology is explored.

The microbiome of Brazilian mangrove sediments as revealed by metagenomics

NARCIS (Netherlands)

Andreote, Fernando Dini; Jiménez Avella, Diego; Chaves, Diego; Dias, Armando Cavalcante Franco; Luvizotto, Danice Mazzer; Dini-Andreote, Francisco; Fasanella, Cristiane Cipola; Lopez, Maryeimy Varon; Baena, Sandra; Taketani, Rodrigo Gouvêa; de Melo, Itamar Soares

2012-01-01

Here we embark in a deep metagenomic survey that revealed the taxonomic and potential metabolic pathways aspects of mangrove sediment microbiology. The extraction of DNA from sediment samples and the direct application of pyrosequencing resulted in approximately 215 Mb of data from four distinct

Sample vial inserts: A better approach for sampling heterogeneous slurry samples in the SRS Defense Waste Processing Facility

International Nuclear Information System (INIS)

Coleman, C.J.; Goode, S.R.

1996-01-01

A convenient and effective new approach for analyzing DWPF samples involves the use of inserts with volumes of 1.5--3 ml placed in the neck of 14 ml sample vials. The inserts have rims that conform to the rim of the vials so that they sit straight and stable in the vial. The DWPF tank sampling system fills the pre-weighed insert rather than the entire vial, so the vial functions only as the insert holder. The shielded cell operator then removes the vial cap and decants the insert containing the sample into a plastic bottle, crucible, etc., for analysis. Inert materials such as Teflon, plastic, and zirconium are used for the insert so it is unnecessary to separate the insert from the sample for most analyses. The key technique advantage of using inserts to take DWPF samples versus filling sample vials is that it provides a convenient and almost foolproof way of obtaining and handling small volumes of slurry samples in a shielded cell without corrupting the sample. Since the insert allows the entire sample to be analyzed, this approach eliminates the errors inherent with subsampling heterogeneous slurries that comprise DWPF samples. Slurry samples can then be analyzed with confidence. Analysis times are dramatically reduced by eliminating the drying and vitrification steps normally used to produce a homogeneous solid sample. Direct dissolution and elemental analysis of slurry samples are achieved in 8 hours or less compared with 40 hours for analysis of vitrified slurry samples. Comparison of samples taken in inserts versus full vials indicate that the insert does not significantly affect sample composition

Micro-PIXE evaluation of radioactive cesium transfer in contaminated soil samples

International Nuclear Information System (INIS)

Fujishiro, F.; Ishii, K.; Matsuyama, S.; Arai, H.; Ishizaki, A.; Osada, N.; Sugai, H.; Kusano, K.; Nozawa, Y.; Yamauchi, S.; Karahashi, M.; Oshikawa, S.; Kikuchi, K.; Koshio, S.; Watanabe, K.; Suzuki, Y.

2014-01-01

Highlights: • There are radioactively contaminated soils having a radioactive cesium transfer of 0.01. • Micro-PIXE analysis has revealed an existence of phosphorus in a contaminated soil. • Radioactive cesium captured by phosphorus compound would be due to radioactive transfer. -- Abstract: Micro-PIXE analysis has been performed on two soil samples with high cesium activity concentrations. These soil samples were contaminated by fallout from the accident at Fukushima Daiichi Nuclear Power Plant. One exhibits a radioactive cesium transfer of ∼0.01, and the other shows a radioactive cesium transfer of less than 0.001, even though both samples have high cesium activity concentrations exceeding 10,000 Bq/kg. X-ray spectra and elemental images of the soil samples revealed the presence of chlorine, which can react with cesium to produce an inorganic soluble compound, and phosphorus-containing cesium-capturable organic compounds

Bacterial diversity characterization in petroleum samples from Brazilian reservoirs

Science.gov (United States)

de Oliveira, Valéria Maia; Sette, Lara Durães; Simioni, Karen Christina Marques; dos Santos Neto, Eugênio Vaz

2008-01-01

This study aimed at evaluating potential differences among the bacterial communities from formation water and oil samples originated from biodegraded and non-biodegraded Brazilian petroleum reservoirs by using a PCR-DGGE based approach. Environmental DNA was isolated and used in PCR reactions with bacterial primers, followed by separation of 16S rDNA fragments in the DGGE. PCR products were also cloned and sequenced, aiming at the taxonomic affiliation of the community members. The fingerprints obtained allowed the direct comparison among the bacterial communities from oil samples presenting distinct degrees of biodegradation, as well as between the communities of formation water and oil sample from the non-biodegraded reservoir. Very similar DGGE band profiles were observed for all samples, and the diversity of the predominant bacterial phylotypes was shown to be low. Cloning and sequencing results revealed major differences between formation water and oil samples from the non-biodegraded reservoir. Bacillus sp. and Halanaerobium sp. were shown to be the predominant components of the bacterial community from the formation water sample, whereas the oil sample also included Alicyclobacillus acidoterrestris, Rhodococcus sp., Streptomyces sp. and Acidithiobacillus ferrooxidans. The PCR-DGGE technique, combined with cloning and sequencing of PCR products, revealed the presence of taxonomic groups not found previously in these samples when using cultivation-based methods and 16S rRNA gene library assembly, confirming the need of a polyphasic study in order to improve the knowledge of the extent of microbial diversity in such extreme environments. PMID:24031244

Negative associations between corpus callosum midsagittal area and IQ in a representative sample of healthy children and adolescents.

Directory of Open Access Journals (Sweden)

Hooman Ganjavi

Full Text Available Documented associations between corpus callosum size and cognitive ability have heretofore been inconsistent potentially owing to differences in sample characteristics, differing methodologies in measuring CC size, or the use of absolute versus relative measures. We investigated the relationship between CC size and intelligence quotient (IQ in the NIH MRI Study of Normal Brain Development sample, a large cohort of healthy children and adolescents (aged six to 18, n = 198 recruited to be representative of the US population. CC midsagittal area was measured using an automated system that partitioned the CC into 25 subregions. IQ was measured using the Wechsler Abbreviated Scale of Intelligence (WASI. After correcting for total brain volume and age, a significant negative correlation was found between total CC midsagittal area and IQ (r = -0.147; p = 0.040. Post hoc analyses revealed a significant negative correlation in children (age<12 (r = -0.279; p = 0.004 but not in adolescents (age≥12 (r = -0.005; p = 0.962. Partitioning the subjects by gender revealed a negative correlation in males (r = -0.231; p = 0.034 but not in females (r = 0.083; p = 0.389. Results suggest that the association between CC and intelligence is mostly driven by male children. In children, a significant gender difference was observed for FSIQ and PIQ, and in males, a significant age-group difference was observed for FSIQ and PIQ. These findings suggest that the correlation between CC midsagittal area and IQ may be related to age and gender.

A bioassay for the detection of benzimidazoles reveals their presence in a range of environmental samples

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Terence S Crofts

2014-11-01

Full Text Available Cobamides are a family of enzyme cofactors that include vitamin B12 (cobalamin and are produced solely by prokaryotes. Structural variability in the lower axial ligand has been observed in cobamides produced by diverse organisms. Of the three classes of lower ligands, the benzimidazoles are uniquely found in cobamides, whereas the purine and phenolic bases have additional biological functions. Many organisms acquire cobamides by salvaging and remodeling cobamides or their precursors from the environment. These processes require free benzimidazoles for incorporation as lower ligands, though the presence of benzimidazoles in the environment has not been previously investigated. Here, we report a new purification method and bioassay to measure the total free benzimidazole content of samples from microbial communities and laboratory media components. The bioassay relies on the calcofluor-bright phenotype of a bluB mutant of the model cobalamin-producing bacterium Sinorhizobium meliloti. The concentrations of individual benzimidazoles in these samples were measured by liquid chromatography-tandem mass spectrometry. Several benzimidazoles were detected in subpicomolar to subnanomolar concentrations in host-associated and environmental samples. In addition, benzimidazoles were found to be common contaminants of laboratory media components. These results suggest that benzimidazoles present in the environment and in laboratory media have the potential to influence microbial metabolic activities.

Revealed social preference for potable groundwater: An Eastern Iowa case study

Science.gov (United States)

Raunikar, R. P.; Bernknopf, R. L.; Forney, W.; Mishra, S.

2011-12-01

The spatially explicit land use and land cover information provided by Landsat moderate-resolution land imagery (MRLI) is needed to more efficiently balance the production of goods and services over landscapes. For example, economic trade-offs are needed to provide both clean groundwater resources and other non-environmental goods and services produced by activities that affect the vadose zone and thus contribute to contamination of groundwater. These trade-off choices are made by numerous economic agents and are constrained by many social institutions including governmental regulations at many levels, contractual obligations and traditions. In effect, on a social level, society acts as if it values groundwater by foregoing other goods to protect these resources. The result of the protection afforded to groundwater resources is observable by measuring contamination in well samples. This observed level of groundwater contamination risk is the revealed preference of society as a whole for clean groundwater. We observed the risk of groundwater contamination in a sampling of well data from our study area (35 counties of Eastern Iowa.) We used a proportional hazard model to quantify the nitrate contamination survival implied by the panel of 19,873 well data, where remaining below a 10 mg/ml maximum contamination level (MCL) is defined as survival. We tested the data for evidence that the levels of protection provided to these resources is correlated with aquifer and vadose zone characteristics and geographic location and whether it changed over time and with economic and other conditions. We demonstrate the use of a nitrate conditioned hazard function for projecting the survival of wells based on nitrate exposure information over the 1940 to 2010 time period. We discuss results of simulations of the survival process that demonstrate the economic significance of this approach. We find that aquifer survival has been significantly improving over time. The principle of

Biological Sampling Variability Study

Energy Technology Data Exchange (ETDEWEB)

Amidan, Brett G. [Pacific Northwest National Lab. (PNNL), Richland, WA (United States); Hutchison, Janine R. [Pacific Northwest National Lab. (PNNL), Richland, WA (United States)

2016-11-08

There are many sources of variability that exist in the sample collection and analysis process. This paper addresses many, but not all, sources of variability. The main focus of this paper was to better understand and estimate variability due to differences between samplers. Variability between days was also studied, as well as random variability within each sampler. Experiments were performed using multiple surface materials (ceramic and stainless steel), multiple contaminant concentrations (10 spores and 100 spores), and with and without the presence of interfering material. All testing was done with sponge sticks using 10-inch by 10-inch coupons. Bacillus atrophaeus was used as the BA surrogate. Spores were deposited using wet deposition. Grime was coated on the coupons which were planned to include the interfering material (Section 3.3). Samples were prepared and analyzed at PNNL using CDC protocol (Section 3.4) and then cultured and counted. Five samplers were trained so that samples were taken using the same protocol. Each sampler randomly sampled eight coupons each day, four coupons with 10 spores deposited and four coupons with 100 spores deposited. Each day consisted of one material being tested. The clean samples (no interfering materials) were run first, followed by the dirty samples (coated with interfering material). There was a significant difference in recovery efficiency between the coupons with 10 spores deposited (mean of 48.9%) and those with 100 spores deposited (mean of 59.8%). There was no general significant difference between the clean and dirty (containing interfering material) coupons or between the two surface materials; however, there was a significant interaction between concentration amount and presence of interfering material. The recovery efficiency was close to the same for coupons with 10 spores deposited, but for the coupons with 100 spores deposited, the recovery efficiency for the dirty samples was significantly larger (65

Why weight? Modelling sample and observational level variability improves power in RNA-seq analyses.

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Liu, Ruijie; Holik, Aliaksei Z; Su, Shian; Jansz, Natasha; Chen, Kelan; Leong, Huei San; Blewitt, Marnie E; Asselin-Labat, Marie-Liesse; Smyth, Gordon K; Ritchie, Matthew E

2015-09-03

Variations in sample quality are frequently encountered in small RNA-sequencing experiments, and pose a major challenge in a differential expression analysis. Removal of high variation samples reduces noise, but at a cost of reducing power, thus limiting our ability to detect biologically meaningful changes. Similarly, retaining these samples in the analysis may not reveal any statistically significant changes due to the higher noise level. A compromise is to use all available data, but to down-weight the observations from more variable samples. We describe a statistical approach that facilitates this by modelling heterogeneity at both the sample and observational levels as part of the differential expression analysis. At the sample level this is achieved by fitting a log-linear variance model that includes common sample-specific or group-specific parameters that are shared between genes. The estimated sample variance factors are then converted to weights and combined with observational level weights obtained from the mean-variance relationship of the log-counts-per-million using 'voom'. A comprehensive analysis involving both simulations and experimental RNA-sequencing data demonstrates that this strategy leads to a universally more powerful analysis and fewer false discoveries when compared to conventional approaches. This methodology has wide application and is implemented in the open-source 'limma' package. © The Author(s) 2015. Published by Oxford University Press on behalf of Nucleic Acids Research.

Physicochemical state of the nanotopographic surface of commercially pure titanium following anodization-hydrothermal treatment reveals significantly improved hydrophilicity and surface energy profiles.

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Takebe, Jun; Ito, Shigeki; Miura, Shingo; Miyata, Kyohei; Ishibashi, Kanji

2012-01-01

A method of coating commercially pure titanium (cpTi) implants with a highly crystalline, thin hydroxyapatite (HA) layer using discharge anodic oxidation followed by hydrothermal treatment (Spark discharged Anodic oxidation treatment ; SA-treated cpTi) has been reported for use in clinical dentistry. We hypothesized that a thin HA layer with high crystallinity and nanostructured anodic titanium oxide film on such SA-treated cpTi implant surfaces might be a crucial function of their surface-specific potential energy. To test this, we analyzed anodic oxide (AO) cpTi and SA-treated cpTi disks by SEM and AFM. Contact angles and surface free energy of each disk surface was measured using FAMAS software. High-magnification SEM and AFM revealed the nanotopographic structure of the anodic titanium oxide film on SA-treated cpTi; however, this was not observed on the AO cpTi surface. The contact angle and surface free energy measurements were also significantly different between AO cpTi and SA-treated cpTi surfaces (Tukey's, P<0.05). These data indicated that the change of physicochemical properties of an anodic titanium oxide film with HA crystals on an SA-treated cpTi surface may play a key role in the phenomenon of osteoconduction during the process of osseointegration. Copyright © 2011 Elsevier B.V. All rights reserved.

Museum samples reveal rapid evolution by wild honey bees exposed to a novel parasite.

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Mikheyev, Alexander S; Tin, Mandy M Y; Arora, Jatin; Seeley, Thomas D

2015-08-06

Understanding genetic changes caused by novel pathogens and parasites can reveal mechanisms of adaptation and genetic robustness. Using whole-genome sequencing of museum and modern specimens, we describe the genomic changes in a wild population of honey bees in North America following the introduction of the ectoparasitic mite, Varroa destructor. Even though colony density in the study population is the same today as in the past, a major loss of haplotypic diversity occurred, indicative of a drastic mitochondrial bottleneck, caused by massive colony mortality. In contrast, nuclear genetic diversity did not change, though hundreds of genes show signs of selection. The genetic diversity within each bee colony, particularly as a consequence of polyandry by queens, may enable preservation of genetic diversity even during population bottlenecks. These findings suggest that genetically diverse honey bee populations can recover from introduced diseases by evolving rapid tolerance, while maintaining much of the standing genetic variation.

Sample Entropy and Traditional Measures of Heart Rate Dynamics Reveal Different Modes of Cardiovascular Control During Low Intensity Exercise

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Matthias Weippert

2014-10-01

Full Text Available Nonlinear parameters of heart rate variability (HRV have proven their prognostic value in clinical settings, but their physiological background is not very well established. We assessed the effects of low intensity isometric (ISO and dynamic (DYN exercise of the lower limbs on heart rate matched intensity on traditional and entropy measures of HRV. Due to changes of afferent feedback under DYN and ISO a distinct autonomic response, mirrored by HRV measures, was hypothesized. Five-minute inter-beat interval measurements of 43 healthy males (26.0 ± 3.1 years were performed during rest, DYN and ISO in a randomized order. Blood pressures and rate pressure product were higher during ISO vs. DYN (p < 0.001. HRV indicators SDNN as well as low and high frequency power were significantly higher during ISO (p < 0.001 for all measures. Compared to DYN, sample entropy (SampEn was lower during ISO (p < 0.001. Concluding, contraction mode itself is a significant modulator of the autonomic cardiovascular response to exercise. Compared to DYN, ISO evokes a stronger blood pressure response and an enhanced interplay between both autonomic branches. Non-linear HRV measures indicate a more regular behavior under ISO. Results support the view of the reciprocal antagonism being only one of many modes of autonomic heart rate control. Under different conditions; the identical “end product” heart rate might be achieved by other modes such as sympathovagal co-activation as well.

On peculiarities of distribution of some elements in vegetation samples

International Nuclear Information System (INIS)

Bakiev, S.A.; Rakhmanov, J.; Khakimov, Z.M.; Turayev, S.

2005-01-01

This work is devoted to the neutron-activation analysis of medicines of vegetation origin and some herbs, vegetables, fruits and cereals, which are used in oriental medicine, in order to reveal peculiarities of distribution of studied elements in them and possible relations between this distribution and parameters of oriental medicine. The sampling involving 85 species and their preparation for analysis, as well as complex of necessary methodological studies were performed and the method of sample analysis for 14 macro- and microelements (Na, Al, Cl, K, Sc, Mn, Fe, Co, Cu, Zn, Br, J, La, Au) was developed. The studies carried out have enabled one to obtain data on concentrations of these elements and to reveal peculiarities of their distribution in the samples under interest. It was revealed herbs, fruits and cereals with pronounced higher concentrations (with respect to the mean values) of one or another element, which are perhaps concentrators of those elements, as well as samples with lower concentrations of elements (see table). It is indicative that in all herbs only enhanced concentrations of elements are observed, but in fruits and cereals-only lowered concentrations of elements. These results can be of interest for geochemical ecology, dietology, therapy, as well as for activities on correction of elemental content of ecosystems, including soils, and alive organisms It is suggested to continue studies with extension of range of object types and analysed elements. Mathematical analysis of the obtained results was performed with comparison of concentrations of a number of elements in the different objects with classifying parameters ('cold-hot' and 'dry-wet') of these objects according to oriental medicine. In the current stage of studies no relation between these parameters and concentrations has been found. It does not mean that there are not such relations at all, they may be revealed with extension and development of our' studies.

Temporal Sampling of White Band Disease Infected Corals Reveals Complex and Dynamic Bacterial Communities

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Gignoux-Wolfsohn, S.; Vollmer, S. V.; Aronson, F. M.

2016-02-01

White band disease (WBD) is a coral disease that is currently decimating populations of the endangered staghorn coral, Acropora cervicornis and elkhorn coral, A. palmata across the Caribbean. Since it was first reported in 1979, WBD has killed 95% of these critical reef-building Caribbean corals. WBD is infectious; it can be transmitted through the water column or by a corallivorous snail. While previous research shows that WBD is likely caused by bacteria, identification of a specific pathogen or pathogens has remained elusive. Much of the difficulty of understanding the etiology of the disease comes from a lack of information about how existing bacterial communities respond to disease and separating initial from secondary colonizers. In order to address this lack of information, we performed a fully-crossed tank infection experiment. We exposed healthy corals from two different sites to disease and healthy (control) homogenates from both sites, replicating genotype across tanks. We sampled every coral at three time points: before inoculation with the homogenate, after inoculation, and when the coral showed signs of disease. We then performed 16S rRNA gene sequencing on the Illumina HiSeq 2000. We saw significant differences between time points and disease state. Interestingly, at the first time point (time one) we observed differences between genotypes: every fragment from some genotypes was dominated by Endozoicomonas, while other genotypes were not dominated by one family. At time two we saw an increase in abundance of Alteromonadaceae and Flavobacteriaceae in all corals, and a larger increase in disease-exposed corals. At time three, we saw another increase in Flavobacteriaceae abundance in diseased corals, as well as an introduction of Francisella to diseased corals. While Flavobacteriaceae and Francisella were proposed as potential pathogens, their increase at time three suggests they may be secondary colonizers or opportunists. In genotypes that were

The significance of Sampling Design on Inference: An Analysis of Binary Outcome Model of Children’s Schooling Using Indonesian Large Multi-stage Sampling Data

OpenAIRE

Ekki Syamsulhakim

2008-01-01

This paper aims to exercise a rather recent trend in applied microeconometrics, namely the effect of sampling design on statistical inference, especially on binary outcome model. Many theoretical research in econometrics have shown the inappropriateness of applying i.i.dassumed statistical analysis on non-i.i.d data. These research have provided proofs showing that applying the iid-assumed analysis on a non-iid observations would result in an inflated standard errors which could make the esti...

Fine-scale genetic structure and cryptic associations reveal evidence of kin-based sociality in the African forest elephant.

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Stephanie G Schuttler

Full Text Available Spatial patterns of relatedness within animal populations are important in the evolution of mating and social systems, and have the potential to reveal information on species that are difficult to observe in the wild. This study examines the fine-scale genetic structure and connectivity of groups within African forest elephants, Loxodonta cyclotis, which are often difficult to observe due to forest habitat. We tested the hypothesis that genetic similarity will decline with increasing geographic distance, as we expect kin to be in closer proximity, using spatial autocorrelation analyses and Tau K(r tests. Associations between individuals were investigated through a non-invasive genetic capture-recapture approach using network models, and were predicted to be more extensive than the small groups found in observational studies, similar to fission-fusion sociality found in African savanna (Loxodonta africana and Asian (Elephas maximus species. Dung samples were collected in Lopé National Park, Gabon in 2008 and 2010 and genotyped at 10 microsatellite loci, genetically sexed, and sequenced at the mitochondrial DNA control region. We conducted analyses on samples collected at three different temporal scales: a day, within six-day sampling sessions, and within each year. Spatial autocorrelation and Tau K(r tests revealed genetic structure, but results were weak and inconsistent between sampling sessions. Positive spatial autocorrelation was found in distance classes of 0-5 km, and was strongest for the single day session. Despite weak genetic structure, individuals within groups were significantly more related to each other than to individuals between groups. Social networks revealed some components to have large, extensive groups of up to 22 individuals, and most groups were composed of individuals of the same matriline. Although fine-scale population genetic structure was weak, forest elephants are typically found in groups consisting of kin and

Sputum microbiota in tuberculosis as revealed by 16S rRNA pyrosequencing.

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Man Kit Cheung

Full Text Available BACKGROUND: Tuberculosis (TB remains a global threat in the 21st century. Traditional studies of the disease are focused on the single pathogen Mycobacterium tuberculosis. Recent studies have revealed associations of some diseases with an imbalance in the microbial community. Characterization of the TB microbiota could allow a better understanding of the disease. METHODOLOGY/PRINCIPAL FINDINGS: Here, the sputum microbiota in TB infection was examined by using 16S rRNA pyrosequencing. A total of 829,873 high-quality sequencing reads were generated from 22 TB and 14 control sputum samples. Firmicutes, Proteobacteria, Bacteroidetes, Actinobacteria, and Fusobacteria were the five major bacterial phyla recovered, which together composed over 98% of the microbial community. Proteobacteria and Bacteroidetes were more represented in the TB samples and Firmicutes was more predominant in the controls. Sixteen major bacterial genera were recovered. Streptococcus, Neisseria and Prevotella were the most predominant genera, which were dominated by several operational taxonomic units grouped at a 97% similarity level. Actinomyces, Fusobacterium, Leptotrichia, Prevotella, Streptococcus, and Veillonella were found in all TB samples, possibly representing the core genera in TB sputum microbiota. The less represented genera Mogibacterium, Moryella and Oribacterium were enriched statistically in the TB samples, while a genus belonging to the unclassified Lactobacillales was enriched in the controls. The diversity of microbiota was similar in the TB and control samples. CONCLUSIONS/SIGNIFICANCE: The composition and diversity of sputum microbiota in TB infection was characterized for the first time by using high-throughput pyrosequencing. It lays the framework for examination of potential roles played by the diverse microbiota in TB pathogenesis and progression, and could ultimately facilitate advances in TB treatment.

Influence of Ongoing Task Difficulty and Motivation Level on Children's Prospective Memory in a Chinese Sample.

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Han, Pi-Guo; Han, Lei; Bian, Yu-Long; Tian, Yu; Xu, Min-Xia; Gao, Feng-Qiang

2017-01-01

Prospective memory (PM) is the process associated with the task of realizing delayed intentions in the future. Researchers distinguish two types of PM, namely time-based PM (tbPM) and event-based PM (ebPM). Experiment 1 investigated the developmental trajectory of 3- to 5-year-old preschool children's PM ability, and the occurrence of delayed retrieval (children execute the PM task in a larger window of opportunity) in both tbPM and ebPM tasks. Results revealed that the 5-year-old children outperformed the 3- and 4-year-old children in PM. Moreover, delayed retrieval was more likely to occur in tbPM task than in ebPM task. In Experiment 2, the influence of ongoing task (OT) difficulty on PM performance was investigated with a sample of 5-year-old children. Results revealed no significant effect of OT difficulty on PM performance. In Experiment 3, we improved children's motivation level to complete the OT, then explored the influence of OT difficulty on children's PM performance. Results revealed that the effect of OT difficulty on PM performance became significant after increasing the children's motivation to complete the OT. These results provide insights into the mechanism of attentional resource allocation in PM tasks and have crucial educational and social implications.

The microbiome of Brazilian mangrove sediments as revealed by metagenomics.

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Fernando Dini Andreote

Full Text Available Here we embark in a deep metagenomic survey that revealed the taxonomic and potential metabolic pathways aspects of mangrove sediment microbiology. The extraction of DNA from sediment samples and the direct application of pyrosequencing resulted in approximately 215 Mb of data from four distinct mangrove areas (BrMgv01 to 04 in Brazil. The taxonomic approaches applied revealed the dominance of Deltaproteobacteria and Gammaproteobacteria in the samples. Paired statistical analysis showed higher proportions of specific taxonomic groups in each dataset. The metabolic reconstruction indicated the possible occurrence of processes modulated by the prevailing conditions found in mangrove sediments. In terms of carbon cycling, the sequences indicated the prevalence of genes involved in the metabolism of methane, formaldehyde, and carbon dioxide. With respect to the nitrogen cycle, evidence for sequences associated with dissimilatory reduction of nitrate, nitrogen immobilization, and denitrification was detected. Sequences related to the production of adenylsulfate, sulfite, and H(2S were relevant to the sulphur cycle. These data indicate that the microbial core involved in methane, nitrogen, and sulphur metabolism consists mainly of Burkholderiaceae, Planctomycetaceae, Rhodobacteraceae, and Desulfobacteraceae. Comparison of our data to datasets from soil and sea samples resulted in the allotment of the mangrove sediments between those samples. The results of this study add valuable data about the composition of microbial communities in mangroves and also shed light on possible transformations promoted by microbial organisms in mangrove sediments.

The microbiome of Brazilian mangrove sediments as revealed by metagenomics.

Science.gov (United States)

Andreote, Fernando Dini; Jiménez, Diego Javier; Chaves, Diego; Dias, Armando Cavalcante Franco; Luvizotto, Danice Mazzer; Dini-Andreote, Francisco; Fasanella, Cristiane Cipola; Lopez, Maryeimy Varon; Baena, Sandra; Taketani, Rodrigo Gouvêa; de Melo, Itamar Soares

2012-01-01

Here we embark in a deep metagenomic survey that revealed the taxonomic and potential metabolic pathways aspects of mangrove sediment microbiology. The extraction of DNA from sediment samples and the direct application of pyrosequencing resulted in approximately 215 Mb of data from four distinct mangrove areas (BrMgv01 to 04) in Brazil. The taxonomic approaches applied revealed the dominance of Deltaproteobacteria and Gammaproteobacteria in the samples. Paired statistical analysis showed higher proportions of specific taxonomic groups in each dataset. The metabolic reconstruction indicated the possible occurrence of processes modulated by the prevailing conditions found in mangrove sediments. In terms of carbon cycling, the sequences indicated the prevalence of genes involved in the metabolism of methane, formaldehyde, and carbon dioxide. With respect to the nitrogen cycle, evidence for sequences associated with dissimilatory reduction of nitrate, nitrogen immobilization, and denitrification was detected. Sequences related to the production of adenylsulfate, sulfite, and H(2)S were relevant to the sulphur cycle. These data indicate that the microbial core involved in methane, nitrogen, and sulphur metabolism consists mainly of Burkholderiaceae, Planctomycetaceae, Rhodobacteraceae, and Desulfobacteraceae. Comparison of our data to datasets from soil and sea samples resulted in the allotment of the mangrove sediments between those samples. The results of this study add valuable data about the composition of microbial communities in mangroves and also shed light on possible transformations promoted by microbial organisms in mangrove sediments.

Effects of sterilization treatments on the analysis of TOC in water samples.

Science.gov (United States)

Shi, Yiming; Xu, Lingfeng; Gong, Dongqin; Lu, Jun

2010-01-01

Decomposition experiments conducted with and without microbial processes are commonly used to study the effects of environmental microorganisms on the degradation of organic pollutants. However, the effects of biological pretreatment (sterilization) on organic matter often have a negative impact on such experiments. Based on the principle of water total organic carbon (TOC) analysis, the effects of physical sterilization treatments on determination of TOC and other water quality parameters were investigated. The results revealed that two conventional physical sterilization treatments, autoclaving and 60Co gamma-radiation sterilization, led to the direct decomposition of some organic pollutants, resulting in remarkable errors in the analysis of TOC in water samples. Furthermore, the extent of the errors varied with the intensity and the duration of sterilization treatments. Accordingly, a novel sterilization method for water samples, 0.45 microm micro-filtration coupled with ultraviolet radiation (MCUR), was developed in the present study. The results indicated that the MCUR method was capable of exerting a high bactericidal effect on the water sample while significantly decreasing the negative impact on the analysis of TOC and other water quality parameters. Before and after sterilization treatments, the relative errors of TOC determination could be controlled to lower than 3% for water samples with different categories and concentrations of organic pollutants by using MCUR.

Paternally expressed, imprinted insulin-like growth factor-2 in chorionic villi correlates significantly with birth weight.

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Charalambos Demetriou

Full Text Available Fetal growth involves highly complex molecular pathways. IGF2 is a key paternally expressed growth hormone that is critical for in utero growth in mice. Its role in human fetal growth has remained ambiguous, as it has only been studied in term tissues. Conversely the maternally expressed growth suppressor, PHLDA2, has a significant negative correlation between its term placental expression and birth weight.The aim of this study is to address the role in early gestation of expression of IGF1, IGF2, their receptors IGF1R and IGF2R, and PHLDA2 on term birth weight.Real-time quantitative PCR was used to investigate mRNA expression of IGF1, IGF2, IGF1R, IGF2R and PHLDA2 in chorionic villus samples (CVS (n = 260 collected at 11-13 weeks' gestation. Expression was correlated with term birth weight using statistical package R including correction for several confounding factors.Transcript levels of IGF2 and IGF2R revealed a significant positive correlation with birth weight (0.009 and 0.04, respectively. No effect was observed for IGF1, IGF1R or PHLDA2 and birth weight. Critically, small for gestational age (SGA neonates had significantly lower IGF2 levels than appropriate for gestational age neonates (p = 3.6 × 10(-7.Our findings show that IGF2 mRNA levels at 12 weeks gestation could provide a useful predictor of future fetal growth to term, potentially predicting SGA babies. SGA babies are known to be at a higher risk for type 2 diabetes. This research reveals an imprinted, parentally driven rheostat for in utero growth.

Australasian disasters of national significance: an epidemiological analysis, 1900-2012.

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Bradt, David A; Bartley, Bruce; Hibble, Belinda A; Varshney, Kavita

2015-04-01

A regional epidemiological analysis of Australasian disasters in the 20th century to present was undertaken to examine trends in disaster epidemiology; to characterise the impacts on civil society through disaster policy, practice and legislation; and to consider future potential limitations in national disaster resilience. A surveillance definition of disaster was developed conforming to the Centre for Research on the Epidemiology of Disasters (CRED) criteria (≥10 deaths, ≥100 affected, or declaration of state emergency or appeal for international assistance). The authors then applied economic and legislative inclusion criteria to identify additional disasters of national significance. The surveillance definition yielded 165 disasters in the period, from which 65 emerged as disasters of national significance. There were 38 natural disasters, 22 technological disasters, three offshore terrorist attacks and two domestic mass shootings. Geographic analysis revealed that states with major population centres experienced the vast majority of disasters of national significance. Timeline analysis revealed an increasing incidence of disasters since the 1980s, which peaked in the period 2005-2009. Recent seasonal bushfires and floods have incurred the highest death toll and economic losses in Australasian history. Reactive hazard-specific legislation emerged after all terrorist acts and after most disasters of national significance. Timeline analysis reveals an increasing incidence in natural disasters over the past 15 years, with the most lethal and costly disasters occurring in the past 3 years. Vulnerability to disaster in Australasia appears to be increasing. Reactive legislation is a recurrent feature of Australasian disaster response that suggests legislative shortsightedness and a need for comprehensive all-hazards model legislation in the future. © 2015 Australasian College for Emergency Medicine and Australasian Society for Emergency Medicine.

The thresholds for statistical and clinical significance

DEFF Research Database (Denmark)

Jakobsen, Janus Christian; Gluud, Christian; Winkel, Per

2014-01-01

BACKGROUND: Thresholds for statistical significance are insufficiently demonstrated by 95% confidence intervals or P-values when assessing results from randomised clinical trials. First, a P-value only shows the probability of getting a result assuming that the null hypothesis is true and does...... not reflect the probability of getting a result assuming an alternative hypothesis to the null hypothesis is true. Second, a confidence interval or a P-value showing significance may be caused by multiplicity. Third, statistical significance does not necessarily result in clinical significance. Therefore...... of the probability that a given trial result is compatible with a 'null' effect (corresponding to the P-value) divided by the probability that the trial result is compatible with the intervention effect hypothesised in the sample size calculation; (3) adjust the confidence intervals and the statistical significance...

Industrial variographic analysis for continuous sampling system validation

DEFF Research Database (Denmark)

Engström, Karin; Esbensen, Kim Harry

2017-01-01

Karin Engström, LKAB mining, Kiruna, Sweden, continues to present illuminative cases from process industry. Here she reveals more from her ongoing PhD project showing application of variographic characterisation for on-line continuous control of process sampling systems, including the one...

Broad-scale sampling of primary freshwater fish populations reveals the role of intrinsic traits, inter-basin connectivity, drainage area and latitude on shaping contemporary patterns of genetic diversity

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Carla Sousa-Santos

2016-02-01

Full Text Available Background. Worldwide predictions suggest that up to 75% of the freshwater fish species occurring in rivers with reduced discharge could be extinct by 2070 due to the combined effect of climate change and water abstraction. The Mediterranean region is considered to be a hotspot of freshwater fish diversity but also one of the regions where the effects of climate change will be more severe. Iberian cyprinids are currently highly endangered, with over 68% of the species raising some level of conservation concern. Methods. During the FISHATLAS project, the Portuguese hydrographical network was extensively covered (all the 34 river basins and 47 sub-basins in order to contribute with valuable data on the genetic diversity distribution patterns of native cyprinid species. A total of 188 populations belonging to 16 cyprinid species of Squalius, Luciobarbus, Achondrostoma, Iberochondrostoma, Anaecypris and Pseudochondrostoma were characterized, for a total of 3,678 cytochrome b gene sequences. Results. When the genetic diversity of these populations was mapped, it highlighted differences among populations from the same species and between species with identical distribution areas. Factors shaping the contemporary patterns of genetic diversity were explored and the results revealed the role of latitude, inter-basin connectivity, migratory behaviour, species maximum size, species range and other species intrinsic traits in determining the genetic diversity of sampled populations. Contrastingly, drainage area and hydrological regime (permanent vs. temporary seem to have no significant effect on genetic diversity. Species intrinsic traits, maximum size attained, inter-basin connectivity and latitude explained over 30% of the haplotype diversity variance and, generally, the levels of diversity were significantly higher for smaller sized species, from connected and southerly river basins. Discussion. Targeting multiple co-distributed species of primary

Metabolomics reveals variation and correlation among different tissues of olive (Olea europaea L.

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Rao Guodong

2017-09-01

Full Text Available Metabolites in olives are associated with nutritional value and physiological properties. However, comprehensive information regarding the olive metabolome is limited. In this study, we identified 226 metabolites from three different tissues of olive using a non-targeted metabolomic profiling approach, of which 76 named metabolites were confirmed. Further statistical analysis revealed that these 76 metabolites covered different types of primary metabolism and some of the secondary metabolism pathways. One-way analysis of variance (ANOVA statistical assay was performed to calculate the variations within the detected metabolites, and levels of 65 metabolites were differentially expressed in different samples. Hierarchical cluster analysis (HCA dendrograms showed variations among different tissues that were similar to the metabolite profiles observed in new leaves and fruit. Additionally, 5776 metabolite-metabolite correlations were detected by a Pearson correlation coefficient approach. Screening of the calculated correlations revealed 3136, 3025, and 5184 were determined to metabolites and had significant correlations in three different combinations, respectively. This work provides the first comprehensive metabolomic of olive, which will provide new insights into understanding the olive metabolism, and potentially help advance studies in olive metabolic engineering.

Museum samples reveal rapid evolution by wild honey bees exposed to a novel parasite

Science.gov (United States)

Mikheyev, Alexander S.; Tin, Mandy M. Y.; Arora, Jatin; Seeley, Thomas D.

2015-01-01

Understanding genetic changes caused by novel pathogens and parasites can reveal mechanisms of adaptation and genetic robustness. Using whole-genome sequencing of museum and modern specimens, we describe the genomic changes in a wild population of honey bees in North America following the introduction of the ectoparasitic mite, Varroa destructor. Even though colony density in the study population is the same today as in the past, a major loss of haplotypic diversity occurred, indicative of a drastic mitochondrial bottleneck, caused by massive colony mortality. In contrast, nuclear genetic diversity did not change, though hundreds of genes show signs of selection. The genetic diversity within each bee colony, particularly as a consequence of polyandry by queens, may enable preservation of genetic diversity even during population bottlenecks. These findings suggest that genetically diverse honey bee populations can recover from introduced diseases by evolving rapid tolerance, while maintaining much of the standing genetic variation. PMID:26246313

Statistical methods for detecting differentially abundant features in clinical metagenomic samples.

