Optimal treatment sequence in COPD: Can a consensus be found?

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J. Ferreira

2016-01-01

Full Text Available There is currently no consensus on the treatment sequence in chronic obstructive pulmonary disease (COPD, although it is recognized that early diagnosis is of paramount importance to start treatment in the early stages of the disease. Although it is fairly consensual that initial treatment should be with an inhaled short-acting beta agonist, a short-acting muscarinic antagonist, a long-acting beta-agonist or a long-acting muscarinic antagonist. As the disease progresses, several therapeutic options are available, and which to choose at each disease stage remains controversial. When and in which patients to use dual bronchodilation? When to use inhaled corticosteroids? And triple therapy? Are the existing non-inhaled therapies, such as mucolytic agents, antibiotics, phosphodiesterase-4 inhibitors, methylxanthines and immunostimulating agents, useful? If so, which patients would benefit? Should co-morbitities be taken into account when choosing COPD therapy for a patient?This paper reviews current guidelines and available evidence and proposes a therapeutic scheme for COPD patients. We also propose a treatment algorithm in the hope that it will help physicians to decide the best approach for their patients. The authors conclude that, at present, a full consensus on optimal treatment sequence in COPD cannot be found, mainly due to disease heterogeneity and lack of biomarkers to guide treatment. For the time being, and although some therapeutic approaches are consensual, treatment of COPD should be patient-oriented. Keywords: COPD, Treatment sequence, SABA, SAMA, LABA, LAMA, ICS, Triple therapy, Non-inhaled therapies

Generating Stimuli for Neuroscience Using PsychoPy.

Science.gov (United States)

Peirce, Jonathan W

2008-01-01

PsychoPy is a software library written in Python, using OpenGL to generate very precise visual stimuli on standard personal computers. It is designed to allow the construction of as wide a variety of neuroscience experiments as possible, with the least effort. By writing scripts in standard Python syntax users can generate an enormous variety of visual and auditory stimuli and can interact with a wide range of external hardware (enabling its use in fMRI, EEG, MEG etc.). The structure of scripts is simple and intuitive. As a result, new experiments can be written very quickly, and trying to understand a previously written script is easy, even with minimal code comments. PsychoPy can also generate movies and image sequences to be used in demos or simulated neuroscience experiments. This paper describes the range of tools and stimuli that it provides and the environment in which experiments are conducted.

CUDArray: CUDA-based NumPy

DEFF Research Database (Denmark)

Larsen, Anders Boesen Lindbo

This technical report introduces CUDArray – a CUDA-accelerated subset of the NumPy library. The goal of CUDArray is to combine the ease of development from NumPy with the computational power of Nvidia GPUs in a lightweight and extensible framework. Since the motivation behind CUDArray is to facil......This technical report introduces CUDArray – a CUDA-accelerated subset of the NumPy library. The goal of CUDArray is to combine the ease of development from NumPy with the computational power of Nvidia GPUs in a lightweight and extensible framework. Since the motivation behind CUDArray...

Image-guided preoperative prediction of pyramidal tract side effect in deep brain stimulation: proof of concept and application to the pyramidal tract side effect induced by pallidal stimulation.

Science.gov (United States)

Baumgarten, Clement; Zhao, Yulong; Sauleau, Paul; Malrain, Cecile; Jannin, Pierre; Haegelen, Claire

2016-04-01

Deep brain stimulation of the medial globus pallidus (GPm) is a surgical procedure for treating patients suffering from Parkinson's disease. Its therapeutic effect may be limited by the presence of pyramidal tract side effect (PTSE). PTSE is a contraction time-locked to the stimulation when the current spreading reaches the motor fibers of the pyramidal tract within the internal capsule. The objective of the study was to propose a preoperative predictive model of PTSE. A machine learning-based method called PyMAN (PTSE model based on artificial neural network) accounting for the current used in stimulation, the three-dimensional electrode coordinates and the angle of the trajectory, was designed to predict the occurrence of PTSE. Ten patients implanted in the GPm have been tested by a clinician to create a labeled dataset of the stimulation parameters that trigger PTSE. The kappa index value between the data predicted by PyMAN and the labeled data was 0.78. Further evaluation studies are desirable to confirm whether PyMAN could be a reliable tool for assisting the surgeon to prevent PTSE during the preoperative planning.

Targeted disruption of py235ebp-1: Invasion of erythrocytes by Plasmodium yoelii using an alternative py235 erythrocyte binding protein

KAUST Repository

Ogun, Solabomi A.

2011-02-17

Plasmodium yoelii YM asexual blood stage parasites express multiple members of the py235 gene family, part of the super-family of genes including those coding for Plasmodium vivax reticulocyte binding proteins and Plasmodium falciparum RH proteins. We previously identified a Py235 erythrocyte binding protein (Py235EBP-1, encoded by the PY01365 gene) that is recognized by protective mAb 25.77. Proteins recognized by a second protective mAb 25.37 have been identified by mass spectrometry and are encoded by two genes, PY01185 and PY05995/PY03534. We deleted the PY01365 gene and examined the phenotype. The expression of the members of the py235 family in both the WT and gene deletion parasites was measured by quantitative RT-PCR and RNA-Seq. py235ebp-1 expression was undetectable in the knockout parasite, but transcription of other members of the family was essentially unaffected. The knockout parasites continued to react with mAb 25.77; and the 25.77-binding proteins in these parasites were the PY01185 and PY05995/PY03534 products. The PY01185 product was also identified as erythrocyte binding. There was no clear change in erythrocyte invasion profile suggesting that the PY01185 gene product (designated PY235EBP-2) is able to fulfill the role of EBP-1 by serving as an invasion ligand although the molecular details of its interaction with erythrocytes have not been examined. The PY01365, PY01185, and PY05995/PY03534 genes are part of a distinct subset of the py235 family. In P. falciparum, the RH protein genes are under epigenetic control and expression correlates with binding to distinct erythrocyte receptors and specific invasion pathways, whereas in P. yoelii YM all the genes are expressed and deletion of one does not result in upregulation of another. We propose that simultaneous expression of multiple Py235 ligands enables invasion of a wide range of host erythrocytes even in the presence of antibodies to one or more of the proteins and that this functional

Targeted disruption of py235ebp-1: Invasion of erythrocytes by Plasmodium yoelii using an alternative py235 erythrocyte binding protein

KAUST Repository

Ogun, Solabomi A.; Tewari, Rita; Otto, Thomas D.; Howell, Steven A.; Knuepfer, Ellen; Cunningham, Deirdre A.; Xu, Zhengyao; Pain, Arnab; Holder, Anthony A.

2011-01-01

Plasmodium yoelii YM asexual blood stage parasites express multiple members of the py235 gene family, part of the super-family of genes including those coding for Plasmodium vivax reticulocyte binding proteins and Plasmodium falciparum RH proteins. We previously identified a Py235 erythrocyte binding protein (Py235EBP-1, encoded by the PY01365 gene) that is recognized by protective mAb 25.77. Proteins recognized by a second protective mAb 25.37 have been identified by mass spectrometry and are encoded by two genes, PY01185 and PY05995/PY03534. We deleted the PY01365 gene and examined the phenotype. The expression of the members of the py235 family in both the WT and gene deletion parasites was measured by quantitative RT-PCR and RNA-Seq. py235ebp-1 expression was undetectable in the knockout parasite, but transcription of other members of the family was essentially unaffected. The knockout parasites continued to react with mAb 25.77; and the 25.77-binding proteins in these parasites were the PY01185 and PY05995/PY03534 products. The PY01185 product was also identified as erythrocyte binding. There was no clear change in erythrocyte invasion profile suggesting that the PY01185 gene product (designated PY235EBP-2) is able to fulfill the role of EBP-1 by serving as an invasion ligand although the molecular details of its interaction with erythrocytes have not been examined. The PY01365, PY01185, and PY05995/PY03534 genes are part of a distinct subset of the py235 family. In P. falciparum, the RH protein genes are under epigenetic control and expression correlates with binding to distinct erythrocyte receptors and specific invasion pathways, whereas in P. yoelii YM all the genes are expressed and deletion of one does not result in upregulation of another. We propose that simultaneous expression of multiple Py235 ligands enables invasion of a wide range of host erythrocytes even in the presence of antibodies to one or more of the proteins and that this functional

Targeted disruption of py235ebp-1: invasion of erythrocytes by Plasmodium yoelii using an alternative Py235 erythrocyte binding protein.

Directory of Open Access Journals (Sweden)

Solabomi A Ogun

2011-02-01

Full Text Available Plasmodium yoelii YM asexual blood stage parasites express multiple members of the py235 gene family, part of the super-family of genes including those coding for Plasmodium vivax reticulocyte binding proteins and Plasmodium falciparum RH proteins. We previously identified a Py235 erythrocyte binding protein (Py235EBP-1, encoded by the PY01365 gene that is recognized by protective mAb 25.77. Proteins recognized by a second protective mAb 25.37 have been identified by mass spectrometry and are encoded by two genes, PY01185 and PY05995/PY03534. We deleted the PY01365 gene and examined the phenotype. The expression of the members of the py235 family in both the WT and gene deletion parasites was measured by quantitative RT-PCR and RNA-Seq. py235ebp-1 expression was undetectable in the knockout parasite, but transcription of other members of the family was essentially unaffected. The knockout parasites continued to react with mAb 25.77; and the 25.77-binding proteins in these parasites were the PY01185 and PY05995/PY03534 products. The PY01185 product was also identified as erythrocyte binding. There was no clear change in erythrocyte invasion profile suggesting that the PY01185 gene product (designated PY235EBP-2 is able to fulfill the role of EBP-1 by serving as an invasion ligand although the molecular details of its interaction with erythrocytes have not been examined. The PY01365, PY01185, and PY05995/PY03534 genes are part of a distinct subset of the py235 family. In P. falciparum, the RH protein genes are under epigenetic control and expression correlates with binding to distinct erythrocyte receptors and specific invasion pathways, whereas in P. yoelii YM all the genes are expressed and deletion of one does not result in upregulation of another. We propose that simultaneous expression of multiple Py235 ligands enables invasion of a wide range of host erythrocytes even in the presence of antibodies to one or more of the proteins and that this

AMS 4.0: consensus prediction of post-translational modifications in protein sequences.

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Plewczynski, Dariusz; Basu, Subhadip; Saha, Indrajit

2012-08-01

We present here the 2011 update of the AutoMotif Service (AMS 4.0) that predicts the wide selection of 88 different types of the single amino acid post-translational modifications (PTM) in protein sequences. The selection of experimentally confirmed modifications is acquired from the latest UniProt and Phospho.ELM databases for training. The sequence vicinity of each modified residue is represented using amino acids physico-chemical features encoded using high quality indices (HQI) obtaining by automatic clustering of known indices extracted from AAindex database. For each type of the numerical representation, the method builds the ensemble of Multi-Layer Perceptron (MLP) pattern classifiers, each optimising different objectives during the training (for example the recall, precision or area under the ROC curve (AUC)). The consensus is built using brainstorming technology, which combines multi-objective instances of machine learning algorithm, and the data fusion of different training objects representations, in order to boost the overall prediction accuracy of conserved short sequence motifs. The performance of AMS 4.0 is compared with the accuracy of previous versions, which were constructed using single machine learning methods (artificial neural networks, support vector machine). Our software improves the average AUC score of the earlier version by close to 7 % as calculated on the test datasets of all 88 PTM types. Moreover, for the selected most-difficult sequence motifs types it is able to improve the prediction performance by almost 32 %, when compared with previously used single machine learning methods. Summarising, the brainstorming consensus meta-learning methodology on the average boosts the AUC score up to around 89 %, averaged over all 88 PTM types. Detailed results for single machine learning methods and the consensus methodology are also provided, together with the comparison to previously published methods and state-of-the-art software tools. The

Generating stimuli for neuroscience using PsychoPy

Directory of Open Access Journals (Sweden)

Jonathan W Peirce

2009-01-01

Full Text Available PsychoPy is a software library written in Python, using OpenGL to generate very precise visual stimuli on standard personal computers. It is designed to allow the construction of as wide a variety of neuroscience experiments as possible, with the least effort. By writing scripts in standard Python syntax users can generate an enormous variety of visual and auditory stimuli and can interact with a wide range of external hardware (enabling its use in fMRI, EEG, MEG etc.. The structure of scripts is simple and intuitive. As a result, new experiments can be written very quickly, and trying to understand a previously written script is easy, even with minimal code comments. PsychoPy can also generate movies and image sequences to be used in demos or simulated neuroscience experiments. This paper describes the range of tools and stimuli that it provides and the environment in which experiments are conducted.

Generation and Characterization of HIV-1 Transmitted and Founder Virus Consensus Sequence from Intravenous Drug Users in Xinjiang, China.

Science.gov (United States)

Li, Fan; Ma, Liying; Feng, Yi; Hu, Jing; Ni, Na; Ruan, Yuhua; Shao, Yiming

2017-06-01

HIV-1 transmission in intravenous drug users (IDUs) has been characterized by high genetic multiplicity and suggests a greater challenge for HIV-1 infection blocking. We investigated a total of 749 sequences of full-length gp160 gene obtained by single genome sequencing (SGS) from 22 HIV-1 early infected IDUs in Xinjiang province, northwest China, and generated a transmitted and founder virus (T/F virus) consensus sequence (IDU.CON). The T/F virus was classified as subtype CRF07_BC and predicted to be CCR5-tropic virus. The variable region (V1, V2, and V4 loop) of IDU.CON showed length variation compared with the heterosexual T/F virus consensus sequence (HSX.CON) and homosexual T/F virus consensus sequence (MSM.CON). A total of 26 N-linked glycosylation sites were discovered in the IDU.CON sequence, which is less than that of MSM.CON and HSX.CON. Characterization of T/F virus from IDUs highlights the genetic make-up and complexity of virus near the moment of transmission or in early infection preceding systemic dissemination and is important toward the development of an effective HIV-1 preventive methods, including vaccines.

SymPy: symbolic computing in Python

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Aaron Meurer

2017-01-01

Full Text Available SymPy is an open source computer algebra system written in pure Python. It is built with a focus on extensibility and ease of use, through both interactive and programmatic applications. These characteristics have led SymPy to become a popular symbolic library for the scientific Python ecosystem. This paper presents the architecture of SymPy, a description of its features, and a discussion of select submodules. The supplementary material provide additional examples and further outline details of the architecture and features of SymPy.

PyMidas: Interface from Python to Midas

Science.gov (United States)

Maisala, Sami; Oittinen, Tero

2014-01-01

PyMidas is an interface between Python and MIDAS, the major ESO legacy general purpose data processing system. PyMidas allows a user to exploit both the rich legacy of MIDAS software and the power of Python scripting in a unified interactive environment. PyMidas also allows the usage of other Python-based astronomical analysis systems such as PyRAF.

Image-guided preoperative prediction of pyramidal tract side effect in deep brain stimulation

Science.gov (United States)

Baumgarten, C.; Zhao, Y.; Sauleau, P.; Malrain, C.; Jannin, P.; Haegelen, C.

2016-03-01

Deep brain stimulation of the medial globus pallidus is a surgical procedure for treating patients suffering from Parkinson's disease. Its therapeutic effect may be limited by the presence of pyramidal tract side effect (PTSE). PTSE is a contraction time-locked to the stimulation when the current spreading reaches the motor fibers of the pyramidal tract within the internal capsule. The lack of side-effect predictive model leads the neurologist to secure an optimal electrode placement by iterating clinical testing on an awake patient during the surgical procedure. The objective of the study was to propose a preoperative predictive model of PTSE. A machine learning based method called PyMAN (for Pyramidal tract side effect Model based on Artificial Neural network) that accounted for the current of the stimulation, the 3D electrode coordinates and the angle of the trajectory, was designed to predict the occurrence of PTSE. Ten patients implanted in the medial globus pallidus have been tested by a clinician to create a labeled dataset of the stimulation parameters that trigger PTSE. The kappa index value between the data predicted by PyMAN and the labeled data was .78. Further evaluation studies are desirable to confirm whether PyMAN could be a reliable tool for assisting the surgeon to prevent PTSE during the preoperative planning.

Python bindings for C++ using PyROOT/cppyy: the experience from PyCool in COOL

CERN Multimedia

CERN. Geneva

2016-01-01

The COOL software is used by the ATLAS and LHCb experiments to handle the time variation and versioning of their conditions data, using a variety of different relational database technologies. While the COOL core libraries are written in C++ and are integrated in the experiment C++ frameworks, a package offering Python bindings of the COOL C++ APIs, PyCool, is also provided and has been an essential component of the ATLAS conditions data management toolkit for over 10 years. Almost since the beginning, the implementation of PyCool has been based on ROOT to generate Python bindings for C++, initially using Reflex and PyROOT in ROOT5 and more recently using clang and cppyy in ROOT6. This presentation will describe the PyCool experience with using ROOT to generate Python bindings for C++, throughout the many evolutions of the underlying technology.

Isolation and functional characterization of an ammonium transporter gene, PyAMT1, related to nitrogen assimilation in the marine macroalga Pyropia yezoensis (Rhodophyta).

Science.gov (United States)

Kakinuma, Makoto; Nakamoto, Chika; Kishi, Kazuki; Coury, Daniel A; Amano, Hideomi

2017-07-01

Ammonium and nitrate are the primary nitrogen sources in natural environments, and are essential for growth and development in photosynthetic eukaryotes. In this study, we report on the isolation and characterization of an ammonium transporter gene (PyAMT1) which performs a key function in nitrogen (N) metabolism of Pyropia yezoensis thalli. The predicted length of PyAMT1 was 483 amino acids (AAs). The AA sequence included 11 putative transmembrane domains and showed approximately 33-44% identity to algal and plant AMT1 AA sequences. Functional complementation in an AMT-defective yeast mutant indicated that PyAMT1 mediated ammonium transport across the plasma membrane. Expression analysis showed that the PyAMT1 mRNA level was strongly induced by N-deficiency, and was more highly suppressed by resupply of inorganic-N than organic-N. These results suggest that PyAMT1 plays important roles in the ammonium transport system, and is highly regulated in response to external/internal N-status. Copyright © 2016 Elsevier Ltd. All rights reserved.

The urinary microbiome and its contribution to lower urinary tract symptoms; ICI-RS 2015.

Science.gov (United States)

Drake, Marcus J; Morris, Nicola; Apostolidis, Apostolos; Rahnama'i, Mohammad S; Marchesi, Julian R

2017-04-01

The microbiome is the term used for the symbiotic microbial colonisation of healthy organs. Studies have found bacterial identifiers within voided urine which is apparently sterile on conventional laboratory culture, and accordingly there may be health and disease implications. The International Consultation on Incontinence Research Society (ICI-RS) established a literature review and expert consensus discussion focussed on the increasing awareness of the urinary microbiome, and potential research priorities. The consensus considered the discrepancy between findings of conventional clinical microbiology methods, which generally rely on culture parameters predisposed towards certain "expected" organisms. Discrepancy between selective culture and RNA sequencing to study species-specific 16S ribosomal RNA is increasingly clear, and highlights the possibility that protective or harmful bacteria may be overlooked where microbiological methods are selective. There are now strong signals of the existence of a "core" urinary microbiome for the human urinary tract, particularly emerging with ageing. The consensus reviewed the potential relationship between a patient's microbiome and lower urinary tract dysfunction, whether low-count bacteriuria may be clinically significant and mechanisms which could associate micro-organisms with lower urinary tract symptoms. Key research priorities identified include the need to establish the scope of microbiome across the range of normality and clinical presentations, and gain consensus on testing protocols. Proteomics to study enzymatic and other functions may be necessary, since different bacteria may have overlapping phenotype. Longitudinal studies into risk factors for exposure, cumulative risk, and emergence of disease need to undertaken. Neurourol. Urodynam. 36:850-853, 2017. © 2017 Wiley Periodicals, Inc. © 2017 Wiley Periodicals, Inc.

Mutations in SOX17 are Associated with Congenital Anomalies of the Kidney and the Urinary Tract

Science.gov (United States)

Gimelli, Stefania; Caridi, Gianluca; Beri, Silvana; McCracken, Kyle; Bocciardi, Renata; Zordan, Paola; Dagnino, Monica; Fiorio, Patrizia; Murer, Luisa; Benetti, Elisa; Zuffardi, Orsetta; Giorda, Roberto; Wells, James M; Gimelli, Giorgio; Ghiggeri, Gian Marco

2010-01-01

Congenital anomalies of the kidney and the urinary tract (CAKUT) represent a major source of morbidity and mortality in children. Several factors (PAX, SOX,WNT, RET, GDFN, and others) play critical roles during the differentiation process that leads to the formation of nephron epithelia. We have identified mutations in SOX17, an HMG-box transcription factor and Wnt signaling antagonist, in eight patients with CAKUT (seven vesico-ureteric reflux, one pelvic obstruction). One mutation, c.775T>A (p.Y259N), recurred in six patients. Four cases derived from two small families; renal scars with urinary infection represented the main symptom at presentation in all but two patients. Transfection studies indicated a 5–10-fold increase in the levels of the mutant protein relative to wild-type SOX17 in transfected kidney cells. Moreover we observed a corresponding increase in the ability of SOX17 p.Y259N to inhibit Wnt/β-catenin transcriptional activity, which is known to regulate multiple stages of kidney and urinary tract development. In conclusion, SOX17 p.Y259N mutation is recurrent in patients with CAKUT. Our data shows that this mutation correlates with an inappropriate accumulation of SOX17-p.Y259N protein and inhibition of the β-catenin/Wnt signaling pathway. These data indicate a role of SOX17 in human kidney and urinary tract development and implicate the SOX17–p.Y259N mutation as a causative factor in CAKUT. Hum Mutat 31:1352–1359, 2010. © 2010 Wiley-Liss, Inc. PMID:20960469

Construction of a virtual Mycobacterium tuberculosis consensus genome and its application to data from a next generation sequencer.

Science.gov (United States)

Okumura, Kayo; Kato, Masako; Kirikae, Teruo; Kayano, Mitsunori; Miyoshi-Akiyama, Tohru

2015-03-20

Although Mycobacterium tuberculosis isolates are consisted of several different lineages and the epidemiology analyses are usually assessed relative to a particular reference genome, M. tuberculosis H37Rv, which might introduce some biased results. Those analyses are essentially based genome sequence information of M. tuberculosis and could be performed in sillico in theory, with whole genome sequence (WGS) data available in the databases and obtained by next generation sequencers (NGSs). As an approach to establish higher resolution methods for such analyses, whole genome sequences of the M. tuberculosis complexes (MTBCs) strains available on databases were aligned to construct virtual reference genome sequences called the consensus sequence (CS), and evaluated its feasibility in in sillico epidemiological analyses. The consensus sequence (CS) was successfully constructed and utilized to perform phylogenetic analysis, evaluation of read mapping efficacy, which is crucial for detecting single nucleotide polymorphisms (SNPs), and various MTBC typing methods virtually including spoligotyping, VNTR, Long sequence polymorphism and Beijing typing. SNPs detected based on CS, in comparison with H37Rv, were utilized in concatemer-based phylogenetic analysis to determine their reliability relative to a phylogenetic tree based on whole genome alignment as the gold standard. Statistical comparison of phylogenic trees based on CS with that of H37Rv indicated the former showed always better results that that of later. SNP detection and concatenation with CS was advantageous because the frequency of crucial SNPs distinguishing among strain lineages was higher than those of H37Rv. The number of SNPs detected was lower with the consensus than with the H37Rv sequence, resulting in a significant reduction in computational time. Performance of each virtual typing was satisfactory and accorded with those published when those are available. These results indicated that virtual CS

pyGeno: A Python package for precision medicine and proteogenomics [version 2; referees: 1 approved, 2 approved with reservations

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Tariq Daouda

2016-05-01

Full Text Available pyGeno is a Python package mainly intended for precision medicine applications that revolve around genomics and proteomics. It integrates reference sequences and annotations from Ensembl, genomic polymorphisms from the dbSNP database and data from next-gen sequencing into an easy to use, memory-efficient and fast framework, therefore allowing the user to easily explore subject-specific genomes and proteomes. Compared to a standalone program, pyGeno gives the user access to the complete expressivity of Python, a general programming language. Its range of application therefore encompasses both short scripts and large scale genome-wide studies.

Prediction of Protein Structural Classes for Low-Similarity Sequences Based on Consensus Sequence and Segmented PSSM

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Yunyun Liang

2015-01-01

Full Text Available Prediction of protein structural classes for low-similarity sequences is useful for understanding fold patterns, regulation, functions, and interactions of proteins. It is well known that feature extraction is significant to prediction of protein structural class and it mainly uses protein primary sequence, predicted secondary structure sequence, and position-specific scoring matrix (PSSM. Currently, prediction solely based on the PSSM has played a key role in improving the prediction accuracy. In this paper, we propose a novel method called CSP-SegPseP-SegACP by fusing consensus sequence (CS, segmented PsePSSM, and segmented autocovariance transformation (ACT based on PSSM. Three widely used low-similarity datasets (1189, 25PDB, and 640 are adopted in this paper. Then a 700-dimensional (700D feature vector is constructed and the dimension is decreased to 224D by using principal component analysis (PCA. To verify the performance of our method, rigorous jackknife cross-validation tests are performed on 1189, 25PDB, and 640 datasets. Comparison of our results with the existing PSSM-based methods demonstrates that our method achieves the favorable and competitive performance. This will offer an important complementary to other PSSM-based methods for prediction of protein structural classes for low-similarity sequences.

78 FR 28643 - Program Year (PY) 2013 Workforce Investment Act (WIA) Allotments; PY 2013 Wagner-Peyser Act Final...

Science.gov (United States)

2013-05-15

...This notice announces allotments for PY 2013 for WIA Title I Youth, Adults and Dislocated Worker Activities programs; final allotments for Employment Service (ES) activities under the Wagner- Peyser Act for PY 2013 and Workforce Information Grants allotments for PY 2013. Allotments for the Work Opportunity Tax Credits will be announced separately. WIA allotments for States and the State final allotments for the Wagner-Peyser Act are based on formulas defined in their respective statutes. The WIA allotments for the outlying areas are based on a formula determined by the Secretary of Labor (Secretary). As required by WIA section 182(d), on February 17, 2000, a notice of the discretionary formula for allocating PY 2000 funds for the outlying areas (American Samoa, Guam, Marshall Islands, Micronesia, Northern Marianas, Palau, and the Virgin Islands) was published in the Federal Register at 65 FR 8236 (February 17, 2000) which included both the rationale for the formula and methodology. The formula for PY 2013 is the same as used for PY 2000 and is described in the section on Youth Activities program allotments. Comments are invited on the formula used to allot funds to the outlying areas.

International consensus statement regarding the use of animal models for research on anastomoses in the lower gastrointestinal tract.

Science.gov (United States)

Bosmans, Joanna W A M; Moossdorff, Martine; Al-Taher, Mahdi; van Beek, Lotte; Derikx, Joep P M; Bouvy, Nicole D

2016-05-01

This project aimed to reach consensus on the most appropriate animal models and outcome measures in research on anastomoses in the lower gastrointestinal tract (GIT). The physiology of anastomotic healing remains an important research topic in gastrointestinal surgery. Recent results from experimental studies are limited with regard to comparability and clinical translation. PubMed and EMBASE were searched for experimental studies investigating anastomotic healing in the lower GIT published between January 1, 2000 and December 31, 2014 to assess currently used models. All corresponding authors were invited for a Delphi-based analysis that consisted of two online survey rounds followed by a final online recommendation survey to reach consensus on the discussed topics. Two hundred seventy-seven original articles were retrieved and 167 articles were included in the systematic review. Mice, rats, rabbits, pigs, and dogs are currently being used as animal models, with a large variety in surgical techniques and outcome measures. Forty-four corresponding authors participated in the Delphi analysis. In the first two rounds, 39/44 and 35/39 participants completed the survey. In the final meeting, 35 experts reached consensus on 76/122 items in six categories. Mouse, rat, and pig are considered appropriate animal models; rabbit and dog should be abandoned in research regarding bowel anastomoses. ARRIVE guidelines should be followed more strictly. Consensus was reached on several recommendations for the use of animal models and outcome measurements in research on anastomoses of the lower GIT. Future research should take these suggestions into account to facilitate comparison and clinical translation of results.

PyCSP - Communicating Sequential Processes for Python

DEFF Research Database (Denmark)

Vinter, Brian; Bjørndalen, John Markus; Anshus, Otto Johan

CSP presently supports the core CSP abstractions. We introduce the PyCSP library, its implementation, a few performance benchmarks, and show example code using PyCSP. An early prototype of PyCSP has been used in this year's Extreme Multiprogramming Class at the CS department, university of Copenhagen......The Python programming language is effective for rapidly specifying programs and experimenting with them. It is increasingly being used in computational sciences, and in teaching computer science. CSP is effective for describing concurrency. It has become especially relevant with the emergence...... of commodity multi-core architectures. We are interested in exploring how a combination of Python and CSP can benefit both the computational sciences and the hands-on teaching of distributed and parallel computing in computer science. To make this possible, we have developed PyCSP, a CSP library for Python. Py...

PyXNAT: XNAT in Python

Directory of Open Access Journals (Sweden)

Yannick eSchwartz

2012-05-01

Full Text Available As neuroimaging databases grow in size and complexity, the time researchers spend investigating and managing the data increases to the expense of data analysis. As a result, investigators rely more and more heavily on scripting using high-level languages to automate data management and processing tasks. For this, a structured and programatic access to the data store is necessary. Web services are a first step toward this goal. They however lack in functionality and ease of use because they provide only low level interfaces to databases. We introduce here {PyXNAT}, a Python module that interacts with The Extensible Neuroimaging Archive Toolkit (XNAT through native Python calls across multiple operating systems. The choice of Python enables {PyXNAT} to expose the XNAT Web Services and unify their features with a higher level and more expressive language. {PyXNAT} provides XNAT users direct access to all the scientific packages in Python. Finally {PyXNAT} aims to be efficient and easy to use, both as a backend library to build XNAT clients and as an alternative frontend from the command line.

PyXNAT: XNAT in Python.

Science.gov (United States)

Schwartz, Yannick; Barbot, Alexis; Thyreau, Benjamin; Frouin, Vincent; Varoquaux, Gaël; Siram, Aditya; Marcus, Daniel S; Poline, Jean-Baptiste

2012-01-01

As neuroimaging databases grow in size and complexity, the time researchers spend investigating and managing the data increases to the expense of data analysis. As a result, investigators rely more and more heavily on scripting using high-level languages to automate data management and processing tasks. For this, a structured and programmatic access to the data store is necessary. Web services are a first step toward this goal. They however lack in functionality and ease of use because they provide only low-level interfaces to databases. We introduce here PyXNAT, a Python module that interacts with The Extensible Neuroimaging Archive Toolkit (XNAT) through native Python calls across multiple operating systems. The choice of Python enables PyXNAT to expose the XNAT Web Services and unify their features with a higher level and more expressive language. PyXNAT provides XNAT users direct access to all the scientific packages in Python. Finally PyXNAT aims to be efficient and easy to use, both as a back-end library to build XNAT clients and as an alternative front-end from the command line.

AtomPy: An Open Atomic Data Curation Environment for Astrophysical Applications

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Claudio Mendoza

2014-05-01

Full Text Available We present a cloud-computing environment, referred to as AtomPy, based on Google-Drive Sheets and Pandas (Python Data Analysis Library DataFrames to promote community-driven curation of atomic data for astrophysical applications, a stage beyond database development. The atomic model for each ionic species is contained in a multi-sheet workbook, tabulating representative sets of energy levels, A-values and electron impact effective collision strengths from different sources. The relevant issues that AtomPy intends to address are: (i data quality by allowing open access to both data producers and users; (ii comparisons of different datasets to facilitate accuracy assessments; (iii downloading to local data structures (i.e., Pandas DataFrames for further manipulation and analysis by prospective users; and (iv data preservation by avoiding the discard of outdated sets. Data processing workflows are implemented by means of IPython Notebooks, and collaborative software developments are encouraged and managed within the GitHub social network. The facilities of AtomPy are illustrated with the critical assessment of the transition probabilities for ions in the hydrogen and helium isoelectronic sequences with atomic number Z ≤ 10.

PyBioMed: a python library for various molecular representations of chemicals, proteins and DNAs and their interactions.

Science.gov (United States)

Dong, Jie; Yao, Zhi-Jiang; Zhang, Lin; Luo, Feijun; Lin, Qinlu; Lu, Ai-Ping; Chen, Alex F; Cao, Dong-Sheng

2018-03-20

With the increasing development of biotechnology and informatics technology, publicly available data in chemistry and biology are undergoing explosive growth. Such wealthy information in these data needs to be extracted and transformed to useful knowledge by various data mining methods. Considering the amazing rate at which data are accumulated in chemistry and biology fields, new tools that process and interpret large and complex interaction data are increasingly important. So far, there are no suitable toolkits that can effectively link the chemical and biological space in view of molecular representation. To further explore these complex data, an integrated toolkit for various molecular representation is urgently needed which could be easily integrated with data mining algorithms to start a full data analysis pipeline. Herein, the python library PyBioMed is presented, which comprises functionalities for online download for various molecular objects by providing different IDs, the pretreatment of molecular structures, the computation of various molecular descriptors for chemicals, proteins, DNAs and their interactions. PyBioMed is a feature-rich and highly customized python library used for the characterization of various complex chemical and biological molecules and interaction samples. The current version of PyBioMed could calculate 775 chemical descriptors and 19 kinds of chemical fingerprints, 9920 protein descriptors based on protein sequences, more than 6000 DNA descriptors from nucleotide sequences, and interaction descriptors from pairwise samples using three different combining strategies. Several examples and five real-life applications were provided to clearly guide the users how to use PyBioMed as an integral part of data analysis projects. By using PyBioMed, users are able to start a full pipelining from getting molecular data, pretreating molecules, molecular representation to constructing machine learning models conveniently. PyBioMed provides

Magnetic resonance urography: application in urinary tract obstruction

International Nuclear Information System (INIS)

Martin, J.; Malet, A.; Rue, M.; Villajos, M.; Martin, C.; Garcia, D.; Prats, J.

1999-01-01

To compare magnetic resonance urography (MRU) and conventional intravenous urography (IVU) in the assessment of the upper urinary tract in patients with obstructive uropathy. Twenty-three patients suspected of having urinary tract obstruction were examined by IVU and MRU, MRU imaging was performed with a 1.0 Tesla multicoil unit. The images were obtained with two MR sequences: a) half-Fourier single shot turbo spin echo (HASTE), and b) highly T2-weighted turbo spin echo (TSE) based on fast acquisition with the relaxation and enhancement (RARE) method. The images were examined independently by four radiologists. Two radiologists reviewed the IVU images by consensus and two reviewed the MRU images by consensus. The incidencences of dilatation and of stricture were calculated and the McNemar test was used to compare the two techniques. The mean duration of MRU was 11 minutes (range: 7 to 25 minutes), while the mean duration of IVU was 363 minutes (range: 45 to 2,160 minutes). IVU took more than 150 minutes to complete in over 50% of the patients. Twenty.one patients presented dilatation of the pyelocaliceal system. MRU disclosed the urinary tract dilatation in all 21 cases, while IVU detected it in 15 (65%: p=0.03). The causes of obstruction were neoplasm (n=9), calculi (n=6) and extrinsic stricture (n=6). MRU is much more reliable and rapid in the detection of dilatation and the site of obstruction in patients with obstructive uropathy, and could be used as an alternative to IVU in certain cases. (Author) 13 refs

PySE: Software for extracting sources from radio images

Science.gov (United States)

Carbone, D.; Garsden, H.; Spreeuw, H.; Swinbank, J. D.; van der Horst, A. J.; Rowlinson, A.; Broderick, J. W.; Rol, E.; Law, C.; Molenaar, G.; Wijers, R. A. M. J.

2018-04-01

PySE is a Python software package for finding and measuring sources in radio telescope images. The software was designed to detect sources in the LOFAR telescope images, but can be used with images from other radio telescopes as well. We introduce the LOFAR Telescope, the context within which PySE was developed, the design of PySE, and describe how it is used. Detailed experiments on the validation and testing of PySE are then presented, along with results of performance testing. We discuss some of the current issues with the algorithms implemented in PySE and their interaction with LOFAR images, concluding with the current status of PySE and its future development.

pyXSIM: Synthetic X-ray observations generator

Science.gov (United States)

ZuHone, John A.; Hallman, Eric. J.

2016-08-01

pyXSIM simulates X-ray observations from astrophysical sources. X-rays probe the high-energy universe, from hot galaxy clusters to compact objects such as neutron stars and black holes and many interesting sources in between. pyXSIM generates synthetic X-ray observations of these sources from a wide variety of models, whether from grid-based simulation codes such as FLASH (ascl:1010.082), Enzo (ascl:1010.072), and Athena (ascl:1010.014), to particle-based codes such as Gadget (ascl:0003.001) and AREPO, and even from datasets that have been created “by hand”, such as from NumPy arrays. pyXSIM can also manipulate the synthetic observations it produces in various ways and export the simulated X-ray events to other software packages to simulate the end products of specific X-ray observatories. pyXSIM is an implementation of the PHOX (ascl:1112.004) algorithm and was initially the photon_simulator analysis module in yt (ascl:1011.022); it is dependent on yt.

Accurate RNA consensus sequencing for high-fidelity detection of transcriptional mutagenesis-induced epimutations.

Science.gov (United States)

Reid-Bayliss, Kate S; Loeb, Lawrence A

2017-08-29

Transcriptional mutagenesis (TM) due to misincorporation during RNA transcription can result in mutant RNAs, or epimutations, that generate proteins with altered properties. TM has long been hypothesized to play a role in aging, cancer, and viral and bacterial evolution. However, inadequate methodologies have limited progress in elucidating a causal association. We present a high-throughput, highly accurate RNA sequencing method to measure epimutations with single-molecule sensitivity. Accurate RNA consensus sequencing (ARC-seq) uniquely combines RNA barcoding and generation of multiple cDNA copies per RNA molecule to eliminate errors introduced during cDNA synthesis, PCR, and sequencing. The stringency of ARC-seq can be scaled to accommodate the quality of input RNAs. We apply ARC-seq to directly assess transcriptome-wide epimutations resulting from RNA polymerase mutants and oxidative stress.

Molecular design of sequence specific DNA alkylating agents.

Science.gov (United States)

Minoshima, Masafumi; Bando, Toshikazu; Shinohara, Ken-ichi; Sugiyama, Hiroshi

2009-01-01

Sequence-specific DNA alkylating agents have great interest for novel approach to cancer chemotherapy. We designed the conjugates between pyrrole (Py)-imidazole (Im) polyamides and DNA alkylating chlorambucil moiety possessing at different positions. The sequence-specific DNA alkylation by conjugates was investigated by using high-resolution denaturing polyacrylamide gel electrophoresis (PAGE). The results showed that polyamide chlorambucil conjugates alkylate DNA at flanking adenines in recognition sequences of Py-Im polyamides, however, the reactivities and alkylation sites were influenced by the positions of conjugation. In addition, we synthesized conjugate between Py-Im polyamide and another alkylating agent, 1-(chloromethyl)-5-hydroxy-1,2-dihydro-3H-benz[e]indole (seco-CBI). DNA alkylation reactivies by both alkylating polyamides were almost comparable. In contrast, cytotoxicities against cell lines differed greatly. These comparative studies would promote development of appropriate sequence-specific DNA alkylating polyamides against specific cancer cells.

SunPy: Python for Solar Physics

Science.gov (United States)

Bobra, M.; Inglis, A. R.; Mumford, S.; Christe, S.; Freij, N.; Hewett, R.; Ireland, J.; Martinez Oliveros, J. C.; Reardon, K.; Savage, S. L.; Shih, A. Y.; Pérez-Suárez, D.

2017-12-01

SunPy is a community-developed open-source software library for solar physics. It is written in Python, a free, cross-platform, general-purpose, high-level programming language which is being increasingly adopted throughout the scientific community. SunPy aims to provide the software for obtaining and analyzing solar and heliospheric data. This poster introduces a new major release, SunPy version 0.8. The first major new feature introduced is Fido, the new primary interface to download data. It provides a consistent and powerful search interface to all major data providers including the VSO and the JSOC, as well as individual data sources such as GOES XRS time series. It is also easy to add new data sources as they become available, i.e. DKIST. The second major new feature is the SunPy coordinate framework. This provides a powerful way of representing coordinates, allowing simple and intuitive conversion between coordinate systems and viewpoints of different instruments (i.e., Solar Orbiter and the Parker Solar Probe), including transformation to astrophysical frames like ICRS. Other new features including new timeseries capabilities with better support for concatenation and metadata, updated documentation and example gallery. SunPy is distributed through pip and conda and all of its code is publicly available (sunpy.org).

Defining a conformational consensus motif in cotransin-sensitive signal sequences: a proteomic and site-directed mutagenesis study.

Directory of Open Access Journals (Sweden)

Wolfgang Klein

Full Text Available The cyclodepsipeptide cotransin was described to inhibit the biosynthesis of a small subset of proteins by a signal sequence-discriminatory mechanism at the Sec61 protein-conducting channel. However, it was not clear how selective cotransin is, i.e. how many proteins are sensitive. Moreover, a consensus motif in signal sequences mediating cotransin sensitivity has yet not been described. To address these questions, we performed a proteomic study using cotransin-treated human hepatocellular carcinoma cells and the stable isotope labelling by amino acids in cell culture technique in combination with quantitative mass spectrometry. We used a saturating concentration of cotransin (30 micromolar to identify also less-sensitive proteins and to discriminate the latter from completely resistant proteins. We found that the biosynthesis of almost all secreted proteins was cotransin-sensitive under these conditions. In contrast, biosynthesis of the majority of the integral membrane proteins was cotransin-resistant. Cotransin sensitivity of signal sequences was neither related to their length nor to their hydrophobicity. Instead, in the case of signal anchor sequences, we identified for the first time a conformational consensus motif mediating cotransin sensitivity.

Defining a Conformational Consensus Motif in Cotransin-Sensitive Signal Sequences: A Proteomic and Site-Directed Mutagenesis Study

Science.gov (United States)

Klein, Wolfgang; Westendorf, Carolin; Schmidt, Antje; Conill-Cortés, Mercè; Rutz, Claudia; Blohs, Marcus; Beyermann, Michael; Protze, Jonas; Krause, Gerd; Krause, Eberhard; Schülein, Ralf

2015-01-01

The cyclodepsipeptide cotransin was described to inhibit the biosynthesis of a small subset of proteins by a signal sequence-discriminatory mechanism at the Sec61 protein-conducting channel. However, it was not clear how selective cotransin is, i.e. how many proteins are sensitive. Moreover, a consensus motif in signal sequences mediating cotransin sensitivity has yet not been described. To address these questions, we performed a proteomic study using cotransin-treated human hepatocellular carcinoma cells and the stable isotope labelling by amino acids in cell culture technique in combination with quantitative mass spectrometry. We used a saturating concentration of cotransin (30 micromolar) to identify also less-sensitive proteins and to discriminate the latter from completely resistant proteins. We found that the biosynthesis of almost all secreted proteins was cotransin-sensitive under these conditions. In contrast, biosynthesis of the majority of the integral membrane proteins was cotransin-resistant. Cotransin sensitivity of signal sequences was neither related to their length nor to their hydrophobicity. Instead, in the case of signal anchor sequences, we identified for the first time a conformational consensus motif mediating cotransin sensitivity. PMID:25806945

Genetic stability of the VHSV consensus sequence of G-gene in diagnostic samples from an acute outbreak

DEFF Research Database (Denmark)

Einer-Jensen, Katja; Ahrens, Peter; Lorenzen, Niels

2006-01-01

The negative stranded RNA virus viral haemorrhagic septicaemia virus (VHSV) is an important disease-causing agent in aquacultured fish and internationally harmonized diagnostic procedures are continuously under development. The present study concerns the suitability of genotyping by sequencing...... collected tissue material as well as from inoculated cell culture. No nucleotide substitutions where identified when aligning the obtained sequence data for the two sample types. The presented data indicate that the overall consensus sequence of the virus outbreak was stable during the survey...

PyCoTools: A Python Toolbox for COPASI.

Science.gov (United States)

Welsh, Ciaran M; Fullard, Nicola; Proctor, Carole J; Martinez-Guimera, Alvaro; Isfort, Robert J; Bascom, Charles C; Tasseff, Ryan; Przyborski, Stefan A; Shanley, Daryl P

2018-05-22

COPASI is an open source software package for constructing, simulating and analysing dynamic models of biochemical networks. COPASI is primarily intended to be used with a graphical user interface but often it is desirable to be able to access COPASI features programmatically, with a high level interface. PyCoTools is a Python package aimed at providing a high level interface to COPASI tasks with an emphasis on model calibration. PyCoTools enables the construction of COPASI models and the execution of a subset of COPASI tasks including time courses, parameter scans and parameter estimations. Additional 'composite' tasks which use COPASI tasks as building blocks are available for increasing parameter estimation throughput, performing identifiability analysis and performing model selection. PyCoTools supports exploratory data analysis on parameter estimation data to assist with troubleshooting model calibrations. We demonstrate PyCoTools by posing a model selection problem designed to show case PyCoTools within a realistic scenario. The aim of the model selection problem is to test the feasibility of three alternative hypotheses in explaining experimental data derived from neonatal dermal fibroblasts in response to TGF-β over time. PyCoTools is used to critically analyse the parameter estimations and propose strategies for model improvement. PyCoTools can be downloaded from the Python Package Index (PyPI) using the command 'pip install pycotools' or directly from GitHub (https://github.com/CiaranWelsh/pycotools). Documentation at http://pycotools.readthedocs.io. Supplementary data are available at Bioinformatics.

Experiences using SciPy for computer vision research

Energy Technology Data Exchange (ETDEWEB)

Eads, Damian R [Los Alamos National Laboratory; Rosten, Edward J [Los Alamos National Laboratory

2008-01-01

SciPy is an effective tool suite for prototyping new algorithms. We share some of our experiences using it for the first time to support our research in object detection. SciPy makes it easy to integrate C code, which is essential when algorithms operating on large data sets cannot be vectorized. The universality of Python, the language in which SciPy was written, gives the researcher access to a broader set of non-numerical libraries to support GUI development, interface with databases, manipulate graph structures. render 3D graphics, unpack binary files, etc. Python's extensive support for operator overloading makes SciPy's syntax as succinct as its competitors, MATLAB, Octave, and R. More profoundly, we found it easy to rework research code written with SciPy into a production application, deployable on numerous platforms.

Presence of a consensus DNA motif at nearby DNA sequence of the mutation susceptible CG nucleotides.

Science.gov (United States)

Chowdhury, Kaushik; Kumar, Suresh; Sharma, Tanu; Sharma, Ankit; Bhagat, Meenakshi; Kamai, Asangla; Ford, Bridget M; Asthana, Shailendra; Mandal, Chandi C

2018-01-10

Complexity in tissues affected by cancer arises from somatic mutations and epigenetic modifications in the genome. The mutation susceptible hotspots present within the genome indicate a non-random nature and/or a position specific selection of mutation. An association exists between the occurrence of mutations and epigenetic DNA methylation. This study is primarily aimed at determining mutation status, and identifying a signature for predicting mutation prone zones of tumor suppressor (TS) genes. Nearby sequences from the top five positions having a higher mutation frequency in each gene of 42 TS genes were selected from a cosmic database and were considered as mutation prone zones. The conserved motifs present in the mutation prone DNA fragments were identified. Molecular docking studies were done to determine putative interactions between the identified conserved motifs and enzyme methyltransferase DNMT1. Collective analysis of 42 TS genes found GC as the most commonly replaced and AT as the most commonly formed residues after mutation. Analysis of the top 5 mutated positions of each gene (210 DNA segments for 42 TS genes) identified that CG nucleotides of the amino acid codons (e.g., Arginine) are most susceptible to mutation, and found a consensus DNA "T/AGC/GAGGA/TG" sequence present in these mutation prone DNA segments. Similar to TS genes, analysis of 54 oncogenes not only found CG nucleotides of the amino acid Arg as the most susceptible to mutation, but also identified the presence of similar consensus DNA motifs in the mutation prone DNA fragments (270 DNA segments for 54 oncogenes) of oncogenes. Docking studies depicted that, upon binding of DNMT1 methylates to this consensus DNA motif (C residues of CpG islands), mutation was likely to occur. Thus, this study proposes that DNMT1 mediated methylation in chromosomal DNA may decrease if a foreign DNA segment containing this consensus sequence along with CG nucleotides is exogenously introduced to dividing

DNA bending in solution: NMR studies on the structural roles of A/T tracts and the sequences at the junction

Energy Technology Data Exchange (ETDEWEB)

Gupta, G. (Los Alamos National Lab., NM (USA)); Umemoto, K.; Sarma, M.H.; Sarma, R.H. (State Univ. of New York, Albany (USA))

1989-01-01

A summary of ID/2D-NMR studies on d(GA{sub 4}T{sub 4}C){sub 2}, and (GA{sub 4}U{sub 4}C){sub 2}, and d(GT{sub 4}A{sub 4}C){sub 2} in solution is reported in this article. Results of these studies indicate one important structural property of A {center dot} T pairs, i.e., A {center dot} T pairs are propeller twisted, which results in a series of interstrand bifurcated H-bonds inside the A/T tract. The structural similarity of d(GA{sub 4}T{sub 4}C){sub 2} and d(GA{sub 4}U{sub 4}C){sub 2} suggests that the methyl group of thymine may be of little consequence as far as this structural peculiarity of the A/T tract is concerned. Comparison of d(GA{sub 4}T{sub 4}C){sub 2} (i.e., junction B-DNA model) and d(GT{sub 4}A{sub 4}C){sub 2} (i.e., straight B-DNA model) structures shows that not only the structural peculiarity of the A/T tract but also the sequence that joins two neighboring A/T tracts play crucial roles in DNA bending. In other words, when two A/T tracts are joined at the A {yields} T sequence, a junction is created, whereas when two A/T tracts are connected at the T {yields} A sequence, no discontinuity is observed.

web2py Application Development Cookbook

CERN Document Server

Mulone, Pablo Martin; Gordon, Richard

2012-01-01

This is a cookbook and you may read the chapters in any order. The recipes need not be read sequentially. There are a good amount of code examples and relevant screenshots to ease learning pains. The target audience are Python developers with basic knowledge of web2py who want to gain further knowledge of web2py

DendroPy: a Python library for phylogenetic computing.

Science.gov (United States)

Sukumaran, Jeet; Holder, Mark T

2010-06-15

DendroPy is a cross-platform library for the Python programming language that provides for object-oriented reading, writing, simulation and manipulation of phylogenetic data, with an emphasis on phylogenetic tree operations. DendroPy uses a splits-hash mapping to perform rapid calculations of tree distances, similarities and shape under various metrics. It contains rich simulation routines to generate trees under a number of different phylogenetic and coalescent models. DendroPy's data simulation and manipulation facilities, in conjunction with its support of a broad range of phylogenetic data formats (NEXUS, Newick, PHYLIP, FASTA, NeXML, etc.), allow it to serve a useful role in various phyloinformatics and phylogeographic pipelines. The stable release of the library is available for download and automated installation through the Python Package Index site (http://pypi.python.org/pypi/DendroPy), while the active development source code repository is available to the public from GitHub (http://github.com/jeetsukumaran/DendroPy).

Magnetic resonance urography in pediatrics: utilization of ultrafast single-shot spin echo sequences

International Nuclear Information System (INIS)

Martin, C.; Martin, J.; Duran, C.; Rigol, S.; Rojo, J. C.

1999-01-01

To determine the value of magnetic resonance urography (MRU) using ultrafast single-shot (SS) rapid acquisition with relaxation enhancement (RARE) and half-Fourier (HF) SS-RARE (SS-HF-RARE or HASTE) in the evaluation of congenital urinary tract anomalies in pediatric patients, and their possible application as alternatives to intravenous urography (IVU). Eighteen children (11 boys and 7 girls) aged 2 months to 15 years (mean: 5 years) with a total of 19 congenital urinary tract anomalies were studies by MU using SS-RARE and HASTE sequences in a 1 Tesla scanner. All the patients had previously been studies by ultrasound (US) and IVU. Twelve patients required anesthesia. The images were acquired by means of a HASTE sequence with multisection technique (TR, infinite; TE e f, 87 msec; echo train, 128; interval between echoes, 10.9 msec; total acquisition time, 13 sections/12 seconds), and SS-RARE (TR, infinite; TE e f, 1.100 msec; echo train, 240, and acquisition time, 7 seconds). Four radiologists evaluated the images independently; two who reviewed the IV images in consensus and two who reviewed the MRU images in consensus. The images were evaluated to assess the dilatation of the urinary tract and their utility in detecting the level and cause of the obstruction. MRU images revealed the urinary tract dilation, the level of the obstruction and the type of anomaly in 18 patients (100%), while IVU provided this information in only 10 [ sensitivity, 53%, 95% confidence interval (29%, 76%)]. The mean time required for MRU was 20 minutes (range: 7 to 30 minutes), while that of IVU was 1,242 minutes (range: 45 to 1,440 minutes). MRU using ultrafast single-short spin echo sequences is a rapid and effective technique that permits and excellent evaluation of congenital urinary tract anomalies in pediatric patients and does not require the administration of contrast media or ionizing radiation. (Author) 10 refs

Creating Physics Aware Games using PyGame and PyODE

Directory of Open Access Journals (Sweden)

2010-09-01

Full Text Available This paper is a tutorial on how to use a popular physics engine and tie it up to a simple 2D game. It is structured as a tutorial for creating a simple game that uses the engine and a graphics library. The graphics library being used will be PyGame (which are Python bindings for the popular SDL library originally developed by Loki Entertainment Software and the physics engine being used will be PyODE (which are Python bindings for the Open Dynamics Engine. A few toy programs will be written and discussed to introduce the components and the bulk of the paper will be the development of a simple game. The game which will be developed is a clone of “The incredible machine” (which is a famous game  published by Sierra Entertainment in 1992.

Synthesis and DNA binding properties of 1-(3-aminopropyl)-imidazole-containing triamide f-Im*PyIm: a novel diamino polyamide designed to target 5'-ACGCGT-3'.

Science.gov (United States)

Satam, Vijay; Babu, Balaji; Porte, Alexander; Savagian, Mia; Lee, Megan; Smeltzer, Thomas; Liu, Yang; Ramos, Joseph; Wilson, W David; Lin, Shicai; Kiakos, Kostantinos; Hartley, John A; Lee, Moses

2012-09-15

A novel diamino/dicationic polyamide f-Im(*)PyIm (5) that contains an orthogonally positioned aminopropyl chain on an imidazole (Im(*)) moiety was designed to target 5'-ACGCGT-3'. The DNA binding properties of the diamino polyamide 5, determined by CD, ΔT(M), DNase I footprinting, SPR, and ITC studies, were compared with those of its monoamino/monocationic counterpart f-ImPyIm (1) and its diamino/dicationic isomer f-ImPy(*)Im (2), which has the aminopropyl group attached to the central pyrrole unit (Py(*)). The results gave evidence for the minor groove binding and selectivity of polyamide 5 for the cognate sequence 5'-ACGCGT-3', and with strong affinity (K(eq)=2.3×10(7) M(-1)). However, the binding affinities varied according to the order: f-ImPy(*)Im (2)>f-ImPyIm (1)≥f-Im(*)PyIm (5) confirming that the second amino group can improve affinity, but its position within the polyamide can affect affinity. Copyright © 2012 Elsevier Ltd. All rights reserved.

SpiceyPy, a Python Wrapper for SPICE

Science.gov (United States)

Annex, A.

2017-06-01

SpiceyPy is an open source Python wrapper for the NAIF SPICE toolkit. It is available for macOS, Linux, and Windows platforms and for Python versions 2.7.x and 3.x as well as Anaconda. SpiceyPy can be installed by running: “pip install spiceypy.”

PyPDB: a Python API for the Protein Data Bank.

Science.gov (United States)

Gilpin, William

2016-01-01

We have created a Python programming interface for the RCSB Protein Data Bank (PDB) that allows search and data retrieval for a wide range of result types, including BLAST and sequence motif queries. The API relies on the existing XML-based API and operates by creating custom XML requests from native Python types, allowing extensibility and straightforward modification. The package has the ability to perform many types of advanced search of the PDB that are otherwise only available through the PDB website. PyPDB is implemented exclusively in Python 3 using standard libraries for maximal compatibility. The most up-to-date version, including iPython notebooks containing usage tutorials, is available free-of-charge under an open-source MIT license via GitHub at https://github.com/williamgilpin/pypdb, and the full API reference is at http://williamgilpin.github.io/pypdb_docs/html/. The latest stable release is also available on PyPI. wgilpin@stanford.edu. © The Author 2015. Published by Oxford University Press. All rights reserved. For Permissions, please e-mail: journals.permissions@oup.com.

Genome Sequences of Shewanella baltica and Shewanella morhuae Strains Isolated from the Gastrointestinal Tract of Freshwater Fish.

Science.gov (United States)

Castillo, Daniel; Gram, Lone; Dailey, Frank E

2018-06-21

We present here the genome sequences of Shewanella baltica strain CW2 and Shewanella morhuae strain CW7, isolated from the gastrointestinal tract of Salvelinus namaycush (lean lake trout) and Coregonus clupeaformis (whitefish), respectively. These genome sequences provide insights into the niche adaptation of these specific species in freshwater systems. Copyright © 2018 Castillo et al.

Vaporization of GaI3Py adduct

International Nuclear Information System (INIS)

Timoshkina, A.Yu.; Grigor'ev, A.A.; Suvorov, A.V.

1995-01-01

Processes of GaI 3 Py complex vaporization have been studied by mass-spectrometric, tensimetric and calorimetric methods. It is shown that adduct transformation into vapour is accompanied by its thermal dissociation. Thermodynamic characteristics of evaporation and dissociation of GaI 3 Py complex have been obtained. 14 refs., 2 figs., 6 tabs

pyIAST: Ideal adsorbed solution theory (IAST) Python package

Science.gov (United States)

Simon, Cory M.; Smit, Berend; Haranczyk, Maciej

2016-03-01

Ideal adsorbed solution theory (IAST) is a widely-used thermodynamic framework to readily predict mixed-gas adsorption isotherms from a set of pure-component adsorption isotherms. We present an open-source, user-friendly Python package, pyIAST, to perform IAST calculations for an arbitrary number of components. pyIAST supports several common analytical models to characterize the pure-component isotherms from experimental or simulated data. Alternatively, pyIAST can use numerical quadrature to compute the spreading pressure for IAST calculations by interpolating the pure-component isotherm data. pyIAST can also perform reverse IAST calculations, where one seeks the required gas phase composition to yield a desired adsorbed phase composition.

Py4Syn: Python for synchrotrons.

Science.gov (United States)

Slepicka, H H; Canova, H F; Beniz, D B; Piton, J R

2015-09-01

In this report, Py4Syn, an open-source Python-based library for data acquisition, device manipulation, scan routines and other helper functions, is presented. Driven by easy-to-use and scalability ideals, Py4Syn offers control system agnostic solution and high customization level for scans and data output, covering distinct techniques and facilities. Here, most of the library functionalities are described, examples of use are shown and ideas for future implementations are presented.

Optimizing Python-based ROOT I/O with PyPy's Tracing JIT

CERN Multimedia

CERN. Geneva

2012-01-01

The Python programming language allows objects and classes to respond dynamically to the execution environment. Most of this, however, is made possible through language hooks which by definition can not be optimized and thus tend to be slow. The PyPy implementation of Python includes a tracing just in time compiler (JIT), which allows similar dynamic responses but at the interpreter-, rather than the application-level. Therefore, it is possible to fully remove the hooks, leaving only the dynamic response, in the optimization stage for hot loops, if the types of interest are opened up to the JIT. A general opening up of types to the JIT, based on reflection information, has already been developed (cppyy). The work described in this paper takes it one step further by customizing access to ROOT I/O to the JIT, allowing for automatic selective reading, judicious caching, and buffer tuning.

PyParse: a semiautomated system for scoring spoken recall data.

Science.gov (United States)

Solway, Alec; Geller, Aaron S; Sederberg, Per B; Kahana, Michael J

2010-02-01

Studies of human memory often generate data on the sequence and timing of recalled items, but scoring such data using conventional methods is difficult or impossible. We describe a Python-based semiautomated system that greatly simplifies this task. This software, called PyParse, can easily be used in conjunction with many common experiment authoring systems. Scored data is output in a simple ASCII format and can be accessed with the programming language of choice, allowing for the identification of features such as correct responses, prior-list intrusions, extra-list intrusions, and repetitions.

PyTrilinos: Recent Advances in the Python Interface to Trilinos

Directory of Open Access Journals (Sweden)

William F. Spotz

2012-01-01

Full Text Available PyTrilinos is a set of Python interfaces to compiled Trilinos packages. This collection supports serial and parallel dense linear algebra, serial and parallel sparse linear algebra, direct and iterative linear solution techniques, algebraic and multilevel preconditioners, nonlinear solvers and continuation algorithms, eigensolvers and partitioning algorithms. Also included are a variety of related utility functions and classes, including distributed I/O, coloring algorithms and matrix generation. PyTrilinos vector objects are compatible with the popular NumPy Python package. As a Python front end to compiled libraries, PyTrilinos takes advantage of the flexibility and ease of use of Python, and the efficiency of the underlying C++, C and Fortran numerical kernels. This paper covers recent, previously unpublished advances in the PyTrilinos package.

First full-length genome sequence of the polerovirus luffa aphid-borne yellows virus (LABYV) reveals the presence of at least two consensus sequences in an isolate from Thailand.

Science.gov (United States)

Knierim, Dennis; Maiss, Edgar; Kenyon, Lawrence; Winter, Stephan; Menzel, Wulf

2015-10-01

Luffa aphid-borne yellows virus (LABYV) was proposed as the name for a previously undescribed polerovirus based on partial genome sequences obtained from samples of cucurbit plants collected in Thailand between 2008 and 2013. In this study, we determined the first full-length genome sequence of LABYV. Based on phylogenetic analysis and genome properties, it is clear that this virus represents a distinct species in the genus Polerovirus. Analysis of sequences from sample TH24, which was collected in 2010 from a luffa plant in Thailand, reveals the presence of two different full-length genome consensus sequences.

Identification of Phosphorylation Consensus Sequences and Endogenous Neuronal Substrates of the Psychiatric Risk Kinase TNIK.

Science.gov (United States)

Wang, Qi; Amato, Stephen P; Rubitski, David M; Hayward, Matthew M; Kormos, Bethany L; Verhoest, Patrick R; Xu, Lan; Brandon, Nicholas J; Ehlers, Michael D

2016-02-01

Traf2- and Nck-interacting kinase (TNIK) is a serine/threonine kinase highly expressed in the brain and enriched in the postsynaptic density of glutamatergic synapses in the mammalian brain. Accumulating genetic evidence and functional data have implicated TNIK as a risk factor for psychiatric disorders. However, the endogenous substrates of TNIK in neurons are unknown. Here, we describe a novel selective small molecule inhibitor of the TNIK kinase family. Using this inhibitor, we report the identification of endogenous neuronal TNIK substrates by immunoprecipitation with a phosphomotif antibody followed by mass spectrometry. Phosphorylation consensus sequences were defined by phosphopeptide sequence analysis. Among the identified substrates were members of the delta-catenin family including p120-catenin, δ-catenin, and armadillo repeat gene deleted in velo-cardio-facial syndrome (ARVCF), each of which is linked to psychiatric or neurologic disorders. Using p120-catenin as a representative substrate, we show TNIK-induced p120-catenin phosphorylation in cells requires intact kinase activity and phosphorylation of TNIK at T181 and T187 in the activation loop. Addition of the small molecule TNIK inhibitor or knocking down TNIK by two shRNAs reduced endogenous p120-catenin phosphorylation in cells. Together, using a TNIK inhibitor and phosphomotif antibody, we identify endogenous substrates of TNIK in neurons, define consensus sequences for TNIK, and suggest signaling pathways by which TNIK influences synaptic development and function linked to psychiatric and neurologic disorders. Copyright © 2016 by The American Society for Pharmacology and Experimental Therapeutics.

GPU-powered model analysis with PySB/cupSODA.

Science.gov (United States)

Harris, Leonard A; Nobile, Marco S; Pino, James C; Lubbock, Alexander L R; Besozzi, Daniela; Mauri, Giancarlo; Cazzaniga, Paolo; Lopez, Carlos F

2017-11-01

A major barrier to the practical utilization of large, complex models of biochemical systems is the lack of open-source computational tools to evaluate model behaviors over high-dimensional parameter spaces. This is due to the high computational expense of performing thousands to millions of model simulations required for statistical analysis. To address this need, we have implemented a user-friendly interface between cupSODA, a GPU-powered kinetic simulator, and PySB, a Python-based modeling and simulation framework. For three example models of varying size, we show that for large numbers of simulations PySB/cupSODA achieves order-of-magnitude speedups relative to a CPU-based ordinary differential equation integrator. The PySB/cupSODA interface has been integrated into the PySB modeling framework (version 1.4.0), which can be installed from the Python Package Index (PyPI) using a Python package manager such as pip. cupSODA source code and precompiled binaries (Linux, Mac OS/X, Windows) are available at github.com/aresio/cupSODA (requires an Nvidia GPU; developer.nvidia.com/cuda-gpus). Additional information about PySB is available at pysb.org. paolo.cazzaniga@unibg.it or c.lopez@vanderbilt.edu. Supplementary data are available at Bioinformatics online. © The Author(s) 2017. Published by Oxford University Press.

Design and rationale of the Procalcitonin Antibiotic Consensus Trial (ProACT), a multicenter randomized trial of procalcitonin antibiotic guidance in lower respiratory tract infection.

Science.gov (United States)

Huang, David T; Angus, Derek C; Chang, Chung-Chou H; Doi, Yohei; Fine, Michael J; Kellum, John A; Peck-Palmer, Octavia M; Pike, Francis; Weissfeld, Lisa A; Yabes, Jonathan; Yealy, Donald M

2017-08-29

Overuse of antibiotics is a major public health problem, contributing to growing antibiotic resistance. Procalcitonin has been reported to be commonly elevated in bacterial, but not viral infection. Multiple European trials found procalcitonin-guided care reduced antibiotic use in lower respiratory tract infection, with no apparent harm. However, applicability to US practice is limited due to trial design features impractical in the US, between-country differences, and residual safety concerns. The Procalcitonin Antibiotic Consensus Trial (ProACT) is a multicenter randomized trial to determine the impact of a procalcitonin antibiotic prescribing guideline, implemented with basic reproducible strategies, in US patients with lower respiratory tract infection. We describe the trial methods using the Consolidated Standards of Reporting Trials (CONSORT) framework, and the rationale for key design decisions, including choice of eligibility criteria, choice of control arm, and approach to guideline implementation. ClinicalTrials.gov NCT02130986 . Registered May 1, 2014.

Synthesis and evaluation of sequence-specific DNA alkylating agents: effect of alkylation subunits.

Science.gov (United States)

Shimizu, Tatsuhiko; Sasaki, Shunta; Minoshima, Masafumi; Shinohara, Ken-ichi; Bando, Toshikazu; Sugiyama, Hiroshi

2006-01-01

We have demonstrated that hairpin pyrrole (Py)- imidazole (Im) polyamide-CBI conjugates selectively alkylate predetermined sequences. In this study, we investigated the effect of alkylation subunits, for example conjugates 1-4 with three types of DNA alkylating units, and Py-Im polyamides with indole linker. Conjugate 3 and 4 selectively alkylated the predetermined sequences as described previously, while conjugates 1 and 2 alkylate at mismatched sites.

PyPSA: Python for Power System Analysis

Directory of Open Access Journals (Sweden)

Thomas Brown

2018-01-01

Full Text Available Python for Power System Analysis (PyPSA is a free software toolbox for simulating and optimising modern electrical power systems over multiple periods. PyPSA includes models for conventional generators with unit commitment, variable renewable generation, storage units, coupling to other energy sectors, and mixed alternating and direct current networks. It is designed to be easily extensible and to scale well with large networks and long time series. In this paper the basic functionality of PyPSA is described, including the formulation of the full power flow equations and the multi-period optimisation of operation and investment with linear power flow equations. PyPSA is positioned in the existing free software landscape as a bridge between traditional power flow analysis tools for steady-state analysis and full multi-period energy system models. The functionality is demonstrated on two open datasets of the transmission system in Germany (based on SciGRID and Europe (based on GridKit.   Funding statement: This research was conducted as part of the CoNDyNet project, which is supported by the German Federal Ministry of Education and Research under grant no. 03SF0472C. The responsibility for the contents lies solely with the authors

PlasmaPy: initial development of a Python package for plasma physics

Science.gov (United States)

Murphy, Nicholas; Leonard, Andrew J.; Stańczak, Dominik; Haggerty, Colby C.; Parashar, Tulasi N.; Huang, Yu-Min; PlasmaPy Community

2017-10-01

We report on initial development of PlasmaPy: an open source community-driven Python package for plasma physics. PlasmaPy seeks to provide core functionality that is needed for the formation of a fully open source Python ecosystem for plasma physics. PlasmaPy prioritizes code readability, consistency, and maintainability while using best practices for scientific computing such as version control, continuous integration testing, embedding documentation in code, and code review. We discuss our current and planned capabilities, including features presently under development. The development roadmap includes features such as fluid and particle simulation capabilities, a Grad-Shafranov solver, a dispersion relation solver, atomic data retrieval methods, and tools to analyze simulations and experiments. We describe several ways to contribute to PlasmaPy. PlasmaPy has a code of conduct and is being developed under a BSD license, with a version 0.1 release planned for 2018. The success of PlasmaPy depends on active community involvement, so anyone interested in contributing to this project should contact the authors. This work was partially supported by the U.S. Department of Energy.

uPy: a ubiquitous computer graphics Python API with Biological Modeling Applications

Science.gov (United States)

Autin, L.; Johnson, G.; Hake, J.; Olson, A.; Sanner, M.

2015-01-01

In this paper we describe uPy, an extension module for the Python programming language that provides a uniform abstraction of the APIs of several 3D computer graphics programs called hosts, including: Blender, Maya, Cinema4D, and DejaVu. A plugin written with uPy is a unique piece of code that will run in all uPy-supported hosts. We demonstrate the creation of complex plug-ins for molecular/cellular modeling and visualization and discuss how uPy can more generally simplify programming for many types of projects (not solely science applications) intended for multi-host distribution. uPy is available at http://upy.scripps.edu PMID:24806987

Bioaccumulation study of acrylate monomers in algae (Chlorella Kessleri) by PY-GC and PY-GC/MS

International Nuclear Information System (INIS)

Halas, L.; Orinak, A.; Adamova, M.; Ladomersky, J.

2004-01-01

Acrylate monomers methylmethacrylate (MMA) and cyclohexylmethacrylate (CHMA) bioaccumulation has been determined in aquatic organism, algae (Chlorella kessleri). Algae were collected in amount of 0.4 mg and directly injected to the paralytic cell. In algae bodies accumulated monomers were analysed by pyrolysis gas chromatography (Py-GC) and pyrolysis gas chromatography coupled with mass spectrometry (Py-GC/MS). Traces of the accumulated monomers in algae body can be determined after 1-, 2 -, 3-weeks of incubation. Maximum content of MMA was determined after 3-week of experiment, contrariwise in the case of CHMA after 2-week exposition. Relationship with pyrolysis temperature has also been studied. (authors)

Extensible, Reusable, and Reproducible Computing: A Case Study of PySPH

International Nuclear Information System (INIS)

Ramachandran, Prabhu

2016-01-01

In this work, the Smoothed Particle Hydrodynamics (SPH) technique is considered as an example of a typical computational research area. PySPH is an open source framework for SPH computations. PySPH is designed to be easy to use. The framework allows a user to implement an entire simulation in pure Python. It is designed to make it easy for scientists to reuse their code and extend the work of others. These important features allow PySPH to facilitate reproducible computational research. Based on the experience with PySPH, general recommendations are suggested for other computational researchers. (paper)

uPy: a ubiquitous CG Python API with biological-modeling applications.

Science.gov (United States)

Autin, Ludovic; Johnson, Graham; Hake, Johan; Olson, Arthur; Sanner, Michel

2012-01-01

The uPy Python extension module provides a uniform abstraction of the APIs of several 3D computer graphics programs (called hosts), including Blender, Maya, Cinema 4D, and DejaVu. A plug-in written with uPy can run in all uPy-supported hosts. Using uPy, researchers have created complex plug-ins for molecular and cellular modeling and visualization. uPy can simplify programming for many types of projects (not solely science applications) intended for multihost distribution. It's available at http://upy.scripps.edu. The first featured Web extra is a video that shows interactive analysis of a calcium dynamics simulation. YouTube URL: http://youtu.be/wvs-nWE6ypo. The second featured Web extra is a video that shows rotation of the HIV virus. YouTube URL: http://youtu.be/vEOybMaRoKc.

Programming biological models in Python using PySB.

Science.gov (United States)

Lopez, Carlos F; Muhlich, Jeremy L; Bachman, John A; Sorger, Peter K

2013-01-01

Mathematical equations are fundamental to modeling biological networks, but as networks get large and revisions frequent, it becomes difficult to manage equations directly or to combine previously developed models. Multiple simultaneous efforts to create graphical standards, rule-based languages, and integrated software workbenches aim to simplify biological modeling but none fully meets the need for transparent, extensible, and reusable models. In this paper we describe PySB, an approach in which models are not only created using programs, they are programs. PySB draws on programmatic modeling concepts from little b and ProMot, the rule-based languages BioNetGen and Kappa and the growing library of Python numerical tools. Central to PySB is a library of macros encoding familiar biochemical actions such as binding, catalysis, and polymerization, making it possible to use a high-level, action-oriented vocabulary to construct detailed models. As Python programs, PySB models leverage tools and practices from the open-source software community, substantially advancing our ability to distribute and manage the work of testing biochemical hypotheses. We illustrate these ideas using new and previously published models of apoptosis.

Aggregation behavior of gemini pyrrolidine-based ionic liquids 1,1'-(butane-1,4-diyl)bis(1-alkylpyrrolidinium) bromide ([C(n)py-4-C(n)py][Br2]) in aqueous solution.

Science.gov (United States)

Zhang, Shaohua; Yan, Han; Zhao, Mingwei; Zheng, Liqiang

2012-04-15

Three gemini pyrrolidine-based ionic liquids, 1,1'-(butane-1,4-diyl)bis(1-alkylpyrrolidinium) bromide ([C(n)py-4-C(n)py][Br(2)], n=10, 12, 14), were synthesized. Their aggregation behavior in aqueous solution was systematically investigated by surface tension, electrical conductivity, and steady-state fluorescence. Compared with their corresponding monomers, N-alkyl-N-methylpyrrolidinium bromide (C(n)MPB), [C(n)py-4-C(n)py][Br(2)], have higher surface activity. The special structure of [C(n)py-4-C(n)py][Br(2)] that has a spacer in their hydrophilic head groups results in a lower surface excess concentration (Γ(max)) and a larger molecular cross-sectional area (A(min)). Electrical conductivity studies show a lower degree of counter-ion binding to the aggregates. A smaller aggregation number (N(agg)) is observed by the pyrene fluorescence quenching method. A series of thermodynamic parameters (ΔG(agg)(0),ΔH(agg)(0),-TΔS(agg)(0)) of aggregation derived from electrical conductivity indicate that the aggregation of [C(n)py-4-C(n)py][Br(2)] is enthalpy-driven, while aggregation of C(n)MPB is entropy-driven at low temperatures but enthalpy-driven at high temperatures. Copyright © 2012 Elsevier Inc. All rights reserved.

Optimizing python-based ROOT I/O with PyPy's tracing just-in-time compiler

Science.gov (United States)

Tlp Lavrijsen, Wim

2012-12-01

The Python programming language allows objects and classes to respond dynamically to the execution environment. Most of this, however, is made possible through language hooks which by definition can not be optimized and thus tend to be slow. The PyPy implementation of Python includes a tracing just in time compiler (JIT), which allows similar dynamic responses but at the interpreter-, rather than the application-level. Therefore, it is possible to fully remove the hooks, leaving only the dynamic response, in the optimization stage for hot loops, if the types of interest are opened up to the JIT. A general opening up of types to the JIT, based on reflection information, has already been developed (cppyy). The work described in this paper takes it one step further by customizing access to ROOT I/O to the JIT, allowing for fully automatic optimizations.

Optimizing python-based ROOT I/O with PyPy's tracing just-in-time compiler

International Nuclear Information System (INIS)

Lavrijsen, Wim TLP

2012-01-01

The Python programming language allows objects and classes to respond dynamically to the execution environment. Most of this, however, is made possible through language hooks which by definition can not be optimized and thus tend to be slow. The PyPy implementation of Python includes a tracing just in time compiler (JIT), which allows similar dynamic responses but at the interpreter-, rather than the application-level. Therefore, it is possible to fully remove the hooks, leaving only the dynamic response, in the optimization stage for hot loops, if the types of interest are opened up to the JIT. A general opening up of types to the JIT, based on reflection information, has already been developed (cppyy). The work described in this paper takes it one step further by customizing access to ROOT I/O to the JIT, allowing for fully automatic optimizations.

PySE: Python Source Extractor for radio astronomical images

Science.gov (United States)

Spreeuw, Hanno; Swinbank, John; Molenaar, Gijs; Staley, Tim; Rol, Evert; Sanders, John; Scheers, Bart; Kuiack, Mark

2018-05-01

PySE finds and measures sources in radio telescope images. It is run with several options, such as the detection threshold (a multiple of the local noise), grid size, and the forced clean beam fit, followed by a list of input image files in standard FITS or CASA format. From these, PySe provides a list of found sources; information such as the calculated background image, source list in different formats (e.g. text, region files importable in DS9), and other data may be saved. PySe can be integrated into a pipeline; it was originally written as part of the LOFAR Transient Detection Pipeline (TraP, ascl:1412.011).

Space Charge Modules for PyHEADTAIL

CERN Multimedia

Oeftiger, Adrian

2016-01-01

PyHEADTAIL is a 6D tracking tool developed at CERN to simulate collective effects. We present recent developments of the direct space charge (SC) suite, which is available for both the CPU and GPU. A new 3D particle-in-cell solver with open boundary conditions has been implemented. For the transverse plane, there is a semi-analytical Bassetti-Erskine model as well as 2D self-consistent particle-in-cell solvers with both open and closed boundary conditions. For the longitudinal plane, PyHEADTAIL offers line density derivative models. Simulations with these models are benchmarked with experiments at the injection plateau of CERN’s SPS.

ConStruct: Improved construction of RNA consensus structures

Directory of Open Access Journals (Sweden)

Steger Gerhard

2008-04-01

Full Text Available Abstract Background Aligning homologous non-coding RNAs (ncRNAs correctly in terms of sequence and structure is an unresolved problem, due to both mathematical complexity and imperfect scoring functions. High quality alignments, however, are a prerequisite for most consensus structure prediction approaches, homology searches, and tools for phylogeny inference. Automatically created ncRNA alignments often need manual corrections, yet this manual refinement is tedious and error-prone. Results We present an extended version of CONSTRUCT, a semi-automatic, graphical tool suitable for creating RNA alignments correct in terms of both consensus sequence and consensus structure. To this purpose CONSTRUCT combines sequence alignment, thermodynamic data and various measures of covariation. One important feature is that the user is guided during the alignment correction step by a consensus dotplot, which displays all thermodynamically optimal base pairs and the corresponding covariation. Once the initial alignment is corrected, optimal and suboptimal secondary structures as well as tertiary interaction can be predicted. We demonstrate CONSTRUCT's ability to guide the user in correcting an initial alignment, and show an example for optimal secondary consensus structure prediction on very hard to align SECIS elements. Moreover we use CONSTRUCT to predict tertiary interactions from sequences of the internal ribosome entry site of CrP-like viruses. In addition we show that alignments specifically designed for benchmarking can be easily be optimized using CONSTRUCT, although they share very little sequence identity. Conclusion CONSTRUCT's graphical interface allows for an easy alignment correction based on and guided by predicted and known structural constraints. It combines several algorithms for prediction of secondary consensus structure and even tertiary interactions. The CONSTRUCT package can be downloaded from the URL listed in the Availability and

ObsPy: A Python Toolbox for Seismology - Recent Developments and Applications

Science.gov (United States)

Megies, T.; Krischer, L.; Barsch, R.; Sales de Andrade, E.; Beyreuther, M.

2014-12-01

ObsPy (http://www.obspy.org) is a community-driven, open-source project dedicated to building a bridge for seismology into the scientific Python ecosystem. It offersa) read and write support for essentially all commonly used waveform, station, and event metadata file formats with a unified interface,b) a comprehensive signal processing toolbox tuned to the needs of seismologists,c) integrated access to all large data centers, web services and databases, andd) convenient wrappers to legacy codes like libtau and evalresp.Python, currently the most popular language for teaching introductory computer science courses at top-ranked U.S. departments, is a full-blown programming language with the flexibility of an interactive scripting language. Its extensive standard library and large variety of freely available high quality scientific modules cover most needs in developing scientific processing workflows. Together with packages like NumPy, SciPy, Matplotlib, IPython, Pandas, lxml, and PyQt, ObsPy enables the construction of complete workflows in Python. These vary from reading locally stored data or requesting data from one or more different data centers through to signal analysis and data processing and on to visualizations in GUI and web applications, output of modified/derived data and the creation of publication-quality figures.ObsPy enjoys a large world-wide rate of adoption in the community. Applications successfully using it include time-dependent and rotational seismology, big data processing, event relocations, and synthetic studies about attenuation kernels and full-waveform inversions to name a few examples. All functionality is extensively documented and the ObsPy tutorial and gallery give a good impression of the wide range of possible use cases.We will present the basic features of ObsPy, new developments and applications, and a roadmap for the near future and discuss the sustainability of our open-source development model.

PySSM: A Python Module for Bayesian Inference of Linear Gaussian State Space Models

Directory of Open Access Journals (Sweden)

Christopher Strickland

2014-04-01

Full Text Available PySSM is a Python package that has been developed for the analysis of time series using linear Gaussian state space models. PySSM is easy to use; models can be set up quickly and efficiently and a variety of different settings are available to the user. It also takes advantage of scientific libraries NumPy and SciPy and other high level features of the Python language. PySSM is also used as a platform for interfacing between optimized and parallelized Fortran routines. These Fortran routines heavily utilize basic linear algebra and linear algebra Package functions for maximum performance. PySSM contains classes for filtering, classical smoothing as well as simulation smoothing.

Scripting MODFLOW model development using Python and FloPy

Science.gov (United States)

Bakker, Mark; Post, Vincent E. A.; Langevin, Christian D.; Hughes, Joseph D.; White, Jeremy; Starn, Jeffrey; Fienen, Michael N.

2016-01-01

Graphical user interfaces (GUIs) are commonly used to construct and postprocess numerical groundwater flow and transport models. Scripting model development with the programming language Python is presented here as an alternative approach. One advantage of Python is that there are many packages available to facilitate the model development process, including packages for plotting, array manipulation, optimization, and data analysis. For MODFLOW-based models, the FloPy package was developed by the authors to construct model input files, run the model, and read and plot simulation results. Use of Python with the available scientific packages and FloPy facilitates data exploration, alternative model evaluations, and model analyses that can be difficult to perform with GUIs. Furthermore, Python scripts are a complete, transparent, and repeatable record of the modeling process. The approach is introduced with a simple FloPy example to create and postprocess a MODFLOW model. A more complicated capture-fraction analysis with a real-world model is presented to demonstrate the types of analyses that can be performed using Python and FloPy.

Programmēšanas spēle "PyDrone"

OpenAIRE

Siliņš, Viesturs

2010-01-01

Darbā “Programmēšanas spēle “PyDrone”” ir dokumentēta atvērtā koda programmas PyDrone izstrāde. PyDrone ir programmēšanas spēle, kas paredzēta izklaidei un izglītošanai, spēles veidā iepazīstinot cilvēkus ar programmēšanu. Programma izstrādāta, izmantojot Python programmēšanas valodu. Programma izstrādāta, izmantojot spējo metodiku programmizstrādes principus. Atslēgvārdi: Python, spējās metodikas, programmēšanas spēle.

MagPy: A Python toolbox for controlling Magstim transcranial magnetic stimulators.

Science.gov (United States)

McNair, Nicolas A

2017-01-30

To date, transcranial magnetic stimulation (TMS) studies manipulating stimulation parameters have largely used blocked paradigms. However, altering these parameters on a trial-by-trial basis in Magstim stimulators is complicated by the need to send regular (1Hz) commands to the stimulator. Additionally, effecting such control interferes with the ability to send TMS pulses or simultaneously present stimuli with high-temporal precision. This manuscript presents the MagPy toolbox, a Python software package that provides full control over Magstim stimulators via the serial port. It is able to maintain this control with no impact on concurrent processing, such as stimulus delivery. In addition, a specially-designed "QuickFire" serial cable is specified that allows MagPy to trigger TMS pulses with very low-latency. In a series of experimental simulations, MagPy was able to maintain uninterrupted remote control over the connected Magstim stimulator across all testing sessions. In addition, having MagPy enabled had no effect on stimulus timing - all stimuli were presented for precisely the duration specified. Finally, using the QuickFire cable, MagPy was able to elicit TMS pulses with sub-millisecond latencies. The MagPy toolbox allows for experiments that require manipulating stimulation parameters from trial to trial. Furthermore, it can achieve this in contexts that require tight control over timing, such as those seeking to combine TMS with fMRI or EEG. Together, the MagPy toolbox and QuickFire serial cable provide an effective means for controlling Magstim stimulators during experiments while ensuring high-precision timing. Copyright © 2016 Elsevier B.V. All rights reserved.

Molecular phylogeny of 21 tropical bamboo species reconstructed by integrating non-coding internal transcribed spacer (ITS1 and 2) sequences and their consensus secondary structure.

Science.gov (United States)

Ghosh, Jayadri Sekhar; Bhattacharya, Samik; Pal, Amita

2017-06-01

The unavailability of the reproductive structure and unpredictability of vegetative characters for the identification and phylogenetic study of bamboo prompted the application of molecular techniques for greater resolution and consensus. We first employed internal transcribed spacer (ITS1, 5.8S rRNA and ITS2) sequences to construct the phylogenetic tree of 21 tropical bamboo species. While the sequence alone could grossly reconstruct the traditional phylogeny amongst the 21-tropical species studied, some anomalies were encountered that prompted a further refinement of the phylogenetic analyses. Therefore, we integrated the secondary structure of the ITS sequences to derive individual sequence-structure matrix to gain more resolution on the phylogenetic reconstruction. The results showed that ITS sequence-structure is the reliable alternative to the conventional phenotypic method for the identification of bamboo species. The best-fit topology obtained by the sequence-structure based phylogeny over the sole sequence based one underscores closer clustering of all the studied Bambusa species (Sub-tribe Bambusinae), while Melocanna baccifera, which belongs to Sub-Tribe Melocanneae, disjointedly clustered as an out-group within the consensus phylogenetic tree. In this study, we demonstrated the dependability of the combined (ITS sequence+structure-based) approach over the only sequence-based analysis for phylogenetic relationship assessment of bamboo.

pyNSMC: A Python Module for Null-Space Monte Carlo Uncertainty Analysis

Science.gov (United States)

White, J.; Brakefield, L. K.

2015-12-01

The null-space monte carlo technique is a non-linear uncertainty analyses technique that is well-suited to high-dimensional inverse problems. While the technique is powerful, the existing workflow for completing null-space monte carlo is cumbersome, requiring the use of multiple commandline utilities, several sets of intermediate files and even a text editor. pyNSMC is an open-source python module that automates the workflow of null-space monte carlo uncertainty analyses. The module is fully compatible with the PEST and PEST++ software suites and leverages existing functionality of pyEMU, a python framework for linear-based uncertainty analyses. pyNSMC greatly simplifies the existing workflow for null-space monte carlo by taking advantage of object oriented design facilities in python. The core of pyNSMC is the ensemble class, which draws and stores realized random vectors and also provides functionality for exporting and visualizing results. By relieving users of the tedium associated with file handling and command line utility execution, pyNSMC instead focuses the user on the important steps and assumptions of null-space monte carlo analysis. Furthermore, pyNSMC facilitates learning through flow charts and results visualization, which are available at many points in the algorithm. The ease-of-use of the pyNSMC workflow is compared to the existing workflow for null-space monte carlo for a synthetic groundwater model with hundreds of estimable parameters.

pyBSM: A Python package for modeling imaging systems

Science.gov (United States)

LeMaster, Daniel A.; Eismann, Michael T.

2017-05-01

There are components that are common to all electro-optical and infrared imaging system performance models. The purpose of the Python Based Sensor Model (pyBSM) is to provide open source access to these functions for other researchers to build upon. Specifically, pyBSM implements much of the capability found in the ERIM Image Based Sensor Model (IBSM) V2.0 along with some improvements. The paper also includes two use-case examples. First, performance of an airborne imaging system is modeled using the General Image Quality Equation (GIQE). The results are then decomposed into factors affecting noise and resolution. Second, pyBSM is paired with openCV to evaluate performance of an algorithm used to detect objects in an image.

PyNEST: a convenient interface to the NEST simulator

Directory of Open Access Journals (Sweden)

Jochen M Eppler

2009-01-01

Full Text Available The neural simulation tool NEST (http://www.nest-initiative.org is a simulator for heterogeneous networks of point neurons or neurons with a small number of compartments. It aims at simulations of large neural systems with more than 10^4 neurons and 10^7 to 10^9 synapses. NEST is implemented in C++ and can be used on a large range of architectures from single-core laptops over multi-core desktop computers to super-computers with thousands of processor cores. Python (http://www.python.org is a modern programming language that has recently received considerable attention in Computational Neuroscience. Python is easy to learn and has many extension modules for scientific computing (e.g. http://www.scipy.org. In this contribution we describe PyNEST, the new user interface to NEST. PyNEST combines NEST’s efficient simulation kernel with the simplicity and flexibility of Python. Compared to NEST’s native simulation language SLI, PyNEST makes it easier to set up simulations, generate stimuli, and analyze simulation results. We describe how PyNEST connects NEST and Python and how it is implemented. With a number of examples, we illustrate how it is used.

Development of p-y curves of laterally loaded piles in cohesionless soil.

Science.gov (United States)

Khari, Mahdy; Kassim, Khairul Anuar; Adnan, Azlan

2014-01-01

The research on damages of structures that are supported by deep foundations has been quite intensive in the past decade. Kinematic interaction in soil-pile interaction is evaluated based on the p-y curve approach. Existing p-y curves have considered the effects of relative density on soil-pile interaction in sandy soil. The roughness influence of the surface wall pile on p-y curves has not been emphasized sufficiently. The presented study was performed to develop a series of p-y curves for single piles through comprehensive experimental investigations. Modification factors were studied, namely, the effects of relative density and roughness of the wall surface of pile. The model tests were subjected to lateral load in Johor Bahru sand. The new p-y curves were evaluated based on the experimental data and were compared to the existing p-y curves. The soil-pile reaction for various relative density (from 30% to 75%) was increased in the range of 40-95% for a smooth pile at a small displacement and 90% at a large displacement. For rough pile, the ratio of dense to loose relative density soil-pile reaction was from 2.0 to 3.0 at a small to large displacement. Direct comparison of the developed p-y curve shows significant differences in the magnitude and shapes with the existing load-transfer curves. Good comparison with the experimental and design studies demonstrates the multidisciplinary applications of the present method.

Development of p-y Curves of Laterally Loaded Piles in Cohesionless Soil

Science.gov (United States)

Khari, Mahdy; Kassim, Khairul Anuar; Adnan, Azlan

2014-01-01

The research on damages of structures that are supported by deep foundations has been quite intensive in the past decade. Kinematic interaction in soil-pile interaction is evaluated based on the p-y curve approach. Existing p-y curves have considered the effects of relative density on soil-pile interaction in sandy soil. The roughness influence of the surface wall pile on p-y curves has not been emphasized sufficiently. The presented study was performed to develop a series of p-y curves for single piles through comprehensive experimental investigations. Modification factors were studied, namely, the effects of relative density and roughness of the wall surface of pile. The model tests were subjected to lateral load in Johor Bahru sand. The new p-y curves were evaluated based on the experimental data and were compared to the existing p-y curves. The soil-pile reaction for various relative density (from 30% to 75%) was increased in the range of 40–95% for a smooth pile at a small displacement and 90% at a large displacement. For rough pile, the ratio of dense to loose relative density soil-pile reaction was from 2.0 to 3.0 at a small to large displacement. Direct comparison of the developed p-y curve shows significant differences in the magnitude and shapes with the existing load-transfer curves. Good comparison with the experimental and design studies demonstrates the multidisciplinary applications of the present method. PMID:24574932

Development of p-y Curves of Laterally Loaded Piles in Cohesionless Soil

Directory of Open Access Journals (Sweden)

Mahdy Khari

2014-01-01

Full Text Available The research on damages of structures that are supported by deep foundations has been quite intensive in the past decade. Kinematic interaction in soil-pile interaction is evaluated based on the p-y curve approach. Existing p-y curves have considered the effects of relative density on soil-pile interaction in sandy soil. The roughness influence of the surface wall pile on p-y curves has not been emphasized sufficiently. The presented study was performed to develop a series of p-y curves for single piles through comprehensive experimental investigations. Modification factors were studied, namely, the effects of relative density and roughness of the wall surface of pile. The model tests were subjected to lateral load in Johor Bahru sand. The new p-y curves were evaluated based on the experimental data and were compared to the existing p-y curves. The soil-pile reaction for various relative density (from 30% to 75% was increased in the range of 40–95% for a smooth pile at a small displacement and 90% at a large displacement. For rough pile, the ratio of dense to loose relative density soil-pile reaction was from 2.0 to 3.0 at a small to large displacement. Direct comparison of the developed p-y curve shows significant differences in the magnitude and shapes with the existing load-transfer curves. Good comparison with the experimental and design studies demonstrates the multidisciplinary applications of the present method.

PyR@TE. Renormalization group equations for general gauge theories

Science.gov (United States)

Lyonnet, F.; Schienbein, I.; Staub, F.; Wingerter, A.

2014-03-01

Although the two-loop renormalization group equations for a general gauge field theory have been known for quite some time, deriving them for specific models has often been difficult in practice. This is mainly due to the fact that, albeit straightforward, the involved calculations are quite long, tedious and prone to error. The present work is an attempt to facilitate the practical use of the renormalization group equations in model building. To that end, we have developed two completely independent sets of programs written in Python and Mathematica, respectively. The Mathematica scripts will be part of an upcoming release of SARAH 4. The present article describes the collection of Python routines that we dubbed PyR@TE which is an acronym for “Python Renormalization group equations At Two-loop for Everyone”. In PyR@TE, once the user specifies the gauge group and the particle content of the model, the routines automatically generate the full two-loop renormalization group equations for all (dimensionless and dimensionful) parameters. The results can optionally be exported to LaTeX and Mathematica, or stored in a Python data structure for further processing by other programs. For ease of use, we have implemented an interactive mode for PyR@TE in form of an IPython Notebook. As a first application, we have generated with PyR@TE the renormalization group equations for several non-supersymmetric extensions of the Standard Model and found some discrepancies with the existing literature. Catalogue identifier: AERV_v1_0 Program summary URL:http://cpc.cs.qub.ac.uk/summaries/AERV_v1_0.html Program obtainable from: CPC Program Library, Queen’s University, Belfast, N. Ireland Licensing provisions: Standard CPC licence, http://cpc.cs.qub.ac.uk/licence/licence.html No. of lines in distributed program, including test data, etc.: 924959 No. of bytes in distributed program, including test data, etc.: 495197 Distribution format: tar.gz Programming language: Python. Computer

WILBER and PyWEED: Event-based Seismic Data Request Tools

Science.gov (United States)

Falco, N.; Clark, A.; Trabant, C. M.

2017-12-01

WILBER and PyWEED are two user-friendly tools for requesting event-oriented seismic data. Both tools provide interactive maps and other controls for browsing and filtering event and station catalogs, and downloading data for selected event/station combinations, where the data window for each event/station pair may be defined relative to the arrival time of seismic waves from the event to that particular station. Both tools allow data to be previewed visually, and can download data in standard miniSEED, SAC, and other formats, complete with relevant metadata for performing instrument correction. WILBER is a web application requiring only a modern web browser. Once the user has selected an event, WILBER identifies all data available for that time period, and allows the user to select stations based on criteria such as the station's distance and orientation relative to the event. When the user has finalized their request, the data is collected and packaged on the IRIS server, and when it is ready the user is sent a link to download. PyWEED is a downloadable, cross-platform (Macintosh / Windows / Linux) application written in Python. PyWEED allows a user to select multiple events and stations, and will download data for each event/station combination selected. PyWEED is built around the ObsPy seismic toolkit, and allows direct interaction and control of the application through a Python interactive console.

Comparative analysis of seven viral nuclear export signals (NESs reveals the crucial role of nuclear export mediated by the third NES consensus sequence of nucleoprotein (NP in influenza A virus replication.

Directory of Open Access Journals (Sweden)

Nopporn Chutiwitoonchai

Full Text Available The assembly of influenza virus progeny virions requires machinery that exports viral genomic ribonucleoproteins from the cell nucleus. Currently, seven nuclear export signal (NES consensus sequences have been identified in different viral proteins, including NS1, NS2, M1, and NP. The present study examined the roles of viral NES consensus sequences and their significance in terms of viral replication and nuclear export. Mutation of the NP-NES3 consensus sequence resulted in a failure to rescue viruses using a reverse genetics approach, whereas mutation of the NS2-NES1 and NS2-NES2 sequences led to a strong reduction in viral replication kinetics compared with the wild-type sequence. While the viral replication kinetics for other NES mutant viruses were also lower than those of the wild-type, the difference was not so marked. Immunofluorescence analysis after transient expression of NP-NES3, NS2-NES1, or NS2-NES2 proteins in host cells showed that they accumulated in the cell nucleus. These results suggest that the NP-NES3 consensus sequence is mostly required for viral replication. Therefore, each of the hydrophobic (Φ residues within this NES consensus sequence (Φ1, Φ2, Φ3, or Φ4 was mutated, and its viral replication and nuclear export function were analyzed. No viruses harboring NP-NES3 Φ2 or Φ3 mutants could be rescued. Consistent with this, the NP-NES3 Φ2 and Φ3 mutants showed reduced binding affinity with CRM1 in a pull-down assay, and both accumulated in the cell nucleus. Indeed, a nuclear export assay revealed that these mutant proteins showed lower nuclear export activity than the wild-type protein. Moreover, the Φ2 and Φ3 residues (along with other Φ residues within the NP-NES3 consensus were highly conserved among different influenza A viruses, including human, avian, and swine. Taken together, these results suggest that the Φ2 and Φ3 residues within the NP-NES3 protein are important for its nuclear export function

The fast azimuthal integration Python library: pyFAI.

Science.gov (United States)

Ashiotis, Giannis; Deschildre, Aurore; Nawaz, Zubair; Wright, Jonathan P; Karkoulis, Dimitrios; Picca, Frédéric Emmanuel; Kieffer, Jérôme

2015-04-01

pyFAI is an open-source software package designed to perform azimuthal integration and, correspondingly, two-dimensional regrouping on area-detector frames for small- and wide-angle X-ray scattering experiments. It is written in Python (with binary submodules for improved performance), a language widely accepted and used by the scientific community today, which enables users to easily incorporate the pyFAI library into their processing pipeline. This article focuses on recent work, especially the ease of calibration, its accuracy and the execution speed for integration.

Adopción por primera vez de la NIIF para las PyMEs en PyMEs argentinas: análisis normativo y cuestiones de aplicación

OpenAIRE

Rondi, Gustavo R.; Casal, María del Carmen; Galante, Marcelo Javier; Gómez, Melisa

2013-01-01

En el desarrollo de este trabajo se abordan las situaciones y dificultades de orden práctico que pueden presentarse cuando una PyME argentina decide adoptar por primera vez la NIIF para las PyMEs. Para ello, se han analizado el tratamiento que la NIIF para las PyMEs y las normas contables argentinas contemplan para los cambios de políticas contables; las simplificaciones, exenciones especiales y requerimientos específicos que la NIIF establece en su adopción por primera vez; y las principales...

Experimental measurements of U24Py nanocluster behavior in aqueous solution

Energy Technology Data Exchange (ETDEWEB)

Flynn, Shannon L.; Szymanowski, Jennifer E.S.; Fein, Jeremy B. [Univ. of Notre Dame, IN (United States). Department of Civil and Environmental Engineering and Earth Sciences; Dembowski, Mateusz [Univ. of Notre Dame, IN (United States). Department of Chemistry and Biochemistry; Burns, Peter C. [Univ. of Notre Dame, IN (United States). Department of Civil and Environmental Engineering and Earth Sciences; Univ. of Notre Dame, IN (United States). Department of Chemistry and Biochemistry

2016-07-01

Uranyl peroxide nanoclusters may impact the mobility and partitioning of uranium at contaminated sites and could be used in the isolation of uranium during the reprocessing of nuclear waste. Their behavior in aqueous systems must be better understood to predict the environmental fate of uranyl peroxide nanoclusters and for their use in engineered systems. The aqueous stability of only one uranyl peroxide nanocluster, U60 (K{sub 16}Li{sub 44}[UO{sub 2}(O{sub 2})OH]{sub 60}), has been studied to date [Flynn, S. L., Szymanowski, J. E. S., Gao, Y., Liu, T., Burns, P. C., Fein, J. B.: Experimental measurements of U60 nanocluster stability in aqueous solution. Geochemica et Cosmochimica Acta 156, 94-105 (2015)]. In this study, we measured the aqueous stability of a second uranyl peroxide nanocluster, U24Py (Na{sub 30}[(UO{sub 2}){sub 24}(O{sub 2}){sub 24}(HP{sub 2}O{sub 7}){sub 6}(H{sub 2}P{sub 2}O{sub 7}){sub 6}]), in batch systems as a function of time, pH, and nanocluster concentration, and then compared the aqueous behavior of U24Py to U60 to determine whether the size and morphology differences result in differences in their aqueous behaviors. Systems containing U24Py nanoclusters took over 30 days to achieve steady-state concentrations of monomeric U, Na, and P, illustrating slower reaction kinetics than parallel U60 systems. Furthermore, U24Py exhibited lower stability in solution than U60, with an average of 72% of the total mass in each nanocluster suspension being associated with the U24Py nanocluster, whereas 97% was associated with the U60 nanocluster in parallel experiments [Flynn, S. L., Szymanowski, J. E. S., Gao, Y., Liu, T., Burns, P. C., Fein, J. B.: Experimental measurements of U60 nanocluster stability in aqueous solution. Geochemica et Cosmochimica Acta 156, 94-105 (2015)]. The measurements from the batch experiments were used to calculate ion activity product (IAP) values for the reaction between the U24Py nanocluster and its constituent monomeric

Context based computational analysis and characterization of ARS consensus sequences (ACS of Saccharomyces cerevisiae genome

Directory of Open Access Journals (Sweden)

Vinod Kumar Singh

2016-09-01

Full Text Available Genome-wide experimental studies in Saccharomyces cerevisiae reveal that autonomous replicating sequence (ARS requires an essential consensus sequence (ACS for replication activity. Computational studies identified thousands of ACS like patterns in the genome. However, only a few hundreds of these sites act as replicating sites and the rest are considered as dormant or evolving sites. In a bid to understand the sequence makeup of replication sites, a content and context-based analysis was performed on a set of replicating ACS sequences that binds to origin-recognition complex (ORC denoted as ORC-ACS and non-replicating ACS sequences (nrACS, that are not bound by ORC. In this study, DNA properties such as base composition, correlation, sequence dependent thermodynamic and DNA structural profiles, and their positions have been considered for characterizing ORC-ACS and nrACS. Analysis reveals that ORC-ACS depict marked differences in nucleotide composition and context features in its vicinity compared to nrACS. Interestingly, an A-rich motif was also discovered in ORC-ACS sequences within its nucleosome-free region. Profound changes in the conformational features, such as DNA helical twist, inclination angle and stacking energy between ORC-ACS and nrACS were observed. Distribution of ACS motifs in the non-coding segments points to the locations of ORC-ACS which are found far away from the adjacent gene start position compared to nrACS thereby enabling an accessible environment for ORC-proteins. Our attempt is novel in considering the contextual view of ACS and its flanking region along with nucleosome positioning in the S. cerevisiae genome and may be useful for any computational prediction scheme.

Fetal Urinary Tract Anomalies: Review of Pathophysiology, Imaging, and Management.

Science.gov (United States)

Mileto, Achille; Itani, Malak; Katz, Douglas S; Siebert, Joseph R; Dighe, Manjiri K; Dubinsky, Theodore J; Moshiri, Mariam

2018-05-01

Common fetal anomalies of the kidneys and urinary tract encompass a complex spectrum of abnormalities that can be detected prenatally by ultrasound. Common fetal anomalies of the kidneys and urinary tract can affect amniotic fluid volume production with the development of oligohydramnios or anhydramnios, resulting in fetal pulmonary hypoplasia and, potentially, abnormal development of other fetal structures. We provide an overview of common fetal anomalies of the kidneys and urinary tract with an emphasis on sonographic patterns as well as pathologic and postnatal correlation, along with brief recommendations for postnatal management. Of note, we render an updated classification of fetal abnormalities of the kidneys and urinary tract based on the presence or absence of associated urinary tract dilation. In addition, we review the 2014 classification of urinary tract dilation based on the Linthicum multidisciplinary consensus panel.

PyElph - a software tool for gel images analysis and phylogenetics

Directory of Open Access Journals (Sweden)

Pavel Ana Brânduşa

2012-01-01

(Random Amplification of Polymorphic DNA and STR (Short Tandem Repeat. The similarity between the DNA sequences is computed and used to generate phylogenetic trees which are very useful for population genetics studies and taxonomic classification. Conclusions PyElph decreases the effort and time spent processing data from gel images by providing an automatic step-by-step gel image analysis system with a friendly Graphical User Interface. The proposed free software tool is suitable for researchers and students which do not have access to expensive commercial software and image acquisition devices.

IdentiPy: an extensible search engine for protein identification in shotgun proteomics.

Science.gov (United States)

Levitsky, Lev I; Ivanov, Mark V; Lobas, Anna A; Bubis, Julia A; Tarasova, Irina A; Solovyeva, Elizaveta M; Pridatchenko, Marina L; Gorshkov, Mikhail V

2018-04-23

We present an open-source, extensible search engine for shotgun proteomics. Implemented in Python programming language, IdentiPy shows competitive processing speed and sensitivity compared with the state-of-the-art search engines. It is equipped with a user-friendly web interface, IdentiPy Server, enabling the use of a single server installation accessed from multiple workstations. Using a simplified version of X!Tandem scoring algorithm and its novel ``auto-tune'' feature, IdentiPy outperforms the popular alternatives on high-resolution data sets. Auto-tune adjusts the search parameters for the particular data set, resulting in improved search efficiency and simplifying the user experience. IdentiPy with the auto-tune feature shows higher sensitivity compared with the evaluated search engines. IdentiPy Server has built-in post-processing and protein inference procedures and provides graphic visualization of the statistical properties of the data set and the search results. It is open-source and can be freely extended to use third-party scoring functions or processing algorithms, and allows customization of the search workflow for specialized applications.

A branch point consensus from Arabidopsis found by non-circular analysis allows for better prediction of acceptor sites

DEFF Research Database (Denmark)

Tolstrup, Niels; Rouzé, Pierre; Brunak, Søren

1997-01-01

Little knowledge exists about branch points in plants; it has even been claimed that plant introns lack conserved branch point sequences similar to those found in vertebrate introns. A putative branch point consensus sequence for Arabidopsis thaliana resembling the well known metazoan consensus s...... in the recognition of true acceptor sites; the false positive rate being reduced by a factor of 2. We take this as an indication that the consensus found here is the genuine one and that the branch point does play a role in the proper recognition of the acceptor site in plants.......Little knowledge exists about branch points in plants; it has even been claimed that plant introns lack conserved branch point sequences similar to those found in vertebrate introns. A putative branch point consensus sequence for Arabidopsis thaliana resembling the well known metazoan consensus...... sequence has been proposed, but this is based on search of sequences similar to those in yeast and metazoa. Here we present a novel consensus sequence found by a non-circular approach. A hidden Markov model with a fixed A nucleotide was trained on sequences upstream of the acceptor site. The consensus...

ncRNA consensus secondary structure derivation using grammar strings.

Science.gov (United States)

Achawanantakun, Rujira; Sun, Yanni; Takyar, Seyedeh Shohreh

2011-04-01

Many noncoding RNAs (ncRNAs) function through both their sequences and secondary structures. Thus, secondary structure derivation is an important issue in today's RNA research. The state-of-the-art structure annotation tools are based on comparative analysis, which derives consensus structure of homologous ncRNAs. Despite promising results from existing ncRNA aligning and consensus structure derivation tools, there is a need for more efficient and accurate ncRNA secondary structure modeling and alignment methods. In this work, we introduce a consensus structure derivation approach based on grammar string, a novel ncRNA secondary structure representation that encodes an ncRNA's sequence and secondary structure in the parameter space of a context-free grammar (CFG) and a full RNA grammar including pseudoknots. Being a string defined on a special alphabet constructed from a grammar, grammar string converts ncRNA alignment into sequence alignment. We derive consensus secondary structures from hundreds of ncRNA families from BraliBase 2.1 and 25 families containing pseudoknots using grammar string alignment. Our experiments have shown that grammar string-based structure derivation competes favorably in consensus structure quality with Murlet and RNASampler. Source code and experimental data are available at http://www.cse.msu.edu/~yannisun/grammar-string.

Dispel4py: An Open-Source Python library for Data-Intensive Seismology

Science.gov (United States)

Filgueira, Rosa; Krause, Amrey; Spinuso, Alessandro; Klampanos, Iraklis; Danecek, Peter; Atkinson, Malcolm

2015-04-01

Scientific workflows are a necessary tool for many scientific communities as they enable easy composition and execution of applications on computing resources while scientists can focus on their research without being distracted by the computation management. Nowadays, scientific communities (e.g. Seismology) have access to a large variety of computing resources and their computational problems are best addressed using parallel computing technology. However, successful use of these technologies requires a lot of additional machinery whose use is not straightforward for non-experts: different parallel frameworks (MPI, Storm, multiprocessing, etc.) must be used depending on the computing resources (local machines, grids, clouds, clusters) where applications are run. This implies that for achieving the best applications' performance, users usually have to change their codes depending on the features of the platform selected for running them. This work presents dispel4py, a new open-source Python library for describing abstract stream-based workflows for distributed data-intensive applications. Special care has been taken to provide dispel4py with the ability to map abstract workflows to different platforms dynamically at run-time. Currently dispel4py has four mappings: Apache Storm, MPI, multi-threading and sequential. The main goal of dispel4py is to provide an easy-to-use tool to develop and test workflows in local resources by using the sequential mode with a small dataset. Later, once a workflow is ready for long runs, it can be automatically executed on different parallel resources. dispel4py takes care of the underlying mappings by performing an efficient parallelisation. Processing Elements (PE) represent the basic computational activities of any dispel4Py workflow, which can be a seismologic algorithm, or a data transformation process. For creating a dispel4py workflow, users only have to write very few lines of code to describe their PEs and how they are

Genomic Variability of Haemophilus influenzae Isolated from Mexican Children Determined by Using Enterobacterial Repetitive Intergenic Consensus Sequences and PCR

OpenAIRE

Gomez-De-Leon, Patricia; Santos, Jose I.; Caballero, Javier; Gomez, Demostenes; Espinosa, Luz E.; Moreno, Isabel; Piñero, Daniel; Cravioto, Alejandro

2000-01-01

Genomic fingerprints from 92 capsulated and noncapsulated strains of Haemophilus influenzae from Mexican children with different diseases and healthy carriers were generated by PCR using the enterobacterial repetitive intergenic consensus (ERIC) sequences. A cluster analysis by the unweighted pair-group method with arithmetic averages based on the overall similarity as estimated from the characteristics of the genomic fingerprints, was conducted to group the strains. A total of 69 fingerprint...

PyFDAP: automated analysis of fluorescence decay after photoconversion (FDAP) experiments.

Science.gov (United States)

Bläßle, Alexander; Müller, Patrick

2015-03-15

We developed the graphical user interface PyFDAP for the fitting of linear and non-linear decay functions to data from fluorescence decay after photoconversion (FDAP) experiments. PyFDAP structures and analyses large FDAP datasets and features multiple fitting and plotting options. PyFDAP was written in Python and runs on Ubuntu Linux, Mac OS X and Microsoft Windows operating systems. The software, a user guide and a test FDAP dataset are freely available for download from http://people.tuebingen.mpg.de/mueller-lab. © The Author 2014. Published by Oxford University Press. All rights reserved. For Permissions, please e-mail: journals.permissions@oup.com.