Directory of Open Access Journals (Sweden)

James Robert White

2009-04-01

Full Text Available Numerous studies are currently underway to characterize the microbial communities inhabiting our world. These studies aim to dramatically expand our understanding of the microbial biosphere and, more importantly, hope to reveal the secrets of the complex symbiotic relationship between us and our commensal bacterial microflora. An important prerequisite for such discoveries are computational tools that are able to rapidly and accurately compare large datasets generated from complex bacterial communities to identify features that distinguish them.We present a statistical method for comparing clinical metagenomic samples from two treatment populations on the basis of count data (e.g. as obtained through sequencing to detect differentially abundant features. Our method, Metastats, employs the false discovery rate to improve specificity in high-complexity environments, and separately handles sparsely-sampled features using Fisher's exact test. Under a variety of simulations, we show that Metastats performs well compared to previously used methods, and significantly outperforms other methods for features with sparse counts. We demonstrate the utility of our method on several datasets including a 16S rRNA survey of obese and lean human gut microbiomes, COG functional profiles of infant and mature gut microbiomes, and bacterial and viral metabolic subsystem data inferred from random sequencing of 85 metagenomes. The application of our method to the obesity dataset reveals differences between obese and lean subjects not reported in the original study. For the COG and subsystem datasets, we provide the first statistically rigorous assessment of the differences between these populations. The methods described in this paper are the first to address clinical metagenomic datasets comprising samples from multiple subjects. Our methods are robust across datasets of varied complexity and sampling level. While designed for metagenomic applications, our software

Monitoring prion protein expression in complex biological samples by SERS for diagnostic applications

Energy Technology Data Exchange (ETDEWEB)

Manno, D; Filippo, E; Fiore, R; Serra, A [Dipartimento di Scienza dei Materiali, Universita del Salento, Lecce (Italy); Urso, E; Rizzello, A; Maffia, M [Dipartimento di Scienze e Tecnologie Biologiche ed Ambientali, Universita del Salento, Lecce (Italy)

2010-04-23

Surface-enhanced Raman spectroscopy (SERS) allows a new insight into the analysis of cell physiology. In this work, the difficulty of producing suitable substrates that, besides permitting the amplification of the Raman signal, do not interact with the biological material causing alteration, has been overcome by a combined method of hydrothermal green synthesis and thermal annealing. The SERS analysis of the cell membrane has been performed with special attention to the cellular prion protein PrP{sup C}. In addition, SERS has also been used to reveal the prion protein-Cu(II) interaction in four different cell models (B104, SH-SY5Y, GN11, HeLa), expressing PrP{sup C} at different levels. A significant implication of the current work consists of the intriguing possibility of revealing and quantifying prion protein expression in complex biological samples by a cheap SERS-based method, replacing the expensive and time-consuming immuno-assay systems commonly employed.

Monitoring prion protein expression in complex biological samples by SERS for diagnostic applications

International Nuclear Information System (INIS)

Manno, D; Filippo, E; Fiore, R; Serra, A; Urso, E; Rizzello, A; Maffia, M

2010-01-01

Surface-enhanced Raman spectroscopy (SERS) allows a new insight into the analysis of cell physiology. In this work, the difficulty of producing suitable substrates that, besides permitting the amplification of the Raman signal, do not interact with the biological material causing alteration, has been overcome by a combined method of hydrothermal green synthesis and thermal annealing. The SERS analysis of the cell membrane has been performed with special attention to the cellular prion protein PrP C . In addition, SERS has also been used to reveal the prion protein-Cu(II) interaction in four different cell models (B104, SH-SY5Y, GN11, HeLa), expressing PrP C at different levels. A significant implication of the current work consists of the intriguing possibility of revealing and quantifying prion protein expression in complex biological samples by a cheap SERS-based method, replacing the expensive and time-consuming immuno-assay systems commonly employed.

Pathway-based outlier method reveals heterogeneous genomic structure of autism in blood transcriptome.

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Campbell, Malcolm G; Kohane, Isaac S; Kong, Sek Won

2013-09-24

Decades of research strongly suggest that the genetic etiology of autism spectrum disorders (ASDs) is heterogeneous. However, most published studies focus on group differences between cases and controls. In contrast, we hypothesized that the heterogeneity of the disorder could be characterized by identifying pathways for which individuals are outliers rather than pathways representative of shared group differences of the ASD diagnosis. Two previously published blood gene expression data sets--the Translational Genetics Research Institute (TGen) dataset (70 cases and 60 unrelated controls) and the Simons Simplex Consortium (Simons) dataset (221 probands and 191 unaffected family members)--were analyzed. All individuals of each dataset were projected to biological pathways, and each sample's Mahalanobis distance from a pooled centroid was calculated to compare the number of case and control outliers for each pathway. Analysis of a set of blood gene expression profiles from 70 ASD and 60 unrelated controls revealed three pathways whose outliers were significantly overrepresented in the ASD cases: neuron development including axonogenesis and neurite development (29% of ASD, 3% of control), nitric oxide signaling (29%, 3%), and skeletal development (27%, 3%). Overall, 50% of cases and 8% of controls were outliers in one of these three pathways, which could not be identified using group comparison or gene-level outlier methods. In an independently collected data set consisting of 221 ASD and 191 unaffected family members, outliers in the neurogenesis pathway were heavily biased towards cases (20.8% of ASD, 12.0% of control). Interestingly, neurogenesis outliers were more common among unaffected family members (Simons) than unrelated controls (TGen), but the statistical significance of this effect was marginal (Chi squared P < 0.09). Unlike group difference approaches, our analysis identified the samples within the case and control groups that manifested each expression

Significant reduction of saturation magnetization and microwave-reflection loss in barium-natural ferrite via Nd3+ substitution

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Widanarto, W.; Ardenti, E.; Ghoshal, S. K.; Kurniawan, C.; Effendi, M.; Cahyanto, W. T.

2018-06-01

To minimize the signal degradation, many electronic devices require efficient microwave absorbers with very low reflection-losses within the X-band. We prepared a series of trivalent neodymium-ion (Nd3+) substituted barium-natural ferrite using a modified solid-state reaction method. The effect of the Nd3+-ion content on the structure, surface morphology, magnetic properties, and microwave reflection loss was studied. The composites were characterized using X-ray diffraction, a vibrating sample magnetometer, scanning electron microscopy, and a vector network analyzer. The XRD patterns of the sample without Nd3+ reveal the presence of BaFe12O19 (hexagonal) and BaFe2O4 (rhombohedral) phases. Furthermore, a new hexagonal crystal phase of Ba6Nd2Fe4O15 appeared after substituting Nd3+. The average size of the prepared barium-natural ferrite particles was estimated to be between 0.4 and 0.8 μm. Both saturation magnetization and microwave reflection losses of these barium-ferrites were significantly reduced by increasing the Nd3+ content.

Changing relationships with significant others: Reflections of ...

African Journals Online (AJOL)

Symbolic interactionism provides the framework for analysing the building of relationships between elite athletes and their significant others. In-depth interviews were conducted with elite throwers and decathlon athletes. The sample included current (n=15) and retired (n=5) student-athletes, parents (n=5), coaches (n=2) ...

RNA-Seq analysis during the life cycle of Cryptosporidium parvum reveals significant differential gene expression between proliferating stages in the intestine and infectious sporozoites.

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Lippuner, Christoph; Ramakrishnan, Chandra; Basso, Walter U; Schmid, Marc W; Okoniewski, Michal; Smith, Nicholas C; Hässig, Michael; Deplazes, Peter; Hehl, Adrian B

2018-05-01

Cryptosporidium parvum is a major cause of diarrhoea in humans and animals. There are no vaccines and few drugs available to control C. parvum. In this study, we used RNA-Seq to compare gene expression in sporozoites and intracellular stages of C. parvum to identify genes likely to be important for successful completion of the parasite's life cycle and, thereby, possible targets for drugs or vaccines. We identified 3774 protein-encoding transcripts in C. parvum. Applying a stringent cut-off of eight fold for determination of differential expression, we identified 173 genes (26 coding for predicted secreted proteins) upregulated in sporozoites. On the other hand, expression of 1259 genes was upregulated in intestinal stages (merozoites/gamonts) with a gene ontology enrichment for 63 biological processes and upregulation of 117 genes in 23 metabolic pathways. There was no clear stage specificity of expression of AP2-domain containing transcription factors, although sporozoites had a relatively small repertoire of these important regulators. Our RNA-Seq analysis revealed a new calcium-dependent protein kinase, bringing the total number of known calcium-dependent protein kinases (CDPKs) in C. parvum to 11. One of these, CDPK1, was expressed in all stages, strengthening the notion that it is a valid drug target. By comparing parasites grown in vivo (which produce bona fide thick-walled oocysts) and in vitro (which are arrested in sexual development prior to oocyst generation) we were able to confirm that genes encoding oocyst wall proteins are expressed in gametocytes and that the proteins are stockpiled rather than generated de novo in zygotes. RNA-Seq analysis of C. parvum revealed genes expressed in a stage-specific manner and others whose expression is required at all stages of development. The functional significance of these can now be addressed through recent advances in transgenics for C. parvum, and may lead to the identification of viable drug and vaccine

Excess fertilizer responsive miRNAs revealed in Linum usitatissimum L.

Science.gov (United States)

Melnikova, Nataliya V; Dmitriev, Alexey A; Belenikin, Maxim S; Speranskaya, Anna S; Krinitsina, Anastasia A; Rachinskaia, Olga A; Lakunina, Valentina A; Krasnov, George S; Snezhkina, Anastasiya V; Sadritdinova, Asiya F; Uroshlev, Leonid A; Koroban, Nadezda V; Samatadze, Tatiana E; Amosova, Alexandra V; Zelenin, Alexander V; Muravenko, Olga V; Bolsheva, Nadezhda L; Kudryavtseva, Anna V

2015-02-01

Effective fertilizer application is necessary to increase crop yields and reduce risk of plant overdosing. It is known that expression level of microRNAs (miRNAs) alters in plants under different nutrient concentrations in soil. The aim of our study was to identify and characterize miRNAs with expression alterations under excessive fertilizer in agriculturally important crop - flax (Linum usitatissimum L.). We have sequenced small RNAs in flax grown under normal and excessive fertilizer using Illumina GAIIx. Over 14 million raw reads was obtained for two small RNA libraries. 84 conserved miRNAs from 20 families were identified. Differential expression was revealed for several flax miRNAs under excessive fertilizer according to high-throughput sequencing data. For 6 miRNA families (miR395, miR169, miR408, miR399, miR398 and miR168) expression level alterations were evaluated on the extended sampling using qPCR. Statistically significant up-regulation was revealed for miR395 under excessive fertilizer. It is known that target genes of miR395 are involved in sulfate uptake and assimilation. However, according to our data alterations of the expression level of miR395 could be associated not only with excess sulfur application, but also with redundancy of other macro- and micronutrients. Furthermore expression level was evaluated for miRNAs and their predicted targets. The negative correlation between miR399 expression and expression of its predicted target ubiquitin-conjugating enzyme E2 gene was shown in flax for the first time. So we suggested miR399 involvement in phosphate regulation in L. usitatissimum. Revealed in our study expression alterations contribute to miRNA role in flax response to excessive fertilizer. Copyright © 2014 Elsevier B.V. and Société française de biochimie et biologie Moléculaire (SFBBM). All rights reserved.

Optimization of sampling parameters for standardized exhaled breath sampling.

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Doran, Sophie; Romano, Andrea; Hanna, George B

2017-09-05

The lack of standardization of breath sampling is a major contributing factor to the poor repeatability of results and hence represents a barrier to the adoption of breath tests in clinical practice. On-line and bag breath sampling have advantages but do not suit multicentre clinical studies whereas storage and robust transport are essential for the conduct of wide-scale studies. Several devices have been developed to control sampling parameters and to concentrate volatile organic compounds (VOCs) onto thermal desorption (TD) tubes and subsequently transport those tubes for laboratory analysis. We conducted three experiments to investigate (i) the fraction of breath sampled (whole vs. lower expiratory exhaled breath); (ii) breath sample volume (125, 250, 500 and 1000ml) and (iii) breath sample flow rate (400, 200, 100 and 50 ml/min). The target VOCs were acetone and potential volatile biomarkers for oesophago-gastric cancer belonging to the aldehyde, fatty acids and phenol chemical classes. We also examined the collection execution time and the impact of environmental contamination. The experiments showed that the use of exhaled breath-sampling devices requires the selection of optimum sampling parameters. The increase in sample volume has improved the levels of VOCs detected. However, the influence of the fraction of exhaled breath and the flow rate depends on the target VOCs measured. The concentration of potential volatile biomarkers for oesophago-gastric cancer was not significantly different between the whole and lower airway exhaled breath. While the recovery of phenols and acetone from TD tubes was lower when breath sampling was performed at a higher flow rate, other VOCs were not affected. A dedicated 'clean air supply' overcomes the contamination from ambient air, but the breath collection device itself can be a source of contaminants. In clinical studies using VOCs to diagnose gastro-oesophageal cancer, the optimum parameters are 500mls sample volume

A novel sample preparation method to avoid influence of embedding medium during nano-indentation

Science.gov (United States)

Meng, Yujie; Wang, Siqun; Cai, Zhiyong; Young, Timothy M.; Du, Guanben; Li, Yanjun

2013-02-01

The effect of the embedding medium on the nano-indentation measurements of lignocellulosic materials was investigated experimentally using nano-indentation. Both the reduced elastic modulus and the hardness of non-embedded cell walls were found to be lower than those of the embedded samples, proving that the embedding medium used for specimen preparation on cellulosic material during nano-indentation can modify cell-wall properties. This leads to structural and chemical changes in the cell-wall constituents, changes that may significantly alter the material properties. Further investigation was carried out to detect the influence of different vacuum times on the cell-wall mechanical properties during the embedding procedure. Interpretation of the statistical analysis revealed no linear relationships between vacuum time and the mechanical properties of cell walls. The quantitative measurements confirm that low-viscosity resin has a rapid penetration rate early in the curing process. Finally, a novel sample preparation method aimed at preventing resin diffusion into lignocellulosic cell walls was developed using a plastic film to wrap the sample before embedding. This method proved to be accessible and straightforward for many kinds of lignocellulosic material, but is especially suitable for small, soft samples.

Individual differences in fluid intelligence predicts inattentional blindness in a sample of older adults: a preliminary study.

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O'Shea, Deirdre M; Fieo, Robert A

2015-07-01

Previous research has shown that aging increases susceptibility to inattentional blindness (Graham and Burke, Psychol Aging 26:162, 2011) as well as individual differences in cognitive ability related to working memory and executive functions in separate studies. Therefore, the present study was conducted in an attempt to bridge a gap that involved investigating 'age-sensitive' cognitive abilities that may predict inattentional blindness in a sample of older adults. We investigated whether individual differences in general fluid intelligence and speed of processing would predict inattentional blindness in our sample of older adults. Thirty-six healthy older adults took part in the study. Using the inattentional blindness paradigm developed by Most et al. (Psychol Rev 112:217, 2005), we investigated whether rates of inattentional blindness could be predicted by participant's performance on the Raven's Advanced Progressive Matrices and a choice-reaction time task. A Mann-Whitney U test revealed that a higher score on the Raven's Advanced Progressive Matrices was significantly associated with lower incidences of inattentional blindness. However, a t test revealed that choice-reaction times were not significantly associated with inattentional blindness. Preliminary results from the present study suggest that individual differences in general fluid intelligence are predictive of inattentional blindness in older adults but not speed of processing. Moreover, our findings are consistent with previous studies that have suggested executive attention control may be the source of these individual differences. These findings also highlight the association between attention and general fluid intelligence and how it may impact environmental awareness. Future research would benefit from repeating these analyses in a larger sample and also including a younger comparison group.

Quantitative Tissue Proteomics Analysis Reveals Versican as Potential Biomarker for Early-Stage Hepatocellular Carcinoma.

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Naboulsi, Wael; Megger, Dominik A; Bracht, Thilo; Kohl, Michael; Turewicz, Michael; Eisenacher, Martin; Voss, Don Marvin; Schlaak, Jörg F; Hoffmann, Andreas-Claudius; Weber, Frank; Baba, Hideo A; Meyer, Helmut E; Sitek, Barbara

2016-01-04

Hepatocellular carcinoma (HCC) is one of the most aggressive tumors, and the treatment outcome of this disease is improved when the cancer is diagnosed at an early stage. This requires biomarkers allowing an accurate and early tumor diagnosis. To identify potential markers for such applications, we analyzed a patient cohort consisting of 50 patients (50 HCC and 50 adjacent nontumorous tissue samples as controls) using two independent proteomics approaches. We performed label-free discovery analysis on 19 HCC and corresponding tissue samples. The data were analyzed considering events known to take place in early events of HCC development, such as abnormal regulation of Wnt/b-catenin and activation of receptor tyrosine kinases (RTKs). 31 proteins were selected for verification experiments. For this analysis, the second set of the patient cohort (31 HCC and corresponding tissue samples) was analyzed using selected (multiple) reaction monitoring (SRM/MRM). We present the overexpression of ATP-dependent RNA helicase (DDX39), Fibulin-5 (FBLN5), myristoylated alanine-rich C-kinase substrate (MARCKS), and Serpin H1 (SERPINH1) in HCC for the first time. We demonstrate Versican core protein (VCAN) to be significantly associated with well differentiated and low-stage HCC. We revealed for the first time the evidence of VCAN as a potential biomarker for early-HCC diagnosis.

Gender differences in the structural connectome of the teenage brain revealed by generalized q-sampling MRI

Directory of Open Access Journals (Sweden)

Yeu-Sheng Tyan

2017-01-01

Full Text Available The question of whether there are biological differences between male and female brains is a fraught one, and political positions and prior expectations seem to have a strong influence on the interpretation of scientific data in this field. This question is relevant to issues of gender differences in the prevalence of psychiatric conditions, including autism, attention deficit hyperactivity disorder (ADHD, Tourette's syndrome, schizophrenia, dyslexia, depression, and eating disorders. Understanding how gender influences vulnerability to these conditions is significant. Diffusion magnetic resonance imaging (dMRI provides a non-invasive method to investigate brain microstructure and the integrity of anatomical connectivity. Generalized q-sampling imaging (GQI has been proposed to characterize complicated fiber patterns and distinguish fiber orientations, providing an opportunity for more accurate, higher-order descriptions through the water diffusion process. Therefore, we aimed to investigate differences in the brain's structural network between teenage males and females using GQI. This study included 59 (i.e., 33 males and 26 females age- and education-matched subjects (age range: 13 to 14 years. The structural connectome was obtained by graph theoretical and network-based statistical (NBS analyses. Our findings show that teenage male brains exhibit better intrahemispheric communication, and teenage female brains exhibit better interhemispheric communication. Our results also suggest that the network organization of teenage male brains is more local, more segregated, and more similar to small-world networks than teenage female brains. We conclude that the use of an MRI study with a GQI-based structural connectomic approach like ours presents novel insights into network-based systems of the brain and provides a new piece of the puzzle regarding gender differences.

Gender differences in the structural connectome of the teenage brain revealed by generalized q-sampling MRI.

Science.gov (United States)

Tyan, Yeu-Sheng; Liao, Jan-Ray; Shen, Chao-Yu; Lin, Yu-Chieh; Weng, Jun-Cheng

2017-01-01

The question of whether there are biological differences between male and female brains is a fraught one, and political positions and prior expectations seem to have a strong influence on the interpretation of scientific data in this field. This question is relevant to issues of gender differences in the prevalence of psychiatric conditions, including autism, attention deficit hyperactivity disorder (ADHD), Tourette's syndrome, schizophrenia, dyslexia, depression, and eating disorders. Understanding how gender influences vulnerability to these conditions is significant. Diffusion magnetic resonance imaging (dMRI) provides a non-invasive method to investigate brain microstructure and the integrity of anatomical connectivity. Generalized q-sampling imaging (GQI) has been proposed to characterize complicated fiber patterns and distinguish fiber orientations, providing an opportunity for more accurate, higher-order descriptions through the water diffusion process. Therefore, we aimed to investigate differences in the brain's structural network between teenage males and females using GQI. This study included 59 (i.e., 33 males and 26 females) age- and education-matched subjects (age range: 13 to 14 years). The structural connectome was obtained by graph theoretical and network-based statistical (NBS) analyses. Our findings show that teenage male brains exhibit better intrahemispheric communication, and teenage female brains exhibit better interhemispheric communication. Our results also suggest that the network organization of teenage male brains is more local, more segregated, and more similar to small-world networks than teenage female brains. We conclude that the use of an MRI study with a GQI-based structural connectomic approach like ours presents novel insights into network-based systems of the brain and provides a new piece of the puzzle regarding gender differences.

Rapid immunohistochemical diagnosis of tobacco mosaic virus disease by microwave-assisted plant sample preparation

Science.gov (United States)

Zellnig, Günther; Möstl, Stefan; Zechmann, Bernd

2013-01-01

Immunoelectron microscopy is a powerful method to diagnose viral diseases and to study the distribution of the viral agent within plant cells and tissues. Nevertheless, current protocols for the immunological detection of viral diseases with transmission electron microscopy (TEM) in plants take between 3 and 6 days and are therefore not suited for rapid diagnosis of virus diseases in plants. In this study, we describe a method that allows rapid cytohistochemical detection of tobacco mosaic virus (TMV) in leaves of tobacco plants. With the help of microwave irradiation, sample preparation of the leaves was reduced to 90 min. After sample sectioning, virus particles were stained on the sections by immunogold labelling of the viral coat protein, which took 100 min. After investigation with the TEM, a clear visualization of TMV in tobacco cells was achieved altogether in about half a day. Comparison of gold particle density by image analysis revealed that samples prepared with the help of microwave irradiation yielded significantly higher gold particle density as samples prepared conventionally at room temperature. This study clearly demonstrates that microwave-assisted plant sample preparation in combination with cytohistochemical localization of viral coat protein is well suited for rapid diagnosis of plant virus diseases in altogether about half a day by TEM. PMID:23580761

Contaminant Gradients in Trees: Directional Tree Coring Reveals Boundaries of Soil and Soil-Gas Contamination with Potential Applications in Vapor Intrusion Assessment.

Science.gov (United States)

Wilson, Jordan L; Samaranayake, V A; Limmer, Matthew A; Schumacher, John G; Burken, Joel G

2017-12-19

Contaminated sites pose ecological and human-health risks through exposure to contaminated soil and groundwater. Whereas we can readily locate, monitor, and track contaminants in groundwater, it is harder to perform these tasks in the vadose zone. In this study, tree-core samples were collected at a Superfund site to determine if the sample-collection location around a particular tree could reveal the subsurface location, or direction, of soil and soil-gas contaminant plumes. Contaminant-centroid vectors were calculated from tree-core data to reveal contaminant distributions in directional tree samples at a higher resolution, and vectors were correlated with soil-gas characterization collected using conventional methods. Results clearly demonstrated that directional tree coring around tree trunks can indicate gradients in soil and soil-gas contaminant plumes, and the strength of the correlations were directly proportionate to the magnitude of tree-core concentration gradients (spearman's coefficient of -0.61 and -0.55 in soil and tree-core gradients, respectively). Linear regression indicates agreement between the concentration-centroid vectors is significantly affected by in planta and soil concentration gradients and when concentration centroids in soil are closer to trees. Given the existing link between soil-gas and vapor intrusion, this study also indicates that directional tree coring might be applicable in vapor intrusion assessment.

Lunar Sample Compendium

Science.gov (United States)

Meyer, Charles

2005-01-01

The purpose of the Lunar Sample Compendium will be to inform scientists, astronauts and the public about the various lunar samples that have been returned from the Moon. This Compendium will be organized rock by rock in the manor of a catalog, but will not be as comprehensive, nor as complete, as the various lunar sample catalogs that are available. Likewise, this Compendium will not duplicate the various excellent books and reviews on the subject of lunar samples (Cadogen 1981, Heiken et al. 1991, Papike et al. 1998, Warren 2003, Eugster 2003). However, it is thought that an online Compendium, such as this, will prove useful to scientists proposing to study individual lunar samples and should help provide backup information for lunar sample displays. This Compendium will allow easy access to the scientific literature by briefly summarizing the significant findings of each rock along with the documentation of where the detailed scientific data are to be found. In general, discussion and interpretation of the results is left to the formal reviews found in the scientific literature. An advantage of this Compendium will be that it can be updated, expanded and corrected as need be.

Probing Genomic Aspects of the Multi-Host Pathogen Clostridium perfringens Reveals Significant Pangenome Diversity, and a Diverse Array of Virulence Factors.

Science.gov (United States)

Kiu, Raymond; Caim, Shabhonam; Alexander, Sarah; Pachori, Purnima; Hall, Lindsay J

2017-01-01

Clostridium perfringens is an important cause of animal and human infections, however information about the genetic makeup of this pathogenic bacterium is currently limited. In this study, we sought to understand and characterise the genomic variation, pangenomic diversity, and key virulence traits of 56 C. perfringens strains which included 51 public, and 5 newly sequenced and annotated genomes using Whole Genome Sequencing. Our investigation revealed that C. perfringens has an "open" pangenome comprising 11667 genes and 12.6% of core genes, identified as the most divergent single-species Gram-positive bacterial pangenome currently reported. Our computational analyses also defined C. perfringens phylogeny (16S rRNA gene) in relation to some 25 Clostridium species, with C. baratii and C. sardiniense determined to be the closest relatives. Profiling virulence-associated factors confirmed presence of well-characterised C. perfringens -associated exotoxins genes including α-toxin ( plc ), enterotoxin ( cpe ), and Perfringolysin O ( pfo or pfoA ), although interestingly there did not appear to be a close correlation with encoded toxin type and disease phenotype. Furthermore, genomic analysis indicated significant horizontal gene transfer events as defined by presence of prophage genomes, and notably absence of CRISPR defence systems in >70% (40/56) of the strains. In relation to antimicrobial resistance mechanisms, tetracycline resistance genes ( tet ) and anti-defensins genes ( mprF ) were consistently detected in silico ( tet : 75%; mprF : 100%). However, pre-antibiotic era strain genomes did not encode for tet , thus implying antimicrobial selective pressures in C. perfringens evolutionary history over the past 80 years. This study provides new genomic understanding of this genetically divergent multi-host bacterium, and further expands our knowledge on this medically and veterinary important pathogen.

RAPID-COMMUNICATION Genetic diversity and differentiation in natural populations of Arapaima gigas from lower Amazon revealed by microsatellites.

Science.gov (United States)

Fazzi-Gomes, P F; Melo, N; Palheta, G; Guerreiro, S; Amador, M; Ribeiro-Dos-Santos, A K; Santos, S; Hamoy, I

2017-02-08

Genetic variability is one of the important criteria for species conservation decisions. This study aimed to analyze the genetic diversity and the population differentiation of two natural populations of Arapaima gigas, a species with a long history of being commercially exploited. We collected 87 samples of A. gigas from Grande Curuai Lake and Paru Lake, located in the Lower Amazon region of Amazônia, Brazil, and genotyped these samples using a multiplex panel of microsatellite markers. Our results showed that the populations of A. gigas analyzed had high levels of genetic variability, which were similar to those described in previous studies. These two populations had a significant population differentiation supported by the estimates of F ST and R ST (0.06), by Bayesian analysis (K = 2), and by population assignment tests, which revealed a moderate genetic distance.

Potential link between body dysmorphic disorder symptoms and alexithymia in an eating-disordered treatment-seeking sample.

Science.gov (United States)

Fenwick, Andrea Siân; Sullivan, Karen Anne

2011-09-30

This study aimed to explore the manifestation of body dysmorphic disorder symptoms in a sample of people with eating disorders and to investigate possible associations between body dysmorphia and alexithymia. Forty patients currently seeking treatment for an eating disorder completed a battery of six measures assessing alexithymia, mood, eating behaviours, weight-related body image, body dysmorphia and non-weight related body image. Significant moderate positive correlations (Pearson's r) between selected variables were found, suggesting that participants with high levels of dysmorphic concern (imagined ugliness) have more difficulty with the affective elements of alexithymia, that is, identifying and describing feelings. When depression, eating attitudes, and weight-related body image concerns were controlled for, significant moderate positive correlations between this alexithymia factor and dysmorphic concerns remained present. An independent-samples t-test between eating-disordered participants with and without symptoms of body dysmorphic disorder (BDD) revealed significant group differences in difficulties identifying feelings. This pattern of results was replicated when the groups were identified on the basis of dysmorphic concerns, as opposed to BDD symptoms. This study highlights the associations between alexithymia and body dysmorphia that have not previously been demonstrated. Copyright © 2011 Elsevier Ltd. All rights reserved.

Operational air sampling report

International Nuclear Information System (INIS)

Lyons, C.L.

1994-03-01

Nevada Test Site vertical shaft and tunnel events generate beta/gamma fission products. The REECo air sampling program is designed to measure these radionuclides at various facilities supporting these events. The current testing moratorium and closure of the Decontamination Facility has decreased the scope of the program significantly. Of the 118 air samples collected in the only active tunnel complex, only one showed any airborne fission products. Tritiated water vapor concentrations were very similar to previously reported levels. The 206 air samples collected at the Area-6 decontamination bays and laundry were again well below any Derived Air Concentration calculation standard. Laboratory analyses of these samples were negative for any airborne fission products

Transcriptome classification reveals molecular subtypes in psoriasis

Directory of Open Access Journals (Sweden)

Ainali Chrysanthi

2012-09-01

Full Text Available Abstract Background Psoriasis is an immune-mediated disease characterised by chronically elevated pro-inflammatory cytokine levels, leading to aberrant keratinocyte proliferation and differentiation. Although certain clinical phenotypes, such as plaque psoriasis, are well defined, it is currently unclear whether there are molecular subtypes that might impact on prognosis or treatment outcomes. Results We present a pipeline for patient stratification through a comprehensive analysis of gene expression in paired lesional and non-lesional psoriatic tissue samples, compared with controls, to establish differences in RNA expression patterns across all tissue types. Ensembles of decision tree predictors were employed to cluster psoriatic samples on the basis of gene expression patterns and reveal gene expression signatures that best discriminate molecular disease subtypes. This multi-stage procedure was applied to several published psoriasis studies and a comparison of gene expression patterns across datasets was performed. Conclusion Overall, classification of psoriasis gene expression patterns revealed distinct molecular sub-groups within the clinical phenotype of plaque psoriasis. Enrichment for TGFb and ErbB signaling pathways, noted in one of the two psoriasis subgroups, suggested that this group may be more amenable to therapies targeting these pathways. Our study highlights the potential biological relevance of using ensemble decision tree predictors to determine molecular disease subtypes, in what may initially appear to be a homogenous clinical group. The R code used in this paper is available upon request.

Evidence of significant covalent bonding in Au(CN)(2)(-).

Science.gov (United States)

Wang, Xue-Bin; Wang, Yi-Lei; Yang, Jie; Xing, Xiao-Peng; Li, Jun; Wang, Lai-Sheng

2009-11-18

The Au(CN)(2)(-) ion is the most stable Au compound known for centuries, yet a detailed understanding of its chemical bonding is still lacking. Here we report direct experimental evidence of significant covalent bonding character in the Au-C bonds in Au(CN)(2)(-) using photoelectron spectroscopy and comparisons with its lighter congeners, Ag(CN)(2)(-) and Cu(CN)(2)(-). Vibrational progressions in the Au-C stretching mode were observed for all detachment transitions for Au(CN)(2)(-), in contrast to the atomic-like transitions for Cu(CN)(2)(-), revealing the Au-C covalent bonding character. In addition, rich electronic structural information was obtained for Au(CN)(2)(-) by employing 118 nm detachment photons. Density functional theory and high-level ab initio calculations were carried out to understand the photoelectron spectra and obtain insight into the nature of the chemical bonding in the M(CN)(2)(-) complexes. Significant covalent character in the Au-C bonding due to the strong relativistic effects was revealed in Au(CN)(2)(-), consistent with its high stability.

Methane hydrate distribution from prolonged and repeated formation in natural and compacted sand samples: X-ray CT observations

Energy Technology Data Exchange (ETDEWEB)

Rees, E.V.L.; Kneafsey, T.J.; Seol, Y.

2010-07-01

To study physical properties of methane gas hydrate-bearing sediments, it is necessary to synthesize laboratory samples due to the limited availability of cores from natural deposits. X-ray computed tomography (CT) and other observations have shown gas hydrate to occur in a number of morphologies over a variety of sediment types. To aid in understanding formation and growth patterns of hydrate in sediments, methane hydrate was repeatedly formed in laboratory-packed sand samples and in a natural sediment core from the Mount Elbert Stratigraphic Test Well. CT scanning was performed during hydrate formation and decomposition steps, and periodically while the hydrate samples remained under stable conditions for up to 60 days. The investigation revealed the impact of water saturation on location and morphology of hydrate in both laboratory and natural sediments during repeated hydrate formations. Significant redistribution of hydrate and water in the samples was observed over both the short and long term.

Significant genetic differentiation between native and introduced silver carp (Hypophthalmichthys molitrix) inferred from mtDNA analysis

Science.gov (United States)

Li, S.-F.; Xu, J.-W.; Yang, Q.-L.; Wang, C.H.; Chapman, D.C.; Lu, G.

2011-01-01

Silver carp Hypophthalmichthys molitrix (Cyprinidae) is native to China and has been introduced to over 80 countries. The extent of genetic diversity in introduced silver carp and the genetic divergence between introduced and native populations remain largely unknown. In this study, 241 silver carp sampled from three major native rivers and two non-native rivers (Mississippi River and Danube River) were analyzed using nucleotide sequences of mitochondrial COI gene and D-loop region. A total of 73 haplotypes were observed, with no haplotype found common to all the five populations and eight haplotypes shared by two to four populations. As compared with introduced populations, all native populations possess both higher haplotype diversity and higher nucleotide diversity, presumably a result of the founder effect. Significant genetic differentiation was revealed between native and introduced populations as well as among five sampled populations, suggesting strong selection pressures might have occurred in introduced populations. Collectively, this study not only provides baseline information for sustainable use of silver carp in their native country (i.e., China), but also offers first-hand genetic data for the control of silver carp in countries (e.g., the United States) where they are considered invasive.

The petrology, geochronology and significance of Granite Harbour Intrusive Complex xenoliths and outcrop sampled in western McMurdo Sound, Southern Victoria Land, Antarctica

International Nuclear Information System (INIS)

Martin, A.P.; Cooper, A.F.; Price, R.C.; Turnbull, R.E.; Roberts, N.M.W.

2015-01-01

Granite Harbour Intrusive Complex xenoliths in McMurdo Volcanic Group rocks and in situ outcrops have been studied from Mount Morning, western McMurdo Sound, Antarctica. Calc-alkalic samples have whole rock signatures and normative compositions similar to the Dry Valleys 1b suite, and zircon grains in one specimen yield a 545.2 ± 4.4 Ma crystallisation age. This supports subduction-related magmatism initiating in Southern Victoria Land by 545 Ma. A second group of xenoliths is alkalic, with titanite grains in one xenolith from this group dated at 538 ± 8 Ma. Whole rock chemistry, normative compositions and geochronology of the alkalic group are comparable to the Koettlitz Glacier Alkaline Suite (KGAS). The position of a proposed lower crustal discontinuity that may form a significant basement suture in the McMurdo Sound region is newly constrained to the east of Mount Morning, perhaps along the trace of the Discovery Glacier. The boundary between East and West Antarctica may also pass along the trace of the Discovery Glacier if, as previously hypothesised, its location is controlled by the basement suture. A significant basement suture may also have provided the necessary egress for the (regionally) early and sustained magmatic activity observed at Mount Morning over the last 24 million years. (author).

Concepts in sample size determination

Directory of Open Access Journals (Sweden)

Umadevi K Rao

2012-01-01

Full Text Available Investigators involved in clinical, epidemiological or translational research, have the drive to publish their results so that they can extrapolate their findings to the population. This begins with the preliminary step of deciding the topic to be studied, the subjects and the type of study design. In this context, the researcher must determine how many subjects would be required for the proposed study. Thus, the number of individuals to be included in the study, i.e., the sample size is an important consideration in the design of many clinical studies. The sample size determination should be based on the difference in the outcome between the two groups studied as in an analytical study, as well as on the accepted p value for statistical significance and the required statistical power to test a hypothesis. The accepted risk of type I error or alpha value, which by convention is set at the 0.05 level in biomedical research defines the cutoff point at which the p value obtained in the study is judged as significant or not. The power in clinical research is the likelihood of finding a statistically significant result when it exists and is typically set to >80%. This is necessary since the most rigorously executed studies may fail to answer the research question if the sample size is too small. Alternatively, a study with too large a sample size will be difficult and will result in waste of time and resources. Thus, the goal of sample size planning is to estimate an appropriate number of subjects for a given study design. This article describes the concepts in estimating the sample size.

Ad-Hoc vs. Standardized and Optimized Arthropod Diversity Sampling

Directory of Open Access Journals (Sweden)

Pedro Cardoso

2009-09-01

Full Text Available The use of standardized and optimized protocols has been recently advocated for different arthropod taxa instead of ad-hoc sampling or sampling with protocols defined on a case-by-case basis. We present a comparison of both sampling approaches applied for spiders in a natural area of Portugal. Tests were made to their efficiency, over-collection of common species, singletons proportions, species abundance distributions, average specimen size, average taxonomic distinctness and behavior of richness estimators. The standardized protocol revealed three main advantages: (1 higher efficiency; (2 more reliable estimations of true richness; and (3 meaningful comparisons between undersampled areas.

Quantitative portable gamma spectroscopy sample analysis for non-standard sample geometries

International Nuclear Information System (INIS)

Enghauser, M.W.; Ebara, S.B.

1997-01-01

Utilizing a portable spectroscopy system, a quantitative method for analysis of samples containing a mixture of fission and activation products in nonstandard geometries was developed. The method can be used with various sample and shielding configurations where analysis on a laboratory based gamma spectroscopy system is impractical. The portable gamma spectroscopy method involves calibration of the detector and modeling of the sample and shielding to identify and quantify the radionuclides present in the sample. The method utilizes the intrinsic efficiency of the detector and the unattenuated gamma fluence rate at the detector surface per unit activity from the sample to calculate the nuclide activity and Minimum Detectable Activity (MDA). For a complex geometry, a computer code written for shielding applications (MICROSHIELD) is utilized to determine the unattenuated gamma fluence rate per unit activity at the detector surface. Lastly, the method is only applicable to nuclides which emit gamma rays and cannot be used for pure beta emitters. In addition, if sample self absorption and shielding is significant, the attenuation will result in high MDA's for nuclides which solely emit low energy gamma rays. The following presents the analysis technique and presents verification results demonstrating the accuracy of the method

Improved Culture Medium (TiKa) for Mycobacterium avium Subspecies Paratuberculosis (MAP) Matches qPCR Sensitivity and Reveals Significant Proportions of Non-viable MAP in Lymphoid Tissue of Vaccinated MAP Challenged Animals

DEFF Research Database (Denmark)

Bull, Tim J.; Munshil, Tulika; Melvang, Heidi Mikkelsen

2017-01-01

The quantitative detection of viable pathogen load is an important tool in determining the degree of infection in animals and contamination of foodstuffs. Current conventional culture methods are limited in their ability to determine these levels in Mycobacterium avium subspecies paratuberculosis......Ka culture equates well with qPCR and provides important evidence that accuracy in estimating viable MAP load using DNA tests alone may vary significantly between samples of mucosal and lymphatic origin....... (MAP) due to slow growth, clumping and low recoverability issues. The principle goal of this study was to evaluate a novel culturing process (TiKa) with unique ability to stimulate MAP growth from low sample loads and dilutions. We demonstrate it was able to stimulate a mean 29-fold increase...