A Distributed Python HPC Framework: ODIN, PyTrilinos, & Seamless

Energy Technology Data Exchange (ETDEWEB)

Grant, Robert [Enthought, Inc., Austin, TX (United States)

2015-11-23

Under this grant, three significant software packages were developed or improved, all with the goal of improving the ease-of-use of HPC libraries. The first component is a Python package, named DistArray (originally named Odin), that provides a high-level interface to distributed array computing. This interface is based on the popular and widely used NumPy package and is integrated with the IPython project for enhanced interactive parallel distributed computing. The second Python package is the Distributed Array Protocol (DAP) that enables separate distributed array libraries to share arrays efficiently without copying or sending messages. If a distributed array library supports the DAP, it is then automatically able to communicate with any other library that also supports the protocol. This protocol allows DistArray to communicate with the Trilinos library via PyTrilinos, which was also enhanced during this project. A third package, PyTrilinos, was extended to support distributed structured arrays (in addition to the unstructured arrays of its original design), allow more flexible distributed arrays (i.e., the restriction to double precision data was lifted), and implement the DAP. DAP support includes both exporting the protocol so that external packages can use distributed Trilinos data structures, and importing the protocol so that PyTrilinos can work with distributed data from external packages.

PyQuant: A Versatile Framework for Analysis of Quantitative Mass Spectrometry Data.

Science.gov (United States)

Mitchell, Christopher J; Kim, Min-Sik; Na, Chan Hyun; Pandey, Akhilesh

2016-08-01

Quantitative mass spectrometry data necessitates an analytical pipeline that captures the accuracy and comprehensiveness of the experiments. Currently, data analysis is often coupled to specific software packages, which restricts the analysis to a given workflow and precludes a more thorough characterization of the data by other complementary tools. To address this, we have developed PyQuant, a cross-platform mass spectrometry data quantification application that is compatible with existing frameworks and can be used as a stand-alone quantification tool. PyQuant supports most types of quantitative mass spectrometry data including SILAC, NeuCode, (15)N, (13)C, or (18)O and chemical methods such as iTRAQ or TMT and provides the option of adding custom labeling strategies. In addition, PyQuant can perform specialized analyses such as quantifying isotopically labeled samples where the label has been metabolized into other amino acids and targeted quantification of selected ions independent of spectral assignment. PyQuant is capable of quantifying search results from popular proteomic frameworks such as MaxQuant, Proteome Discoverer, and the Trans-Proteomic Pipeline in addition to several standalone search engines. We have found that PyQuant routinely quantifies a greater proportion of spectral assignments, with increases ranging from 25-45% in this study. Finally, PyQuant is capable of complementing spectral assignments between replicates to quantify ions missed because of lack of MS/MS fragmentation or that were omitted because of issues such as spectra quality or false discovery rates. This results in an increase of biologically useful data available for interpretation. In summary, PyQuant is a flexible mass spectrometry data quantification platform that is capable of interfacing with a variety of existing formats and is highly customizable, which permits easy configuration for custom analysis. © 2016 by The American Society for Biochemistry and Molecular Biology

PyECLOUD and build-up simulations at CERN

International Nuclear Information System (INIS)

Iadarola, G; Rumolo, G

2013-01-01

PyECLOUD is a newly developed code for the simulation of the electron cloud (EC) build-up in particle accelerators. Almost entirely written in Python, it is mostly based on the physical models already used in the ECLOUD code but, thanks to the implementation of new optimized algorithms, it exhibits a significantly improved performance in accuracy, speed, reliability and flexibility. Such new features of PyECLOUD have been already broadly exploited to study EC observations in the Large Hadron Collider (LHC) and its injector chain as well as for the extrapolation to high luminosity upgrade scenarios. (author)

A complex array of Hpr consensus DNA recognition sequences proximal to the enterotoxin gene in Clostridium perfringens type A.

Science.gov (United States)

Brynestad, S; Iwanejko, L A; Stewart, G S; Granum, P E

1994-01-01

Enterotoxin production in Clostridium perfringens is both strain dependent and sporulation associated. Underlying these phenotypic observations must lie a genetic and molecular explanation and the principal keys will be held within the DNA sequence both upstream and downstream of the structural gene cpe. In accordance with the above we have sequenced 4.1 kbp of DNA upstream of cpe in the type strain NCTC 8239. A region of DNA extending up to 1.5 kb 5' to cpe is conserved in all enterotoxin-positive strains. This region contains a putative ORF with substantial homology to an ORF in the Salmonella typhimurium IS200 insertion element and, in addition, contains multiple perfect consensus DNA-binding sequences for the Bacillus subtilis transition state regulator Hpr. The detailed structural elements revealed by the sequence analysis are presented and used to develop a new perspective on the molecular basis of enterotoxin production in this important food-poisoning bacterium.

Software news and update PyFrag - Streamlining your reaction path analysis

NARCIS (Netherlands)

van Zeist, W.-J.; Fonseca Guerra, C.; Bickelhaupt, F.M.

2008-01-01

The PyFrag program (released as PyFrag2007.01) is a "wrap-around" for the Amsterdam Density Functional (ADF) package and facilitates the extension of the fragment analysis method implemented in ADF along an entire potential energy surface. The purpose is to make analyses of reaction paths and other

PyRosetta: a script-based interface for implementing molecular modeling algorithms using Rosetta

OpenAIRE

Chaudhury, Sidhartha; Lyskov, Sergey; Gray, Jeffrey J.

2010-01-01

Summary: PyRosetta is a stand-alone Python-based implementation of the Rosetta molecular modeling package that allows users to write custom structure prediction and design algorithms using the major Rosetta sampling and scoring functions. PyRosetta contains Python bindings to libraries that define Rosetta functions including those for accessing and manipulating protein structure, calculating energies and running Monte Carlo-based simulations. PyRosetta can be used in two ways: (i) interactive...

PyPedia: using the wiki paradigm as crowd sourcing environment for bioinformatics protocols.

Science.gov (United States)

Kanterakis, Alexandros; Kuiper, Joël; Potamias, George; Swertz, Morris A

2015-01-01

Today researchers can choose from many bioinformatics protocols for all types of life sciences research, computational environments and coding languages. Although the majority of these are open source, few of them possess all virtues to maximize reuse and promote reproducible science. Wikipedia has proven a great tool to disseminate information and enhance collaboration between users with varying expertise and background to author qualitative content via crowdsourcing. However, it remains an open question whether the wiki paradigm can be applied to bioinformatics protocols. We piloted PyPedia, a wiki where each article is both implementation and documentation of a bioinformatics computational protocol in the python language. Hyperlinks within the wiki can be used to compose complex workflows and induce reuse. A RESTful API enables code execution outside the wiki. Initial content of PyPedia contains articles for population statistics, bioinformatics format conversions and genotype imputation. Use of the easy to learn wiki syntax effectively lowers the barriers to bring expert programmers and less computer savvy researchers on the same page. PyPedia demonstrates how wiki can provide a collaborative development, sharing and even execution environment for biologists and bioinformaticians that complement existing resources, useful for local and multi-center research teams. PyPedia is available online at: http://www.pypedia.com. The source code and installation instructions are available at: https://github.com/kantale/PyPedia_server. The PyPedia python library is available at: https://github.com/kantale/pypedia. PyPedia is open-source, available under the BSD 2-Clause License.

PyKE3: data analysis tools for NASA's Kepler, K2, and TESS missions

Science.gov (United States)

Hedges, Christina L.; Cardoso, Jose Vinicius De Miranda; Barentsen, Geert; Gully-Santiago, Michael A.; Cody, Ann Marie; Barclay, Thomas; Still, Martin; BAY AREA ENVIRONMENTAL RESEARCH IN

2018-01-01

The PyKE package is a set of easy to use tools for working with Kepler/K2 data. This includes tools to correct light curves for cotrending basis vectors, turn the raw Target Pixel File data into motion corrected light curves, check for exoplanet false positives and run new PSF photometry. We are now releasing PyKE 3, which is compatible with Python 3, is pip installable and no longer depends on PyRAF. Tools are available both as Python routines and from the command line. New tutorials are available and under construction for users to learn about Kepler and K2 data and how to best use it for their science goals. PyKE is open source and welcomes contributions from the community. Routines and more information are available on the PyKE repository on GitHub.

pyAmpli: an amplicon-based variant filter pipeline for targeted resequencing data.

Science.gov (United States)

Beyens, Matthias; Boeckx, Nele; Van Camp, Guy; Op de Beeck, Ken; Vandeweyer, Geert

2017-12-14

Haloplex targeted resequencing is a popular method to analyze both germline and somatic variants in gene panels. However, involved wet-lab procedures may introduce false positives that need to be considered in subsequent data-analysis. No variant filtering rationale addressing amplicon enrichment related systematic errors, in the form of an all-in-one package, exists to our knowledge. We present pyAmpli, a platform independent parallelized Python package that implements an amplicon-based germline and somatic variant filtering strategy for Haloplex data. pyAmpli can filter variants for systematic errors by user pre-defined criteria. We show that pyAmpli significantly increases specificity, without reducing sensitivity, essential for reporting true positive clinical relevant mutations in gene panel data. pyAmpli is an easy-to-use software tool which increases the true positive variant call rate in targeted resequencing data. It specifically reduces errors related to PCR-based enrichment of targeted regions.

PySLHA: a Pythonic interface to SUSY Les Houches accord data

International Nuclear Information System (INIS)

Buckley, Andy

2015-01-01

This paper describes the PySLHA package, a Python language module and program collection for reading, writing and visualising SUSY model data in the SLHA format. PySLHA can read and write SLHA data in a very general way, including the official SLHA2 extension and user customisations, and with arbitrarily deep indexing of data block entries and a dedicated, intuitive interface for particle data and decay information. The draft SLHA3 XSECTION feature is also fully supported. PySLHA can additionally read and write the legacy ISAWIG model format, and provides format conversion scripts. A publication-quality mass spectrum and decay chain plotting tool, slhaplot, is included in the package. (orig.)

PyRosetta: a script-based interface for implementing molecular modeling algorithms using Rosetta.

Science.gov (United States)

Chaudhury, Sidhartha; Lyskov, Sergey; Gray, Jeffrey J

2010-03-01

PyRosetta is a stand-alone Python-based implementation of the Rosetta molecular modeling package that allows users to write custom structure prediction and design algorithms using the major Rosetta sampling and scoring functions. PyRosetta contains Python bindings to libraries that define Rosetta functions including those for accessing and manipulating protein structure, calculating energies and running Monte Carlo-based simulations. PyRosetta can be used in two ways: (i) interactively, using iPython and (ii) script-based, using Python scripting. Interactive mode contains a number of help features and is ideal for beginners while script-mode is best suited for algorithm development. PyRosetta has similar computational performance to Rosetta, can be easily scaled up for cluster applications and has been implemented for algorithms demonstrating protein docking, protein folding, loop modeling and design. PyRosetta is a stand-alone package available at http://www.pyrosetta.org under the Rosetta license which is free for academic and non-profit users. A tutorial, user's manual and sample scripts demonstrating usage are also available on the web site.

pySPACE-a signal processing and classification environment in Python.

Science.gov (United States)

Krell, Mario M; Straube, Sirko; Seeland, Anett; Wöhrle, Hendrik; Teiwes, Johannes; Metzen, Jan H; Kirchner, Elsa A; Kirchner, Frank

2013-01-01

In neuroscience large amounts of data are recorded to provide insights into cerebral information processing and function. The successful extraction of the relevant signals becomes more and more challenging due to increasing complexities in acquisition techniques and questions addressed. Here, automated signal processing and machine learning tools can help to process the data, e.g., to separate signal and noise. With the presented software pySPACE (http://pyspace.github.io/pyspace), signal processing algorithms can be compared and applied automatically on time series data, either with the aim of finding a suitable preprocessing, or of training supervised algorithms to classify the data. pySPACE originally has been built to process multi-sensor windowed time series data, like event-related potentials from the electroencephalogram (EEG). The software provides automated data handling, distributed processing, modular build-up of signal processing chains and tools for visualization and performance evaluation. Included in the software are various algorithms like temporal and spatial filters, feature generation and selection, classification algorithms, and evaluation schemes. Further, interfaces to other signal processing tools are provided and, since pySPACE is a modular framework, it can be extended with new algorithms according to individual needs. In the presented work, the structural hierarchies are described. It is illustrated how users and developers can interface the software and execute offline and online modes. Configuration of pySPACE is realized with the YAML format, so that programming skills are not mandatory for usage. The concept of pySPACE is to have one comprehensive tool that can be used to perform complete signal processing and classification tasks. It further allows to define own algorithms, or to integrate and use already existing libraries.

ObsPy: A Python Toolbox for Seismology

Science.gov (United States)

Krischer, Lion; Megies, Tobias; Sales de Andrade, Elliott; Barsch, Robert; MacCarthy, Jonathan

2017-04-01

In recent years the Python ecosystem evolved into one of the most powerful and productive scientific environments across disciplines. ObsPy (https://www.obspy.org) is a fully community-driven, open-source project dedicated to providing a bridge for seismology into that ecosystem. It does so by offering Read and write support for essentially every commonly used data format in seismology with a unified interface and automatic format detection. This includes waveform data (MiniSEED, SAC, SEG-Y, Reftek, …) as well as station (SEED, StationXML, …) and event meta information (QuakeML, ZMAP, …). Integrated access to the largest data centers, web services, and real-time data streams (FDSNWS, ArcLink, SeedLink, ...). A powerful signal processing toolbox tuned to the specific needs of seismologists. Utility functionality like travel time calculations with the TauP method, geodetic functions, and data visualizations. ObsPy has been in constant development for more than seven years and is developed and used by scientists around the world with successful applications in all branches of seismology. Additionally it nowadays serves as the foundation for a large number of more specialized packages. This presentation will give a short overview of the capabilities of ObsPy and point out several representative or new use cases. Additionally we will discuss the road ahead as well as the long-term sustainability of open-source scientific software.

PyClaw: Accessible, Extensible, Scalable Tools for Wave Propagation Problems

KAUST Repository

Ketcheson, David I.; Mandli, Kyle; Ahmadia, Aron; Alghamdi, Amal; de Luna, Manuel Quezada; Parsani, Matteo; Knepley, Matthew G.; Emmett, Matthew

2012-01-01

Development of scientific software involves tradeoffs between ease of use, generality, and performance. We describe the design of a general hyperbolic PDE solver that can be operated with the convenience of MATLAB yet achieves efficiency near that of hand-coded Fortran and scales to the largest supercomputers. This is achieved by using Python for most of the code while employing automatically wrapped Fortran kernels for computationally intensive routines, and using Python bindings to interface with a parallel computing library and other numerical packages. The software described here is PyClaw, a Python-based structured grid solver for general systems of hyperbolic PDEs [K. T. Mandli et al., PyClaw Software, Version 1.0, http://numerics.kaust.edu.sa/pyclaw/ (2011)]. PyClaw provides a powerful and intuitive interface to the algorithms of the existing Fortran codes Clawpack and SharpClaw, simplifying code development and use while providing massive parallelism and scalable solvers via the PETSc library. The package is further augmented by use of PyWENO for generation of efficient high-order weighted essentially nonoscillatory reconstruction code. The simplicity, capability, and performance of this approach are demonstrated through application to example problems in shallow water flow, compressible flow, and elasticity.

PyClaw: Accessible, Extensible, Scalable Tools for Wave Propagation Problems

KAUST Repository

Ketcheson, David I.

2012-08-15

Development of scientific software involves tradeoffs between ease of use, generality, and performance. We describe the design of a general hyperbolic PDE solver that can be operated with the convenience of MATLAB yet achieves efficiency near that of hand-coded Fortran and scales to the largest supercomputers. This is achieved by using Python for most of the code while employing automatically wrapped Fortran kernels for computationally intensive routines, and using Python bindings to interface with a parallel computing library and other numerical packages. The software described here is PyClaw, a Python-based structured grid solver for general systems of hyperbolic PDEs [K. T. Mandli et al., PyClaw Software, Version 1.0, http://numerics.kaust.edu.sa/pyclaw/ (2011)]. PyClaw provides a powerful and intuitive interface to the algorithms of the existing Fortran codes Clawpack and SharpClaw, simplifying code development and use while providing massive parallelism and scalable solvers via the PETSc library. The package is further augmented by use of PyWENO for generation of efficient high-order weighted essentially nonoscillatory reconstruction code. The simplicity, capability, and performance of this approach are demonstrated through application to example problems in shallow water flow, compressible flow, and elasticity.

Imaging strategies in pediatric urinary tract infection

Energy Technology Data Exchange (ETDEWEB)

Dacher, Jean-Nicolas [University of Rouen, Quant-IF Laboratory, School of Medicine and Pharmacy, Rouen (France); Rouen University Hospital Charles Nicolle, Department of Radiology, Rouen (France); UFR Medecine Pharmacie de Rouen, Laboratoire Quant-If, Rouen (France); Hitzel, Anne; Vera, Pierre [University of Rouen, Quant-IF Laboratory, School of Medicine and Pharmacy, Rouen (France); CRLCC Henri Becquerel, Department of Nuclear Medicine, Rouen (France); Avni, Fred E. [Free University of Brussels, Department of Radiology, Erasmus Hospital, Brussels (Belgium)

2005-07-01

This article is focused on the controversial topic of imaging strategies in pediatric urinary tract infection. A review of the recent literature illustrates the complementary roles of ultrasound, diagnostic radiology and nuclear medicine. The authors stress the key role of ultrasound which has recently been debated. The commonly associated vesicoureteric reflux has to be classified as congenital or secondary due to voiding dysfunction. A series of frequently asked questions are addressed in a second section. The proposed answers are not the product of a consensus but should rather be considered as proposals to enrich the ongoing debate concerning the evaluation of urinary tract infection in children. (orig.)

Imaging strategies in pediatric urinary tract infection

International Nuclear Information System (INIS)

Dacher, Jean-Nicolas; Hitzel, Anne; Vera, Pierre; Avni, Fred E.

2005-01-01

This article is focused on the controversial topic of imaging strategies in pediatric urinary tract infection. A review of the recent literature illustrates the complementary roles of ultrasound, diagnostic radiology and nuclear medicine. The authors stress the key role of ultrasound which has recently been debated. The commonly associated vesicoureteric reflux has to be classified as congenital or secondary due to voiding dysfunction. A series of frequently asked questions are addressed in a second section. The proposed answers are not the product of a consensus but should rather be considered as proposals to enrich the ongoing debate concerning the evaluation of urinary tract infection in children. (orig.)

Nostoc PCC7524, a cyanobacterium which contains five sequence-specific deoxyribonucleases

NARCIS (Netherlands)

Reaston, J.; Duybesteyn, M.G.C.; Waard, Adrian de

1982-01-01

Five nucleotide sequence-specific deoxyribonucleases present in cell-free extracts of the filamentous cyanobacterium Nostoc PCC7524 have been purified and characterized. One of these enzymes, designated Nsp(7524)I cleaves at a new kind of nucleotide sequence i.e. 5'-PuCATG λ Py-3'. The other four

Rice MEL2, the RNA recognition motif (RRM) protein, binds in vitro to meiosis-expressed genes containing U-rich RNA consensus sequences in the 3'-UTR.

Science.gov (United States)

Miyazaki, Saori; Sato, Yutaka; Asano, Tomoya; Nagamura, Yoshiaki; Nonomura, Ken-Ichi

2015-10-01

Post-transcriptional gene regulation by RNA recognition motif (RRM) proteins through binding to cis-elements in the 3'-untranslated region (3'-UTR) is widely used in eukaryotes to complete various biological processes. Rice MEIOSIS ARRESTED AT LEPTOTENE2 (MEL2) is the RRM protein that functions in the transition to meiosis in proper timing. The MEL2 RRM preferentially associated with the U-rich RNA consensus, UUAGUU[U/A][U/G][A/U/G]U, dependently on sequences and proportionally to MEL2 protein amounts in vitro. The consensus sequences were located in the putative looped structures of the RNA ligand. A genome-wide survey revealed a tendency of MEL2-binding consensus appearing in 3'-UTR of rice genes. Of 249 genes that conserved the consensus in their 3'-UTR, 13 genes spatiotemporally co-expressed with MEL2 in meiotic flowers, and included several genes whose function was supposed in meiosis; such as Replication protein A and OsMADS3. The proteome analysis revealed that the amounts of small ubiquitin-related modifier-like protein and eukaryotic translation initiation factor3-like protein were dramatically altered in mel2 mutant anthers. Taken together with transcriptome and gene ontology results, we propose that the rice MEL2 is involved in the translational regulation of key meiotic genes on 3'-UTRs to achieve the faithful transition of germ cells to meiosis.

No. 250-Recurrent Urinary Tract Infection.

Science.gov (United States)

Epp, Annette; Larochelle, Annick

2017-10-01

To provide an update of the definition, epidemiology, clinical presentation, investigation, treatment, and prevention of recurrent urinary tract infections in women. Continuous antibiotic prophylaxis, post-coital antibiotic prophylaxis, and acute self-treatment are all efficient alternatives to prevent recurrent urinary tract infection. Vaginal estrogen and cranberry juice can also be effective prophylaxis alternatives. A search of PubMed and The Cochrane Library for articles published in English identified the most relevant literature. Results were restricted to systematic reviews, randomized control trials/controlled clinical trials, and observational studies. There were no date restrictions. This update is the consensus of the Sub-Committee on Urogynaecology of the Society of Obstetricians and Gynaecologists of Canada. Recommendations were made according to the guidelines developed by the Canadian Task Force on Preventive Health Care (Table 1). Recurrent urinary tract infections need careful investigation and can be efficiently treated and prevented. Different prophylaxis options can be selected according to each patient's characteristics. Copyright © 2017. Published by Elsevier Inc.

Quality indicators for diagnosis and treatment of respiratory tract infections in general practice: a modified Delphi study

DEFF Research Database (Denmark)

Hansen, Malene Plejdrup; Bjerrum, Lars; Gahrn-Hansen, Bente

2010-01-01

was achieved in both Delphi rounds. A total of 41 of the proposed 59 quality indicators attained consensus. None of the quality indicators focusing on the diagnostic process achieved consensus. Consensus was attained for 14 quality indicators focusing on the decision regarding antibiotic treatment and for 27...... quality indicators focusing on the choice of antibiotics. CONCLUSION: This study resulted in a final set of 41 quality indicators concerning respiratory tract infections in general practice. These quality indicators may be used to strengthen general practitioners' focus on their management of patients......OBJECTIVE: To develop a set of quality indicators focusing on the diagnosis and treatment of respiratory tract infections in general practice. DESIGN: A modified 2-round Delphi study. SETTING: General practice. SUBJECTS: A panel of 27 experts (13 countries) comprising mainly general practitioners...

PyRosetta: a script-based interface for implementing molecular modeling algorithms using Rosetta

Science.gov (United States)

Chaudhury, Sidhartha; Lyskov, Sergey; Gray, Jeffrey J.

2010-01-01

Summary: PyRosetta is a stand-alone Python-based implementation of the Rosetta molecular modeling package that allows users to write custom structure prediction and design algorithms using the major Rosetta sampling and scoring functions. PyRosetta contains Python bindings to libraries that define Rosetta functions including those for accessing and manipulating protein structure, calculating energies and running Monte Carlo-based simulations. PyRosetta can be used in two ways: (i) interactively, using iPython and (ii) script-based, using Python scripting. Interactive mode contains a number of help features and is ideal for beginners while script-mode is best suited for algorithm development. PyRosetta has similar computational performance to Rosetta, can be easily scaled up for cluster applications and has been implemented for algorithms demonstrating protein docking, protein folding, loop modeling and design. Availability: PyRosetta is a stand-alone package available at http://www.pyrosetta.org under the Rosetta license which is free for academic and non-profit users. A tutorial, user's manual and sample scripts demonstrating usage are also available on the web site. Contact: pyrosetta@graylab.jhu.edu PMID:20061306

pySPACE - A Signal Processing and Classification Environment in Python

Directory of Open Access Journals (Sweden)

Mario Michael Krell

2013-12-01

Full Text Available In neuroscience large amounts of data are recorded to provide insights into cerebral information processing and function. The successful extraction of the relevant signals becomes more and more challenging due to increasing complexities in acquisition techniques and questions addressed. Here, automated signal processing and machine learning tools can help to process the data, e.g., to separate signal and noise. With the presented software pySPACE (http://pyspace.github.io/pyspace, signal processing algorithms can be compared and applied automatically on time series data, either with the aim of finding a suitable preprocessing, or of training supervised algorithms to classify the data. pySPACE originally has been built to process multi-sensor windowed time series data, like event-related potentials from the electroencephalogram (EEG. The software provides automated data handling, distributed processing, modular build-up of signal processing chains and tools for visualization and performance evaluation. Included in the software are various algorithms like temporal and spatial filters, feature generation and selection, classification algorithms and evaluation schemes. Further, interfaces to other signal processing tools are provided and, since pySPACE is a modular framework, it can be extended with new algorithms according to individual needs. In the presented work, the structural hierarchies are described. It is illustrated how users and developers can interface the software and execute offline and online modes. Configuration of pySPACE is realized with the YAML format, so that programming skills are not mandatory for usage. The concept of pySPACE is to have one comprehensive tool that can be used to perform complete signal processing and classification tasks. It further allows to define own algorithms, or to integrate and use already existing libraries.

Dielectric Properties of SiCf/PyC/SiC Composites After Oxidation

Institute of Scientific and Technical Information of China (English)

SONG Huihui; ZHOU Wancheng; LUO Fa; QING Yuchang; CHEN Malin; LI Zhimin

2016-01-01

In this paper, the SiC fiber-reinforced SiC matrix composites with a 0.15mm thick pyrocarbon interphase (notedas SiCf/PyC/SiC) were prepared by chemical vapor infiltration (CVI). The SiCf/PyC/SiC were oxidized in air at 950℃ for 50h. The dielectric properties after this high temperature oxidation were investigated in X-band from room temperature (RT) to 700℃. Results suggested that:e' of the SiCf/PyC/SiC after oxidation increased at first then de-creased with temperature elevating;e" increased with temperature raising in the temperature range studied.

pyJac: Analytical Jacobian generator for chemical kinetics

Science.gov (United States)

Niemeyer, Kyle E.; Curtis, Nicholas J.; Sung, Chih-Jen

2017-06-01

Accurate simulations of combustion phenomena require the use of detailed chemical kinetics in order to capture limit phenomena such as ignition and extinction as well as predict pollutant formation. However, the chemical kinetic models for hydrocarbon fuels of practical interest typically have large numbers of species and reactions and exhibit high levels of mathematical stiffness in the governing differential equations, particularly for larger fuel molecules. In order to integrate the stiff equations governing chemical kinetics, generally reactive-flow simulations rely on implicit algorithms that require frequent Jacobian matrix evaluations. Some in situ and a posteriori computational diagnostics methods also require accurate Jacobian matrices, including computational singular perturbation and chemical explosive mode analysis. Typically, finite differences numerically approximate these, but for larger chemical kinetic models this poses significant computational demands since the number of chemical source term evaluations scales with the square of species count. Furthermore, existing analytical Jacobian tools do not optimize evaluations or support emerging SIMD processors such as GPUs. Here we introduce pyJac, a Python-based open-source program that generates analytical Jacobian matrices for use in chemical kinetics modeling and analysis. In addition to producing the necessary customized source code for evaluating reaction rates (including all modern reaction rate formulations), the chemical source terms, and the Jacobian matrix, pyJac uses an optimized evaluation order to minimize computational and memory operations. As a demonstration, we first establish the correctness of the Jacobian matrices for kinetic models of hydrogen, methane, ethylene, and isopentanol oxidation (number of species ranging 13-360) by showing agreement within 0.001% of matrices obtained via automatic differentiation. We then demonstrate the performance achievable on CPUs and GPUs using py

Continuous degradation of trichloroethylene by Xanthobacter sp. strain Py2 during growth on propene.

OpenAIRE

Reij, M W; Kieboom, J; de Bont, J A; Hartmans, S

1995-01-01

Propene-grown Xanthobacter sp. strain Py2 cells can degrade trichloroethylene (TCE), but the transformation capacity of such cells was limited and depended on both the TCE concentration and the biomass concentration. Toxic metabolites presumably accumulated extracellularly, because the fermentation of glucose by yeast cells was inhibited by TCE degradation products formed by strain Py2. The affinity of the propene monooxygenase for TCE was low, and this allowed strain Py2 to grow on propene i...

The coordination chemistry of the neutral tris-2-pyridyl silicon ligand [PhSi(6-Me-2-py)3].

Science.gov (United States)

Plajer, Alex J; Colebatch, Annie L; Enders, Markus; García-Romero, Álvaro; Bond, Andrew D; García-Rodríguez, Raúl; Wright, Dominic S

2018-05-22

Difficulties in the preparation of neutral ligands of the type [RSi(2-py)3] (where 2-py is an unfunctionalised 2-pyridyl ring unit) have thwarted efforts to expand the coordination chemistry of ligands of this type. However, simply switching the pyridyl substituents to 6-methyl-pyridyl groups (6-Me-2-py) in the current paper has allowed smooth, high-yielding access to the [PhSi(6-Me-2-py)3] ligand (1), and the first exploration of its coordination chemistry with transition metals. The synthesis, single-crystal X-ray structures and solution dynamics of the new complexes [{PhSi(6-Me-2-py)3}CuCH3CN][PF6], [{PhSi(6-Me-2-py)3}CuCH3CN][CuCl2], [{PhSi(6-Me-2-py)3}FeCl2], [{PhSi(6-Me-2-py)3}Mo(CO)3] and [{PhSi(6-Me-2-py)3}CoCl2] are reported. The paramagnetic Fe2+ and Co2+ complexes show strongly shifted NMR resonances for the coordinated pyridyl units due to large Fermi-contact shifts. However, magnetic anisotropy also leads to considerable pseudo-contact shifts so that both contributions have to be included in the paramagnetic NMR analysis.

The PyZgoubi framework and the simulation of dynamic aperture in fixed-field alternating-gradient accelerators

International Nuclear Information System (INIS)

Tygier, S.; Appleby, R.B.; Garland, J.M.; Hock, K.; Owen, H.; Kelliher, D.J.; Sheehy, S.L.

2015-01-01

We present PyZgoubi, a framework that has been developed based on the tracking engine Zgoubi to model, optimise and visualise the dynamics in particle accelerators, especially fixed-field alternating-gradient (FFAG) accelerators. We show that PyZgoubi abstracts Zgoubi by wrapping it in an easy-to-use Python framework in order to allow simple construction, parameterisation, visualisation and optimisation of FFAG accelerator lattices. Its object oriented design gives it the flexibility and extensibility required for current novel FFAG design. We apply PyZgoubi to two example FFAGs; this includes determining the dynamic aperture of the PAMELA medical FFAG in the presence of magnet misalignments, and illustrating how PyZgoubi may be used to optimise FFAGs. We also discuss a robust definition of dynamic aperture in an FFAG and show its implementation in PyZgoubi

The PyZgoubi framework and the simulation of dynamic aperture in fixed-field alternating-gradient accelerators

Energy Technology Data Exchange (ETDEWEB)

Tygier, S., E-mail: sam.tygier@hep.manchester.ac.uk [Cockcroft Accelerator Group, The University of Manchester (United Kingdom); Appleby, R.B., E-mail: robert.appleby@manchester.ac.uk [Cockcroft Accelerator Group, The University of Manchester (United Kingdom); Garland, J.M. [Cockcroft Accelerator Group, The University of Manchester (United Kingdom); Hock, K. [University of Liverpool (United Kingdom); Owen, H. [Cockcroft Accelerator Group, The University of Manchester (United Kingdom); Kelliher, D.J.; Sheehy, S.L. [STFC Rutherford Appleton Laboratory (United Kingdom)

2015-03-01

We present PyZgoubi, a framework that has been developed based on the tracking engine Zgoubi to model, optimise and visualise the dynamics in particle accelerators, especially fixed-field alternating-gradient (FFAG) accelerators. We show that PyZgoubi abstracts Zgoubi by wrapping it in an easy-to-use Python framework in order to allow simple construction, parameterisation, visualisation and optimisation of FFAG accelerator lattices. Its object oriented design gives it the flexibility and extensibility required for current novel FFAG design. We apply PyZgoubi to two example FFAGs; this includes determining the dynamic aperture of the PAMELA medical FFAG in the presence of magnet misalignments, and illustrating how PyZgoubi may be used to optimise FFAGs. We also discuss a robust definition of dynamic aperture in an FFAG and show its implementation in PyZgoubi.

PyCorrFit-generic data evaluation for fluorescence correlation spectroscopy.

Science.gov (United States)

Müller, Paul; Schwille, Petra; Weidemann, Thomas

2014-09-01

We present a graphical user interface (PyCorrFit) for the fitting of theoretical model functions to experimental data obtained by fluorescence correlation spectroscopy (FCS). The program supports many data file formats and features a set of tools specialized in FCS data evaluation. The Python source code is freely available for download from the PyCorrFit web page at http://pycorrfit.craban.de. We offer binaries for Ubuntu Linux, Mac OS X and Microsoft Windows. © The Author 2014. Published by Oxford University Press.

Mecanismos para la internacionalización de las PyMES

OpenAIRE

Zapata, Cristina I.

2008-01-01

Las empresas PyMEs son conscientes de la importancia que el proceso exportador tiene para el crecimiento y muchas veces hasta para su supervivencia. El comercio internacional representa un papel cada vez más relevante en el aporte a la actividad extractiva, industrial y de servicios de un país como Argentina. Las motivaciones y el desarrollo de estrategias de Marketing Internacional son la base para el logro del proceso exportación de las empresas PyME de Argentina. Facultad de Ciencias Ec...

Progress on Fabrication of Planar Diffusion Couples with Representative TRISO PyC/SiC Microstructure

Energy Technology Data Exchange (ETDEWEB)

Hunn, John D. [Oak Ridge National Lab. (ORNL), Oak Ridge, TN (United States); Jolly, Brian C. [Oak Ridge National Lab. (ORNL), Oak Ridge, TN (United States); Gerczak, Tyler J. [Oak Ridge National Lab. (ORNL), Oak Ridge, TN (United States); Campbell, Anne A. [Oak Ridge National Lab. (ORNL), Oak Ridge, TN (United States); Schumacher, Austin T. [Oak Ridge National Lab. (ORNL), Oak Ridge, TN (United States)

2017-10-01

Release of fission products from tristructural-isotropic (TRISO) coated particle fuel limits the fuel’s operational lifetime and creates potential safety and maintenance concerns. A need for diffusion analysis in representative TRISO layers exists to provide fuel performance models with high fidelity data to improve fuel performance and efficiency. An effort has been initiated to better understand fission product transport in, and release from, quality TRISO fuel by investigating diffusion couples with representative pyrocarbon (PyC) and silicon carbide (SiC). Here planar PyC/SiC diffusion couples are being developed with representative PyC/SiC layers using a fluidized bed chemical vapor deposition (FBCVD) system identical to those used to produce laboratory-scale TRISO fuel for the Advanced Gas Reactor Fuel Qualification and Development Program’s (AGR) first fuel irradiation. The diffusivity of silver, the silver and palladium system, europium, and strontium in the PyC/SiC will be studied at elevated temperatures and under high temperature neutron irradiation. The study also includes a comparative study of PyC/SiC diffusion couples with varying TRISO layer properties to understand the influence of SiC microstructure (grain size) and the PyC/SiC interface on fission product transport. The first step in accomplishing these goals is the development of the planar diffusion couples. The diffusion couple construction consists of multiple steps which includes fabrication of the primary PyC/SiC structures with targeted layer properties, introduction of fission product species and seal coating to create an isolated system. Coating development has shown planar PyC/SiC diffusion couples with similar properties to AGR TRISO fuel can be produced. A summary of the coating development process, characterization methods, and status are presented.

GillesPy: A Python Package for Stochastic Model Building and Simulation

OpenAIRE

Abel, John H.; Drawert, Brian; Hellander, Andreas; Petzold, Linda R.

2016-01-01

GillesPy is an open-source Python package for model construction and simulation of stochastic biochemical systems. GillesPy consists of a Python framework for model building and an interface to the StochKit2 suite of efficient simulation algorithms based on the Gillespie stochastic simulation algorithms (SSA). To enable intuitive model construction and seamless integration into the scientific Python stack, we present an easy to understand, action-oriented programming interface. Here, we descr...

77 FR 15804 - Employment and Training Administration Program Year (PY) 2012 Workforce Investment Act (WIA...

Science.gov (United States)

2012-03-16

...This notice announces allotments for PY 2012 for WIA Title I Youth, Adults and Dislocated Worker Activities programs; final allotments for Employment Service (ES) activities under the Wagner- Peyser Act for PY 2012 and Workforce Information Grants allotments for PY 2012. Allotments for the Work Opportunity Tax Credits will be announced separately. WIA allotments for States and the State final allotments for the Wagner-Peyser Act are based on formulas defined in their respective statutes. The WIA allotments for the outlying areas are based on a formula determined by the Secretary of Labor (Secretary). As required by WIA section 182(d), on February 17, 2000, a notice of the discretionary formula for allocating PY 2000 funds for the outlying areas (American Samoa, Guam, Marshall Islands, Micronesia, Northern Marianas, Palau, and the Virgin Islands) was published in the Federal Register at 65 FR 8236 (February 17, 2000). The rationale for the formula and methodology was fully explained in the February 17, 2000, Federal Register notice. The formula for PY 2012 is the same as used for PY 2000 and is described in the section on Youth Activities program allotments. Comments are invited on the formula used to allot funds to the outlying areas.

NumPy 1.5 Beginner's Guide

CERN Document Server

Idris, Ivan

2011-01-01

The book is written in beginner's guide style with each aspect of NumPy demonstrated by real world examples. There is appropriate explained code with the required screenshots thrown in for the novice. This book is for the programmer, scientist or engineer, who has basic Python knowledge and would like to be able to do numerical computations with Python.

Statistical properties and fractals of nucleotide clusters in DNA sequences

International Nuclear Information System (INIS)

Sun Tingting; Zhang Linxi; Chen Jin; Jiang Zhouting

2004-01-01

Statistical properties of nucleotide clusters in DNA sequences and their fractals are investigated in this paper. The average size of nucleotide clusters in non-coding sequence is larger than that in coding sequence. We investigate the cluster-size distribution P(S) for human chromosomes 21 and 22, and the results are different from previous works. The cluster-size distribution P(S 1 +S 2 ) with the total size of sequential Pu-cluster and Py-cluster S 1 +S 2 is studied. We observe that P(S 1 +S 2 ) follows an exponential decay both in coding and non-coding sequences. However, we get different results for human chromosomes 21 and 22. The probability distribution P(S 1 ,S 2 ) of nucleotide clusters with the size of sequential Pu-cluster and Py-cluster S 1 and S 2 respectively, is also examined. In the meantime, some of the linear correlations are obtained in the double logarithmic plots of the fluctuation F(l) versus nucleotide cluster distance l along the DNA chain. The power spectrums of nucleotide clusters are also discussed, and it is concluded that the curves are flat and hardly changed and the 1/3 frequency is neither observed in coding sequence nor in non-coding sequence. These investigations can provide some insights into the nucleotide clusters of DNA sequences

Diagnosis of pediatric urinary tract infections

Directory of Open Access Journals (Sweden)

Jeng-Daw Tsai

2016-09-01

Full Text Available Urinary tract infection (UTI is the second common infection in children. The diagnosis of UTI in infants and children can be difficult. Good history taking and physical examination are corner stones of good care of UTI. In addition, this article reviewed current evident on the methods of urine specimen collection and various diagnostic criteria to reach the diagnosis of UTI. Asian Guideline for UTI in children is highlighted to increase consensus of the diagnosis of UTI.

Diagnosis of pediatric urinary tract infections

OpenAIRE

Jeng-Daw Tsai; Chun-Chen Lin; Stephan S. Yang

2016-01-01

Urinary tract infection (UTI) is the second common infection in children. The diagnosis of UTI in infants and children can be difficult. Good history taking and physical examination are corner stones of good care of UTI. In addition, this article reviewed current evident on the methods of urine specimen collection and various diagnostic criteria to reach the diagnosis of UTI. Asian Guideline for UTI in children is highlighted to increase consensus of the diagnosis of UTI.

pyAudioAnalysis: An Open-Source Python Library for Audio Signal Analysis.

Science.gov (United States)

Giannakopoulos, Theodoros

2015-01-01

Audio information plays a rather important role in the increasing digital content that is available today, resulting in a need for methodologies that automatically analyze such content: audio event recognition for home automations and surveillance systems, speech recognition, music information retrieval, multimodal analysis (e.g. audio-visual analysis of online videos for content-based recommendation), etc. This paper presents pyAudioAnalysis, an open-source Python library that provides a wide range of audio analysis procedures including: feature extraction, classification of audio signals, supervised and unsupervised segmentation and content visualization. pyAudioAnalysis is licensed under the Apache License and is available at GitHub (https://github.com/tyiannak/pyAudioAnalysis/). Here we present the theoretical background behind the wide range of the implemented methodologies, along with evaluation metrics for some of the methods. pyAudioAnalysis has been already used in several audio analysis research applications: smart-home functionalities through audio event detection, speech emotion recognition, depression classification based on audio-visual features, music segmentation, multimodal content-based movie recommendation and health applications (e.g. monitoring eating habits). The feedback provided from all these particular audio applications has led to practical enhancement of the library.

PyDBS: an automated image processing workflow for deep brain stimulation surgery.

Science.gov (United States)

D'Albis, Tiziano; Haegelen, Claire; Essert, Caroline; Fernández-Vidal, Sara; Lalys, Florent; Jannin, Pierre

2015-02-01

Deep brain stimulation (DBS) is a surgical procedure for treating motor-related neurological disorders. DBS clinical efficacy hinges on precise surgical planning and accurate electrode placement, which in turn call upon several image processing and visualization tasks, such as image registration, image segmentation, image fusion, and 3D visualization. These tasks are often performed by a heterogeneous set of software tools, which adopt differing formats and geometrical conventions and require patient-specific parameterization or interactive tuning. To overcome these issues, we introduce in this article PyDBS, a fully integrated and automated image processing workflow for DBS surgery. PyDBS consists of three image processing pipelines and three visualization modules assisting clinicians through the entire DBS surgical workflow, from the preoperative planning of electrode trajectories to the postoperative assessment of electrode placement. The system's robustness, speed, and accuracy were assessed by means of a retrospective validation, based on 92 clinical cases. The complete PyDBS workflow achieved satisfactory results in 92 % of tested cases, with a median processing time of 28 min per patient. The results obtained are compatible with the adoption of PyDBS in clinical practice.

Probabilistic programming in Python using PyMC3

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John Salvatier

2016-04-01

Full Text Available Probabilistic programming allows for automatic Bayesian inference on user-defined probabilistic models. Recent advances in Markov chain Monte Carlo (MCMC sampling allow inference on increasingly complex models. This class of MCMC, known as Hamiltonian Monte Carlo, requires gradient information which is often not readily available. PyMC3 is a new open source probabilistic programming framework written in Python that uses Theano to compute gradients via automatic differentiation as well as compile probabilistic programs on-the-fly to C for increased speed. Contrary to other probabilistic programming languages, PyMC3 allows model specification directly in Python code. The lack of a domain specific language allows for great flexibility and direct interaction with the model. This paper is a tutorial-style introduction to this software package.

Dominant obligate anaerobes revealed in lower respiratory tract infection in horses by 16S rRNA gene sequencing.

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Kinoshita, Yuta; Niwa, Hidekazu; Katayama, Yoshinari; Hariu, Kazuhisa

2014-04-01

Obligate anaerobes are important etiological agents in pneumonia or pleuropneumonia in horses, because they are isolated more commonly from ill horses that have died or been euthanized than from those that survive. We performed bacterial identification and antimicrobial susceptibility testing for obligate anaerobes to establish effective antimicrobial therapy. We used 16S rRNA gene sequencing to identify 58 obligate anaerobes and compared the results with those from a phenotypic identification kit. The identification results of 16S rRNA gene sequencing were more reliable than those of the commercial kit. We concluded that genera Bacteroides and Prevotella-especially B. fragilis and P. heparinolytica-are dominant anaerobes in lower respiratory tract infection in horses; these organisms were susceptible to metronidazole, imipenem and clindamycin.

SpacePy - a Python-based library of tools for the space sciences

International Nuclear Information System (INIS)

Morley, Steven K.; Welling, Daniel T.; Koller, Josef; Larsen, Brian A.; Henderson, Michael G.

2010-01-01

Space science deals with the bodies within the solar system and the interplanetary medium; the primary focus is on atmospheres and above - at Earth the short timescale variation in the the geomagnetic field, the Van Allen radiation belts and the deposition of energy into the upper atmosphere are key areas of investigation. SpacePy is a package for Python, targeted at the space sciences, that aims to make basic data analysis, modeling and visualization easier. It builds on the capabilities of the well-known NumPy and MatPlotLib packages. Publication quality output direct from analyses is emphasized. The SpacePy project seeks to promote accurate and open research standards by providing an open environment for code development. In the space physics community there has long been a significant reliance on proprietary languages that restrict free transfer of data and reproducibility of results. By providing a comprehensive, open-source library of widely used analysis and visualization tools in a free, modern and intuitive language, we hope that this reliance will be diminished. SpacePy includes implementations of widely used empirical models, statistical techniques used frequently in space science (e.g. superposed epoch analysis), and interfaces to advanced tools such as electron drift shell calculations for radiation belt studies. SpacePy also provides analysis and visualization tools for components of the Space Weather Modeling Framework - currently this only includes the BATS-R-US 3-D magnetohydrodynamic model and the RAM ring current model - including streamline tracing in vector fields. Further development is currently underway. External libraries, which include well-known magnetic field models, high-precision time conversions and coordinate transformations are wrapped for access from Python using SWIG and f2py. The rest of the tools have been implemented directly in Python. The provision of open-source tools to perform common tasks will provide openness in the

AutoPyFactory: A Scalable Flexible Pilot Factory Implementation

International Nuclear Information System (INIS)

Caballero, J; Hover, J; Love, P; Stewart, G A

2012-01-01

The ATLAS experiment at the CERN LHC is one of the largest users of grid computing infrastructure, which is a central part of the experiment's computing operations. Considerable efforts have been made to use grid technology in the most efficient and effective way, including the use of a pilot job based workload management framework. In this model the experiment submits ‘pilot’ jobs to sites without payload. When these jobs begin to run they contact a central service to pick-up a real payload to execute. The first generation of pilot factories were usually specific to a single Virtual Organization (VO), and were bound to the particular architecture of that VO's distributed processing. A second generation provides factories which are more flexible, not tied to any particular VO, and provide new and improved features such as monitoring, logging, profiling, etc. In this paper we describe this key part of the ATLAS pilot architecture, a second generation pilot factory, AutoPyFactory. AutoPyFactory has a modular design and is highly configurable. It is able to send different types of pilots to sites and exploit different submission mechanisms and queue characteristics. It is tightly integrated with the PanDA job submission framework, coupling pilot flow to the amount of work the site has to run. It gathers information from many sources in order to correctly configure itself for a site and its decision logic can easily be updated. Integrated into AutoPyFactory is a flexible system for delivering both generic and specific job wrappers which can perform many useful actions before starting to run end-user scientific applications, e.g., validation of the middleware, node profiling and diagnostics, and monitoring. AutoPyFactory also has a robust monitoring system that has been invaluable in establishing a reliable pilot factory service for ATLAS.

PyRETIS: A well-done, medium-sized python library for rare events.

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Lervik, Anders; Riccardi, Enrico; van Erp, Titus S

2017-10-30

Transition path sampling techniques are becoming common approaches in the study of rare events at the molecular scale. More efficient methods, such as transition interface sampling (TIS) and replica exchange transition interface sampling (RETIS), allow the investigation of rare events, for example, chemical reactions and structural/morphological transitions, in a reasonable computational time. Here, we present PyRETIS, a Python library for performing TIS and RETIS simulations. PyRETIS directs molecular dynamics (MD) simulations in order to sample rare events with unbiased dynamics. PyRETIS is designed to be easily interfaced with any molecular simulation package and in the present release, it has been interfaced with GROMACS and CP2K, for classical and ab initio MD simulations, respectively. © 2017 Wiley Periodicals, Inc. © 2017 Wiley Periodicals, Inc.

PyOperators: Operators and solvers for high-performance computing

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Chanial, P.; Barbey, N.

2012-12-01

PyOperators is a publicly available library that provides basic operators and solvers for small-to-very large inverse problems ({http://pchanial.github.com/pyoperators}). It forms the backbone of the package PySimulators, which implements specific operators to construct an instrument model and means to conveniently represent a map, a timeline or a time-dependent observation ({http://pchanial.github.com/pysimulators}). Both are part of the Tamasis (Tools for Advanced Map-making, Analysis and SImulations of Submillimeter surveys) toolbox, aiming at providing versatile, reliable, easy-to-use, and optimal map-making tools for Herschel and future generation of sub-mm instruments. The project is a collaboration between 4 institutes (ESO Garching, IAS Orsay, CEA Saclay, Univ. Leiden).

PyNCS: a microkernel for high-level definition and configuration of neuromorphic electronic systems

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Fabio eStefanini

2014-08-01

Full Text Available Neuromorphic hardware offers an electronic substrate for the realization of asynchronousevent-based sensory-motor systems and large-scale spiking neural network architectures. Inorder to characterize these systems, configure them, and carry out modeling experiments, it isoften necessary to interface them to workstations. The software used for this purpose typicallyconsists of a large monolithic block of code highly specific to the hardware setup used. While thisapproach can lead to highly integrated hardware/software systems, it hampers the developmentof modular and neuromorphic infrastructures. To alleviate this problem, we propose PyNCS,an open-source front-end for the definition of neural network models that is interfaced to thehardware through a set of Python Application Programming Interfaces (APIs. The designof PyNCS promotes modularity, portability and expandability and separates implementationfrom hardware description. The high-level front-end that comes with PyNCS includes tools todefine neural network models as well as to create, monitor and analyze spiking data. Here wereport the design philosophy behind the PyNCS framework and describe its implementation.We demonstrate its functionality with two representative case studies, one using an event-based neuromorphic vision sensor, and one using a set of multi-neuron devices for carryingout a cognitive decision-making task involving state-dependent computation. PyNCS, alreadyapplicable to a wide range of existing spike-based neuromorphic setups, will accelerate thedevelopment of hybrid software/hardware neuromorphic systems, thanks to its code flexibility.The code developed is open-source and available online at https://github.com/inincs/pyNCS.

Capping Layer (CL) Induced Antidamping in CL/Py/β-W System (CL: Al, β-Ta, Cu, β-W).

Science.gov (United States)

Behera, Nilamani; Guha, Puspendu; Pandya, Dinesh K; Chaudhary, Sujeet

2017-09-13

For achieving ultrafast switching speed and minimizing dissipation losses, the spin-based data storage device requires a control on effective damping (α eff ) of nanomagnetic bits. Incorporation of interfacial antidamping spin orbit torque (SOT) in spintronic devices therefore has high prospects for enhancing their performance efficiency. Clear evidence of such an interfacial antidamping is found in Al capped Py(15 nm)/β-W(t W )/Si (Py = Ni 81 Fe 19 and t W = thickness of β-W), which is in contrast to the increase of α eff (i.e., damping) usually associated with spin pumping as seen in Py(15 nm)/β-W(t W )/Si system. Because of spin pumping, the interfacial spin mixing conductance (g ↑↓ ) at Py/β-W interface and spin diffusion length (λ SD ) of β-W are found to be 1.63(±0.02) × 10 18 m -2 (1.44(±0.02) × 10 18 m -2 ) and 1.42(±0.19) nm (1.00(±0.10) nm) for Py(15 nm)/β-W(t W )/Si (β-W(t W )/Py(15 nm)/Si) bilayer systems. Other different nonmagnetic capping layers (CL), namely, β-W(2 nm), Cu(2 nm), and β-Ta(2,3,4 nm) were also grown over the same Py(15 nm)/β-W(t W ). However, antidamping is seen only in β-Ta(2,3 nm)/Py(15 nm)/β-W(t W )/Si. This decrease in α eff is attributed to the interfacial Rashba like SOT generated by nonequilibrium spin accumulation subsequent to the spin pumping. Contrary to this, when interlayer positions of Py(15 nm) and β-W(t W ) is interchanged irrespective of the fixed top nonmagnetic layer, an increase of α eff is observed, which is ascribed to spin pumping from Py to β-W layer.

The Metalloporphyrin Antioxidant, MnTE-2-PyP, Inhibits Th2 Cell Immune Responses in an Asthma Model

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Paiboon Jungsuwadee

2012-08-01

Full Text Available MnTE-2-PyP, a superoxide dismutase mimetic, inhibited OVA-induced airway inflammation in mice suggesting an effect on Th2 responsiveness. Thus, we hypothesized that MnTE-2-PyP may alter dendritic cell-Th2 interactions. Bone marrow derived dendritic cells (DC and OVA_323-339-specific Th2 cells were cultured separately in the presence or absence of MnTE-2-PyP for 3 days prior to the co-culturing of the two cell types in the presence of an OVA_323-339 peptide and in some cases stimulated with CD3/CD28. MnTE-2-PyP-pretreated DC inhibited IL-4, IL-5 and IFNγ production and inhibited Th2 cell proliferation in the DC-Th2 co-culturing system in the presence of the OVA_323-339 peptide. Similar results were obtained using the CD3/CD28 cell-activation system; the addition of MnTE-2-PyP inhibited Th2 cell proliferation. MnTE-2-PyP suppressed CD25 expression on OVA-specific Th2 cells, which implied that MnTE-2-PyP can inhibit the activation of Th2 cells. MnTE-2-PyP also down-regulated co-stimulatory molecules: CD40, CD80 and CD86 on immature DC. Our studies suggest that the major mechanism by which MnTE-2-PyP inhibits airway inflammation is by acting on the DC and suppressing Th2 cell proliferation and activation.

PyMICE: APython library for analysis of IntelliCage data.

Science.gov (United States)

Dzik, Jakub M; Puścian, Alicja; Mijakowska, Zofia; Radwanska, Kasia; Łęski, Szymon

2018-04-01

IntelliCage is an automated system for recording the behavior of a group of mice housed together. It produces rich, detailed behavioral data calling for new methods and software for their analysis. Here we present PyMICE, a free and open-source library for analysis of IntelliCage data in the Python programming language. We describe the design and demonstrate the use of the library through a series of examples. PyMICE provides easy and intuitive access to IntelliCage data, and thus facilitates the possibility of using numerous other Python scientific libraries to form a complete data analysis workflow.

PyGaze: an open-source, cross-platform toolbox for minimal-effort programming of eyetracking experiments.

Science.gov (United States)

Dalmaijer, Edwin S; Mathôt, Sebastiaan; Van der Stigchel, Stefan

2014-12-01

The PyGaze toolbox is an open-source software package for Python, a high-level programming language. It is designed for creating eyetracking experiments in Python syntax with the least possible effort, and it offers programming ease and script readability without constraining functionality and flexibility. PyGaze can be used for visual and auditory stimulus presentation; for response collection via keyboard, mouse, joystick, and other external hardware; and for the online detection of eye movements using a custom algorithm. A wide range of eyetrackers of different brands (EyeLink, SMI, and Tobii systems) are supported. The novelty of PyGaze lies in providing an easy-to-use layer on top of the many different software libraries that are required for implementing eyetracking experiments. Essentially, PyGaze is a software bridge for eyetracking research.

ChemoPy: freely available python package for computational biology and chemoinformatics.

Science.gov (United States)

Cao, Dong-Sheng; Xu, Qing-Song; Hu, Qian-Nan; Liang, Yi-Zeng

2013-04-15

Molecular representation for small molecules has been routinely used in QSAR/SAR, virtual screening, database search, ranking, drug ADME/T prediction and other drug discovery processes. To facilitate extensive studies of drug molecules, we developed a freely available, open-source python package called chemoinformatics in python (ChemoPy) for calculating the commonly used structural and physicochemical features. It computes 16 drug feature groups composed of 19 descriptors that include 1135 descriptor values. In addition, it provides seven types of molecular fingerprint systems for drug molecules, including topological fingerprints, electro-topological state (E-state) fingerprints, MACCS keys, FP4 keys, atom pairs fingerprints, topological torsion fingerprints and Morgan/circular fingerprints. By applying a semi-empirical quantum chemistry program MOPAC, ChemoPy can also compute a large number of 3D molecular descriptors conveniently. The python package, ChemoPy, is freely available via http://code.google.com/p/pychem/downloads/list, and it runs on Linux and MS-Windows. Supplementary data are available at Bioinformatics online.

Chimaeric Virus-Like Particles Derived from Consensus Genome Sequences of Human Rotavirus Strains Co-Circulating in Africa

Science.gov (United States)

Jere, Khuzwayo C.; O'Neill, Hester G.; Potgieter, A. Christiaan; van Dijk, Alberdina A.