Pure versus combined Merkel cell carcinomas: immunohistochemical evaluation of cellular proteins (p53, Bcl-2, and c-kit) reveals significant overexpression of p53 in combined tumors.

Science.gov (United States)

Lai, Jonathan H; Fleming, Kirsten E; Ly, Thai Yen; Pasternak, Sylvia; Godlewski, Marek; Doucette, Steve; Walsh, Noreen M

2015-09-01

Merkel cell polyomavirus is of oncogenic significance in approximately 80% of Merkel cell carcinomas. Morphological subcategories of the tumor differ in regard to viral status, the rare combined type being uniformly virus negative and the predominant pure type being mainly virus positive. Indications that different biological subsets of the tumor exist led us to explore this diversity. In an Eastern Canadian cohort of cases (75 patients; mean age, 76 years [range, 43-91]; male/female ratio, 43:32; 51 [68%] pure and 24 [34%] combined tumors), we semiquantitatively compared the immunohistochemical expression of 3 cellular proteins (p53, Bcl-2, and c-kit) in pure versus combined groups. Viral status was known in a subset of cases. The significant overexpression of p53 in the combined group (mean [SD], 153.8 [117.8] versus 121.6 [77.9]; P = .01) and the increased epidermal expression of this protein (p53 patches) in the same group lend credence to a primary etiologic role for sun damage in these cases. Expression of Bcl-2 and c-kit did not differ significantly between the 2 morphological groups. A relative increase in c-kit expression was significantly associated with a virus-negative status (median [interquartile range], 100 [60-115] versus 70 [0-100]; P = .03). Emerging data reveal divergent biological pathways in Merkel cell carcinoma, each with a characteristic immunohistochemical profile. Virus-positive tumors (all pure) exhibit high retinoblastoma protein and low p53 expression, whereas virus-negative cases (few pure and all combined) show high p53 and relatively high c-kit expression. The potential biological implications of this dichotomy call for consistent stratification of these tumors in future studies. Copyright © 2015 Elsevier Inc. All rights reserved.

Knowledge-fused differential dependency network models for detecting significant rewiring in biological networks.

Science.gov (United States)

Tian, Ye; Zhang, Bai; Hoffman, Eric P; Clarke, Robert; Zhang, Zhen; Shih, Ie-Ming; Xuan, Jianhua; Herrington, David M; Wang, Yue

2014-07-24

Modeling biological networks serves as both a major goal and an effective tool of systems biology in studying mechanisms that orchestrate the activities of gene products in cells. Biological networks are context-specific and dynamic in nature. To systematically characterize the selectively activated regulatory components and mechanisms, modeling tools must be able to effectively distinguish significant rewiring from random background fluctuations. While differential networks cannot be constructed by existing knowledge alone, novel incorporation of prior knowledge into data-driven approaches can improve the robustness and biological relevance of network inference. However, the major unresolved roadblocks include: big solution space but a small sample size; highly complex networks; imperfect prior knowledge; missing significance assessment; and heuristic structural parameter learning. To address these challenges, we formulated the inference of differential dependency networks that incorporate both conditional data and prior knowledge as a convex optimization problem, and developed an efficient learning algorithm to jointly infer the conserved biological network and the significant rewiring across different conditions. We used a novel sampling scheme to estimate the expected error rate due to "random" knowledge. Based on that scheme, we developed a strategy that fully exploits the benefit of this data-knowledge integrated approach. We demonstrated and validated the principle and performance of our method using synthetic datasets. We then applied our method to yeast cell line and breast cancer microarray data and obtained biologically plausible results. The open-source R software package and the experimental data are freely available at http://www.cbil.ece.vt.edu/software.htm. Experiments on both synthetic and real data demonstrate the effectiveness of the knowledge-fused differential dependency network in revealing the statistically significant rewiring in biological

The rumen microbial metaproteome as revealed by SDS-PAGE.

Science.gov (United States)

Snelling, Timothy J; Wallace, R John

2017-01-07

Ruminal digestion is carried out by large numbers of bacteria, archaea, protozoa and fungi. Understanding the microbiota is important because ruminal fermentation dictates the efficiency of feed utilisation by the animal and is also responsible for major emissions of the greenhouse gas, methane. Recent metagenomic and metatranscriptomic studies have helped to elucidate many features of the composition and activity of the microbiota. The metaproteome provides complementary information to these other -omics technologies. The aim of this study was to explore the metaproteome of bovine and ovine ruminal digesta using 2D SDS-PAGE. Digesta samples were taken via ruminal fistulae and by gastric intubation, or at slaughter, and stored in glycerol at -80 °C. A protein extraction protocol was developed to maximise yield and representativeness of the protein content. The proteome of ruminal digesta taken from dairy cows fed a high concentrate diet was dominated by a few very highly expressed proteins, which were identified by LC-MS/MS to be structural proteins, such as actin and α- and β-tubulins, derived from ciliate protozoa. Removal of protozoa from digesta before extraction of proteins revealed the prokaryotic metaproteome, which was dominated by enzymes involved in glycolysis, such as glyceraldehyde-3-phosphate dehydrogenase, phosphoenolpyruvate carboxykinase, phosphoglycerate kinase and triosephosphate isomerase. The enzymes were predominantly from the Firmicutes and Bacteroidetes phyla. Enzymes from methanogenic archaea were also abundant, consistent with the importance of methane formation in the rumen. Gels from samples from dairy cows fed a high proportion of grass silage were consistently obscured by co-staining of humic compounds. Samples from beef cattle and fattening lambs receiving a predominantly concentrate diet produced clearer gels, but the pattern of spots was inconsistent between samples, making comparisons difficult. This work demonstrated for the

Population-based resequencing revealed an ancestral winter group of cultivated flax: implication for flax domestication processes

Science.gov (United States)

Fu, Yong-Bi

2012-01-01

Cultivated flax (Linum usitatissimum L.) is the earliest oil and fiber crop and its early domestication history may involve multiple events of domestication for oil, fiber, capsular indehiscence, and winter hardiness. Genetic studies have demonstrated that winter cultivated flax is closely related to oil and fiber cultivated flax and shows little relatedness to its progenitor, pale flax (L. bienne Mill.), but winter hardiness is one major characteristic of pale flax. Here, we assessed the genetic relationships of 48 Linum samples representing pale flax and four trait-specific groups of cultivated flax (dehiscent, fiber, oil, and winter) through population-based resequencing at 24 genomic regions, and revealed a winter group of cultivated flax that displayed close relatedness to the pale flax samples. Overall, the cultivated flax showed a 27% reduction of nucleotide diversity when compared with the pale flax. Recombination frequently occurred at these sampled genomic regions, but the signal of selection and bottleneck was relatively weak. These findings provide some insight into the impact and processes of flax domestication and are significant for expanding our knowledge about early flax domestication, particularly for winter hardiness. PMID:22822439

Isolation of Microsporum gypseum in soil samples from different geographical regions of Brazil, evaluation of the extracellular proteolytic enzymes activities (keratinase and elastase and molecular sequencing of selected strains

Directory of Open Access Journals (Sweden)

Mauro Cintra Giudice

2012-09-01

Full Text Available A survey of Microsporum gypseum was conducted in soil samples in different geographical regions of Brazil. The isolation of dermatophyte from soil samples was performed by hair baiting technique and the species were identified by morphology studies. We analyzed 692 soil samples and the recuperating rate was 19.2%. The activities of keratinase and elastase were quantitatively performed in 138 samples. The sequencing of the ITS region of rDNA was performed in representatives samples. M. gypseum isolates showed significant quantitative differences in the expression of both keratinase and elastase, but no significant correlation was observed between these enzymes. The sequencing of the representative samples revealed the presence of two teleomorphic species of M. gypseum (Arthroderma gypseum and A. incurvatum. The enzymatic activities may play an important role in the pathogenicity and a probable adaptation of this fungus to the animal parasitism. Using the phenotypical and molecular analysis, the Microsporum identification and their teleomorphic states will provide a useful and reliable identification system.

Networks of Food Sharing Reveal the Functional Significance of Multilevel Sociality in Two Hunter-Gatherer Groups.

Science.gov (United States)

Dyble, Mark; Thompson, James; Smith, Daniel; Salali, Gul Deniz; Chaudhary, Nikhil; Page, Abigail E; Vinicuis, Lucio; Mace, Ruth; Migliano, Andrea Bamberg

2016-08-08

Like many other mammalian and primate societies [1-4], humans are said to live in multilevel social groups, with individuals situated in a series of hierarchically structured sub-groups [5, 6]. Although this multilevel social organization has been described among contemporary hunter-gatherers [5], questions remain as to the benefits that individuals derive from living in such groups. Here, we show that food sharing among two populations of contemporary hunter-gatherers-the Palanan Agta (Philippines) and Mbendjele BaYaka (Republic of Congo)-reveals similar multilevel social structures, with individuals situated in households, within sharing clusters of 3-4 households, within the wider residential camps, which vary in size. We suggest that these groupings serve to facilitate inter-sexual provisioning, kin provisioning, and risk reduction reciprocity, three levels of cooperation argued to be fundamental in human societies [7, 8]. Humans have a suite of derived life history characteristics including a long childhood and short inter-birth intervals that make offspring energetically demanding [9] and have moved to a dietary niche that often involves the exploitation of difficult to acquire foods with highly variable return rates [10-12]. This means that human foragers face both day-to-day and more long-term energetic deficits that conspire to make humans energetically interdependent. We suggest that a multilevel social organization allows individuals access to both the food sharing partners required to buffer themselves against energetic shortfalls and the cooperative partners required for skill-based tasks such as cooperative foraging. Copyright © 2016 Elsevier Ltd. All rights reserved.

Transcriptomic analysis of the late stages of grapevine (Vitis vinifera cv. Cabernet Sauvignon) berry ripening reveals significant induction of ethylene signaling and flavor pathways in the skin.

Science.gov (United States)

Cramer, Grant R; Ghan, Ryan; Schlauch, Karen A; Tillett, Richard L; Heymann, Hildegarde; Ferrarini, Alberto; Delledonne, Massimo; Zenoni, Sara; Fasoli, Marianna; Pezzotti, Mario

2014-12-19

Grapevine berry, a nonclimacteric fruit, has three developmental stages; the last one is when berry color and sugar increase. Flavors derived from terpenoid and fatty acid metabolism develop at the very end of this ripening stage. The transcriptomic response of pulp and skin of Cabernet Sauvignon berries in the late stages of ripening between 22 and 37 °Brix was assessed using whole-genome micorarrays. The transcript abundance of approximately 18,000 genes changed with °Brix and tissue type. There were a large number of changes in many gene ontology (GO) categories involving metabolism, signaling and abiotic stress. GO categories reflecting tissue differences were overrepresented in photosynthesis, isoprenoid metabolism and pigment biosynthesis. Detailed analysis of the interaction of the skin and pulp with °Brix revealed that there were statistically significantly higher abundances of transcripts changing with °Brix in the skin that were involved in ethylene signaling, isoprenoid and fatty acid metabolism. Many transcripts were peaking around known optimal fruit stages for flavor production. The transcript abundance of approximately two-thirds of the AP2/ERF superfamily of transcription factors changed during these developmental stages. The transcript abundance of a unique clade of ERF6-type transcription factors had the largest changes in the skin and clustered with genes involved in ethylene, senescence, and fruit flavor production including ACC oxidase, terpene synthases, and lipoxygenases. The transcript abundance of important transcription factors involved in fruit ripening was also higher in the skin. A detailed analysis of the transcriptome dynamics during late stages of ripening of grapevine berries revealed that these berries went through massive transcriptional changes in gene ontology categories involving chemical signaling and metabolism in both the pulp and skin, particularly in the skin. Changes in the transcript abundance of genes involved in

Green approaches in sample preparation of bioanalytical samples prior to chromatographic analysis.

Science.gov (United States)

Filippou, Olga; Bitas, Dimitrios; Samanidou, Victoria

2017-02-01

Sample preparation is considered to be the most challenging step of the analytical procedure, since it has an effect on the whole analytical methodology, therefore it contributes significantly to the greenness or lack of it of the entire process. The elimination of the sample treatment steps, pursuing at the same time the reduction of the amount of the sample, strong reductions in consumption of hazardous reagents and energy also maximizing safety for operators and environment, the avoidance of the use of big amount of organic solvents, form the basis for greening sample preparation and analytical methods. In the last decade, the development and utilization of greener and sustainable microextraction techniques is an alternative to classical sample preparation procedures. In this review, the main green microextraction techniques (solid phase microextraction, stir bar sorptive extraction, hollow-fiber liquid phase microextraction, dispersive liquid - liquid microextraction, etc.) will be presented, with special attention to bioanalytical applications of these environment-friendly sample preparation techniques which comply with the green analytical chemistry principles. Copyright © 2016 Elsevier B.V. All rights reserved.

Clinical Significance of CK19 Negative Breast Cancer

Energy Technology Data Exchange (ETDEWEB)

Fujisue, Mamiko, E-mail: nishimura.reiki@cityhosp-kumamoto.jp; Nishimura, Reiki; Okumura, Yasuhiro [Department of Breast and Endocrine Surgery, Kumamoto City Hospital, 1-1-60 Kotoh, Kumamoto City, Kumamoto 862-8505 (Japan); Tashima, Rumiko [Department of Surgery, Kumamoto City Hospital, 1-1-60 Kotoh, Kumamoto City, Kumamoto 862-8505 (Japan); Nishiyama, Yasuyuki; Osako, Tomofumi [Department of Breast and Endocrine Surgery, Kumamoto City Hospital, 1-1-60 Kotoh, Kumamoto City, Kumamoto 862-8505 (Japan); Toyozumi, Yasuo; Arima, Nobuyuki [Department of Pathology, Kumamoto City Hospital, 1-1-60 Kotoh, Kumamoto City, Kumamoto 862-8505 (Japan)

2012-12-21

Analysis of sentinel lymph nodes (SLNs) by means of One-Step Nucleic Acid Amplification (OSNA) is gaining widespread use as a quick and accurate method. This assay detects the expression level of cytokeratin 19 (CK19) which is present in some but not all breast tumors. In this study, the clinical significance of negative CK19 was investigated in 219 cases of primary breast cancer. In 179 patients with clinically negative nodes, OSNA and imprint smear cytology of SLN were performed simultaneously. The OSNA revealed a node-positive rate of 24.6%. Negative CK19 correlated significantly with negative ER/PgR and higher Ki-67 values, and marginally with higher nuclear grade and p53 overexpression. The triple negative subtype showed lower CK19 expression. OSNA revealed that one of the negative CK19 cases was actually a false negative but this was corrected with the use of the imprint smear cytology. In conclusion, CK19 negativity reflected the aggressiveness of primary breast cancer. OSNA assay used to analyze SLN was useful, but there is a possibility that it will mistakenly detect false negatives in CK19 negative tumors. Therefore, in tumors with negative CK19, the imprint smear cytology may be more useful in cases with macrometastasis.

Clinical Significance of CK19 Negative Breast Cancer

Directory of Open Access Journals (Sweden)

Nobuyuki Arima

2012-12-01

Full Text Available Analysis of sentinel lymph nodes (SLNs by means of One-Step Nucleic Acid Amplification (OSNA is gaining widespread use as a quick and accurate method. This assay detects the expression level of cytokeratin 19 (CK19 which is present in some but not all breast tumors. In this study, the clinical significance of negative CK19 was investigated in 219 cases of primary breast cancer. In 179 patients with clinically negative nodes, OSNA and imprint smear cytology of SLN were performed simultaneously. The OSNA revealed a node-positive rate of 24.6%. Negative CK19 correlated significantly with negative ER/PgR and higher Ki-67 values, and marginally with higher nuclear grade and p53 overexpression. The triple negative subtype showed lower CK19 expression. OSNA revealed that one of the negative CK19 cases was actually a false negative but this was corrected with the use of the imprint smear cytology. In conclusion, CK19 negativity reflected the aggressiveness of primary breast cancer. OSNA assay used to analyze SLN was useful, but there is a possibility that it will mistakenly detect false negatives in CK19 negative tumors. Therefore, in tumors with negative CK19, the imprint smear cytology may be more useful in cases with macrometastasis.

Clinical Significance of CK19 Negative Breast Cancer

International Nuclear Information System (INIS)

Fujisue, Mamiko; Nishimura, Reiki; Okumura, Yasuhiro; Tashima, Rumiko; Nishiyama, Yasuyuki; Osako, Tomofumi; Toyozumi, Yasuo; Arima, Nobuyuki

2012-01-01

Analysis of sentinel lymph nodes (SLNs) by means of One-Step Nucleic Acid Amplification (OSNA) is gaining widespread use as a quick and accurate method. This assay detects the expression level of cytokeratin 19 (CK19) which is present in some but not all breast tumors. In this study, the clinical significance of negative CK19 was investigated in 219 cases of primary breast cancer. In 179 patients with clinically negative nodes, OSNA and imprint smear cytology of SLN were performed simultaneously. The OSNA revealed a node-positive rate of 24.6%. Negative CK19 correlated significantly with negative ER/PgR and higher Ki-67 values, and marginally with higher nuclear grade and p53 overexpression. The triple negative subtype showed lower CK19 expression. OSNA revealed that one of the negative CK19 cases was actually a false negative but this was corrected with the use of the imprint smear cytology. In conclusion, CK19 negativity reflected the aggressiveness of primary breast cancer. OSNA assay used to analyze SLN was useful, but there is a possibility that it will mistakenly detect false negatives in CK19 negative tumors. Therefore, in tumors with negative CK19, the imprint smear cytology may be more useful in cases with macrometastasis

Diagnosing phenotypes of single-sample individuals by edge biomarkers.

Science.gov (United States)

Zhang, Wanwei; Zeng, Tao; Liu, Xiaoping; Chen, Luonan

2015-06-01

Network or edge biomarkers are a reliable form to characterize phenotypes or diseases. However, obtaining edges or correlations between molecules for an individual requires measurement of multiple samples of that individual, which are generally unavailable in clinical practice. Thus, it is strongly demanded to diagnose a disease by edge or network biomarkers in one-sample-for-one-individual context. Here, we developed a new computational framework, EdgeBiomarker, to integrate edge and node biomarkers to diagnose phenotype of each single test sample. By applying the method to datasets of lung and breast cancer, it reveals new marker genes/gene-pairs and related sub-networks for distinguishing earlier and advanced cancer stages. Our method shows advantages over traditional methods: (i) edge biomarkers extracted from non-differentially expressed genes achieve better cross-validation accuracy of diagnosis than molecule or node biomarkers from differentially expressed genes, suggesting that certain pathogenic information is only present at the level of network and under-estimated by traditional methods; (ii) edge biomarkers categorize patients into low/high survival rate in a more reliable manner; (iii) edge biomarkers are significantly enriched in relevant biological functions or pathways, implying that the association changes in a network, rather than expression changes in individual molecules, tend to be causally related to cancer development. The new framework of edge biomarkers paves the way for diagnosing diseases and analyzing their molecular mechanisms by edges or networks in one-sample-for-one-individual basis. This also provides a powerful tool for precision medicine or big-data medicine. © The Author (2015). Published by Oxford University Press on behalf of Journal of Molecular Cell Biology, IBCB, SIBS, CAS. All rights reserved.

Comparative Study of 11 Honey Samples Sold in Riyadh Saudi Arabia

OpenAIRE

Al Tufail, M. A. [محمد عبد الله الطفيل; Al Araidh, I. A. [ابراهيم عبد الله العريض

2006-01-01

11 honey various samples commercially available in Saudi Arabia, were subjected to chemical, toxicological and bacteriological tests. The samples were checked for As and CN, presence of pollens, and for bacteria contamination. The carbohydrate profile was analyzed with HPLC. Fe, P, Ca, K, and Mg were measured with colorimetry. Toxic metals, As, Pb, Sb, Tl, and Hg were determined with ICP-MS. The samples were investigated by GC-MS. The investigation revealed the presence of syringaldehyde, men...

[Mutism and acute behavioral disorders revealing MELAS syndrome].

Science.gov (United States)

Coomans, H; Barroso, B; Bertandeau, E; Bonnan, M; Dakar, A; Demasles, S; Garraud, S; Krim, E; Martin-Négrier, M-L

2011-11-01

MELAS syndrome (mitochondrial encephalomyopathy, lactic acidosis and stroke-like episodes) is a rare genetic mitochondrial disease which can cause cerebral (cerebrovascular accident, migraine, mental deterioration..), sensorial (bilateral symmetrical deafness) and peripheral (muscular involvement, neuropathy) disorders potentially associated with diabetes, renal or cardiac disorders, or growth retardation. Eighty percent of the patients have the 3243 A>G mutation in the leucine RNA transfer gene. Clinical manifestations leading to discovery of the mutation can be extremely varied, affecting patients of different age groups. We report the case of a 49-year-old man who presented acute fits of confusion followed by mutism and praxic disorders. History taking revealed recently diagnosed type 2 diabetes, axonal neuropathy, and bilateral symmetrical deafness requiring hearing aids. The initial MRI showed FLAIR sequences with bi-parietal abnormalities, no signs of recent stroke on the DW/B10000 sequences, and basal ganglia calcifications. Blood tests and morphological findings ruled out a vascular origin. Search for lactic acidosis remained constantly negative in blood samples despite positive cerebrospinal fluid samples (N×3). The 3243 A>G mitochondrial DNA mutation was identified. The neuropsychological evaluation revealed a serious dysexecutive syndrome with a major impact on the patient's self sufficiency. Neurocognitive disorders are not common in MELAS syndrome. Brain MRI results and the presence of extra-neurological signs can be helpful for diagnosis. Copyright © 2011 Elsevier Masson SAS. All rights reserved.

Sampling for Beryllium Surface Contamination using Wet, Dry and Alcohol Wipe Sampling

Energy Technology Data Exchange (ETDEWEB)

Kerr, Kent [Central Missouri State Univ., Warrensburg, MO (United States)

2004-12-01

This research project was conducted at the National Nuclear Security Administration's Kansas City Plant, operated by Honeywell Federal Manufacturing and Technologies, in conjunction with the Safety Sciences Department of Central Missouri State University, to compare relative removal efficiencies of three wipe sampling techniques currently used at Department of Energy facilities. Efficiencies of removal of beryllium contamination from typical painted surfaces were tested by wipe sampling with dry Whatman 42 filter paper, with water-moistened (Ghost Wipe) materials, and by methanol-moistened wipes. Test plates were prepared using 100 mm X 15 mm Pyrex Petri dishes with interior surfaces spray painted with a bond coat primer. To achieve uniform deposition over the test plate surface, 10 ml aliquots of solution containing 1 beryllium and 0.1 ml of metal working fluid were transferred to the test plates and subsequently evaporated. Metal working fluid was added to simulate the slight oiliness common on surfaces in metal working shops where fugitive oil mist accumulates over time. Sixteen test plates for each wipe method (dry, water, and methanol) were processed and sampled using a modification of wiping patterns recommended by OSHA Method 125G. Laboratory and statistical analysis showed that methanol-moistened wipe sampling removed significantly more (about twice as much) beryllium/oil-film surface contamination as water-moistened wipes (p< 0.001), which removed significantly more (about twice as much) residue as dry wipes (p <0.001). Evidence for beryllium sensitization via skin exposure argues in favor of wipe sampling with wetting agents that provide enhanced residue removal efficiency.

Sampling the Mouse Hippocampal Dentate Gyrus

OpenAIRE

Lisa Basler; Lisa Basler; Stephan Gerdes; David P. Wolfer; David P. Wolfer; David P. Wolfer; Lutz Slomianka; Lutz Slomianka

2017-01-01

Sampling is a critical step in procedures that generate quantitative morphological data in the neurosciences. Samples need to be representative to allow statistical evaluations, and samples need to deliver a precision that makes statistical evaluations not only possible but also meaningful. Sampling generated variability should, e.g., not be able to hide significant group differences from statistical detection if they are present. Estimators of the coefficient of error (CE) have been develope...

Probing Genomic Aspects of the Multi-Host Pathogen Clostridium perfringens Reveals Significant Pangenome Diversity, and a Diverse Array of Virulence Factors

Directory of Open Access Journals (Sweden)

Raymond Kiu

2017-12-01

Full Text Available Clostridium perfringens is an important cause of animal and human infections, however information about the genetic makeup of this pathogenic bacterium is currently limited. In this study, we sought to understand and characterise the genomic variation, pangenomic diversity, and key virulence traits of 56 C. perfringens strains which included 51 public, and 5 newly sequenced and annotated genomes using Whole Genome Sequencing. Our investigation revealed that C. perfringens has an “open” pangenome comprising 11667 genes and 12.6% of core genes, identified as the most divergent single-species Gram-positive bacterial pangenome currently reported. Our computational analyses also defined C. perfringens phylogeny (16S rRNA gene in relation to some 25 Clostridium species, with C. baratii and C. sardiniense determined to be the closest relatives. Profiling virulence-associated factors confirmed presence of well-characterised C. perfringens-associated exotoxins genes including α-toxin (plc, enterotoxin (cpe, and Perfringolysin O (pfo or pfoA, although interestingly there did not appear to be a close correlation with encoded toxin type and disease phenotype. Furthermore, genomic analysis indicated significant horizontal gene transfer events as defined by presence of prophage genomes, and notably absence of CRISPR defence systems in >70% (40/56 of the strains. In relation to antimicrobial resistance mechanisms, tetracycline resistance genes (tet and anti-defensins genes (mprF were consistently detected in silico (tet: 75%; mprF: 100%. However, pre-antibiotic era strain genomes did not encode for tet, thus implying antimicrobial selective pressures in C. perfringens evolutionary history over the past 80 years. This study provides new genomic understanding of this genetically divergent multi-host bacterium, and further expands our knowledge on this medically and veterinary important pathogen.

Determinants of renewable energy growth: A global sample analysis

International Nuclear Information System (INIS)

Aguirre, Mariana; Ibikunle, Gbenga

2014-01-01

We investigate factors influencing country-level renewable energy growth by applying FEVD and PCSE estimation methods in a unique sample analysis. With a longer time series (1990–2010) and a broader sample size of countries (including Brazil, Russia, India, China and South Africa) than previous studies, our results reveal new insights. The results suggest that certain government-backed energy policies impede renewable energy investments, thus implying significant failures in policy design. These policies may be failing mainly because of uncertainty and the likelihood of discontinuity. Weak voluntary approaches are introduced in order to satisfy public demand for more sustainable investments and programmes; we find that these may have negative influences on the growth of renewables as well. The insight gained is consistent over the estimation methods employed. - Highlights: • Some public energy policies are shown to impede renewable energy investments; this implies failure in policy design. • Environmental concern is shown to drive renewables investment but energy security concerns do not seem to influence renewables investment. • Results suggest that countries are likely to reduce renewables commitments when under pressure to ensure energy supply. • Results seem to underscore the policy lobbying strength of the traditional energy mix industries

Gene Expression Profiling Reveals a Massive, Aneuploidy-Dependent Transcriptional Deregulation and Distinct Differences between Lymph Node–Negative and Lymph Node–Positive Colon Carcinomas

Science.gov (United States)

Grade, Marian; Hörmann, Patrick; Becker, Sandra; Hummon, Amanda B.; Wangsa, Danny; Varma, Sudhir; Simon, Richard; Liersch, Torsten; Becker, Heinz; Difilippantonio, Michael J.; Ghadimi, B. Michael; Ried, Thomas

2016-01-01

To characterize patterns of global transcriptional deregulation in primary colon carcinomas, we did gene expression profiling of 73 tumors [Unio Internationale Contra Cancrum stage II (n = 33) and stage III (n = 40)] using oligonucleotide microarrays. For 30 of the tumors, expression profiles were compared with those from matched normal mucosa samples. We identified a set of 1,950 genes with highly significant deregulation between tumors and mucosa samples (P 5-fold average expression difference between normal colon mucosa and carcinomas, including up-regulation of MYC and of HMGA1, a putative oncogene. Furthermore, we identified 68 genes that were significantly differentially expressed between lymph node–negative and lymph node–positive tumors (P deregulated genes were validated using quantitative real-time reverse transcription-PCR in >40 tumor and normal mucosa samples with good concordance between the techniques. Finally, we established a relationship between specific genomic imbalances, which were mapped for 32 of the analyzed colon tumors by comparative genomic hybridization, and alterations of global transcriptional activity. Previously, we had conducted a similar analysis of primary rectal carcinomas. The systematic comparison of colon and rectal carcinomas revealed a significant overlap of genomic imbalances and transcriptional deregulation, including activation of the Wnt/β-catenin signaling cascade, suggesting similar pathogenic pathways. PMID:17210682

NMR-Based Metabonomic Investigation of Heat Stress in Myotubes Reveals a Time-Dependent Change in the Metabolites

DEFF Research Database (Denmark)

Straadt, Ida K; Young, Jette F; Bross, Peter

2010-01-01

NMR-based metabonomics was applied to elucidate the time-dependent stress responses in mouse myotubes after heat exposure of either 42 or 45 degrees C for 1 h. Principal component analysis (PCA) revealed that the gradual time-dependent changes in metabolites contributing to the clustering...... and separation of the control samples from the different time points after heat stress primarily are in the metabolites glucose, leucine, lysine, phenylalanine, creatine, glutamine, and acetate. In addition, PC scores revealed a maximum change in metabolite composition 4 h after the stress exposure; thereafter......, samples returned toward control samples, however, without reaching the control samples even 10 h after stress. The results also indicate that the myotubes efficiently regulate the pH level by release of lactate to the culture medium at a heat stress level of 42 degrees C, which is a temperature level...

Significant strain accumulation between the deformation front and landward out-of-sequence thrusts in accretionary wedge of SW Taiwan revealed by cGPS and SAR interferometry

Science.gov (United States)

Tsai, M. C.

2017-12-01

High strain accumulation across the fold-and-thrust belt in Southwestern Taiwan are revealed by the Continuous GPS (cGPS) and SAR interferometry. This high strain is generally accommodated by the major active structures in fold-and-thrust belt of western Foothills in SW Taiwan connected to the accretionary wedge in the incipient are-continent collision zone. The active structures across the high strain accumulation include the deformation front around the Tainan Tableland, the Hochiali, Hsiaokangshan, Fangshan and Chishan faults. Among these active structures, the deformation pattern revealed from cGPS and SAR interferometry suggest that the Fangshan transfer fault may be a left-lateral fault zone with thrust component accommodating the westward differential motion of thrust sheets on both side of the fault. In addition, the Chishan fault connected to the splay fault bordering the lower-slope and upper-slope of the accretionary wedge which could be the major seismogenic fault and an out-of-sequence thrust fault in SW Taiwan. The big earthquakes resulted from the reactivation of out-of-sequence thrusts have been observed along the Nankai accretionary wedge, thus the assessment of the major seismogenic structures by strain accumulation between the frontal décollement and out-of-sequence thrusts is a crucial topic. According to the background seismicity, the low seismicity and mid-crust to mantle events are observed inland and the lower- and upper- slope domain offshore SW Taiwan, which rheologically implies the upper crust of the accretionary wedge is more or less aseimic. This result may suggest that the excess fluid pressure from the accretionary wedge not only has significantly weakened the prism materials as well as major fault zone, but also makes the accretionary wedge landward extension, which is why the low seismicity is observed in SW Taiwan area. Key words: Continuous GPS, SAR interferometry, strain rate, out-of-sequence thrust.

Revealing Rembrandt

Directory of Open Access Journals (Sweden)

Andrew J Parker

2014-04-01

Full Text Available The power and significance of artwork in shaping human cognition is self-evident. The starting point for our empirical investigations is the view that the task of neuroscience is to integrate itself with other forms of knowledge, rather than to seek to supplant them. In our recent work, we examined a particular aspect of the appreciation of artwork using present-day functional magnetic resonance imaging (fMRI. Our results emphasised the continuity between viewing artwork and other human cognitive activities. We also showed that appreciation of a particular aspect of artwork, namely authenticity, depends upon the co-ordinated activity between the brain regions involved in multiple decision making and those responsible for processing visual information. The findings about brain function probably have no specific consequences for understanding how people respond to the art of Rembrandt in comparison with their response to other artworks. However, the use of images of Rembrandt’s portraits, his most intimate and personal works, clearly had a significant impact upon our viewers, even though they have been spatially confined to the interior of an MRI scanner at the time of viewing. Neuroscientific studies of humans viewing artwork have the capacity to reveal the diversity of human cognitive responses that may be induced by external advice or context as people view artwork in a variety of frameworks and settings.

Body image and eating disordered behavior in a community sample of Black and Hispanic women.

Science.gov (United States)

Hrabosky, Joshua I; Grilo, Carlos M

2007-01-01

The current study examined body image concerns and eating disordered behaviors in a community sample of Black and Hispanic women. In addition, this study explored whether there are ethnic differences in the correlates or in the prediction of body image concerns. Participants were 120 (67 Black and 53 Hispanic) women who responded to advertisements to participate in a study of women and health. Participants completed a battery of established self-report measures to assess body image, eating disordered behaviors, and associated psychological domains. Black and Hispanic women did not differ significantly in their self-reports of body image, eating disordered behaviors, or associated psychological measures. Comparisons performed separately within both ethnic groups revealed significant differences by weight status, with a general graded patterning of greater concerns in obese than overweight than average weight groups. In terms of predicting body image, multiple regression analyses testing a number of variables, including BMI, performed separately for Black and Hispanic women revealed that eating concern and depressive affect were significant predictors of body image concern for both groups. Overall, Black and Hispanic women differed little in their self-reports of body image, eating-disordered features, and depressive affect. Higher weight was associated with a general pattern of increased body image concerns and features of eating disorders in both groups and with binge eating in Black women. Eating concerns and depressive affect emerged as significant independent predictors of body image for both ethnic groups.

Sampling and farm stories prompt consumers to buy specialty cheeses

OpenAIRE

Reed, Barbara A.; Bruhn, Christine M.

2003-01-01

California specialty cheese makers need information on what drives product sales so they can effectively market their products. Focus group and telephone research revealed that specialty cheese consumers have a strong preference for sampling cheese before making a purchase. Consumers also rely heavily on staff recommendations to select cheese. They appreciate unlimited sampling in an unhurried, low-pressure environment. Specialty cheese consumers consider themselves “food experimenters”; they...

Novel loci and pathways significantly associated with longevity

DEFF Research Database (Denmark)

Zeng, Yi; Nie, Chao; Min, Junxia

2016-01-01

Only two genome-wide significant loci associated with longevity have been identified so far, probably because of insufficient sample sizes of centenarians, whose genomes may harbor genetic variants associated with health and longevity. Here we report a genome-wide association study (GWAS) of Han ...

High rates of hybridisation reveal fragile reproductive barriers between endangered Australian sea snakes

DEFF Research Database (Denmark)

Sanders, Kate L; Redsted Rasmussen, Arne; Guinea, Michael L.

2014-01-01

designations, but revealed high frequencies of hybrids on all four reefs and individuals of pure A. fuscus ancestry only at Scott and (historically) Ashmore. Most unexpectedly, 95% of snakes sampled at Hibernia were hybrids that resembled A. laevis in phenotype, revealing a collapse of reproductive barriers...... (‘reverse speciation’) at this reef. These results have dire implications for the conservation status of A. fuscus, and highlight the fragility of reproductive barriers in a recent marine radiation....

Aggregation and sampling in deterministic chaos: implications for chaos identification in hydrological processes

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J. D. Salas

2005-01-01

Full Text Available A review of the literature reveals conflicting results regarding the existence and inherent nature of chaos in hydrological processes such as precipitation and streamflow, i.e. whether they are low dimensional chaotic or stochastic. This issue is examined further in this paper, particularly the effect that certain types of transformations, such as aggregation and sampling, may have on the identification of the dynamics of the underlying system. First, we investigate the dynamics of daily streamflows for two rivers in Florida, one with strong surface and groundwater storage contributions and the other with a lesser basin storage contribution. Based on estimates of the delay time, the delay time window, and the correlation integral, our results suggest that the river with the stronger basin storage contribution departs significantly from the behavior of a chaotic system, while the departure is less significant for the river with the smaller basin storage contribution. We pose the hypothesis that the chaotic behavior depicted on continuous precipitation fields or small time-step precipitation series becomes less identifiable as the aggregation (or sampling time step increases. Similarly, because streamflows result from a complex transformation of precipitation that involves accumulating and routing excess rainfall throughout the basin and adding surface and groundwater flows, the end result may be that streamflows at the outlet of the basin depart from low dimensional chaotic behavior. We also investigate the effect of aggregation and sampling using series derived from the Lorenz equations and show that, as the aggregation and sampling scales increase, the chaotic behavior deteriorates and eventually ceases to show evidence of low dimensional determinism.

Satisfaction with life scale in a representative sample of Spanish adults: validation and normative data.

Science.gov (United States)

Vázquez, Carmelo; Duque, Almudena; Hervás, Gonzalo

2013-01-01

The Satisfaction with Life Scale (SWLS) is a measure widely used to assess life satisfaction. This paper aims to test its psychometric properties, factor structure, and distribution scores across age, gender, education, and employment status. For this purpose, a representative sample of the Spanish population (N = 2,964) was used. Although analyses showed no significant differences across age or gender, participants with higher education level and those who held an occupation were more satisfied with their lives. Confirmatory factor analysis revealed a unifactorial structure with significant correlations between the SWLS, and subjective happiness and social support. The internal consistency of the scale was .88. Thus, our results indicate that the Spanish version of the SWLS is a valid and reliable measure of life satisfaction within the Spanish context.

Phylogenetic analysis reveals two genotypes of the emerging fungus Mucor indicus, an opportunistic human pathogen in immunocompromised patients.

Science.gov (United States)

Taj-Aldeen, Saad J; Almaslamani, Muna; Theelen, Bart; Boekhout, Teun

2017-07-12

Mucormycosis is a rare fungal infection caused by Mucor indicus. Phylogenetic analysis of many M. indicus isolates, mainly sampled from different clinical and environmental specimens collected worldwide, revealed two genotypes, I and II, based on ITS and D1/D2 LSU rDNA sequences. A retrospective review of the literature revealed 13 cases. Eight (76.9%) patients had disseminated infections, and the overall mortality rate was 30.7%. A pulmonary infection caused by M. indicus genotype I in a liver transplant recipient was disseminated to include the skin and was successfully treated with liposomal amphotericin B and aggressive surgery. M. indicus can infect a wide variety of patients with no real preference for the site of infection. We concluded that M. indicus has emerged as a significant cause of invasive mycosis in severely immunocompromised patients worldwide. Early diagnosis and initiation of appropriate therapy could enhance survival in these immunocompromised patient populations.

Benchmarking sample preparation/digestion protocols reveals tube-gel being a fast and repeatable method for quantitative proteomics.

Science.gov (United States)

Muller, Leslie; Fornecker, Luc; Van Dorsselaer, Alain; Cianférani, Sarah; Carapito, Christine

2016-12-01

Sample preparation, typically by in-solution or in-gel approaches, has a strong influence on the accuracy and robustness of quantitative proteomics workflows. The major benefit of in-gel procedures is their compatibility with detergents (such as SDS) for protein solubilization. However, SDS-PAGE is a time-consuming approach. Tube-gel (TG) preparation circumvents this drawback as it involves directly trapping the sample in a polyacrylamide gel matrix without electrophoresis. We report here the first global label-free quantitative comparison between TG, stacking gel (SG), and basic liquid digestion (LD). A series of UPS1 standard mixtures (at 0.5, 1, 2.5, 5, 10, and 25 fmol) were spiked in a complex yeast lysate background. TG preparation allowed more yeast proteins to be identified than did the SG and LD approaches, with mean numbers of 1979, 1788, and 1323 proteins identified, respectively. Furthermore, the TG method proved equivalent to SG and superior to LD in terms of the repeatability of the subsequent experiments, with mean CV for yeast protein label-free quantifications of 7, 9, and 10%. Finally, known variant UPS1 proteins were successfully detected in the TG-prepared sample within a complex background with high sensitivity. All the data from this study are accessible on ProteomeXchange (PXD003841). © 2016 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Epidemiology of mixed martial arts and youth violence in an ethnically diverse sample.

Science.gov (United States)

Hishinuma, Earl S; Umemoto, Karen N; Nguyen, Toan Gia; Chang, Janice Y; Bautista, Randy Paul M

2012-01-01

Mixed martial arts' (MMAs) growing international popularity has rekindled the discussion on the advantages (e.g., exercise) and disadvantages (e.g., possible injury) of contact sports. This study was the first of its kind to examine the psychosocial aspects of MMA and youth violence using an epidemiologic approach with an Asian American and Pacific Islander (AAPI) adolescent sample (N = 881). The results were consistent with the increased popularity of MMA with 52% (adolescent males = 73%, adolescent females = 39%) enjoying watching MMA and 24% (adolescent males = 39%, adolescent females = 13%) practicing professional fight moves with friends. Although statistically significant ethnic differences were found for the two MMA items on a bivariate level, these findings were not statistically significant when considering other variables in the model. The bivariate results revealed a cluster of risk-protective factors. Regarding the multiple regression findings, although enjoying watching MMA remained associated with positive attitudes toward violence and practicing fight moves remained associated with negative out-group orientation, the MMA items were not associated with unique variances of youth violence perpetration and victimization. Implications included the need for further research that includes other diverse samples, more comprehensive and objective MMA and violence measures, and observational and intervention longitudinal studies.

An empirical comparison of respondent-driven sampling, time location sampling, and snowball sampling for behavioral surveillance in men who have sex with men, Fortaleza, Brazil.

Science.gov (United States)

Kendall, Carl; Kerr, Ligia R F S; Gondim, Rogerio C; Werneck, Guilherme L; Macena, Raimunda Hermelinda Maia; Pontes, Marta Kerr; Johnston, Lisa G; Sabin, Keith; McFarland, Willi

2008-07-01

Obtaining samples of populations at risk for HIV challenges surveillance, prevention planning, and evaluation. Methods used include snowball sampling, time location sampling (TLS), and respondent-driven sampling (RDS). Few studies have made side-by-side comparisons to assess their relative advantages. We compared snowball, TLS, and RDS surveys of men who have sex with men (MSM) in Forteleza, Brazil, with a focus on the socio-economic status (SES) and risk behaviors of the samples to each other, to known AIDS cases and to the general population. RDS produced a sample with wider inclusion of lower SES than snowball sampling or TLS-a finding of health significance given the majority of AIDS cases reported among MSM in the state were low SES. RDS also achieved the sample size faster and at lower cost. For reasons of inclusion and cost-efficiency, RDS is the sampling methodology of choice for HIV surveillance of MSM in Fortaleza.

Evaluating significance in linear mixed-effects models in R.

Science.gov (United States)

Luke, Steven G

2017-08-01

Mixed-effects models are being used ever more frequently in the analysis of experimental data. However, in the lme4 package in R the standards for evaluating significance of fixed effects in these models (i.e., obtaining p-values) are somewhat vague. There are good reasons for this, but as researchers who are using these models are required in many cases to report p-values, some method for evaluating the significance of the model output is needed. This paper reports the results of simulations showing that the two most common methods for evaluating significance, using likelihood ratio tests and applying the z distribution to the Wald t values from the model output (t-as-z), are somewhat anti-conservative, especially for smaller sample sizes. Other methods for evaluating significance, including parametric bootstrapping and the Kenward-Roger and Satterthwaite approximations for degrees of freedom, were also evaluated. The results of these simulations suggest that Type 1 error rates are closest to .05 when models are fitted using REML and p-values are derived using the Kenward-Roger or Satterthwaite approximations, as these approximations both produced acceptable Type 1 error rates even for smaller samples.

High Throughput qPCR Expression Profiling of Circulating MicroRNAs Reveals Minimal Sex- and Sample Timing-Related Variation in Plasma of Healthy Volunteers.

Directory of Open Access Journals (Sweden)

Catherine Mooney

Full Text Available MicroRNAs are a class of small non-coding RNA that regulate gene expression at a post-transcriptional level. MicroRNAs have been identified in various body fluids under normal conditions and their stability as well as their dysregulation in disease opens up a new field for biomarker study. However, diurnal and day-to-day variation in plasma microRNA levels, and differential regulation between males and females, may affect biomarker stability. A QuantStudio 12K Flex Real-Time PCR System was used to profile plasma microRNA levels using OpenArray in male and female healthy volunteers, in the morning and afternoon, and at four time points over a one month period. Using this system we were able to run four OpenArray plates in a single run, the equivalent of 32 traditional 384-well qPCR plates or 12,000 data points. Up to 754 microRNAs can be identified in a single plasma sample in under two hours. 108 individual microRNAs were identified in at least 80% of all our samples which compares favourably with other reports of microRNA profiles in serum or plasma in healthy adults. Many of these microRNAs, including miR-16-5p, miR-17-5p, miR-19a-3p, miR-24-3p, miR-30c-5p, miR-191-5p, miR-223-3p and miR-451a are highly expressed and consistent with previous studies using other platforms. Overall, microRNA levels were very consistent between individuals, males and females, and time points and we did not detect significant differences in levels of microRNAs. These results suggest the suitability of this platform for microRNA profiling and biomarker discovery and suggest minimal confounding influence of sex or sample timing. However, the platform has not been subjected to rigorous validation which must be demonstrated in future biomarker studies where large differences may exist between disease and control samples.

Cross-hemispheric dopamine projections have functional significance

Science.gov (United States)

Fox, Megan E.; Mikhailova, Maria A.; Bass, Caroline E.; Takmakov, Pavel; Gainetdinov, Raul R.; Budygin, Evgeny A.; Wightman, R. Mark

2016-01-01

Dopamine signaling occurs on a subsecond timescale, and its dysregulation is implicated in pathologies ranging from drug addiction to Parkinson’s disease. Anatomic evidence suggests that some dopamine neurons have cross-hemispheric projections, but the significance of these projections is unknown. Here we report unprecedented interhemispheric communication in the midbrain dopamine system of awake and anesthetized rats. In the anesthetized rats, optogenetic and electrical stimulation of dopamine cells elicited physiologically relevant dopamine release in the contralateral striatum. Contralateral release differed between the dorsal and ventral striatum owing to differential regulation by D2-like receptors. In the freely moving animals, simultaneous bilateral measurements revealed that dopamine release synchronizes between hemispheres and intact, contralateral projections can release dopamine in the midbrain of 6-hydroxydopamine–lesioned rats. These experiments are the first, to our knowledge, to show cross-hemispheric synchronicity in dopamine signaling and support a functional role for contralateral projections. In addition, our data reveal that psychostimulants, such as amphetamine, promote the coupling of dopamine transients between hemispheres. PMID:27298371

Uranium and coexisting element behaviour in surface waters and associated sediments with varied sampling techniques used for uranium exploration

International Nuclear Information System (INIS)

Wenrich-Verbeek, K.J.

1977-01-01

Optimum sampling methods in surface water and associated sediments for use in uranium exploration are being studied at thirty sites in Colorado, New Mexico, Arizona and Utah. For water samples, filtering is recommended to increase sample homogeneity and reproducibility because for most elements studied water samples which were allowed to remain unfiltered until time of analysis contained higher concentrations than field-filtered samples of the same waters. Acidification of unfiltered samples resulted in still higher concentrations. This is predominantly because of leaching of the elements from the suspended fraction. U in water correslates directly with Ca, Mg, Na, K, Ba, B, Li and As. In stream sediments, U and other trace elements are concentrated in the finer size fractions. Accordingly, in prospecting, grain size fractions less than 90 μm (170 mesh) should be analyzed for U. A greater number of elements (21) show a significant positive correlation with U in stream sediments than in water. Results have revealed that anomalous concentrations of U found in water may not be detected in associated sediments and vice versa. Hence, sampling of both surface water and coexisting sediment is strongly recommended

Comparative metatranscriptomics reveals decline of a neustonic planktonic population

KAUST Repository

Mojib, Nazia; Thimma, Manjula; Kumaran, M.; Sougrat, Rachid; Irigoien, Xabier

2016-01-01

The neuston layer in tropical seas provides a good model to study the effects of increased levels of different stressors (e.g., temperature, ultraviolet radiation and Trichodesmium blooms). Here, we use a comparative in situ metatranscriptomics approach to reveal the functional genomic composition of metabolically active neustonic mesozooplankton community in response to the summer conditions in the Red Sea. The neustonic population exhibited changes in composition and abundance with a significant decline in copepods and appendicularia in July, when Trichodesmium cells were more abundant along with high temperatures and UV-B radiation. Nearly 23,000 genes were differentially expressed at the community level when the metatranscriptomes of the neustonic zooplankton were compared in April, July, and October. On a wider Phylum level, the genes related to oxidative phosphorylation, carbon, nucleotides, amino acids, and lipids were significantly overrepresented in both arthropods and chordates in April and October. On organism level for copepods, expression of genes responsive to oxidative stress, defense against bacteria, immune response, and virus reproduction were increased along with the observed increased appearance of copepod carcasses in the samples collected during July. The differences in expression correspond either to secondary effects of the Trichodesmium bloom or more likely to the increased UV-B radiation in July. Given the dearth of information on the zooplankton gene expression in response to environmental stimuli, our study provides the first transcriptome landscape of the mesozooplankton community during a period of increased mortality of the copepod and appendicularia population.

Comparative metatranscriptomics reveals decline of a neustonic planktonic population

KAUST Repository

Mojib, Nazia

2016-10-20

The neuston layer in tropical seas provides a good model to study the effects of increased levels of different stressors (e.g., temperature, ultraviolet radiation and Trichodesmium blooms). Here, we use a comparative in situ metatranscriptomics approach to reveal the functional genomic composition of metabolically active neustonic mesozooplankton community in response to the summer conditions in the Red Sea. The neustonic population exhibited changes in composition and abundance with a significant decline in copepods and appendicularia in July, when Trichodesmium cells were more abundant along with high temperatures and UV-B radiation. Nearly 23,000 genes were differentially expressed at the community level when the metatranscriptomes of the neustonic zooplankton were compared in April, July, and October. On a wider Phylum level, the genes related to oxidative phosphorylation, carbon, nucleotides, amino acids, and lipids were significantly overrepresented in both arthropods and chordates in April and October. On organism level for copepods, expression of genes responsive to oxidative stress, defense against bacteria, immune response, and virus reproduction were increased along with the observed increased appearance of copepod carcasses in the samples collected during July. The differences in expression correspond either to secondary effects of the Trichodesmium bloom or more likely to the increased UV-B radiation in July. Given the dearth of information on the zooplankton gene expression in response to environmental stimuli, our study provides the first transcriptome landscape of the mesozooplankton community during a period of increased mortality of the copepod and appendicularia population.

Association between virtues and posttraumatic growth: preliminary evidence from a Chinese community sample after earthquakes

Directory of Open Access Journals (Sweden)

Wenjie Duan

2015-04-01

Full Text Available Objective. Relationship, vitality, and conscientiousness are three fundamental virtues that have been recently identified as important individual differences to health, well being, and positive development. This cross-sectional study attempted to explore the relationship between the three constructs and post-traumatic growth (PTG in three directions, including indirect trauma samples without post-traumatic stress disorder (PTSD, direct trauma samples without PTSD, and direct trauma samples with PTSD.Methods. A total of 340 community participants from Sichuan Province, Mainland China involved in the study, most of which experienced Wenchuan and Lushan Earthquake. Participants were required to complete the self-reported questionnaire packages at one time point for obtaining their scores on virtues (Chinese Virtues Questionnaire, PTSD (PTSD Checklist-Specific, and PTG (Post-traumatic Growth Inventory-Chinese.Results. Significant and positive correlations between the three virtues and PTG were identified (r = .39–.56; p < .01. Further regression analysis by stepwise method reveled that: in the indirect trauma samples, vitality explained 32% variance of PTG. In reference to the direct trauma sample without PTSD, both relationship and conscientiousness explained 32% variance of PTG, whereas in the direct trauma sample with PTSD, only conscientiousness accounted for 31% the variance in PTG.Conclusion.This cross-sectional investigation partly revealed the roles of different virtues in trauma context. Findings suggest important implications for strengths-based treatment.

Off-road sampling reveals a different grassland bird community than roadside sampling: implications for survey design and estimates to guide conservation

Directory of Open Access Journals (Sweden)

Troy I. Wellicome

2014-06-01

concern. Our results highlight the need to develop appropriate corrections for bias in estimates derived from roadside sampling, and the need to design surveys that sample bird communities across a more representative cross-section of the landscape, both near and far from roads.

Active Listening Attitude Scale (ALAS: Reliability and Validity in a Nationwide Sample of Greek Educators

Directory of Open Access Journals (Sweden)

Ntina Kourmousi

2017-03-01

Full Text Available The present study examined the Active Listening Attitude Scale (ALAS validity and reliability in a sample of 3955 Greek educators. The sample was randomly split and an exploratory factor analysis (EFA was conducted in the even subsample to evaluate the scale’s construct validity. A confirmatory factor analysis (CFA was performed in the odd subsample to confirm the three-factor model identified by the EFA. The chi square test (χ2 of the model was significant (p < 0.05, due to the large sample size. The root mean square error of approximation (RMSEA, the comparative fit index (CFI and the goodness of fit index (GFI values were 0.079, 0.969 and 0.960, respectively, further supporting the fit of the three-factor model. Cronbach’s alpha coefficient was used to test internal consistency reliability and was satisfactory exceeding 0.72 for ALAS subscales. The intercorrelations of the three subscales were all positive and significant (p < 0.001, ranging from 0.20 to 0.42. Student’s t-tests and the computation of effect sizes revealed that women scored higher on Listening Skill and Conversation Opportunity, while principals and participants trained on mental health promotion scored higher on all three subscales. The analyses confirmed the three-factor model of ALAS and demonstrated its validity and reliability in measuring Greek teachers’ active listening attitudes.

The significance of deaf identity for psychological well-being

DEFF Research Database (Denmark)

Chapman, Madeleine; Dammeyer, Jesper

2017-01-01

of psychological well-being than those with a marginal identity. Further, it found that additional disability, educational level, and feeling discriminated against significantly and independently explained the degree of psychological well-being. Results are discussed here with respect to social identity theory......Research has paid attention to how deaf identity affects life outcomes such as psychological well-being. However, studies are often carried out with small samples and without controlling for other variables. This study examined how different forms of identity—deaf, hearing, bicultural (deaf...... and hearing), and marginal (neither deaf nor hearing)—were associated with levels of psychological well-being and a number of other variables. The sample was 742 adults with hearing loss in Denmark. The study found that those with a deaf, hearing or bicultural identity had significantly higher levels...

Micro-PIXE evaluation of radioactive cesium transfer in contaminated soil samples

Science.gov (United States)

Fujishiro, F.; Ishii, K.; Matsuyama, S.; Arai, H.; Ishizaki, A.; Osada, N.; Sugai, H.; Kusano, K.; Nozawa, Y.; Yamauchi, S.; Karahashi, M.; Oshikawa, S.; Kikuchi, K.; Koshio, S.; Watanabe, K.; Suzuki, Y.

2014-01-01

Micro-PIXE analysis has been performed on two soil samples with high cesium activity concentrations. These soil samples were contaminated by fallout from the accident at Fukushima Daiichi Nuclear Power Plant. One exhibits a radioactive cesium transfer of ˜0.01, and the other shows a radioactive cesium transfer of less than 0.001, even though both samples have high cesium activity concentrations exceeding 10,000 Bq/kg. X-ray spectra and elemental images of the soil samples revealed the presence of chlorine, which can react with cesium to produce an inorganic soluble compound, and phosphorus-containing cesium-capturable organic compounds.

MR diffusion histology and micro-tractography reveal mesoscale features of the human cerebellum.

Science.gov (United States)

Dell'Acqua, Flavio; Bodi, Istvan; Slater, David; Catani, Marco; Modo, Michel

2013-12-01

After 140 years from the discovery of Golgi's black reaction, the study of connectivity of the cerebellum remains a fascinating yet challenging task. Current histological techniques provide powerful methods for unravelling local axonal architecture, but the relatively low volume of data that can be acquired in a reasonable amount of time limits their application to small samples. State-of-the-art in vivo magnetic resonance imaging (MRI) methods, such as diffusion tractography techniques, can reveal trajectories of the major white matter pathways, but their correspondence with underlying anatomy is yet to be established. Hence, a significant gap exists between these two approaches as neither of them can adequately describe the three-dimensional complexity of fibre architecture at the level of the mesoscale (from a few millimetres to micrometres). In this study, we report the application of MR diffusion histology and micro-tractography methods to reveal the combined cytoarchitectural organisation and connectivity of the human cerebellum at a resolution of 100-μm (2 nl/voxel volume). Results show that the diffusion characteristics for each layer of the cerebellar cortex correctly reflect the known cellular composition and its architectural pattern. Micro-tractography also reveals details of the axonal connectivity of individual cerebellar folia and the intra-cortical organisation of the different cerebellar layers. The direct correspondence between MR diffusion histology and micro-tractography with immunohistochemistry indicates that these approaches have the potential to complement traditional histology techniques by providing a non-destructive, quantitative and three-dimensional description of the microstructural organisation of the healthy and pathological tissue.

Gaussian graphical modeling reveals specific lipid correlations in glioblastoma cells

Science.gov (United States)

Mueller, Nikola S.; Krumsiek, Jan; Theis, Fabian J.; Böhm, Christian; Meyer-Bäse, Anke

2011-06-01

Advances in high-throughput measurements of biological specimens necessitate the development of biologically driven computational techniques. To understand the molecular level of many human diseases, such as cancer, lipid quantifications have been shown to offer an excellent opportunity to reveal disease-specific regulations. The data analysis of the cell lipidome, however, remains a challenging task and cannot be accomplished solely based on intuitive reasoning. We have developed a method to identify a lipid correlation network which is entirely disease-specific. A powerful method to correlate experimentally measured lipid levels across the various samples is a Gaussian Graphical Model (GGM), which is based on partial correlation coefficients. In contrast to regular Pearson correlations, partial correlations aim to identify only direct correlations while eliminating indirect associations. Conventional GGM calculations on the entire dataset can, however, not provide information on whether a correlation is truly disease-specific with respect to the disease samples and not a correlation of control samples. Thus, we implemented a novel differential GGM approach unraveling only the disease-specific correlations, and applied it to the lipidome of immortal Glioblastoma tumor cells. A large set of lipid species were measured by mass spectrometry in order to evaluate lipid remodeling as a result to a combination of perturbation of cells inducing programmed cell death, while the other perturbations served solely as biological controls. With the differential GGM, we were able to reveal Glioblastoma-specific lipid correlations to advance biomedical research on novel gene therapies.

Social attribution test--multiple choice (SAT-MC) in schizophrenia: comparison with community sample and relationship to neurocognitive, social cognitive and symptom measures.

Science.gov (United States)

Bell, Morris D; Fiszdon, Joanna M; Greig, Tamasine C; Wexler, Bruce E

2010-09-01

This is the first report on the use of the Social Attribution Task - Multiple Choice (SAT-MC) to assess social cognitive impairments in schizophrenia. The SAT-MC was originally developed for autism research, and consists of a 64-second animation showing geometric figures enacting a social drama, with 19 multiple choice questions about the interactions. Responses from 85 community-dwelling participants and 66 participants with SCID confirmed schizophrenia or schizoaffective disorders (Scz) revealed highly significant group differences. When the two samples were combined, SAT-MC scores were significantly correlated with other social cognitive measures, including measures of affect recognition, theory of mind, self-report of egocentricity and the Social Cognition Index from the MATRICS battery. Using a cut-off score, 53% of Scz were significantly impaired on SAT-MC compared with 9% of the community sample. Most Scz participants with impairment on SAT-MC also had impairment on affect recognition. Significant correlations were also found with neurocognitive measures but with less dependence on verbal processes than other social cognitive measures. Logistic regression using SAT-MC scores correctly classified 75% of both samples. Results suggest that this measure may have promise, but alternative versions will be needed before it can be used in pre-post or longitudinal designs. (c) 2009 Elsevier B.V. All rights reserved.

[Distribution Characteristics of Heavy Metals in Environmental Samples Around Electroplating Factories and the Health Risk Assessment].

Science.gov (United States)

Guo, Peng-ran; Lei, Yong-qian; Zhou, Qiao-li; Wang, Chang; Pan, Jia-chuan

2015-09-01

This study aimed to investigate the pollution degree and human health risk of heavy metals in soil and air samples around electroplating factories. Soil, air and waste gas samples were collected to measure 8 heavy metals (As, Cd, Cr, Cu, Hg, Ni, Pb and Zn) in two electroplating factories, located in Baiyun district of Guangzhou city. Geoaccumulation index and USEPA Risk Assessment Guidance for Superfund (RAGS) were respectively carried out. Results showed that concentrations of Hg and Pb in waste gas and Cr in air samples were higher than limits of the corresponding quality standards, and concentrations of Cd, Hg and Zn in soil samples reached the moderate pollution level. The HQ and HI of exposure by heavy metals in air and soil samples were both lower than 1, indicating that there was no non-carcinogen risk. CRAs and CRCr in soil samples were beyond the maximum acceptable level of carcinogen risk (10(-4)), and the contribution rate of CRCr to TCR was over 81%. CRCr, CRNi and TCR in air samples were in range of 10(-6) - 10(-4), indicating there was possibly carcinogen risk but was acceptable risk. CR values for children were higher than adults in soils, but were higher for adults in air samples. Correlation analysis revealed that concentrations of heavy metals in soils were significantly correlated with these in waste gas samples, and PCA data showed pollution sources of Cd, Hg and Zn in soils were different from other metals.

Bacterial community profiling of milk samples as a means to understand culture-negative bovine clinical mastitis.

Science.gov (United States)

Kuehn, Joanna S; Gorden, Patrick J; Munro, Daniel; Rong, Ruichen; Dong, Qunfeng; Plummer, Paul J; Wang, Chong; Phillips, Gregory J

2013-01-01

Inflammation and infection of bovine mammary glands, commonly known as mastitis, imposes significant losses each year in the dairy industry worldwide. While several different bacterial species have been identified as causative agents of mastitis, many clinical mastitis cases remain culture negative, even after enrichment for bacterial growth. To understand the basis for this increasingly common phenomenon, the composition of bacterial communities from milk samples was analyzed using culture independent pyrosequencing of amplicons of 16S ribosomal RNA genes (16S rDNA). Comparisons were made of the microbial community composition of culture negative milk samples from mastitic quarters with that of non-mastitic quarters from the same animals. Genomic DNA from culture-negative clinical and healthy quarter sample pairs was isolated, and amplicon libraries were prepared using indexed primers specific to the V1-V2 region of bacterial 16S rRNA genes and sequenced using the Roche 454 GS FLX with titanium chemistry. Evaluation of the taxonomic composition of these samples revealed significant differences in the microbiota in milk from mastitic and healthy quarters. Statistical analysis identified seven bacterial genera that may be mainly responsible for the observed microbial community differences between mastitic and healthy quarters. Collectively, these results provide evidence that cases of culture negative mastitis can be associated with bacterial species that may be present below culture detection thresholds used here. The application of culture-independent bacterial community profiling represents a powerful approach to understand long-standing questions in animal health and disease.

Broken home or drug using peers : "Significant relations"?

NARCIS (Netherlands)

Quensel, S; McArdle, P; Brinkley, A; Wiegersma, A; Blom, M; Fitzgerald, M; Johnson, R; Kolte, B; Michels, [No Value; Pierolini, A; Pos, R; Stoeckel, [No Value

2002-01-01

This study reports the results of a comparative survey with representative samples of 3,386 school attending youths, most of whom were 15 years of age and residing in five European cities. We found significant but low correlations between the type of family structure (intact family, model family,

Testing the effects of educational toilet posters: a novel way of reducing haemolysis of blood samples within ED.

Science.gov (United States)

Corkill, David

2012-02-01

Haemolysed blood samples are an unnecessary burden on Emergency Departments (ED) as they increase workloads and drive down efficiencies. Little empirical data exists that demonstrates the effectiveness of educational posters displayed in staff toilet cubicles. This study explored the impact educational toilet posters have on reducing haemolysis rates within the ED. A time series study of the clinical effect of educational toilet posters on reducing haemolysis rates throughout a 12 month period at the Gold Coast Hospital ED was undertaken. The GCH ED is a tertiary emergency service that has approximately 66,000 patient presentations per year. Data was collected prospectively. Analysis was undertaken to investigate the effects on total number of haemolysed samples and those clinically significant samples with a haemolytic index >3. Further investigation explored the specific effects on medical and nursing staff. Analysis undertaken using an independent t-test found that the pre-intervention data demonstrates a medium haemolysis rate of 4.92% (SD=1.04). This is a statistically significantly different (t=3.56, df=50, p=0.001) from the median post intervention data of 3.95% (SD=0.84). The difference of 0.97% (95%CI=0.42, 1.52) represents a 19.72% reduction in clinically significant haemolysed samples over the study period. This study reveals that the use of educational toilet posters had a positive impact on reducing the rates of haemolysed samples collected within the ED. This simple and cost effective educational initiative changed the behaviour of clinical staff. Further investigation is warranted to examine the impact of educational toilet posters on additional clinical scenarios. Crown Copyright © 2011. Published by Elsevier Ltd. All rights reserved.

Genotyping of samples from German patients with ocular, cerebral and systemic toxoplasmosis reveals a predominance of Toxoplasma gondii type II.

Science.gov (United States)

Herrmann, Daland C; Maksimov, Pavlo; Hotop, Andrea; Groß, Uwe; Däubener, Walter; Liesenfeld, Oliver; Pleyer, Uwe; Conraths, Franz J; Schares, Gereon

2014-10-01

Toxoplasmosis is an important zoonosis transmitted from animals to humans world-wide. In order to determine Toxoplasma gondii genotypes in individuals living in Germany and to compare findings with those in animals, we analysed nine independent and unlinked genetic markers (nSAG2, SAG3, BTUB, GRA6, c22-8, c29-2, L358, PK1 and Apico) by PCR-RFLP in 83 archived T. gondii-positive DNA samples from patients with ocular toxoplasmosis (n=35), toxoplasmic encephalitis (n=32), systemic toxoplasmosis after bone-marrow transplantation (n=15) and congenital toxoplasmosis (n=1). In 46 of these 83 samples the presence of T. gondii DNA was confirmed by conventional end-point PCR. Among these, 17 T. gondii-positive samples were typed at all nine loci. The majority (15/17, 88.2%) of these samples were of T. gondii type II (i.e., including both, the Apico type II and Apico type I variants). In addition, in one sample a T. gondii type II/type III allele combination and in another sample a T. gondii genotype displaying type III alleles at all markers was observed. In the remaining 11 samples, in which T. gondii could only be partially typed, exclusively type II (n=10) or type III (n=1) alleles were observed. Results of the present study suggest that the majority of patients in Germany are infected with type II T. gondii regardless of the clinical manifestation of toxoplasmosis. This finding is in accord with the predominance of type II T. gondii in oocysts isolated from cats and in tissues of other intermediate hosts in Germany. Copyright © 2014 Elsevier GmbH. All rights reserved.

Diverse sampling of East African haemosporidians reveals chiropteran origin of malaria parasites in primates and rodents.

Science.gov (United States)

Lutz, Holly L; Patterson, Bruce D; Kerbis Peterhans, Julian C; Stanley, William T; Webala, Paul W; Gnoske, Thomas P; Hackett, Shannon J; Stanhope, Michael J

2016-06-01

Phylogenies of parasites provide hypotheses on the history of their movements between hosts, leading to important insights regarding the processes of host switching that underlie modern-day epidemics. Haemosporidian (malaria) parasites lack a well resolved phylogeny, which has impeded the study of evolutionary processes associated with host-switching in this group. Here we present a novel phylogenetic hypothesis that suggests bats served as the ancestral hosts of malaria parasites in primates and rodents. Expanding upon current taxon sampling of Afrotropical bat and bird parasites, we find strong support for all major nodes in the haemosporidian tree using both Bayesian and maximum likelihood approaches. Our analyses support a single transition of haemosporidian parasites from saurian to chiropteran hosts, and do not support a monophyletic relationship between Plasmodium parasites of birds and mammals. We find, for the first time, that Hepatocystis and Plasmodium parasites of mammals represent reciprocally monophyletic evolutionary lineages. These results highlight the importance of broad taxonomic sampling when analyzing phylogenetic relationships, and have important implications for our understanding of key host switching events in the history of malaria parasite evolution. Copyright © 2016 Elsevier Inc. All rights reserved.

Sampling procedure in a willow plantation for chemical elements important for biomass combustion quality

DEFF Research Database (Denmark)

Liu, Na; Nielsen, Henrik Kofoed; Jørgensen, Uffe

2015-01-01

clone ‘Tordis’, and to reveal the relationship between sampling position, shoot diameters, and distribution of elements. Five Tordis willow shoots were cut into 10–50 cm sections from base to top. The ash content and concentration of twelve elements (Al, Ca, Cd, Cu, Fe, K, Mg, Mn, Na, P, Si, and Zn......Willow (Salix spp.) is expected to contribute significantly to the woody bioenergy system in the future, so more information on how to sample the quality of the willow biomass is needed. The objectives of this study were to investigate the spatial variation of elements within shoots of a willow......) in each section were determined. The results showed large spatial variation in the distribution of most elements along the length of the willow shoots. Concentrations of elements in 2-year old shoots of the willow clone Tordis were fairly stable within the range of 100–285 cm above ground and resembled...

Interpreting Statistical Significance Test Results: A Proposed New "What If" Method.

Science.gov (United States)

Kieffer, Kevin M.; Thompson, Bruce

As the 1994 publication manual of the American Psychological Association emphasized, "p" values are affected by sample size. As a result, it can be helpful to interpret the results of statistical significant tests in a sample size context by conducting so-called "what if" analyses. However, these methods can be inaccurate…

Male infertility is significantly associated with multiple deletions in an 8.7-kb segment of sperm mtDNA in Pakistan.

Science.gov (United States)

Mughal, Irfan Afzal; Irfan, Asma; Jahan, Sarwat; Hameed, Abdul

2017-06-12

This study aimed to find a link between sperm mitochondrial DNA mutations and male infertility in Pakistan. DNA from semen samples was extracted and amplified by PCR using 7.8-kb deletion-specific primers. The PCR products were separated on agarose gel, visualized under UV-illumination, and then photographed. The results were genotyped and the data were analyzed using SPSS. Deletion analysis of the 8.7-kb fragment by long PCR revealed multiple deletions. The frequency of deletion was much higher in infertile groups as compared to the control group. Further, on comparison between different subtypes of infertile groups, the deletions were highest in the oligoasthenoteratozoospermia (OAT) group. The statistical analysis of case and control groups showed a significant association of the 8.7-kb deletion with human male infertile groups (P = 0.031), and particularly a very significant association with the OAT subgroup (P = 0.019). A significant association has been found between human male infertility and mtDNA deletions in an 8.7-kb segment of sperm mtDNA in a Pakistani population.

Cannabis, motivation, and life satisfaction in an internet sample

Directory of Open Access Journals (Sweden)

Wilcox Rand

2006-01-01

Full Text Available Abstract Although little evidence supports cannabis-induced amotivational syndrome, sources continue to assert that the drug saps motivation 1, which may guide current prohibitions. Few studies report low motivation in chronic users; another reveals that they have higher subjective wellbeing. To assess differences in motivation and subjective wellbeing, we used a large sample (N = 487 and strict definitions of cannabis use (7 days/week and abstinence (never. Standard statistical techniques showed no differences. Robust statistical methods controlling for heteroscedasticity, non-normality and extreme values found no differences in motivation but a small difference in subjective wellbeing. Medical users of cannabis reporting health problems tended to account for a significant portion of subjective wellbeing differences, suggesting that illness decreased wellbeing. All p-values were above p = .05. Thus, daily use of cannabis does not impair motivation. Its impact on subjective wellbeing is small and may actually reflect lower wellbeing due to medical symptoms rather than actual consumption of the plant.

Nanoscale imaging and identification of four-component carbon sample

Energy Technology Data Exchange (ETDEWEB)

Sheremet, Evgeniya S [ORNL; Rodriguez, Raul [Chemnitz University of Technology, Germany; Agapov, Alexander L [ORNL; Sokolov, Alexei P [ORNL; Hietschold, Michael [Chemnitz University of Technology, Germany; Zahn, Dietrich [Chemnitz University of Technology, Germany

2015-01-01

We demonstrate the unprecedented chemical imaging of individual constituents in a four-component sample made of several carbon allotropes: single-wall carbon nanotubes, graphene oxide, C₆₀ fullerene, and an organic residue. This represents a significant advance with respect to previous works that were mainly limited to systems with one or two components having very different chemical composition. Despite the spectral and spatial overlap from different components, plasmon-based nanospectroscopy allows the discrimination of all individual carbon nanomaterials here investigated. Among other physical insights such as doping observed in carbon nanotubes, the detailed chemical imaging of graphene oxide reveals higher defect concentration at the flake edges similarly to the case of graphene. We found that the organic residue has either low adsorption or lack of resonant enhancement on GO, in contrast to graphene, suggesting a decreased van der Waals interaction. Furthermore, this report paves the way for routine nanoscale analysis of complex carbon systems with spatial resolution of 15 nm and below.

Diversity of Microbial Communities in Production and Injection Waters of Algerian Oilfields Revealed by 16S rRNA Gene Amplicon 454 Pyrosequencing

Science.gov (United States)

Lenchi, Nesrine; İnceoğlu, Özgül; Kebbouche-Gana, Salima; Gana, Mohamed Lamine; Llirós, Marc; Servais, Pierre; García-Armisen, Tamara

2013-01-01

The microorganisms inhabiting many petroleum reservoirs are multi-extremophiles capable of surviving in environments with high temperature, pressure and salinity. Their activity influences oil quality and they are an important reservoir of enzymes of industrial interest. To study these microbial assemblages and to assess any modifications that may be caused by industrial practices, the bacterial and archaeal communities in waters from four Algerian oilfields were described and compared. Three different types of samples were analyzed: production waters from flooded wells, production waters from non-flooded wells and injection waters used for flooding (water-bearing formations). Microbial communities of production and injection waters appeared to be significantly different. From a quantitative point of view, injection waters harbored roughly ten times more microbial cells than production waters. Bacteria dominated in injection waters, while Archaea dominated in production waters. Statistical analysis based on the relative abundance and bacterial community composition (BCC) revealed significant differences between production and injection waters at both OTUs0.03 and phylum level. However, no significant difference was found between production waters from flooded and non-flooded wells, suggesting that most of the microorganisms introduced by the injection waters were unable to survive in the production waters. Furthermore, a Venn diagram generated to compare the BCC of production and injection waters of one flooded well revealed only 4% of shared bacterial OTUs. Phylogenetic analysis of bacterial sequences indicated that Alpha-, Beta- and Gammaproteobacteria were the main classes in most of the water samples. Archaeal sequences were only obtained from production wells and each well had a unique archaeal community composition, mainly belonging to Methanobacteria, Methanomicrobia, Thermoprotei and Halobacteria classes. Many of the bacterial genera retrieved had already

Introduction of e-learning in dental radiology reveals significantly improved results in final examination.

Science.gov (United States)

Meckfessel, Sandra; Stühmer, Constantin; Bormann, Kai-Hendrik; Kupka, Thomas; Behrends, Marianne; Matthies, Herbert; Vaske, Bernhard; Stiesch, Meike; Gellrich, Nils-Claudius; Rücker, Martin

2011-01-01

Because a traditionally instructed dental radiology lecture course is very time-consuming and labour-intensive, online courseware, including an interactive-learning module, was implemented to support the lectures. The purpose of this study was to evaluate the perceptions of students who have worked with web-based courseware as well as the effect on their results in final examinations. Users (n(3+4)=138) had access to the e-program from any networked computer at any time. Two groups (n(3)=71, n(4)=67) had to pass a final exam after using the e-course. Results were compared with two groups (n(1)=42, n(2)=48) who had studied the same content by attending traditional lectures. In addition a survey of the students was statistically evaluated. Most of the respondents reported a positive attitude towards e-learning and would have appreciated more access to computer-assisted instruction. Two years after initiating the e-course the failure rate in the final examination dropped significantly, from 40% to less than 2%. The very positive response to the e-program and improved test scores demonstrated the effectiveness of our e-course as a learning aid. Interactive modules in step with clinical practice provided learning that is not achieved by traditional teaching methods alone. To what extent staff savings are possible is part of a further study. Copyright © 2010 European Association for Cranio-Maxillo-Facial Surgery. Published by Elsevier Ltd. All rights reserved.