2014-01-01

Rotavirus virus-like particles (RV-VLPs) are potential alternative non-live vaccine candidates due to their high immunogenicity. They mimic the natural conformation of native viral proteins but cannot replicate because they do not contain genomic material which makes them safe. To date, most RV-VLPs have been derived from cell culture adapted strains or common G1 and G3 rotaviruses that have been circulating in communities for some time. In this study, chimaeric RV-VLPs were generated from the consensus sequences of African rotaviruses (G2, G8, G9 or G12 strains associated with either P[4], P[6] or P[8] genotypes) characterised directly from human stool samples without prior adaptation of the wild type strains to cell culture. Codon-optimised sequences for insect cell expression of genome segments 2 (VP2), 4 (VP4), 6 (VP6) and 9 (VP7) were cloned into a modified pFASTBAC vector, which allowed simultaneous expression of up to four genes using the Bac-to-Bac Baculovirus Expression System (BEVS; Invitrogen). Several combinations of the genome segments originating from different field strains were cloned to produce double-layered RV-VLPs (dRV-VLP; VP2/6), triple-layered RV-VLPs (tRV-VLP; VP2/6/7 or VP2/6/7/4) and chimaeric tRV-VLPs. The RV-VLPs were produced by infecting Spodoptera frugiperda 9 and Trichoplusia ni cells with recombinant baculoviruses using multi-cistronic, dual co-infection and stepwise-infection expression strategies. The size and morphology of the RV-VLPs, as determined by transmission electron microscopy, revealed successful production of RV-VLPs. The novel approach of producing tRV-VLPs, by using the consensus insect cell codon-optimised nucleotide sequence derived from dsRNA extracted directly from clinical specimens, should speed-up vaccine research and development by by-passing the need to adapt rotaviruses to cell culture. Other problems associated with cell culture adaptation, such as possible changes in epitopes, can also be circumvented

PyNCS: a microkernel for high-level definition and configuration of neuromorphic electronic systems.

Science.gov (United States)

Stefanini, Fabio; Neftci, Emre O; Sheik, Sadique; Indiveri, Giacomo

2014-01-01

Neuromorphic hardware offers an electronic substrate for the realization of asynchronous event-based sensory-motor systems and large-scale spiking neural network architectures. In order to characterize these systems, configure them, and carry out modeling experiments, it is often necessary to interface them to workstations. The software used for this purpose typically consists of a large monolithic block of code which is highly specific to the hardware setup used. While this approach can lead to highly integrated hardware/software systems, it hampers the development of modular and reconfigurable infrastructures thus preventing a rapid evolution of such systems. To alleviate this problem, we propose PyNCS, an open-source front-end for the definition of neural network models that is interfaced to the hardware through a set of Python Application Programming Interfaces (APIs). The design of PyNCS promotes modularity, portability and expandability and separates implementation from hardware description. The high-level front-end that comes with PyNCS includes tools to define neural network models as well as to create, monitor and analyze spiking data. Here we report the design philosophy behind the PyNCS framework and describe its implementation. We demonstrate its functionality with two representative case studies, one using an event-based neuromorphic vision sensor, and one using a set of multi-neuron devices for carrying out a cognitive decision-making task involving state-dependent computation. PyNCS, already applicable to a wide range of existing spike-based neuromorphic setups, will accelerate the development of hybrid software/hardware neuromorphic systems, thanks to its code flexibility. The code is open-source and available online at https://github.com/inincs/pyNCS.

PyNCS: a microkernel for high-level definition and configuration of neuromorphic electronic systems

Science.gov (United States)

Stefanini, Fabio; Neftci, Emre O.; Sheik, Sadique; Indiveri, Giacomo

2014-01-01

Neuromorphic hardware offers an electronic substrate for the realization of asynchronous event-based sensory-motor systems and large-scale spiking neural network architectures. In order to characterize these systems, configure them, and carry out modeling experiments, it is often necessary to interface them to workstations. The software used for this purpose typically consists of a large monolithic block of code which is highly specific to the hardware setup used. While this approach can lead to highly integrated hardware/software systems, it hampers the development of modular and reconfigurable infrastructures thus preventing a rapid evolution of such systems. To alleviate this problem, we propose PyNCS, an open-source front-end for the definition of neural network models that is interfaced to the hardware through a set of Python Application Programming Interfaces (APIs). The design of PyNCS promotes modularity, portability and expandability and separates implementation from hardware description. The high-level front-end that comes with PyNCS includes tools to define neural network models as well as to create, monitor and analyze spiking data. Here we report the design philosophy behind the PyNCS framework and describe its implementation. We demonstrate its functionality with two representative case studies, one using an event-based neuromorphic vision sensor, and one using a set of multi-neuron devices for carrying out a cognitive decision-making task involving state-dependent computation. PyNCS, already applicable to a wide range of existing spike-based neuromorphic setups, will accelerate the development of hybrid software/hardware neuromorphic systems, thanks to its code flexibility. The code is open-source and available online at https://github.com/inincs/pyNCS. PMID:25232314

WekaPyScript: Classification, Regression, and Filter Schemes for WEKA Implemented in Python

Directory of Open Access Journals (Sweden)

Christopher Beckham

2016-08-01

Full Text Available WekaPyScript is a package for the machine learning software WEKA that allows learning algorithms and preprocessing methods for classification and regression to be written in Python, as opposed to WEKA’s implementation language, Java. This opens up WEKA to its machine learning and scientific computing ecosystem. Furthermore, due to Python’s minimalist syntax, learning algorithms and preprocessing methods can be prototyped easily and utilised from within WEKA. WekaPyScript works by running a local Python server using the host’s installation of Python; as a result, any libraries installed in the host installation can be leveraged when writing a script for WekaPyScript. Three example scripts (two learning algorithms and one preprocessing method are presented.

GillesPy: A Python Package for Stochastic Model Building and Simulation.

Science.gov (United States)

Abel, John H; Drawert, Brian; Hellander, Andreas; Petzold, Linda R

2016-09-01

GillesPy is an open-source Python package for model construction and simulation of stochastic biochemical systems. GillesPy consists of a Python framework for model building and an interface to the StochKit2 suite of efficient simulation algorithms based on the Gillespie stochastic simulation algorithms (SSA). To enable intuitive model construction and seamless integration into the scientific Python stack, we present an easy to understand, action-oriented programming interface. Here, we describe the components of this package and provide a detailed example relevant to the computational biology community.

Zn(II) coordination polymer of an in situ generated 4-pyridyl (4Py) attached bis(amido)phosphate ligand, [PO2(NH4Py)2]- showing preferential water uptake over aliphatic alcohols.

Science.gov (United States)

Gupta, Arvind K; Nagarkar, Sanjog S; Boomishankar, Ramamoorthy

2013-08-14

Two polymorphic 2D-coordination polymers of composition [ZnL(HCO2)]∞ were synthesized from an in situ generated ligand [PO2(NH(4)Py)2](-) (L(-)). The ligand L(-) was generated by a facile metal-assisted P-N bond hydrolysis reaction from the corresponding phosphonium salt 1, [P(NH(4)Py)4]Cl, or from the neutral phosphoric triamide 2, [PO(NH(4)Py)3]. The de-solvated sample of the polymer [ZnL(HCO2)]∞ features polar micropores and shows a type I isotherm for CO2 sorption whereas a type II behaviour was observed for N2. The vapour sorption isotherm of the de-solvated sample of [ZnL(HCO2)]∞ shows preferential adsorption of water vapour over aliphatic alcohols.

In vitro site selection of a consensus binding site for the Drosophila melanogaster Tbx20 homolog midline.

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Nima Najand

Full Text Available We employed in vitro site selection to identify a consensus binding sequence for the Drosophila melanogaster Tbx20 T-box transcription factor homolog Midline. We purified a bacterially expressed T-box DNA binding domain of Midline, and used it in four rounds of precipitation and polymerase-chain-reaction based amplification. We cloned and sequenced 54 random oligonucleotides selected by Midline. Electromobility shift-assays confirmed that 27 of these could bind the Midline T-box. Sequence alignment of these 27 clones suggests that Midline binds as a monomer to a consensus sequence that contains an AGGTGT core. Thus, the Midline consensus binding site we define in this study is similar to that defined for vertebrate Tbx20, but differs from a previously reported Midline binding sequence derived through site selection.

Pediatric urinary tract infection

Energy Technology Data Exchange (ETDEWEB)

Blickman, J.G.

1991-02-06

Acute urinary tract infection (UTI) is an important cause of morbidity in children and may be complicated by congenital urinary tract abnormalities of a functional or anatomic nature which, predispose to recurrent UTI's that in turn may lead to renal failure and hypertension. Early radiologic and ultrasonographic investigations may reveal these anatomic anomalies in particular because the urinary tract, specifically in children, is not readily accessible to adequate clinical examinations Excretory urography (EU) has been considered as the 'gold standard' of upper urinary tract visualization, while the voiding cystourethrogram (VCUG) was thought to be the preferential method of imaging of the lower urinary tract. Recently, major technical advances have altered this commonly accepted diagnostic workup. Although ultrasonography, radio-nuclide scanning and urodynamics have become important contributors to the understanding of pathophysiology of UTI's their value and place in assessment of the sequence of imaging has not been comprehensively studied. This thesis deals about the optimization of the choice and the order of the different imaging techniques used in the evaluation of children, younger than six year with UTI. (author). 243 refs.; 23 figs.; 8 tabs.

Pediatric urinary tract infection

International Nuclear Information System (INIS)

Blickman, J.G.

1991-01-01

Acute urinary tract infection (UTI) is an important cause of morbidity in children and may be complicated by congenital urinary tract abnormalities of a functional or anatomic nature which, predispose to recurrent UTI's that in turn may lead to renal failure and hypertension. Early radiologic and ultrasonographic investigations may reveal these anatomic anomalies in particular because the urinary tract, specifically in children, is not readily accessible to adequate clinical examinations Excretory urography (EU) has been considered as the 'gold standard' of upper urinary tract visualization, while the voiding cystourethrogram (VCUG) was thought to be the preferential method of imaging of the lower urinary tract. Recently, major technical advances have altered this commonly accepted diagnostic workup. Although ultrasonography, radio-nuclide scanning and urodynamics have become important contributors to the understanding of pathophysiology of UTI's their value and place in assessment of the sequence of imaging has not been comprehensively studied. This thesis deals about the optimization of the choice and the order of the different imaging techniques used in the evaluation of children, younger than six year with UTI. (author). 243 refs.; 23 figs.; 8 tabs

InteractiveROSETTA: a graphical user interface for the PyRosetta protein modeling suite.

Science.gov (United States)

Schenkelberg, Christian D; Bystroff, Christopher

2015-12-15

Modern biotechnical research is becoming increasingly reliant on computational structural modeling programs to develop novel solutions to scientific questions. Rosetta is one such protein modeling suite that has already demonstrated wide applicability to a number of diverse research projects. Unfortunately, Rosetta is largely a command-line-driven software package which restricts its use among non-computational researchers. Some graphical interfaces for Rosetta exist, but typically are not as sophisticated as commercial software. Here, we present InteractiveROSETTA, a graphical interface for the PyRosetta framework that presents easy-to-use controls for several of the most widely used Rosetta protocols alongside a sophisticated selection system utilizing PyMOL as a visualizer. InteractiveROSETTA is also capable of interacting with remote Rosetta servers, facilitating sophisticated protocols that are not accessible in PyRosetta or which require greater computational resources. InteractiveROSETTA is freely available at https://github.com/schenc3/InteractiveROSETTA/releases and relies upon a separate download of PyRosetta which is available at http://www.pyrosetta.org after obtaining a license (free for academic use). © The Author 2015. Published by Oxford University Press. All rights reserved. For Permissions, please e-mail: journals.permissions@oup.com.

PyMES INNOVADORAS. Cambio de Estrategias e Instrumentos

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Juan Gonzalo Castellanos

2003-07-01

Full Text Available ¿Cómo hacer que las PyMES aumenten el valor de sus productos y servicios? ¿Cómo incorporar valor-conocimiento a la totalidad de la organización? Se intenta en este escrito introducir algunos conceptos útiles para comprender mejor la compleja realidad de los pequeños y medianos negocios en el mercado de hoy. En este artículo se trabajan conceptos relativos a la innovación como actividad primordial e integradora en el quehacer de una empresa competitiva y se revisan los resultados de diversos estudios sobre innovación y PyMES en el mundo desarrollado y en desarrollo, incluyendo los resultados del análisis de los casos elaborados dentro del ejercicio que promueve la Escuela de Administración de Negocios EAN en la línea de investigación sobre pequeñas y medianas empresas.

Replacing the IRAF/PyRAF Code-base at STScI: The Advanced Camera for Surveys (ACS)

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Lucas, Ray A.; Desjardins, Tyler D.; STScI ACS (Advanced Camera for Surveys) Team

2018-06-01

IRAF/PyRAF are no longer viable on the latest hardware often used by HST observers, therefore STScI no longer actively supports IRAF or PyRAF for most purposes. STScI instrument teams are in the process of converting all of our data processing and analysis code from IRAF/PyRAF to Python, including our calibration reference file pipelines and data reduction software. This is exemplified by our latest ACS Data Handbook, version 9.0, which was recently published in February 2018. Examples of IRAF and PyRAF commands have now been replaced by code blocks in Python, with references linked to documentation on how to download and install the latest Python software via Conda and AstroConda. With the temporary exception of the ACS slitless spectroscopy tool aXe, all ACS-related software is now independent of IRAF/PyRAF. A concerted effort has been made across STScI divisions to help the astronomical community transition from IRAF/PyRAF to Python, with tools such as Python Jupyter notebooks being made to give users workable examples. In addition to our code changes, the new ACS data handbook discusses the latest developments in charge transfer efficiency (CTE) correction, bias de-striping, and updates to the creation and format of calibration reference files among other topics.

ObsPy: A Python toolbox for seismology - Sustainability, New Features, and Applications

Science.gov (United States)

Krischer, L.; Megies, T.; Sales de Andrade, E.; Barsch, R.; MacCarthy, J.

2016-12-01

ObsPy (https://www.obspy.org) is a community-driven, open-source project dedicated to offer a bridge for seismology into the scientific Python ecosystem. Amongst other things, it provides Read and write support for essentially every commonly used data format in seismology with a unified interface. This includes waveform data as well as station and event meta information. A signal processing toolbox tuned to the specific needs of seismologists. Integrated access to the largest data centers, web services, and databases. Wrappers around third party codes like libmseed and evalresp. Using ObsPy enables users to take advantage of the vast scientific ecosystem that has developed around Python. In contrast to many other programming languages and tools, Python is simple enough to enable an exploratory and interactive coding style desired by many scientists. At the same time it is a full-fledged programming language usable by software engineers to build complex and large programs. This combination makes it very suitable for use in seismology where research code often must be translated to stable and production ready environments, especially in the age of big data. ObsPy has seen constant development for more than six years and enjoys a large rate of adoption in the seismological community with thousands of users. Successful applications include time-dependent and rotational seismology, big data processing, event relocations, and synthetic studies about attenuation kernels and full-waveform inversions to name a few examples. Additionally it sparked the development of several more specialized packages slowly building a modern seismological ecosystem around it. We will present a short overview of the capabilities of ObsPy and point out several representative use cases and more specialized software built around ObsPy. Additionally we will discuss new and upcoming features, as well as the sustainability of open-source scientific software.

ObsPy - A Python Toolbox for Seismology - and Applications

Science.gov (United States)

Krischer, L.; Megies, T.; Barsch, R.; MacCarthy, J.; Lecocq, T.; Koymans, M. R.; Carothers, L.; Eulenfeld, T.; Reyes, C. G.; Falco, N.; Sales de Andrade, E.

2017-12-01

Recent years witnessed the evolution of Python's ecosystem into one of the most powerful and productive scientific environments across disciplines. ObsPy (https://www.obspy.org) is a fully community driven, open-source project dedicated to provide a bridge for seismology into that ecosystem. It is a Python toolbox offering: Read and write support for essentially every commonly used data format in seismology with a unified interface and automatic format detection. This includes waveform data (MiniSEED, SAC, SEG-Y, Reftek, …) as well as station (SEED, StationXML, SC3ML, …) and event meta information (QuakeML, ZMAP, …). Integrated access to the largest data centers, web services, and real-time data streams (FDSNWS, ArcLink, SeedLink, ...). A powerful signal processing toolbox tuned to the specific needs of seismologists. Utility functionality like travel time calculations with the TauP method, geodetic functions, and data visualizations. ObsPy has been in constant development for more than eight years and is developed and used by scientists around the world with successful applications in all branches of seismology. Additionally it nowadays serves as the foundation for a large number of more specialized packages. Newest features include: Full interoperability of SEED and StationXML/Inventory objects Access to the Nominal Response Library (NRL) for easy and quick creation of station metadata from scratch Support for the IRIS Federated Catalog Service Improved performance of the EarthWorm client Several improvements to MiniSEED read/write module Improved plotting capabilities for PPSD (spectrograms, PSD of discrete frequencies over time, ..) Support for.. Reading ArcLink Inventory XML Reading Reftek data format Writing SeisComp3 ML (SC3ML) Writing StationTXT format This presentation will give a short overview of the capabilities of ObsPy and point out several representative or new use cases and show-case some projects that are based on ObsPy, e.g.: seismo

Three Unique Implementations of Processes for PyCSP

DEFF Research Database (Denmark)

Friborg, Rune Møllegaard; Bjørndalen, John Markus; Vinter, Brian

2009-01-01

In this work we motivate and describe three unique implementations of processes for PyCSP: process, thread and greenlet based. The overall purpose is to demonstrate the feasibility of Communicating Sequential Processes as a framework for different application types and target platforms. The result...

Thermal spin current generation and spin transport in Pt/magnetic-insulator/Py heterostructures

Science.gov (United States)

Chen, Ching-Tzu; Safranski, Christopher; Krivorotov, Ilya; Sun, Jonathan

Magnetic insulators can transmit spin current via magnon propagation while blocking charge current. Furthermore, under Joule heating, magnon flow as a result of the spin Seeback effect can generate additional spin current. Incorporating magnetic insulators in a spin-orbit torque magnetoresistive memory device can potentially yield high switching efficiencies. Here we report the DC magneto-transport studies of these two effects in Pt/magnetic-insulator/Py heterostructures, using ferrimagnetic CoFexOy (CFO) and antiferromagnet NiO as the model magnetic insulators. We observe the presence and absence of the inverse spin-Hall signals from the thermal spin current in Pt/CFO/Py and Pt/NiO/Py structures. These results are consistent with our spin-torque FMR linewidths in comparison. We will also report investigations into the magnetic field-angle dependence of these observations.

Endemic and Epidemic Lineages of Escherichia coli that Cause Urinary Tract Infections

Science.gov (United States)

Tabor, Helen; Tellis, Patricia; Vincent, Caroline; Tellier, Pierre-Paul

2008-01-01

Women with urinary tract infections (UTIs) in California, USA (1999–2001), were infected with closely related or indistinguishable strains of Escherichia coli (clonal groups), which suggests point source dissemination. We compared strains of UTI-causing E. coli in California with strains causing such infections in Montréal, Québec, Canada. Urine specimens from women with community-acquired UTIs in Montréal (2006) were cultured for E. coli. Isolates that caused 256 consecutive episodes of UTI were characterized by antimicrobial drug susceptibility profile, enterobacterial repetitive intergenic consensus 2 PCR, serotyping, XbaI and NotI pulsed-field gel electrophoresis, multilocus sequence typing, and phylogenetic typing. We confirmed the presence of drug-resistant, genetically related, and temporally clustered E. coli clonal groups that caused community-acquired UTIs in unrelated women in 2 locations and 2 different times. Two clonal groups were identified in both locations. Epidemic transmission followed by endemic transmission of UTI-causing clonal groups may explain these clusters of UTI cases. PMID:18826822

ImagePy: an open-source, Python-based and platform-independent software package for boimage analysis.

Science.gov (United States)

Wang, Anliang; Yan, Xiaolong; Wei, Zhijun

2018-04-27

This note presents the design of a scalable software package named ImagePy for analysing biological images. Our contribution is concentrated on facilitating extensibility and interoperability of the software through decoupling the data model from the user interface. Especially with assistance from the Python ecosystem, this software framework makes modern computer algorithms easier to be applied in bioimage analysis. ImagePy is free and open source software, with documentation and code available at https://github.com/Image-Py/imagepy under the BSD license. It has been tested on the Windows, Mac and Linux operating systems. wzjdlut@dlut.edu.cn or yxdragon@imagepy.org.

pyPaSWAS : Python-based multi-core CPU and GPU sequence alignment

NARCIS (Netherlands)

Warris, Sven; Timal, N Roshan N; Kempenaar, Marcel; Poortinga, Arne M; van de Geest, Henri; Varbanescu, Ana L; Nap, Jan-Peter

2018-01-01

BACKGROUND: Our previously published CUDA-only application PaSWAS for Smith-Waterman (SW) sequence alignment of any type of sequence on NVIDIA-based GPUs is platform-specific and therefore adopted less than could be. The OpenCL language is supported more widely and allows use on a variety of

PyMercury: Interactive Python for the Mercury Monte Carlo Particle Transport Code

International Nuclear Information System (INIS)

Iandola, F.N.; O'Brien, M.J.; Procassini, R.J.

2010-01-01

Monte Carlo particle transport applications are often written in low-level languages (C/C++) for optimal performance on clusters and supercomputers. However, this development approach often sacrifices straightforward usability and testing in the interest of fast application performance. To improve usability, some high-performance computing applications employ mixed-language programming with high-level and low-level languages. In this study, we consider the benefits of incorporating an interactive Python interface into a Monte Carlo application. With PyMercury, a new Python extension to the Mercury general-purpose Monte Carlo particle transport code, we improve application usability without diminishing performance. In two case studies, we illustrate how PyMercury improves usability and simplifies testing and validation in a Monte Carlo application. In short, PyMercury demonstrates the value of interactive Python for Monte Carlo particle transport applications. In the future, we expect interactive Python to play an increasingly significant role in Monte Carlo usage and testing.

Particular Candida albicans strains in the digestive tract of dyspeptic patients, identified by multilocus sequence typing.

Directory of Open Access Journals (Sweden)

Yan-Bing Gong

Full Text Available BACKGROUND: Candida albicans is a human commensal that is also responsible for chronic gastritis and peptic ulcerous disease. Little is known about the genetic profiles of the C. albicans strains in the digestive tract of dyspeptic patients. The aim of this study was to evaluate the prevalence, diversity, and genetic profiles among C. albicans isolates recovered from natural colonization of the digestive tract in the dyspeptic patients. METHODS AND FINDINGS: Oral swab samples (n = 111 and gastric mucosa samples (n = 102 were obtained from a group of patients who presented dyspeptic symptoms or ulcer complaints. Oral swab samples (n = 162 were also obtained from healthy volunteers. C. albicans isolates were characterized and analyzed by multilocus sequence typing. The prevalence of Candida spp. in the oral samples was not significantly different between the dyspeptic group and the healthy group (36.0%, 40/111 vs. 29.6%, 48/162; P > 0.05. However, there were significant differences between the groups in the distribution of species isolated and the genotypes of the C. albicans isolates. C. albicans was isolated from 97.8% of the Candida-positive subjects in the dyspeptic group, but from only 56.3% in the healthy group (P < 0.001. DST1593 was the dominant C. albicans genotype from the digestive tract of the dyspeptic group (60%, 27/45, but not the healthy group (14.8%, 4/27 (P < 0.001. CONCLUSIONS: Our data suggest a possible link between particular C. albicans strain genotypes and the host microenvironment. Positivity for particular C. albicans genotypes could signify susceptibility to dyspepsia.

PyMOOSE: interoperable scripting in Python for MOOSE

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Subhasis Ray

2008-12-01

Full Text Available Python is emerging as a common scripting language for simulators. This opens up many possibilities for interoperability in the form of analysis, interfaces, and communications between simulators. We report the integration of Python scripting with the Multi-scale Object Oriented Simulation Environment (MOOSE. MOOSE is a general-purpose simulation system for compartmental neuronal models and for models of signaling pathways based on chemical kinetics. We show how the Python-scripting version of MOOSE, PyMOOSE, combines the power of a compiled simulator with the versatility and ease of use of Python. We illustrate this by using Python numerical libraries to analyze MOOSE output online, and by developing a GUI in Python/Qt for a MOOSE simulation. Finally, we build and run a composite neuronal/signaling model that uses both the NEURON and MOOSE numerical engines, and Python as a bridge between the two. Thus PyMOOSE has a high degree of interoperability with analysis routines, with graphical toolkits, and with other simulators.

SINA: accurate high-throughput multiple sequence alignment of ribosomal RNA genes.

Science.gov (United States)

Pruesse, Elmar; Peplies, Jörg; Glöckner, Frank Oliver

2012-07-15

In the analysis of homologous sequences, computation of multiple sequence alignments (MSAs) has become a bottleneck. This is especially troublesome for marker genes like the ribosomal RNA (rRNA) where already millions of sequences are publicly available and individual studies can easily produce hundreds of thousands of new sequences. Methods have been developed to cope with such numbers, but further improvements are needed to meet accuracy requirements. In this study, we present the SILVA Incremental Aligner (SINA) used to align the rRNA gene databases provided by the SILVA ribosomal RNA project. SINA uses a combination of k-mer searching and partial order alignment (POA) to maintain very high alignment accuracy while satisfying high throughput performance demands. SINA was evaluated in comparison with the commonly used high throughput MSA programs PyNAST and mothur. The three BRAliBase III benchmark MSAs could be reproduced with 99.3, 97.6 and 96.1 accuracy. A larger benchmark MSA comprising 38 772 sequences could be reproduced with 98.9 and 99.3% accuracy using reference MSAs comprising 1000 and 5000 sequences. SINA was able to achieve higher accuracy than PyNAST and mothur in all performed benchmarks. Alignment of up to 500 sequences using the latest SILVA SSU/LSU Ref datasets as reference MSA is offered at http://www.arb-silva.de/aligner. This page also links to Linux binaries, user manual and tutorial. SINA is made available under a personal use license.

MnTE-2-PyP modulates thiol oxidation in a hydrogen peroxide-mediated manner in a human prostate cancer cell.

Science.gov (United States)

Tong, Qiang; Zhu, Yuxiang; Galaske, Joseph W; Kosmacek, Elizabeth A; Chatterjee, Arpita; Dickinson, Bryan C; Oberley-Deegan, Rebecca E

2016-12-01

To improve the treatment of advanced prostate cancer, the development of effective and innovative antitumor agents is needed. Our previous work demonstrated that the ROS (reactive oxygen species) scavenger, MnTE-2-PyP, inhibited human prostate cancer growth and also inhibited prostate cancer migration and invasion. We showed that MnTE-2-PyP treatment altered the affinity of the histone acetyltransferase enzyme, p300, to bind to DNA. We speculate that this may be one mechanism by which MnTE-2-PyP inhibits prostate cancer progression. Specifically, MnTE-2-PyP decreased p300/HIF-1/CREB complex (p300/hypoxia-inducible factor-1/cAMP response element-binding protein) binding to a specific hypoxia-response element (HRE) motif within the plasminogen activator inhibitor-1 (PAI-1) gene promoter region, and consequently, repressed PAI-1 expression. However, it remains unclear how MnTE-2-PyP reduces p300 complex binding affinity to the promoter region of specific genes. In this study, we found that overexpression of Cu/ZnSOD (superoxide dismutase 1, SOD1) significantly suppressed PAI-1 gene expression and p300 complex binding to the promoter region of PAI-1 gene, just as was observed in cells treated with MnTE-2-PyP. Furthermore, catalase (CAT) overexpression rescued the inhibition of PAI-1 expression and p300 binding by MnTE-2-PyP. Taken together, the above findings suggest that hydrogen peroxide (H 2 O 2 ) is likely the mediator through which MnTE-2-PyP inhibits the PAI-1 expression and p300 complex binding in PC3 cells. To confirm this, we measured the production of H 2 O 2 following overexpression of SOD1 or catalase with MnTE-2-PyP treatment in the presence or absence of radiation. We found that MnTE-2-PyP increased the intracellular steady-state levels of H 2 O 2 and increased nuclear H 2 O 2 levels. As expected, catalase overexpression significantly decreased the levels of intracellular H 2 O 2 induced by MnTE-2-PyP. We then determined if this increased H 2 O 2

LANL12-RS-107J PYTHON Radiography Analysis Tool (PyRAT). Mid-Year Deliverable Report for FY15

International Nuclear Information System (INIS)

Temple, Brian Allen; Armstrong, Jerawan Chudoung

2015-01-01

This document is a mid-year report on a deliverable for the PYTHON Radiography Analysis Tool (PyRAT) for project LANL12-RS-107J in FY15. The deliverable is deliverable number 2 in the work package and is titled ''Add the ability to read in more types of image file formats in PyRAT''. Right now PyRAT can only read in uncompressed TIF files (tiff files). It is planned to expand the file formats that can be read by PyRAT, making it easier to use in more situations. A summary of the file formats added include jpeg, jpg, png and formatted ASCII files.

Predicting Consensus Structures for RNA Alignments Via Pseudo-Energy Minimization

Directory of Open Access Journals (Sweden)

Junilda Spirollari

2009-01-01

Full Text Available Thermodynamic processes with free energy parameters are often used in algorithms that solve the free energy minimization problem to predict secondary structures of single RNA sequences. While results from these algorithms are promising, an observation is that single sequence-based methods have moderate accuracy and more information is needed to improve on RNA secondary structure prediction, such as covariance scores obtained from multiple sequence alignments. We present in this paper a new approach to predicting the consensus secondary structure of a set of aligned RNA sequences via pseudo-energy minimization. Our tool, called RSpredict, takes into account sequence covariation and employs effective heuristics for accuracy improvement. RSpredict accepts, as input data, a multiple sequence alignment in FASTA or ClustalW format and outputs the consensus secondary structure of the input sequences in both the Vienna style Dot Bracket format and the Connectivity Table format. Our method was compared with some widely used tools including KNetFold, Pfold and RNAalifold. A comprehensive test on different datasets including Rfam sequence alignments and a multiple sequence alignment obtained from our study on the Drosophila X chromosome reveals that RSpredict is competitive with the existing tools on the tested datasets. RSpredict is freely available online as a web server and also as a jar file for download at http:// datalab.njit.edu/biology/RSpredict.

A universal protocol to generate consensus level genome sequences for foot-and-mouth disease virus and other positive-sense polyadenylated RNA viruses using the Illumina MiSeq.

Science.gov (United States)

Logan, Grace; Freimanis, Graham L; King, David J; Valdazo-González, Begoña; Bachanek-Bankowska, Katarzyna; Sanderson, Nicholas D; Knowles, Nick J; King, Donald P; Cottam, Eleanor M

2014-09-30

Next-Generation Sequencing (NGS) is revolutionizing molecular epidemiology by providing new approaches to undertake whole genome sequencing (WGS) in diagnostic settings for a variety of human and veterinary pathogens. Previous sequencing protocols have been subject to biases such as those encountered during PCR amplification and cell culture, or are restricted by the need for large quantities of starting material. We describe here a simple and robust methodology for the generation of whole genome sequences on the Illumina MiSeq. This protocol is specific for foot-and-mouth disease virus (FMDV) or other polyadenylated RNA viruses and circumvents both the use of PCR and the requirement for large amounts of initial template. The protocol was successfully validated using five FMDV positive clinical samples from the 2001 epidemic in the United Kingdom, as well as a panel of representative viruses from all seven serotypes. In addition, this protocol was successfully used to recover 94% of an FMDV genome that had previously been identified as cell culture negative. Genome sequences from three other non-FMDV polyadenylated RNA viruses (EMCV, ERAV, VESV) were also obtained with minor protocol amendments. We calculated that a minimum coverage depth of 22 reads was required to produce an accurate consensus sequence for FMDV O. This was achieved in 5 FMDV/O/UKG isolates and the type O FMDV from the serotype panel with the exception of the 5' genomic termini and area immediately flanking the poly(C) region. We have developed a universal WGS method for FMDV and other polyadenylated RNA viruses. This method works successfully from a limited quantity of starting material and eliminates the requirement for genome-specific PCR amplification. This protocol has the potential to generate consensus-level sequences within a routine high-throughput diagnostic environment.

Assessment of p-y curves from numerical methods for a non-slender monopile in cohesionless soil

Energy Technology Data Exchange (ETDEWEB)

Ibsen, L. B.; Ravn Roesen, H. [Aalborg Univ. Dept. of Civil Engineering, Aalborg (Denmark); Hansen, Mette; Kirk Wolf, T. [COWI, Kgs. Lyngby (Denmark); Lange Rasmussen, K. [Niras, Aalborg (Denmark)

2013-06-15

In current design the monopile is a widely used solution as foundation of offshore wind turbines. Winds and waves subject the monopile to considerable lateral loads. The behaviour of monopiles under lateral loading is not fully understood and the current design guidances apply the p-y curve method in a Winkler model approach. The p-y curve method was originally developed for jag-piles used in the oil and gas industry which are much more slender than the monopile foundation. In recent years the 3D finite element analysis has become a tool in the investigation of complex geotechnical situations, such as the laterally loaded monopile. In this paper a 3D FEA is conducted as basis of an extraction of p-y curves, as a basis for an evaluation of the traditional curves. Two different methods are applied to create a list of data points used for the p-y curves: A force producing a similar response as seen in the ULS situation is applied stepwise; hereby creating the most realistic soil response. This method, however, does not generate sufficient data points around the rotation point of the pile. Therefore, also a forced horizontal displacement of the entire pile is applied, whereby displacements are created over the entire length of the pile. The response is extracted from the interface and the nearby soil elements respectively, as to investigate the influence this has on the computed curves. p-y curves are obtained near the rotation point by evaluation of soil response during a prescribed displacement but the response is not in clear agreement with the response during an applied load. Two different material models are applied. It is found that the applied material models have a significant influence on the stiffness of the evaluated p-y curves. The p-y curves evaluated by means of FEA are compared to the conventional p-y curve formulation which provides a much stiffer response. It is found that the best response is computed by implementing the Hardening Soil model and

PROSPECT improves cis-acting regulatory element prediction by integrating expression profile data with consensus pattern searches

Science.gov (United States)

Fujibuchi, Wataru; Anderson, John S. J.; Landsman, David

2001-01-01

Consensus pattern and matrix-based searches designed to predict cis-acting transcriptional regulatory sequences have historically been subject to large numbers of false positives. We sought to decrease false positives by incorporating expression profile data into a consensus pattern-based search method. We have systematically analyzed the expression phenotypes of over 6000 yeast genes, across 121 expression profile experiments, and correlated them with the distribution of 14 known regulatory elements over sequences upstream of the genes. Our method is based on a metric we term probabilistic element assessment (PEA), which is a ranking of potential sites based on sequence similarity in the upstream regions of genes with similar expression phenotypes. For eight of the 14 known elements that we examined, our method had a much higher selectivity than a naïve consensus pattern search. Based on our analysis, we have developed a web-based tool called PROSPECT, which allows consensus pattern-based searching of gene clusters obtained from microarray data. PMID:11574681

An International Continence Society (ICS) report on the terminology for adult neurogenic lower urinary tract dysfunction (ANLUTD).

Science.gov (United States)

Gajewski, Jerzy B; Schurch, Brigitte; Hamid, Rizwan; Averbeck, Márcio; Sakakibara, Ryuji; Agrò, Enrico F; Dickinson, Tamara; Payne, Christopher K; Drake, Marcus J; Haylen, Bernie T

2018-03-01

The terminology for adult neurogenic lower urinary tract dysfunction (ANLUTD) should be defined and organized in a clinically based consensus Report. This Report has been created by a Working Group under the auspices and guidelines of the International Continence Society (ICS) Standardization Steering Committee (SSC) assisted at intervals by external referees. All relevant definitions for ANLUTD were updated on the basis of research over the last 14 years. An extensive process of 18 rounds of internal and external review was involved to exhaustively examine each definition, with decision-making by collective opinion (consensus). A Terminology Report for ANLUTD, encompassing 97 definitions (42 NEW and 8 CHANGED, has been developed. It is clinically based with the most common diagnoses defined. Clarity and user-friendliness have been key aims to make it interpretable by practitioners and trainees in all the different groups involved not only in lower urinary tract dysfunction but additionally in many other medical specialties. A consensus-based Terminology Report for ANLUTD has been produced to aid clinical practice and research. © 2017 Wiley Periodicals, Inc.

PyPathway: Python Package for Biological Network Analysis and Visualization.

Science.gov (United States)

Xu, Yang; Luo, Xiao-Chun

2018-05-01

Life science studies represent one of the biggest generators of large data sets, mainly because of rapid sequencing technological advances. Biological networks including interactive networks and human curated pathways are essential to understand these high-throughput data sets. Biological network analysis offers a method to explore systematically not only the molecular complexity of a particular disease but also the molecular relationships among apparently distinct phenotypes. Currently, several packages for Python community have been developed, such as BioPython and Goatools. However, tools to perform comprehensive network analysis and visualization are still needed. Here, we have developed PyPathway, an extensible free and open source Python package for functional enrichment analysis, network modeling, and network visualization. The network process module supports various interaction network and pathway databases such as Reactome, WikiPathway, STRING, and BioGRID. The network analysis module implements overrepresentation analysis, gene set enrichment analysis, network-based enrichment, and de novo network modeling. Finally, the visualization and data publishing modules enable users to share their analysis by using an easy web application. For package availability, see the first Reference.

PyContact: Rapid, Customizable, and Visual Analysis of Noncovalent Interactions in MD Simulations.

Science.gov (United States)

Scheurer, Maximilian; Rodenkirch, Peter; Siggel, Marc; Bernardi, Rafael C; Schulten, Klaus; Tajkhorshid, Emad; Rudack, Till

2018-02-06

Molecular dynamics (MD) simulations have become ubiquitous in all areas of life sciences. The size and model complexity of MD simulations are rapidly growing along with increasing computing power and improved algorithms. This growth has led to the production of a large amount of simulation data that need to be filtered for relevant information to address specific biomedical and biochemical questions. One of the most relevant molecular properties that can be investigated by all-atom MD simulations is the time-dependent evolution of the complex noncovalent interaction networks governing such fundamental aspects as molecular recognition, binding strength, and mechanical and structural stability. Extracting, evaluating, and visualizing noncovalent interactions is a key task in the daily work of structural biologists. We have developed PyContact, an easy-to-use, highly flexible, and intuitive graphical user interface-based application, designed to provide a toolkit to investigate biomolecular interactions in MD trajectories. PyContact is designed to facilitate this task by enabling identification of relevant noncovalent interactions in a comprehensible manner. The implementation of PyContact as a standalone application enables rapid analysis and data visualization without any additional programming requirements, and also preserves full in-program customization and extension capabilities for advanced users. The statistical analysis representation is interactively combined with full mapping of the results on the molecular system through the synergistic connection between PyContact and VMD. We showcase the capabilities and scientific significance of PyContact by analyzing and visualizing in great detail the noncovalent interactions underlying the ion permeation pathway of the human P2X 3 receptor. As a second application, we examine the protein-protein interaction network of the mechanically ultrastable cohesin-dockering complex. Copyright © 2017 Biophysical Society

PyCDT: A Python toolkit for modeling point defects in semiconductors and insulators

Science.gov (United States)

Broberg, Danny; Medasani, Bharat; Zimmermann, Nils E. R.; Yu, Guodong; Canning, Andrew; Haranczyk, Maciej; Asta, Mark; Hautier, Geoffroy

2018-05-01

Point defects have a strong impact on the performance of semiconductor and insulator materials used in technological applications, spanning microelectronics to energy conversion and storage. The nature of the dominant defect types, how they vary with processing conditions, and their impact on materials properties are central aspects that determine the performance of a material in a certain application. This information is, however, difficult to access directly from experimental measurements. Consequently, computational methods, based on electronic density functional theory (DFT), have found widespread use in the calculation of point-defect properties. Here we have developed the Python Charged Defect Toolkit (PyCDT) to expedite the setup and post-processing of defect calculations with widely used DFT software. PyCDT has a user-friendly command-line interface and provides a direct interface with the Materials Project database. This allows for setting up many charged defect calculations for any material of interest, as well as post-processing and applying state-of-the-art electrostatic correction terms. Our paper serves as a documentation for PyCDT, and demonstrates its use in an application to the well-studied GaAs compound semiconductor. We anticipate that the PyCDT code will be useful as a framework for undertaking readily reproducible calculations of charged point-defect properties, and that it will provide a foundation for automated, high-throughput calculations.

Applications of the PyTOPKAPI model to ungauged catchments

African Journals Online (AJOL)

Many catchments in developing countries are poorly gauged/totally ungauged which hinders water resource ... INTRODUCTION ... focusing on the output of model calibration and validation. The last .... The improved PyTOPKAPI model is coded in Python ...... computer program for estimating streamflow statistics for ungaged.

ObsPy – What can it do for data centers and observatories?

Directory of Open Access Journals (Sweden)

Joachim Wassermann

2011-04-01

Full Text Available Data acquisition by seismic centers relies on real-time systems, like SeisComP3, Antelope and Earthworm. However, these are complex systems that are designed for fast and precisely defined standard real-time analyses. Therefore, it is not a simple task to access or modify internal routines, and to integrate them into custom-processing workflows or to perform in-depth data analyses. Often a library is necessary that provides convenient access to data and allows easy control over all of the operations that are to be performed on the data. ObsPy is such a library, which is designed to access and process seismological waveform data and metadata. We use short and simple examples here to demonstrate how effective it is to use Python for seismological data analysis. Then, we illustrate the general capabilities of ObsPy, and highlight some of its specific aspects that are relevant for seismological data centers and observatories, through presentation of real-world examples. Finally, we demonstrate how the ObsPy library can be used to develop custom graphical user interface applications.

Automated degenerate PCR primer design for high-throughput sequencing improves efficiency of viral sequencing

Directory of Open Access Journals (Sweden)

Li Kelvin

2012-11-01

Full Text Available Abstract Background In a high-throughput environment, to PCR amplify and sequence a large set of viral isolates from populations that are potentially heterogeneous and continuously evolving, the use of degenerate PCR primers is an important strategy. Degenerate primers allow for the PCR amplification of a wider range of viral isolates with only one set of pre-mixed primers, thus increasing amplification success rates and minimizing the necessity for genome finishing activities. To successfully select a large set of degenerate PCR primers necessary to tile across an entire viral genome and maximize their success, this process is best performed computationally. Results We have developed a fully automated degenerate PCR primer design system that plays a key role in the J. Craig Venter Institute’s (JCVI high-throughput viral sequencing pipeline. A consensus viral genome, or a set of consensus segment sequences in the case of a segmented virus, is specified using IUPAC ambiguity codes in the consensus template sequence to represent the allelic diversity of the target population. PCR primer pairs are then selected computationally to produce a minimal amplicon set capable of tiling across the full length of the specified target region. As part of the tiling process, primer pairs are computationally screened to meet the criteria for successful PCR with one of two described amplification protocols. The actual sequencing success rates for designed primers for measles virus, mumps virus, human parainfluenza virus 1 and 3, human respiratory syncytial virus A and B and human metapneumovirus are described, where >90% of designed primer pairs were able to consistently successfully amplify >75% of the isolates. Conclusions Augmenting our previously developed and published JCVI Primer Design Pipeline, we achieved similarly high sequencing success rates with only minor software modifications. The recommended methodology for the construction of the consensus

Von Willebrand disease and other bleeding disorders in women: consensus on diagnosis and management from an international expert panel

NARCIS (Netherlands)

James, Andra H.; Kouides, Peter A.; Abdul-Kadir, Rezan; Edlund, Mans; Federici, Augusto B.; Halimeh, Susan; Kamphuisen, Pieter W.; Konkle, Barbara A.; Martínez-Perez, Oscar; McLintock, Claire; Peyvandi, Flora; Winikoff, Rochelle

2009-01-01

Reproductive tract bleeding in women is a naturally occurring event during menstruation and childbirth. In women with menorrhagia, however, congenital bleeding disorders historically have been underdiagnosed. This consensus is intended to allow physicians to better recognize bleeding disorders as a

Canadian Cardiovascular Society 2009 Consensus Conference on the management of adults with congenital heart disease: Outflow tract obstruction, coarctation of the aorta, tetralogy of Fallot, Ebstein anomaly and Marfan’s syndrome

Science.gov (United States)

Silversides, Candice K; Beauchesne, Luc; Bradley, Timothy; Connelly, Michael; Niwa, Koichiro; Mulder, Barbara; Webb, Gary; Colman, Jack; Therrien, Judith

2010-01-01

With advances in pediatric cardiology and cardiac surgery, the population of adults with congenital heart disease (CHD) has increased. In the current era, there are more adults with CHD than children. This population has many unique issues and needs. Since the 2001 Canadian Cardiovascular Society Consensus Conference report on the management of adults with CHD, there have been significant advances in the field of adult CHD. Therefore, new clinical guidelines have been written by Canadian adult CHD physicians in collaboration with an international panel of experts in the field. Part II of the guidelines includes recommendations for the care of patients with left ventricular outflow tract obstruction and bicuspid aortic valve disease, coarctation of the aorta, right ventricular outflow tract obstruction, tetralogy of Fallot, Ebstein anomaly and Marfan’s syndrome. Topics addressed include genetics, clinical outcomes, recommended diagnostic workup, surgical and interventional options, treatment of arrhythmias, assessment of pregnancy risk and follow-up requirements. The complete document consists of four manuscripts that are published online in the present issue of The Canadian Journal of Cardiology. The complete document and references can also be found at www.ccs.ca or www.cachnet.org. PMID:20352138

The SOD Mimic, MnTE-2-PyP, Protects from Chronic Fibrosis and Inflammation in Irradiated Normal Pelvic Tissues

Directory of Open Access Journals (Sweden)

Shashank Shrishrimal

2017-11-01

Full Text Available Pelvic radiation for cancer therapy can damage a variety of normal tissues. In this study, we demonstrate that radiation causes acute changes to pelvic fibroblasts such as the transformation to myofibroblasts and the induction of senescence, which persist months after radiation. The addition of the manganese porphyrin, MnTE-2-PyP, resulted in protection of these acute changes in fibroblasts and this protection persisted months following radiation exposure. Specifically, at two months post-radiation, MnTE-2-PyP inhibited the number of α-smooth muscle actin positive fibroblasts induced by radiation and at six months post-radiation, MnTE-2-PyP significantly reduced collagen deposition (fibrosis in the skin and bladder tissues of irradiated mice. Radiation also resulted in changes to T cells. At two months post-radiation, there was a reduction of Th1-producing splenocytes, which resulted in reduced Th1:Th2 ratios. MnTE-2-PyP maintained Th1:Th2 ratios similar to unirradiated mice. At six months post-radiation, increased T cells were observed in the adipose tissues. MnTE-2-PyP treatment inhibited this increase. Thus, MnTE-2-PyP treatment maintains normal fibroblast function and T cell immunity months after radiation exposure. We believe that one of the reasons MnTE-2-PyP is a potent radioprotector is due to its protection of multiple cell types from radiation damage.

Clinical implications of the microbiome in urinary tract diseases.

Science.gov (United States)

Hiergeist, Andreas; Gessner, André

2017-03-01

The purpose of this review is to outline and evaluate the most recent literature on the role of the microbiome in urinary tract diseases. High throughput molecular DNA sequencing of bacterial 16S rRNA genes enabled the analysis of complex microbial communities inhabiting the human urinary tract. Several recent studies have identified bacterial taxa of the urinary microbiome to impact urinary tract diseases including interstitial cystitis, urgency urinary incontinence or calcium oxalate stone formation. Furthermore, treatment of urinary tract infections by antibiotics globally impacts community profiles of the intestinal microbiota and might indirectly influence human health. Alternative treatment options like application of probiotics for the treatment of urinary tract infections are currently under investigation. The urinary microbiome and its relationship to urinary tract diseases is currently under comprehensive investigation. Further studies are needed to shed light on the role of commensal microbiota for urinary tract infections.

Catalytic pyrolysis of Laminaria japonica over nanoporous catalysts using Py-GC/MS

Directory of Open Access Journals (Sweden)

Jeon Jong-Ki

2011-01-01

Full Text Available Abstract The catalytic pyrolysis of Laminaria japonica was carried out over a hierarchical meso-MFI zeolite (Meso-MFI and nanoporous Al-MCM-48 using pyrolysis gas chromatography/mass spectrometry (Py-GC/MS. The effect of the catalyst type on the product distribution and chemical composition of the bio-oil was examined using Py-GC/MS. The Meso-MFI exhibited a higher activity in deoxygenation and aromatization during the catalytic pyrolysis of L. japonica. Meanwhile, the catalytic activity of Al-MCM-48 was lower than that of Meso-MFI due to its weak acidity.

Reactivity toward alcohols of (Ru/sup IV/ = O/sup 2-/) unit in trans-(RuCl(O)(py)/sub 4/)/sup +/

Energy Technology Data Exchange (ETDEWEB)

Aoyagi, Kimitake; Nagao, Hirotaka; Yukawa, Yasuhiko; Ogura, Mariko; Kuwayama, Akito; Howell, F S; Mukaida, Masao; Kakihana, Hidetake

1986-12-01

The reactivity with alcohol of trans-(RuCl(O)(py)/sub 4/)/sup +/ was investigated. In MeOH, trans-(RuCl(OH)(py)/sub 4/)/sup +/ was confirmed to exist as a precursor in the formation of trans-(RuCl(OMe)(py)/sub 4/)/sup +/. The reaction progress was traced by spectrometrical and /sup 18/O-labelling experiments.

Consensus on consensus: a synthesis of consensus estimates on human-caused global warming

Science.gov (United States)

Cook, John; Oreskes, Naomi; Doran, Peter T.; Anderegg, William R. L.; Verheggen, Bart; Maibach, Ed W.; Carlton, J. Stuart; Lewandowsky, Stephan; Skuce, Andrew G.; Green, Sarah A.; Nuccitelli, Dana; Jacobs, Peter; Richardson, Mark; Winkler, Bärbel; Painting, Rob; Rice, Ken

2016-04-01

The consensus that humans are causing recent global warming is shared by 90%-100% of publishing climate scientists according to six independent studies by co-authors of this paper. Those results are consistent with the 97% consensus reported by Cook et al (Environ. Res. Lett. 8 024024) based on 11 944 abstracts of research papers, of which 4014 took a position on the cause of recent global warming. A survey of authors of those papers (N = 2412 papers) also supported a 97% consensus. Tol (2016 Environ. Res. Lett. 11 048001) comes to a different conclusion using results from surveys of non-experts such as economic geologists and a self-selected group of those who reject the consensus. We demonstrate that this outcome is not unexpected because the level of consensus correlates with expertise in climate science. At one point, Tol also reduces the apparent consensus by assuming that abstracts that do not explicitly state the cause of global warming (‘no position’) represent non-endorsement, an approach that if applied elsewhere would reject consensus on well-established theories such as plate tectonics. We examine the available studies and conclude that the finding of 97% consensus in published climate research is robust and consistent with other surveys of climate scientists and peer-reviewed studies.

Is There a Consensus on Consensus Methodology? Descriptions and Recommendations for Future Consensus Research.

Science.gov (United States)

Waggoner, Jane; Carline, Jan D; Durning, Steven J

2016-05-01

The authors of this article reviewed the methodology of three common consensus methods: nominal group process, consensus development panels, and the Delphi technique. The authors set out to determine how a majority of researchers are conducting these studies, how they are analyzing results, and subsequently the manner in which they are reporting their findings. The authors conclude with a set of guidelines and suggestions designed to aid researchers who choose to use the consensus methodology in their work.Overall, researchers need to describe their inclusion criteria. In addition to this, on the basis of the current literature the authors found that a panel size of 5 to 11 members was most beneficial across all consensus methods described. Lastly, the authors agreed that the statistical analyses done in consensus method studies should be as rigorous as possible and that the predetermined definition of consensus must be included in the ultimate manuscript. More specific recommendations are given for each of the three consensus methods described in the article.

Multiple splicing defects in an intronic false exon.

Science.gov (United States)

Sun, H; Chasin, L A

2000-09-01

Splice site consensus sequences alone are insufficient to dictate the recognition of real constitutive splice sites within the typically large transcripts of higher eukaryotes, and large numbers of pseudoexons flanked by pseudosplice sites with good matches to the consensus sequences can be easily designated. In an attempt to identify elements that prevent pseudoexon splicing, we have systematically altered known splicing signals, as well as immediately adjacent flanking sequences, of an arbitrarily chosen pseudoexon from intron 1 of the human hprt gene. The substitution of a 5' splice site that perfectly matches the 5' consensus combined with mutation to match the CAG/G sequence of the 3' consensus failed to get this model pseudoexon included as the central exon in a dhfr minigene context. Provision of a real 3' splice site and a consensus 5' splice site and removal of an upstream inhibitory sequence were necessary and sufficient to confer splicing on the pseudoexon. This activated context also supported the splicing of a second pseudoexon sequence containing no apparent enhancer. Thus, both the 5' splice site sequence and the polypyrimidine tract of the pseudoexon are defective despite their good agreement with the consensus. On the other hand, the pseudoexon body did not exert a negative influence on splicing. The introduction into the pseudoexon of a sequence selected for binding to ASF/SF2 or its replacement with beta-globin exon 2 only partially reversed the effect of the upstream negative element and the defective polypyrimidine tract. These results support the idea that exon-bridging enhancers are not a prerequisite for constitutive exon definition and suggest that intrinsically defective splice sites and negative elements play important roles in distinguishing the real splicing signal from the vast number of false splicing signals.

The antioxidant, MnTE-2-PyP, prevents side-effects incurred by prostate cancer irradiation.

Directory of Open Access Journals (Sweden)

Rebecca E Oberley-Deegan

Full Text Available Prostate cancer is the most commonly diagnosed cancer, with an estimated 240,000 new cases reported annually in the United States. Due to early detection and advances in therapies, more than 90% of patients will survive 10 years post diagnosis and treatment. Radiation is a treatment option often used to treat localized disease; however, while radiation is very effective at killing tumor cells, normal tissues are damaged as well. Potential side-effects due to prostate cancer-related radiation therapy include bowel inflammation, erectile dysfunction, urethral stricture, rectal bleeding and incontinence. Currently, radiation therapy for prostate cancer does not include the administration of therapeutic agents to reduce these side effects and protect normal tissues from radiation-induced damage. In the current study, we show that the small molecular weight antioxidant, MnTE-2-PyP, protects normal tissues from radiation-induced damage in the lower abdomen in rats. Specifically, MnTE-2-PyP protected skin, prostate, and testes from radiation-induced damage. MnTE-2-PyP also protected from erectile dysfunction, a persistent problem regardless of the type of radiation techniques used because the penile neurovascular bundles lay in the peripheral zones of the prostate, where most prostate cancers reside. Based on previous studies showing that MnTE-2-PyP, in combination with radiation, further reduces subcutaneous tumor growth, we believe that MnTE-2-PyP represents an excellent radioprotectant in combination radiotherapy for cancer in general and specifically for prostate cancer.

MnTM-4-PyP modulates endogenous antioxidant responses and protects primary cortical neurons against oxidative stress.

Science.gov (United States)

Cheng, Kuo-Yuan; Guo, Fei; Lu, Jia-Qi; Cao, Yuan-Zhao; Wang, Tian-Chang; Yang, Qi; Xia, Qing

2015-05-01

Oxidative stress is a direct cause of injury in various neural diseases. Manganese porphyrins (MnPs), a large category of superoxide dismutase (SOD) mimics, shown universally to have effects in numerous neural disease models in vivo. Given their complex intracellular redox activities, detailed mechanisms underlying the biomedical efficacies are not fully elucidated. This study sought to investigate the regulation of endogenous antioxidant systems by a MnP (MnTM-4-PyP) and its role in the protection against neural oxidative stress. Primary cortical neurons were treated with MnTM-4-PyP prior to hydrogen peroxide-induced oxidative stress. MnTM-4-PyP increased cell viability, reduced intracellular level of reactive oxygen species, inhibited mitochondrial apoptotic pathway, and ameliorated endoplasmic reticulum function. The protein levels and activities of endogenous SODs were elevated, but not those of catalase. SOD2 transcription was promoted in a transcription factor-specific manner. Additionally, we found FOXO3A and Sirt3 levels also increased. These effects were not observed with MnTM-4-PyP alone. Induction of various levels of endogenous antioxidant responses by MnTM-4-PyP has indispensable functions in its protection for cortical neurons against hydrogen peroxide-induced oxidative stress. © 2014 John Wiley & Sons Ltd.

Synthesis of Cyclic Py-Im Polyamide Libraries

OpenAIRE

Li, Benjamin C.; Montgomery, David C.; Puckett, James W.; Dervan, Peter B.

2013-01-01

Cyclic Py-Im polyamides containing two GABA turn units exhibit enhanced DNA binding affinity, but extensive studies of their biological properties have been hindered due to synthetic inaccessibility. A facile modular approach toward cyclic polyamides has been developed via microwave-assisted solid-phase synthesis of hairpin amino acid oligomer intermediates followed by macrocyclization. A focused library of cyclic polyamides 1–7 targeted to the androgen response element (ARE) and the estrogen...

Cofactor specificity switch in Shikimate dehydrogenase by rational design and consensus engineering.