Targeted Gene-Silencing Reveals the Functional Significance of Myocardin Signaling in the Failing Heart

Science.gov (United States)

Torrado, Mario; Iglesias, Raquel; Centeno, Alberto; López, Eduardo; Mikhailov, Alexander T.

2011-01-01

Background Myocardin (MYOCD), a potent transcriptional coactivator of smooth muscle (SM) and cardiac genes, is upregulated in failing myocardium in animal models and human end-stage heart failure (HF). However, the molecular and functional consequences of myocd upregulation in HF are still unclear. Methodology/Principal Findings The goal of the present study was to investigate if targeted inhibition of upregulated expression of myocd could influence failing heart gene expression and function. To this end, we used the doxorubicin (Dox)-induced diastolic HF (DHF) model in neonatal piglets, in which, as we show, not only myocd but also myocd-dependent SM-marker genes are highly activated in failing left ventricular (LV) myocardium. In this model, intra-myocardial delivery of short-hairpin RNAs, designed to target myocd variants expressed in porcine heart, leads on day 2 post-delivery to: (1) a decrease in the activated expression of myocd and myocd-dependent SM-marker genes in failing myocardium to levels seen in healthy control animals, (2) amelioration of impaired diastolic dysfunction, and (3) higher survival rates of DHF piglets. The posterior restoration of elevated myocd expression (on day 7 post-delivery) led to overexpression of myocd-dependent SM-marker genes in failing LV-myocardium that was associated with a return to altered diastolic function. Conclusions/Significance These data provide the first evidence that a moderate inhibition (e.g., normalization) of the activated MYOCD signaling in the diseased heart may be promising from a therapeutic point of view. PMID:22028870

Targeted gene-silencing reveals the functional significance of myocardin signaling in the failing heart.

Directory of Open Access Journals (Sweden)

Mario Torrado

Full Text Available BACKGROUND: Myocardin (MYOCD, a potent transcriptional coactivator of smooth muscle (SM and cardiac genes, is upregulated in failing myocardium in animal models and human end-stage heart failure (HF. However, the molecular and functional consequences of myocd upregulation in HF are still unclear. METHODOLOGY/PRINCIPAL FINDINGS: The goal of the present study was to investigate if targeted inhibition of upregulated expression of myocd could influence failing heart gene expression and function. To this end, we used the doxorubicin (Dox-induced diastolic HF (DHF model in neonatal piglets, in which, as we show, not only myocd but also myocd-dependent SM-marker genes are highly activated in failing left ventricular (LV myocardium. In this model, intra-myocardial delivery of short-hairpin RNAs, designed to target myocd variants expressed in porcine heart, leads on day 2 post-delivery to: (1 a decrease in the activated expression of myocd and myocd-dependent SM-marker genes in failing myocardium to levels seen in healthy control animals, (2 amelioration of impaired diastolic dysfunction, and (3 higher survival rates of DHF piglets. The posterior restoration of elevated myocd expression (on day 7 post-delivery led to overexpression of myocd-dependent SM-marker genes in failing LV-myocardium that was associated with a return to altered diastolic function. CONCLUSIONS/SIGNIFICANCE: These data provide the first evidence that a moderate inhibition (e.g., normalization of the activated MYOCD signaling in the diseased heart may be promising from a therapeutic point of view.

Sampling in ecology and evolution - bridging the gap between theory and practice

Science.gov (United States)

Albert, C.H.; Yoccoz, N.G.; Edwards, T.C.; Graham, C.H.; Zimmermann, N.E.; Thuiller, W.

2010-01-01

Sampling is a key issue for answering most ecological and evolutionary questions. The importance of developing a rigorous sampling design tailored to specific questions has already been discussed in the ecological and sampling literature and has provided useful tools and recommendations to sample and analyse ecological data. However, sampling issues are often difficult to overcome in ecological studies due to apparent inconsistencies between theory and practice, often leading to the implementation of simplified sampling designs that suffer from unknown biases. Moreover, we believe that classical sampling principles which are based on estimation of means and variances are insufficient to fully address many ecological questions that rely on estimating relationships between a response and a set of predictor variables over time and space. Our objective is thus to highlight the importance of selecting an appropriate sampling space and an appropriate sampling design. We also emphasize the importance of using prior knowledge of the study system to estimate models or complex parameters and thus better understand ecological patterns and processes generating these patterns. Using a semi-virtual simulation study as an illustration we reveal how the selection of the space (e.g. geographic, climatic), in which the sampling is designed, influences the patterns that can be ultimately detected. We also demonstrate the inefficiency of common sampling designs to reveal response curves between ecological variables and climatic gradients. Further, we show that response-surface methodology, which has rarely been used in ecology, is much more efficient than more traditional methods. Finally, we discuss the use of prior knowledge, simulation studies and model-based designs in defining appropriate sampling designs. We conclude by a call for development of methods to unbiasedly estimate nonlinear ecologically relevant parameters, in order to make inferences while fulfilling requirements of

Species Richness and Diversity Reveal that Human-Modified ...

African Journals Online (AJOL)

Family diversity and richness showed no significant differences across the sites. The spider species consisted of primarily three functional groups: ground wanderers, web builders and plant wanderers, and showed no within-group differences in abundance between sites. Similarity index between the study sites revealed a ...

18S rDNA Sequences from Microeukaryotes Reveal Oil Indicators in Mangrove Sediment

Science.gov (United States)

Santos, Henrique F.; Cury, Juliano C.; Carmo, Flavia L.; Rosado, Alexandre S.; Peixoto, Raquel S.

2010-01-01

Background Microeukaryotes are an effective indicator of the presence of environmental contaminants. However, the characterisation of these organisms by conventional tools is often inefficient, and recent molecular studies have revealed a great diversity of microeukaryotes. The full extent of this diversity is unknown, and therefore, the distribution, ecological role and responses to anthropogenic effects of microeukaryotes are rather obscure. The majority of oil from oceanic oil spills (e.g., the May 2010 accident in the Gulf of Mexico) converges on coastal ecosystems such as mangroves, which are threatened with worldwide disappearance, highlighting the need for efficient tools to indicate the presence of oil in these environments. However, no studies have used molecular methods to assess the effects of oil contamination in mangrove sediment on microeukaryotes as a group. Methodology/Principal Findings We evaluated the population dynamics and the prevailing 18S rDNA phylotypes of microeukaryotes in mangrove sediment microcosms with and without oil contamination, using PCR/DGGE and clone libraries. We found that microeukaryotes are useful for monitoring oil contamination in mangroves. Our clone library analysis revealed a decrease in both diversity and species richness after contamination. The phylogenetic group that showed the greatest sensitivity to oil was the Nematoda. After contamination, a large increase in the abundance of the groups Bacillariophyta (diatoms) and Biosoecida was detected. The oil-contaminated samples were almost entirely dominated by organisms related to Bacillariophyta sp. and Cafeteria minima, which indicates that these groups are possible targets for biomonitoring oil in mangroves. The DGGE fingerprints also indicated shifts in microeukaryote profiles; specific band sequencing indicated the appearance of Bacillariophyta sp. only in contaminated samples and Nematoda only in non-contaminated sediment. Conclusions/Significance We believe that

3-dimensional examination of the adult mouse subventricular zone reveals lineage-specific microdomains.

Science.gov (United States)

Azim, Kasum; Fiorelli, Roberto; Zweifel, Stefan; Hurtado-Chong, Anahi; Yoshikawa, Kazuaki; Slomianka, Lutz; Raineteau, Olivier

2012-01-01

Recent studies suggest that the subventricular zone (SVZ) of the lateral ventricle is populated by heterogeneous populations of stem and progenitor cells that, depending on their exact location, are biased to acquire specific neuronal fates. This newly described heterogeneity of SVZ stem and progenitor cells underlines the necessity to develop methods for the accurate quantification of SVZ stem and progenitor subpopulations. In this study, we provide 3-dimensional topographical maps of slow cycling "stem" cells and progenitors based on their unique cell cycle properties. These maps revealed that both cell populations are present throughout the lateral ventricle wall as well as in discrete regions of the dorsal wall. Immunodetection of transcription factors expressed in defined progenitor populations further reveals that divergent lineages have clear regional enrichments in the rostro-caudal as well as in the dorso-ventral span of the lateral ventricle. Thus, progenitors expressing Tbr2 and Dlx2 were confined to dorsal and dorso-lateral regions of the lateral ventricle, respectively, while Mash1+ progenitors were more homogeneously distributed. All cell populations were enriched in the rostral-most region of the lateral ventricle. This diversity and uneven distribution greatly impede the accurate quantification of SVZ progenitor populations. This is illustrated by measuring the coefficient of error of estimates obtained by using increasing section sampling interval. Based on our empirical data, we provide such estimates for all progenitor populations investigated in this study. These can be used in future studies as guidelines to judge if the precision obtained with a sampling scheme is sufficient to detect statistically significant differences between experimental groups if a biological effect is present. Altogether, our study underlines the need to consider the SVZ of the lateral ventricle as a complex 3D structure and define methods to accurately assess neural

Quantitative PCR Profiling of Escherichia coli in Livestock Feces Reveals Increased Population Resilience Relative to Culturable Counts under Temperature Extremes.

Science.gov (United States)

Oliver, David M; Bird, Clare; Burd, Emmy; Wyman, Michael

2016-09-06

The relationship between culturable counts (CFU) and quantitative PCR (qPCR) cell equivalent counts of Escherichia coli in dairy feces exposed to different environmental conditions and temperature extremes was investigated. Fecal samples were collected in summer and winter from dairy cowpats held under two treatments: field-exposed versus polytunnel-protected. A significant correlation in quantified E. coli was recorded between the qPCR and culture-based methods (r = 0.82). Evaluation of the persistence profiles of E. coli over time revealed no significant difference in the E. coli numbers determined as either CFU or gene copies during the summer for the field-exposed cowpats, whereas significantly higher counts were observed by qPCR for the polytunnel-protected cowpats, which were exposed to higher ambient temperatures. In winter, the qPCR returned significantly higher counts of E. coli for the field-exposed cowpats, thus representing a reversal of the findings from the summer sampling campaign. Results from this study suggest that with increasing time post-defecation and with the onset of challenging environmental conditions, such as extremes in temperature, culture-based counts begin to underestimate the true resilience of viable E. coli populations in livestock feces. This is important not only in the long term as the Earth changes in response to climate-change drivers but also in the short term during spells of extremely cold or hot weather.

Sampling Lesbian, Gay, and Bisexual Populations

Science.gov (United States)

Meyer, Ilan H.; Wilson, Patrick A.

2009-01-01

Sampling has been the single most influential component of conducting research with lesbian, gay, and bisexual (LGB) populations. Poor sampling designs can result in biased results that will mislead other researchers, policymakers, and practitioners. Investigators wishing to study LGB populations must therefore devote significant energy and…

Estimation of radioecological parameters of soil samples from a phosphatic area

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Harb Shaaban

2016-01-01

Full Text Available The activity concentrations of natural radionuclides (226Ra, 232Th, and 40K for a set of 31 agricultural soil samples from the Nile River banks in the area of El-Sebaiya city, Aswan Governorate, Egypt were measured by gamma-spectrometry. The study revealed that the average activity concentrations of natural radionuclides 226Ra, 232Th, and 40K were 23.2 ± 2.8Bq/kg, 21.1 ± 2.8 Bq/kg, and 218.6 ± 3.7 Bq/kg, respectively. The obtained results of the activity concentrations are within the range of values reported for neighbouring areas in Egypt. The values obtained for the hazard indices and the representative level index in all sampling sites were lower than unity, showing that there is no significant risk arising from the exposure to the soil in the studied area. The absorbed dose rate and annual effective dose in air outdoors and indoors were calculated from 226Ra, 232Th, and 40K in soil, the average values being 32.64 nGy/h, 40.06 µSv, and 160.25 µSv, respectively. The absorbed dose rate at the eastof El-Sebaiya city is higher than that obtained for the west because of higher concentrations of tri-calcium phosphate in the soil. The studied area is not significantly affected by the industrial activities, except for a few isolated spots.

Sampling Modification Effects in the Subgingival Microbiome Profile of Healthy Children

Science.gov (United States)

Santigli, Elisabeth; Trajanoski, Slave; Eberhard, Katharina; Klug, Barbara

2017-01-01

Background: Oral microbiota are considered major players in the development of periodontal diseases. Thorough knowledge of intact subgingival microbiomes is required to elucidate microbial shifts from health to disease. Aims: This comparative study investigated the subgingival microbiome of healthy children, possible inter- and intra-individual effects of modified sampling, and basic comparability of subgingival microprints. Methods: In five 10-year-old children, biofilm was collected from the upper first premolars and first molars using sterilized, UV-treated paper-points inserted into the subgingival sulcus at eight sites. After supragingival cleaning using an electric toothbrush and water, sampling was performed, firstly, excluding (Mode A) and, secondly, including (Mode B) cleansing with sterile cotton pellets. DNA was extracted from the pooled samples, and primers targeting 16S rRNA hypervariable regions V5 and V6 were used for 454-pyrosequencing. Wilcoxon signed rank test and t-test were applied to compare sampling modes. Principal coordinate analysis (PCoA) and average agglomerative hierarchical clustering were calculated with unweighted UniFrac distance matrices. Sample grouping was tested with permutational MANOVA (Adonis). Results: Data filtering and quality control yielded 67,218 sequences with an average sequence length of 243bp (SD 6.52; range 231–255). Actinobacteria (2.8–24.6%), Bacteroidetes (9.2–25.1%), Proteobacteria (4.9–50.6%), Firmicutes (16.5–57.4%), and Fusobacteria (2.2–17.1%) were the five major phyla found in all samples. Differences in microbial abundances between sampling modes were not evident. High sampling numbers are needed to achieve significance for rare bacterial phyla. Samples taken from one individual using different sampling modes were more similar to each other than to other individuals' samples. PCoA and hierarchical clustering showed a grouping of the paired samples. Permutational MANOVA did not reveal sample

Sampling Modification Effects in the Subgingival Microbiome Profile of Healthy Children.

Science.gov (United States)

Santigli, Elisabeth; Trajanoski, Slave; Eberhard, Katharina; Klug, Barbara

2016-01-01

Background: Oral microbiota are considered major players in the development of periodontal diseases. Thorough knowledge of intact subgingival microbiomes is required to elucidate microbial shifts from health to disease. Aims: This comparative study investigated the subgingival microbiome of healthy children, possible inter- and intra-individual effects of modified sampling, and basic comparability of subgingival microprints. Methods: In five 10-year-old children, biofilm was collected from the upper first premolars and first molars using sterilized, UV-treated paper-points inserted into the subgingival sulcus at eight sites. After supragingival cleaning using an electric toothbrush and water, sampling was performed, firstly, excluding (Mode A) and, secondly, including (Mode B) cleansing with sterile cotton pellets. DNA was extracted from the pooled samples, and primers targeting 16S rRNA hypervariable regions V5 and V6 were used for 454-pyrosequencing. Wilcoxon signed rank test and t -test were applied to compare sampling modes. Principal coordinate analysis (PCoA) and average agglomerative hierarchical clustering were calculated with unweighted UniFrac distance matrices. Sample grouping was tested with permutational MANOVA (Adonis). Results: Data filtering and quality control yielded 67,218 sequences with an average sequence length of 243bp (SD 6.52; range 231-255). Actinobacteria (2.8-24.6%), Bacteroidetes (9.2-25.1%), Proteobacteria (4.9-50.6%), Firmicutes (16.5-57.4%), and Fusobacteria (2.2-17.1%) were the five major phyla found in all samples. Differences in microbial abundances between sampling modes were not evident. High sampling numbers are needed to achieve significance for rare bacterial phyla. Samples taken from one individual using different sampling modes were more similar to each other than to other individuals' samples. PCoA and hierarchical clustering showed a grouping of the paired samples. Permutational MANOVA did not reveal sample grouping by

[Formula: see text]Determination of the smoking gun of intent: significance testing of forced choice results in social security claimants.

Science.gov (United States)

Binder, Laurence M; Chafetz, Michael D

2018-01-01

Significantly below-chance findings on forced choice tests have been described as revealing "the smoking gun of intent" that proved malingering. The issues of probability levels, one-tailed vs. two-tailed tests, and the combining of PVT scores on significantly below-chance findings were addressed in a previous study, with a recommendation of a probability level of .20 to test the significance of below-chance results. The purpose of the present study was to determine the rate of below-chance findings in a Social Security Disability claimant sample using the previous recommendations. We compared the frequency of below-chance results on forced choice performance validity tests (PVTs) at two levels of significance, .05 and .20, and when using significance testing on individual subtests of the PVTs compared with total scores in claimants for Social Security Disability in order to determine the rate of the expected increase. The frequency of significant results increased with the higher level of significance for each subtest of the PVT and when combining individual test sections to increase the number of test items, with up to 20% of claimants showing significantly below-chance results at the higher p-value. These findings are discussed in light of Social Security Administration policy, showing an impact on policy issues concerning child abuse and neglect, and the importance of using these techniques in evaluations for Social Security Disability.

Comprehensive Genomic Profiling of Esthesioneuroblastoma Reveals Additional Treatment Options.

Science.gov (United States)

Gay, Laurie M; Kim, Sungeun; Fedorchak, Kyle; Kundranda, Madappa; Odia, Yazmin; Nangia, Chaitali; Battiste, James; Colon-Otero, Gerardo; Powell, Steven; Russell, Jeffery; Elvin, Julia A; Vergilio, Jo-Anne; Suh, James; Ali, Siraj M; Stephens, Philip J; Miller, Vincent A; Ross, Jeffrey S

2017-07-01

Esthesioneuroblastoma (ENB), also known as olfactory neuroblastoma, is a rare malignant neoplasm of the olfactory mucosa. Despite surgical resection combined with radiotherapy and adjuvant chemotherapy, ENB often relapses with rapid progression. Current multimodality, nontargeted therapy for relapsed ENB is of limited clinical benefit. We queried whether comprehensive genomic profiling (CGP) of relapsed or refractory ENB can uncover genomic alterations (GA) that could identify potential targeted therapies for these patients. CGP was performed on formalin-fixed, paraffin-embedded sections from 41 consecutive clinical cases of ENBs using a hybrid-capture, adaptor ligation based next-generation sequencing assay to a mean coverage depth of 593X. The results were analyzed for base substitutions, insertions and deletions, select rearrangements, and copy number changes (amplifications and homozygous deletions). Clinically relevant GA (CRGA) were defined as GA linked to drugs on the market or under evaluation in clinical trials. A total of 28 ENBs harbored GA, with a mean of 1.5 GA per sample. Approximately half of the ENBs (21, 51%) featured at least one CRGA, with an average of 1 CRGA per sample. The most commonly altered gene was TP53 (17%), with GA in PIK3CA , NF1 , CDKN2A , and CDKN2C occurring in 7% of samples. We report comprehensive genomic profiles for 41 ENB tumors. CGP revealed potential new therapeutic targets, including targetable GA in the mTOR, CDK and growth factor signaling pathways, highlighting the clinical value of genomic profiling in ENB. Comprehensive genomic profiling of 41 relapsed or refractory ENBs reveals recurrent alterations or classes of mutation, including amplification of tyrosine kinases encoded on chromosome 5q and mutations affecting genes in the mTOR/PI3K pathway. Approximately half of the ENBs (21, 51%) featured at least one clinically relevant genomic alteration (CRGA), with an average of 1 CRGA per sample. The most commonly altered

MicroRNA expression data reveals a signature of kidney damage following ischemia reperfusion injury.

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Michael D Shapiro

Full Text Available Ischemia reperfusion injury (IRI is a leading cause of acute kidney injury, a common problem worldwide associated with significant morbidity and mortality. We have recently examined the role of microRNAs (miRs in renal IRI using expression profiling. Here we conducted mathematical analyses to determine if differential expression of miRs can be used to define a biomarker of renal IRI. Principal component analysis (PCA was combined with spherical geometry to determine whether samples that underwent renal injury as a result of IRI can be distinguished from controls based on alterations in miR expression using our data set consisting of time series measuring 571 miRs. Using PCA, we examined whether changes in miR expression in the kidney following IRI have a distinct direction when compared to controls based on the trajectory of the first three principal components (PCs for our time series. We then used Monte Carlo methods and spherical geometry to assess the statistical significance of these directions. We hypothesized that if IRI and control samples exhibit distinct directions, then miR expression can be used as a biomarker of injury. Our data reveal that the pattern of miR expression in the kidney following IRI has a distinct direction based on the trajectory of the first three PCs and can be distinguished from changes observed in sham controls. Analyses of samples from immunodeficient mice indicated that the changes in miR expression observed following IRI were lymphocyte independent, and therefore represent a kidney intrinsic response to injury. Together, these data strongly support the notion that IRI results in distinct changes in miR expression that can be used as a biomarker of injury.

Joint importance sampling of low-order volumetric scattering

DEFF Research Database (Denmark)

Georgiev, Iliyan; Křivánek, Jaroslav; Hachisuka, Toshiya

2013-01-01

Central to all Monte Carlo-based rendering algorithms is the construction of light transport paths from the light sources to the eye. Existing rendering approaches sample path vertices incrementally when constructing these light transport paths. The resulting probability density is thus a product...... of the conditional densities of each local sampling step, constructed without explicit control over the form of the final joint distribution of the complete path. We analyze why current incremental construction schemes often lead to high variance in the presence of participating media, and reveal...... that such approaches are an unnecessary legacy inherited from traditional surface-based rendering algorithms. We devise joint importance sampling of path vertices in participating media to construct paths that explicitly account for the product of all scattering and geometry terms along a sequence of vertices instead...

Lack of tissue renewal in human adult Achilles tendon is revealed by nuclear bomb C

DEFF Research Database (Denmark)

Heinemeier, Katja Maria; Schjerling, Peter; Heinemeier, J.

2013-01-01

the 14C bomb-pulse method. This method takes advantage of the dramatic increase in atmospheric levels of 14C, produced by nuclear bomb tests in 1955-1963, which is reflected in all living organisms. Levels of 14C were measured in 28 forensic samples of Achilles tendon core and 4 skeletal muscle samples...... is revealed by nuclear bomb 14C....

Intensity of Love in a Community Sample of Spanish Couples in the Region of Madrid.

Science.gov (United States)

Cuenca-Montesino, María Luisa; Graña, José Luis; O'Leary, K Daniel

2015-10-13

Intensity of love was examined in a representative community sample of 2,988 couples, from the Region of Madrid (Spain). Gender differences revealed no significant differences in intensity of love. Twenty-five percent of the participants who were in a relationship of less than 10 years and eleven percent of the participants in a relationship of more than 30 years reported being "very intensely in love" F(3, 5.972) = 191.32, p love for both men and women. Affection was also positively associated with intense love for men (r = .47, p love for women (r = .15, p love for male or females. As predicted, love declined significantly in the first decade of marriage, but not much after that. The percentage of men and women who reported being intensely in love was lower than that obtained in the U.S.

Predicting protein-ATP binding sites from primary sequence through fusing bi-profile sampling of multi-view features

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Zhang Ya-Nan

2012-05-01

Full Text Available Abstract Background Adenosine-5′-triphosphate (ATP is one of multifunctional nucleotides and plays an important role in cell biology as a coenzyme interacting with proteins. Revealing the binding sites between protein and ATP is significantly important to understand the functionality of the proteins and the mechanisms of protein-ATP complex. Results In this paper, we propose a novel framework for predicting the proteins’ functional residues, through which they can bind with ATP molecules. The new prediction protocol is achieved by combination of sequence evolutional information and bi-profile sampling of multi-view sequential features and the sequence derived structural features. The hypothesis for this strategy is single-view feature can only represent partial target’s knowledge and multiple sources of descriptors can be complementary. Conclusions Prediction performances evaluated by both 5-fold and leave-one-out jackknife cross-validation tests on two benchmark datasets consisting of 168 and 227 non-homologous ATP binding proteins respectively demonstrate the efficacy of the proposed protocol. Our experimental results also reveal that the residue structural characteristics of real protein-ATP binding sites are significant different from those normal ones, for example the binding residues do not show high solvent accessibility propensities, and the bindings prefer to occur at the conjoint points between different secondary structure segments. Furthermore, results also show that performance is affected by the imbalanced training datasets by testing multiple ratios between positive and negative samples in the experiments. Increasing the dataset scale is also demonstrated useful for improving the prediction performances.

Determination of Sodium Benzoate and Potassium Sorbate in “Doogh” Samples in Post Market Surveillance in Iran 2012

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B. Akbari-adergani

2013-06-01

Full Text Available Sodium benzoate and potassium sorbate are two major chemical preservatives which are used in Doogh (Iranian traditional dairy drink. In this study, a total of 27 commercial brands of highly consumed of Doogh samples were analyzed. The means and standard deviation for concentration of these preservatives based on HPLC results for analysis of benzoate and sorbate were 195·9 (SD 1·8 and 328·8 (SD 2·1 mg.Kg-1 respectively. The minimum and maximum of benzoate content in various brands were 18.3 and 2345.1 mg.Kg-1 and for sorbate were not detected and 4961.3 mg.Kg-1 respectively. The study revealed that there was not significant difference in preservative concentration in the samples that belonged to various dates. However, a few samples had a high preservative concentration, which could be a risk factor for human health, especially when their intake was being occurred by various foodstuffs simultaneously.

Bacterial microbiota compositions of naturally fermented milk are shaped by both geographic origin and sample type.

Science.gov (United States)

Zhong, Z; Hou, Q; Kwok, L; Yu, Z; Zheng, Y; Sun, Z; Menghe, B; Zhang, H

2016-10-01

Naturally fermented dairy products contain a rich microbial biodiversity. This study aimed to provide an overview on the bacterial microbiota biodiversity of 85 samples, previously collected across a wide region of China, Mongolia, and Russia. Data from these 85 samples, including 55 yogurts, 18 naturally fermented yak milks, 6 koumisses, and 6 cheeses, were retrieved and collectively analyzed. The most prevalent phyla shared across samples were Firmicutes, Proteobacteria, Bacteroidetes, and Actinobacteria, which together accounted for 99% of bacterial sequences. The predominant genera were Lactobacillus, Lactococcus, Streptococcus, Acetobacter, Acinetobacter, Leuconostoc, and Macrococcus, which together corresponded to 96.63% of bacterial sequences. Further multivariate statistical analyses revealed significant differences in the microbiota structure across sample geographic origin and type. First, on the principal coordinate score plot, samples representing the 3 main sample collection regions (Russia, Xinjiang, and Tibet) were mostly located respectively in the upper left, lower right, and lower left quadrants, although slight overlapping occurred. In contrast, samples from the minor sampling areas (Inner Mongolia, Mongolia, Gansu, and Sichuan) were predominantly distributed in the lower left quadrant. These results suggest a possible association between sample geographical origin and microbiota composition. Second, bacterial microbiota structure was stratified by sample type. In particular, the microbiota of cheese was largely distinct from the other sample types due to its high abundances of Lactococcus and Streptococcus. The fermented yak milk microbiota was most like that of the yogurts. Koumiss samples had the lowest microbial diversity and richness. In conclusion, both geographic origin and sample type shape the microbial diversity of naturally fermented milk. Copyright © 2016 American Dairy Science Association. Published by Elsevier Inc. All rights

Characteristic Performance Evaluation of a new SAGe Well Detector for Small and Large Sample Geometries

International Nuclear Information System (INIS)

Adekola, A.S.; Colaresi, J.; Douwen, J.; Jaederstroem, H.; Mueller, W.F.; Yocum, K.M.; Carmichael, K.

2015-01-01

Environmental scientific research requires a detector that has sensitivity low enough to reveal the presence of any contaminant in the sample at a reasonable counting time. Canberra developed the germanium detector geometry called Small Anode Germanium (SAGe) Well detector, which is now available commercially. The SAGe Well detector is a new type of low capacitance germanium well detector manufactured using small anode technology capable of advancing many environmental scientific research applications. The performance of this detector has been evaluated for a range of sample sizes and geometries counted inside the well, and on the end cap of the detector. The detector has energy resolution performance similar to semi-planar detectors, and offers significant improvement over the existing coaxial and Well detectors. Energy resolution performance of 750 eV Full Width at Half Maximum (FWHM) at 122 keV γ-ray energy and resolution of 2.0 - 2.3 keV FWHM at 1332 keV γ-ray energy are guaranteed for detector volumes up to 425 cm 3 . The SAGe Well detector offers an optional 28 mm well diameter with the same energy resolution as the standard 16 mm well. Such outstanding resolution performance will benefit environmental applications in revealing the detailed radionuclide content of samples, particularly at low energy, and will enhance the detection sensitivity resulting in reduced counting time. The detector is compatible with electric coolers without any sacrifice in performance and supports the Canberra Mathematical efficiency calibration method (In situ Object Calibration Software or ISOCS, and Laboratory Source-less Calibration Software or LABSOCS). In addition, the SAGe Well detector supports true coincidence summing available in the ISOCS/LABSOCS framework. The improved resolution performance greatly enhances detection sensitivity of this new detector for a range of sample sizes and geometries counted inside the well. This results in lower minimum detectable

Characteristic Performance Evaluation of a new SAGe Well Detector for Small and Large Sample Geometries

Energy Technology Data Exchange (ETDEWEB)

Adekola, A.S.; Colaresi, J.; Douwen, J.; Jaederstroem, H.; Mueller, W.F.; Yocum, K.M.; Carmichael, K. [Canberra Industries Inc., 800 Research Parkway, Meriden, CT 06450 (United States)

2015-07-01

Environmental scientific research requires a detector that has sensitivity low enough to reveal the presence of any contaminant in the sample at a reasonable counting time. Canberra developed the germanium detector geometry called Small Anode Germanium (SAGe) Well detector, which is now available commercially. The SAGe Well detector is a new type of low capacitance germanium well detector manufactured using small anode technology capable of advancing many environmental scientific research applications. The performance of this detector has been evaluated for a range of sample sizes and geometries counted inside the well, and on the end cap of the detector. The detector has energy resolution performance similar to semi-planar detectors, and offers significant improvement over the existing coaxial and Well detectors. Energy resolution performance of 750 eV Full Width at Half Maximum (FWHM) at 122 keV γ-ray energy and resolution of 2.0 - 2.3 keV FWHM at 1332 keV γ-ray energy are guaranteed for detector volumes up to 425 cm{sup 3}. The SAGe Well detector offers an optional 28 mm well diameter with the same energy resolution as the standard 16 mm well. Such outstanding resolution performance will benefit environmental applications in revealing the detailed radionuclide content of samples, particularly at low energy, and will enhance the detection sensitivity resulting in reduced counting time. The detector is compatible with electric coolers without any sacrifice in performance and supports the Canberra Mathematical efficiency calibration method (In situ Object Calibration Software or ISOCS, and Laboratory Source-less Calibration Software or LABSOCS). In addition, the SAGe Well detector supports true coincidence summing available in the ISOCS/LABSOCS framework. The improved resolution performance greatly enhances detection sensitivity of this new detector for a range of sample sizes and geometries counted inside the well. This results in lower minimum detectable

Social marketing campaign significantly associated with increases in syphilis testing among gay and bisexual men in San Francisco.

Science.gov (United States)

Montoya, Jorge A; Kent, Charlotte K; Rotblatt, Harlan; McCright, Jacque; Kerndt, Peter R; Klausner, Jeffrey D

2005-07-01

Between 1999 and 2002, San Francisco experienced a sharp increase in early syphilis among gay and bisexual men. In response, the San Francisco Department of Public Health launched a social marketing campaign to increase testing for syphilis, and awareness and knowledge about syphilis among gay and bisexual men. A convenience sample of 244 gay and bisexual men (18-60 years of age) were surveyed to evaluate the effectiveness of the campaign. Respondents were interviewed to elicit unaided and aided awareness about the campaign, knowledge about syphilis, recent sexual behaviors, and syphilis testing behavior. After controlling for other potential confounders, unaided campaign awareness was a significant correlate of having a syphilis test in the last 6 months (odds ratio, 3.21; 95% confidence interval, 1.30-7.97) compared with no awareness of the campaign. A comparison of respondents aware of the campaign with those not aware also revealed significant increases in awareness and knowledge about syphilis. The Healthy Penis 2002 campaign achieved its primary objective of increasing syphilis testing, and awareness and knowledge about syphilis among gay and bisexual men in San Francisco.

Diagnostic herd sensitivity using environmental samples

DEFF Research Database (Denmark)

Vigre, Håkan; Josefsen, Mathilde Hartmann; Seyfarth, Anne Mette

either at farm or slaughter. Three sample matrices were collected; dust samples (5 environmental swabs), nasal swabs (10 pools with 5 animals per pool) and air samples (1 filter). Based on the assumption that MRSA occurred in all 48 herds the overall herd sensitivity was 58% for nasal swabs, 33% for dust....... In our example, the prevalence of infected pigs in each herd was estimated from the pooled samples of nasal swabs. Logistic regression was used to estimate the effect of animal prevalence on the probability to detect MRSA in the dust and air samples at herd level. The results show a significant increase...

Expression of small leucine-rich extracellular matrix proteoglycans biglycan and lumican reveals oral lichen planus malignant potential.

Science.gov (United States)

Lončar-Brzak, Božana; Klobučar, Marko; Veliki-Dalić, Irena; Sabol, Ivan; Kraljević Pavelić, Sandra; Krušlin, Božo; Mravak-Stipetić, Marinka

2018-03-01

The aim of this study was to examine molecular alterations on the protein level in lesions of oral lichen planus (OLP), oral squamous cell carcinoma (OSCC) and healthy mucosa. Global protein profiling methods based on liquid chromatography coupled to mass spectrometry (LC-MS) were used, with a special emphasis on evaluation of deregulated extracellular matrix molecules expression, as well as on analyses of IG2F and IGFR2 expression in healthy mucosa, OLP and OSCC tissues by comparative semi-quantitative immunohistochemistry. Mass spectrometry-based proteomics profiling of healthy mucosa, OLP and OSCC tissues (and accompanied histologically unaltered tissues, respectively) identified 55 extracellular matrix proteins. Twenty among identified proteins were common to all groups of samples. Expression of small leucine-rich extracellular matrix proteoglycans lumican and biglycan was found both in OSCC and OLP and they were validated by Western blot analysis as putative biomarkers. A significant increase (p < 0.05) of biglycan expression in OLP-AT group was determined in comparison with OLP-T group, while lumican showed significant up-regulation (p < 0.05) in OLP-T and OSCC-T groups vs. adjacent and control tissue groups. Biglycan expression was only determined in OSCC-AT group. Immunohistochemical analysis of IGF2 and IG2FR expression revealed no significant difference among groups of samples. Biglycan and lumican were identified as important pathogenesis biomarkers of OLP that point to its malignant potential.

Molecular-based rapid inventories of sympatric diversity: a comparison of DNA barcode clustering methods applied to geography-based vs clade-based sampling of amphibians.

Science.gov (United States)

Paz, Andrea; Crawford, Andrew J

2012-11-01

Molecular markers offer a universal source of data for quantifying biodiversity. DNA barcoding uses a standardized genetic marker and a curated reference database to identify known species and to reveal cryptic diversity within wellsampled clades. Rapid biological inventories, e.g. rapid assessment programs (RAPs), unlike most barcoding campaigns, are focused on particular geographic localities rather than on clades. Because of the potentially sparse phylogenetic sampling, the addition of DNA barcoding to RAPs may present a greater challenge for the identification of named species or for revealing cryptic diversity. In this article we evaluate the use of DNA barcoding for quantifying lineage diversity within a single sampling site as compared to clade-based sampling, and present examples from amphibians. We compared algorithms for identifying DNA barcode clusters (e.g. species, cryptic species or Evolutionary Significant Units) using previously published DNA barcode data obtained from geography-based sampling at a site in Central Panama, and from clade-based sampling in Madagascar. We found that clustering algorithms based on genetic distance performed similarly on sympatric as well as clade-based barcode data, while a promising coalescent-based method performed poorly on sympatric data. The various clustering algorithms were also compared in terms of speed and software implementation. Although each method has its shortcomings in certain contexts, we recommend the use of the ABGD method, which not only performs fairly well under either sampling method, but does so in a few seconds and with a user-friendly Web interface.

Polybrominated diphenyl ethers in water, sediment, soil, and biological samples from different industrial areas in Zhejiang, China

International Nuclear Information System (INIS)

Wang, Junxia; Lin, Zhenkun; Lin, Kuangfei; Wang, Chunyan; Zhang, Wei; Cui, Changyuan; Lin, Junda; Dong, Qiaoxiang; Huang, Changjiang

2011-01-01

Highlights: ► We examined PBDE concentrations in various matrices from different industrial areas. ► Elevated PBDE levels were found in areas with low-voltage electrical manufactures. ► Areas with e-waste recycling activities also had higher PBDE concentrations. ► PBDE content and composition in water samples varied from one area to another. ► PBDE composition in sediment/soil and biological samples was predominated by BDE-209. - Abstract: Polybrominated diphenyl ethers (PBDEs) have been used extensively in electrical and electronic products, but little is known about their distribution in the environment surrounding the manufacturing factories. This study reports PBDE contamination in various matrices from the location (Liushi, Zhejiang province) that produces more than 70% of the low-voltage electrical appliances in China. Additionally, PBDE contamination was compared with other industries such as the e-waste recycling business (Fengjiang) in the same region. Specifically, we measured seven PBDE congeners (BDEs – 47, 99, 100, 153, 154, 183, and 209) in water, sediment, soil, plant, and animal tissues from four different areas in this region. The present study revealed elevated PBDE concentrations in all matrices collected from Liushi and Fengjiang in comparison with highly industrialized areas without significant PBDE contamination sources. In water samples, there were large variations of PBDE content and composition across different areas. In sediment/soil and biological samples, BDE-209 was the predominant congener and this could be due to the abundant usage of deca-BDE mixtures in China. Our findings provide the very first data on PBDE contamination in the local environments surrounding the electronics industry, and also reveal widespread PBDE contamination in highly industrialized coastal regions of China.

"What If" Analyses: Ways to Interpret Statistical Significance Test Results Using EXCEL or "R"

Science.gov (United States)

Ozturk, Elif

2012-01-01

The present paper aims to review two motivations to conduct "what if" analyses using Excel and "R" to understand the statistical significance tests through the sample size context. "What if" analyses can be used to teach students what statistical significance tests really do and in applied research either prospectively to estimate what sample size…

Metabolomics of dates (Phoenix dactylifera) reveals a highly dynamic ripening process accounting for major variation in fruit composition.