Science.gov (United States)

García-Guevara, Fernando; Bravo, Iris; Martínez-Anaya, Claudia; Segovia, Lorenzo

2017-08-01

Consensus engineering has been used to design more stable variants using the most frequent amino acid at each site of a multiple sequence alignment; sometimes consensus engineering modifies function, but efforts have mainly been focused on studying stability. Here we constructed a consensus Rossmann domain for the Shikimate dehydrogenase enzyme; separately we decided to switch the cofactor specificity through rational design in the Escherichia coli Shikimate dehydrogenase enzyme and then analyzed the effect of consensus mutations on top of our design. We found that consensus mutations closest to the 2' adenine moiety increased the activity in our design. Consensus engineering has been shown to result in more stable proteins and our findings suggest it could also be used as a complementary tool for increasing or modifying enzyme activity during design. © The Author 2017. Published by Oxford University Press. All rights reserved. For Permissions, please e-mail: journals.permissions@oup.com.

Evaluación de un proyecto de éxito para PyMEs costarricenses

OpenAIRE

Quesada Pineda, Henry

2013-01-01

Los investigadores Henry Quesada y Marcela Meneses, de la Escuela de Ingeniería en Producción Industrial del Instituto Tecnológico de Costa Rica (TEC), realizaron una investigación durante el periodo 2007 a 2008 con la intención de identificar si existe un patrón en un modelo de negocios para pequeñas y medianas empresas (PyMEs) que les haya permitido ser competitivas a escala nacional o internacional. El aporte económico de las PyMEs en Costa Rica ha sido documentado en muchas investigacione...

PyCOOL — A Cosmological Object-Oriented Lattice code written in Python

International Nuclear Information System (INIS)

Sainio, J.

2012-01-01

There are a number of different phenomena in the early universe that have to be studied numerically with lattice simulations. This paper presents a graphics processing unit (GPU) accelerated Python program called PyCOOL that solves the evolution of scalar fields in a lattice with very precise symplectic integrators. The program has been written with the intention to hit a sweet spot of speed, accuracy and user friendliness. This has been achieved by using the Python language with the PyCUDA interface to make a program that is easy to adapt to different scalar field models. In this paper we derive the symplectic dynamics that govern the evolution of the system and then present the implementation of the program in Python and PyCUDA. The functionality of the program is tested in a chaotic inflation preheating model, a single field oscillon case and in a supersymmetric curvaton model which leads to Q-ball production. We have also compared the performance of a consumer graphics card to a professional Tesla compute card in these simulations. We find that the program is not only accurate but also very fast. To further increase the usefulness of the program we have equipped it with numerous post-processing functions that provide useful information about the cosmological model. These include various spectra and statistics of the fields. The program can be additionally used to calculate the generated curvature perturbation. The program is publicly available under GNU General Public License at https://github.com/jtksai/PyCOOL. Some additional information can be found from http://www.physics.utu.fi/tiedostot/theory/particlecosmology/pycool/

PyCOOL — A Cosmological Object-Oriented Lattice code written in Python

Energy Technology Data Exchange (ETDEWEB)

Sainio, J., E-mail: jani.sainio@utu.fi [Turku School of Economics, University of Turku, Rehtorinpellonkatu 3, FI-20500 Turku (Finland); Department of Physics and Astronomy, University of Turku, FI-20014 Turku (Finland)

2012-04-01

There are a number of different phenomena in the early universe that have to be studied numerically with lattice simulations. This paper presents a graphics processing unit (GPU) accelerated Python program called PyCOOL that solves the evolution of scalar fields in a lattice with very precise symplectic integrators. The program has been written with the intention to hit a sweet spot of speed, accuracy and user friendliness. This has been achieved by using the Python language with the PyCUDA interface to make a program that is easy to adapt to different scalar field models. In this paper we derive the symplectic dynamics that govern the evolution of the system and then present the implementation of the program in Python and PyCUDA. The functionality of the program is tested in a chaotic inflation preheating model, a single field oscillon case and in a supersymmetric curvaton model which leads to Q-ball production. We have also compared the performance of a consumer graphics card to a professional Tesla compute card in these simulations. We find that the program is not only accurate but also very fast. To further increase the usefulness of the program we have equipped it with numerous post-processing functions that provide useful information about the cosmological model. These include various spectra and statistics of the fields. The program can be additionally used to calculate the generated curvature perturbation. The program is publicly available under GNU General Public License at https://github.com/jtksai/PyCOOL. Some additional information can be found from http://www.physics.utu.fi/tiedostot/theory/particlecosmology/pycool/.

Enabling grand-canonical Monte Carlo : extending the flexibility of GROMACS through the GromPy python interface module

NARCIS (Netherlands)

Pool, René; Heringa, Jaap; Hoefling, Martin; Schulz, Roland; Smith, Jeremy C; Feenstra, K Anton

2012-01-01

We report on a python interface to the GROMACS molecular simulation package, GromPy (available at https://github.com/GromPy). This application programming interface (API) uses the ctypes python module that allows function calls to shared libraries, for example, written in C. To the best of our

Quality indicators for the diagnosis and antibiotic treatment of acute respiratory tract infections in general practice

DEFF Research Database (Denmark)

Saust, Laura Trolle; Bjerrum, Lars; Arpi, Magnus

2017-01-01

Objective: To develop quality indicators for the diagnosis and antibiotic treatment of acute respiratory tract infections, tailored to the Danish general practice setting. Design: A RAND/UCLA Appropriateness Method was used. Setting: General practice. Subjects: A panel of nine experts, mainly...... general practitioners, was asked to rate the relevance of 64 quality indicators for the diagnosis and antibiotic treatment of acute respiratory tract infections based on guidelines. Subsequently, a face-to-face meeting was held to resolve misinterpretations and to achieve consensus. Main outcome measures...

Towards a consensus Y-chromosomal phylogeny and Y-SNP set in forensics in the next-generation sequencing era.

Science.gov (United States)

Larmuseau, Maarten H D; Van Geystelen, Anneleen; Kayser, Manfred; van Oven, Mannis; Decorte, Ronny

2015-03-01

Currently, several different Y-chromosomal phylogenies and haplogroup nomenclatures are presented in scientific literature and at conferences demonstrating the present diversity in Y-chromosomal phylogenetic trees and Y-SNP sets used within forensic and anthropological research. This situation can be ascribed to the exponential growth of the number of Y-SNPs discovered due to mostly next-generation sequencing (NGS) studies. As Y-SNPs and their respective phylogenetic positions are important in forensics, such as for male lineage characterization and paternal bio-geographic ancestry inference, there is a need for forensic geneticists to know how to deal with these newly identified Y-SNPs and phylogenies, especially since these phylogenies are often created with other aims than to carry out forensic genetic research. Therefore, we give here an overview of four categories of currently used Y-chromosomal phylogenies and the associated Y-SNP sets in scientific research in the current NGS era. We compare these categories based on the construction method, their advantages and disadvantages, the disciplines wherein the phylogenetic tree can be used, and their specific relevance for forensic geneticists. Based on this overview, it is clear that an up-to-date reduced tree with a consensus Y-SNP set and a stable nomenclature will be the most appropriate reference resource for forensic research. Initiatives to reach such an international consensus are therefore highly recommended. Copyright © 2014 Elsevier Ireland Ltd. All rights reserved.

PyMEs : Guía de comunicación para exportación

OpenAIRE

Barandiain, Dolores; Feiteler, Daniela Elizabeth; Longarzo, María Florencia

2007-01-01

Esta guía de comunicación está dirigida al empresario PyME que pretende insertarse en la actividad exportadora o que aspira a mejorar dicho proceso. Este material tiene como objetivo aportar herramientas útiles, prácticas y claras vinculadas a la comunicación, entendiendo el concepto como un valor agregado en la gestión de las PyMEs que exportan. Cualquier acción que la empresa realice va a construir un sentido en el destinatario. A partir de aquí, se plantea la Guía de Comunicación para Expo...

PyFly: A fast, portable aerodynamics simulator

KAUST Repository

Garcia, D.; Ghommem, M.; Collier, N.; Varga, B.O.N.; Calo, V.M.

2018-01-01

We present a fast, user-friendly implementation of a potential flow solver based on the unsteady vortex lattice method (UVLM), namely PyFly. UVLM computes the aerodynamic loads applied on lifting surfaces while capturing the unsteady effects such as the added mass forces, the growth of bound circulation, and the wake while assuming that the flow separation location is known a priori. This method is based on discretizing the body surface into a lattice of vortex rings and relies on the Biot–Savart law to construct the velocity field at every point in the simulated domain. We introduce the pointwise approximation approach to simulate the interactions of the far-field vortices to overcome the computational burden associated with the classical implementation of UVLM. The computational framework uses the Python programming language to provide an easy to handle user interface while the computational kernels are written in Fortran. The mixed language approach enables high performance regarding solution time and great flexibility concerning easiness of code adaptation to different system configurations and applications. The computational tool predicts the unsteady aerodynamic behavior of multiple moving bodies (e.g., flapping wings, rotating blades, suspension bridges) subject to incoming air. The aerodynamic simulator can also deal with enclosure effects, multi-body interactions, and B-spline representation of body shapes. We simulate different aerodynamic problems to illustrate the usefulness and effectiveness of PyFly.

PyFly: A fast, portable aerodynamics simulator

KAUST Repository

Garcia, D.

2018-03-18

We present a fast, user-friendly implementation of a potential flow solver based on the unsteady vortex lattice method (UVLM), namely PyFly. UVLM computes the aerodynamic loads applied on lifting surfaces while capturing the unsteady effects such as the added mass forces, the growth of bound circulation, and the wake while assuming that the flow separation location is known a priori. This method is based on discretizing the body surface into a lattice of vortex rings and relies on the Biot–Savart law to construct the velocity field at every point in the simulated domain. We introduce the pointwise approximation approach to simulate the interactions of the far-field vortices to overcome the computational burden associated with the classical implementation of UVLM. The computational framework uses the Python programming language to provide an easy to handle user interface while the computational kernels are written in Fortran. The mixed language approach enables high performance regarding solution time and great flexibility concerning easiness of code adaptation to different system configurations and applications. The computational tool predicts the unsteady aerodynamic behavior of multiple moving bodies (e.g., flapping wings, rotating blades, suspension bridges) subject to incoming air. The aerodynamic simulator can also deal with enclosure effects, multi-body interactions, and B-spline representation of body shapes. We simulate different aerodynamic problems to illustrate the usefulness and effectiveness of PyFly.

R2R - software to speed the depiction of aesthetic consensus RNA secondary structures

Directory of Open Access Journals (Sweden)

Weinberg Zasha

2011-01-01

Full Text Available Abstract Background With continuing identification of novel structured noncoding RNAs, there is an increasing need to create schematic diagrams showing the consensus features of these molecules. RNA structural diagrams are typically made either with general-purpose drawing programs like Adobe Illustrator, or with automated or interactive programs specific to RNA. Unfortunately, the use of applications like Illustrator is extremely time consuming, while existing RNA-specific programs produce figures that are useful, but usually not of the same aesthetic quality as those produced at great cost in Illustrator. Additionally, most existing RNA-specific applications are designed for drawing single RNA molecules, not consensus diagrams. Results We created R2R, a computer program that facilitates the generation of aesthetic and readable drawings of RNA consensus diagrams in a fraction of the time required with general-purpose drawing programs. Since the inference of a consensus RNA structure typically requires a multiple-sequence alignment, the R2R user annotates the alignment with commands directing the layout and annotation of the RNA. R2R creates SVG or PDF output that can be imported into Adobe Illustrator, Inkscape or CorelDRAW. R2R can be used to create consensus sequence and secondary structure models for novel RNA structures or to revise models when new representatives for known RNA classes become available. Although R2R does not currently have a graphical user interface, it has proven useful in our efforts to create 100 schematic models of distinct noncoding RNA classes. Conclusions R2R makes it possible to obtain high-quality drawings of the consensus sequence and structural models of many diverse RNA structures with a more practical amount of effort. R2R software is available at http://breaker.research.yale.edu/R2R and as an Additional file.

R2R - software to speed the depiction of aesthetic consensus RNA secondary structures

Science.gov (United States)

2011-01-01

Background With continuing identification of novel structured noncoding RNAs, there is an increasing need to create schematic diagrams showing the consensus features of these molecules. RNA structural diagrams are typically made either with general-purpose drawing programs like Adobe Illustrator, or with automated or interactive programs specific to RNA. Unfortunately, the use of applications like Illustrator is extremely time consuming, while existing RNA-specific programs produce figures that are useful, but usually not of the same aesthetic quality as those produced at great cost in Illustrator. Additionally, most existing RNA-specific applications are designed for drawing single RNA molecules, not consensus diagrams. Results We created R2R, a computer program that facilitates the generation of aesthetic and readable drawings of RNA consensus diagrams in a fraction of the time required with general-purpose drawing programs. Since the inference of a consensus RNA structure typically requires a multiple-sequence alignment, the R2R user annotates the alignment with commands directing the layout and annotation of the RNA. R2R creates SVG or PDF output that can be imported into Adobe Illustrator, Inkscape or CorelDRAW. R2R can be used to create consensus sequence and secondary structure models for novel RNA structures or to revise models when new representatives for known RNA classes become available. Although R2R does not currently have a graphical user interface, it has proven useful in our efforts to create 100 schematic models of distinct noncoding RNA classes. Conclusions R2R makes it possible to obtain high-quality drawings of the consensus sequence and structural models of many diverse RNA structures with a more practical amount of effort. R2R software is available at http://breaker.research.yale.edu/R2R and as an Additional file. PMID:21205310

R2R--software to speed the depiction of aesthetic consensus RNA secondary structures.

Science.gov (United States)

Weinberg, Zasha; Breaker, Ronald R

2011-01-04

With continuing identification of novel structured noncoding RNAs, there is an increasing need to create schematic diagrams showing the consensus features of these molecules. RNA structural diagrams are typically made either with general-purpose drawing programs like Adobe Illustrator, or with automated or interactive programs specific to RNA. Unfortunately, the use of applications like Illustrator is extremely time consuming, while existing RNA-specific programs produce figures that are useful, but usually not of the same aesthetic quality as those produced at great cost in Illustrator. Additionally, most existing RNA-specific applications are designed for drawing single RNA molecules, not consensus diagrams. We created R2R, a computer program that facilitates the generation of aesthetic and readable drawings of RNA consensus diagrams in a fraction of the time required with general-purpose drawing programs. Since the inference of a consensus RNA structure typically requires a multiple-sequence alignment, the R2R user annotates the alignment with commands directing the layout and annotation of the RNA. R2R creates SVG or PDF output that can be imported into Adobe Illustrator, Inkscape or CorelDRAW. R2R can be used to create consensus sequence and secondary structure models for novel RNA structures or to revise models when new representatives for known RNA classes become available. Although R2R does not currently have a graphical user interface, it has proven useful in our efforts to create 100 schematic models of distinct noncoding RNA classes. R2R makes it possible to obtain high-quality drawings of the consensus sequence and structural models of many diverse RNA structures with a more practical amount of effort. R2R software is available at http://breaker.research.yale.edu/R2R and as an Additional file.

PyMES COLOMBIANAS Y LA GESTIÓN DEL CONOCIMIENTO

Directory of Open Access Journals (Sweden)

Andrea Carolina Bustos Claro

2003-07-01

Full Text Available En los últimos años, la adaptación de modelos e-business se ha convertido en un elemento de vital importancia para las organizaciones, hasta el punto de creer que ésta es la mejor forma de crear una ventaja competitiva en el mercado global. Sin embargo, es necesario tener presente que la existencia de la tecnología por sí sola, no asegura el éxito. Se requiere además del cambio de algunos paradigmas organizacionales: lacultura, los niveles jerárquicos y el manejo que se le da a la información y a la comunicación. Gracias a los resultados obtenidos en el proyecto “Indicadores Pragmáticos de Gestión del Conocimiento aplicado a páginas Web de PyMES colombianas”, adelantado por el Centro de Investigaciones de la EAN, se ha logrado un acercamiento a la situación actual de las páginas Web de las PyMES y su desempeño en la red.

AutoPyFactory: A Scalable Flexible Pilot Factory Implementation

CERN Document Server

Caballero, J; The ATLAS collaboration; Love, P; Stewart, G

2012-01-01

The ATLAS experiment at the CERN LHC is one of the largest users of grid computing infrastructure, which is a central part of the experiment’s computing operations. Considerable efforts have been made to use grid technology in the most efficient and effective way, including the use of a pilot job based workload management framework. In this model the experiment submits ’pilot’ jobs to sites without payload. When these jobs begin to run they contact a central service to retrieve a real payload to execute. The first generation of pilot factories were usually specific to a single VO, and were bound to the particular architecture of that VO’s distributed processing. A second generation provides factories which are more flexible, not tied to any particular VO, and provide new or improved features such as monitoring, logging, profiling, etc. In this paper we describe this key part of the ATLAS pilot architecture, a second generation pilot factory, AutoPyFactory. AutoPyFactory has a modular design and is hig...

Synthesis of Pt-Ru PSB-Py catalysis by {gamma}-irradiation and their electrocatalytic efficiency for methanol oxidation

Energy Technology Data Exchange (ETDEWEB)

Yoon, Jung Ah; Sim, Kwang Sik; Choi, Seong Ho [Hannam University, Daejeon (Korea, Republic of); Jung, Sung Hee [Korea Atomic Energy Research Institute, Daejeon (Korea, Republic of)

2009-09-15

We report here that deposition of Pt-Ru catalysis on the surface of core-shell conductive balls by radiation-chemical reduction of Pt and Ru ions, in order to use as catalysis in a fuel cell. The poly(styrene-co-4-vinylphenylboronic acid)-pyrrole (PSB-Py) with core-shell structure was obtained by in situ polymerization of pyrrole in the presence of the poly(styrene-co-4-vinylphenylboronic acid) (PSB). Subsequently, Pt-Ru catalysis were deposited onto PSB-Py ball by {gamma}-irradiation, in the presence/absence of poly(vinypyrolidone) (PVP) to prepare electrocatalysis for a fuel cell. The catalytic efficiency of Pt-Ru PSB-Py catalyst was examined for carbon monoxide (CO) stripping and methanol oxidation.

Synthesis of Pt-Ru PSB-Py catalysis by γ-irradiation and their electrocatalytic efficiency for methanol oxidation

International Nuclear Information System (INIS)

Yoon, Jung Ah; Sim, Kwang Sik; Choi, Seong Ho; Jung, Sung Hee

2009-01-01

We report here that deposition of Pt-Ru catalysis on the surface of core-shell conductive balls by radiation-chemical reduction of Pt and Ru ions, in order to use as catalysis in a fuel cell. The poly(styrene-co-4-vinylphenylboronic acid)-pyrrole (PSB-Py) with core-shell structure was obtained by in situ polymerization of pyrrole in the presence of the poly(styrene-co-4-vinylphenylboronic acid) (PSB). Subsequently, Pt-Ru catalysis were deposited onto PSB-Py ball by γ-irradiation, in the presence/absence of poly(vinypyrolidone) (PVP) to prepare electrocatalysis for a fuel cell. The catalytic efficiency of Pt-Ru PSB-Py catalyst was examined for carbon monoxide (CO) stripping and methanol oxidation

pyGFC - A Python Extension to the C++ Geodesy Foundation Classes

National Research Council Canada - National Science Library

Nguyen, Binh Q

2008-01-01

.... Army Research Laboratory (ARL). The pyGFC module was created to support the visualization of network topologies using the ARL Topodef tool, a graphical design and animation tool for custom-designing and editing a mobility scenario...

Sampled-Data Consensus of Linear Multi-agent Systems With Packet Losses.

Science.gov (United States)

Zhang, Wenbing; Tang, Yang; Huang, Tingwen; Kurths, Jurgen

In this paper, the consensus problem is studied for a class of multi-agent systems with sampled data and packet losses, where random and deterministic packet losses are considered, respectively. For random packet losses, a Bernoulli-distributed white sequence is used to describe packet dropouts among agents in a stochastic way. For deterministic packet losses, a switched system with stable and unstable subsystems is employed to model packet dropouts in a deterministic way. The purpose of this paper is to derive consensus criteria, such that linear multi-agent systems with sampled-data and packet losses can reach consensus. By means of the Lyapunov function approach and the decomposition method, the design problem of a distributed controller is solved in terms of convex optimization. The interplay among the allowable bound of the sampling interval, the probability of random packet losses, and the rate of deterministic packet losses are explicitly derived to characterize consensus conditions. The obtained criteria are closely related to the maximum eigenvalue of the Laplacian matrix versus the second minimum eigenvalue of the Laplacian matrix, which reveals the intrinsic effect of communication topologies on consensus performance. Finally, simulations are given to show the effectiveness of the proposed results.In this paper, the consensus problem is studied for a class of multi-agent systems with sampled data and packet losses, where random and deterministic packet losses are considered, respectively. For random packet losses, a Bernoulli-distributed white sequence is used to describe packet dropouts among agents in a stochastic way. For deterministic packet losses, a switched system with stable and unstable subsystems is employed to model packet dropouts in a deterministic way. The purpose of this paper is to derive consensus criteria, such that linear multi-agent systems with sampled-data and packet losses can reach consensus. By means of the Lyapunov function

Management of urinary tract infection in solid organ transplant recipients: Consensus statement of the Group for the Study of Infection in Transplant Recipients (GESITRA) of the Spanish Society of Infectious Diseases and Clinical Microbiology (SEIMC) and the Spanish Network for Research in Infectious Diseases (REIPI).

Science.gov (United States)

Vidal, Elisa; Cervera, Carlos; Cordero, Elisa; Armiñanzas, Carlos; Carratalá, Jordi; Cisneros, José Miguel; Fariñas, M Carmen; López-Medrano, Francisco; Moreno, Asunción; Muñoz, Patricia; Origüen, Julia; Sabé, Núria; Valerio, Maricela; Torre-Cisneros, Julián

2015-12-01

Urinary tract infections (UTIs) are one of the most common infections in solid organ transplant (SOT) recipients. Experienced SOT researchers and clinicians have developed and implemented this consensus document in support of the optimal management of these patients. A systematic review was conducted, and evidence levels based on the available literature are given for each recommendation. This article was written in accordance with international recommendations on consensus statements and the recommendations of the Appraisal of Guidelines for Research and Evaluation II (AGREE II). Recommendations are provided on the management of asymptomatic bacteriuria, and prophylaxis and treatment of UTI in SOT recipients. The diagnostic-therapeutic management of recurrent UTI and the role of infection in kidney graft rejection or dysfunction are reviewed. Finally, recommendations on antimicrobials and immunosuppressant interactions are also included. The latest scientific information on UTI in SOT is incorporated in this consensus document. Copyright © 2015 Elsevier España, S.L.U. y Sociedad Española de Enfermedades Infecciosas y Microbiología Clínica. All rights reserved.

Generating Stimuli for Neuroscience Using PsychoPy

OpenAIRE

Peirce, Jonathan W.

2009-01-01

PsychoPy is a software library written in Python, using OpenGL to generate very precise visual stimuli on standard personal computers. It is designed to allow the construction of as wide a variety of neuroscience experiments as possible, with the least effort. By writing scripts in standard Python syntax users can generate an enormous variety of visual and auditory stimuli and can interact with a wide range of external hardware (enabling its use in fMRI, EEG, MEG etc.). The structure of scrip...

Role of spin mixing conductance in spin pumping: Enhancement of spin pumping efficiency in Ta/Cu/Py structures

Energy Technology Data Exchange (ETDEWEB)

Deorani, Praveen; Yang, Hyunsoo, E-mail: eleyang@nus.edu.sg [Department of Electrical and Computer Engineering, National University of Singapore, 117576 Singapore (Singapore)

2013-12-02

From spin pumping measurements in Ta/Py devices for different thicknesses of Ta, we determine the spin Hall angle to be 0.021–0.033 and spin diffusion length to be 8 nm in Ta. We have also studied the effect of changing the properties of non-magnet/ferromagnet interface by adding a Cu interlayer. The experimental results show that the effective spin mixing conductance increases in the presence of Cu interlayer for Ta/Cu/Py devices whereas it decreases in Pt/Cu/Py devices. Our findings allow the tunability of the spin pumping efficiency by adding a thin interlayer at the non-magnet/ferromagnet interface.

The PyRosetta Toolkit: a graphical user interface for the Rosetta software suite.

Science.gov (United States)

Adolf-Bryfogle, Jared; Dunbrack, Roland L

2013-01-01

The Rosetta Molecular Modeling suite is a command-line-only collection of applications that enable high-resolution modeling and design of proteins and other molecules. Although extremely useful, Rosetta can be difficult to learn for scientists with little computational or programming experience. To that end, we have created a Graphical User Interface (GUI) for Rosetta, called the PyRosetta Toolkit, for creating and running protocols in Rosetta for common molecular modeling and protein design tasks and for analyzing the results of Rosetta calculations. The program is highly extensible so that developers can add new protocols and analysis tools to the PyRosetta Toolkit GUI.

Development of a decision aid for the treatment of benign prostatic hyperplasia : A four stage method using a Delphi consensus study

NARCIS (Netherlands)

Lamers, Romy E D; Cuypers, Maarten; Garvelink, Mirjam M.; Bosch, J. L H Ruud; Kil, Paul J M

2016-01-01

Objective: To develop a web-based decision aid (DA) for the treatment of lower urinary tract symptoms due to benign prostatic hyperplasia (LUTS/BPH). Methods: From February-September 2014 we performed a four-stage development method: 1: Two-round Delphi consensus method among urologists, 2:

PyPedal, an open source software package for pedigree analysis

Science.gov (United States)

The open source software package PyPedal (http://pypedal.sourceforge.net/) was first released in 2002, and provided users with a set of simple tools for manipulating pedigrees. Its flexibility has been demonstrated by its used in a number of settings for large and small populations. After substantia...

Characterization of arene di-oxygenases involved in polycyclic aromatic hydrocarbons biodegradation in Mycobacterium sp. 6PY1; Caracterisation d'arene dioxygenases impliquees dans la biodegradation des hydrocarbures aromatiques polycycliques chez Mycobacterium sp. 6PY1

Energy Technology Data Exchange (ETDEWEB)

Kuony, S.

2005-06-15

This thesis deals with the bacterial biodegradation of pollutants called polycyclic aromatic hydrocarbons (PAHs). The bacterium Mycobacterium sp. 6PY1 was isolated from a polluted soil for its ability to use pyrene, a 4-ring PAH, as sole source of carbon and energy. To learn about the pyrene metabolic pathway, the identification of the enzymes involved in this process has been undertaken using a proteomic approach. This approach revealed the occurrence of two ring-hydroxylating di-oxygenases in strain 6PY1, which could catalyze the initial attack of pyrene. The goal of this study was to clone the genes encoding the di-oxygenases identified in Mycobacterium sp. 6PY1, over-express these genes in an heterologous system in order to facilitate the purification of the corresponding enzymes, and determine the biochemical and catalytic properties of these enzymes. The pdoA1B1 genes encoding the terminal component of a di-oxygenase were cloned and over-expressed in Escherichia coli. The catalytic properties of this enzyme, called Pdo1, were determined in vivo by measuring the oxidation products of 2- to 4-ring PAHs by gas chromatography coupled to mass spectrometry (GC-MS). Analysis of the selectivity of the enzyme, as determined using GC-MS, showed that Pdo1 preferentially oxidized 3- or 4-ring PAHs, including phenanthrene and pyrene, but was inactive on di-aromatic compounds such as naphthalene and biphenyl. Pdo1 was unstable and was therefore purified in inactive form. The genes encoding a second di-oxygenase component were found in a locus containing two other catabolic genes. The pdoA2B2 genes encoded an enzyme called Pdo2 showing a narrow specificity towards 2- to 3-ring PAHs, and a high preference for phenanthrene. Pdo2 is an a3{beta}3 hexamer, containing [2Fe-2S] Rieske clusters which confer it a characteristic absorbance spectrum. A third set of genes possibly encoding another di-oxygenase was discovered in the genome of Mycobacterium sp. 6PY1. This set is closely

Compartmentalization of HIV-1 within the female genital tract is due to monotypic and low-diversity variants not distinct viral populations.

Science.gov (United States)

Bull, Marta; Learn, Gerald; Genowati, Indira; McKernan, Jennifer; Hitti, Jane; Lockhart, David; Tapia, Kenneth; Holte, Sarah; Dragavon, Joan; Coombs, Robert; Mullins, James; Frenkel, Lisa

2009-09-22

Compartmentalization of HIV-1 between the genital tract and blood was noted in half of 57 women included in 12 studies primarily using cell-free virus. To further understand differences between genital tract and blood viruses of women with chronic HIV-1 infection cell-free and cell-associated virus populations were sequenced from these tissues, reasoning that integrated viral DNA includes variants archived from earlier in infection, and provides a greater array of genotypes for comparisons. Multiple sequences from single-genome-amplification of HIV-1 RNA and DNA from the genital tract and blood of each woman were compared in a cross-sectional study. Maximum likelihood phylogenies were evaluated for evidence of compartmentalization using four statistical tests. Genital tract and blood HIV-1 appears compartmentalized in 7/13 women by >/=2 statistical analyses. These subjects' phylograms were characterized by low diversity genital-specific viral clades interspersed between clades containing both genital and blood sequences. Many of the genital-specific clades contained monotypic HIV-1 sequences. In 2/7 women, HIV-1 populations were significantly compartmentalized across all four statistical tests; both had low diversity genital tract-only clades. Collapsing monotypic variants into a single sequence diminished the prevalence and extent of compartmentalization. Viral sequences did not demonstrate tissue-specific signature amino acid residues, differential immune selection, or co-receptor usage. In women with chronic HIV-1 infection multiple identical sequences suggest proliferation of HIV-1-infected cells, and low diversity tissue-specific phylogenetic clades are consistent with bursts of viral replication. These monotypic and tissue-specific viruses provide statistical support for compartmentalization of HIV-1 between the female genital tract and blood. However, the intermingling of these clades with clades comprised of both genital and blood sequences and the absence

seismic-py: Reading seismic data with Python

Directory of Open Access Journals (Sweden)

2008-08-01

Full Text Available The field of seismic exploration of the Earth has changed
dramatically over the last half a century. The Society of Exploration
Geophysicists (SEG has worked to create standards to store the vast
amounts of seismic data in a way that will be portable across computer
architectures. However, it has been impossible to predict the needs of the
immense range of seismic data acquisition systems. As a result, vendors have
had to bend the rules to accommodate the needs of new instruments and
experiment types. For low level access to seismic data, there is need for a
standard open source library to allow access to a wide range of vendor data
files that can handle all of the variations. A new seismic software package,
seismic-py, provides an infrastructure for creating and managing drivers for
each particular format. Drivers can be derived from one of the known formats
and altered to handle any slight variations. Alternatively drivers can be
developed from scratch for formats that are very different from any previously
defined format. Python has been the key to making driver development easy
and efficient to implement. The goal of seismic-py is to be the base system
that will power a wide range of experimentation with seismic data and at the
same time provide clear documentation for the historical record of seismic
data formats.

Fisher.py: Fisher Matrix Manipulation and Confidence Contour Plotting

Science.gov (United States)

Coe, Dan

2010-10-01

Fisher.py allows you to combine constraints from multiple experiments (e.g., weak lensing + supernovae) and add priors (e.g., a flat universe) simply and easily. Calculate parameter uncertainties and plot confidence ellipses. Fisher matrix expectations for several experiments are included as calculated by myself (time delays) and the Dark Energy Task Force (WL/SN/BAO/CL/CMB), or provide your own.

Enabling grand-canonical Monte Carlo: extending the flexibility of GROMACS through the GromPy python interface module.

Science.gov (United States)

Pool, René; Heringa, Jaap; Hoefling, Martin; Schulz, Roland; Smith, Jeremy C; Feenstra, K Anton

2012-05-05

We report on a python interface to the GROMACS molecular simulation package, GromPy (available at https://github.com/GromPy). This application programming interface (API) uses the ctypes python module that allows function calls to shared libraries, for example, written in C. To the best of our knowledge, this is the first reported interface to the GROMACS library that uses direct library calls. GromPy can be used for extending the current GROMACS simulation and analysis modes. In this work, we demonstrate that the interface enables hybrid Monte-Carlo/molecular dynamics (MD) simulations in the grand-canonical ensemble, a simulation mode that is currently not implemented in GROMACS. For this application, the interplay between GromPy and GROMACS requires only minor modifications of the GROMACS source code, not affecting the operation, efficiency, and performance of the GROMACS applications. We validate the grand-canonical application against MD in the canonical ensemble by comparison of equations of state. The results of the grand-canonical simulations are in complete agreement with MD in the canonical ensemble. The python overhead of the grand-canonical scheme is only minimal. Copyright © 2012 Wiley Periodicals, Inc.

PyGPlates - a GPlates Python library for data analysis through space and deep geological time

Science.gov (United States)

Williams, Simon; Cannon, John; Qin, Xiaodong; Müller, Dietmar

2017-04-01

A fundamental consideration for studying the Earth through deep time is that the configurations of the continents, tectonic plates, and plate boundaries are continuously changing. Within a diverse range of fields including geodynamics, paleoclimate, and paleobiology, the importance of considering geodata in their reconstructed context across previous cycles of supercontinent aggregation, dispersal and ocean basin evolution is widely recognised. Open-source software tools such as GPlates provide paleo-geographic information systems for geoscientists to combine a wide variety of geodata and examine them within tectonic reconstructions through time. The availability of such powerful tools also brings new challenges - we want to learn something about the key associations between reconstructed plate motions and the geological record, but the high-dimensional parameter space is difficult for a human being to visually comprehend and quantify these associations. To achieve true spatio-temporal data-mining, new tools are needed. Here, we present a further development of the GPlates ecosystem - a Python-based tool for geotectonic analysis. In contrast to existing GPlates tools that are built around a graphical user interface (GUI) and interactive visualisation, pyGPlates offers a programming interface for the automation of quantitative plate tectonic analysis or arbitrary complexity. The vast array of open-source Python-based tools for data-mining, statistics and machine learning can now be linked to pyGPlates, allowing spatial data to be seamlessly analysed in space and geological "deep time", and with the ability to spread large computations across multiple processors. The presentation will illustrate a range of example applications, both simple and advanced. Basic examples include data querying, filtering, and reconstruction, and file-format conversions. For the innovative study of plate kinematics, pyGPlates has been used to explore the relationships between absolute

Mutations in DSTYK and dominant urinary tract malformations.

Science.gov (United States)

Sanna-Cherchi, Simone; Sampogna, Rosemary V; Papeta, Natalia; Burgess, Katelyn E; Nees, Shannon N; Perry, Brittany J; Choi, Murim; Bodria, Monica; Liu, Yan; Weng, Patricia L; Lozanovski, Vladimir J; Verbitsky, Miguel; Lugani, Francesca; Sterken, Roel; Paragas, Neal; Caridi, Gianluca; Carrea, Alba; Dagnino, Monica; Materna-Kiryluk, Anna; Santamaria, Giuseppe; Murtas, Corrado; Ristoska-Bojkovska, Nadica; Izzi, Claudia; Kacak, Nilgun; Bianco, Beatrice; Giberti, Stefania; Gigante, Maddalena; Piaggio, Giorgio; Gesualdo, Loreto; Vukic, Durdica Kosuljandic; Vukojevic, Katarina; Saraga-Babic, Mirna; Saraga, Marijan; Gucev, Zoran; Allegri, Landino; Latos-Bielenska, Anna; Casu, Domenica; State, Matthew; Scolari, Francesco; Ravazzolo, Roberto; Kiryluk, Krzysztof; Al-Awqati, Qais; D'Agati, Vivette D; Drummond, Iain A; Tasic, Velibor; Lifton, Richard P; Ghiggeri, Gian Marco; Gharavi, Ali G

2013-08-15

Congenital abnormalities of the kidney and the urinary tract are the most common cause of pediatric kidney failure. These disorders are highly heterogeneous, and the etiologic factors are poorly understood. We performed genomewide linkage analysis and whole-exome sequencing in a family with an autosomal dominant form of congenital abnormalities of the kidney or urinary tract (seven affected family members). We also performed a sequence analysis in 311 unrelated patients, as well as histologic and functional studies. Linkage analysis identified five regions of the genome that were shared among all affected family members. Exome sequencing identified a single, rare, deleterious variant within these linkage intervals, a heterozygous splice-site mutation in the dual serine-threonine and tyrosine protein kinase gene (DSTYK). This variant, which resulted in aberrant splicing of messenger RNA, was present in all affected family members. Additional, independent DSTYK mutations, including nonsense and splice-site mutations, were detected in 7 of 311 unrelated patients. DSTYK is highly expressed in the maturing epithelia of all major organs, localizing to cell membranes. Knockdown in zebrafish resulted in developmental defects in multiple organs, which suggested loss of fibroblast growth factor (FGF) signaling. Consistent with this finding is the observation that DSTYK colocalizes with FGF receptors in the ureteric bud and metanephric mesenchyme. DSTYK knockdown in human embryonic kidney cells inhibited FGF-stimulated phosphorylation of extracellular-signal-regulated kinase (ERK), the principal signal downstream of receptor tyrosine kinases. We detected independent DSTYK mutations in 2.3% of patients with congenital abnormalities of the kidney or urinary tract, a finding that suggests that DSTYK is a major determinant of human urinary tract development, downstream of FGF signaling. (Funded by the National Institutes of Health and others.).

Construction of three metal-organic frameworks based on multifunctional T-shaped tripodal ligands, H3PyImDC

KAUST Repository

Jing, Xuemin

2010-08-04

Three novel metal-organic frameworks (MOFs), |(C3H 7NO)2(H2O)|[Zn3(C10H 5N3O4)3(C3H 7NO)2] (1), |(H2O)5(H 3O)(NO3)|[Nd2(C10H5N 3O4)3(H2O)4] (2), and |(H2O)2|[Nd3(C10H5N 3O4)3(C10H4N 3O4)] (3), based on the T-shaped tripodal ligands 2-(pyridine-4-yl)-1H-4,5-imidazoledicarboxylic acid and 2-(pyridine-3-yl)-1H-4, 5-imidazoledicarboxylic acid (H3PyImDC), have been constructed under solvo-/hydrothermal conditions. The diverse coordination modes of H 3PyImDC ligands have afforded the assembly of three novel compounds. In compound 1, two oxygen atoms and three nitrogen atoms of the H 3PyImDC ligand, a T-shaped linker, coordinate to two zinc centers to form a novel bbm net with two distinct channels along the [100] and [001] directions. In compound 2, H3PyImDC ligands coordinate to neodymium centers to form a ladder-like chain which then interacts with a water molecules chain via hydrogen-bondings to construct a 3D supermolecular structure. In compound 3, H3PyImDC ligands, a T-shaped linker, coordinate to neodymium centers to form a (3,6)-connected net with an ant topology. In compounds 1-3, the two H3PyImDC ligands exhibit different coordination modes with zinc and neodymium centers, which afforded the expected structural diversity. Additionally, all three compounds exhibit strong fluorescence emissions in the solid state at room temperature. © 2010 American Chemical Society.

Genome Sequence of a Novel Archaeal Rudivirus Recovered from a Mexican Hot Spring

DEFF Research Database (Denmark)

Servín-Garcidueñas, L; Peng, X; Garrett, R

2013-01-01

We report the consensus genome sequence of a novel GC-rich rudivirus, designated SMR1 (Sulfolobales Mexican rudivirus 1), assembled from a high-throughput sequenced environmental sample from a hot spring in Los Azufres National Park in western Mexico.......We report the consensus genome sequence of a novel GC-rich rudivirus, designated SMR1 (Sulfolobales Mexican rudivirus 1), assembled from a high-throughput sequenced environmental sample from a hot spring in Los Azufres National Park in western Mexico....

Psi4NumPy: An Interactive Quantum Chemistry Programming Environment for Reference Implementations and Rapid Development.

Science.gov (United States)

Smith, Daniel G A; Burns, Lori A; Sirianni, Dominic A; Nascimento, Daniel R; Kumar, Ashutosh; James, Andrew M; Schriber, Jeffrey B; Zhang, Tianyuan; Zhang, Boyi; Abbott, Adam S; Berquist, Eric J; Lechner, Marvin H; Cunha, Leonardo A; Heide, Alexander G; Waldrop, Jonathan M; Takeshita, Tyler Y; Alenaizan, Asem; Neuhauser, Daniel; King, Rollin A; Simmonett, Andrew C; Turney, Justin M; Schaefer, Henry F; Evangelista, Francesco A; DePrince, A Eugene; Crawford, T Daniel; Patkowski, Konrad; Sherrill, C David

2018-06-11

Psi4NumPy demonstrates the use of efficient computational kernels from the open-source Psi4 program through the popular NumPy library for linear algebra in Python to facilitate the rapid development of clear, understandable Python computer code for new quantum chemical methods, while maintaining a relatively low execution time. Using these tools, reference implementations have been created for a number of methods, including self-consistent field (SCF), SCF response, many-body perturbation theory, coupled-cluster theory, configuration interaction, and symmetry-adapted perturbation theory. Furthermore, several reference codes have been integrated into Jupyter notebooks, allowing background, underlying theory, and formula information to be associated with the implementation. Psi4NumPy tools and associated reference implementations can lower the barrier for future development of quantum chemistry methods. These implementations also demonstrate the power of the hybrid C++/Python programming approach employed by the Psi4 program.

Effects of Diameter on Initial Stiffness of P-Y Curves for Large-Diameter Piles in Sand

DEFF Research Database (Denmark)

Sørensen, Søren Peder Hyldal; Ibsen, Lars Bo; Augustesen, Anders Hust

2010-01-01

is developed for slender piles with diameters up to approximately 2.0 m. Hence, the method is not validated for piles with diameters of 4–6 m. The aim of the paper is to extend the p-y curve method to large-diameter non-slender piles in sand by considering the effects of the pile diameter on the soil-pile...... interaction. Hence, a modified expression for the p-y curves for statically loaded piles in sand is proposed in which the initial slope of the p-y curves depends on the depth below the soil surface, the pile diameter and the internal angle of friction. The evaluation is based on three-dimensional numerical...... analyses by means of the commercial program FLAC3D incorporating a Mohr-Coulomb failure criterion. The numerical model is validated with laboratory tests in a pressure tank at Aalborg University....

Determination of p-y Curves for Bucket Foundations in Silt and Sand Using Finite Element Modelling

DEFF Research Database (Denmark)

Vethanayagam, Vinojan; Ibsen, Lars Bo

slender than the tested piles. The suction bucket has a slenderness ratio of 0.5-1, thus its response is a rigid movement, where slender piles undergoes a flexible movement. Due to the importance of precise estimations, p-y formulations for suction buckets in drained and undrained silt are sought...... developed with use of finite element. In general the developed p-y formulations for the drained and undrained silt are fairly precise. Furthermore, the same method and basic formulation of the drained silt is applied to data of the drained sand from Østergaard et al. [2015]. The developed formulation...... herefore shows to be more versatile and precise than the formulation suggested by Østergaard et al. [2015]. The developed p-y formulations are functions of the effective vertical in-situ stress, soil stiffness, diameter of the bucket and the internal friction angle/the undrained shear strength....

PyCPR - a python-based implementation of the Conjugate Peak Refinement (CPR) algorithm for finding transition state structures.

Science.gov (United States)

Gisdon, Florian J; Culka, Martin; Ullmann, G Matthias

2016-10-01

Conjugate peak refinement (CPR) is a powerful and robust method to search transition states on a molecular potential energy surface. Nevertheless, the method was to the best of our knowledge so far only implemented in CHARMM. In this paper, we present PyCPR, a new Python-based implementation of the CPR algorithm within the pDynamo framework. We provide a detailed description of the theory underlying our implementation and discuss the different parts of the implementation. The method is applied to two different problems. First, we illustrate the method by analyzing the gauche to anti-periplanar transition of butane using a semiempirical QM method. Second, we reanalyze the mechanism of a glycyl-radical enzyme, namely of 4-hydroxyphenylacetate decarboxylase (HPD) using QM/MM calculations. In the end, we suggest a strategy how to use our implementation of the CPR algorithm. The integration of PyCPR into the framework pDynamo allows the combination of CPR with the large variety of methods implemented in pDynamo. PyCPR can be used in combination with quantum mechanical and molecular mechanical methods (and hybrid methods) implemented directly in pDynamo, but also in combination with external programs such as ORCA using pDynamo as interface. PyCPR is distributed as free, open source software and can be downloaded from http://www.bisb.uni-bayreuth.de/index.php?page=downloads . Graphical Abstract PyCPR is a search tool for finding saddle points on the potential energy landscape of a molecular system.

Genome-wide conserved consensus transcription factor binding motifs are hyper-methylated

Directory of Open Access Journals (Sweden)

Down Thomas A

2010-09-01

Full Text Available Abstract Background DNA methylation can regulate gene expression by modulating the interaction between DNA and proteins or protein complexes. Conserved consensus motifs exist across the human genome ("predicted transcription factor binding sites": "predicted TFBS" but the large majority of these are proven by chromatin immunoprecipitation and high throughput sequencing (ChIP-seq not to be biological transcription factor binding sites ("empirical TFBS". We hypothesize that DNA methylation at conserved consensus motifs prevents promiscuous or disorderly transcription factor binding. Results Using genome-wide methylation maps of the human heart and sperm, we found that all conserved consensus motifs as well as the subset of those that reside outside CpG islands have an aggregate profile of hyper-methylation. In contrast, empirical TFBS with conserved consensus motifs have a profile of hypo-methylation. 40% of empirical TFBS with conserved consensus motifs resided in CpG islands whereas only 7% of all conserved consensus motifs were in CpG islands. Finally we further identified a minority subset of TF whose profiles are either hypo-methylated or neutral at their respective conserved consensus motifs implicating that these TF may be responsible for establishing or maintaining an un-methylated DNA state, or whose binding is not regulated by DNA methylation. Conclusions Our analysis supports the hypothesis that at least for a subset of TF, empirical binding to conserved consensus motifs genome-wide may be controlled by DNA methylation.

Enterobacterial repetitive intergenic consensus sequences and the PCR to generate fingerprints of genomic DNAs from Vibrio cholerae O1, O139, and non-O1 strains.

OpenAIRE

Rivera, I G; Chowdhury, M A; Huq, A; Jacobs, D; Martins, M T; Colwell, R R

1995-01-01

Enterobacterial repetitive intergenic consensus (ERIC) sequence polymorphism was studied in Vibrio Cholerae strains isolated before and after the cholera epidemic in Brazil (in 1991), along with epidemic strains from Peru, Mexico, and India, by PCR. A total of 17 fingerprint patterns (FPs) were detected in the V. cholerae strains examined; 96.7% of the toxigenic V. cholerae O1 strains and 100% of the O139 serogroup strains were found to belong to the same FP group comprising four fragments (F...

Dissecting direct and indirect readout of cAMP receptor protein DNA binding using an inosine and 2,6-diaminopurine in vitro selection system

DEFF Research Database (Denmark)

Lindemose, Søren; Nielsen, Peter E.; Møllegaard, Niels Erik

2008-01-01

The DNA interaction of the Escherichia coli cyclic AMP receptor protein (CRP) represents a typical example of a dual recognition mechanism exhibiting both direct and indirect readout. We have dissected the direct and indirect components of DNA recognition by CRP employing in vitro selection...... is functionally intact. The majority of the selected sites contain the natural consensus sequence TGTGAN(6)TCACA (i.e. TITIDN(6)TCDCD). Thus, direct readout of the consensus sequence is independent of minor groove conformation. Consequently, the indirect readout known to occur in the TG/CA base pair step (primary...... kink site) in the consensus sequence is not affected by I-D substitutions. In contrast, the flanking regions are selected as I/C rich sequences (mostly I-tracts) instead of A/T rich sequences which are known to strongly increase CRP binding, thereby demonstrating almost exclusive indirect readout...

PyFolding: Open-Source Graphing, Simulation, and Analysis of the Biophysical Properties of Proteins.

Science.gov (United States)

Lowe, Alan R; Perez-Riba, Albert; Itzhaki, Laura S; Main, Ewan R G

2018-02-06

For many years, curve-fitting software has been heavily utilized to fit simple models to various types of biophysical data. Although such software packages are easy to use for simple functions, they are often expensive and present substantial impediments to applying more complex models or for the analysis of large data sets. One field that is reliant on such data analysis is the thermodynamics and kinetics of protein folding. Over the past decade, increasingly sophisticated analytical models have been generated, but without simple tools to enable routine analysis. Consequently, users have needed to generate their own tools or otherwise find willing collaborators. Here we present PyFolding, a free, open-source, and extensible Python framework for graphing, analysis, and simulation of the biophysical properties of proteins. To demonstrate the utility of PyFolding, we have used it to analyze and model experimental protein folding and thermodynamic data. Examples include: 1) multiphase kinetic folding fitted to linked equations, 2) global fitting of multiple data sets, and 3) analysis of repeat protein thermodynamics with Ising model variants. Moreover, we demonstrate how PyFolding is easily extensible to novel functionality beyond applications in protein folding via the addition of new models. Example scripts to perform these and other operations are supplied with the software, and we encourage users to contribute notebooks and models to create a community resource. Finally, we show that PyFolding can be used in conjunction with Jupyter notebooks as an easy way to share methods and analysis for publication and among research teams. Copyright © 2017 Biophysical Society. Published by Elsevier Inc. All rights reserved.

pyPcazip: A PCA-based toolkit for compression and analysis of molecular simulation data

Directory of Open Access Journals (Sweden)

Ardita Shkurti

2016-01-01

Full Text Available The biomolecular simulation community is currently in need of novel and optimised software tools that can analyse and process, in reasonable timescales, the large generated amounts of molecular simulation data. In light of this, we have developed and present here pyPcazip: a suite of software tools for compression and analysis of molecular dynamics (MD simulation data. The software is compatible with trajectory file formats generated by most contemporary MD engines such as AMBER, CHARMM, GROMACS and NAMD, and is MPI parallelised to permit the efficient processing of very large datasets. pyPcazip is a Unix based open-source software (BSD licenced written in Python.

PyMS: a Python toolkit for processing of gas chromatography-mass spectrometry (GC-MS data. Application and comparative study of selected tools

Directory of Open Access Journals (Sweden)

O'Callaghan Sean

2012-05-01

Full Text Available Abstract Background Gas chromatography–mass spectrometry (GC-MS is a technique frequently used in targeted and non-targeted measurements of metabolites. Most existing software tools for processing of raw instrument GC-MS data tightly integrate data processing methods with graphical user interface facilitating interactive data processing. While interactive processing remains critically important in GC-MS applications, high-throughput studies increasingly dictate the need for command line tools, suitable for scripting of high-throughput, customized processing pipelines. Results PyMS comprises a library of functions for processing of instrument GC-MS data developed in Python. PyMS currently provides a complete set of GC-MS processing functions, including reading of standard data formats (ANDI- MS/NetCDF and JCAMP-DX, noise smoothing, baseline correction, peak detection, peak deconvolution, peak integration, and peak alignment by dynamic programming. A novel common ion single quantitation algorithm allows automated, accurate quantitation of GC-MS electron impact (EI fragmentation spectra when a large number of experiments are being analyzed. PyMS implements parallel processing for by-row and by-column data processing tasks based on Message Passing Interface (MPI, allowing processing to scale on multiple CPUs in distributed computing environments. A set of specifically designed experiments was performed in-house and used to comparatively evaluate the performance of PyMS and three widely used software packages for GC-MS data processing (AMDIS, AnalyzerPro, and XCMS. Conclusions PyMS is a novel software package for the processing of raw GC-MS data, particularly suitable for scripting of customized processing pipelines and for data processing in batch mode. PyMS provides limited graphical capabilities and can be used both for routine data processing and interactive/exploratory data analysis. In real-life GC-MS data processing scenarios PyMS performs

Anatomy and Physiology of the Urinary Tract: Relation to Host Defense and Microbial Infection.

Science.gov (United States)

Hickling, Duane R; Sun, Tung-Tien; Wu, Xue-Ru

2015-08-01

The urinary tract exits to a body surface area that is densely populated by a wide range of microbes. Yet, under most normal circumstances, it is typically considered sterile, i.e., devoid of microbes, a stark contrast to the gastrointestinal and upper respiratory tracts where many commensal and pathogenic microbes call home. Not surprisingly, infection of the urinary tract over a healthy person's lifetime is relatively infrequent, occurring once or twice or not at all for most people. For those who do experience an initial infection, the great majority (70% to 80%) thankfully do not go on to suffer from multiple episodes. This is a far cry from the upper respiratory tract infections, which can afflict an otherwise healthy individual countless times. The fact that urinary tract infections are hard to elicit in experimental animals except with inoculum 3-5 orders of magnitude greater than the colony counts that define an acute urinary infection in humans (105 cfu/ml), also speaks to the robustness of the urinary tract defense. How can the urinary tract be so effective in fending off harmful microbes despite its orifice in a close vicinity to that of the microbe-laden gastrointestinal tract? While a complete picture is still evolving, the general consensus is that the anatomical and physiological integrity of the urinary tract is of paramount importance in maintaining a healthy urinary tract. When this integrity is breached, however, the urinary tract can be at a heightened risk or even recurrent episodes of microbial infections. In fact, recurrent urinary tract infections are a significant cause of morbidity and time lost from work and a major challenge to manage clinically. Additionally, infections of the upper urinary tract often require hospitalization and prolonged antibiotic therapy. In this chapter, we provide an overview of the basic anatomy and physiology of the urinary tract with an emphasis on their specific roles in host defense. We also highlight the

Modeling plate shell structures using pyFormex

DEFF Research Database (Denmark)

Bagger, Anne; Verhegghe, Benedict; Hertz, Kristian Dahl

2009-01-01

A shell structure made of glass combines a light-weight structural concept with glass’ high permeability to light. If the geometry of the structure is plane-based facetted (plate shell structure), the glass elements will be plane panes, and these glass panes will comprise the primary load...... (plate shells and triangulated lattice shells) may not differ in complexity regarding the topology, but when it comes to the practical generation of the geometry, e.g. in CAD, the plate shell is far more troublesome to handle than the triangulated geometry. The free software tool “pyFormex”, developed...

A full-fledged micromagnetic code in fewer than 70 lines of NumPy

International Nuclear Information System (INIS)

Abert, Claas; Bruckner, Florian; Vogler, Christoph; Windl, Roman; Thanhoffer, Raphael; Suess, Dieter

2015-01-01

We present a complete micromagnetic finite-difference code in fewer than 70 lines of Python. The code makes a large use of the NumPy library and computes the exchange field by finite differences and the demagnetization field with a fast convolution algorithm. Since the magnetization in finite-difference micromagnetics is represented by a multi-dimensional array and the NumPy library features a rich interface for this data structure, the code we present is an ideal starting point for the development of novel algorithms. - Highlights: • A very concise but complete micromagnetic code written in Python is presented. • An introduction to finite-difference micromagnetics is provided. • The code is a perfect starting point for the development of novel algorithms

International interlaboratory study comparing single organism 16S rRNA gene sequencing data: Beyond consensus sequence comparisons

Science.gov (United States)

Olson, Nathan D.; Lund, Steven P.; Zook, Justin M.; Rojas-Cornejo, Fabiola; Beck, Brian; Foy, Carole; Huggett, Jim; Whale, Alexandra S.; Sui, Zhiwei; Baoutina, Anna; Dobeson, Michael; Partis, Lina; Morrow, Jayne B.

2015-01-01

This study presents the results from an interlaboratory sequencing study for which we developed a novel high-resolution method for comparing data from different sequencing platforms for a multi-copy, paralogous gene. The combination of PCR amplification and 16S ribosomal RNA gene (16S rRNA) sequencing has revolutionized bacteriology by enabling rapid identification, frequently without the need for culture. To assess variability between laboratories in sequencing 16S rRNA, six laboratories sequenced the gene encoding the 16S rRNA from Escherichia coli O157:H7 strain EDL933 and Listeria monocytogenes serovar 4b strain NCTC11994. Participants performed sequencing methods and protocols available in their laboratories: Sanger sequencing, Roche 454 pyrosequencing®, or Ion Torrent PGM®. The sequencing data were evaluated on three levels: (1) identity of biologically conserved position, (2) ratio of 16S rRNA gene copies featuring identified variants, and (3) the collection of variant combinations in a set of 16S rRNA gene copies. The same set of biologically conserved positions was identified for each sequencing method. Analytical methods using Bayesian and maximum likelihood statistics were developed to estimate variant copy ratios, which describe the ratio of nucleotides at each identified biologically variable position, as well as the likely set of variant combinations present in 16S rRNA gene copies. Our results indicate that estimated variant copy ratios at biologically variable positions were only reproducible for high throughput sequencing methods. Furthermore, the likely variant combination set was only reproducible with increased sequencing depth and longer read lengths. We also demonstrate novel methods for evaluating variable positions when comparing multi-copy gene sequence data from multiple laboratories generated using multiple sequencing technologies. PMID:27077030

International interlaboratory study comparing single organism 16S rRNA gene sequencing data: Beyond consensus sequence comparisons

Directory of Open Access Journals (Sweden)

Nathan D. Olson

2015-03-01

Full Text Available This study presents the results from an interlaboratory sequencing study for which we developed a novel high-resolution method for comparing data from different sequencing platforms for a multi-copy, paralogous gene. The combination of PCR amplification and 16S ribosomal RNA gene (16S rRNA sequencing has revolutionized bacteriology by enabling rapid identification, frequently without the need for culture. To assess variability between laboratories in sequencing 16S rRNA, six laboratories sequenced the gene encoding the 16S rRNA from Escherichia coli O157:H7 strain EDL933 and Listeria monocytogenes serovar 4b strain NCTC11994. Participants performed sequencing methods and protocols available in their laboratories: Sanger sequencing, Roche 454 pyrosequencing®, or Ion Torrent PGM®. The sequencing data were evaluated on three levels: (1 identity of biologically conserved position, (2 ratio of 16S rRNA gene copies featuring identified variants, and (3 the collection of variant combinations in a set of 16S rRNA gene copies. The same set of biologically conserved positions was identified for each sequencing method. Analytical methods using Bayesian and maximum likelihood statistics were developed to estimate variant copy ratios, which describe the ratio of nucleotides at each identified biologically variable position, as well as the likely set of variant combinations present in 16S rRNA gene copies. Our results indicate that estimated variant copy ratios at biologically variable positions were only reproducible for high throughput sequencing methods. Furthermore, the likely variant combination set was only reproducible with increased sequencing depth and longer read lengths. We also demonstrate novel methods for evaluating variable positions when comparing multi-copy gene sequence data from multiple laboratories generated using multiple sequencing technologies.

Urinary tract infections in children: EAU/ESPU guidelines.

Science.gov (United States)

Stein, Raimund; Dogan, Hasan S; Hoebeke, Piet; Kočvara, Radim; Nijman, Rien J M; Radmayr, Christian; Tekgül, Serdar

2015-03-01

In 30% of children with urinary tract anomalies, urinary tract infection (UTI) can be the first sign. Failure to identify patients at risk can result in damage to the upper urinary tract. To provide recommendations for the diagnosis, treatment, and imaging of children presenting with UTI. The recommendations were developed after a review of the literature and a search of PubMed and Embase. A consensus decision was adopted when evidence was low. UTIs are classified according to site, episode, symptoms, and complicating factors. For acute treatment, site and severity are the most important. Urine sampling by suprapubic aspiration or catheterisation has a low contamination rate and confirms UTI. Using a plastic bag to collect urine, a UTI can only be excluded if the dipstick is negative for both leukocyte esterase and nitrite or microscopic analysis is negative for both pyuria and bacteriuria. A clean voided midstream urine sample after cleaning the external genitalia has good diagnostic accuracy in toilet-trained children. In children with febrile UTI, antibiotic treatment should be initiated as soon as possible to eradicate infection, prevent bacteraemia, improve outcome, and reduce the likelihood of renal involvement. Ultrasound of the urinary tract is advised to exclude obstructive uropathy. Depending on sex, age, and clinical presentation, vesicoureteral reflux should be excluded. Antibacterial prophylaxis is beneficial. In toilet-trained children, bladder and bowel dysfunction needs to be excluded. The level of evidence is high for the diagnosis of UTI and treatment in children but not for imaging to identify patients at risk for upper urinary tract damage. In these guidelines, we looked at the diagnosis, treatment, and imaging of children with urinary tract infection. There are strong recommendations on diagnosis and treatment; we also advise exclusion of obstructive uropathy within 24h and later vesicoureteral reflux, if indicated. Copyright © 2014 European

A study of polymerization of aspen (Populus) wood lipophilic extractives by SEC and Py-GC/MS

CSIR Research Space (South Africa)

Sithole, Bruce

2013-03-01

Full Text Available ) Orig inal manuscript received 13 June 2012, revision accepted 31 October 2012 Vol 66 No 1 January - March 2013 1 PEER REVIEWED A study of polymerization of aspen (Populus) wood lipophilic extractives by SEC and Py-GC/MS BRUCE SITHOLE1*, LUC... of polymerized wood resin that will be difficult to remove if present in pulp and paper products. On the other hand, these problems may be minor compared to using unseasoned wood. KEYWORDS: Aspen, extractives, polymerization, size exclusion chromatography, Py...

The sequence specificity of UV-induced DNA damage in a systematically altered DNA sequence.

Science.gov (United States)

Khoe, Clairine V; Chung, Long H; Murray, Vincent

2018-06-01

The sequence specificity of UV-induced DNA damage was investigated in a specifically designed DNA plasmid using two procedures: end-labelling and linear amplification. Absorption of UV photons by DNA leads to dimerisation of pyrimidine bases and produces two major photoproducts, cyclobutane pyrimidine dimers (CPDs) and pyrimidine(6-4)pyrimidone photoproducts (6-4PPs). A previous study had determined that two hexanucleotide sequences, 5'-GCTC*AC and 5'-TATT*AA, were high intensity UV-induced DNA damage sites. The UV clone plasmid was constructed by systematically altering each nucleotide of these two hexanucleotide sequences. One of the main goals of this study was to determine the influence of single nucleotide alterations on the intensity of UV-induced DNA damage. The sequence 5'-GCTC*AC was designed to examine the sequence specificity of 6-4PPs and the highest intensity 6-4PP damage sites were found at 5'-GTTC*CC nucleotides. The sequence 5'-TATT*AA was devised to investigate the sequence specificity of CPDs and the highest intensity CPD damage sites were found at 5'-TTTT*CG nucleotides. It was proposed that the tetranucleotide DNA sequence, 5'-YTC*Y (where Y is T or C), was the consensus sequence for the highest intensity UV-induced 6-4PP adduct sites; while it was 5'-YTT*C for the highest intensity UV-induced CPD damage sites. These consensus tetranucleotides are composed entirely of consecutive pyrimidines and must have a DNA conformation that is highly productive for the absorption of UV photons. Crown Copyright © 2018. Published by Elsevier B.V. All rights reserved.

A genosensor for detection of consensus DNA sequence of Dengue virus using ZnO/Pt-Pd nanocomposites.

Science.gov (United States)

Singhal, Chaitali; Pundir, C S; Narang, Jagriti

2017-11-15

An electrochemical genosensor based on Zinc oxide/platinum-palladium (ZnO/Pt-Pd) modified fluorine doped tin oxide (FTO) glass plate was fabricated for detection of consensus DNA sequence of Dengue virus (DENV) using methylene blue (MB) as an intercalating agent. To achieve it, probe DNA (PDNA) was immobilized on the surface of ZnO/Pt-Pd nanocomposites modified FTO electrode. The synthesized nano-composites were characterized by high resolution transmission electron microscopy (HRTEM), energy dispersive X-ray analysis (EDX), atomic force microscopy (AFM), scanning electron microscopy (SEM), UV-Vis spectroscopy, X-ray diffraction (XRD) analysis and Fourier transform infra-red (FTIR) spectroscopy. This PDNA modified electrode (PDNA/ZnO/Pt-Pd/FTO) served as a signal amplification platform for the detection of the target hybridized DNA (TDNA). The hybridization between PDNA and TDNA was detected by reduction in current, generated by interaction of anionic mediator, i.e., methylene blue (MB) with free guanine (3'G) of ssDNA. The sensor showed a dynamic linear range of 1 × 10 -6 M to 100 × 10 -6 M with LOD as 4.3 × 10 -5 M and LOQ as 9.5 × 10 -5 M. Till date, majorly serotype specific biosensors for dengue detection have been developed. The genosensor reported here eliminates the possibility of false result as in case of serotype specific DNA sensor. This is the report where conserved sequences present in all the serotypes of Dengue virus has been employed for fabrication of a genosensor. Copyright © 2017 Elsevier B.V. All rights reserved.

SWMM5 Application Programming Interface and PySWMM: A Python Interfacing Wrapper

Science.gov (United States)

In support of the OpenWaterAnalytics open source initiative, the PySWMM project encompasses the development of a Python interfacing wrapper to SWMM5 with parallel ongoing development of the USEPA Stormwater Management Model (SWMM5) application programming interface (API). ...

A Naturally Transmitted Epitheliotropic Polyomavirus Pathogenic in Immunodeficient Rats: Characterization, Transmission, and Preliminary Epidemiologic Studies.

Science.gov (United States)

Besch-Williford, Cynthia; Pesavento, Patricia; Hamilton, Shari; Bauer, Beth; Kapusinszky, Beatrix; Phan, Tung; Delwart, Eric; Livingston, Robert; Cushing, Susan; Watanabe, Rie; Levin, Stephen; Berger, Diana; Myles, Matthew

2017-07-01

We report the identification, pathogenesis, and transmission of a novel polyomavirus in severe combined immunodeficient F344 rats with null Prkdc and interleukin 2 receptor gamma genes. Infected rats experienced weight loss, decreased fecundity, and mortality. Large basophilic intranuclear inclusions were observed in epithelium of the respiratory tract, salivary and lacrimal glands, uterus, and prostate gland. Unbiased viral metagenomic sequencing of lesioned tissues identified a novel polyomavirus, provisionally named Rattus norvegicus polyomavirus 2 (RatPyV2), which clustered with Washington University (WU) polyomavirus in the Wuki clade of the Betapolyomavirus genus. In situ hybridization analyses and quantitative polymerase chain reaction (PCR) results demonstrated viral nucleic acids in epithelium of respiratory, glandular, and reproductive tissues. Polyomaviral disease was reproduced in Foxn1 rnu nude rats cohoused with infected rats or experimentally inoculated with virus. After development of RatPyV2-specific diagnostic assays, a survey of immune-competent rats from North American research institutions revealed detection of RatPyV2 in 7 of 1,000 fecal samples by PCR and anti-RatPyV2 antibodies in 480 of 1,500 serum samples. These findings suggest widespread infection in laboratory rat populations, which may have profound implications for established models of respiratory injury. Additionally, RatPyV2 infection studies may provide an important system to investigate the pathogenesis of WU polyomavirus diseases of man.

Bus.py: A GridLAB-D Communication Interface for Smart Distribution Grid Simulations

Energy Technology Data Exchange (ETDEWEB)

Hansen, Timothy M.; Palmintier, Bryan; Suryanarayanan, Siddharth; Maciejewski, Anthony A.; Siegel, Howard Jay

2015-07-03

As more Smart Grid technologies (e.g., distributed photovoltaic, spatially distributed electric vehicle charging) are integrated into distribution grids, static distribution simulations are no longer sufficient for performing modeling and analysis. GridLAB-D is an agent-based distribution system simulation environment that allows fine-grained end-user models, including geospatial and network topology detail. A problem exists in that, without outside intervention, once the GridLAB-D simulation begins execution, it will run to completion without allowing the real-time interaction of Smart Grid controls, such as home energy management systems and aggregator control. We address this lack of runtime interaction by designing a flexible communication interface, Bus.py (pronounced bus-dot-pie), that uses Python to pass messages between one or more GridLAB-D instances and a Smart Grid simulator. This work describes the design and implementation of Bus.py, discusses its usefulness in terms of some Smart Grid scenarios, and provides an example of an aggregator-based residential demand response system interacting with GridLAB-D through Bus.py. The small scale example demonstrates the validity of the interface and shows that an aggregator using said interface is able to control residential loads in GridLAB-D during runtime to cause a reduction in the peak load on the distribution system in (a) peak reduction and (b) time-of-use pricing cases.

PyForecastTools

Energy Technology Data Exchange (ETDEWEB)

2017-09-22

The PyForecastTools package provides Python routines for calculating metrics for model validation, forecast verification and model comparison. For continuous predictands the package provides functions for calculating bias (mean error, mean percentage error, median log accuracy, symmetric signed bias), and for calculating accuracy (mean squared error, mean absolute error, mean absolute scaled error, normalized RMSE, median symmetric accuracy). Convenience routines to calculate the component parts (e.g. forecast error, scaled error) of each metric are also provided. To compare models the package provides: generic skill score; percent better. Robust measures of scale including median absolute deviation, robust standard deviation, robust coefficient of variation and the Sn estimator are all provided by the package. Finally, the package implements Python classes for NxN contingency tables. In the case of a multi-class prediction, accuracy and skill metrics such as proportion correct and the Heidke and Peirce skill scores are provided as object methods. The special case of a 2x2 contingency table inherits from the NxN class and provides many additional metrics for binary classification: probability of detection, probability of false detection, false alarm ration, threat score, equitable threat score, bias. Confidence intervals for many of these quantities can be calculated using either the Wald method or Agresti-Coull intervals.

Expert consensus document: The International Scientific Association for Probiotics and Prebiotics (ISAPP) consensus statement on the definition and scope of prebiotics.

Science.gov (United States)

Gibson, Glenn R; Hutkins, Robert; Sanders, Mary Ellen; Prescott, Susan L; Reimer, Raylene A; Salminen, Seppo J; Scott, Karen; Stanton, Catherine; Swanson, Kelly S; Cani, Patrice D; Verbeke, Kristin; Reid, Gregor

2017-08-01

In December 2016, a panel of experts in microbiology, nutrition and clinical research was convened by the International Scientific Association for Probiotics and Prebiotics to review the definition and scope of prebiotics. Consistent with the original embodiment of prebiotics, but aware of the latest scientific and clinical developments, the panel updated the definition of a prebiotic: a substrate that is selectively utilized by host microorganisms conferring a health benefit. This definition expands the concept of prebiotics to possibly include non-carbohydrate substances, applications to body sites other than the gastrointestinal tract, and diverse categories other than food. The requirement for selective microbiota-mediated mechanisms was retained. Beneficial health effects must be documented for a substance to be considered a prebiotic. The consensus definition applies also to prebiotics for use by animals, in which microbiota-focused strategies to maintain health and prevent disease is as relevant as for humans. Ultimately, the goal of this Consensus Statement is to engender appropriate use of the term 'prebiotic' by relevant stakeholders so that consistency and clarity can be achieved in research reports, product marketing and regulatory oversight of the category. To this end, we have reviewed several aspects of prebiotic science including its development, health benefits and legislation.

Actividades predominantes a nivel nacional, regional y local de las PyMEs industriales argentinas

Directory of Open Access Journals (Sweden)

Roark, Geraldina Yesica

2013-06-01

Full Text Available La creciente importancia e interés que han ido adquiriendo las Pequeñas y Medianas empresas (PyMEs en la actividad económica del país, ha originado la realización de diversos estudios, tanto de instituciones públicas como privadas, que a través de encuestas y registros han caracterizado diferentes temáticas para este tipo de empresas.En este contexto, el Departamento de Ingeniería Industrial de la Facultad de Ingeniería, perteneciente a la Universidad Nacional del Centro de la Provincia de Buenos Aires (UNCPBA, ubicado en la ciudad de Olavarría, se encuentra actualmente desarrollando un proyecto de investigación denominado "Cadena de valor e impacto de las actividades clave en la conducta competitiva de las PyMEs" con el objeto de evaluar sus cadenas de valor y generar propuestas de mejora que impacten positivamente en su competitividad y sustentabilidad en el sector al que pertenecen. Consecuentemente, la relevancia del presente estudio se focaliza en determinar las actividades predominantes de las PyMEs argentinas, a nivel nacional, regional y local, de forma tal de fundamentar la elección de la población objeto de estudio del citado proyecto.

Consensus recommendations for MS cortical lesion scoring using double inversion recovery MRI

DEFF Research Database (Denmark)

Geurts, J J G; Roosendaal, S D; Calabrese, M

2011-01-01

Different double inversion recovery (DIR) sequences are currently used in multiple sclerosis (MS) research centers to visualize cortical lesions, making it difficult to compare published data. This study aimed to formulate consensus recommendations for scoring cortical lesions in patients with MS...

Complete genome sequence of bacteriocin-producing Lactobacillus plantarum KLDS1.0391, a probiotic strain with gastrointestinal tract resistance and adhesion to the intestinal epithelial cells.

Science.gov (United States)

Jia, Fang-Fang; Zhang, Lu-Ji; Pang, Xue-Hui; Gu, Xin-Xi; Abdelazez, Amro; Liang, Yu; Sun, Si-Rui; Meng, Xiang-Chen

2017-10-01

Lactobacillus plantarum KLDS1.0391 is a probiotic strain isolated from the traditional fermented dairy products and identified to produce bacteriocin against Gram-positive and Gram-negative bacteria. Previous studies showed that the strain has a high resistance to gastrointestinal stress and has a high adhesion ability to the intestinal epithelial cells (Caco-2). We reported the entire genome sequence of this strain, which contains a circular 2,886,607-bp chromosome and three circular plasmids. Genes, which are related to the biosynthesis of bacteriocins, the stress resistance to gastrointestinal tract environment and adhesive performance, were identified. Whole genome sequence of Lactobacillus plantarum KLDS1.0391 will be helpful for its applications in food industry. Copyright © 2017 Elsevier Inc. All rights reserved.

pyOpenMS: a Python-based interface to the OpenMS mass-spectrometry algorithm library.

Science.gov (United States)

Röst, Hannes L; Schmitt, Uwe; Aebersold, Ruedi; Malmström, Lars

2014-01-01

pyOpenMS is an open-source, Python-based interface to the C++ OpenMS library, providing facile access to a feature-rich, open-source algorithm library for MS-based proteomics analysis. It contains Python bindings that allow raw access to the data structures and algorithms implemented in OpenMS, specifically those for file access (mzXML, mzML, TraML, mzIdentML among others), basic signal processing (smoothing, filtering, de-isotoping, and peak-picking) and complex data analysis (including label-free, SILAC, iTRAQ, and SWATH analysis tools). pyOpenMS thus allows fast prototyping and efficient workflow development in a fully interactive manner (using the interactive Python interpreter) and is also ideally suited for researchers not proficient in C++. In addition, our code to wrap a complex C++ library is completely open-source, allowing other projects to create similar bindings with ease. The pyOpenMS framework is freely available at https://pypi.python.org/pypi/pyopenms while the autowrap tool to create Cython code automatically is available at https://pypi.python.org/pypi/autowrap (both released under the 3-clause BSD licence). © 2014 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

PyTranSpot: A tool for multiband light curve modeling of planetary transits and stellar spots

Science.gov (United States)

Juvan, Ines G.; Lendl, M.; Cubillos, P. E.; Fossati, L.; Tregloan-Reed, J.; Lammer, H.; Guenther, E. W.; Hanslmeier, A.

2018-02-01

Several studies have shown that stellar activity features, such as occulted and non-occulted starspots, can affect the measurement of transit parameters biasing studies of transit timing variations and transmission spectra. We present PyTranSpot, which we designed to model multiband transit light curves showing starspot anomalies, inferring both transit and spot parameters. The code follows a pixellation approach to model the star with its corresponding limb darkening, spots, and transiting planet on a two dimensional Cartesian coordinate grid. We combine PyTranSpot with a Markov chain Monte Carlo framework to study and derive exoplanet transmission spectra, which provides statistically robust values for the physical properties and uncertainties of a transiting star-planet system. We validate PyTranSpot's performance by analyzing eleven synthetic light curves of four different star-planet systems and 20 transit light curves of the well-studied WASP-41b system. We also investigate the impact of starspots on transit parameters and derive wavelength dependent transit depth values for WASP-41b covering a range of 6200-9200 Å, indicating a flat transmission spectrum.

A consensus linkage map of lentil based on DArT markers from three RIL mapping populations.

Directory of Open Access Journals (Sweden)

Duygu Ates

Full Text Available Lentil (Lens culinaris ssp. culinaris Medikus is a diploid (2n = 2x = 14, self-pollinating grain legume with a haploid genome size of about 4 Gbp and is grown throughout the world with current annual production of 4.9 million tonnes.A consensus map of lentil (Lens culinaris ssp. culinaris Medikus was constructed using three different lentils recombinant inbred line (RIL populations, including "CDC Redberry" x "ILL7502" (LR8, "ILL8006" x "CDC Milestone" (LR11 and "PI320937" x "Eston" (LR39.The lentil consensus map was composed of 9,793 DArT markers, covered a total of 977.47 cM with an average distance of 0.10 cM between adjacent markers and constructed 7 linkage groups representing 7 chromosomes of the lentil genome. The consensus map had no gap larger than 12.67 cM and only 5 gaps were found to be between 12.67 cM and 6.0 cM (on LG3 and LG4. The localization of the SNP markers on the lentil consensus map were in general consistent with their localization on the three individual genetic linkage maps and the lentil consensus map has longer map length, higher marker density and shorter average distance between the adjacent markers compared to the component linkage maps.This high-density consensus map could provide insight into the lentil genome. The consensus map could also help to construct a physical map using a Bacterial Artificial Chromosome library and map based cloning studies. Sequence information of DArT may help localization of orientation scaffolds from Next Generation Sequencing data.

A consensus linkage map of lentil based on DArT markers from three RIL mapping populations.

Science.gov (United States)

Ates, Duygu; Aldemir, Secil; Alsaleh, Ahmad; Erdogmus, Semih; Nemli, Seda; Kahriman, Abdullah; Ozkan, Hakan; Vandenberg, Albert; Tanyolac, Bahattin

2018-01-01

Lentil (Lens culinaris ssp. culinaris Medikus) is a diploid (2n = 2x = 14), self-pollinating grain legume with a haploid genome size of about 4 Gbp and is grown throughout the world with current annual production of 4.9 million tonnes. A consensus map of lentil (Lens culinaris ssp. culinaris Medikus) was constructed using three different lentils recombinant inbred line (RIL) populations, including "CDC Redberry" x "ILL7502" (LR8), "ILL8006" x "CDC Milestone" (LR11) and "PI320937" x "Eston" (LR39). The lentil consensus map was composed of 9,793 DArT markers, covered a total of 977.47 cM with an average distance of 0.10 cM between adjacent markers and constructed 7 linkage groups representing 7 chromosomes of the lentil genome. The consensus map had no gap larger than 12.67 cM and only 5 gaps were found to be between 12.67 cM and 6.0 cM (on LG3 and LG4). The localization of the SNP markers on the lentil consensus map were in general consistent with their localization on the three individual genetic linkage maps and the lentil consensus map has longer map length, higher marker density and shorter average distance between the adjacent markers compared to the component linkage maps. This high-density consensus map could provide insight into the lentil genome. The consensus map could also help to construct a physical map using a Bacterial Artificial Chromosome library and map based cloning studies. Sequence information of DArT may help localization of orientation scaffolds from Next Generation Sequencing data.

A high density barley microsatellite consensus map with 775 SSR loci

NARCIS (Netherlands)

Varshney, R.K.; Marcel, T.C.; Ramsay, L.; Russell, J.; Roder, M.S.; Stein, N.; Waugh, R.; Langridge, P.; Niks, R.E.; Graner, A.

2007-01-01

A microsatellite or simple sequence repeat (SSR) consensus map of barley was constructed by joining six independent genetic maps based on the mapping populations 'Igri x Franka', 'Steptoe x Morex', 'OWBRec x OWBDom', 'Lina x Canada Park', 'L94 x Vada' and 'SusPtrit x Vada'. Segregation data for

Comparison of two Next Generation sequencing platforms for full genome sequencing of Classical Swine Fever Virus

DEFF Research Database (Denmark)

Fahnøe, Ulrik; Pedersen, Anders Gorm; Höper, Dirk

2013-01-01

to the consensus sequence. Additionally, we got an average sequence depth for the genome of 4000 for the Iontorrent PGM and 400 for the FLX platform making the mapping suitable for single nucleotide variant (SNV) detection. The analysis revealed a single non-silent SNV A10665G leading to the amino acid change D......Next Generation Sequencing (NGS) is becoming more adopted into viral research and will be the preferred technology in the years to come. We have recently sequenced several strains of Classical Swine Fever Virus (CSFV) by NGS on both Genome Sequencer FLX (GS FLX) and Iontorrent PGM platforms...

Delay-Induced Consensus and Quasi-Consensus in Multi-Agent Dynamical Systems

NARCIS (Netherlands)

Yu, Wenwu; Chen, Guanrong; Cao, Ming; Ren, Wei

2013-01-01

This paper studies consensus and quasi-consensus in multi-agent dynamical systems. A linear consensus protocol in the second-order dynamics is designed where both the current and delayed position information is utilized. Time delay, in a common perspective, can induce periodic oscillations or even

Python for data analysis data wrangling with Pandas, NumPy, and IPython

CERN Document Server

McKinney, Wes

2017-01-01

Get complete instructions for manipulating, processing, cleaning, and crunching datasets in Python. Updated for Python 3.6, the second edition of this hands-on guide is packed with practical case studies that show you how to solve a broad set of data analysis problems effectively. You’ll learn the latest versions of pandas, NumPy, IPython, and Jupyter in the process. Written by Wes McKinney, the creator of the Python pandas project, this book is a practical, modern introduction to data science tools in Python. It’s ideal for analysts new to Python and for Python programmers new to data science and scientific computing. Data files and related material are available on GitHub. Use the IPython shell and Jupyter notebook for exploratory computing Learn basic and advanced features in NumPy (Numerical Python) Get started with data analysis tools in the pandas library Use flexible tools to load, clean, transform, merge, and reshape data Create informative visualizations with matplotlib ...

Assessment of p-y Curves from Numerical Methods for a non-Slender Monopile in Cohesionless Soil

DEFF Research Database (Denmark)

Ibsen, Lars Bo; Roesen, Hanne Ravn; Wolf, Torben K.

2013-01-01

In current design the stiff large diameter monopile is a widely used solution as foundation of offshore wind turbines. Winds and waves subject the monopile to considerable lateral loads. The current design guidances apply the p-y curve method with formulations for the curves based on slender piles....... However, the behaviour of the stiff monopiles during lateral loading is not fully understood. In this paper case study from Barrow Offshore Wind Farm is used in a 3D finite element model. The analysis forms a basis for extraction of p-y curves which are used in an evaluation of the traditional curves...

Assessment of p-y Curves from Numerical Methods for a non-Slender Monopile in Cohesionless Soil

DEFF Research Database (Denmark)

Wolf, Torben K.; Rasmussen, Kristian L.; Hansen, Mette

In current design the stiff large diameter monopile is a widely used solution as foundation of offshore wind turbines. Winds and waves subject the monopile to considerable lateral loads. The current design guidances apply the p-y curve method with formulations for the curves based on slender piles....... However, the behaviour of the stiff monopiles during lateral loading is not fully understood. In this paper case study from Barrow Offshore Wind Farm is used in a 3D finite element model. The analysis forms a basis for extraction of p-y curves which are used in an evaluation of the traditional curves...

Principales prácticas de recursos humanos de las PyMEs industriales exitosas.

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Liliana Rocío López Suárez

2013-04-01

Full Text Available El éxito competitivo de la PyME depende en parte de la buena gestión de recursos humanos,por lo que no darle el valor que requiere constituye una de las principales causas de fracasode estas empresas. La responsabilidad de la gestión eficaz de los recursos humanos recae fundamentalmenteen los directivos. La presente investigación tiene como objetivo identificarlos estilos de dirección y las principales prácticas de recursos humanos que llevan a cabo lasPyMEs industriales exitosas de México y España. Para alcanzar los objetivos antes reseñados,se ha realizado un análisis documental, así como entrevistas en profundidad a expertosen el área de recursos humanos. En este trabajo se presentan los principales resultados conrespecto a las prácticas mencionadas.

Phylogenetic Trees From Sequences

Science.gov (United States)

Ryvkin, Paul; Wang, Li-San

In this chapter, we review important concepts and approaches for phylogeny reconstruction from sequence data.We first cover some basic definitions and properties of phylogenetics, and briefly explain how scientists model sequence evolution and measure sequence divergence. We then discuss three major approaches for phylogenetic reconstruction: distance-based phylogenetic reconstruction, maximum parsimony, and maximum likelihood. In the third part of the chapter, we review how multiple phylogenies are compared by consensus methods and how to assess confidence using bootstrapping. At the end of the chapter are two sections that list popular software packages and additional reading.

On the tradeoffs of programming language choice for numerical modelling in geoscience. A case study comparing modern Fortran, C++/Blitz++ and Python/NumPy.

Science.gov (United States)

Jarecka, D.; Arabas, S.; Fijalkowski, M.; Gaynor, A.

2012-04-01

The language of choice for numerical modelling in geoscience has long been Fortran. A choice of a particular language and coding paradigm comes with different set of tradeoffs such as that between performance, ease of use (and ease of abuse), code clarity, maintainability and reusability, availability of open source compilers, debugging tools, adequate external libraries and parallelisation mechanisms. The availability of trained personnel and the scale and activeness of the developer community is of importance as well. We present a short comparison study aimed at identification and quantification of these tradeoffs for a particular example of an object oriented implementation of a parallel 2D-advection-equation solver in Python/NumPy, C++/Blitz++ and modern Fortran. The main angles of comparison will be complexity of implementation, performance of various compilers or interpreters and characterisation of the "added value" gained by a particular choice of the language. The choice of the numerical problem is dictated by the aim to make the comparison useful and meaningful to geoscientists. Python is chosen as a language that traditionally is associated with ease of use, elegant syntax but limited performance. C++ is chosen for its traditional association with high performance but even higher complexity and syntax obscurity. Fortran is included in the comparison for its widespread use in geoscience often attributed to its performance. We confront the validity of these traditional views. We point out how the usability of a particular language in geoscience depends on the characteristics of the language itself and the availability of pre-existing software libraries (e.g. NumPy, SciPy, PyNGL, PyNIO, MPI4Py for Python and Blitz++, Boost.Units, Boost.MPI for C++). Having in mind the limited complexity of the considered numerical problem, we present a tentative comparison of performance of the three implementations with different open source compilers including CPython and

4-Pyridone-3-carboxamide-1-β-d-ribonucleoside Triphosphate (4PyTP, a Novel NAD+ Metabolite Accumulating in Erythrocytes of Uremic Children: A Biomarker for a Toxic NAD+ Analogue in Other Tissues?

Directory of Open Access Journals (Sweden)

Elizabeth A. Carrey

2011-06-01

Full Text Available We have identified a novel nucleotide, 4-pyridone 3/5-carboxamide ribonucleoside triphosphate (4PyTP, which accumulates in human erythrocytes during renal failure. Using plasma and erythrocyte extracts obtained from children with chronic renal failure we show that the concentration of 4PyTP is increased, as well as other soluble NAD+ metabolites (nicotinamide, N1-methylnicotinamide and 4Py-riboside and the major nicotinamide metabolite N1-methyl-2-pyridone-5-carboxamide (2PY, with increasing degrees of renal failure. We noted that 2PY concentration was highest in the plasma of haemodialysis patients, while 4PyTP was highest in erythrocytes of children undergoing peritoneal dialysis: its concentration correlated closely with 4Py-riboside, an authentic precursor of 4PyTP, in the plasma. In the dialysis patients, GTP concentration was elevated: similar accumulation was noted previously, as a paradoxical effect in erythrocytes during treatment with immunosuppressants such as ribavirin and mycophenolate mofetil, which deplete GTP through inhibition of IMP dehydrogenase in nucleated cells such as lymphocytes. We predict that 4Py-riboside and 4Py-nucleotides bind to this enzyme and alter its activity. The enzymes that regenerate NAD+ from nicotinamide riboside also convert the drugs tiazofurin and benzamide riboside into NAD+ analogues that inhibit IMP dehydrogenase more effectively than the related ribosides: we therefore propose that the accumulation of 4PyTP in erythrocytes during renal failure is a marker for the accumulation of a related toxic NAD+ analogue that inhibits IMP dehydrogenase in other cells.

Learning SciPy for numerical and scientific computing

CERN Document Server

Silva

2013-01-01

A step-by-step practical tutorial with plenty of examples on research-based problems from various areas of science, that prove how simple, yet effective, it is to provide solutions based on SciPy. This book is targeted at anyone with basic knowledge of Python, a somewhat advanced command of mathematics/physics, and an interest in engineering or scientific applications---this is broadly what we refer to as scientific computing.This book will be of critical importance to programmers and scientists who have basic Python knowledge and would like to be able to do scientific and numerical computatio

Spin crossover behaviour in Hofmann-like coordination polymer Fe(py)2[Pd(CN)4] with 57Fe Mössbauer spectra

Science.gov (United States)

Kitazawa, Takafumi; Kishida, Takanori; Kawasaki, Takeshi; Takahashi, Masashi

2017-11-01

We have prepared the 2D spin crossover complexes Fe(L)2Pd(CN)4 (L = py : 1a; py-D5 : 1b and py-15N : 1c). 1a has been characterised by 57Fe Mossbauer spectroscopic measurements, single crystal X-ray determination and SQUID measurements. The Mössbauer spectra for 1a indicate that the iron(II) spin states are in high spin states at 298 K and are in low spin states at 77 K. The crystal structures of 1a at 298 K and 90 K also show the high spin state and the low spin state respectively, associated with the Fe(II)-N distances. The spin transition temperature range of 1a is higher than that of Fe(py)2Ni(CN)4 since Pd(II) ions are larger and heavier than Ni(II) ions. SQUID data indicate isotope effects among 1a, 1b and 1c are observed in very small shifts of the transition temperatures probably due to larger and heavier Pd(II) ions. The delicate shifts would be associated with subtle balances between different vibrations around Fe(II) atoms and electronic factors.

MRI of the brain stem using fluid attenuated inversion recivery pulse sequences

International Nuclear Information System (INIS)

De Coene, B.; Hajnal, J.V.; Pennock, J.M.; Bydder, G.M.

1993-01-01

Heavily T2-weighted fluid-attenuated inversion recovery (FLAIR) sequences with inversion times of 2000-2500 ms and echo times of 130-200 ms were used to image the brain stem of a normal adult and five patients. These sequences produce high signal from many white matter tracts and display high lesion contrast. The corticospinal and parietopontine tracts, lateral and medial lemnisci, superior and inferior cerebellar peduncles, medial longitudinal fasciculi, thalamo-olivary tracts the cuneate and gracile fasiculi gave high signal and were directly visualised. The oculomotor and trigeminal nerves were demonstrated within the brain stem. Lesions not seen with conventional T2-weighted spin echo sequences were seen with high contrast in patients with infarction, multiple sclerosis, sarcoidosis, chunt obstruction and metastatic tumour. The anatomical detail and high lesion contrast given by the FLAIR pulse sequence appear likely to be of value in diagnosis of disease in the brain stem. (orig.)

Fractional anisotropy in white matter tracts of very-low-birth-weight infants

Energy Technology Data Exchange (ETDEWEB)

Dudink, Jeroen; Conneman, Nikk; Goudoever, Johannes van; Govaert, Paul [Erasmus MC-Sophia Children' s Hospital, Division of Neonatology, Department of Paediatrics, P.O. Box 2060, Rotterdam (Netherlands); Lequin, Maarten [Erasmus MC-Sophia Children' s Hospital, Division of Paediatrics, Department of Radiology, Rotterdam (Netherlands); Pul, Carola van [Maxima Medical Center, Department of Clinical Physics, Veldhoven (Netherlands); Buijs, Jan [Maxima Medical Center, Division of Neonatology, Department of Paediatrics, Veldhoven (Netherlands)

2007-12-15

Advances in neonatal intensive care have not yet reduced the high incidence of neurodevelopmental disability among very-low-birth-weight (VLBW) infants. As neurological deficits are related to white-matter injury, early detection is important. Diffusion tensor imaging (DTI) could be an excellent tool for assessment of white-matter injury. To provide DTI fractional anisotropy (FA) reference values for white-matter tracts of VLBW infants for clinical use. We retrospectively analysed DTI images of 28 VLBW infants (26-32 weeks gestational age) without evidence of white-matter abnormalities on conventional MRI sequences, and normal developmental outcome (assessed at age 1-3 years). For DTI an echoplanar sequence with diffusion gradient (b = 1,000 s/mm{sup 2}) applied in 25 non-collinear directions was used. We measured FA and apparent diffusion coefficient (ADC) of different white-matter tracts in the first 4 days of life. A statistically significant correlation was found between gestational age and FA of the posterior limb of the internal capsule in VLBW infants (r = 0.495, P<0.01). Values of FA and ADC were measured in white-matter tracts of VLBW infants. FA of the pyramidal tracts measured in the first few days after birth is related to gestational age. (orig.)

Fractional anisotropy in white matter tracts of very-low-birth-weight infants

International Nuclear Information System (INIS)

Dudink, Jeroen; Conneman, Nikk; Goudoever, Johannes van; Govaert, Paul; Lequin, Maarten; Pul, Carola van; Buijs, Jan

2007-01-01

Advances in neonatal intensive care have not yet reduced the high incidence of neurodevelopmental disability among very-low-birth-weight (VLBW) infants. As neurological deficits are related to white-matter injury, early detection is important. Diffusion tensor imaging (DTI) could be an excellent tool for assessment of white-matter injury. To provide DTI fractional anisotropy (FA) reference values for white-matter tracts of VLBW infants for clinical use. We retrospectively analysed DTI images of 28 VLBW infants (26-32 weeks gestational age) without evidence of white-matter abnormalities on conventional MRI sequences, and normal developmental outcome (assessed at age 1-3 years). For DTI an echoplanar sequence with diffusion gradient (b = 1,000 s/mm 2 ) applied in 25 non-collinear directions was used. We measured FA and apparent diffusion coefficient (ADC) of different white-matter tracts in the first 4 days of life. A statistically significant correlation was found between gestational age and FA of the posterior limb of the internal capsule in VLBW infants (r = 0.495, P<0.01). Values of FA and ADC were measured in white-matter tracts of VLBW infants. FA of the pyramidal tracts measured in the first few days after birth is related to gestational age. (orig.)

PyTRiP - a toolbox and GUI for the proton/ion therapy planning system TRiP

International Nuclear Information System (INIS)

Toftegaard, J; Bassler, N; Petersen, J B

2014-01-01

Purpose: Only very few treatment planning systems (TPS) are capable of handling heavy ions. Commercial heavy ion TPS are costly and normally restrict the possibility to implement new functionalities. PyTRiP provides Python bindings and a platform-independent graphical user interface (GUI) for the heavy ion treatment program TRiP, and adds seamless support of DICOM files. We aim to provide a front-end for TRiP which does not require any special computer skills. Methods: PyTRiP is written in Python combined with C for fast computing. Routines for DICOM file import/export to TRiPs native file format are implemented. The GUI comes as an executable with all its dependencies including PyTRiP making it easy to install on Windows, Mac and Linux. Results: PyTRiP is a comprehensive toolbox for handling TRiP. Treatment plans are handled using an object oriented structure. Bindings to TRiP (which only runs on Linux, either locally or on a remote server) are performed through a single function call. GUI users can intuitively create treatment plans without much knowledge about the TRiP user interface. Advanced users still have full access to all TRiP functionality. The user interface comes with a comprehensive plotting tool, which can visualize 2D contours, volume histograms, as well as dose- and linear energy transfer (LET) distributions. Conclusion: We developed a powerful toolbox for ion therapy research using TRiP as backend. The corresponding GUI allows to easily and intuitively create, calculate and visualize treatment plans. TRiP is thereby more accessible and simpler to use.

Formula Translation in Blitz++, NumPy and Modern Fortran: A Case Study of the Language Choice Tradeoffs

Directory of Open Access Journals (Sweden)

Sylwester Arabas

2014-01-01

Full Text Available Three object-oriented implementations of a prototype solver of the advection equation are introduced. The presented programs are based on Blitz++ (C++, NumPy (Python and Fortran's built-in array containers. The solvers constitute implementations of the Multidimensional Positive-Definite Advective Transport Algorithm (MPDATA. The introduced codes serve as examples for how the application of object-oriented programming (OOP techniques and new language constructs from C++11 and Fortran 2008 allow to reproduce the mathematical notation used in the literature within the program code. A discussion on the tradeoffs of the programming language choice is presented. The main angles of comparison are code brevity and syntax clarity (and hence maintainability and auditability as well as performance. All performance tests are carried out using free and open-source compilers. In the case of Python, a significant performance gain is observed when switching from the standard interpreter (CPython to the PyPy implementation of Python. Entire source code of all three implementations is embedded in the text and is licensed under the terms of the GNU GPL license.

Metagenomic analysis of viral diversity in respiratory samples from patients with respiratory tract infections in Kuwait.

Science.gov (United States)

Madi, Nada; Al-Nakib, Widad; Mustafa, Abu Salim; Habibi, Nazima

2018-03-01

A metagenomic approach based on target independent next-generation sequencing has become a known method for the detection of both known and novel viruses in clinical samples. This study aimed to use the metagenomic sequencing approach to characterize the viral diversity in respiratory samples from patients with respiratory tract infections. We have investigated 86 respiratory samples received from various hospitals in Kuwait between 2015 and 2016 for the diagnosis of respiratory tract infections. A metagenomic approach using the next-generation sequencer to characterize viruses was used. According to the metagenomic analysis, an average of 145, 019 reads were identified, and 2% of these reads were of viral origin. Also, metagenomic analysis of the viral sequences revealed many known respiratory viruses, which were detected in 30.2% of the clinical samples. Also, sequences of non-respiratory viruses were detected in 14% of the clinical samples, while sequences of non-human viruses were detected in 55.8% of the clinical samples. The average genome coverage of the viruses was 12% with the highest genome coverage of 99.2% for respiratory syncytial virus, and the lowest was 1% for torque teno midi virus 2. Our results showed 47.7% agreement between multiplex Real-Time PCR and metagenomics sequencing in the detection of respiratory viruses in the clinical samples. Though there are some difficulties in using this method to clinical samples such as specimen quality, these observations are indicative of the promising utility of the metagenomic sequencing approach for the identification of respiratory viruses in patients with respiratory tract infections. © 2017 Wiley Periodicals, Inc.

Consensus recommendation for India and Bangladesh for the use of pneumococcal vaccine in mass gatherings with special reference to Hajj pilgrims

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Dilip Mathai

2016-01-01

Full Text Available Respiratory tract infections are prevalent among Hajj pilgrims with pneumonia being a leading cause of hospitalization. Streptococcus pneumoniae is a common pathogen isolated from patients with pneumonia and respiratory tract infections during Hajj. There is a significant burden of pneumococcal disease in India, which can be prevented. Guidelines for preventive measures and adult immunization have been published in India, but the implementation of the guidelines is low. Data from Bangladesh are available about significant mortality due to respiratory infections; however, literature regarding guidelines for adult immunization is limited. There is a need for extensive awareness programs across India and Bangladesh. Hence, there was a general consensus about the necessity for a rapid and urgent implementation of measures to prevent respiratory infections in pilgrims traveling to Hajj. About ten countries have developed recommendations for pneumococcal vaccination in Hajj pilgrims: France, the USA, Kuwait, Qatar, Bahrain, the UAE (Dubai Health Authority, Singapore, Malaysia, Egypt, and Indonesia. At any given point whether it is Hajj or Umrah, more than a million people are present in the holy places of Mecca and Madina. Therefore, the preventive measures taken for Hajj apply for Umrah as well. This document puts forward the consensus recommendations by a group of twenty doctors following a closed-door discussion based on the scientific evidence available for India and Bangladesh regarding the prevention of respiratory tract infections in Hajj pilgrims.

Angiotensin-converting enzyme inhibitor treatment and the development of urinary tract infections : a prescription sequence symmetry analysis

NARCIS (Netherlands)

Pouwels, Koen B; Visser, Sipke T; Bos, H Jens; Hak, Eelko

2013-01-01

BACKGROUND: Angiotensin-converting enzyme inhibitors (ACEi) can reduce urine output, especially when treatment is first started. Since bacterial clearance from the urinary tract is dependent on urine output, it was hypothesized that ACEi may also increase the risk of urinary tract infections (UTIs).

PyCCF: Python Cross Correlation Function for reverberation mapping studies

Science.gov (United States)

Sun, Mouyuan; Grier, C. J.; Peterson, B. M.

2018-05-01

PyCCF emulates a Fortran program written by B. Peterson for use with reverberation mapping. The code cross correlates two light curves that are unevenly sampled using linear interpolation and measures the peak and centroid of the cross-correlation function. In addition, it is possible to run Monto Carlo iterations using flux randomization and random subset selection (RSS) to produce cross-correlation centroid distributions to estimate the uncertainties in the cross correlation results.

Human adenovirus serotype 12 virion precursors pMu and pVI are cleaved at amino-terminal and carboxy-terminal sites that conform to the adenovirus 2 endoproteinase cleavage consensus sequence.

Science.gov (United States)

Freimuth, P; Anderson, C W

1993-03-01

The sequence of a 1158-base pair fragment of the human adenovirus serotype 12 (Ad12) genome was determined. This segment encodes the precursors for virion components Mu and VI. Both Ad12 precursors contain two sequences that conform to a consensus sequence motif for cleavage by the endoproteinase of adenovirus 2 (Ad2). Analysis of the amino terminus of VI and of the peptide fragments found in Ad12 virions demonstrated that these sites are cleaved during Ad12 maturation. This observation suggests that the recognition motif for adenovirus endoproteinases is highly conserved among human serotypes. The adenovirus 2 endoproteinase polypeptide requires additional co-factors for activity (C. W. Anderson, Protein Expression Purif., 1993, 4, 8-15). Synthetic Ad12 or Ad2 pVI carboxy-terminal peptides each permitted efficient cleavage of an artificial endoproteinase substrate by recombinant Ad2 endoproteinase polypeptide.

Genome sequence of Lactobacillus rhamnosus ATCC 8530.

Science.gov (United States)

Pittet, Vanessa; Ewen, Emily; Bushell, Barry R; Ziola, Barry

2012-02-01

Lactobacillus rhamnosus is found in the human gastrointestinal tract and is important for probiotics. We became interested in L. rhamnosus isolate ATCC 8530 in relation to beer spoilage and hops resistance. We report here the genome sequence of this isolate, along with a brief comparison to other available L. rhamnosus genome sequences.

Genome Sequence of Lactobacillus rhamnosus ATCC 8530

OpenAIRE

Pittet, Vanessa; Ewen, Emily; Bushell, Barry R.; Ziola, Barry

2012-01-01

Lactobacillus rhamnosus is found in the human gastrointestinal tract and is important for probiotics. We became interested in L. rhamnosus isolate ATCC 8530 in relation to beer spoilage and hops resistance. We report here the genome sequence of this isolate, along with a brief comparison to other available L. rhamnosus genome sequences.

Un modelo asociativo con base tecnológica para la competitividad de PyMes: caso floricultor colombiano

OpenAIRE

Giraldo, Olga Lucia; Herrera, Andrea

2004-01-01

La globalización ha abierto los mercados haciendo que la tecnología desempeñe un papel clave en la búsqueda y logro de competitividad. Este estudio, basado en el enfoque de cluster, primero analiza la competitividad a la luz del diamante de Porter, de las PyMes colombianas centrándose en el sector floricultor; segundo estudia las áreas donde las tecnologías de información tendrían mayor impacto; y tercero propone soluciones asociativas, basadas en el modelo de ASP, para lograr que las PyMes t...

Prediction of antigenic epitopes on protein surfaces by consensus scoring

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Zhang Chi

2009-09-01

Full Text Available Abstract Background Prediction of antigenic epitopes on protein surfaces is important for vaccine design. Most existing epitope prediction methods focus on protein sequences to predict continuous epitopes linear in sequence. Only a few structure-based epitope prediction algorithms are available and they have not yet shown satisfying performance. Results We present a new antigen Epitope Prediction method, which uses ConsEnsus Scoring (EPCES from six different scoring functions - residue epitope propensity, conservation score, side-chain energy score, contact number, surface planarity score, and secondary structure composition. Applied to unbounded antigen structures from an independent test set, EPCES was able to predict antigenic eptitopes with 47.8% sensitivity, 69.5% specificity and an AUC value of 0.632. The performance of the method is statistically similar to other published methods. The AUC value of EPCES is slightly higher compared to the best results of existing algorithms by about 0.034. Conclusion Our work shows consensus scoring of multiple features has a better performance than any single term. The successful prediction is also due to the new score of residue epitope propensity based on atomic solvent accessibility.

Perprof-py: A Python Package for Performance Profile of Mathematical Optimization Software

Directory of Open Access Journals (Sweden)

Abel Soares Siqueira

2016-04-01

Full Text Available A very important area of research in the field of Mathematical Optimization is the benchmarking of optimization packages to compare solvers. During benchmarking, one usually collects a large amount of information like CPU time, number of functions evaluations, number of iterations, and much more. This information, if presented as tables, can be difficult to analyze and compare due to large amount of data. Therefore tools to better process and understand optimization benchmark data have been developed. One of the most widespread tools is the Performance Profile graphics proposed by Dolan and Moré [2]. In this context, this paper describes perprof-py, a free/open source software that creates 'Performance Profile' graphics. This software produces graphics in PDF using LaTeX with PGF/TikZ [22] and PGFPLOTS [4] packages, in PNG using matplotlib [9], and in HTML using Bokeh [1]. Perprof-py can also be easily extended to be used with other plot libraries. It is implemented in Python 3 with support for internationalization, and is under the General Public License Version 3 (GPLv3.

PyChimera: use UCSF Chimera modules in any Python 2.7 project.

Science.gov (United States)

Rodríguez-Guerra Pedregal, Jaime; Maréchal, Jean-Didier

2018-05-15

UCSF Chimera is a powerful visualization tool remarkably present in the computational chemistry and structural biology communities. Built on a C++ core wrapped under a Python 2.7 environment, one could expect to easily import UCSF Chimera's arsenal of resources in custom scripts or software projects. Nonetheless, this is not readily possible if the script is not executed within UCSF Chimera due to the isolation of the platform. UCSF ChimeraX, successor to the original Chimera, partially solves the problem but yet major upgrades need to be undergone so that this updated version can offer all UCSF Chimera features. PyChimera has been developed to overcome these limitations and provide access to the UCSF Chimera codebase from any Python 2.7 interpreter, including interactive programming with tools like IPython and Jupyter Notebooks, making it easier to use with additional third-party software. PyChimera is LGPL-licensed and available at https://github.com/insilichem/pychimera. jaime.rodriguezguerra@uab.cat or jeandidier.marechal@uab.cat. Supplementary data are available at Bioinformatics online.

ObsPy: Establishing and maintaining an open-source community package

Science.gov (United States)

Krischer, L.; Megies, T.; Barsch, R.

2017-12-01

Python's ecosystem evolved into one of the most powerful and productive research environment across disciplines. ObsPy (https://obspy.org) is a fully community driven, open-source project dedicated to provide a bridge for seismology into that ecosystem. It does so by offering Read and write support for essentially every commonly used data format in seismology, Integrated access to the largest data centers, web services, and real-time data streams, A powerful signal processing toolbox tuned to the specific needs of seismologists, and Utility functionality like travel time calculations, geodetic functions, and data visualizations. ObsPy has been in constant unfunded development for more than eight years and is developed and used by scientists around the world with successful applications in all branches of seismology. By now around 70 people directly contributed code to ObsPy and we aim to make it a self-sustaining community project.This contributions focusses on several meta aspects of open-source software in science, in particular how we experienced them. During the panel we would like to discuss obvious questions like long-term sustainability with very limited to no funding, insufficient computer science training in many sciences, and gaining hard scientific credits for software development, but also the following questions: How to best deal with the fact that a lot of scientific software is very specialized thus usually solves a complex problem but at the same time can only ever reach a limited pool of developers and users by virtue of it being so specialized? Therefore the "many eyes on the code" approach to develop and improve open-source software only applies in a limited fashion. An initial publication for a significant new scientific software package is fairly straightforward. How to on-board and motivate potential new contributors when they can no longer be lured by a potential co-authorship? When is spending significant time and effort on reusable

PyORBIT: A Python Shell For ORBIT

Energy Technology Data Exchange (ETDEWEB)

Jean-Francois Ostiguy; Jeffrey Holmes

2003-07-01

ORBIT is code developed at SNS to simulate beam dynamics in accumulation rings and synchrotrons. The code is structured as a collection of external C++ modules for SuperCode, a high level interpreter shell developed at LLNL in the early 1990s. SuperCode is no longer actively supported and there has for some time been interest in replacing it by a modern scripting language, while preserving the feel of the original ORBIT program. In this paper, we describe a new version of ORBIT where the role of SuperCode is assumed by Python, a free, well-documented and widely supported object-oriented scripting language. We also compare PyORBIT to ORBIT from the standpoint of features, performance and future expandability.

PyORBIT: A Python Shell For ORBIT

International Nuclear Information System (INIS)

Jean-Francois Ostiguy; Jeffrey Holmes

2003-01-01

ORBIT is code developed at SNS to simulate beam dynamics in accumulation rings and synchrotrons. The code is structured as a collection of external C++ modules for SuperCode, a high level interpreter shell developed at LLNL in the early 1990s. SuperCode is no longer actively supported and there has for some time been interest in replacing it by a modern scripting language, while preserving the feel of the original ORBIT program. In this paper, we describe a new version of ORBIT where the role of SuperCode is assumed by Python, a free, well-documented and widely supported object-oriented scripting language. We also compare PyORBIT to ORBIT from the standpoint of features, performance and future expandability

Sequence stratigraphic interpretation of parts of Anambra Basin, Nigeria using geophysical well logs and biostratigraphic data

Science.gov (United States)

Anakwuba, E. K.; Ajaegwu, N. E.; Ejeke, C. F.; Onyekwelu, C. U.; Chinwuko, A. I.

2018-03-01

The Anambra basin constitutes the southeastern lower portion of the Benue Trough, which is a large structural depression that is divided into lower, middle and upper parts; and is one of the least studied inland sedimentary basins in Nigeria. Sequence stratigraphic interpretation had been carried out in parts of the Anambra Basin using data from three wells (Alo-1 Igbariam-1 and Ajire-1). Geophysical well logs and biostratigraphic data were integrated in order to identify key bounding surfaces, subdivide the sediment packages, correlate sand continuity and interpret the environment of deposition in the fields. Biostratigraphic interpretation, using foraminifera and plankton population and diversity, reveals five maximum flooding surfaces (MFS) in the fields. Five sequence boundaries (SB) were also identified using the well log analysis. Four 3rd order genetic sequences bounded by maximum flooding surfaces (MFS-1 to MFS-6) were identified in the areas; four complete sequences and one incomplete sequence were identified in both Alo-1 and Igbariam-1 wells while Ajire-1 has an no complete sequence. The identified system tracts delineated comprises Lowstand Systems Tracts (progradational to aggradational to retrogradational packages), Transgressive Systems Tracts (retrogradational packages) and Highstand Systems Tracts (aggradational to progradational packages) in each well. The sand continuity across the fields reveal sands S1 to S5 where S1 is present in Ajire-1 well and Igbariam-1 well but not in Alo-1 well. The sands S4 to S5 run across the three fields at different depths. The formations penetrated by the wells starting from the base are; Nkporo Formation (Campanian), Mamu Formation (Late Campanian to Early Maastrichtian), Ajali Sandstone (Maastrichtian), Nsukka Formation (Late Maastrichtian to Early Palaeocene), Imo Formation (Palaeocene) and Nanka Sand (Eocene). The environments of deposition revealed are from coastal to bathyal. The sands of lowstand system

Quality indicators for the diagnosis and antibiotic treatment of acute respiratory tract infections in general practice

DEFF Research Database (Denmark)

Saust, Laura Trolle; Bjerrum, Lars; Arpi, Magnus

2017-01-01

Objective: To develop quality indicators for the diagnosis and antibiotic treatment of acute respiratory tract infections, tailored to the Danish general practice setting. Design: A RAND/UCLA Appropriateness Method was used. Setting: General practice. Subjects: A panel of nine experts, mainly...... general practitioners, was asked to rate the relevance of 64 quality indicators for the diagnosis and antibiotic treatment of acute respiratory tract infections based on guidelines. Subsequently, a face-to-face meeting was held to resolve misinterpretations and to achieve consensus. Main outcome measures...... indicators focusing on the diagnostic process and 19 indicators focusing on the decision about antibiotic treatment and choice of antibiotics, respectively. Conclusion: These newly developed quality indicators may be used to strengthen Danish general practitioners’ focus on their management of patients...

pyRMSD: a Python package for efficient pairwise RMSD matrix calculation and handling.

Science.gov (United States)

Gil, Víctor A; Guallar, Víctor

2013-09-15

We introduce pyRMSD, an open source standalone Python package that aims at offering an integrative and efficient way of performing Root Mean Square Deviation (RMSD)-related calculations of large sets of structures. It is specially tuned to do fast collective RMSD calculations, as pairwise RMSD matrices, implementing up to three well-known superposition algorithms. pyRMSD provides its own symmetric distance matrix class that, besides the fact that it can be used as a regular matrix, helps to save memory and increases memory access speed. This last feature can dramatically improve the overall performance of any Python algorithm using it. In addition, its extensibility, testing suites and documentation make it a good choice to those in need of a workbench for developing or testing new algorithms. The source code (under MIT license), installer, test suites and benchmarks can be found at https://pele.bsc.es/ under the tools section. victor.guallar@bsc.es Supplementary data are available at Bioinformatics online.