Science.gov (United States)

Diboun, Ilhame; Mathew, Sweety; Al-Rayyashi, Maryam; Elrayess, Mohamed; Torres, Maria; Halama, Anna; Méret, Michaël; Mohney, Robert P; Karoly, Edward D; Malek, Joel; Suhre, Karsten

2015-12-16

Dates are tropical fruits with appreciable nutritional value. Previous attempts at global metabolic characterization of the date metabolome were constrained by small sample size and limited geographical sampling. In this study, two independent large cohorts of mature dates exhibiting substantial diversity in origin, varieties and fruit processing conditions were measured by metabolomics techniques in order to identify major determinants of the fruit metabolome. Multivariate analysis revealed a first principal component (PC1) significantly associated with the dates' countries of production. The availability of a smaller dataset featuring immature dates from different development stages served to build a model of the ripening process in dates, which helped reveal a strong ripening signature in PC1. Analysis revealed enrichment in the dry type of dates amongst fruits with early ripening profiles at one end of PC1 as oppose to an overrepresentation of the soft type of dates with late ripening profiles at the other end of PC1. Dry dates are typical to the North African region whilst soft dates are more popular in the Gulf region, which partly explains the observed association between PC1 and geography. Analysis of the loading values, expressing metabolite correlation levels with PC1, revealed enrichment patterns of a comprehensive range of metabolite classes along PC1. Three distinct metabolic phases corresponding to known stages of date ripening were observed: An early phase enriched in regulatory hormones, amines and polyamines, energy production, tannins, sucrose and anti-oxidant activity, a second phase with on-going phenylpropanoid secondary metabolism, gene expression and phospholipid metabolism and a late phase with marked sugar dehydration activity and degradation reactions leading to increased volatile synthesis. These data indicate the importance of date ripening as a main driver of variation in the date metabolome responsible for their diverse nutritional and

Quantifying the Clinical Significance of Cannabis Withdrawal

Science.gov (United States)

Allsop, David J.; Copeland, Jan; Norberg, Melissa M.; Fu, Shanlin; Molnar, Anna; Lewis, John; Budney, Alan J.

2012-01-01

Background and Aims Questions over the clinical significance of cannabis withdrawal have hindered its inclusion as a discrete cannabis induced psychiatric condition in the Diagnostic and Statistical Manual of Mental Disorders (DSM IV). This study aims to quantify functional impairment to normal daily activities from cannabis withdrawal, and looks at the factors predicting functional impairment. In addition the study tests the influence of functional impairment from cannabis withdrawal on cannabis use during and after an abstinence attempt. Methods and Results A volunteer sample of 49 non-treatment seeking cannabis users who met DSM-IV criteria for dependence provided daily withdrawal-related functional impairment scores during a one-week baseline phase and two weeks of monitored abstinence from cannabis with a one month follow up. Functional impairment from withdrawal symptoms was strongly associated with symptom severity (p = 0.0001). Participants with more severe cannabis dependence before the abstinence attempt reported greater functional impairment from cannabis withdrawal (p = 0.03). Relapse to cannabis use during the abstinence period was associated with greater functional impairment from a subset of withdrawal symptoms in high dependence users. Higher levels of functional impairment during the abstinence attempt predicted higher levels of cannabis use at one month follow up (p = 0.001). Conclusions Cannabis withdrawal is clinically significant because it is associated with functional impairment to normal daily activities, as well as relapse to cannabis use. Sample size in the relapse group was small and the use of a non-treatment seeking population requires findings to be replicated in clinical samples. Tailoring treatments to target withdrawal symptoms contributing to functional impairment during a quit attempt may improve treatment outcomes. PMID:23049760

Quantifying the clinical significance of cannabis withdrawal.

Directory of Open Access Journals (Sweden)

David J Allsop

Full Text Available Questions over the clinical significance of cannabis withdrawal have hindered its inclusion as a discrete cannabis induced psychiatric condition in the Diagnostic and Statistical Manual of Mental Disorders (DSM IV. This study aims to quantify functional impairment to normal daily activities from cannabis withdrawal, and looks at the factors predicting functional impairment. In addition the study tests the influence of functional impairment from cannabis withdrawal on cannabis use during and after an abstinence attempt.A volunteer sample of 49 non-treatment seeking cannabis users who met DSM-IV criteria for dependence provided daily withdrawal-related functional impairment scores during a one-week baseline phase and two weeks of monitored abstinence from cannabis with a one month follow up. Functional impairment from withdrawal symptoms was strongly associated with symptom severity (p=0.0001. Participants with more severe cannabis dependence before the abstinence attempt reported greater functional impairment from cannabis withdrawal (p=0.03. Relapse to cannabis use during the abstinence period was associated with greater functional impairment from a subset of withdrawal symptoms in high dependence users. Higher levels of functional impairment during the abstinence attempt predicted higher levels of cannabis use at one month follow up (p=0.001.Cannabis withdrawal is clinically significant because it is associated with functional impairment to normal daily activities, as well as relapse to cannabis use. Sample size in the relapse group was small and the use of a non-treatment seeking population requires findings to be replicated in clinical samples. Tailoring treatments to target withdrawal symptoms contributing to functional impairment during a quit attempt may improve treatment outcomes.

Interval sampling methods and measurement error: a computer simulation.

Science.gov (United States)

Wirth, Oliver; Slaven, James; Taylor, Matthew A

2014-01-01

A simulation study was conducted to provide a more thorough account of measurement error associated with interval sampling methods. A computer program simulated the application of momentary time sampling, partial-interval recording, and whole-interval recording methods on target events randomly distributed across an observation period. The simulation yielded measures of error for multiple combinations of observation period, interval duration, event duration, and cumulative event duration. The simulations were conducted up to 100 times to yield measures of error variability. Although the present simulation confirmed some previously reported characteristics of interval sampling methods, it also revealed many new findings that pertain to each method's inherent strengths and weaknesses. The analysis and resulting error tables can help guide the selection of the most appropriate sampling method for observation-based behavioral assessments. © Society for the Experimental Analysis of Behavior.

Detecting significant changes in protein abundance

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Kai Kammers

2015-06-01

Full Text Available We review and demonstrate how an empirical Bayes method, shrinking a protein's sample variance towards a pooled estimate, leads to far more powerful and stable inference to detect significant changes in protein abundance compared to ordinary t-tests. Using examples from isobaric mass labelled proteomic experiments we show how to analyze data from multiple experiments simultaneously, and discuss the effects of missing data on the inference. We also present easy to use open source software for normalization of mass spectrometry data and inference based on moderated test statistics.

Antimicrobial potential and phyto chemical analysis of different solvent extracted samples of viola pilosa

International Nuclear Information System (INIS)

Bakht, J.; Panni, M. K.; Shafi, M.

2017-01-01

Investigation of susceptibility of medicinal plants for bacterial pathogens is significant for suitable choice of treatment. Different solvent extracted samples of Viola pilosa shoots were investigated for their antibacterial and phytochemical activities using 0.5, 1 and 2 mg disc-1 concentrations. The antibacterial bioassay was assayed by disc diffusion method against six microbes. The studies revealed that ethyl acetate extracted fractions resulted in maximum growth inhibition of Pseudomonas aeruginosa and Staphylococcus aureus at 2000 mu g disc-1 concentration. Similarly, Xanthomonas campestris and Klebsiella pneumonia were found more susceptible to n-butanol extract. Maximum reduction in the activity of B. subtilis and E. coli was recorded by n-hexane fractions at two mg per disc. The most susceptible microbe was Pseudomonas aeruginosa. The results further revealed that all the tested microbes were found completely resistant to water extracted fractions at all the tested concentrations measuring 0% ZI. Phytochemical analysis showed the presence of various bioactive compounds including flavonoids, glycosides, proteins, fats, alkaloids, steroids, saponins, carbohydrates and tannins. (author)

Blood sampling and hemolysis affect concentration of plasma metabolites

DEFF Research Database (Denmark)

Theil, Peter Kappel; Pedersen, Lene Juul; Jensen, Margit Bak

2012-01-01

design and blood was collected after restraint via vein puncture 1, 4, 11, and 23 h after morning feeding. Plasma samples were categorized as without or with minor or major hemolysis [clear (n = 218), yellow (n = 97), or red (n = 37)] upon centrifugation. Plasma NEFA (P ...Two experiments were carried out to reveal and quantify plasma metabolites that are sensitive to hemolysis and animal stress due to the blood sampling procedure (vein puncture vs. catheter). In Exp. 1, 48 sows were fed 4 diets either once (0800 h) or twice daily (0800 h and 1500 h) in a crossover......, a subset of samples from 24 sows fed twice daily in Exp. 1 was combined with data obtained from 30 sows sampled using jugular vein catheters. All sows in Exp. 2 were fed twice daily (0800 h and 1500 h) and blood samples collected repeatedly 1, 4, 11, and 23 h after morning feeding (other conditions were...

Genome Wide Expression Profiling of Cancer Cell Lines Cultured in Microgravity Reveals Significant Dysregulation of Cell Cycle and MicroRNA Gene Networks.

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Prasanna Vidyasekar

Full Text Available Zero gravity causes several changes in metabolic and functional aspects of the human body and experiments in space flight have demonstrated alterations in cancer growth and progression. This study reports the genome wide expression profiling of a colorectal cancer cell line-DLD-1, and a lymphoblast leukemic cell line-MOLT-4, under simulated microgravity in an effort to understand central processes and cellular functions that are dysregulated among both cell lines. Altered cell morphology, reduced cell viability and an aberrant cell cycle profile in comparison to their static controls were observed in both cell lines under microgravity. The process of cell cycle in DLD-1 cells was markedly affected with reduced viability, reduced colony forming ability, an apoptotic population and dysregulation of cell cycle genes, oncogenes, and cancer progression and prognostic markers. DNA microarray analysis revealed 1801 (upregulated and 2542 (downregulated genes (>2 fold in DLD-1 cultures under microgravity while MOLT-4 cultures differentially expressed 349 (upregulated and 444 (downregulated genes (>2 fold under microgravity. The loss in cell proliferative capacity was corroborated with the downregulation of the cell cycle process as demonstrated by functional clustering of DNA microarray data using gene ontology terms. The genome wide expression profile also showed significant dysregulation of post transcriptional gene silencing machinery and multiple microRNA host genes that are potential tumor suppressors and proto-oncogenes including MIR22HG, MIR17HG and MIR21HG. The MIR22HG, a tumor-suppressor gene was one of the highest upregulated genes in the microarray data showing a 4.4 log fold upregulation under microgravity. Real time PCR validated the dysregulation in the host gene by demonstrating a 4.18 log fold upregulation of the miR-22 microRNA. Microarray data also showed dysregulation of direct targets of miR-22, SP1, CDK6 and CCNA2.

Abrasive supply for ancient Egypt revealed

International Nuclear Information System (INIS)

Peltz, C.; Bichler, M.

2008-01-01

In the framework of the major research scheme 'Synchronization of Civilizations in the Eastern Mediterranean Region in the 2nd Millennium B.C' instrumental neutron activation analysis (INAA) was used to determine 30 elements in pumice from archaeological excavations to reveal their specific volcanic origin. In ancient time, the widespread pumiceous products of several eruptions in the Aegean region have been used as abrasive tools and were therefore popular trade objects. The correlation of such archaeological findings to a specific eruption of known age would therefore allow to certify a maximum age of the respective stratum ('dating by first appearance'). Pumices from the Aegean region can easily be distinguished by their trace element distribution patterns. This has been shown by previous studies of the group. The elements Al, Ba, Ca, Ce, Co, Cr, Cs, Dy, Eu, Fe, Hf, K, La, Lu, Mn, Na, Nd, Rb, Sb, Sc, Sm, Ta, Tb, Th, Ti, U, V, Yb, Zr and Zn were determined in 16 samples of pumice lumps from excavations in Tell-el-Dab'a and Tell-el-Herr (Egypt). Two irradiation cycles and five measurement runs were applied. To show the accuracy of the results obtained, typical samples of the most important pumice sources in the Aegean region, particularly from Milos, Nisyros, Kos and Thera were analyzed together with the Egyptian samples of unknown origin. A reliable identification of the samples is achieved by comparing these results to the database compiled in previous studies. The geographical positions of these islands are shown. Within the error range, most of the elements determined in typical representatives of Milos, Nisyros, Kos and Santorini were in perfect agreement with values from the literature. On the basis of the Cluster graphics presented, it is possible to relate unknown pumice to its primary source, just by comparing the relation of a few elements, like Ta-Eu and Th-Hf. One concludes that all samples except one can be related to the Minoan eruption of Thera

Sample size estimation and sampling techniques for selecting a representative sample

Directory of Open Access Journals (Sweden)

Aamir Omair

2014-01-01

Full Text Available Introduction: The purpose of this article is to provide a general understanding of the concepts of sampling as applied to health-related research. Sample Size Estimation: It is important to select a representative sample in quantitative research in order to be able to generalize the results to the target population. The sample should be of the required sample size and must be selected using an appropriate probability sampling technique. There are many hidden biases which can adversely affect the outcome of the study. Important factors to consider for estimating the sample size include the size of the study population, confidence level, expected proportion of the outcome variable (for categorical variables/standard deviation of the outcome variable (for numerical variables, and the required precision (margin of accuracy from the study. The more the precision required, the greater is the required sample size. Sampling Techniques: The probability sampling techniques applied for health related research include simple random sampling, systematic random sampling, stratified random sampling, cluster sampling, and multistage sampling. These are more recommended than the nonprobability sampling techniques, because the results of the study can be generalized to the target population.

Light and electron microscopy of the European beaver (Castor fiber) stomach reveal unique morphological features with possible general biological significance.

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Ziółkowska, Natalia; Lewczuk, Bogdan; Petryński, Wojciech; Palkowska, Katarzyna; Prusik, Magdalena; Targońska, Krystyna; Giżejewski, Zygmunt; Przybylska-Gornowicz, Barbara

2014-01-01

Anatomical, histological, and ultrastructural studies of the European beaver stomach revealed several unique morphological features. The prominent attribute of its gross morphology was the cardiogastric gland (CGG), located near the oesophageal entrance. Light microscopy showed that the CGG was formed by invaginations of the mucosa into the submucosa, which contained densely packed proper gastric glands comprised primarily of parietal and chief cells. Mucous neck cells represented beaver stomach was the presence of specific mucus with a thickness up to 950 µm (in frozen, unfixed sections) that coated the mucosa. Our observations suggest that the formation of this mucus is complex and includes the secretory granule accumulation in the cytoplasm of pit cells, the granule aggregation inside cells, and the incorporation of degenerating cells into the mucus.

Automated gray level index measurements reveal only minor cytoarchitectonic changes of Brodmann area 9 in schizophrenia.

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Tepest, Ralf; Vogeley, Kai; Viebahn, Bettina; Schneider-Axmann, Thomas; Honer, William G; Falkai, Peter

2008-07-15

Using an automatized gray level index (GLI) method, we recently found cytoarchitectonic abnormalities in schizophrenia in Brodmann area 10 (BA10) [Vogeley, K., Tepest, R., Schneider-Axmann, T., Hutte, H., Zilles, K., Honer, W.G., Falkai, P., 2003. Automated image analysis of disturbed cytoarchitecture in Brodmann area 10 in schizophrenia, Schizophrenia Research 62, 133-140]. As another potential key region involved in the pathophysiology of schizophrenia, we have now investigated BA9 in the same sample consisting of 20 schizophrenic cases and 20 controls. The GLI value represents the area-percentage covered by perikarya in measuring fields of microscopic images. BA9 was analyzed with respect to the factors diagnosis and gender for six different compartments approximately corresponding to the neocortical layers. The main result in BA9 was a significant interaction of diagnosis and gender for GLI in layers IV and V on the left side. Subsequent analyses separately performed concerning gender revealed a significant GLI increase in layer V on the left side in male patients compared with controls. However, after an adjustment of error probabilities for multiple testing, differences did not reach significance. No GLI difference was observed in the sample between diagnostic groups for females and between the diagnostic groups in general. Comparisons with our BA10 results suggest that cytoarchitectural changes relevant to schizophrenia appear different in various Brodmann areas. Since increases in GLI were found only in selected layers (V and VI) of BA9, these findings do not support a generalized neuropil reduction across all cortical layers.

Study of the formation of duricrusts on the martian surface and their effect on sampling equipment

Science.gov (United States)

Kömle, Norbert; Pitcher, Craig; Gao, Yang; Richter, Lutz

2017-01-01

The Powdered Sample Dosing and Distribution System (PSDDS) of the ExoMars rover will be required to handle and contain samples of Mars regolith for long periods of time. Cementation of the regolith, caused by water and salts in the soil, results in clumpy material and a duricrust layer forming on the surface. It is therefore possible that material residing in the sampling system may cement, and could potentially hinder its operation. There has yet to be an investigation into the formation of duricrusts under simulated Martian conditions, or how this may affect the performance of sample handling mechanisms. Therefore experiments have been performed to create a duricrust and to explore the cementation of Mars analogues, before performing a series of tests on a qualification model of the PSDDS under simulated Martian conditions. It was possible to create a consolidated crust of cemented material several millimetres deep, with the material below remaining powder-like. It was seen that due to the very low permeability of the Montmorillonite component material, diffusion of water through the material was quickly blocked, resulting in a sample with an inhomogeneous water content. Additionally, samples with a water mass content of 10% or higher would cement into a single solid piece. Finally, tests with the PSDDS revealed that samples with a water mass content of just 5% created small clumps with significant internal cohesion, blocking the sample funnels and preventing transportation of the material. These experiments have highlighted that the cementation of regolith in Martian conditions must be taken into consideration in the design of sample handling instruments.

Impact of shrinking measurement error budgets on qualification metrology sampling and cost

Science.gov (United States)

Sendelbach, Matthew; Sarig, Niv; Wakamoto, Koichi; Kim, Hyang Kyun (Helen); Isbester, Paul; Asano, Masafumi; Matsuki, Kazuto; Vaid, Alok; Osorio, Carmen; Archie, Chas

2014-04-01

When designing an experiment to assess the accuracy of a tool as compared to a reference tool, semiconductor metrologists are often confronted with the situation that they must decide on the sampling strategy before the measurements begin. This decision is usually based largely on the previous experience of the metrologist and the available resources, and not on the statistics that are needed to achieve acceptable confidence limits on the final result. This paper shows a solution to this problem, called inverse TMU analysis, by presenting statistically-based equations that allow the user to estimate the needed sampling after providing appropriate inputs, allowing him to make important "risk vs. reward" sampling, cost, and equipment decisions. Application examples using experimental data from scatterometry and critical dimension scanning electron microscope (CD-SEM) tools are used first to demonstrate how the inverse TMU analysis methodology can be used to make intelligent sampling decisions before the start of the experiment, and then to reveal why low sampling can lead to unstable and misleading results. A model is developed that can help an experimenter minimize the costs associated both with increased sampling and with making wrong decisions caused by insufficient sampling. A second cost model is described that reveals the inadequacy of current TEM (Transmission Electron Microscopy) sampling practices and the enormous costs associated with TEM sampling that is needed to provide reasonable levels of certainty in the result. These high costs reach into the tens of millions of dollars for TEM reference metrology as the measurement error budgets reach angstrom levels. The paper concludes with strategies on how to manage and mitigate these costs.

Three-year-olds obey the sample size principle of induction: the influence of evidence presentation and sample size disparity on young children's generalizations.

Science.gov (United States)

Lawson, Chris A

2014-07-01

Three experiments with 81 3-year-olds (M=3.62years) examined the conditions that enable young children to use the sample size principle (SSP) of induction-the inductive rule that facilitates generalizations from large rather than small samples of evidence. In Experiment 1, children exhibited the SSP when exemplars were presented sequentially but not when exemplars were presented simultaneously. Results from Experiment 3 suggest that the advantage of sequential presentation is not due to the additional time to process the available input from the two samples but instead may be linked to better memory for specific individuals in the large sample. In addition, findings from Experiments 1 and 2 suggest that adherence to the SSP is mediated by the disparity between presented samples. Overall, these results reveal that the SSP appears early in development and is guided by basic cognitive processes triggered during the acquisition of input. Copyright © 2013 Elsevier Inc. All rights reserved.

Catch me if you can: Comparing ballast water sampling skids to traditional net sampling

Science.gov (United States)

Bradie, Johanna; Gianoli, Claudio; Linley, Robert Dallas; Schillak, Lothar; Schneider, Gerd; Stehouwer, Peter; Bailey, Sarah

2018-03-01

With the recent ratification of the International Convention for the Control and Management of Ships' Ballast Water and Sediments, 2004, it will soon be necessary to assess ships for compliance with ballast water discharge standards. Sampling skids that allow the efficient collection of ballast water samples in a compact space have been developed for this purpose. We ran 22 trials on board the RV Meteor from June 4-15, 2015 to evaluate the performance of three ballast water sampling devices (traditional plankton net, Triton sampling skid, SGS sampling skid) for three organism size classes: ≥ 50 μm, ≥ 10 μm to Natural sea water was run through the ballast water system and untreated samples were collected using paired sampling devices. Collected samples were analyzed in parallel by multiple analysts using several different analytic methods to quantify organism concentrations. To determine whether there were differences in the number of viable organisms collected across sampling devices, results were standardized and statistically treated to filter out other sources of variability, resulting in an outcome variable representing the mean difference in measurements that can be attributed to sampling devices. These results were tested for significance using pairwise Tukey contrasts. Differences in organism concentrations were found in 50% of comparisons between sampling skids and the plankton net for ≥ 50 μm, and ≥ 10 μm to < 50 μm size classes, with net samples containing either higher or lower densities. There were no differences for < 10 μm organisms. Future work will be required to explicitly examine the potential effects of flow velocity, sampling duration, sampled volume, and organism concentrations on sampling device performance.

Sample size calculation in metabolic phenotyping studies.

Science.gov (United States)

Billoir, Elise; Navratil, Vincent; Blaise, Benjamin J

2015-09-01

The number of samples needed to identify significant effects is a key question in biomedical studies, with consequences on experimental designs, costs and potential discoveries. In metabolic phenotyping studies, sample size determination remains a complex step. This is due particularly to the multiple hypothesis-testing framework and the top-down hypothesis-free approach, with no a priori known metabolic target. Until now, there was no standard procedure available to address this purpose. In this review, we discuss sample size estimation procedures for metabolic phenotyping studies. We release an automated implementation of the Data-driven Sample size Determination (DSD) algorithm for MATLAB and GNU Octave. Original research concerning DSD was published elsewhere. DSD allows the determination of an optimized sample size in metabolic phenotyping studies. The procedure uses analytical data only from a small pilot cohort to generate an expanded data set. The statistical recoupling of variables procedure is used to identify metabolic variables, and their intensity distributions are estimated by Kernel smoothing or log-normal density fitting. Statistically significant metabolic variations are evaluated using the Benjamini-Yekutieli correction and processed for data sets of various sizes. Optimal sample size determination is achieved in a context of biomarker discovery (at least one statistically significant variation) or metabolic exploration (a maximum of statistically significant variations). DSD toolbox is encoded in MATLAB R2008A (Mathworks, Natick, MA) for Kernel and log-normal estimates, and in GNU Octave for log-normal estimates (Kernel density estimates are not robust enough in GNU octave). It is available at http://www.prabi.fr/redmine/projects/dsd/repository, with a tutorial at http://www.prabi.fr/redmine/projects/dsd/wiki. © The Author 2015. Published by Oxford University Press. For Permissions, please email: journals.permissions@oup.com.

'Intelligent' approach to radioimmunoassay sample counting employing a microprocessor controlled sample counter

International Nuclear Information System (INIS)

Ekins, R.P.; Sufi, S.; Malan, P.G.

1977-01-01

The enormous impact on medical science in the last two decades of microanalytical techniques employing radioisotopic labels has, in turn, generated a large demand for automatic radioisotopic sample counters. Such instruments frequently comprise the most important item of capital equipment required in the use of radioimmunoassay and related techniques and often form a principle bottleneck in the flow of samples through a busy laboratory. It is therefore particularly imperitive that such instruments should be used 'intelligently' and in an optimal fashion to avoid both the very large capital expenditure involved in the unnecessary proliferation of instruments and the time delays arising from their sub-optimal use. The majority of the current generation of radioactive sample counters nevertheless rely on primitive control mechanisms based on a simplistic statistical theory of radioactive sample counting which preclude their efficient and rational use. The fundamental principle upon which this approach is based is that it is useless to continue counting a radioactive sample for a time longer than that required to yield a significant increase in precision of the measurement. Thus, since substantial experimental errors occur during sample preparation, these errors should be assessed and must be releted to the counting errors for that sample. It is the objective of this presentation to demonstrate that the combination of a realistic statistical assessment of radioactive sample measurement, together with the more sophisticated control mechanisms that modern microprocessor technology make possible, may often enable savings in counter usage of the order of 5-10 fold to be made. (orig.) [de

Diversity and structure of soil bacterial communities in the Fildes Region (maritime Antarctica as revealed by 454 pyrosequencing

Directory of Open Access Journals (Sweden)

Neng Fei eWang

2015-10-01

Full Text Available This study assessed the diversity and composition of bacterial communities in four different soils (human-, penguin-, seal-colony impacted soils and pristine soil in the Fildes Region (King George Island, Antarctica using 454 pyrosequencing with bacterial-specific primers targeting the 16S rRNA gene. Proteobacteria, Actinobacteria, Acidobacteria, and Verrucomicrobia were abundant phyla in almost all the soil samples. The four types of soils were significantly different in geochemical properties and bacterial community structure. Thermotogae, Cyanobacteria, Fibrobacteres, Deinococcus-Thermus, and Chlorobi obviously varied in their abundance among the 4 soil types. Considering all the samples together, members of the genera Gaiella, Chloracidobacterium, Nitrospira, Polaromonas, Gemmatimonas, Sphingomonas and Chthoniobacter were found to predominate, whereas members of the genera Chamaesiphon, Herbaspirillum, Hirschia, Nevskia, Nitrosococcus, Rhodococcus, Rhodomicrobium, and Xanthomonas varied obviously in their abundance among the four soil types. Distance-based redundancy analysis revealed that pH (p < 0.01, phosphate phosphorus (p < 0.01, organic carbon (p < 0.05, and organic nitrogen (p < 0.05 were the most significant factors that correlated with the community distribution of soil bacteria. To our knowledge, this is the first study to explore the soil bacterial communities in human-, penguin-, and seal- colony impacted soils from ice-free areas in maritime Antarctica using high-throughput pyrosequencing.

Non-suicidal self-injury, suicidal ideation, and suicide attempt: prevalence and predictors in a sample of youth offenders in the UK

OpenAIRE

Spink, Alisa; Dhingra, Katie; Debowska, Agata; Boduszek, Daniel

2017-01-01

The aim of this study was to examine the prevalence and correlates of suicide attempts (SA), suicidal ideation (SI), and non-suicidal self-injury (NSSI) within a sample of community-based youth offenders (M age = 15.33 years) engaging with a Youth Offending Team (YOT). Findings revealed the highest prevalence rates for NSSI (20.6%), followed by SI (12.7%), and SA (5.9%). SA and SI were significantly correlated with trauma exposure, self-esteem, and posttraumatic stress disorder (PTSD). NSSI f...

Trace metals analysis in molybdenite mineral sample

International Nuclear Information System (INIS)

Tamrakar, Praveen Kumar; Pitre, K.S.

2000-01-01

DC polarography and other related techniques, viz., DPP and DPASV have been successfully used for the simultaneous determination of trace metals in molybdenite mineral sample. The polarograms and voltammograms of sample solution have been recorded in 0.1 M (NH 4 ) 2 tartrate supporting electrolyte at two different pH values i.e., 2.7±0.1 and 9.0±0.1. The results indicate the presence of Cu 2+ , Mo 6+ , Cd 2+ , Ni 2+ , In 3+ , Fe 3+ and W 6+ metal ions in the sample. For the determination of tungsten(VI), 11 M HCl has been used as supporting electrolyte. Tungsten(VI) produces a well defined wave/peak with E 1/2 /Ep=-0.42V/-0.48V vs SCE in 11 M HCl. The quantitative analysis by the method of standard addition shows the mineral sample to have the following composition, Cu 2+ ( 14.83), Mo 6+ (253.70), Cd 2+ (41.36), Ni 2+ (16.08), In 3+ (3.06), Fe 3+ (83.00)and W 6+ (4.14 )mg/g of the sample. Statistical treatment of the observed voltammetric data reveals high accuracy and good precision of determination. The observed voltammetric results are comparable with those obtained using AAS method. (author)

Contamination-free Ge-based graphene as revealed by graphene enhanced secondary ion mass spectrometry (GESIMS)

Science.gov (United States)

Michałowski, P. P.; Pasternak, I.; Strupiński, W.

2018-01-01

In this study, we demonstrate that graphene grown on Ge does not contain any copper contamination, and identify some of the errors affecting the accuracy of commonly used measurement methods. Indeed, one of these, the secondary ion mass spectrometry (SIMS) technique, reveals copper contamination in Ge-based graphene but does not take into account the effect of the presence of the graphene layer. We have shown that this layer increases negative ionization significantly, and thus yields false results, but also that the graphene enhances, by an order of two, the magnitude of the intensity of SIMS signals when compared with a similar graphene-free sample, enabling much better detection limits. This forms the basis of a new measurement procedure, graphene enhanced SIMS (GESIMS) (pending European patent application no. EP 16461554.4), which allows for the precise estimation of the realistic distribution of dopants and contamination in graphene. In addition, we present evidence that the GESIMS effect leads to unexpected mass interferences with double-ionized species, and that these interferences are negligible in samples without graphene. The GESIMS method also shows that graphene transferred from Cu results in increased copper contamination.

Australian attitudes to DNA sample banks and genetic screening.

Science.gov (United States)

Williams, Carolyn

2005-11-01

An exploration via an anonymous questionnaire of Australian public attitudes towards medical genetics and sample banking revealed the overwhelming majority views these developments with thoughtful confidence. Continued public education and awareness of these issues will allow the public to make informed decisions and enhance vigilance towards the sometimes misleading coverage in the press and media.

Life-table studies revealed significant effects of deforestation on the development and survivorship of Anopheles minimus larvae.

Science.gov (United States)

Wang, Xiaoming; Zhou, Guofa; Zhong, Daibin; Wang, Xiaoling; Wang, Ying; Yang, Zhaoqing; Cui, Liwang; Yan, Guiyun

2016-06-06

Many developing countries are experiencing rapid ecological changes such as deforestation and shifting agricultural practices. These environmental changes may have an important consequence on malaria due to their impact on vector survival and reproduction. Despite intensive deforestation and malaria transmission in the China-Myanmar border area, the impact of deforestation on malaria vectors in the border area is unknown. We conducted life table studies on Anopheles minimus larvae to determine the pupation rate and development time in microcosms under deforested, banana plantation, and forested environments. The pupation rate of An. minimus was 3.8 % in the forested environment. It was significantly increased to 12.5 % in banana plantations and to 52.5 % in the deforested area. Deforestation reduced larval-to-pupal development time by 1.9-3.3 days. Food supplementation to aquatic habitats in forested environments and banana plantations significantly increased larval survival rate to a similar level as in the deforested environment. Deforestation enhanced the survival and development of An. minimus larvae, a major malaria vector in the China-Myanmar border area. Experimental determination of the life table parameters on mosquito larvae under a variety of environmental conditions is valuable to model malaria transmission dynamics and impact by climate and environmental changes.

Experimental breakdown of selected anodized aluminum samples in dilute plasmas

Science.gov (United States)

Grier, Norman T.; Domitz, Stanley

1992-01-01

Anodized aluminum samples representative of Space Station Freedom structural material were tested for electrical breakdown under space plasma conditions. In space, this potential arises across the insulating anodized coating when the spacecraft structure is driven to a negative bias relative to the external plasma potential due to plasma-surface interaction phenomena. For anodized materials used in the tests, it was found that breakdown voltage varied from 100 to 2000 volts depending on the sample. The current in the arcs depended on the sample, the capacitor, and the voltage. The level of the arc currents varied from 60 to 1000 amperes. The plasma number density varied from 3 x 10 exp 6 to 10 exp 3 ions per cc. The time between arcs increased as the number density was lowered. Corona testing of anodized samples revealed that samples with higher corona inception voltage had higher arcing inception voltages. From this it is concluded that corona testing may provide a method of screening the samples.

Examination of weight control practices in a non-clinical sample of college women.

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Hayes, S; Napolitano, M A

2012-09-01

The current study examined healthy weight control practices among a sample of college women enrolled at an urban university (N=715; age=19.87±1.16; 77.2% Caucasian; 13.4% African American, 7.2% Asian, 2.2% other races). Participants completed measures as part of an on-line study about health habits, behaviors, and attitudes. Items from the Three Factor Eating Questionnaire were selected and evaluated with exploratory factor analysis to create a healthy weight control practices scale. Results revealed that college women, regardless of weight status, used a comparable number (four of eight) of practices. Examination of racial differences between Caucasian and African American women revealed that normal weight African American women used significantly fewer strategies than Caucasian women. Of note, greater use of healthy weight control practices was associated with higher cognitive restraint, drive for thinness, minutes of physical activity, and more frequent use of compensatory strategies. Higher scores on measures of binge and disinhibited eating, body dissatisfaction, negative affect, and depressive symptoms were associated with greater use of healthy weight control practices by underweight/normal weight but not by overweight/obese college women. Results suggest that among a sample of college females, a combination of healthy and potentially unhealthy weight control practices occurs. Implications of the findings suggest the need for effective weight management and eating disorder prevention programs for this critical developmental life stage. Such programs should be designed to help students learn how to appropriately use healthy weight control practices, as motivations for use may vary by weight status.

Detection and Molecular Characterization of Gemycircularvirus from Environmental Samples in Brazil.

Science.gov (United States)

da Silva Assis, Matheus Ribeiro; Vieira, Carmen Baur; Fioretti, Julia Monassa; Rocha, Mônica Simões; de Almeida, Pedro Ivo Neves; Miagostovich, Marize Pereira; Fumian, Tulio Machado

2016-12-01

Gemycircularvirus (GemyCV) is a group of viruses which has been recently proposed as a new viral genus detected in fecal and environmental samples around the world. GemyCVs have been detected in human blood, brain tissue, cerebrospinal fluid, and stool sample. In the present study, we demonstrate for the first time, through molecular detection and characterization, the presence of GemyCVs in environmental samples from Brazil. Our results show a percentage of positivity ranging from 69 (25/36) to 97 % (35/36) in river water samples collected in Manaus, Amazon region, and wastewater from a wastewater treatment plant located in Rio de Janeiro, respectively, revealing GemyCVs as an important environmental contaminant.

Scalability on LHS (Latin Hypercube Sampling) samples for use in uncertainty analysis of large numerical models

International Nuclear Information System (INIS)

Baron, Jorge H.; Nunez Mac Leod, J.E.

2000-01-01

The present paper deals with the utilization of advanced sampling statistical methods to perform uncertainty and sensitivity analysis on numerical models. Such models may represent physical phenomena, logical structures (such as boolean expressions) or other systems, and various of their intrinsic parameters and/or input variables are usually treated as random variables simultaneously. In the present paper a simple method to scale-up Latin Hypercube Sampling (LHS) samples is presented, starting with a small sample and duplicating its size at each step, making it possible to use the already run numerical model results with the smaller sample. The method does not distort the statistical properties of the random variables and does not add any bias to the samples. The results is a significant reduction in numerical models running time can be achieved (by re-using the previously run samples), keeping all the advantages of LHS, until an acceptable representation level is achieved in the output variables. (author)

Neurochemical Metabolomics Reveals Disruption to Sphingolipid Metabolism Following Chronic Haloperidol Administration.

Science.gov (United States)

McClay, Joseph L; Vunck, Sarah A; Batman, Angela M; Crowley, James J; Vann, Robert E; Beardsley, Patrick M; van den Oord, Edwin J

2015-09-01

Haloperidol is an effective antipsychotic drug for treatment of schizophrenia, but prolonged use can lead to debilitating side effects. To better understand the effects of long-term administration, we measured global metabolic changes in mouse brain following 3 mg/kg/day haloperidol for 28 days. These conditions lead to movement-related side effects in mice akin to those observed in patients after prolonged use. Brain tissue was collected following microwave tissue fixation to arrest metabolism and extracted metabolites were assessed using both liquid and gas chromatography mass spectrometry (MS). Over 300 unique compounds were identified across MS platforms. Haloperidol was found to be present in all test samples and not in controls, indicating experimental validity. Twenty-one compounds differed significantly between test and control groups at the p < 0.05 level. Top compounds were robust to analytical method, also being identified via partial least squares discriminant analysis. Four compounds (sphinganine, N-acetylornithine, leucine and adenosine diphosphate) survived correction for multiple testing in a non-parametric analysis using false discovery rate threshold < 0.1. Pathway analysis of nominally significant compounds (p < 0.05) revealed significant findings for sphingolipid metabolism (p = 0.015) and protein biosynthesis (p = 0.024). Altered sphingolipid metabolism is suggestive of disruptions to myelin. This interpretation is supported by our observation of elevated N-acetyl-aspartyl-glutamate in the haloperidol-treated mice (p = 0.004), a marker previously associated with demyelination. This study further demonstrates the utility of murine neurochemical metabolomics as a method to advance understanding of CNS drug effects.

Proteomic Analysis of Hylocereus polyrhizus Reveals Metabolic Pathway Changes

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Qingzhu Hua

2016-09-01

Full Text Available Red dragon fruit or red pitaya (Hylocereus polyrhizus is the only edible fruit that contains betalains. The color of betalains ranges from red and violet to yellow in plants. Betalains may also serve as an important component of health-promoting and disease-preventing functional food. Currently, the biosynthetic and regulatory pathways for betalain production remain to be fully deciphered. In this study, isobaric tags for relative and absolute quantitation (iTRAQ-based proteomic analyses were used to reveal the molecular mechanism of betalain biosynthesis in H. polyrhizus fruits at white and red pulp stages, respectively. A total of 1946 proteins were identified as the differentially expressed between the two samples, and 936 of them were significantly highly expressed at the red pulp stage of H. polyrhizus. RNA-seq and iTRAQ analyses showed that some transcripts and proteins were positively correlated; they belonged to “phenylpropanoid biosynthesis”, “tyrosine metabolism”, “flavonoid biosynthesis”, “ascorbate and aldarate metabolism”, “betalains biosynthesis” and “anthocyanin biosynthesis”. In betalains biosynthesis pathway, several proteins/enzymes such as polyphenol oxidase, CYP76AD3 and 4,5-dihydroxy-phenylalanine (DOPA dioxygenase extradiol-like protein were identified. The present study provides a new insight into the molecular mechanism of the betalain biosynthesis at the posttranscriptional level.

Carbon Isotopic Ratios of Amino Acids in Stardust-Returned Samples

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Elsila, Jamie E.; Glavin, Daniel P.; Dworkin, Jason P.