Identification of Meconopsis species by a DNA barcode sequence ...

African Journals Online (AJOL)

Deoxyribonucleic acid (DNA) barcoding is a novel technology that uses a standard DNA sequence to facilitate species identification. Species identification is necessary for the authentication of traditional plant based medicines. Although a consensus has not been agreed regarding which DNA sequences can be used as ...

Involvement of an ATP-dependent carboxylase in a CO2-dependent pathway of acetone metabolism by Xanthobacter strain Py2.

OpenAIRE

Sluis, M K; Small, F J; Allen, J R; Ensign, S A

1996-01-01

The metabolism of acetone by the aerobic bacterium Xanthobacter strain Py2 was investigated. Cell suspensions of Xanthobacter strain Py2 grown with propylene or glucose as carbon sources were unable to metabolize acetone. The addition of acetone to cultures grown with propylene or glucose resulted in a time-dependent increase in acetone-degrading activity. The degradation of acetone by these cultures was prevented by the addition of rifampin and chloramphenicol, demonstrating that new protein...

Laboratory Diagnosis of Parasites from the Gastrointestinal Tract.

Science.gov (United States)

Garcia, Lynne S; Arrowood, Michael; Kokoskin, Evelyne; Paltridge, Graeme P; Pillai, Dylan R; Procop, Gary W; Ryan, Norbert; Shimizu, Robyn Y; Visvesvara, Govinda

2018-01-01

This Practical Guidance for Clinical Microbiology document on the laboratory diagnosis of parasites from the gastrointestinal tract provides practical information for the recovery and identification of relevant human parasites. The document is based on a comprehensive literature review and expert consensus on relevant diagnostic methods. However, it does not include didactic information on human parasite life cycles, organism morphology, clinical disease, pathogenesis, treatment, or epidemiology and prevention. As greater emphasis is placed on neglected tropical diseases, it becomes highly probable that patients with gastrointestinal parasitic infections will become more widely recognized in areas where parasites are endemic and not endemic. Generally, these methods are nonautomated and require extensive bench experience for accurate performance and interpretation. Copyright © 2017 American Society for Microbiology.

Mechanical behavior of SiCf/SiC composites with alternating PyC/SiC multilayer interphases

International Nuclear Information System (INIS)

Yu, Haijiao; Zhou, Xingui; Zhang, Wei; Peng, Huaxin; Zhang, Changrui

2013-01-01

Highlights: ► Superior combination of flexural strength and fracture toughness of the 3D SiC/SiC composite was achieved by interface tailoring. ► Resulted composite possesses a much higher flexural strength and fracture toughness than its counterparts in literatures. ► Mechanisms that PyC/SiC multilayer coatings improve the mechanical properties were illustrated. -- Abstract: In order to tailor the fiber–matrix interface of continuous silicon carbide fiber reinforced silicon carbide (SiC f /SiC) composites for improved fracture toughness, alternating pyrolytic carbon/silicon carbide (PyC/SiC) multilayer coatings were applied to the KD-I SiC fibers using chemical vapor deposition (CVD) method. Three dimensional (3D) KD-I SiC f /SiC composites reinforced by these coated fibers were fabricated using a precursor infiltration and pyrolysis (PIP) process. The interfacial characteristics were determined by the fiber push-out test and microstructural examination using scanning electron microscopy (SEM). The effect of interface coatings on composite mechanical properties was evaluated by single-edge notched beam (SENB) test and three-point bending test. The results indicate that the PyC/SiC multilayer coatings led to an optimum interfacial bonding between fibers and matrix and greatly improved the fracture toughness of the composites.

PyMEs y crecimiento económico : Estado de situación de Argentina y su comparación con Brasil y Canadá

OpenAIRE

De Simone Martin, Mara

2017-01-01

Descripción del estado de situación en Argentina, Brasil y Canadá respecto de la contribución de las PyMES al PBI y Empleo. Organismos o políticas de Apoyo a las PyMES. Incubadoras de Negocios. Durante los últimos 15 años, Argentina muestra muy pocas PyMES y bajo PBI comparada con Brasil y Canadá aún cuando se contemplen paralelismos geopolíticos, similitudes en PBI per Cápita (Argentina-Brasil) o PEA (Argentina-Canadá), entre otras muchas otras variables. Argentina no cuenta con un...

Functional promoter upstream p53 regulatory sequence of IGFBP3 that is silenced by tumor specific methylation

International Nuclear Information System (INIS)

Hanafusa, Tadashi; Shinji, Toshiyuki; Shiraha, Hidenori; Nouso, Kazuhiro; Iwasaki, Yoshiaki; Yumoto, Eichiro; Ono, Toshiro; Koide, Norio

2005-01-01

Insulin-like growth factor binding protein (IGFBP)-3 functions as a carrier of insulin-like growth factors (IGFs) in circulation and a mediator of the growth suppression signal in cells. There are two reported p53 regulatory regions in the IGFBP3 gene; one upstream of the promoter and one intronic. We previously reported a hot spot of promoter hypermethylation of IGFBP-3 in human hepatocellular carcinomas and derivative cell lines. As the hot spot locates at the putative upstream p53 consensus sequences, these p53 consensus sequences are really functional is a question to be answered. In this study, we examined the p53 consensus sequences upstream of the IGFBP-3 promoter for the p53 induced expression of IGFBP-3. Deletion, mutagenesis, and methylation constructs of IGFBP-3 promoter were assessed in the human hepatoblastoma cell line HepG2 for promoter activity. Deletions and mutations of these sequences completely abolished the expression of IGFBP-3 in the presence of p53 overexpression. In vitro methylation of these p53 consensus sequences also suppressed IGFBP-3 expression. In contrast, the expression of IGFBP-3 was not affected in the absence of p53 overexpression. Further, we observed by electrophoresis mobility shift assay that p53 binding to the promoter region was diminished when methylated. From these observations, we conclude that four out of eleven p53 consensus sequences upstream of the IGFBP-3 promoter are essential for the p53 induced expression of IGFBP-3, and hypermethylation of these sequences selectively suppresses p53 induced IGFBP-3 expression in HepG2 cells

White matter tracts associated with set-shifting in healthy aging.

Science.gov (United States)

Perry, Michele E; McDonald, Carrie R; Hagler, Donald J; Gharapetian, Lusineh; Kuperman, Joshua M; Koyama, Alain K; Dale, Anders M; McEvoy, Linda K

2009-11-01

Attentional set-shifting ability, commonly assessed with the Trail Making Test (TMT), decreases with increasing age in adults. Since set-shifting performance relies on activity in widespread brain regions, deterioration of the white matter tracts that connect these regions may underlie the age-related decrease in performance. We used an automated fiber tracking method to investigate the relationship between white matter integrity in several cortical association tracts and TMT performance in a sample of 24 healthy adults, 21-80 years. Diffusion tensor images were used to compute average fractional anisotropy (FA) for five cortical association tracts, the corpus callosum (CC), and the corticospinal tract (CST), which served as a control. Results showed that advancing age was associated with declines in set-shifting performance and with decreased FA in the CC and in association tracts that connect frontal cortex to more posterior brain regions, including the inferior fronto-occipital fasciculus (IFOF), uncinate fasciculus (UF), and superior longitudinal fasciculus (SLF). Declines in average FA in these tracts, and in average FA of the right inferior longitudinal fasciculus (ILF), were associated with increased time to completion on the set-shifting subtask of the TMT but not with the simple sequencing subtask. FA values in these tracts were strong mediators of the effect of age on set-shifting performance. Automated tractography methods can enhance our understanding of the fiber systems involved in performance of specific cognitive tasks and of the functional consequences of age-related changes in those systems.

Study of the red lacquer from a pair of Namban stirrups by Py-GC/MS

Directory of Open Access Journals (Sweden)

José Carlos Frade

2009-01-01

Full Text Available Oriental lacquer is a material of vegetal origin that is used in the Asian countries as a coating for the most varied kinds of religious and civil use objects. With the Portuguese arrival to the East, the Europeans started to develop a taste for the exotic and exquisite Art of Lacquer. From the 16th century onwards a lacquerware market developed with numerous lacquered objects being brought to Europe. In this work, the red lacquer from a pair of Namban stirrups was studied by Py-GC/MS (pyrolysis-gas chromatography/mass spectrometry. The results were compared with lacquer references, and the lacquer type was identified. Based on the results, the stirrups' lacquering technique and the performance of Py-CG/MS in the identification of oriental lacquers are also discussed.

Characterization of the internationalization process of the Ecuadorian PyME

Directory of Open Access Journals (Sweden)

Wilson Araque Jaramillo

2016-02-01

Full Text Available In this study that is made with a descriptive focus, we can find some instruments that help us understand the potential the internationalization of business has; which are also known as PyME –small and medium sized companies-. This work will contribute to generate key guidelines for the process of management decisions, the design of national and local public politics with questions that will motivate the developing of new research, focusing on commercial internationalization of national production.

Using Py-GC/MS to fingerprint additives associated with paper mill effluent toxicity episodes

CSIR Research Space (South Africa)

Sithole, Bruce

2012-10-01

Full Text Available techniques applicable to mill effluents such as gas chromatography. Py-GC/MS is a powerful analytical technique that can be used to fingerprint these additives. The presence of the additives is confirmed by fingerprint pyrograms of the additives (or...

Integrated consensus genetic and physical maps of flax (Linum usitatissimum L.).

Science.gov (United States)

Cloutier, Sylvie; Ragupathy, Raja; Miranda, Evelyn; Radovanovic, Natasa; Reimer, Elsa; Walichnowski, Andrzej; Ward, Kerry; Rowland, Gordon; Duguid, Scott; Banik, Mitali

2012-12-01

Three linkage maps of flax (Linum usitatissimum L.) were constructed from populations CDC Bethune/Macbeth, E1747/Viking and SP2047/UGG5-5 containing between 385 and 469 mapped markers each. The first consensus map of flax was constructed incorporating 770 markers based on 371 shared markers including 114 that were shared by all three populations and 257 shared between any two populations. The 15 linkage group map corresponds to the haploid number of chromosomes of this species. The marker order of the consensus map was largely collinear in all three individual maps but a few local inversions and marker rearrangements spanning short intervals were observed. Segregation distortion was present in all linkage groups which contained 1-52 markers displaying non-Mendelian segregation. The total length of the consensus genetic map is 1,551 cM with a mean marker density of 2.0 cM. A total of 670 markers were anchored to 204 of the 416 fingerprinted contigs of the physical map corresponding to ~274 Mb or 74 % of the estimated flax genome size of 370 Mb. This high resolution consensus map will be a resource for comparative genomics, genome organization, evolution studies and anchoring of the whole genome shotgun sequence.

The Python ARM Radar Toolkit (Py-ART), a Library for Working with Weather Radar Data in the Python Programming Language

OpenAIRE

Helmus, Jonathan J; Collis, Scott M

2016-01-01

The Python ARM Radar Toolkit is a package for reading, visualizing, correcting and analysing data from weather radars. Development began to meet the needs of the Atmospheric Radiation Measurement Climate Research Facility and has since expanded to provide a general-purpose framework for working with data from weather radars in the Python programming language. The toolkit is built on top of libraries in the Scientific Python ecosystem including NumPy, SciPy, and matplotlib, and makes use of Cy...

Application potential of sequence stratigraphy to prospecting for sandstone-type uranium deposit in continental depositional basins

International Nuclear Information System (INIS)

Li Shengxiang; Chen Zhaobo; Chen Zuyi; Xiang Weidong; Cai Yuqi

2001-01-01

Sequence stratigraphy has been widely used in hydrocarbon exploration and development, and great achievements have been achieved. However, its application to the prospecting for sandstone-type uranium deposits is just beginning. The metallogenic characteristics of sandstone-type uranium deposits and those of oil and gas are compared, and the relationship between sandstone-type uranium metallogenesis and the system tracts of sequence stratigraphy is studied. The authors propose that highest and system tracts are the main targets for prospecting interlayer oxidation zone type sandstone uranium deposits, and the incised valleys of low stand system tracts are favourable places for phreatic oxidation zone type sandstone uranium deposits, and transgressive system tracts are generally unfavorable to the formation of in-situ leachable sandstone-type uranium deposits. Finally, the authors look ahead the application potential of sequence stratigraphy to the prospecting for sandstone-type uranium deposits in continental depositional basins

[Promoting citizen participation in healthcare through PyDEsalud.com].

Science.gov (United States)

Perestelo-Pérez, Lilisbeth; Pérez-Ramos, Jeanette; Abt-Sacks, Analía; Rivero-Santana, Amado; Serrano-Aguilar, Pedro

2013-01-01

This project supports the initiative promoted by the Spanish National Health System to provide informational materials, in printed or interactive format, to encourage public participation in decision making and healthcare. We present the newly created PyDEsalud.com, a web platform aimed at people with chronic diseases with a high socioeconomic impact, such as breast cancer, depression, and diabetes. This platform uses scientific methodology and contains three information service modules (Patients' experiences, Shared decision making, and Research needs), aimed at promoting health education for patients and families. Copyright © 2012 SESPAS. Published by Elsevier Espana. All rights reserved.

4-(2-Tetrathiafulvalenyl-ethenyl)pyridine (TTF-CH=CH-Py) radical cation salts containing poly(beta-diketonate) rare earth complexes: synthesis, crystal structure, photoluminescent and magnetic properties.

Science.gov (United States)

Pointillart, Fabrice; Maury, Olivier; Le Gal, Yann; Golhen, Stéphane; Cador, Olivier; Ouahab, Lahcène

2009-08-03

The reactions between the redox-active 4-(2-tetrathiafulvalenyl-ethenyl)pyridine ligand (TTF-CH=CH-Py) and the tris(1,1,1,5,5,5-hexafluoroacetylacetonate)Ln(III) (Ln = La and Nd) lead to the formation of compounds with the formulas {[La(hfac)(5)][(TTF-CH=CH-Py(*+))](2)} (1), {[Nd(hfac)(4)(H(2)O)][(TTF-CH=CH-Py(*+))]}(2) (2), and {[Nd(hfac)(4)(H(2)O)][(TTF-CH=CH-Py(*+))]}(2)(H(2)O)(C(6)H(14))(0.5) (3) (hfac(-) = 1,1,1,5,5,5-hexafluoroacetylacetonate anion). These compounds have been characterized by single-crystal X-ray diffraction, optical, and magnetic measurements. Compounds 1, 2, and 3 crystallize in the monoclinic C2/c, triclinic P1, and monoclinic P2(1)/c space groups, respectively. La(III) adopts a tetradecahedral geometry, while Nd(III) stands in a distorted capped square antiprism one. In 1, the inorganic network is formed by the [La(hfac)(5)](2-) dianionic complexes, while it is formed by a pseudo-dimeric dianionic unit of formula {[Nd(hfac)(4)(H(2)O)](2)}(2-) in 2 and 3. In all crystal structures, the organic network is constituted by the TTF-CH=CH-Py(*+) radical cations. The inorganic and organic networks interact through intermolecular contacts between the pyridine moieties of the TTF-CH=CH-Py(*+) radical cations and the Ln(III) ions. The luminescence properties of the Nd(III) ions (9400 cm(-1)) and fluorescence band of the TTF-CH=CH-Py(*+) radical cations (10200 cm(-1)) have been observed and studied for compound 2. Complexes 2 and 3 are paramagnetic because of Nd(III) ions. Compound 2 is a paramagnetic luminescent TTF-radical-cation-based material. Resistivity measurements have also been performed on these materials.

Rhinovirus genome variation during chronic upper and lower respiratory tract infections.

Directory of Open Access Journals (Sweden)

Caroline Tapparel

Full Text Available Routine screening of lung transplant recipients and hospital patients for respiratory virus infections allowed to identify human rhinovirus (HRV in the upper and lower respiratory tracts, including immunocompromised hosts chronically infected with the same strain over weeks or months. Phylogenetic analysis of 144 HRV-positive samples showed no apparent correlation between a given viral genotype or species and their ability to invade the lower respiratory tract or lead to protracted infection. By contrast, protracted infections were found almost exclusively in immunocompromised patients, thus suggesting that host factors rather than the virus genotype modulate disease outcome, in particular the immune response. Complete genome sequencing of five chronic cases to study rhinovirus genome adaptation showed that the calculated mutation frequency was in the range observed during acute human infections. Analysis of mutation hot spot regions between specimens collected at different times or in different body sites revealed that non-synonymous changes were mostly concentrated in the viral capsid genes VP1, VP2 and VP3, independent of the HRV type. In an immunosuppressed lung transplant recipient infected with the same HRV strain for more than two years, both classical and ultra-deep sequencing of samples collected at different time points in the upper and lower respiratory tracts showed that these virus populations were phylogenetically indistinguishable over the course of infection, except for the last month. Specific signatures were found in the last two lower respiratory tract populations, including changes in the 5'UTR polypyrimidine tract and the VP2 immunogenic site 2. These results highlight for the first time the ability of a given rhinovirus to evolve in the course of a natural infection in immunocompromised patients and complement data obtained from previous experimental inoculation studies in immunocompetent volunteers.

dispel4py: An Agile Framework for Data-Intensive eScience

OpenAIRE

Filgueira, Rosa; Krause, Amrey; Atkinson, Malcolm; Klampanos, Iraklis; Spinuso, Alessandro; Sanchez-Exposito, Susana

2015-01-01

We present dispel4py a versatile data-intensive kit presented as a standard Python library. It empowers scientists to experiment and test ideas using their familiar rapid-prototyping environment. It delivers mappings to diverse computing infrastructures, including cloud technologies, HPC architectures and specialised data-intensive machines, to move seamlessly into production with large-scale data loads. The mappings are fully automated, so that the encoded data analyses and data handling are...

Transgressive systems tract development and incised-valley fills within a quaternary estuary-shelf system: Virginia inner shelf, USA

Science.gov (United States)

Foyle, A.M.; Oertel, G.F.

1997-01-01

High-frequency Quaternary glacioeustasy resulted in the incision of six moderate- to high-relief fluvial erosion surfaces beneath the Virginia inner shelf and coastal zone along the updip edges of the Atlantic continental margin. Fluvial valleys up to 5 km wide, with up to 37 m of relief and thalweg depths of up to 72 m below modern mean sea level, cut through underlying Pleistocene and Mio-Pliocene strata in response to drops in baselevel on the order of 100 m. Fluvially incised valleys were significantly modified during subsequent marine transgressions as fluvial drainage basins evolved into estuarine embayments (ancestral generations of the Chesapeake Bay). Complex incised-valley fill successions are bounded by, or contain, up to four stacked erosional surfaces (basal fluvial erosion surface, bay ravinement, tidal ravinement, and ebb-flood channel-base diastem) in vertical succession. These surfaces, combined with the transgressive oceanic ravinement that generally caps incised-valley fills, control the lateral and vertical development of intervening seismic facies (depositional systems). Transgressive stratigraphy characterizes the Quaternary section beneath the Virginia inner shelf where six depositional sequences (Sequences I-VI) are identified. Depositional sequences consist primarily of estuarine depositional systems (subjacent to the transgressive oceanic ravinement) and shoreface-shelf depositional systems; highstand systems tract coastal systems are thinly developed. The Quaternary section can be broadly subdivided into two parts. The upper part contains sequences consisting predominantly of inner shelf facies, whereas sequences in the lower part of the section consist predominantly of estuarine facies. Three styles of sequence preservation are identified. Style 1, represented by Sequences VI and V, is characterized by large estuarine systems (ancestral generations of the Chesapeake Bay) that are up to 40 m thick, have hemicylindrical wedge geometries

Gestión de conocimiento en PyME del sector servicios en la ciudad de Chihuahua

Directory of Open Access Journals (Sweden)

María del Carmen Gutiérrez-Diez

2015-01-01

Full Text Available La gestión de conocimiento es fundamental en la sobrevivencia de las PyME. Este trabajo describe los resultados, obtenidos hasta mayo del 2013, donde en particular se estudian los procesos de gestión de conocimiento, en treinta PyME del sector de servicios, ubicadas en la ciudad de Chihuahua. Se usó como marco de referencia el modelo de espiral de creación de conocimiento organizacional de Nonaka y Takeuchi., a partir del cual de evaluaron las dimensiones de Socialización, Interiorización, Exteriorización y Combinación. Se desarrolló y aplicó un instrumento, dirigido a los empleadores. Los resultados fueron analizados a través de una estadistica descriptiva, correlacional y regresión lineal. En los resultados obtenidos, se describen los valores asignados por los empleadores a estas diferentes categorías. Se obtuvo que las categorías de Socialización y Combinación muestran aportaciones más bajas, mientras que Exteriorización, Interiorización y Combinación aportan más al proceso de gestión de conocimiento. Lo anterior permite concluir una clara falta de estrategias y procesos que favorezcan la generación del conocimiento organizacional para estas PyME, en particular en las actividades de Socialización y Combinación.

Urinary tract infection during pregnancy: current concepts on a common multifaceted problem.

Science.gov (United States)

Kalinderi, Kallirhoe; Delkos, Dimitrios; Kalinderis, Michail; Athanasiadis, Apostolos; Kalogiannidis, Ioannis

2018-02-06

Urinary tract infections (UTIs) are the most common bacterial infection in pregnancy, increasing the risk of maternal and neonatal morbidity and mortality. Urinary tract infections may present as asymptomatic bacteriuria, acute cystitis or pyelonephritis. Escherichia coli is the most common pathogen associated with both symptomatic and asymptomatic bacteriuria. If asymptomatic bacteriuria is untreated, up to 30% of mothers develop acute pyelonephritis, with an increased risk of multiple maternal and neonatal complications, such as preeclampsia, preterm birth, intrauterine growth restriction and low birth weight. Urinary tract infection is a common, but preventable cause of pregnancy complications, thus urinary tests, such as urine culture or new technologies such as high-throughput DNA sequence-based analyses, should be used in order to improve antenatal screening of pregnant women.

Monitoring of the upper urinary tract in patients with bladder cancer

Directory of Open Access Journals (Sweden)

Rajinikanth Ayyathurai

2011-01-01

Full Text Available Upper urinary tract (UUT transitional cell carcinoma (TCC is relatively rare tumor. Approximately 0.7-4% of patients with primary bladder cancer develops UUT-TCC. The symptoms related to an UUT-TCC often occur with an advanced stage which leads one to emphasize a surveillance strategy to monitor the UUT to allow for an earlier diagnosis. Although the risk of UUT-TCC after bladder cancer is well established, there is a paucity of recommendations suggesting the optimal method and frequency of monitoring the UUT and there is no consensus among them. This article reviews the recommendations on monitoring the UUT in patients with bladder cancer.

Calcium antagonist binding sites in the rat brain: Quantitative autoradiographic mapping using the 1, 4-dihydropyridines (TH)PN 200-110 and (TH)PY 108-068

Energy Technology Data Exchange (ETDEWEB)

Cortes, R.; Supavilai, P.; Karobath, M.; Palacios, J.M.

1984-01-01

An in vitro autoradiographic technique has been used for the quantitative mapping of calcium antagonist binding sites (CABS) in the rat brain, using the 1, 4-dihydropyridines (TH)PN 200-110 and (TH)PY 108-068 as ligands. CABS were distributed throughout the brain in a highly heterogeneous fashion. The highest densities of CABS were observed in the olfactory bulb, hippocampus and parts of the amygdala. The neocortex was also rich in CABS. The basal ganglia, thalamus and hypothalamus presented intermediate levels of CABS while low densities of sites were seen in areas such as the cerebellum, pons and white matter tracts. The distributions of CABS in brain does not correlate with indexes of brain blood flow, regional glucose utilization or the distributions of receptor binding sites for drugs and neurotransmitters analyzed until now. No correlation exists between CABS distribution and that of any neurotransmitter or brain enzyme described so far. The heterogeneous distributions of CABS is suggestive of a neuronal localization, an idea supported by lesion experiments. (Author).

Bias of purine stretches in sequenced chromosomes

DEFF Research Database (Denmark)

Ussery, David; Soumpasis, Dikeos Mario; Brunak, Søren

2002-01-01

/pur tracts was slightly less than expected, with an average of 0.8%. One of the most surprising findings is a clear difference in the length distributions of the regions studied between prokaryotes and eukaryotes. Whereas short-range correlations can explain the length distributions in prokaryotes......, in eukaryotes there is an abundance of long stretches of purines or alternating purine/pyrimidine tracts, which cannot be explained in this way; these sequences are likely to play an important role in eukaryotic chromosome organisation....

Cloning and Comparative Studies of Seaweed Trehalose-6-Phosphate Synthase Genes

Directory of Open Access Journals (Sweden)

Bin Wang

2010-07-01

Full Text Available The full-length cDNA sequence (3219 base pairs of the trehalose-6-phosphate synthase gene of Porphyra yezoensis (PyTPS was isolated byRACE-PCR and deposited in GenBank (NCBI with the accession number AY729671. PyTPS encodes a protein of 908 amino acids before a stop codon, and has a calculated molecular mass of 101,591 Daltons. The PyTPS protein consists of a TPS domain in the N-terminus and a putative TPP domain at the C-terminus. Homology alignment for PyTPS and the TPS proteins from bacteria, yeast and higher plants indicated that the most closely related sequences to PyTPS were those from higher plants (OsTPS and AtTPS5, whereas the most distant sequence to PyTPS was from bacteria (EcOtsAB. Based on the identified sequence of the PyTPS gene, PCR primers were designed and used to amplify the TPS genes from nine other seaweed species. Sequences of the nine obtained TPS genes were deposited in GenBank (NCBI. All 10 TPS genes encoded peptides of 908 amino acids and the sequences were highly conserved both in nucleotide composition (>94% and in amino acid composition (>96%. Unlike the TPS genes from some other plants, there was no intron in any of the 10 isolated seaweed TPS genes.

Sequence analysis of the G gene of hRSVA ON1 genotype from Egyptian children with acute respiratory tract infections.

Science.gov (United States)

Abdel-Moneim, Ahmed S; Soliman, May S; Kamel, Mahmoud M; El-Kholy, Amani A

2018-03-01

Human respiratory syncytial virus causes severe lower respiratory tract infection in neonates and children. Genotype ON1, with duplication of 72-nt in the G gene, was first detected in Canada and then recorded in other countries. In the current study, we describe the first detection of the ON1 genotype among children in Egypt in 2014/2015. Sequence analysis of the full-attachment G gene revealed that the majority of the strains examined were related to the ON1 genotype and only one sample related to N1 genotype. The Egyptian ON1 strains showed unique non-silent mutations in addition to variable mutations near the antigenic sites in comparison to the original ON1 ancestor strain. Continuous surveillance of hRSV regionally and globally is needed to understand the evolutionary mechanisms and strategies adopted by hRSV and their inducers for better adaption to the host.

The Automation of Stochastization Algorithm with Use of SymPy Computer Algebra Library

Science.gov (United States)

Demidova, Anastasya; Gevorkyan, Migran; Kulyabov, Dmitry; Korolkova, Anna; Sevastianov, Leonid

2018-02-01

SymPy computer algebra library is used for automatic generation of ordinary and stochastic systems of differential equations from the schemes of kinetic interaction. Schemes of this type are used not only in chemical kinetics but also in biological, ecological and technical models. This paper describes the automatic generation algorithm with an emphasis on application details.

Achieving consensus in environmental programs

International Nuclear Information System (INIS)

Kurstedt, H.A.; Jones, R.M.; Walker, J.A.; Middleman, L.I.

1989-01-01

In this paper, the authors describe a research effort on consensus tied to the Environmental Restoration Program (ERP) within the U.S. Department of Energy's Office of Defense Waste and Transportation Management (DWTM). They define consensus and explain why consensus decisions are not merely desirable but necessary in furthering ERP activities. As examples of their planned applied research, the authors first discuss nominal group technique as a representative consensus-generating tool, and conclude by describing the consensus-related mission of the Waste Management Review Group, established to conduct independent, third-party review of DWTM/ERP plans and activities

Achieving consensus in environmental programs

Energy Technology Data Exchange (ETDEWEB)

Kurstedt, Jr., H. A.; Jones, R. M.; Walker, J. A.; Middleman, L. I.

1989-01-01

In this paper, we describe a new research effort on consensus tied to the Environmental Restoration Program (ERP) within the US Department of Energy's Office of Defense Waste and Transportation Management (DWTM). We define consensus and explain why consensus decisions are not merely desirable but necessary in furthering ERP activities. As examples of our planned applied research, we first discuss Nominal Group Technique as a representative consensus-generating tool, and we conclude by describing the consensus-related mission of the Waste Management Review Group, established at Virginia Tech to conduct independent, third-party review of DWTM/ERP plans and activities. 10 refs.

PySpline: A Modern, Cross-Platform Program for the Processing of Raw Averaged XAS Edge and EXAFS Data

International Nuclear Information System (INIS)

Tenderholt, Adam; Hedman, Britt; Hodgson, Keith O.

2007-01-01

PySpline is a modern computer program for processing raw averaged XAS and EXAFS data using an intuitive approach which allows the user to see the immediate effect of various processing parameters on the resulting k- and R-space data. The Python scripting language and Qt and Qwt widget libraries were chosen to meet the design requirement that it be cross-platform (i.e. versions for Windows, Mac OS X, and Linux). PySpline supports polynomial pre- and post-edge background subtraction, splining of the EXAFS region with a multi-segment polynomial spline, and Fast Fourier Transform (FFT) of the resulting k3-weighted EXAFS data

Purification and characterization of acetone carboxylase from Xanthobacter strain Py2

OpenAIRE

Sluis, Miriam K.; Ensign, Scott A.

1997-01-01

Acetone metabolism in the aerobic bacterium Xanthobacter strain Py2 proceeds by a carboxylation reaction forming acetoacetate as the first detectable product. In this study, acetone carboxylase, the enzyme catalyzing this reaction, has been purified to homogeneity and characterized. Acetone carboxylase was comprised of three polypeptides with molecular weights of 85,300, 78,300, and 19,600 arranged in an α2β2γ2 quaternary structure. The carboxylation of acetone was coupled to the hydrolysis o...

NxRepair: error correction in de novo sequence assembly using Nextera mate pairs

Directory of Open Access Journals (Sweden)

Rebecca R. Murphy

2015-06-01

Full Text Available Scaffolding errors and incorrect repeat disambiguation during de novo assembly can result in large scale misassemblies in draft genomes. Nextera mate pair sequencing data provide additional information to resolve assembly ambiguities during scaffolding. Here, we introduce NxRepair, an open source toolkit for error correction in de novo assemblies that uses Nextera mate pair libraries to identify and correct large-scale errors. We show that NxRepair can identify and correct large scaffolding errors, without use of a reference sequence, resulting in quantitative improvements in the assembly quality. NxRepair can be downloaded from GitHub or PyPI, the Python Package Index; a tutorial and user documentation are also available.

prepare_taxa_charts.py: A Python program to automate generation of publication ready taxonomic pie chart images from QIIME.

Science.gov (United States)

Lakhujani, Vijay; Badapanda, Chandan

2017-06-01

QIIME (Quantitative Insights Into Microbial Ecology) is one of the most popular open-source bioinformatics suite for performing metagenome, 16S rRNA amplicon and Internal Transcribed Spacer (ITS) data analysis. Although, it is very comprehensive and powerful tool, it lacks a method to provide publication ready taxonomic pie charts. The script plot_taxa_summary . py bundled with QIIME generate a html file and a folder containing taxonomic pie chart and legend as separate images. The images have randomly generated alphanumeric names. Therefore, it is difficult to associate the pie chart with the legend and the corresponding sample identifier. Even if the option to have the legend within the html file is selected while executing plot_taxa_summary . py , it is very tedious to crop a complete image (having both the pie chart and the legend) due to unequal image sizes. It requires a lot of time to manually prepare the pie charts for multiple samples for publication purpose. Moreover, there are chances of error while identifying the pie chart and legend pair due to random alphanumeric names of the images. To bypass all these bottlenecks and make this process efficient, we have developed a python based program, prepare_taxa_charts . py , to automate the renaming, cropping and merging of taxonomic pie chart and corresponding legend image into a single, good quality publication ready image. This program not only augments the functionality of plot_taxa_summary . py but is also very fast in terms of CPU time and user friendly.

Full trans-activation mediated by the immediate-early protein of equine herpesvirus 1 requires a consensus TATA box, but not its cognate binding sequence.

Science.gov (United States)

Kim, Seong K; Shakya, Akhalesh K; O'Callaghan, Dennis J

2016-01-04

The immediate-early protein (IEP) of equine herpesvirus 1 (EHV-1) has extensive homology to the IEP of alphaherpesviruses and possesses domains essential for trans-activation, including an acidic trans-activation domain (TAD) and binding domains for DNA, TFIIB, and TBP. Our data showed that the IEP directly interacted with transcription factor TFIIA, which is known to stabilize the binding of TBP and TFIID to the TATA box of core promoters. When the TATA box of the EICP0 promoter was mutated to a nonfunctional TATA box, IEP-mediated trans-activation was reduced from 22-fold to 7-fold. The IEP trans-activated the viral promoters in a TATA motif-dependent manner. Our previous data showed that the IEP is able to repress its own promoter when the IEP-binding sequence (IEBS) is located within 26-bp from the TATA box. When the IEBS was located at 100 bp upstream of the TATA box, IEP-mediated trans-activation was very similar to that of the minimal IE(nt -89 to +73) promoter lacking the IEBS. As the distance from the IEBS to the TATA box decreased, IEP-mediated trans-activation progressively decreased, indicating that the IEBS located within 100 bp from the TATA box sequence functions as a distance-dependent repressive element. These results indicated that IEP-mediated full trans-activation requires a consensus TATA box of core promoters, but not its binding to the cognate sequence (IEBS). Copyright © 2015 Elsevier B.V. All rights reserved.

Full trans–activation mediated by the immediate–early protein of equine herpesvirus 1 requires a consensus TATA box, but not its cognate binding sequence

Science.gov (United States)

Kim, Seong K.; Shakya, Akhalesh K.; O'Callaghan, Dennis J.

2015-01-01

The immediate-early protein (IEP) of equine herpesvirus 1 (EHV-1) has extensive homology to the IEP of alphaherpesviruses and possesses domains essential for trans-activation, including an acidic trans-activation domain (TAD) and binding domains for DNA, TFIIB, and TBP. Our data showed that the IEP directly interacted with transcription factor TFIIA, which is known to stabilize the binding of TBP and TFIID to the TATA box of core promoters. When the TATA box of the EICP0 promoter was mutated to a nonfunctional TATA box, IEP-mediated trans-activation was reduced from 22-fold to 7-fold. The IEP trans-activated the viral promoters in a TATA motif-dependent manner. Our previous data showed that the IEP is able to repress its own promoter when the IEP-binding sequence (IEBS) is located within 26-bp from the TATA box. When the IEBS was located at 100 bp upstream of the TATA box, IEP-mediated trans-activation was very similar to that of the minimal IE(nt −89 to +73) promoter lacking the IEBS. As the distance from the IEBS to the TATA box decreased, IEP-mediated trans-activation progressively decreased, indicating that the IEBS located within 100 bp from the TATA box sequence functions as a distance-dependent repressive element. These results indicated that IEP-mediated full trans-activation requires a consensus TATA box of core promoters, but not its binding to the cognate sequence (IEBS). PMID:26541315

Stabilizing IkappaBalpha by "consensus" design.

Science.gov (United States)

Ferreiro, Diego U; Cervantes, Carla F; Truhlar, Stephanie M E; Cho, Samuel S; Wolynes, Peter G; Komives, Elizabeth A

2007-01-26

IkappaBalpha is the major regulator of transcription factor NF-kappaB function. The ankyrin repeat region of IkappaBalpha mediates specific interactions with NF-kappaB dimers, but ankyrin repeats 1, 5 and 6 display a highly dynamic character when not in complex with NF-kappaB. Using chemical denaturation, we show here that IkappaBalpha displays two folding transitions: a non-cooperative conversion under weak perturbation, and a major cooperative folding phase upon stronger insult. Taking advantage of a native Trp residue in ankyrin repeat (AR) 6 and engineered Trp residues in AR2, AR4 and AR5, we show that the cooperative transition involves AR2 and AR3, while the non-cooperative transition involves AR5 and AR6. The major structural transition can be affected by single amino acid substitutions converging to the "consensus" ankyrin repeat sequence, increasing the native state stability significantly. We further characterized the structural and dynamic properties of the native state ensemble of IkappaBalpha and the stabilized mutants by H/(2)H exchange mass spectrometry and NMR. The solution experiments were complemented with molecular dynamics simulations to elucidate the microscopic origins of the stabilizing effect of the consensus substitutions, which can be traced to the fast conformational dynamics of the folded ensemble.

Advantages of genome sequencing by long-read sequencer using SMRT technology in medical area.

Science.gov (United States)

Nakano, Kazuma; Shiroma, Akino; Shimoji, Makiko; Tamotsu, Hinako; Ashimine, Noriko; Ohki, Shun; Shinzato, Misuzu; Minami, Maiko; Nakanishi, Tetsuhiro; Teruya, Kuniko; Satou, Kazuhito; Hirano, Takashi

2017-07-01

PacBio RS II is the first commercialized third-generation DNA sequencer able to sequence a single molecule DNA in real-time without amplification. PacBio RS II's sequencing technology is novel and unique, enabling the direct observation of DNA synthesis by DNA polymerase. PacBio RS II confers four major advantages compared to other sequencing technologies: long read lengths, high consensus accuracy, a low degree of bias, and simultaneous capability of epigenetic characterization. These advantages surmount the obstacle of sequencing genomic regions such as high/low G+C, tandem repeat, and interspersed repeat regions. Moreover, PacBio RS II is ideal for whole genome sequencing, targeted sequencing, complex population analysis, RNA sequencing, and epigenetics characterization. With PacBio RS II, we have sequenced and analyzed the genomes of many species, from viruses to humans. Herein, we summarize and review some of our key genome sequencing projects, including full-length viral sequencing, complete bacterial genome and almost-complete plant genome assemblies, and long amplicon sequencing of a disease-associated gene region. We believe that PacBio RS II is not only an effective tool for use in the basic biological sciences but also in the medical/clinical setting.

Elucidation of the sequence selective binding mode of the DNA minor groove binder adozelesin, by high-field 1H NMR and restrained molecular dynamics

International Nuclear Information System (INIS)

Cameron, L.

1999-01-01

indole and benzofuran sub-units and the carbonyl of a central thymine base plus a second, weaker, hydrogen-bond to the exocyclic NH 2 of the guanine. Secondly, covalent modification of an adenine by adozelesin yields a distortional wave which terminates 6 base-pairs upstream in the 5'-direction. 1 H NMR data and the resulting molecular model show that adozelesin lies closer to the modified strand as a consequence of this strong hydrogen-bond and perhaps also of the distorted guanine pushing adozelesin to the opposite side of the groove. No distortion of this kind was noted in the 'A' tract model; however, the 1 H NMR data shows that the adenine bases remain propeller twisted, which is characteristic of macroscopically bent DNA. This molecular model showed that, within this most preferred sequence, adozelesin lay centrally within this straighter 'A' tract, yielding an improved complementary fit of the drug within the DNA minor groove. No hydrogen-bonds were detected. This study indicates the possible role of the ureylene linker in the selective binding of adozelesin to the unpredicted GC-containing consensus sequence. Various other minor groove binders (cyanomorpholinoadriamycin, DSB-120 and sibiromycin) also had their sequence-selectivity properties probed with limited success, owing to their inability to yield a single drug-DNA adduct for high-field NMR study. The adozelesin-DNA self-complementary adduct in this study has provided a new and exciting starting point for rational drug design of an adozelesin dimer, a proposed antineoplastic agent with enhanced sequence-selectivity. These adozelesin-DNA adducts have proved to be an excellent model system to investigate the molecular basis for DNA recognition and binding. (author)

Type 1 fimbrial expression enhances Escherichia coli virulence for the urinary tract

DEFF Research Database (Denmark)

Connell, Hugh; Agace, William; Klemm, Per

1996-01-01

of Escherichia coli for the urinary tract by promoting bacterial persistence and enhancing the inflammatory responce to infection. In a clinical study, we observed that disease severity was greater in children infected with E. coli O1:K1:H7 isolates expressing type 1 fimbriae than in those infected with type 1...... negative isolates of the same serotype. The E. coli O1:K1:H7 isolates had the same electrophoretic type, were hemolysin-negative, expressed P fimbriae, and carried the fim DNA sequences. When tested in a mouse urinary tract infection model, the type 1-positive E. coli O1:K1:H7 isolates survived inhigher...... urinary tract infection model. E. coli CN1016 reconstituted with type 1 fimbriae had restored virulence similar to that of the wild-type parent strain. These results show that type 1 fimbriae in the genetic background of a uropathogenic strain contribute to the pathogenesis of E. coli in the urinary tract....

Risk communication strategies : achieving a multidisciplinary consensus; La communication des risques : un consensus multidisciplinaire

Energy Technology Data Exchange (ETDEWEB)

Robert, B.; Cloutier, I. [Ecole Polytechnique, Montreal, PQ (Canada). Dept. de Mathematiques et de Genie Industriel; Sabourin, J.P. [Ville de Quebec, Quebec, PQ (Canada)

2006-07-01

Risk management related to floods and dam failures requires input from a variety of stakeholders from both the private and the public sector. This paper provided details of a risk management communication strategy based on a consequence approach that established work sequence modes to achieve a multidisciplinary consensus of opinion. The communication of risk was considered as a bilateral exchange of information between concerned parties, who were divided into 2 spheres: (1) a public sphere which included interest groups, government agencies, individuals and the media; and (2) a technical sphere comprised of industry members, scientific experts, and government agencies. Divided between the 2 spheres, government agencies play a distinct role in both the communication and understanding of risk. In Quebec, municipal agencies are required to identify risk and develop plans that ensure public safety. Risk management plans developed by industry members are a valuable source of information for municipal authorities, who can identify vulnerabilities in their own risk communication strategies. In addition, members of the public play an important role in eliciting further risk communications to improve areas of vulnerability. Interest groups can demand further analyses from impartial sources on sensitive issues. Conflicting results offer a plurality of opinions that must be considered to obtain a consensus in risk assessment, which is the ultimate aim of all risk analyses and communications strategies. It was concluded that risk communication strategies benefit from the engagement of a variety of often conflicting views. 8 refs., 3 figs.

Financiamiento de PyMEs en el mercado de Capitales - Viabilidad de la obtención de fondos para Empresas PyMEs del sector del retail

OpenAIRE

Berardo, Carlos Fernando

2014-01-01

En el presente trabajo se analizará la viabilidad que existe para que una empresa PyME acceda a financiarse en el Mercado de Capitales con el fin de reemplazar su actual estructura de financiamiento.- El mismo cuenta con un Marco Teórico donde se expondrán los principales modelos utilizados, entre los cuales puedo enumerar: La Teoría Clásica de las Series de Tiempo, utilizada para estimar la tendencia futura de las ventas; el Modelo de Regresión Lineal Simple, aplicado para conocer ...

Model-based consensus

NARCIS (Netherlands)

Boumans, M.; Martini, C.; Boumans, M.

2014-01-01

The aim of the rational-consensus method is to produce "rational consensus", that is, "mathematical aggregation", by weighing the performance of each expert on the basis of his or her knowledge and ability to judge relevant uncertainties. The measurement of the performance of the experts is based on

Diagnostic imaging of the kidney and the urinary tract in infancy

International Nuclear Information System (INIS)

Troeger, J.; Darge, K.; Rohrschneider, W.

1999-01-01

Imaging flow charts differ in pediatric and general radiology. The reasons are: Different illnesses, different consequences arising out of imaging results and different sequence of imaging methods. Ultrasound is always the first imaging method of the urinary tract in infancy and childhood starts with ultrasound with the exception of severe abdominal trauma which is investigated by computertomography. The decision 'normal or abnormal' is possible using ultrasound in the most pediatric cases. The diagnostic value and significance of ultrasound in infancy and childhood is far better than in general radiology because of the higher resolution of the high-frequency units taken. The result of the ultrasound examination should be the basis for the following imaging procedures. We will describe diagnostic flow charts starting with three important clinical symptoms: Prenatal pathology, urinary tract obstruction and urinary tract infection. (orig.) [de

Improving consensus contact prediction via server correlation reduction.

Science.gov (United States)

Gao, Xin; Bu, Dongbo; Xu, Jinbo; Li, Ming

2009-05-06

Protein inter-residue contacts play a crucial role in the determination and prediction of protein structures. Previous studies on contact prediction indicate that although template-based consensus methods outperform sequence-based methods on targets with typical templates, such consensus methods perform poorly on new fold targets. However, we find out that even for new fold targets, the models generated by threading programs can contain many true contacts. The challenge is how to identify them. In this paper, we develop an integer linear programming model for consensus contact prediction. In contrast to the simple majority voting method assuming that all the individual servers are equally important and independent, the newly developed method evaluates their correlation by using maximum likelihood estimation and extracts independent latent servers from them by using principal component analysis. An integer linear programming method is then applied to assign a weight to each latent server to maximize the difference between true contacts and false ones. The proposed method is tested on the CASP7 data set. If the top L/5 predicted contacts are evaluated where L is the protein size, the average accuracy is 73%, which is much higher than that of any previously reported study. Moreover, if only the 15 new fold CASP7 targets are considered, our method achieves an average accuracy of 37%, which is much better than that of the majority voting method, SVM-LOMETS, SVM-SEQ, and SAM-T06. These methods demonstrate an average accuracy of 13.0%, 10.8%, 25.8% and 21.2%, respectively. Reducing server correlation and optimally combining independent latent servers show a significant improvement over the traditional consensus methods. This approach can hopefully provide a powerful tool for protein structure refinement and prediction use.

Improving consensus contact prediction via server correlation reduction

Directory of Open Access Journals (Sweden)

Xu Jinbo

2009-05-01

Full Text Available Abstract Background Protein inter-residue contacts play a crucial role in the determination and prediction of protein structures. Previous studies on contact prediction indicate that although template-based consensus methods outperform sequence-based methods on targets with typical templates, such consensus methods perform poorly on new fold targets. However, we find out that even for new fold targets, the models generated by threading programs can contain many true contacts. The challenge is how to identify them. Results In this paper, we develop an integer linear programming model for consensus contact prediction. In contrast to the simple majority voting method assuming that all the individual servers are equally important and independent, the newly developed method evaluates their correlation by using maximum likelihood estimation and extracts independent latent servers from them by using principal component analysis. An integer linear programming method is then applied to assign a weight to each latent server to maximize the difference between true contacts and false ones. The proposed method is tested on the CASP7 data set. If the top L/5 predicted contacts are evaluated where L is the protein size, the average accuracy is 73%, which is much higher than that of any previously reported study. Moreover, if only the 15 new fold CASP7 targets are considered, our method achieves an average accuracy of 37%, which is much better than that of the majority voting method, SVM-LOMETS, SVM-SEQ, and SAM-T06. These methods demonstrate an average accuracy of 13.0%, 10.8%, 25.8% and 21.2%, respectively. Conclusion Reducing server correlation and optimally combining independent latent servers show a significant improvement over the traditional consensus methods. This approach can hopefully provide a powerful tool for protein structure refinement and prediction use.

Sampled-data consensus in switching networks of integrators based on edge events

Science.gov (United States)

Xiao, Feng; Meng, Xiangyu; Chen, Tongwen

2015-02-01

This paper investigates the event-driven sampled-data consensus in switching networks of multiple integrators and studies both the bidirectional interaction and leader-following passive reaction topologies in a unified framework. In these topologies, each information link is modelled by an edge of the information graph and assigned a sequence of edge events, which activate the mutual data sampling and controller updates of the two linked agents. Two kinds of edge-event-detecting rules are proposed for the general asynchronous data-sampling case and the synchronous periodic event-detecting case. They are implemented in a distributed fashion, and their effectiveness in reducing communication costs and solving consensus problems under a jointly connected topology condition is shown by both theoretical analysis and simulation examples.

Urinary Tract Infection (UTI)

Science.gov (United States)

... Home A-Z Health Topics Urinary tract infections Urinary tract infections > A-Z Health Topics Urinary tract infections (PDF, ... Embed Subscribe To receive Publications email updates Submit Urinary tract infections Urinary tract infections (UTIs) are most often caused ...

Enrichment and identification of cellulolytic bacteria from the gastrointestinal tract of Giant African snail, Achatina fulica.

Science.gov (United States)

Pawar, Kiran D; Dar, Mudasir A; Rajput, Bharati P; Kulkarni, Girish J

2015-02-01

The cellulolytic bacterial community structure in gastrointestinal (GI) tract of Achatina fulica was studied using culture-independent and -dependent methods by enrichment in carboxymethyl cellulose (CMC). Culture-dependent method indicated that GI tract of snail was dominated by Enterobacteriaceae members. When tested for cellulase activities, all isolates obtained by culture-dependent method showed both or either of CMCase or avicelase activity. Isolate identified as Citrobacter freundii showed highest CMCase and medium avicelase activity. Sequencing of clones from the 16S rRNA gene clone library identified ten operational taxonomic units (OTUs), which were affiliated to Enterobacteriaceae of phylum Gammaproteobacteria. Of these ten OTUs, eight OTUs closely matched with Enterobacter and Klebsiella genera. The most abundant OTU allied to Klebsiella oxytoca accounted for 70 % of the total sequences. The members of Klebsiella and Enterobacter were observed by both methods indicating their dominance among the cellulolytic bacterial community in the GI tract of the snail.

pyPaSWAS

NARCIS (Netherlands)

Warris, Sven; Timal, N.R.N.; Kempenaar, Marcel; Poortinga, Arne M.; Geest, van de Henri; Varbanescu, Ana L.; Nap, Jan Peter

2018-01-01

Background Our previously published CUDA-only application PaSWAS for Smith-Waterman (SW) sequence alignment of any type of sequence on NVIDIA-based GPUs is platform-specific and therefore adopted less than could be. The OpenCL language is supported more widely and allows use on a variety of hardware

Nonhybrid, finished microbial genome assemblies from long-read SMRT sequencing data.

Science.gov (United States)

Chin, Chen-Shan; Alexander, David H; Marks, Patrick; Klammer, Aaron A; Drake, James; Heiner, Cheryl; Clum, Alicia; Copeland, Alex; Huddleston, John; Eichler, Evan E; Turner, Stephen W; Korlach, Jonas

2013-06-01

We present a hierarchical genome-assembly process (HGAP) for high-quality de novo microbial genome assemblies using only a single, long-insert shotgun DNA library in conjunction with Single Molecule, Real-Time (SMRT) DNA sequencing. Our method uses the longest reads as seeds to recruit all other reads for construction of highly accurate preassembled reads through a directed acyclic graph-based consensus procedure, which we follow with assembly using off-the-shelf long-read assemblers. In contrast to hybrid approaches, HGAP does not require highly accurate raw reads for error correction. We demonstrate efficient genome assembly for several microorganisms using as few as three SMRT Cell zero-mode waveguide arrays of sequencing and for BACs using just one SMRT Cell. Long repeat regions can be successfully resolved with this workflow. We also describe a consensus algorithm that incorporates SMRT sequencing primary quality values to produce de novo genome sequence exceeding 99.999% accuracy.

Bacterial diversity in different regions of gastrointestinal tract of Giant African snail (Achatina fulica).

Science.gov (United States)

Pawar, Kiran D; Banskar, Sunil; Rane, Shailendra D; Charan, Shakti S; Kulkarni, Girish J; Sawant, Shailesh S; Ghate, Hemant V; Patole, Milind S; Shouche, Yogesh S

2012-12-01

The gastrointestinal (GI) tract of invasive land snail Achatina fulica is known to harbor metabolically active bacterial communities. In this study, we assessed the bacterial diversity in the different regions of GI tract of Giant African snail, A. fulica by culture-independent and culture-dependent methods. Five 16S rRNA gene libraries from different regions of GI tract of active snails indicated that sequences affiliated to phylum γ-Proteobacteria dominated the esophagus, crop, intestine, and rectum libraries, whereas sequences affiliated to Tenericutes dominated the stomach library. On phylogenetic analysis, 30, 27, 9, 27, and 25 operational taxonomic units (OTUs) from esophagus, crop, stomach, intestine, and rectum libraries were identified, respectively. Estimations of the total bacterial diversity covered along with environmental cluster analysis showed highest bacterial diversity in the esophagus and lowest in the stomach. Thirty-three distinct bacterial isolates were obtained, which belonged to 12 genera of two major bacterial phyla namely γ-Proteobacteria and Firmicutes. Among these, Lactococcus lactis and Kurthia gibsonii were the dominant bacteria present in all GI tract regions. Quantitative real-time polymerase chain reaction (qPCR) analysis indicated significant differences in bacterial load in different GI tract regions of active and estivating snails. The difference in the bacterial load between the intestines of active and estivating snail was maximum. Principal component analysis (PCA) of terminal restriction fragment length polymorphism suggested that bacterial community structure changes only in intestine when snail enters estivation state. © 2012 The Authors. Published by Blackwell Publishing Ltd.

Signs and symptoms of developmental abnormalities of the genitourinary tract

Directory of Open Access Journals (Sweden)

Paulo Cesar Koch Nogueira

2016-06-01

Full Text Available Abstract Objective: The abnormalities of the genitourinary tract development are the leading cause of chronic kidney disease (CKD in children. The diagnosis of this disease in Brazil is late and incomplete, which results in increased morbidity and mortality in this age group. Early diagnosis of this condition is the prerogative of generalist pediatricians, and the aim of this study was to review the clinical signs and symptoms associated with developmental abnormalities of the genitourinary tract. Data sources: Based on the description of a symbolic clinical case, the authors conducted a non-systematic review of medical literature. Data synthesis: The results suggest that the following data should be used as a warning for early diagnosis of affected children: (a combined urinary tract abnormalities (chromosomal abnormalities; sequence of malformations [VACTERLand Prune-Belly]; and musculoskeletal, digestive tract, heart, and nervous system malformations; (b previous history (congenital anomalies of the kidney and urinary tract [CAKUT] in the family, low birth weight, and oligoamnios; (c clinical signs (polyuria/nocturia, urinary tract infection, systemic arterial hypertension, failure to thrive, weak urinary stream, difficulty to start urination, distended bladder, non-monosymptomatic enuresis, urinary/urge incontinence, and bowel and bladder dysfunction; and (d pre- and postnatal ultrasonographic alterations (increased anteroposterior diameter of the renal pelvis, mainly in the third trimester of pregnancy; single kidney; hydronephrosis associated with other abnormalities; and hydronephrosis with parenchymal involvement in the post-neonatal assessment. Conclusion: The suggestions shown here can help the pediatrician to establish clinical hypotheses for the early diagnosis of developmental abnormalities of the genitourinary tract without resorting to expensive and invasive procedures.

NIR and Py-mbms coupled with multivariate data analysis as a high-throughput biomass characterization technique : a review

Directory of Open Access Journals (Sweden)

Li eXiao

2014-08-01

Full Text Available Optimizing the use of lignocellulosic biomass as the feedstock for renewable energy production is currently being developed globally. Biomass is a complex mixture of cellulose, hemicelluloses, lignins, extractives, and proteins; as well as inorganic salts. Cell wall compositional analysis for biomass characterization is laborious and time consuming. In order to characterize biomass fast and efficiently, several high through-put technologies have been successfully developed. Among them, near infrared spectroscopy (NIR and pyrolysis-molecular beam mass spectrometry (Py-mbms are complementary tools and capable of evaluating a large number of raw or modified biomass in a short period of time. NIR shows vibrations associated with specific chemical structures whereas Py-mbms depicts the full range of fragments from the decomposition of biomass. Both NIR vibrations and Py-mbms peaks are assigned to possible chemical functional groups and molecular structures. They provide complementary information of chemical insight of biomaterials. However, it is challenging to interpret the informative results because of the large amount of overlapping bands or decomposition fragments contained in the spectra. In order to improve the efficiency of data analysis, multivariate analysis tools have been adapted to define the significant correlations among data variables, so that the large number of bands/peaks could be replaced by a small number of reconstructed variables representing original variation. Reconstructed data variables are used for sample comparison (principal component analysis and for building regression models (partial least square regression between biomass chemical structures and properties of interests. In this review, the important biomass chemical structures measured by NIR and Py-mbms are summarized. The advantages and disadvantages of conventional data analysis methods and multivariate data analysis methods are introduced, compared and evaluated

Genome Sequence Databases (Overview): Sequencing and Assembly

Energy Technology Data Exchange (ETDEWEB)

Lapidus, Alla L.