2009-01-01

NASA's Stardust spacecraft returned to Earth samples from comet 81P/Wild 2 in January 2006. Preliminary examinations revealed the presence of a suite of organic compounds including several amines and amino acids, but the origin of these compounds could not be identified. Here. we present the carbon isotopic ratios of glycine and E-aminocaproic acid (EACH), the two most abundant amino acids observed, in Stardust-returned foil samples measured by gas chromatography-combustion-isotope ratio crass spectrometry coupled with quadrupole mass spectrometry (GC-QMS/IRMS).

Brief Group Psychoeducation for Bulimia Nervosa: Assessing the Clinical Significance of Change.

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Davis, Ron; And Others

1990-01-01

Brief intervention designed to promote symptom management was completed by 41 women with bulimia nervosa. Findings revealed diversity of outcomes that individuals reported following participation in intervention. Found differential reporting of clinically significant change in favor of specific eating psychopathology relative to personality…

Comparative Tissue Proteomics of Microdissected Specimens Reveals Novel Candidate Biomarkers of Bladder Cancer*

Science.gov (United States)

Chen, Chien-Lun; Chung, Ting; Wu, Chih-Ching; Ng, Kwai-Fong; Yu, Jau-Song; Tsai, Cheng-Han; Chang, Yu-Sun; Liang, Ying; Tsui, Ke-Hung; Chen, Yi-Ting

2015-01-01

More than 380,000 new cases of bladder cancer are diagnosed worldwide, accounting for ∼150,200 deaths each year. To discover potential biomarkers of bladder cancer, we employed a strategy combining laser microdissection, isobaric tags for relative and absolute quantitation labeling, and liquid chromatography-tandem MS (LC-MS/MS) analysis to profile proteomic changes in fresh-frozen bladder tumor specimens. Cellular proteins from four pairs of surgically resected primary bladder cancer tumor and adjacent nontumorous tissue were extracted for use in two batches of isobaric tags for relative and absolute quantitation experiments, which identified a total of 3220 proteins. A DAVID (database for annotation, visualization and integrated discovery) analysis of dysregulated proteins revealed that the three top-ranking biological processes were extracellular matrix organization, extracellular structure organization, and oxidation-reduction. Biological processes including response to organic substances, response to metal ions, and response to inorganic substances were highlighted by up-expressed proteins in bladder cancer. Seven differentially expressed proteins were selected as potential bladder cancer biomarkers for further verification. Immunohistochemical analyses showed significantly elevated levels of three proteins—SLC3A2, STMN1, and TAGLN2—in tumor cells compared with noncancerous bladder epithelial cells, and suggested that TAGLN2 could be a useful tumor tissue marker for diagnosis (AUC = 0.999) and evaluating lymph node metastasis in bladder cancer patients. ELISA results revealed significantly increased urinary levels of both STMN1 and TAGLN2 in bladder cancer subgroups compared with control groups. In comparisons with age-matched hernia urine specimens, urinary TAGLN2 in bladder cancer samples showed the largest fold change (7.13-fold), with an area-under-the-curve value of 0.70 (p < 0.001, n = 205). Overall, TAGLN2 showed the most significant

Reanalysis of RNA-sequencing data reveals several additional fusion genes with multiple isoforms.

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Kangaspeska, Sara; Hultsch, Susanne; Edgren, Henrik; Nicorici, Daniel; Murumägi, Astrid; Kallioniemi, Olli

2012-01-01

RNA-sequencing and tailored bioinformatic methodologies have paved the way for identification of expressed fusion genes from the chaotic genomes of solid tumors. We have recently successfully exploited RNA-sequencing for the discovery of 24 novel fusion genes in breast cancer. Here, we demonstrate the importance of continuous optimization of the bioinformatic methodology for this purpose, and report the discovery and experimental validation of 13 additional fusion genes from the same samples. Integration of copy number profiling with the RNA-sequencing results revealed that the majority of the gene fusions were promoter-donating events that occurred at copy number transition points or involved high-level DNA-amplifications. Sequencing of genomic fusion break points confirmed that DNA-level rearrangements underlie selected fusion transcripts. Furthermore, a significant portion (>60%) of the fusion genes were alternatively spliced. This illustrates the importance of reanalyzing sequencing data as gene definitions change and bioinformatic methods improve, and highlights the previously unforeseen isoform diversity among fusion transcripts.

Reanalysis of RNA-sequencing data reveals several additional fusion genes with multiple isoforms.

Directory of Open Access Journals (Sweden)

Sara Kangaspeska

Full Text Available RNA-sequencing and tailored bioinformatic methodologies have paved the way for identification of expressed fusion genes from the chaotic genomes of solid tumors. We have recently successfully exploited RNA-sequencing for the discovery of 24 novel fusion genes in breast cancer. Here, we demonstrate the importance of continuous optimization of the bioinformatic methodology for this purpose, and report the discovery and experimental validation of 13 additional fusion genes from the same samples. Integration of copy number profiling with the RNA-sequencing results revealed that the majority of the gene fusions were promoter-donating events that occurred at copy number transition points or involved high-level DNA-amplifications. Sequencing of genomic fusion break points confirmed that DNA-level rearrangements underlie selected fusion transcripts. Furthermore, a significant portion (>60% of the fusion genes were alternatively spliced. This illustrates the importance of reanalyzing sequencing data as gene definitions change and bioinformatic methods improve, and highlights the previously unforeseen isoform diversity among fusion transcripts.

The Association Between Psychopathic Personality Traits and Victimization and Exposure to Violence in a Sample of Saudi Arabian Youth.

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Beaver, Kevin M; Al-Ghamdi, Mohammed Said; Kobeisy, Ahmed Nezar; Alqurashi, Fathiyah H; Connolly, Eric J; Schwartz, Joseph A

2016-06-01

Psychopathic personality traits have been shown to increase the odds of a wide range of antisocial outcomes. Very little research, however, has examined the association between psychopathy and the risk of personal victimization. The current study address this gap in the literature by examining the association between scores on the Levenson Self-Report Psychopathy scale and a self-reported measure of victimization by using cross-sectional data drawn from a sample of youth residing in Jeddah, Saudi Arabia (N = 311). The results revealed a positive and statistically significant association between LSPR scores and the odds of being victimized. Additional analyses revealed that two mediators-arrest history and exposure to delinquent peers-were related to personal victimization, but neither of these measures mediated the effects of LSPR scores on victimization. Whether these findings would generalize to other nations remains an issue awaiting future research.

Network analysis of ChIP-Seq data reveals key genes in prostate cancer.

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Zhang, Yu; Huang, Zhen; Zhu, Zhiqiang; Liu, Jianwei; Zheng, Xin; Zhang, Yuhai

2014-09-03

Prostate cancer (PC) is the second most common cancer among men in the United States, and it imposes a considerable threat to human health. A deep understanding of its underlying molecular mechanisms is the premise for developing effective targeted therapies. Recently, deep transcriptional sequencing has been used as an effective genomic assay to obtain insights into diseases and may be helpful in the study of PC. In present study, ChIP-Seq data for PC and normal samples were compared, and differential peaks identified, based upon fold changes (with P-values calculated with t-tests). Annotations of these peaks were performed. Protein-protein interaction (PPI) network analysis was performed with BioGRID and constructed with Cytoscape, following which the highly connected genes were screened. We obtained a total of 5,570 differential peaks, including 3,726 differentially enriched peaks in tumor samples and 1,844 differentially enriched peaks in normal samples. There were eight significant regions of the peaks. The intergenic region possessed the highest score (51%), followed by intronic (31%) and exonic (11%) regions. The analysis revealed the top 35 highly connected genes, which comprised 33 differential genes (such as YWHAQ, tyrosine 3-monooxygenase/tryptophan 5-monooxygenase activation protein and θ polypeptide) from ChIP-Seq data and 2 differential genes retrieved from the PPI network: UBA52 (ubiquitin A-52 residue ribosomal protein fusion product (1) and SUMO2 (SMT3 suppressor of mif two 3 homolog (2) . Our findings regarding potential PC-related genes increase the understanding of PC and provides direction for future research.

Laboratory sample turnaround times: do they cause delays in the ED?

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Gill, Dipender; Galvin, Sean; Ponsford, Mark; Bruce, David; Reicher, John; Preston, Laura; Bernard, Stephani; Lafferty, Jessica; Robertson, Andrew; Rose-Morris, Anna; Stoneham, Simon; Rieu, Romelie; Pooley, Sophie; Weetch, Alison; McCann, Lloyd

2012-02-01

Blood tests are requested for approximately 50% of patients attending the emergency department (ED). The time taken to obtain the results is perceived as a common reason for delay. The objective of this study was therefore to investigate the turnaround time (TAT) for blood results and whether this affects patient length of stay (LOS) and to identify potential areas for improvement. A time-in-motion study was performed at the ED of the John Radcliffe Hospital (JRH), Oxford, UK. The duration of each of the stages leading up to receipt of 101 biochemistry and haematology results was recorded, along with the corresponding patient's LOS. The findings reveal that the mean time for haematology results to become available was 1 hour 6 minutes (95% CI: 29 minutes to 2 hours 13 minutes), while biochemistry samples took 1 hour 42 minutes (95% CI: 1 hour 1 minute to 4 hours 21 minutes), with some positive correlation noted with the patient LOS, but no significant variation between different days or shifts. With the fastest 10% of samples being reported within 35 minutes (haematology) and 1 hour 5 minutes (biochemistry) of request, our study showed that delays can be attributable to laboratory TAT. Given the limited ability to further improve laboratory processes, the solutions to improving TAT need to come from a collaborative and integrated approach that includes strategies before samples reach the laboratory and downstream review of results. © 2010 Blackwell Publishing Ltd.

Social anxiety symptoms and suicidal ideation in a clinical sample of early adolescents: examining loneliness and social support as longitudinal mediators.

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Gallagher, Michelle; Prinstein, Mitchell J; Simon, Valerie; Spirito, Anthony

2014-08-01

Recent research has shown that social anxiety may be related to increased risk for suicidal ideation in teens, although this research largely has been cross-sectional and has not examined potential mediators of this relationship. A clinical sample of 144 early adolescents (72 % female; 12-15 years old) was assessed during psychiatric inpatient hospitalization and followed up at 9 and 18 months post-baseline. Symptoms of social anxiety, depression, suicidal ideation, loneliness, and perceived social support were assessed via structured interviews and self-report instruments. Structural equation modeling revealed a significant direct relationship between social anxiety symptoms at baseline and suicidal ideation at 18 months post-baseline, even after controlling for baseline depressive symptoms and ideation. A second multiple mediation model revealed that baseline social anxiety had a significant indirect effect on suicidal ideation at 18 months post-baseline through loneliness at 9 months post-baseline. Social anxiety did not have a significant indirect effect on suicidal ideation through perceived social support from either parents or close friends. Findings suggest that loneliness may be particularly implicated in the relationship between social anxiety and suicidality in teens. Clinicians should assess and address feelings of loneliness when treating socially anxious adolescents.

A Microbiomic Analysis in African Americans with Colonic Lesions Reveals Streptococcus sp.VT162 as a Marker of Neoplastic Transformation

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Hassan Brim

2017-11-01

Full Text Available Increasing evidence suggests a role of the gut microbiota in colorectal carcinogenesis (CRC. To detect bacterial markers of colorectal cancer in African Americans a metabolomic analysis was performed on fecal water extracts. DNA from stool samples of adenoma and healthy subjects and from colon cancer and matched normal tissues was analyzed to determine the microbiota composition (using 16S rDNA and genomic content (metagenomics. Metagenomic functions with discriminative power between healthy and neoplastic specimens were established. Quantitative Polymerase Chain Reaction (q-PCR using primers and probes specific to Streptococcus sp. VT_162 were used to validate this bacterium association with neoplastic transformation in stool samples from two independent cohorts of African Americans and Chinese patients with colorectal lesions. The metabolomic analysis of adenomas revealed low amino acids content. The microbiota in both cancer vs. normal tissues and adenoma vs. normal stool samples were different at the 16S rRNA gene level. Cross-mapping of metagenomic data led to 9 markers with significant discriminative power between normal and diseased specimens. These markers identified with Streptococcus sp. VT_162. Q-PCR data showed a statistically significant presence of this bacterium in advanced adenoma and cancer samples in an independent cohort of CRC patients. We defined metagenomic functions from Streptococcus sp. VT_162 with discriminative power among cancers vs. matched normal and adenomas vs. healthy subjects’ stools. Streptococcus sp. VT_162 specific 16S rDNA was validated in an independent cohort. These findings might facilitate non-invasive screening for colorectal cancer.

MODIS-Aqua Reveals Evolving Phytoplankton Community Structure During the Arabian Sea Northeast Monsoon

Science.gov (United States)

Werdell, P. Jeremy; Roesler, Collin S.; Goes, Joaquim I.

2016-01-01

Applying a bio-optical model designed to identify the mixotrophic dinoflagellate Noctiluca miliaris to MODIS-Aqua revealed (1) patterns in its spatial distribution not previously seen (including its appearance in places not previously sampled), and (2) the surprising disassociation of total chlorophyll biomass with the presence of N. miliaris.

Spaceflight Alters Bacterial Gene Expression and Virulence and Reveals Role for Global Regulator Hfq

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Wilson, J. W.; Ott, C. M.; zuBentrup, K. Honer; Ramamurthy R.; Quick, L.; Porwollik, S.; Cheng, P.; McClellan, M.; Tsaprailis, G.; Radabaugh, T.;

Quantitative portable gamma-spectroscopy sample analysis for non-standard sample geometries

International Nuclear Information System (INIS)

Ebara, S.B.

1998-01-01

Utilizing a portable spectroscopy system, a quantitative method for analysis of samples containing a mixture of fission and activation products in nonstandard geometries was developed. This method was not developed to replace other methods such as Monte Carlo or Discrete Ordinates but rather to offer an alternative rapid solution. The method can be used with various sample and shielding configurations where analysis on a laboratory based gamma-spectroscopy system is impractical. The portable gamma-spectroscopy method involves calibration of the detector and modeling of the sample and shielding to identify and quantify the radionuclides present in the sample. The method utilizes the intrinsic efficiency of the detector and the unattenuated gamma fluence rate at the detector surface per unit activity from the sample to calculate the nuclide activity and Minimum Detectable Activity (MDA). For a complex geometry, a computer code written for shielding applications (MICROSHIELD) is utilized to determine the unattenuated gamma fluence rate per unit activity at the detector surface. Lastly, the method is only applicable to nuclides which emit gamma-rays and cannot be used for pure beta or alpha emitters. In addition, if sample self absorption and shielding is significant, the attenuation will result in high MDA's for nuclides which solely emit low energy gamma-rays. The following presents the analysis technique and presents verification results using actual experimental data, rather than comparisons to other approximations such as Monte Carlo techniques, to demonstrate the accuracy of the method given a known geometry and source term. (author)

Elevated phenylalanine on newborn screening: follow-up testing may reveal undiagnosed galactosaemia.

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Shakespeare, Lynette; Downing, Melanie; Allen, Joyce; Casbolt, Ann-Marie; Ellin, Sheila; Maloney, Martin; Race, Gillian; Bonham, Jim

2010-11-01

Introduction Newborn screening for phenylketonuria (PKU) can reveal other conditions which lead to an increased blood spot phenylalanine (Phe) concentration. We have investigated the proportion of blood spot samples that gave a positive screen due to clinically significant conditions other than PKU, compared the positive predictive value (PPV) of our referral Phe cut-off with that recommended by the UK Newborn Screening Programme Centre (UKNSPC) (>210 and >240 μmol/L, respectively) and evaluated the effectiveness of reflex testing for galactosaemia using a lower blood spot Phe cut-off concentration of 130 μmol/L. All blood spot samples that screened positive, for an increased Phe concentration, between April 2001 and March 2008, were identified from the records of the Sheffield Newborn Screening Laboratory and the diagnoses noted. In addition, all cases of galactosaemia detected in or notified to our screening laboratory within this time were also examined and the screened Phe concentrations compared. Out of 438,674 babies who were screened, 67 had Phe concentration >210 μmol/L (15 per 100,000). Of these, 40 had PKU or persistent hyperphenylalaninaemia with a Phe concentration identified by screening between 270 and 2350 μmol/L. A further 11 were diagnosed with another clinically significant disorder: galactosaemia (n = 8), biopterin defects (n = 2), tyrosinaemia Type 1 (n = 1). In addition, 16 had transient elevations in Phe. In total, nine cases of galactosaemia were identified, of whom, three had Phe concentrations 240 μmol/L) will not affect the detection rate of classical PKU, but will improve the PPV from 76% to 80%. The use of a lower cut-off (130 μmol/L) for reflex galactosaemia testing enables the timely identification of asymptomatic cases that benefit particularly from early treatment, without prompting any unnecessary clinical referrals or delaying any referrals. This intervention may reduce mortality in this vulnerable group.

Integrated genomic and immunophenotypic classification of pancreatic cancer reveals three distinct subtypes with prognostic/predictive significance.

Science.gov (United States)

Wartenberg, Martin; Cibin, Silvia; Zlobec, Inti; Vassella, Erik; Eppenberger-Castori, Serenella M M; Terracciano, Luigi; Eichmann, Micha; Worni, Mathias; Gloor, Beat; Perren, Aurel; Karamitopoulou, Eva

2018-04-16

Current clinical classification of pancreatic ductal adenocarcinoma (PDAC) is unable to predict prognosis or response to chemo- or immunotherapy and does not take into account the host reaction to PDAC-cells. Our aim is to classify PDAC according to host- and tumor-related factors into clinically/biologically relevant subtypes by integrating molecular and microenvironmental findings. A well-characterized PDAC-cohort (n=110) underwent next-generation sequencing with a hotspot cancer panel, while Next-generation Tissue-Microarrays were immunostained for CD3, CD4, CD8, CD20, PD-L1, p63, hyaluronan-mediated motility receptor (RHAMM) and DNA mismatch-repair proteins. Previous data on FOXP3 were integrated. Immune-cell counts and protein expression were correlated with tumor-derived driver mutations, clinicopathologic features (TNM 8. 2017), survival and epithelial-mesenchymal-transition (EMT)-like tumor budding.  Results: Three PDAC-subtypes were identified: the "immune-escape" (54%), poor in T- and B-cells and enriched in FOXP3+Tregs, with high-grade budding, frequent CDKN2A- , SMAD4- and PIK3CA-mutations and poor outcome; the "immune-rich" (35%), rich in T- and B-cells and poorer in FOXP3+Tregs, with infrequent budding, lower CDKN2A- and PIK3CA-mutation rate and better outcome and a subpopulation with tertiary lymphoid tissue (TLT), mutations in DNA damage response genes (STK11, ATM) and the best outcome; and the "immune-exhausted" (11%) with immunogenic microenvironment and two subpopulations: one with PD-L1-expression and high PIK3CA-mutation rate and a microsatellite-unstable subpopulation with high prevalence of JAK3-mutations. The combination of low budding, low stromal FOXP3-counts, presence of TLTs and absence of CDKN2A-mutations confers significant survival advantage in PDAC-patients. Immune host responses correlate with tumor characteristics leading to morphologically recognizable PDAC-subtypes with prognostic/predictive significance. Copyright ©2018

222Rn in water: A comparison of two sample collection methods and two sample transport methods, and the determination of temporal variation in North Carolina ground water

International Nuclear Information System (INIS)

Hightower, J.H. III

1994-01-01

Objectives of this field experiment were: (1) determine whether there was a statistically significant difference between the radon concentrations of samples collected by EPA's standard method, using a syringe, and an alternative, slow-flow method; (2) determine whether there was a statistically significant difference between the measured radon concentrations of samples mailed vs samples not mailed; and (3) determine whether there was a temporal variation of water radon concentration over a 7-month period. The field experiment was conducted at 9 sites, 5 private wells, and 4 public wells, at various locations in North Carolina. Results showed that a syringe is not necessary for sample collection, there was generally no significant radon loss due to mailing samples, and there was statistically significant evidence of temporal variations in water radon concentrations

Significant association between sulfate-reducing bacteria and uranium-reducing microbial communities as revealed by a combined massively parallel sequencing-indicator species approach.

Science.gov (United States)

Cardenas, Erick; Wu, Wei-Min; Leigh, Mary Beth; Carley, Jack; Carroll, Sue; Gentry, Terry; Luo, Jian; Watson, David; Gu, Baohua; Ginder-Vogel, Matthew; Kitanidis, Peter K; Jardine, Philip M; Zhou, Jizhong; Criddle, Craig S; Marsh, Terence L; Tiedje, James M

2010-10-01

Massively parallel sequencing has provided a more affordable and high-throughput method to study microbial communities, although it has mostly been used in an exploratory fashion. We combined pyrosequencing with a strict indicator species statistical analysis to test if bacteria specifically responded to ethanol injection that successfully promoted dissimilatory uranium(VI) reduction in the subsurface of a uranium contamination plume at the Oak Ridge Field Research Center in Tennessee. Remediation was achieved with a hydraulic flow control consisting of an inner loop, where ethanol was injected, and an outer loop for flow-field protection. This strategy reduced uranium concentrations in groundwater to levels below 0.126 μM and created geochemical gradients in electron donors from the inner-loop injection well toward the outer loop and downgradient flow path. Our analysis with 15 sediment samples from the entire test area found significant indicator species that showed a high degree of adaptation to the three different hydrochemical-created conditions. Castellaniella and Rhodanobacter characterized areas with low pH, heavy metals, and low bioactivity, while sulfate-, Fe(III)-, and U(VI)-reducing bacteria (Desulfovibrio, Anaeromyxobacter, and Desulfosporosinus) were indicators of areas where U(VI) reduction occurred. The abundance of these bacteria, as well as the Fe(III) and U(VI) reducer Geobacter, correlated with the hydraulic connectivity to the substrate injection site, suggesting that the selected populations were a direct response to electron donor addition by the groundwater flow path. A false-discovery-rate approach was implemented to discard false-positive results by chance, given the large amount of data compared.

Sampling criteria in multicollection searching.

Science.gov (United States)

Gilio, A.; Scozzafava, R.; Marchetti, P. G.

In the first stage of the document retrieval process, no information concerning relevance of a particular document is available. On the other hand, computer implementation requires that the analysis be made only for a sample of retrieved documents. This paper addresses the significance and suitability of two different sampling criteria for a multicollection online search facility. The inevitability of resorting to a logarithmic criterion in order to achieve a "spread of representativeness" from the multicollection is demonstrated.

Two-sample discrimination of Poisson means

Science.gov (United States)

Lampton, M.

1994-01-01

This paper presents a statistical test for detecting significant differences between two random count accumulations. The null hypothesis is that the two samples share a common random arrival process with a mean count proportional to each sample's exposure. The model represents the partition of N total events into two counts, A and B, as a sequence of N independent Bernoulli trials whose partition fraction, f, is determined by the ratio of the exposures of A and B. The detection of a significant difference is claimed when the background (null) hypothesis is rejected, which occurs when the observed sample falls in a critical region of (A, B) space. The critical region depends on f and the desired significance level, alpha. The model correctly takes into account the fluctuations in both the signals and the background data, including the important case of small numbers of counts in the signal, the background, or both. The significance can be exactly determined from the cumulative binomial distribution, which in turn can be inverted to determine the critical A(B) or B(A) contour. This paper gives efficient implementations of these tests, based on lookup tables. Applications include the detection of clustering of astronomical objects, the detection of faint emission or absorption lines in photon-limited spectroscopy, the detection of faint emitters or absorbers in photon-limited imaging, and dosimetry.

RELATIONSHIP BETWEEN COMPOSITION AND TOXICITY OF ENGINE EMISSION SAMPLES

Energy Technology Data Exchange (ETDEWEB)

(1)Mauderly, J; Seagrave, J; McDonald; J (2)Eide,I (3)Zielinska, B (4)Lawson, D

2003-08-24

Differences in the lung toxicity and bacterial mutagenicity of seven samples from gasoline and diesel vehicle emissions were reported previously [1]. Filter and vapor-phase semivolatile organic samples were collected from normal and high-emitter gasoline and diesel vehicles operated on chassis dynamometers on the Unified Driving Cycle, and the compositions of the samples were measured in detail. The two fractions of each sample were combined in their original mass collection ratios, and the toxicity of the seven samples was compared by measuring inflammation and tissue damage in rat lungs and mutagenicity in bacteria. There was good agreement among the toxicity response variables in ranking the samples and demonstrating a five-fold range of toxicity. The relationship between chemical composition and toxicity was analyzed by a combination of principal component analysis (PCA) and partial least squares regression (PLS, also known as projection to latent surfaces). The PCA /PLS analysis revealed the chemical constituents co-varying most strongly with toxicity and produced models predicting the relative toxicity of the samples with good accuracy. The results demonstrated the utility of the PCA/PLS approach, which is now being applied to additional samples, and it also provided a starting point for confirming the compounds that actually cause the effects.

Clinical symptoms predict concurrent social and global functioning in an early psychosis sample.

Science.gov (United States)

Cacciotti-Saija, Cristina; Langdon, Robyn; Ward, Philip B; Hickie, Ian B; Guastella, Adam J

2018-04-01

Although well established in chronic schizophrenia, the key determinants of functioning remain unknown during the early phase of a psychotic disorder. The aim of this study was to comprehensively examine the social cognitive, basic neurocognitive and clinical predictors of concurrent social functioning and global functioning in an early psychosis sample. This study examined the relationship between social cognition, basic neurocognition and clinical symptoms with concurrent functioning in 51 early psychosis individuals. Assessments included a range of self-report, observational and clinician-rated measures of cognitive, symptom severity and functioning domains. Results revealed a significant association between self-reported social function and lower levels of both social interaction anxiety and negative psychotic symptoms. A significant association was also observed between lower levels of negative psychotic symptoms and observed social functioning. Lastly, results demonstrated a significant association between reduced negative psychotic symptoms and clinician-rated global functioning. Clinical domains such as negative symptoms and social interaction anxiety significantly contribute to an optimal model predicting outcome during the early phase of a psychotic disorder. These clinical features may also provide useful markers of an individual's capacity for social participation. Clinical implications include the need for early targeted intervention to address social anxiety and negative psychotic symptoms to facilitate optimum patient outcome. © 2015 Wiley Publishing Asia Pty Ltd.

Novel genotype of Ehrlichia canis detected in samples of human blood bank donors in Costa Rica.

Science.gov (United States)

Bouza-Mora, Laura; Dolz, Gaby; Solórzano-Morales, Antony; Romero-Zuñiga, Juan José; Salazar-Sánchez, Lizbeth; Labruna, Marcelo B; Aguiar, Daniel M

2017-01-01

This study focuses on the detection and identification of DNA and antibodies to Ehrlichia spp. in samples of blood bank donors in Costa Rica using molecular and serological techniques. Presence of Ehrlichia canis was determined in 10 (3.6%) out of 280 blood samples using polymerase chain reaction (PCR) targeting the ehrlichial dsb conserved gene. Analysis of the ehrlichial trp36 polymorphic gene in these 10 samples revealed substantial polymorphism among the E. canis genotypes, including divergent tandem repeat sequences. Nucleotide sequences of dsb and trp36 amplicons revealed a novel genotype of E. canis in blood bank donors from Costa Rica. Indirect immunofluorescence assay (IFA) detected antibodies in 35 (35%) of 100 serum samples evaluated. Thirty samples showed low endpoint titers (64-256) to E. canis, whereas five sera yielded high endpoint titers (1024-8192); these five samples were also E. canis-PCR positive. These findings represent the first report of the presence of E. canis in humans in Central America. Copyright © 2016 Elsevier GmbH. All rights reserved.

Assessment of Tools for Marker-Assisted Selection in a Marine Commercial Species: Significant Association between MSTN-1 Gene Polymorphism and Growth Traits

Directory of Open Access Journals (Sweden)

Irma Sánchez-Ramos

2012-01-01

Full Text Available Growth is a priority trait from the point of view of genetic improvement. Molecular markers linked to quantitative trait loci (QTL have been regarded as useful for marker-assisted selection in complex traits as growth. Polymorphisms have been studied in five candidate genes influencing growth in gilthead seabream (Sparus aurata: the growth hormone (GH, insulin-like growth factor-1 (IGF-1, myostatin (MSTN-1, prolactin (PRL, and somatolactin (SL genes. Specimens evaluated were from a commercial broodstock comprising 131 breeders (from which 36 males and 44 females contributed to the progeny. In all samples eleven gene fragments, covering more than 13,000 bp, generated by PCR-RFLP, were analyzed; tests were made for significant associations between these markers and growth traits. ANOVA results showed a significant association between MSTN-1 gene polymorphism and growth traits. Pairwise tests revealed several RFLPs in the MSTN-1 gene with significant heterogeneity of genotypes among size groups. PRL and MSTN-1 genes presented linkage disequilibrium. The MSTN-1 gene was mapped in the centromeric region of a medium-size acrocentric chromosome pair.

Technicians work with Apollo 14 lunar sample material in Lunar Receiving Lab.

Science.gov (United States)

1971-01-01

Glove handlers work with freshly opened Apollo 14 lunar sample material in modularized cabinets in the Lunar Receiving Laboratory at the Manned Spacecraft Center. The glove operator on the right starts to pour fine lunar material which he has just taken from a tote bag. This powdery sample was among the last to be revealed of the 90-odd pounds of material brought back to Earth by the Apollo 14 crewmen.

Quantitative proteomic analysis of human testis reveals system-wide molecular and cellular pathways associated with non-obstructive azoospermia.

Science.gov (United States)

Alikhani, Mehdi; Mirzaei, Mehdi; Sabbaghian, Marjan; Parsamatin, Pouria; Karamzadeh, Razieh; Adib, Samane; Sodeifi, Niloofar; Gilani, Mohammad Ali Sadighi; Zabet-Moghaddam, Masoud; Parker, Lindsay; Wu, Yunqi; Gupta, Vivek; Haynes, Paul A; Gourabi, Hamid; Baharvand, Hossein; Salekdeh, Ghasem Hosseini

2017-06-06

Male infertility accounts for half of the infertility problems experienced by couples. Azoospermia, having no measurable level of sperm in seminal fluid, is one of the known conditions resulting in male infertility. In order to elucidate the complex molecular mechanisms causing male azoospermia, label-free quantitative shotgun proteomics was carried out on testicular tissue specimens from patients with obstructive azoospermia and non-obstructive azoospermia, including maturation arrest (MA) and Sertoli cell only syndrome (SCOS). The abundance of 520 proteins was significantly changed across three groups of samples. We were able to identify several functional biological pathways enriched in azoospermia samples and confirm selected differentially abundant proteins, using multiple histological methods. The results revealed that cell cycle and proteolysis, and RNA splicing were the most significant biological processes impaired by the substantial suppression of proteins related to the aforementioned categories in SCOS tissues. In the MA patient testes, generation of precursor metabolites and energy as well as oxidation-reduction were the most significantly altered processes. Novel candidate proteins identified in this study include key transcription factors, many of which have not previously been shown to be associated with azoospermia. Our findings can provide substantial insights into the molecular regulation of spermatogenesis and human reproduction. The obtained data showed a drastic suppression of proteins involved in spliceosome, cell cycle and proteasome proteins, as well as energy and metabolic production in Sertoli cell only syndrome testis tissue, and to a lesser extent in maturation arrest samples. Moreover, we identified new transcription factors that are highly down-regulated in SCOS and MA patients, thus helping to understand the molecular complexity of spermatogenesis in male infertility. Our findings provide novel candidate protein targets associated

Ananke: temporal clustering reveals ecological dynamics of microbial communities

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Michael W. Hall

2017-09-01

Full Text Available Taxonomic markers such as the 16S ribosomal RNA gene are widely used in microbial community analysis. A common first step in marker-gene analysis is grouping genes into clusters to reduce data sets to a more manageable size and potentially mitigate the effects of sequencing error. Instead of clustering based on sequence identity, marker-gene data sets collected over time can be clustered based on temporal correlation to reveal ecologically meaningful associations. We present Ananke, a free and open-source algorithm and software package that complements existing sequence-identity-based clustering approaches by clustering marker-gene data based on time-series profiles and provides interactive visualization of clusters, including highlighting of internal OTU inconsistencies. Ananke is able to cluster distinct temporal patterns from simulations of multiple ecological patterns, such as periodic seasonal dynamics and organism appearances/disappearances. We apply our algorithm to two longitudinal marker gene data sets: faecal communities from the human gut of an individual sampled over one year, and communities from a freshwater lake sampled over eleven years. Within the gut, the segregation of the bacterial community around a food-poisoning event was immediately clear. In the freshwater lake, we found that high sequence identity between marker genes does not guarantee similar temporal dynamics, and Ananke time-series clusters revealed patterns obscured by clustering based on sequence identity or taxonomy. Ananke is free and open-source software available at https://github.com/beiko-lab/ananke.

Personality in general and clinical samples: Measurement invariance of the Multidimensional Personality Questionnaire.

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Eigenhuis, Annemarie; Kamphuis, Jan H; Noordhof, Arjen

2017-09-01

A growing body of research suggests that the same general dimensions can describe normal and pathological personality, but most of the supporting evidence is exploratory. We aim to determine in a confirmatory framework the extent to which responses on the Multidimensional Personality Questionnaire (MPQ) are identical across general and clinical samples. We tested the Dutch brief form of the MPQ (MPQ-BF-NL) for measurement invariance across a general population subsample (N = 365) and a clinical sample (N = 365), using Multiple Group Confirmatory Factor Analysis (MGCFA) and Multiple Group Exploratory Structural Equation Modeling (MGESEM). As an omnibus personality test, the MPQ-BF-NL revealed strict invariance, indicating absence of bias. Unidimensional per scale tests for measurement invariance revealed that 10% of items appeared to contain bias across samples. Item bias only affected the scale interpretation of Achievement, with individuals from the clinical sample more readily admitting to put high demands on themselves than individuals from the general sample, regardless of trait level. This formal test of equivalence provides strong evidence for the common structure of normal and pathological personality and lends further support to the clinical utility of the MPQ. (PsycINFO Database Record (c) 2017 APA, all rights reserved).

Prognostic significance of snail expression in hilar cholangiocarcinoma

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Kong, Dalu [Department of Hepatobiliary Surgery, Tianjin Medical University Cancer Institute and Hospital, Hexi District, Tianjin (China); Liang, Jun [Department of Oncology, Affiliated Hospital of Medical College, Qingdao University, Qingdao, Shandong Province (China); Li, Rong [Department of Hepatobiliary Surgery, Tianjin Medical University Cancer Institute and Hospital, Hexi District, Tianjin (China); Liu, Shihai [Department of Laboratory Center, Affiliated Hospital of Medical College, Qingdao University, Qingdao, Shandong Province (China); Wang, Jigang [Department of Oncology, Affiliated Hospital of Medical College, Qingdao University, Qingdao, Shandong Province (China); Zhang, Kejun; Chen, Dong [Department of General Surgery, Affiliated Hospital of Medical College, Qingdao University, Qingdao, Shandong Province (China)

2012-05-11

Many patients with hilar cholangiocarcinoma (HC) have a poor prognosis. Snail, a transcription factor and E-cadherin repressor, is a novel prognostic factor in many cancers. The aim of this study was to evaluate the relationship between snail and E-cadherin protein expression and the prognostic significance of snail expression in HC. We examined the protein expression of snail and E-cadherin in HC tissues from 47 patients (22 males and 25 females, mean age 61.2 years) using immunohistochemistry and RT-PCR. Proliferation rate was also evaluated in the same cases by the MIB1 index. High, low and negative snail protein expression was recorded in 18 (38%), 17 (36%), and 12 (26%) cases, respectively, and 40.4% (19/47) cases showed reduced E-cadherin protein expression in HC samples. No significant correlation was found between snail and E-cadherin protein expression levels (P = 0.056). No significant correlation was found between snail protein expression levels and gender, age, tumor grade, vascular or perineural invasion, nodal metastasis and invasion, or proliferative index. Cancer samples with positive snail protein expression were associated with poor survival compared with the negative expresser groups. Kaplan-Meier curves comparing different snail protein expression levels to survival showed highly significant separation (P < 0.0001, log-rank test). With multivariate analysis, only snail protein expression among all parameters was found to influence survival (P = 0.0003). We suggest that snail expression levels can predict poor survival regardless of pathological features and tumor proliferation. Immunohistochemical detection of snail protein expression levels in routine sections may provide the first biological prognostic marker.

On incomplete sampling under birth-death models and connections to the sampling-based coalescent.

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Stadler, Tanja

2009-11-07

The constant rate birth-death process is used as a stochastic model for many biological systems, for example phylogenies or disease transmission. As the biological data are usually not fully available, it is crucial to understand the effect of incomplete sampling. In this paper, we analyze the constant rate birth-death process with incomplete sampling. We derive the density of the bifurcation events for trees on n leaves which evolved under this birth-death-sampling process. This density is used for calculating prior distributions in Bayesian inference programs and for efficiently simulating trees. We show that the birth-death-sampling process can be interpreted as a birth-death process with reduced rates and complete sampling. This shows that joint inference of birth rate, death rate and sampling probability is not possible. The birth-death-sampling process is compared to the sampling-based population genetics model, the coalescent. It is shown that despite many similarities between these two models, the distribution of bifurcation times remains different even in the case of very large population sizes. We illustrate these findings on an Hepatitis C virus dataset from Egypt. We show that the transmission times estimates are significantly different-the widely used Gamma statistic even changes its sign from negative to positive when switching from the coalescent to the birth-death process.

Polybrominated diphenyl ethers in water, sediment, soil, and biological samples from different industrial areas in Zhejiang, China

Energy Technology Data Exchange (ETDEWEB)

Wang, Junxia; Lin, Zhenkun [Zhejiang Provincial Key Lab for Technology and Application of Model Organisms, Institute of Watershed Science and Environmental Ecology, Wenzhou Medical College, Wenzhou 325035 (China); Lin, Kuangfei [School of Resources and Environmental Engineering, East China University of Science and Technology/State Environmental Protection Key Laboratory of Environmental Risk Assessment and Control on Chemical Process, Shanghai 200237 (China); Wang, Chunyan [Zhejiang Provincial Key Lab for Technology and Application of Model Organisms, Institute of Watershed Science and Environmental Ecology, Wenzhou Medical College, Wenzhou 325035 (China); Zhang, Wei [School of Resources and Environmental Engineering, East China University of Science and Technology/State Environmental Protection Key Laboratory of Environmental Risk Assessment and Control on Chemical Process, Shanghai 200237 (China); Cui, Changyuan [Zhejiang Provincial Key Lab for Technology and Application of Model Organisms, Institute of Watershed Science and Environmental Ecology, Wenzhou Medical College, Wenzhou 325035 (China); Lin, Junda [Department of Biological Sciences, Florida Institute of Technology, Melbourne, FL 32901 (United States); Dong, Qiaoxiang, E-mail: dqxdong@163.com [Zhejiang Provincial Key Lab for Technology and Application of Model Organisms, Institute of Watershed Science and Environmental Ecology, Wenzhou Medical College, Wenzhou 325035 (China); Huang, Changjiang, E-mail: cjhuang5711@163.com [Zhejiang Provincial Key Lab for Technology and Application of Model Organisms, Institute of Watershed Science and Environmental Ecology, Wenzhou Medical College, Wenzhou 325035 (China)

2011-12-15

Highlights: Black-Right-Pointing-Pointer We examined PBDE concentrations in various matrices from different industrial areas. Black-Right-Pointing-Pointer Elevated PBDE levels were found in areas with low-voltage electrical manufactures. Black-Right-Pointing-Pointer Areas with e-waste recycling activities also had higher PBDE concentrations. Black-Right-Pointing-Pointer PBDE content and composition in water samples varied from one area to another. Black-Right-Pointing-Pointer PBDE composition in sediment/soil and biological samples was predominated by BDE-209. - Abstract: Polybrominated diphenyl ethers (PBDEs) have been used extensively in electrical and electronic products, but little is known about their distribution in the environment surrounding the manufacturing factories. This study reports PBDE contamination in various matrices from the location (Liushi, Zhejiang province) that produces more than 70% of the low-voltage electrical appliances in China. Additionally, PBDE contamination was compared with other industries such as the e-waste recycling business (Fengjiang) in the same region. Specifically, we measured seven PBDE congeners (BDEs - 47, 99, 100, 153, 154, 183, and 209) in water, sediment, soil, plant, and animal tissues from four different areas in this region. The present study revealed elevated PBDE concentrations in all matrices collected from Liushi and Fengjiang in comparison with highly industrialized areas without significant PBDE contamination sources. In water samples, there were large variations of PBDE content and composition across different areas. In sediment/soil and biological samples, BDE-209 was the predominant congener and this could be due to the abundant usage of deca-BDE mixtures in China. Our findings provide the very first data on PBDE contamination in the local environments surrounding the electronics industry, and also reveal widespread PBDE contamination in highly industrialized coastal regions of China.

The Statistics and Mathematics of High Dimension Low Sample Size Asymptotics.

Science.gov (United States)

Shen, Dan; Shen, Haipeng; Zhu, Hongtu; Marron, J S

2016-10-01

The aim of this paper is to establish several deep theoretical properties of principal component analysis for multiple-component spike covariance models. Our new results reveal an asymptotic conical structure in critical sample eigendirections under the spike models with distinguishable (or indistinguishable) eigenvalues, when the sample size and/or the number of variables (or dimension) tend to infinity. The consistency of the sample eigenvectors relative to their population counterparts is determined by the ratio between the dimension and the product of the sample size with the spike size. When this ratio converges to a nonzero constant, the sample eigenvector converges to a cone, with a certain angle to its corresponding population eigenvector. In the High Dimension, Low Sample Size case, the angle between the sample eigenvector and its population counterpart converges to a limiting distribution. Several generalizations of the multi-spike covariance models are also explored, and additional theoretical results are presented.

Sampling strategies to capture single-cell heterogeneity

OpenAIRE

Satwik Rajaram; Louise E. Heinrich; John D. Gordan; Jayant Avva; Kathy M. Bonness; Agnieszka K. Witkiewicz; James S. Malter; Chloe E. Atreya; Robert S. Warren; Lani F. Wu; Steven J. Altschuler

2017-01-01

Advances in single-cell technologies have highlighted the prevalence and biological significance of cellular heterogeneity. A critical question is how to design experiments that faithfully capture the true range of heterogeneity from samples of cellular populations. Here, we develop a data-driven approach, illustrated in the context of image data, that estimates the sampling depth required for prospective investigations of single-cell heterogeneity from an existing collection of samples. ...

Cognitive Predictors of Verbal Memory in a Mixed Clinical Pediatric Sample

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Shelley C. Heaton

2013-08-01

Full Text Available Verbal memory problems, along with other cognitive difficulties, are common in children diagnosed with neurological and/or psychological disorders. Historically, these “memory problems” have been poorly characterized and often present with a heterogeneous pattern of performance across memory processes, even within a specific diagnostic group. The current study examined archival neuropsychological data from a large mixed clinical pediatric sample in order to understand whether functioning in other cognitive areas (i.e., verbal knowledge, attention, working memory, executive functioning may explain some of the performance variability seen across verbal memory tasks of the Children’s Memory Scale (CMS. Multivariate analyses revealed that among the cognitive functions examined, only verbal knowledge explained a significant amount of variance in overall verbal memory performance. Further univariate analyses examining the component processes of verbal memory indicated that verbal knowledge is specifically related to encoding, but not the retention or retrieval stages. Future research is needed to replicate these findings in other clinical samples, to examine whether verbal knowledge predicts performance on other verbal memory tasks and to explore whether these findings also hold true for visual memory tasks. Successful replication of the current study findings would indicate that interventions targeting verbal encoding deficits should include efforts to improve verbal knowledge.

Child maltreatment and ADHD symptoms in a sample of young adults

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Karoline Sanderud

2016-06-01

Full Text Available Objective: The present study investigated the relationship between different types of childhood maltreatment (emotional, sexual, overall abuse, and no abuse and the symptoms of attention deficit hyperactivity disorder (ADHD in young adulthood. Method: Data were collected from a Danish national study conducted by The Danish National Centre for Social Research in 2008 and 2009. A sample of 4,718 young adults (24 years of age were randomly selected using the total birth cohort of children born in 1984. Structured interviews were conducted with a response rate of 63%, equating to a total sample size of 2,980 participants. Results: Chi-square analyses revealed significant relationships between child maltreatment groups and a probable diagnosis of ADHD using the Adult ADHD Self-Report Scale (ASRS. Binary logistic regression analysis showed that the overall abuse class was more strongly associated with probable ADHD (OR=5.08, followed by emotional abuse (OR=3.09 and sexual abuse (OR=2.07. Conclusions: The results showed that childhood maltreatment was associated with increased risk of ADHD symptoms in young adulthood. The findings of this study are discussed within the existing literature and suggestions for future research are outlined in order to replicate these findings in other adult populations.

Evaluation of the DSM-5 severity indicator for binge eating disorder in a clinical sample

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Grilo, Carlos M.; Ivezaj, Valentina; White, Marney A.

2015-01-01

Objective This study tested the new DSM-5 severity criterion for binge eating disorder (BED) based on frequency of binge-eating in a clinical sample. This study also tested overvaluation of shape/weight as an alternative severity specifier. Method Participants were 834 treatment-seeking adults diagnosed with DSM-5 BED using semistructured diagnostic and eating-disorder interviews. Participants sub-grouped based on DSM-5 severity levels and on overvaluation of shape/weight were compared on demographic and clinical variables. Results Based on DSM-5 severity definitions, 331 (39.7%) participants were categorized as mild, 395 (47.5%) as moderate, 83 (10.0%) as severe, and 25 (3.0%) as extreme. Analyses comparing three (mild, moderate, and severe/extreme) severity groups revealed no significant differences in demographic variables or body mass index (BMI). Analyses revealed significantly higher eating-disorder psychopathology in the severe/extreme than moderate and mild groups and higher depression in moderate and severe/extreme groups than the mild group; effect sizes were small. Participants characterized with overvaluation (N = 449; 54%) versus without overvaluation (N = 384; 46%) did not differ significantly in age, sex, BMI, or binge-eating frequency, but had significantly greater eating-disorder psychopathology and depression. The robustly greater eating-disorder psychopathology and depression levels (medium-to-large effect sizes) in the overvaluation group was observed without attenuation of effect sizes after adjusting for ethnicity/race and binge-eating severity/frequency. Conclusions Our findings provide support for overvaluation of shape/weight as a severity specifier for BED as it provides stronger information about the severity of homogeneous groupings of patients than the DSM-5 rating based on binge-eating. PMID:26114779

Meditation effects within the hippocampal complex revealed by voxel-based morphometry and cytoarchitectonic probabilistic mapping

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Eileen eLuders

2013-07-01

Full Text Available Scientific studies addressing anatomical variations in meditators’ brains have emerged rapidly over the last few years, where significant links are most frequently reported with respect to gray matter (GM. To advance prior work, this study examined GM characteristics in a large sample of 100 subjects (50 meditators, 50 controls, where meditators have been practicing close to twenty years, on average. A standard, whole-brain voxel-based morphometry approach was applied and revealed significant meditation effects in the vicinity of the hippocampus, showing more GM in meditators than in controls as well as positive correlations with the number of years practiced. However, the hippocampal complex is regionally segregated by architecture, connectivity, and functional relevance. Thus, to establish differential effects within the hippocampal formation (cornu ammonis, fascia dentate, entorhinal cortex, subiculum as well as the hippocampal-amygdaloid transition area, we utilized refined cytoarchitectonic probabilistic maps of (peri- hippocampal subsections. Significant meditation effects were observed within the subiculum specifically. Since the subiculum is known to play a key role in stress regulation and meditation is an established form of stress reduction, these GM findings may reflect neuronal preservation in long-term meditators – perhaps due to an attenuated release of stress hormones and decreased neurotoxicity.

Meditation effects within the hippocampal complex revealed by voxel-based morphometry and cytoarchitectonic probabilistic mapping

Science.gov (United States)

Luders, Eileen; Kurth, Florian; Toga, Arthur W.; Narr, Katherine L.; Gaser, Christian

2013-01-01

Scientific studies addressing anatomical variations in meditators' brains have emerged rapidly over the last few years, where significant links are most frequently reported with respect to gray matter (GM). To advance prior work, this study examined GM characteristics in a large sample of 100 subjects (50 meditators, 50 controls), where meditators have been practicing close to 20 years, on average. A standard, whole-brain voxel-based morphometry approach was applied and revealed significant meditation effects in the vicinity of the hippocampus, showing more GM in meditators than in controls as well as positive correlations with the number of years practiced. However, the hippocampal complex is regionally segregated by architecture, connectivity, and functional relevance. Thus, to establish differential effects within the hippocampal formation (cornu ammonis, fascia dentata, entorhinal cortex, subiculum) as well as the hippocampal-amygdaloid transition area, we utilized refined cytoarchitectonic probabilistic maps of (peri-) hippocampal subsections. Significant meditation effects were observed within the subiculum specifically. Since the subiculum is known to play a key role in stress regulation and meditation is an established form of stress reduction, these GM findings may reflect neuronal preservation in long-term meditators—perhaps due to an attenuated release of stress hormones and decreased neurotoxicity. PMID:23847572

Psychological Resilience, Affective Mechanisms, and Symptom Burden in a Tertiary Care Sample of Patients with Fibromyalgia

Science.gov (United States)

McAllister, Samantha J; Vincent, Ann; Hassett, Afton L; Whipple, Mary O; Oh, Terry H; Benzo, Roberto P; Toussaint, Loren L

2014-01-01

Research demonstrates that patients with fibromyalgia who have higher positive and lower negative affect have lower symptom burden. Affect has been shown to be associated with resilience. This study examined the relationship between affect, resilience, and fibromyalgia symptom burden in a clinical sample of patients with fibromyalgia. We hypothesized that (a) positive and negative affect would be associated with fibromyalgia symptom burden; (b) resilience would be associated with positive and negative affect; (c) resilience would be associated with fibromyalgia symptom burden; and (d) the connection between resilience and fibromyalgia symptom burden would be mediated by both positive and negative affect. A sample of 858 patients with fibromyalgia completed questionnaires. Mediation modeling revealed statistically significant direct effects of resilience on fibromyalgia symptom burden (β =−.10, P fibromyalgia symptom burden through affect (β =−.36, P fibromyalgia symptom burden. Our results suggest that improving affect through resiliency training could be studied as a modality for improving fibromyalgia symptom burden. PMID:24376184

Neutron activation analysis of neonate and maternal hair sampled in areas with different levels of pollution

International Nuclear Information System (INIS)

Obrusnik, I.; Skrivanek, O.; Umlaufova, M.; Hovorka, V.

1985-01-01

Instrumental neutron activation analysis was performed on human head hair of newborns and mothers sampled in two areas with different levels of environmental exposure. The group of neonates from the exposed area (polluted by thermal power plants burning brown coal and by chemical industry) exhibited higher levels of several trace elements in hair, e.g. Se, Zn, Hg and Sb in comparison with the control group. Moreover, the mean concentrations of Se, Hg, Zn and Br in neonate hair were found to be higher than in mothers' hair. Although the study revealed statistically significant differences in the composition of neonate hair samples in areas with different levels of environmental exposure, the differences are relatively small. Only a thorough long-term study both with environmental and medical observations can prove a direct connection of the elevated levels of some trace elements in neonate hair with the higher incidence of mental diseaes of children living in the exposed area. (author)

Parabens in 24 h urine samples of the German Environmental Specimen Bank from 1995 to 2012.

Science.gov (United States)

Moos, Rebecca K; Koch, Holger M; Angerer, Jürgen; Apel, Petra; Schröter-Kermani, Christa; Brüning, Thomas; Kolossa-Gehring, Marike

2015-10-01

Parabens are widely used as antimicrobial preservatives in personal care and consumer products, food and pharmaceuticals. Due to their ubiquity, humans are constantly exposed to these chemicals. We assessed exposure to nine parabens (methyl-, ethyl-, n- and iso-propyl-, n- and iso-butyl-, benzyl-, pentyl- and heptyl paraben) in the German population from 1995 to 2012 based on 660 24h urine samples from the German Environmental Specimen Bank (ESB) using on-line HPLC coupled to isotope dilution tandem mass spectrometry. The limit of quantification (LOQ) was 0.5 μg/L for all parabens. We detected methyl-, ethyl- and n-propyl paraben in 79-99% of samples, followed by n-butyl paraben in 40% of samples. We infrequently detected iso-butyl-, iso-propyl- and benzyl paraben in 24%, 4% and 1.4% of samples, respectively. Urinary concentrations were highest for methyl paraben (median 39.8 μg/L; 95th percentile 319 μg/L) followed by n-propyl paraben (4.8 μg/L; 95th percentile 74.0 μg/L) and ethyl paraben (2.1 μg/L; 95th percentile 39.1 μg/L). Women had significantly higher urinary levels for all parabens than men, except for benzyl paraben. Samples from the ESB revealed that over the investigation period of nearly 20 years urinary paraben levels remained surprisingly constant; only methyl paraben had a significant increase, for both men and women. We found strong correlations between methyl- and n-propyl paraben and between n- and iso-butyl paraben. These results indicate that parabens are used in combination and arise from common sources of exposure. Urinary excretion factors are needed to extrapolate from individual urinary concentrations to actual doses. Copyright © 2015 Elsevier GmbH. All rights reserved.

Predicting significant torso trauma.

Science.gov (United States)

Nirula, Ram; Talmor, Daniel; Brasel, Karen

2005-07-01

Identification of motor vehicle crash (MVC) characteristics associated with thoracoabdominal injury would advance the development of automatic crash notification systems (ACNS) by improving triage and response times. Our objective was to determine the relationships between MVC characteristics and thoracoabdominal trauma to develop a torso injury probability model. Drivers involved in crashes from 1993 to 2001 within the National Automotive Sampling System were reviewed. Relationships between torso injury and MVC characteristics were assessed using multivariate logistic regression. Receiver operating characteristic curves were used to compare the model to current ACNS models. There were a total of 56,466 drivers. Age, ejection, braking, avoidance, velocity, restraints, passenger-side impact, rollover, and vehicle weight and type were associated with injury (p < 0.05). The area under the receiver operating characteristic curve (83.9) was significantly greater than current ACNS models. We have developed a thoracoabdominal injury probability model that may improve patient triage when used with ACNS.

Clinicopathological and prognostic significance of GPX2 protein expression in esophageal squamous cell carcinoma

International Nuclear Information System (INIS)

Lei, Zhijin; Tian, Dongping; Zhang, Chong; Zhao, Shukun; Su, Min

2016-01-01

Chaoshan region, a littoral area of Guangdong province in southern China, has a high incidence of esophageal squamous cell carcinoma (ESCC). At present, the prognosis of ESCC is still very poor, therefore, there is urgent need to seek valuable molecular biomarker for prognostic evaluation to guide clinical treatment. GPX2, a selenoprotein, was exclusively expressed in gastrointestinal tract and has an anti-oxidative damage and anti-tumour effect in the progress of tumourigenesis. We collected 161 ESCC patients samples, among which 83 patients were followed up. We employed immunochemistry analysis, western blotting and quantitative real-time PCR for measuring the expression of GPX2 within ESCC samples. We analysed the relationship between the expression of GPX2 and clinicopathological parameters of 161 patients with ESCC by Chi-square or Fisher’s exact test. The survival analysis of GPX2 expression within ESCC tissues was evaluated by the Kaplan-Meier method and Cox-regression. A significant higher expression level of GPX2 was detected in tumour tissues compared to that in non-tumour tissues (P < 0.001). Moreover, GPX2 expression has statistically significant difference in the tumour histological grade of ESCC (P < 0.001), while there was no statistically significant difference in age, sex, tumour size, tumour location, gross morphology and clinical TNM stages (P > 0.05). Meanwhile, the expression of GPX2 protein was obviously down-regulated within poorly differentiated ESCC. Last, survival analysis revealed that tumour histological grade and clinical TNM stages, both of the clinical pathological parameters of ESCC, were associated with the prognosis of patients with ESCC (respectively, P = 0.009, HR (95 % CI) = 1.885 (1.212 ~ 2.932); P = 0.007, HR (95 % CI) = 2.046 (1.318 ~ 3.177)). More importantly, loss expression of GPX2 protein predicted poor prognosis in patients with ESCC (P < 0.001, HR (95 % CI) = 5.700 (2.337 ~ 13.907)). Collectively, these results

Pulsed Direct Current Electrospray: Enabling Systematic Analysis of Small Volume Sample by Boosting Sample Economy.

Science.gov (United States)

Wei, Zhenwei; Xiong, Xingchuang; Guo, Chengan; Si, Xingyu; Zhao, Yaoyao; He, Muyi; Yang, Chengdui; Xu, Wei; Tang, Fei; Fang, Xiang; Zhang, Sichun; Zhang, Xinrong

2015-11-17

We had developed pulsed direct current electrospray ionization mass spectrometry (pulsed-dc-ESI-MS) for systematically profiling and determining components in small volume sample. Pulsed-dc-ESI utilized constant high voltage to induce the generation of single polarity pulsed electrospray remotely. This method had significantly boosted the sample economy, so as to obtain several minutes MS signal duration from merely picoliter volume sample. The elongated MS signal duration enable us to collect abundant MS(2) information on interested components in a small volume sample for systematical analysis. This method had been successfully applied for single cell metabolomics analysis. We had obtained 2-D profile of metabolites (including exact mass and MS(2) data) from single plant and mammalian cell, concerning 1034 components and 656 components for Allium cepa and HeLa cells, respectively. Further identification had found 162 compounds and 28 different modification groups of 141 saccharides in a single Allium cepa cell, indicating pulsed-dc-ESI a powerful tool for small volume sample systematical analysis.

Sampling methods for rumen microbial counts by Real-Time PCR techniques

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S. Puppo

2010-02-01

Full Text Available Fresh rumen samples were withdrawn from 4 cannulated buffalo females fed a fibrous diets in order to quantify bacteria concentration in the rumen by Real-Time PCR techniques. To obtain DNA of a good quality from whole rumen fluid, eight (M1-M8 different pre-filtration methods (cheese cloths, glass-fibre and nylon filter in combination with various centrifugation speeds (1000, 5000 and 14,000 rpm were tested. Genomic DNA extraction was performed either on fresh or frozen samples (-20°C. The quantitative bacteria analysis was realized according to Real-Time PCR procedure for Butyrivibrio fibrisolvens reported in literature. M5 resulted the best sampling procedure allowing to obtain a suitable genomic DNA. No differences were revealed between fresh and frozen samples.

Combined Metabolomic Analysis of Plasma and Urine Reveals AHBA, Tryptophan and Serotonin Metabolism as Potential Risk Factors in Gestational Diabetes Mellitus (GDM

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Miriam Leitner

2017-12-01

Full Text Available Gestational diabetes mellitus during pregnancy has severe implications for the health of the mother and the fetus. Therefore, early prediction and an understanding of the physiology are an important part of prenatal care. Metabolite profiling is a long established method for the analysis and prediction of metabolic diseases. Here, we applied untargeted and targeted metabolomic protocols to analyze plasma and urine samples of pregnant women with and without GDM. Univariate and multivariate statistical analyses of metabolomic profiles revealed markers such as 2-hydroxybutanoic acid (AHBA, 3-hydroxybutanoic acid (BHBA, amino acids valine and alanine, the glucose-alanine-cycle, but also plant-derived compounds like sitosterin as different between control and GDM patients. PLS-DA and VIP analysis revealed tryptophan as a strong variable separating control and GDM. As tryptophan is biotransformed to serotonin we hypothesized whether serotonin metabolism might also be altered in GDM. To test this hypothesis we applied a method for the analysis of serotonin, metabolic intermediates and dopamine in urine by stable isotope dilution direct infusion electrospray ionization mass spectrometry (SID-MS. Indeed, serotonin and related metabolites differ significantly between control and GDM patients confirming the involvement of serotonin metabolism in GDM. Clustered correlation coefficient visualization of metabolite correlation networks revealed the different metabolic signatures between control and GDM patients. Eventually, the combination of selected blood plasma and urine sample metabolites improved the AUC prediction accuracy to 0.99. The detected GDM candidate biomarkers and the related systemic metabolic signatures are discussed in their pathophysiological context. Further studies with larger cohorts are necessary to underpin these observations.

CAFET algorithm reveals Wnt/PCP signature in lung squamous cell carcinoma.

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Yue Hu

Full Text Available We analyzed the gene expression patterns of 138 Non-Small Cell Lung Cancer (NSCLC samples and developed a new algorithm called Coverage Analysis with Fisher's Exact Test (CAFET to identify molecular pathways that are differentially activated in squamous cell carcinoma (SCC and adenocarcinoma (AC subtypes. Analysis of the lung cancer samples demonstrated hierarchical clustering according to the histological subtype and revealed a strong enrichment for the Wnt signaling pathway components in the cluster consisting predominantly of SCC samples. The specific gene expression pattern observed correlated with enhanced activation of the Wnt Planar Cell Polarity (PCP pathway and inhibition of the canonical Wnt signaling branch. Further real time RT-PCR follow-up with additional primary tumor samples and lung cancer cell lines confirmed enrichment of Wnt/PCP pathway associated genes in the SCC subtype. Dysregulation of the canonical Wnt pathway, characterized by increased levels of β-catenin and epigenetic silencing of negative regulators, has been reported in adenocarcinoma of the lung. Our results suggest that SCC and AC utilize different branches of the Wnt pathway during oncogenesis.

Sampling study in milk storage tanks by INAA

International Nuclear Information System (INIS)

Santos, L.G.C.; Nadai Fernandes de, E.A.; Bacchi, M.A.; Tagliaferro, F.S.

2008-01-01

This study investigated the representativeness of samples for assessing chemical elements in milk bulk tanks. Milk samples were collected from a closed tank in a dairy plant and from an open top tank in a dairy farm. Samples were analyzed for chemical elements by instrumental neutron activation analysis (INAA). For both experiments, Br, Ca, Cs, K, Na, Rb and Zn did not present significant differences between samples thereby indicating the appropriateness of the sampling procedure adopted to evaluate the analytes of interest. (author)

Significance levels for studies with correlated test statistics.

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Shi, Jianxin; Levinson, Douglas F; Whittemore, Alice S

2008-07-01

When testing large numbers of null hypotheses, one needs to assess the evidence against the global null hypothesis that none of the hypotheses is false. Such evidence typically is based on the test statistic of the largest magnitude, whose statistical significance is evaluated by permuting the sample units to simulate its null distribution. Efron (2007) has noted that correlation among the test statistics can induce substantial interstudy variation in the shapes of their histograms, which may cause misleading tail counts. Here, we show that permutation-based estimates of the overall significance level also can be misleading when the test statistics are correlated. We propose that such estimates be conditioned on a simple measure of the spread of the observed histogram, and we provide a method for obtaining conditional significance levels. We justify this conditioning using the conditionality principle described by Cox and Hinkley (1974). Application of the method to gene expression data illustrates the circumstances when conditional significance levels are needed.

Detection of HCV core antigen and its diagnostic significance

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YANG Jie

2013-02-01

Full Text Available ObjectiveTo compare the abilities of the hepatitis C virus (HCV core antigen (cAg test and the HCV RNA assay for confirming anti-HCV presence in order to determine the clinical utility of the HCV-cAg as an alternative or confirmatory diagnostic tool. MethodsSerum samples collected from 158 patients diagnosed with HCV infection were subjected to the enzyme-linked immunosorbent assay-based HCV-cAg test. The optical density (OD measured values were used to calculate the ratio of specimen absorbance to the cutoff value (S/CO. Simultaneously, the serum samples were subjected to PCR-based nucleic acid amplification quantitative fluorescence detection of HCV RNA. ResultsNone of the serum samples had a S/CO value ＜1 for the HCV-cAg test (100% negative, but all of the samples had a S/CO value ＞5 (100% positive. The HCV-cAg test sensitivity was 87.05%, specificity was 76.67%, positive predictive value was 9653%, and negative predictive value was 44.23%. As the S/CO value gradually increased, the significantly higher positive coincident rate of the HCV RNA test decreased. The HCV RNA negative coincident rate was significantly higher than that of the HCV-cAg test. HCV-cAg S/CO values between 1 and 2 corresponded to an HCV RNA values between 1.0×103 copies/ml and 1.0×104 copies/ml. The highest S/CO value obtained was 1.992. ConclusionThe HCV-cAg test is comparable to the HCV RNA assay for diagnosing HCV infection.

Analysis of fingerprint samples, testing various conditions, for forensic DNA identification.

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Ostojic, Lana; Wurmbach, Elisa

2017-01-01

Fingerprints can be of tremendous value for forensic biology, since they can be collected from a wide variety of evident types, such as handles of weapons, tools collected in criminal cases, and objects with no apparent staining. DNA obtained from fingerprints varies greatly in quality and quantity, which ultimately affects the quality of the resulting STR profiles. Additional difficulties can arise when fingerprint samples show mixed STR profiles due to the handling of multiple persons. After applying a tested protocol for sample collection (swabbing with 5% Triton X-100), DNA extraction (using an enzyme that works at elevated temperatures), and PCR amplification (AmpFlSTR® Identifiler® using 31cycles) extensive analysis was performed to better understand the challenges inherent to fingerprint samples, with the ultimate goal of developing valuable profiles (≥50% complete). The impact of time on deposited fingerprints was investigated, revealing that while the quality of profiles deteriorated, full STR profiles could still be obtained from samples after 40days of storage at room temperature. By comparing the STR profiles from fingerprints of the dominant versus the non-dominant hand, we found a slightly better quality from the non-dominant hand, which was not always significant. Substrates seem to have greater effects on fingerprints. Tests on glass, plastic, paper and metal (US Quarter dollar, made of Cu and Ni), common substrates in offices and homes, showed best results for glass, followed by plastic and paper, while almost no profiles were obtained from a Quarter dollar. Important for forensic casework, we also assessed three-person mixtures of touched fingerprint samples. Unlike routinely used approaches for sampling evidence, the surface of an object (bottle) was sectioned into six equal parts and separate samples were taken from each section. The samples were processed separately for DNA extraction and STR amplification. The results included a few single

An 'intelligent' approach to radioimmunoassay sample counting employing a microprocessor-controlled sample counter

International Nuclear Information System (INIS)

Ekins, R.P.; Sufi, S.; Malan, P.G.

1978-01-01

The enormous impact on medical science in the last two decades of microanalytical techniques employing radioisotopic labels has, in turn, generated a large demand for automatic radioisotopic sample counters. Such instruments frequently comprise the most important item of capital equipment required in the use of radioimmunoassay and related techniques and often form a principle bottleneck in the flow of samples through a busy laboratory. It is therefore imperative that such instruments should be used 'intelligently' and in an optimal fashion to avoid both the very large capital expenditure involved in the unnecessary proliferation of instruments and the time delays arising from their sub-optimal use. Most of the current generation of radioactive sample counters nevertheless rely on primitive control mechanisms based on a simplistic statistical theory of radioactive sample counting which preclude their efficient and rational use. The fundamental principle upon which this approach is based is that it is useless to continue counting a radioactive sample for a time longer than that required to yield a significant increase in precision of the measurement. Thus, since substantial experimental errors occur during sample preparation, these errors should be assessed and must be related to the counting errors for that sample. The objective of the paper is to demonstrate that the combination of a realistic statistical assessment of radioactive sample measurement, together with the more sophisticated control mechanisms that modern microprocessor technology make possible, may often enable savings in counter usage of the order of 5- to 10-fold to be made. (author)

Characterization of different cassava samples by nuclear magnetic resonance spectroscopy

International Nuclear Information System (INIS)

Iulianelli, Gisele C.V.; Tavares, Maria I.B.

2011-01-01

Cassava root (Manihot esculenta Crantz) is grown in all Brazilian states, being an important product in the diet of Brazilians. For many families of the North and Northeast states, it may represent the main energy source. The cassava root flour has high levels of starch, in addition to containing fiber, lipids and some minerals. There is, however, great genetic variability, which results in differentiation in its chemical composition and structural aspect. Motivated by the economic, nutritional and pharmacological importance of this product, this work is aimed at characterizing six cassava flour samples by NMR spectroscopy. The spectra revealed the main chemical groups. Furthermore, the results confirmed differences on chemical and structural aspect of the samples. For instance, the F1 sample is richer in carbohydrates, while the F4 sample has higher proportion of glycolipids, the F2 sample has higher amylose content and the F6 sample exhibits a greater diversity of glycolipid types. Regarding the molecular structure, the NMR spectra indicated that the F1 sample is more organized at the molecular level, while the F3 and F5 samples are similar in amorphicity and in the molecular packing. (author)

Testing the DSM-5 severity indicator for bulimia nervosa in a treatment-seeking sample.

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Dakanalis, Antonios; Clerici, Massimo; Riva, Giuseppe; Carrà, Giuseppe

2017-03-01

This study tested the new DSM-5 severity criterion for bulimia nervosa (BN) based on the frequency of inappropriate weight compensatory behaviors in a treatment-seeking sample. Participants were 345 adults with DSM-5 BN presenting for treatment. They were sub-grouped based on DSM-5 severity levels and compared on a range of variables of clinical interest and demographics. Based on DSM-5 severity definitions, 27.2 % of the sample was categorized with mild, 26.1 % with moderate, 24.9 % with severe, and 21.8 % with extreme severity of BN. Analyses revealed that the four (mild, moderate, severe, and extreme) severity groups of BN significantly differed from each other in eating disordered and body-related attitudes and behaviors, factors involved in the maintenance process of the disorder, comorbid psychiatric disorders, psychological distress, and psychosocial impairment (medium-to-large effect sizes). No significant between-group differences were observed in demographics, body mass index, or at the age when BN first occurred, lending some credence to recent suggestions that age-at-onset of BN may be more a disorder- than a severity-dependent variable. Collectively, our findings provide support for the severity indicator for BN introduced in the DSM-5 as a means of addressing heterogeneity and variability in the severity of the disorder.

Results of EDS uranium samples characterization after hydrogen loading

International Nuclear Information System (INIS)

Chicea, D.; Dash, J.

2003-01-01

Several experiments of loading natural uranium foils with hydrogen were done. Electrolysis was used for loading hydrogen into uranium, because it is the most efficient way for H loading. The composition of the surface and near surface of the samples was determined using an Oxford EDS spectrometer on a Scanning Electron Microscope, manufactured by ISI. Images were taken with several magnifications up to 3.4KX. Results reveal that when low current density was used, the surface patterns changed from granules on the surface having a typical size of 2-4 microns to pits under the surface having a typical size under one micron. When high current density was used the surface changed and presented deep fissures. The deep fissures are the result of the mechanical strain induced by the lattice expansion caused by hydrogen absorption. The surface composition was determined before and after hydrogen loading. Uranium, thorium platinum and carbon concentration were measured. Experiments suggest that the amount of thorium increases on the uranium sample with the total electric charge transported through electrolyte. Carbon concentration was found to decrease on the surface of the sample as the total electric charge transported through electrolyte increased. Platinum is used in electrolysis experiment as anode primarily because it does not dissolve in electrolyte and therefore it is not electro-deposited on the cathode surface. The results of the platinum concentration measurements on the surface of the samples we loaded with hydrogen reveal that the platinum concentration increased dramatically as the current density increased and that created platinum spots on the cathode surface. Work is in progress on the subject. (authors)

Estimating Sample Size for Usability Testing

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Alex Cazañas

2017-02-01

Full Text Available One strategy used to assure that an interface meets user requirements is to conduct usability testing. When conducting such testing one of the unknowns is sample size. Since extensive testing is costly, minimizing the number of participants can contribute greatly to successful resource management of a project. Even though a significant number of models have been proposed to estimate sample size in usability testing, there is still not consensus on the optimal size. Several studies claim that 3 to 5 users suffice to uncover 80% of problems in a software interface. However, many other studies challenge this assertion. This study analyzed data collected from the user testing of a web application to verify the rule of thumb, commonly known as the “magic number 5”. The outcomes of the analysis showed that the 5-user rule significantly underestimates the required sample size to achieve reasonable levels of problem detection.

Isotope analytics for the evaluation of the feeding influence on the isotope ratio in beef samples; Isotopenanalytik zur Bestimmung des Einflusses der Ernaehrung auf die Isotopenzusammensetzung in Rinderproben

Energy Technology Data Exchange (ETDEWEB)

Herwig, Nadine

2010-11-17

Information about the origin of food and associated production systems has a high significance for food control. An extremely promising approach to obtain such information is the determination of isotope ratios of different elements. In this study the correlation of the isotope ratios C-13/C-12, N-15/N-14, Mg-25/Mg-24, and Sr-87/Sr-86 in bovine samples (milk and urine) and the corresponding isotope ratios in feed was investigated. It was shown that in the bovine samples all four isotope ratios correlate with the isotope composition of the feed. The isotope ratios of strontium and magnesium have the advantage that they directly reflect the isotope ratios of the ingested feed since there is no isotope fractionation in the bovine organism which is in contrast to the case of carbon and nitrogen isotope ratios. From the present feeding study it is evident, that a feed change leads to a significant change in the delta C-13 values in milk and urine within 10 days already. For the deltaN-15 values the feed change was only visible in the bovine urine after 49 days. Investigations of cows from two different regions (Berlin/Germany and Goestling/Austria) kept at different feeding regimes revealed no differences in the N-15/N-14 and Mg-26/Mg-24 isotope ratios. The strongest correlation between the isotope ratio of the bovine samples and the kind of ingested feed was observed for the carbon isotope ratio. With this ratio even smallest differences in the feed composition were traceable in the bovine samples. Since different regions usually coincide with different feeding regimes, carbon isotope ratios can be used to distinguish bovine samples from different regions if the delta C-13 values of the ingested feed are different. Furthermore, the determination of strontium isotope ratios revealed significant differences between bovine and feed samples of Berlin and Goestling due to the different geologic realities. Hence the carbon and strontium isotope ratios allow the best

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

Proteomic profiling in multiple sclerosis clinical courses reveals potential biomarkers of neurodegeneration.

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Maria Liguori

Full Text Available The aim of our project was to perform an exploratory analysis of the cerebrospinal fluid (CSF proteomic profiles of Multiple Sclerosis (MS patients, collected in different phases of their clinical course, in order to investigate the existence of peculiar profiles characterizing the different MS phenotypes. The study was carried out on 24 Clinically Isolated Syndrome (CIS, 16 Relapsing Remitting (RR MS, 11 Progressive (Pr MS patients. The CSF samples were analysed using the Matrix Assisted Laser Desorption Ionisation Time Of Flight (MALDI-TOF mass spectrometer in linear mode geometry and in delayed extraction mode (m/z range: 1000-25000 Da. Peak lists were imported for normalization and statistical analysis. CSF data were correlated with demographic, clinical and MRI parameters. The evaluation of MALDI-TOF spectra revealed 348 peak signals with relative intensity ≥ 1% in the study range. The peak intensity of the signals corresponding to Secretogranin II and Protein 7B2 were significantly upregulated in RRMS patients compared to PrMS (p<0.05, whereas the signals of Fibrinogen and Fibrinopeptide A were significantly downregulated in CIS compared to PrMS patients (p<0.04. Additionally, the intensity of the Tymosin β4 peak was the only signal to be significantly discriminated between the CIS and RRMS patients (p = 0.013. Although with caution due to the relatively small size of the study populations, and considering that not all the findings remained significant after adjustment for multiple comparisons, in our opinion this mass spectrometry evaluation confirms that this technique may provide useful and important information to improve our understanding of the complex pathogenesis of MS.

Human bloodstains on bone artefacts: an SEM intra- and inter-sample comparative study using ratite bird tibiotarsus.

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Hortolà, Policarp

2016-11-01

Apart from their forensic significance in crime investigation, human bloodstains have an anthropological interest due to their occurrence on certain traditional weapons and ritual objects. Previously, a guiding study of erythrocytes in experimental samples including domestic sheep (Ovis aries) tibia was carried out using a scanning electron microscope (SEM). Here, a comparative SEM study to reveal the potential differences in bloodstain surface morphology as a function of intra-sample (smear region) and inter-sample (individual smear, smearing mechanism, bone origin) parameters is reported. A fragment of emu (Dromaius novaehollandiae) tibiotarsus was smeared with an adult man's peripheral blood. After air-drying and storing indoors, the boundary and neighbouring inner areas of the three individual bloodstains obtained were examined via secondary electrons in a variable-pressure SEM working in low-vacuum mode. As a whole, desiccation microcracks were present, the limits between the smear and the substrate appeared poorly defined, and no erythrocyte negative replicas were observed in the examined areas. In addition, a putative fibrin network, more or less embedded in the dried plasma matrix, was observed in the smears' boundary. Regarding the smear region in sliding smears, the periphery and boundary revealed to be different, while the head and tail were similar. Considering individual sliding smears, they had similar characteristics. Relating to the smear region as a function of the smearing mechanism, the periphery was different whether sliding or touching, while the boundary was similar in sliding and touching smears. Concerning the smear region as a function of the bone origin, the periphery revealed to be similar in both ratite and mammalian bone, while the boundary did different in ratite and mammalian bone. The results of this study show that SEM examination can be used fruitfully to detect bloodstains on ratite bone. Combined with previous SEM results in