2009-01-01

From the date its role in heredity was discovered, DNA has been generating interest among scientists from different fields of knowledge: physicists have studied the three dimensional structure of the DNA molecule, biologists tried to decode the secrets of life hidden within these long molecules, and technologists invent and improve methods of DNA analysis. The analysis of the nucleotide sequence of DNA occupies a special place among the methods developed. Thanks to the variety of sequencing technologies available, the process of decoding the sequence of genomic DNA (or whole genome sequencing) has become robust and inexpensive. Meanwhile the assembly of whole genome sequences remains a challenging task. In addition to the need to assemble millions of DNA fragments of different length (from 35 bp (Solexa) to 800 bp (Sanger)), great interest in analysis of microbial communities (metagenomes) of different complexities raises new problems and pushes some new requirements for sequence assembly tools to the forefront. The genome assembly process can be divided into two steps: draft assembly and assembly improvement (finishing). Despite the fact that automatically performed assembly (or draft assembly) is capable of covering up to 98% of the genome, in most cases, it still contains incorrectly assembled reads. The error rate of the consensus sequence produced at this stage is about 1/2000 bp. A finished genome represents the genome assembly of much higher accuracy (with no gaps or incorrectly assembled areas) and quality ({approx}1 error/10,000 bp), validated through a number of computer and laboratory experiments.

Adherence to MRI protocol consensus guidelines in multiple sclerosis: an Australian multi-centre study

International Nuclear Information System (INIS)

Curley, Michael; Josey, Lawrence; Lucas, Robyn; Dear, Keith; Taylor, Bruce V.; Coulthard, Alan; Ausimmune Investigator Group

2012-01-01

Multiple sclerosis (MS) is a debilitating disease that causes significant morbidity within a young demographic. Diagnostic guidelines for MS have evolved, and imaging has played an increasingly important role in diagnosis over the last two decades. For imaging to contribute to diagnosis in a meaningful way, it must be reproducible. Consensus guidelines for MRI in MS exist to define correct sequence type and imaging technique, but it is not clear to what extent they are followed. This study reviewed MRI studies performed on Australian individuals presenting with a first clinical diagnosis of central nervous system demyelination (FCD) for adherence to published guidelines and discussed practical implementation of MS guidelines in light of recent updates. The Ausimmune study was a prospective case control study of Australian participants presenting with FCD from 2003 to 2006. Baseline cranial and spinal cord MRI studies of 226 case participants from four separate Australian regions were reviewed. MRI sequences were classified according to anatomical location, slice plane, tissue weighting and use of gadolinium-containing contrast media. Results were compared with the 2003 Consortium of Multiple Sclerosis Centres MRI protocol for the diagnosis of MS. The composition of core cranial MRI sequences performed varied across the 226 scans. Of the studies, 91% included sagittal fluid attenuated inversion recovery (FLAIR) sequences. Cranial axial T2-weighted, axial FLAIR and axial proton density-weighted sequences were performed in 88%, 60% and 16% (respectively) of scans. Only 25% of the studies included a T1-weighted contrast-enhanced sequence. Concordance with the guidelines in all sequences was very low (2). Only a small number of MRI investigations performed included all of the sequences stipulated by consensus guidelines. This is likely due to poor awareness in the imaging community of the guidelines and the rationale behind certain sequences. Radiologists with a sub

CONSIDERACIONES PRÁCTICAS PARA LA GESTIÓN DEL CAPITAL DE TRABAJO EN LAS PyMES INNOVADORAS

Directory of Open Access Journals (Sweden)

Hugo Alfonso Vargas Arévalo

2003-07-01

Full Text Available Las PyMES se presentan en la actualidad como las principales empresas generadoras de empleo en Colombia. Son además un segmento empresarial de gran importancia por su contribución al PIB. Sin embargo, muchas de ellas adolecen de la gestión necesaria para convertirlas en unidades innovadoras, autosostenibles y en crecimiento. Hay, por ejemplo, una gran dificultad para obtener financiación, para vender, para generar estrategias de asociación, para gestionar recursos humanos. Este artículo se propone unificar algunos conceptos concernientes a la administración de capital de trabajo de las PyMES. Se hace énfasis en la rentabilidad y se aporta un conjunto de recursos estratégicos que puede contribuir a mejorar la gestión de este tipo de empresas en el contexto colombiano.

Metabolism of the synthetic cannabinoid 5F-PY-PICA by human and rat hepatocytes and identification of biliary analytical targets by directional efflux in sandwich-cultured rat hepatocytes using UHPLC-HR-MS/MS

DEFF Research Database (Denmark)

Mardal, Marie; Annaert, Pieter; Noble, Carolina

2018-01-01

Analytical strategies for detecting drugs in biological samples rely on information on metabolism and elimination. 5F-PY-PICA belongs to the group of synthetic cannabinoids that are known to undergo excretion into the bile. The aims of this study were the in vitro identification of metabolites of 5......F-PY-PICA and to determine which analytical targets are excreted into the bile and urine. Metabolites identified after incubation of 5F-PY-PICA with pooled human liver microsomes (pHLM), pooled human hepatocytes (pHH), or suspended and sandwich-cultured rat hepatocytes (SCRH). Rat hepatocytes were......-PY-PICA, M4, and M22 are proposed as analytical targets for bile analysis in forensic screening protocols, whereas M6 should be one of the main urinary targets for 5F-PY-PICA analysis....

Diffusion tensor imaging in children with tuberous sclerosis complex: tract-based spatial statistics assessment of brain microstructural changes.

Science.gov (United States)

Zikou, Anastasia K; Xydis, Vasileios G; Astrakas, Loukas G; Nakou, Iliada; Tzarouchi, Loukia C; Tzoufi, Meropi; Argyropoulou, Maria I

2016-07-01

There is evidence of microstructural changes in normal-appearing white matter of patients with tuberous sclerosis complex. To evaluate major white matter tracts in children with tuberous sclerosis complex using tract-based spatial statistics diffusion tensor imaging (DTI) analysis. Eight children (mean age ± standard deviation: 8.5 ± 5.5 years) with an established diagnosis of tuberous sclerosis complex and 8 age-matched controls were studied. The imaging protocol consisted of T1-weighted high-resolution 3-D spoiled gradient-echo sequence and a spin-echo, echo-planar diffusion-weighted sequence. Differences in the diffusion indices were evaluated using tract-based spatial statistics. Tract-based spatial statistics showed increased axial diffusivity in the children with tuberous sclerosis complex in the superior and anterior corona radiata, the superior longitudinal fascicle, the inferior fronto-occipital fascicle, the uncinate fascicle and the anterior thalamic radiation. No significant differences were observed in fractional anisotropy, mean diffusivity and radial diffusivity between patients and control subjects. No difference was found in the diffusion indices between the baseline and follow-up examination in the patient group. Patients with tuberous sclerosis complex have increased axial diffusivity in major white matter tracts, probably related to reduced axonal integrity.

Diffusion tensor imaging in children with tuberous sclerosis complex: tract-based spatial statistics assessment of brain microstructural changes

International Nuclear Information System (INIS)

Zikou, Anastasia K.; Xydis, Vasileios G.; Tzarouchi, Loukia C.; Argyropoulou, Maria I.; Astrakas, Loukas G.; Nakou, Iliada; Tzoufi, Meropi

2016-01-01

There is evidence of microstructural changes in normal-appearing white matter of patients with tuberous sclerosis complex. To evaluate major white matter tracts in children with tuberous sclerosis complex using tract-based spatial statistics diffusion tensor imaging (DTI) analysis. Eight children (mean age ± standard deviation: 8.5 ± 5.5 years) with an established diagnosis of tuberous sclerosis complex and 8 age-matched controls were studied. The imaging protocol consisted of T1-weighted high-resolution 3-D spoiled gradient-echo sequence and a spin-echo, echo-planar diffusion-weighted sequence. Differences in the diffusion indices were evaluated using tract-based spatial statistics. Tract-based spatial statistics showed increased axial diffusivity in the children with tuberous sclerosis complex in the superior and anterior corona radiata, the superior longitudinal fascicle, the inferior fronto-occipital fascicle, the uncinate fascicle and the anterior thalamic radiation. No significant differences were observed in fractional anisotropy, mean diffusivity and radial diffusivity between patients and control subjects. No difference was found in the diffusion indices between the baseline and follow-up examination in the patient group. Patients with tuberous sclerosis complex have increased axial diffusivity in major white matter tracts, probably related to reduced axonal integrity. (orig.)

Children's UTIs in the new millennium. Diagnosis, investigation, and treatment of childhood urinary tract infections in the year 2001.

Science.gov (United States)

White, C. T.; Matsell, D. G.

2001-01-01

OBJECTIVE: To provide an effective approach for family physicians treating children presenting with urinary tract infections (UTIs). QUALITY OF EVIDENCE: The information presented, and articles quoted, are drawn from both review of the literature and recent consensus guidelines. Data and recommendations come from prospective multicentre trials; retrospective reviews; expert consensus statements; and some smaller trials, commentaries, and editorials. MAIN MESSAGE: Urinary tract infections are often seen in family practice. Diagnosis requires suspicion and a realization that children, especially those younger than 2 years, often have very few, nonspecific signs of infection. Obtaining a proper urine sample is vital, because true infections require radiographic studies. Antibiotic prophylaxis is promoted because of the link between vesicoureteral reflux, recurrent UTIs, and renal scarring and hypertension. We generally provide prophylaxis until children are 3 or 4 years, when risk of damage from reflux is lessened and timely urine samples are easier to obtain for prompt therapy. Surgical opinion is sought only when medical management has failed. Failure is defined as either recurrent infections and pyelonephritis or poor renal growth. CONCLUSION: To diagnose UTIs in children, physicians must suspect them, obtain proper urine samples, order appropriate investigations to rule out underlying anatomic abnormalities, and treat with appropriate antibiotics considering both organism sensitivities and length of therapy. PMID:11561337

Dynamic Average Consensus and Consensusability of General Linear Multiagent Systems with Random Packet Dropout

Directory of Open Access Journals (Sweden)

Wen-Min Zhou

2013-01-01

Full Text Available This paper is concerned with the consensus problem of general linear discrete-time multiagent systems (MASs with random packet dropout that happens during information exchange between agents. The packet dropout phenomenon is characterized as being a Bernoulli random process. A distributed consensus protocol with weighted graph is proposed to address the packet dropout phenomenon. Through introducing a new disagreement vector, a new framework is established to solve the consensus problem. Based on the control theory, the perturbation argument, and the matrix theory, the necessary and sufficient condition for MASs to reach mean-square consensus is derived in terms of stability of an array of low-dimensional matrices. Moreover, mean-square consensusable conditions with regard to network topology and agent dynamic structure are also provided. Finally, the effectiveness of the theoretical results is demonstrated through an illustrative example.

Direct chloroplast sequencing: comparison of sequencing platforms and analysis tools for whole chloroplast barcoding.

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Marta Brozynska

Full Text Available Direct sequencing of total plant DNA using next generation sequencing technologies generates a whole chloroplast genome sequence that has the potential to provide a barcode for use in plant and food identification. Advances in DNA sequencing platforms may make this an attractive approach for routine plant identification. The HiSeq (Illumina and Ion Torrent (Life Technology sequencing platforms were used to sequence total DNA from rice to identify polymorphisms in the whole chloroplast genome sequence of a wild rice plant relative to cultivated rice (cv. Nipponbare. Consensus chloroplast sequences were produced by mapping sequence reads to the reference rice chloroplast genome or by de novo assembly and mapping of the resulting contigs to the reference sequence. A total of 122 polymorphisms (SNPs and indels between the wild and cultivated rice chloroplasts were predicted by these different sequencing and analysis methods. Of these, a total of 102 polymorphisms including 90 SNPs were predicted by both platforms. Indels were more variable with different sequencing methods, with almost all discrepancies found in homopolymers. The Ion Torrent platform gave no apparent false SNP but was less reliable for indels. The methods should be suitable for routine barcoding using appropriate combinations of sequencing platform and data analysis.

PyMes: las grandes organizaciones del mañana, ¿ISO la solucion del hoy?

Directory of Open Access Journals (Sweden)

Placeres, A.

2006-07-01

Full Text Available In this article, we demonstrate the relevance for the companies in terms of maintaining a high competitive ability with their peers, and taking into account the requirement of their clients, trying to procure better tools based upon their financial capabilities, with particular emphasis on PyMes (small and medium-sized companies. This arises from the fact that in order to grow for a company; it should take into account the commitment and variation in this regard, in their clients. In this article the growth options of PyMes based upon the search for standardization, certification and the implementation of their processes with the aid of standard norms such as ISO 9000 are highlighted. This process should be on the basis of the level of the commitment of all their employees, as in the absence of such commitments, such processes will be viewed as unnecessary costs which will not help the growth of the company.

pyLIMA: An Open-source Package for Microlensing Modeling. I. Presentation of the Software and Analysis of Single-lens Models

Science.gov (United States)

Bachelet, E.; Norbury, M.; Bozza, V.; Street, R.

2017-11-01

Microlensing is a unique tool, capable of detecting the “cold” planets between ˜1 and 10 au from their host stars and even unbound “free-floating” planets. This regime has been poorly sampled to date owing to the limitations of alternative planet-finding methods, but a watershed in discoveries is anticipated in the near future thanks to the planned microlensing surveys of WFIRST-AFTA and Euclid's Extended Mission. Of the many challenges inherent in these missions, the modeling of microlensing events will be of primary importance, yet it is often time-consuming, complex, and perceived as a daunting barrier to participation in the field. The large scale of future survey data products will require thorough but efficient modeling software, but, unlike other areas of exoplanet research, microlensing currently lacks a publicly available, well-documented package to conduct this type of analysis. We present version 1.0 of the python Lightcurve Identification and Microlensing Analysis (pyLIMA). This software is written in Python and uses existing packages as much as possible to make it widely accessible. In this paper, we describe the overall architecture of the software and the core modules for modeling single-lens events. To verify the performance of this software, we use it to model both real data sets from events published in the literature and generated test data produced using pyLIMA's simulation module. The results demonstrate that pyLIMA is an efficient tool for microlensing modeling. We will expand pyLIMA to consider more complex phenomena in the following papers.

A first report and complete genome sequence of alfalfa enamovirus from Sudan

Science.gov (United States)

A full genome sequence of a viral pathogen, provisionally named alfalfa enamovirus 2 (AEV-2), was reconstructed from short reads obtained by Illumina RNA sequencing of alfalfa sample originating from Sudan. Ambiguous nucleotides in the resultant consensus assembly and identity of the predicted virus...

Human immunodeficiency viruses appear compartmentalized to the female genital tract in cross-sectional analyses but genital lineages do not persist over time.

Science.gov (United States)

Bull, Marta E; Heath, Laura M; McKernan-Mullin, Jennifer L; Kraft, Kelli M; Acevedo, Luis; Hitti, Jane E; Cohn, Susan E; Tapia, Kenneth A; Holte, Sarah E; Dragavon, Joan A; Coombs, Robert W; Mullins, James I; Frenkel, Lisa M

2013-04-15

Whether unique human immunodeficiency type 1 (HIV) genotypes occur in the genital tract is important for vaccine development and management of drug resistant viruses. Multiple cross-sectional studies suggest HIV is compartmentalized within the female genital tract. We hypothesize that bursts of HIV replication and/or proliferation of infected cells captured in cross-sectional analyses drive compartmentalization but over time genital-specific viral lineages do not form; rather viruses mix between genital tract and blood. Eight women with ongoing HIV replication were studied during a period of 1.5 to 4.5 years. Multiple viral sequences were derived by single-genome amplification of the HIV C2-V5 region of env from genital secretions and blood plasma. Maximum likelihood phylogenies were evaluated for compartmentalization using 4 statistical tests. In cross-sectional analyses compartmentalization of genital from blood viruses was detected in three of eight women by all tests; this was associated with tissue specific clades containing multiple monotypic sequences. In longitudinal analysis, the tissues-specific clades did not persist to form viral lineages. Rather, across women, HIV lineages were comprised of both genital tract and blood sequences. The observation of genital-specific HIV clades only in cross-sectional analysis and an absence of genital-specific lineages in longitudinal analyses suggest a dynamic interchange of HIV variants between the female genital tract and blood.

Investigation of a Quadruplex-Forming Repeat Sequence Highly Enriched in Xanthomonas and Nostoc sp.

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Charlotte Rehm

Full Text Available In prokaryotes simple sequence repeats (SSRs with unit sizes of 1-5 nucleotides (nt are causative for phase and antigenic variation. Although an increased abundance of heptameric repeats was noticed in bacteria, reports about SSRs of 6-9 nt are rare. In particular G-rich repeat sequences with the propensity to fold into G-quadruplex (G4 structures have received little attention. In silico analysis of prokaryotic genomes show putative G4 forming sequences to be abundant. This report focuses on a surprisingly enriched G-rich repeat of the type GGGNATC in Xanthomonas and cyanobacteria such as Nostoc. We studied in detail the genomes of Xanthomonas campestris pv. campestris ATCC 33913 (Xcc, Xanthomonas axonopodis pv. citri str. 306 (Xac, and Nostoc sp. strain PCC7120 (Ana. In all three organisms repeats are spread all over the genome with an over-representation in non-coding regions. Extensive variation of the number of repetitive units was observed with repeat numbers ranging from two up to 26 units. However a clear preference for four units was detected. The strong bias for four units coincides with the requirement of four consecutive G-tracts for G4 formation. Evidence for G4 formation of the consensus repeat sequences was found in biophysical studies utilizing CD spectroscopy. The G-rich repeats are preferably located between aligned open reading frames (ORFs and are under-represented in coding regions or between divergent ORFs. The G-rich repeats are preferentially located within a distance of 50 bp upstream of an ORF on the anti-sense strand or within 50 bp from the stop codon on the sense strand. Analysis of whole transcriptome sequence data showed that the majority of repeat sequences are transcribed. The genetic loci in the vicinity of repeat regions show increased genomic stability. In conclusion, we introduce and characterize a special class of highly abundant and wide-spread quadruplex-forming repeat sequences in bacteria.

Investigation of a Quadruplex-Forming Repeat Sequence Highly Enriched in Xanthomonas and Nostoc sp.

Science.gov (United States)

Rehm, Charlotte; Wurmthaler, Lena A; Li, Yuanhao; Frickey, Tancred; Hartig, Jörg S

2015-01-01

In prokaryotes simple sequence repeats (SSRs) with unit sizes of 1-5 nucleotides (nt) are causative for phase and antigenic variation. Although an increased abundance of heptameric repeats was noticed in bacteria, reports about SSRs of 6-9 nt are rare. In particular G-rich repeat sequences with the propensity to fold into G-quadruplex (G4) structures have received little attention. In silico analysis of prokaryotic genomes show putative G4 forming sequences to be abundant. This report focuses on a surprisingly enriched G-rich repeat of the type GGGNATC in Xanthomonas and cyanobacteria such as Nostoc. We studied in detail the genomes of Xanthomonas campestris pv. campestris ATCC 33913 (Xcc), Xanthomonas axonopodis pv. citri str. 306 (Xac), and Nostoc sp. strain PCC7120 (Ana). In all three organisms repeats are spread all over the genome with an over-representation in non-coding regions. Extensive variation of the number of repetitive units was observed with repeat numbers ranging from two up to 26 units. However a clear preference for four units was detected. The strong bias for four units coincides with the requirement of four consecutive G-tracts for G4 formation. Evidence for G4 formation of the consensus repeat sequences was found in biophysical studies utilizing CD spectroscopy. The G-rich repeats are preferably located between aligned open reading frames (ORFs) and are under-represented in coding regions or between divergent ORFs. The G-rich repeats are preferentially located within a distance of 50 bp upstream of an ORF on the anti-sense strand or within 50 bp from the stop codon on the sense strand. Analysis of whole transcriptome sequence data showed that the majority of repeat sequences are transcribed. The genetic loci in the vicinity of repeat regions show increased genomic stability. In conclusion, we introduce and characterize a special class of highly abundant and wide-spread quadruplex-forming repeat sequences in bacteria.

La contabilidad de costos en el sistema de información contable de las PyME del estado Mérida

OpenAIRE

Chacón P., Galia B.

2011-01-01

El objetivo central de esta investigación es el de analizar la aplicación de la contabilidad de costos como sistema de información que permite el control de la gestión de las PyME del estado Mérida. De la literatura se deriva que la contabilidad de costos es fundamental en la producción de la información que requieren las PyME. Para lograr el objetivo planteado se realizó un estudio empírico en una muestra de 263 empresas del Municipio Libertador del estado Mérida, donde se identifi...

Calcium antagonist binding sites in the rat brain: Quantitative autoradiographic mapping using the 1, 4-Dihydropyridines [3H]PN 200-110 and [3H]PY 108-068

International Nuclear Information System (INIS)

Cortes, R.; Supavilai, P.; Karobath, M.; Palacios, J.M.

1984-01-01

An in vitro autoradiographic technique has been used for the quantitative mapping of calcium antagonist binding sites (CABS) in the rat brain, using the 1, 4-dihydropyridines [ 3 H]PN 200-110 and [ 3 H]PY 108-068 as ligands. CABS were distributed throughout the brain in a highly heterogeneous fashion. The highest densities of CABS were observed in the olfactory bulb, hippocampus and parts of the amygdala. The neocortex was also rich in CABS. The basal ganglia, thalamus and hypothalamus presented intermediate levels of CABS while low densities of sites were seen in areas such as the cerebellum, pons and white matter tracts. The distributions of CABS in brain does not correlate with indexes of brain blood flow, regional glucose utilization or the distributions of receptor binding sites for drugs and neurotransmitters analyzed until now. No correlation exists between CABS distribution and that of any neurotransmitter or brain enzyme described so far. The heterogeneous distributions of CABS is suggestive of a neuronal localization, an idea supported by lesion experiments. (Author)

Late Pleistocene sequence architecture on the geostrophic current-dominated southwest margin of the Ulleung Basin, East Sea

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Choi, Dong-Lim; Shin, Dong-Hyeok; Kum, Byung-Cheol; Jang, Seok; Cho, Jin-Hyung; Jou, Hyeong-Tae; Jang, Nam-Do

2018-06-01

High-resolution multichannel seismic data were collected to identify depositional sequences on the southwestern shelf of the Ulleung Basin, where a unidirectional ocean current is dominant at water depths exceeding 130 m. Four aggradational stratigraphic sequences with a 100,000-year cycle were recognized since marine isotope stage (MIS) 10. These sequences consist only of lowstand systems tracts (LSTs) and falling-stage systems tracts (FSSTs). Prograding wedge-shaped deposits are present in the LSTs near the shelf break. Oblique progradational clinoforms of forced regressive deposits are present in the FSSTs on the outer continental shelf. Each FSST has non-uniform forced regressional stratal geometries, reflecting that the origins of sediments in each depositional sequence changed when sea level was falling. Slump deposits are characteristically developed in the upper layer of the FSSTs, and this was used as evidence to distinguish the sequence boundaries. The subsidence rates around the shelf break reached as much as 0.6 mm/year since MIS 10, which contributed to the well-preserved depositional sequence. During the Quaternary sea-level change, the water depth in the Korea Strait declined and the intensity of the Tsushima Current flowing near the bottom of the inner continental shelf increased. This resulted in greater erosion of sediments that were delivered to the outer continental shelf, which was the main cause of sediment deposition on the deep, low-angled outer shelf. Therefore, a depositional sequence formation model that consists of only FSSTs and LSTs, excluding highstand systems tracts (HSTs) and transgressive systems tracts (TSTs), best explains the depositional sequence beneath this shelf margin dominated by a geostrophic current.

Reconstruction of ancestral RNA sequences under multiple structural constraints.

Science.gov (United States)

Tremblay-Savard, Olivier; Reinharz, Vladimir; Waldispühl, Jérôme

2016-11-11

Secondary structures form the scaffold of multiple sequence alignment of non-coding RNA (ncRNA) families. An accurate reconstruction of ancestral ncRNAs must use this structural signal. However, the inference of ancestors of a single ncRNA family with a single consensus structure may bias the results towards sequences with high affinity to this structure, which are far from the true ancestors. In this paper, we introduce achARNement, a maximum parsimony approach that, given two alignments of homologous ncRNA families with consensus secondary structures and a phylogenetic tree, simultaneously calculates ancestral RNA sequences for these two families. We test our methodology on simulated data sets, and show that achARNement outperforms classical maximum parsimony approaches in terms of accuracy, but also reduces by several orders of magnitude the number of candidate sequences. To conclude this study, we apply our algorithms on the Glm clan and the FinP-traJ clan from the Rfam database. Our results show that our methods reconstruct small sets of high-quality candidate ancestors with better agreement to the two target structures than with classical approaches. Our program is freely available at: http://csb.cs.mcgill.ca/acharnement .

Urinary Tract Health

Science.gov (United States)

... related to the urinary tract health of women: Urinary Tract Infections (UTIs) and Urinary Incontinence (UI). For information on a range of urinary tract health issues for women, men, and children, visit the National Kidney and Urologic Diseases Information ...

Discrimination of bacteria using pyrolysis-gas chromatography-differential mobility spectrometry (Py-GC-DMS) and chemometrics.

Science.gov (United States)

Cheung, William; Xu, Yu; Thomas, C L Paul; Goodacre, Royston

2009-03-01

Discrimination of bacteria was investigated using pyrolysis-gas chromatography-differential mobility spectrometry (Py-GC-DMS). Three strains belonging to the genus Bacillus were investigated and these included two strains of Bacillus subtilis and a single Bacillus megaterium. These were chosen so as to evaluate the possibility of bacterial strain discrimination using Py-GC-DMS. The instrument was constructed in-house and the long-term reproducibility of the instrument was evaluated over a period of 60 days using a Scotch whisky quality control. To assess the reproducibility further each bacterium was cultured six times and each culture was analysed in replicate to give three analytical replicates. The DMS data were generated in both positive and negative modes, and the data in each mode were analysed independently of each other. The Py-GC-DMS data were pre-processed via correlation optimised warping (COW) and asymmetric least square (ALS) to align the DMS chromatograms and to remove any unavoidable baseline shifts, prior to normalisation. Processed chromatograms were analysed using principal component analysis (PCA) followed by supervised learning methodology using partial least squares for discriminant analysis (PLS-DA). It was found that the separations between B. subtilis and B. megaterium can be readily observed by PCA; however, strain discrimination within the two B. subtilis was only possible using supervised learning. As multiple biological replicates were analysed an exhaustive splitting of the training and test sets was undertaken and this allowed correct classification rates (CCRs) to be assessed for the 3375 test sets. It was found that with PLS-DA the negative ion mode DMS data were more discriminatory than the positive mode data.

The pyPHaz software, an interactive tool to analyze and visualize results from probabilistic hazard assessments

Science.gov (United States)

Tonini, Roberto; Selva, Jacopo; Costa, Antonio; Sandri, Laura

2014-05-01

Probabilistic Hazard Assessment (PHA) is becoming an essential tool for risk mitigation policies, since it allows to quantify the hazard due to hazardous phenomena and, differently from the deterministic approach, it accounts for both aleatory and epistemic uncertainties. On the other hand, one of the main disadvantages of PHA methods is that their results are not easy to understand and interpret by people who are not specialist in probabilistic tools. For scientists, this leads to the issue of providing tools that can be easily used and understood by decision makers (i.e., risk managers or local authorities). The work here presented fits into the problem of simplifying the transfer between scientific knowledge and land protection policies, by providing an interface between scientists, who produce PHA's results, and decision makers, who use PHA's results for risk analyses. In this framework we present pyPHaz, an open tool developed and designed to visualize and analyze PHA results due to one or more phenomena affecting a specific area of interest. The software implementation has been fully developed with the free and open-source Python programming language and some featured Python-based libraries and modules. The pyPHaz tool allows to visualize the Hazard Curves (HC) calculated in a selected target area together with different levels of uncertainty (mean and percentiles) on maps that can be interactively created and modified by the user, thanks to a dedicated Graphical User Interface (GUI). Moreover, the tool can be used to compare the results of different PHA models and to merge them, by creating ensemble models. The pyPHaz software has been designed with the features of storing and accessing all the data through a MySQL database and of being able to read as input the XML-based standard file formats defined in the frame of GEM (Global Earthquake Model). This format model is easy to extend also to any other kind of hazard, as it will be shown in the applications

PyMVPA: a unifying approach to the analysis of neuroscientific data

Directory of Open Access Journals (Sweden)

Michael Hanke

2009-02-01

Full Text Available The Python programming language is steadily increasing in popularity as the language of choice for scientific computing. The ability of this scripting environment to access a huge code base in various languages, combined with its syntactical simplicity, make it the ideal tool for implementing and sharing ideas among scientists from numerous fields and with heterogeneous methodological backgrounds. The recent rise of reciprocal interest between the machine learning and neuroscience communities is an example of the desire for an inter-disciplinary transfer of computational methods that can benefit from a Python-based framework. For many years, a large fraction of both research communities have addressed, almost independently, very high-dimensional problems with almost completely non-overlapping methods. However, a number of recently published studies that applied machine learning methods to neuroscience research questions attracted a lot of attention from researchers from both fields, as well as the general public, and showed that this approach can provide novel and fruitful insights into the functioning of the brain. In this article we show how PyMVPA, a specialized Python framework for machine-learning based data analysis, can help to facilitate this inter-disciplinary technology transfer by providing a single interface to a wide array of machine-learning libraries and neural data-processing methods. We demonstrate the general applicability and power of PyMVPA via analyses of a number of neural data modalities, including fMRI, EEG, MEG, and extracellular recordings.

A new fast method for inferring multiple consensus trees using k-medoids.

Science.gov (United States)

Tahiri, Nadia; Willems, Matthieu; Makarenkov, Vladimir

2018-04-05

Gene trees carry important information about specific evolutionary patterns which characterize the evolution of the corresponding gene families. However, a reliable species consensus tree cannot be inferred from a multiple sequence alignment of a single gene family or from the concatenation of alignments corresponding to gene families having different evolutionary histories. These evolutionary histories can be quite different due to horizontal transfer events or to ancient gene duplications which cause the emergence of paralogs within a genome. Many methods have been proposed to infer a single consensus tree from a collection of gene trees. Still, the application of these tree merging methods can lead to the loss of specific evolutionary patterns which characterize some gene families or some groups of gene families. Thus, the problem of inferring multiple consensus trees from a given set of gene trees becomes relevant. We describe a new fast method for inferring multiple consensus trees from a given set of phylogenetic trees (i.e. additive trees or X-trees) defined on the same set of species (i.e. objects or taxa). The traditional consensus approach yields a single consensus tree. We use the popular k-medoids partitioning algorithm to divide a given set of trees into several clusters of trees. We propose novel versions of the well-known Silhouette and Caliński-Harabasz cluster validity indices that are adapted for tree clustering with k-medoids. The efficiency of the new method was assessed using both synthetic and real data, such as a well-known phylogenetic dataset consisting of 47 gene trees inferred for 14 archaeal organisms. The method described here allows inference of multiple consensus trees from a given set of gene trees. It can be used to identify groups of gene trees having similar intragroup and different intergroup evolutionary histories. The main advantage of our method is that it is much faster than the existing tree clustering approaches, while

Antibiotic resistance patterns of community-acquired urinary tract infections in children with vesicoureteral reflux receiving prophylactic antibiotic therapy.

Science.gov (United States)

Cheng, Chi-Hui; Tsai, Ming-Horng; Huang, Yhu-Chering; Su, Lin-Hui; Tsau, Yong-Kwei; Lin, Chi-Jen; Chiu, Cheng-Hsun; Lin, Tzou-Yien

2008-12-01

The goal was to examine bacterial antimicrobial resistance of recurrent urinary tract infections in children receiving antibiotic prophylaxis because of primary vesicoureteral reflux. We reviewed data retrospectively for children with documented vesicoureteral reflux in 2 hospitals during a 5-year follow-up period. The patients were receiving co-trimoxazole, cephalexin, or cefaclor prophylaxis or prophylaxis with a sequence of different antibiotics (alternative monotherapy). Demographic data, degree of vesicoureteral reflux, prophylactic antibiotics prescribed, and antibiotic sensitivity results of first urinary tract infections and breakthrough urinary tract infections were recorded. Three hundred twenty-four patients underwent antibiotic prophylaxis (109 with co-trimoxazole, 100 with cephalexin, 44 with cefaclor, and 71 with alternative monotherapy) in one hospital and 96 children underwent co-trimoxazole prophylaxis in the other hospital. Breakthrough urinary tract infections occurred in patients from both hospitals (20.4% and 25%, respectively). Escherichia coli infection was significantly less common in children receiving antibiotic prophylaxis, compared with their initial episodes of urinary tract infection, at both hospitals. Children receiving cephalosporin prophylaxis were more likely to have an extended-spectrum beta-lactamase-producing organism for breakthrough urinary tract infections, compared with children with co-trimoxazole prophylaxis. Antimicrobial susceptibilities to almost all antibiotics decreased with cephalosporin prophylaxis when recurrent urinary tract infections developed. The extent of decreased susceptibilities was also severe for prophylaxis with a sequence of different antibiotics. However, antimicrobial susceptibilities decreased minimally in co-trimoxazole prophylaxis groups. Children receiving cephalosporin prophylaxis are more likely to have extended-spectrum beta-lactamase-producing bacteria or multidrug-resistant uropathogens

Distribution and sequence homogeneity of an abundant satellite DNA in the beetle, Tenebrio molitor.

Science.gov (United States)

Davis, C A; Wyatt, G R

1989-01-01

The mealworm beetle, Tenebrio molitor, contains an unusually abundant and homogeneous satellite DNA which constitutes up to 60% of its genome. The satellite DNA is shown to be present in all of the chromosomes by in situ hybridization. 18 dimers of the repeat unit were cloned and sequenced. The consensus sequence is 142 nt long and lacks any internal repeat structure. Monomers of the sequence are very similar, showing on average a 2% divergence from the calculated consensus. Variant nucleotides are scattered randomly throughout the sequence although some variants are more common than others. Neighboring repeat units are no more alike than randomly chosen ones. The results suggest that some mechanism, perhaps gene conversion, is acting to maintain the homogeneity of the satellite DNA despite its abundance and distribution on all of the chromosomes. Images PMID:2762148

Detection and typing of human papillomavirus in archival cervical cancer specimens by DNA amplification with consensus primers

NARCIS (Netherlands)

RESNICK, R. M.; Cornelissen, M. T.; WRIGHT, D. K.; EICHINGER, G. H.; FOX, H. S.; ter Schegget, J.; MANOS, M. M.

1990-01-01

We developed a polymerase chain reaction DNA amplification system using two distinct consensus oligonucleotide primer sets for the improved detection and typing of a broad spectrum of human genital papillomavirus (HPV) sequences, including those of novel viruses. The system incorporates one primer

PyGaze: an open-source, cross-platform toolbox for minimal-effort programming of eye-tracking experiments

NARCIS (Netherlands)

Dalmaijer, E.S.; Mathôt, S.; van der Stigchel, S.

2014-01-01

he PyGaze toolbox is an open-source software package for Python, a high-level programming language. It is designed for creating eyetracking experiments in Python syntax with the least possible effort, and it offers programming ease and script readability without constraining functionality and

Sequence Dependent Electrophoretic Separations of DNA in Pluronic F127 Gels

Science.gov (United States)

You, Seungyong; van Winkle, David H.

2010-03-01

Two-dimensional (2-D) electrophoresis has successfully been used to visualize the separation of DNA fragments of the same length. We electrophorese a double-stranded DNA ladder in an Agarose gel for the first dimension and in gels of Pluronic F127 for the second dimension at room temperature. The 1000 bp band that travels together as a single band in an Agarose gel is split into two bands in Pluronic gels. The slower band follows the exponential decay trend that the other ladder constituents do. After sequencing the DNA fragments, the faster band has an apparently random sequence, while the slower band and the others have two A-tracts in each 250 bp segment. The A-tracts consist of a series of at least five adenine bases pairing with thymine bases. This result leads to the conclusion that the migration of the DNA molecules bent with A-tracts is more retarded in Pluronic gels than the wild-type of DNA molecules.

Interfacial microstructure and mechanical properties of Cf/AZ91D composites with TiO2 and PyC fiber coatings.

Science.gov (United States)

Li, Shaolin; Qi, Lehua; Zhang, Ting; Ju, Luyan; Li, Hejun

2017-10-01

In spite of the effectiveness of the fiber coatings on interface modification of carbon fiber reinforced magnesium matrix composites, the cost and exclusive equipment for the coatings preparation are usually ignored during research work. In this paper, pyrolytic carbon (PyC) and TiO 2 were coated on carbon fiber surface to study the effects of fiber coatings on interfacial microstructure and mechanical properties of carbon fiber reinforced AZ91D composites (C f /AZ91D composites). It was indicated that both the two coatings could modify the interface and improve the mechanical properties of the composites. The ultimate tensile strength of the TiO 2 -C f /AZ91D and the PyC-C f /AZ91D composite were 333MPa and 400MPa, which were improved by 41.7% and 70.2% respectively, compared with the untreated-C f /AZ91D composite. The microstructure observation revealed that the strengthening of the composites relied on fiber integrity and moderate interfacial bonding. MgO nano-particles were generated at the interface due to the reaction of TiO 2 with Mg in the TiO 2 -C f /AZ91D composite. The volume expansion resulting from the reaction let to disordered intergranular films and crystal defects at the interface. The fibers were protected and the interfacial reaction was restrained by PyC coating in the PyC-C f /AZ91D composite. The principle to select the coating of fiber was proposed by comparing the effectiveness and cost of the coatings. Copyright © 2017 Elsevier Ltd. All rights reserved.

Association of membrane/lipid rafts with the platelet cytoskeleton and the caveolin PY14: participation in the adhesion process.

Science.gov (United States)

Cerecedo, Doris; Martínez-Vieyra, Ivette; Maldonado-García, Deneb; Hernández-González, Enrique; Winder, Steve J

2015-11-01

Platelets are the most prominent elements of blood tissue involved in hemostasis at sites of blood vessel injury. Platelet cytoskeleton is responsible for their shape modifications observed during activation and adhesion to the substratum; therefore the interactions between cytoskeleton and plasma membrane are critical to modulate blood platelet functions. Several cytoskeletal components and binding partners, as well as enzymes that regulate the cytoskeleton, localize to membrane/lipid rafts (MLR) and regulate lateral diffusion of membrane proteins and lipids. Resting, thrombin-activated, and adherent human platelets were processed for biochemical studies including western-blot and immunprecipitation assays and confocal analysis were performed to characterize the interaction of MLR with the main cytoskeleton elements and β-dystroglycan as well as with the association of caveolin-1 PY14 with focal adhesion proteins. We transfected a megakaryoblast cell line (Meg-01) to deplete β-dystroglycan, subsequent to their differentiation to the platelet progenitors. Our data showed a direct interaction of the MLR with cytoskeleton to regulate platelet shape, while an association of caveolin-1 PY14 with vinculin is needed to establish focal adhesions, which are modulated for β-dystroglycan. In conclusion, caveolin-1 PY14 in association with platelet cytoskeleton participate in focal adhesions dynamics. © 2015 Wiley Periodicals, Inc.

Achieving Consensus Through Professionalized Head Nods

DEFF Research Database (Denmark)

Oshima, Sae

2014-01-01

of nodding in a particular professional-client setting, namely, hair salon interactions. My interest specifically lies in the frequent occurrence of synchronized head nods during the “service-assessment sequence,” where both service provider and customer inspect and determine whether the completed work...... is adequate. I pursue mechanisms of synchronized head nods by revealing exactly how participants collaborate in producing a nod, and how their verbal actions may at times be designed accordingly. In doing so, the study provides insight into what consensus may look like at service encounters in Japan......While the interactional functions of head nodding in everyday Japanese conversation have been frequently studied, a discourse on head nodding as a professional communicative practice has yet to be explored. With the method of multimodal conversation analysis, the current study examines the role...

Using Py-GC/MS to detect and measure silicone defoamers in pulp fibres and mill deposits

CSIR Research Space (South Africa)

Sithole, Bruce

2013-09-01

Full Text Available in deposits. In this work, for the first time, Py-GC/MS has been used to analyse for silicone defoamers in pulp and paper matrices. This work demonstrates that the technique is ideal for analysis and characterisation of silicone defoamers on pulp fibres...

Implicit Consensus: Blockchain with Unbounded Throughput

OpenAIRE

Ren, Zhijie; Cong, Kelong; Pouwelse, Johan; Erkin, Zekeriya

2017-01-01

Recently, the blockchain technique was put in the spotlight as it introduced a systematic approach for multiple parties to reach consensus without needing trust. However, the application of this technique in practice is severely restricted due to its limitations in throughput. In this paper, we propose a novel consensus model, namely the implicit consensus, with a distinctive blockchain-based distributed ledger in which each node holds its individual blockchain. In our system, the consensus i...

Human Immunodeficiency Viruses Appear Compartmentalized to the Female Genital Tract in Cross-Sectional Analyses but Genital Lineages Do Not Persist Over Time

Science.gov (United States)

Bull, Marta E.; Heath, Laura M.; McKernan-Mullin, Jennifer L.; Kraft, Kelli M.; Acevedo, Luis; Hitti, Jane E.; Cohn, Susan E.; Tapia, Kenneth A.; Holte, Sarah E.; Dragavon, Joan A.; Coombs, Robert W.; Mullins, James I.; Frenkel, Lisa M.

2013-01-01

Background. Whether unique human immunodeficiency type 1 (HIV) genotypes occur in the genital tract is important for vaccine development and management of drug resistant viruses. Multiple cross-sectional studies suggest HIV is compartmentalized within the female genital tract. We hypothesize that bursts of HIV replication and/or proliferation of infected cells captured in cross-sectional analyses drive compartmentalization but over time genital-specific viral lineages do not form; rather viruses mix between genital tract and blood. Methods. Eight women with ongoing HIV replication were studied during a period of 1.5 to 4.5 years. Multiple viral sequences were derived by single-genome amplification of the HIV C2-V5 region of env from genital secretions and blood plasma. Maximum likelihood phylogenies were evaluated for compartmentalization using 4 statistical tests. Results. In cross-sectional analyses compartmentalization of genital from blood viruses was detected in three of eight women by all tests; this was associated with tissue specific clades containing multiple monotypic sequences. In longitudinal analysis, the tissues-specific clades did not persist to form viral lineages. Rather, across women, HIV lineages were comprised of both genital tract and blood sequences. Conclusions. The observation of genital-specific HIV clades only in cross-sectional analysis and an absence of genital-specific lineages in longitudinal analyses suggest a dynamic interchange of HIV variants between the female genital tract and blood. PMID:23315326

Establishment of Lactobacillus plantarum strain in honey bee digestive tract monitored using gfp fluorescence.

Science.gov (United States)

Javorský, P; Fecskeová, L Kolesár; Hrehová, L; Sabo, R; Legáth, J; Pristas, P

2017-04-26

Lactic acid bacteria are symbiotic bacteria that naturally reside in the gastrointestinal tract of honey bees. They serve a multitude of functions and are considered beneficial and completely harmless. In our experiments Lactobacillus plantarum strain B35, isolated from honey bee digestive tract, was modified using pAD43-25 plasmid carrying a functional GFP gene sequence (gfpmut3a) and used as a model for monitoring and optimisation of the mode of application. The establishment of this strain in honey bee digestive tract was monitored using GFP fluorescence. Three different modes of oral application of this strain were tested: water suspension of lyophilised bacteria, aerosol application of these bacteria and consumption of sugar honey paste containing the lyophilised lactobacilli. Two days after administration the L. plantarum B35-gfp was present throughout the honey bee digestive tract with 10 4 -10 5 cfu/bee with highest count observed for aerosol application.

PyMVPA: A python toolbox for multivariate pattern analysis of fMRI data.

Science.gov (United States)

Hanke, Michael; Halchenko, Yaroslav O; Sederberg, Per B; Hanson, Stephen José; Haxby, James V; Pollmann, Stefan

2009-01-01

Decoding patterns of neural activity onto cognitive states is one of the central goals of functional brain imaging. Standard univariate fMRI analysis methods, which correlate cognitive and perceptual function with the blood oxygenation-level dependent (BOLD) signal, have proven successful in identifying anatomical regions based on signal increases during cognitive and perceptual tasks. Recently, researchers have begun to explore new multivariate techniques that have proven to be more flexible, more reliable, and more sensitive than standard univariate analysis. Drawing on the field of statistical learning theory, these new classifier-based analysis techniques possess explanatory power that could provide new insights into the functional properties of the brain. However, unlike the wealth of software packages for univariate analyses, there are few packages that facilitate multivariate pattern classification analyses of fMRI data. Here we introduce a Python-based, cross-platform, and open-source software toolbox, called PyMVPA, for the application of classifier-based analysis techniques to fMRI datasets. PyMVPA makes use of Python's ability to access libraries written in a large variety of programming languages and computing environments to interface with the wealth of existing machine learning packages. We present the framework in this paper and provide illustrative examples on its usage, features, and programmability.

Criteria required for an acceptable point-of-care test for UTI detection: Obtaining consensus using the Delphi technique.

Science.gov (United States)

Weir, Nichola-Jane M; Pattison, Sally H; Kearney, Paddy; Stafford, Bob; Gormley, Gerard J; Crockard, Martin A; Gilpin, Deirdre F; Tunney, Michael M; Hughes, Carmel M

2018-01-01

Urinary Tract Infections (UTIs) are common bacterial infections, second only to respiratory tract infections and particularly prevalent within primary care. Conventional detection of UTIs is culture, however, return of results can take between 24 and 72 hours. The introduction of a point of care (POC) test would allow for more timely identification of UTIs, facilitating improved, targeted treatment. This study aimed to obtain consensus on the criteria required for a POC UTI test, to meet patient need within primary care. Criteria for consideration were compiled by the research team. These criteria were validated through a two-round Delphi process, utilising an expert panel of healthcare professionals from across Europe and United States of America. Using web-based questionnaires, panellists recorded their level of agreement with each criterion based on a 5-point Likert Scale, with space for comments. Using median response, interquartile range and comments provided, criteria were accepted/rejected/revised depending on pre-agreed cut-off scores. The first round questionnaire presented thirty-three criteria to the panel, of which 22 were accepted. Consensus was not achieved for the remaining 11 criteria. Following response review, one criterion was removed, while after revision, the remaining 10 criteria entered the second round. Of these, four were subsequently accepted, resulting in 26 criteria considered appropriate for a POC test to detect urinary infections. This study generated an approved set of criteria for a POC test to detect urinary infections. Criteria acceptance and comments provided by the healthcare professionals also supports the development of a multiplex point of care UTI test.

The Limits of Consensus.

Science.gov (United States)

Poster, John B.

Dynamics in the education policy arena suggest that, despite two generations of researchers extolling democratic leadership styles and consensus building over autocratic techniques, wide participation in policymaking and the broadest possible consensus are not always productive: American society has not yet agreed on what schools should…

First brazilian consensus of advanced prostate cancer: recommendations for clinical practice

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Andre Deeke Sasse

Full Text Available ABSTRACT Introduction Prostate cancer still represents a major cause of morbidity, and still about 20% of men with the disease are diagnosed or will progress to the advanced stage without the possibility of curative treatment. Despite the recent advances in scientific and technological knowledge and the availability of new therapies, there is still considerable heterogeneity in the therapeutic approaches for metastatic prostate cancer. Objectives This article presents a summary of the I Brazilian Consensus on Advanced Prostate Cancer, conducted by the Brazilian Society of Urology and Brazilian Society of Clinical Oncology. Materials and Methods Experts were selected by the medical societies involved. Forty issues regarding controversial issues in advanced disease were previously elaborated. The panel met for consensus, with a threshold established for 2/3 of the participants. Results and Conclusions The treatment of advanced prostate cancer is complex, due to the existence of a large number of therapies, with different response profiles and toxicities. The panel addressed recommendations on preferred choice of therapies, indicators that would justify their change, and indicated some strategies for better sequencing of treatment in order to maximize the potential for disease control with the available therapeutic arsenal. The lack of consensus on some topics clearly indicates the absence of strong evidence for some decisions.

PyFLOWGO: An open-source platform for simulation of channelized lava thermo-rheological properties

Science.gov (United States)

Chevrel, Magdalena Oryaëlle; Labroquère, Jérémie; Harris, Andrew J. L.; Rowland, Scott K.

2018-02-01

Lava flow advance can be modeled through tracking the evolution of the thermo-rheological properties of a control volume of lava as it cools and crystallizes. An example of such a model was conceived by Harris and Rowland (2001) who developed a 1-D model, FLOWGO, in which the velocity of a control volume flowing down a channel depends on rheological properties computed following the thermal path estimated via a heat balance box model. We provide here an updated version of FLOWGO written in Python that is an open-source, modern and flexible language. Our software, named PyFLOWGO, allows selection of heat fluxes and rheological models of the user's choice to simulate the thermo-rheological evolution of the lava control volume. We describe its architecture which offers more flexibility while reducing the risk of making error when changing models in comparison to the previous FLOWGO version. Three cases are tested using actual data from channel-fed lava flow systems and results are discussed in terms of model validation and convergence. PyFLOWGO is open-source and packaged in a Python library to be imported and reused in any Python program (https://github.com/pyflowgo/pyflowgo)

ChromaStarPy: A Stellar Atmosphere and Spectrum Modeling and Visualization Lab in Python

Science.gov (United States)

Short, C. Ian; Bayer, Jason H. T.; Burns, Lindsey M.

2018-02-01

We announce ChromaStarPy, an integrated general stellar atmospheric modeling and spectrum synthesis code written entirely in python V. 3. ChromaStarPy is a direct port of the ChromaStarServer (CSServ) Java modeling code described in earlier papers in this series, and many of the associated JavaScript (JS) post-processing procedures have been ported and incorporated into CSPy so that students have access to ready-made data products. A python integrated development environment (IDE) allows a student in a more advanced course to experiment with the code and to graphically visualize intermediate and final results, ad hoc, as they are running it. CSPy allows students and researchers to compare modeled to observed spectra in the same IDE in which they are processing observational data, while having complete control over the stellar parameters affecting the synthetic spectra. We also take the opportunity to describe improvements that have been made to the related codes, ChromaStar (CS), CSServ, and ChromaStarDB (CSDB), that, where relevant, have also been incorporated into CSPy. The application may be found at the home page of the OpenStars project: http://www.ap.smu.ca/OpenStars/.

Magnetic resonance imaging for the clinical management of rectal cancer patients: recommendations from the 2012 European Society of Gastrointestinal and Abdominal Radiology (ESGAR) consensus meeting

Energy Technology Data Exchange (ETDEWEB)

Beets-Tan, Regina G.H. [Maastricht University Medical Centre+, Maastricht (Netherlands); Maastricht University Medical Centre+, Department of Radiology, P.O. Box 5800, AZ, Maastricht (Netherlands); Lambregts, Doenja M.J.; Maas, Monique [Maastricht University Medical Centre+, Maastricht (Netherlands); Bipat, Shandra; Stoker, Jaap [Academic Medical Centre, Amsterdam (Netherlands); Barbaro, Brunella [Catholic University School of Medicine, Rome (Italy); Caseiro-Alves, Filipe; Curvo-Semedo, Luis [Coimbra University Hospitals, Coimbra (Portugal); Fenlon, Helen M. [Mater Misericordiae University Hospital, Dublin (Ireland); Gollub, Marc J. [Memorial Sloan-Kettering Cancer Center, New York (United States); Gourtsoyianni, Sofia [University Hospital of Heraklion, Crete (Greece); Guy' s and St. Thomas' NHS FT, London (United Kingdom); Halligan, Steve; Taylor, Stuart A. [University College London, Centre for Medical Imaging, London (United Kingdom); Hoeffel, Christine [Reims University Hospital, Reims (France); Kim, Seung Ho [Inje University Haeundae Paik Hospital, Busan (Korea, Republic of); Laghi, Andrea [Sapienza - University of Rome, Rome (Italy); Maier, Andrea [Medical University of Vienna, Vienna (Austria); Rafaelsen, Soeren R. [Vejle Hospital, Vejle (Denmark); Torkzad, Michael R. [Uppsala University, Uppsala (Sweden); Blomqvist, Lennart [Karolinska University Hospital and Karolinska Institutet, Stockholm (Sweden)

2013-09-15

To develop guidelines describing a standardised approach regarding the acquisition, interpretation and reporting of magnetic resonance imaging (MRI) for clinical staging and restaging of rectal cancer. A consensus meeting of 14 abdominal imaging experts from the European Society of Gastrointestinal and Abdominal Radiology (ESGAR) was conducted following the RAND-UCLA Appropriateness Method. Two independent (non-voting) chairs facilitated the meeting. Two hundred and thirty-six items were scored by participants for appropriateness and classified subsequently as appropriate or inappropriate (defined by {>=} 80 % consensus) or uncertain (defined by < 80 % consensus). Items not reaching 80 % consensus were noted. Consensus was reached for 88 % of items: recommendations regarding hardware, patient preparation, imaging sequences, angulation, criteria for MRI assessment and MRI reporting were constructed from these. These expert consensus recommendations can be used as clinical guidelines for primary staging and restaging of rectal cancer using MRI. (orig.)

Fast Pyrolysis of Four Lignins from Different Isolation Processes Using Py-GC/MS

OpenAIRE

Lin, Xiaona; Sui, Shujuan; Tan, Shun; Pittman, Charles; Sun, Jianping; Zhang, Zhijun

2015-01-01

Pyrolysis is a promising approach that is being investigated to convert lignin into higher value products including biofuels and phenolic chemicals. In this study, fast pyrolysis of four types of lignin, including milled Amur linden wood lignin (MWL), enzymatic hydrolysis corn stover lignin (EHL), wheat straw alkali lignin (AL) and wheat straw sulfonate lignin (SL), were performed using pyrolysis gas-chromatography/mass spectrometry (Py-GC/MS). Thermogravimetric analysis (TGA) showed that the...

Possibilities of consensus: toward democratic moral discourse.

Science.gov (United States)

Jennings, B

1991-08-01

The concept of consensus is often appealed to in discussions of biomedical ethics and applied ethics, and it plays an important role in many influential ethical theories. Consensus is an especially influential notion among theorists who reject ethical realism and who frame ethics as a practice of discourse rather than a body of objective knowledge. It is also a practically important notion when moral decision making is subject to bureaucratic organization and oversight, as is increasingly becoming the case in medicine. Two models of consensus are examined and criticized: pluralistic consensus and overlapping consensus. As an alternative to these models, the paper argues that consensus refers to the dialogic aspects of a broader normative conception of democratic moral agency. When the preconditions for that dialogic democratic practice are met, consensus has a justificatory role in ethics; when they are not, consensus, as distinct from mere agreement, does not emerge and can have no moral authority.

The Python Spectral Analysis Tool (PySAT): A Powerful, Flexible, Preprocessing and Machine Learning Library and Interface

Science.gov (United States)

Anderson, R. B.; Finch, N.; Clegg, S. M.; Graff, T. G.; Morris, R. V.; Laura, J.; Gaddis, L. R.

2017-12-01

Machine learning is a powerful but underutilized approach that can enable planetary scientists to derive meaningful results from the rapidly-growing quantity of available spectral data. For example, regression methods such as Partial Least Squares (PLS) and Least Absolute Shrinkage and Selection Operator (LASSO), can be used to determine chemical concentrations from ChemCam and SuperCam Laser-Induced Breakdown Spectroscopy (LIBS) data [1]. Many scientists are interested in testing different spectral data processing and machine learning methods, but few have the time or expertise to write their own software to do so. We are therefore developing a free open-source library of software called the Python Spectral Analysis Tool (PySAT) along with a flexible, user-friendly graphical interface to enable scientists to process and analyze point spectral data without requiring significant programming or machine-learning expertise. A related but separately-funded effort is working to develop a graphical interface for orbital data [2]. The PySAT point-spectra tool includes common preprocessing steps (e.g. interpolation, normalization, masking, continuum removal, dimensionality reduction), plotting capabilities, and capabilities to prepare data for machine learning such as creating stratified folds for cross validation, defining training and test sets, and applying calibration transfer so that data collected on different instruments or under different conditions can be used together. The tool leverages the scikit-learn library [3] to enable users to train and compare the results from a variety of multivariate regression methods. It also includes the ability to combine multiple "sub-models" into an overall model, a method that has been shown to improve results and is currently used for ChemCam data [4]. Although development of the PySAT point-spectra tool has focused primarily on the analysis of LIBS spectra, the relevant steps and methods are applicable to any spectral data. The

Development of a decision aid for the treatment of benign prostatic hyperplasia: A four stage method using a Delphi consensus study.

Science.gov (United States)

Lamers, Romy E D; Cuypers, Maarten; Garvelink, Mirjam M; de Vries, Marieke; Bosch, J L H Ruud; Kil, Paul J M

2016-07-01

To develop a web-based decision aid (DA) for the treatment of lower urinary tract symptoms due to benign prostatic hyperplasia (LUTS/BPH). From February-September 2014 we performed a four-stage development method: 1: Two-round Delphi consensus method among urologists, 2: Identifying patients' needs and expectations, 3: Development of DA content and structure, 4: Usability testing with LUTS/BPH patients. 1 (N=15): Dutch urologists reached consensus on 61% of the statements concerning users' criteria, decision options, structure, and medical content. 2 (N=24): Consensus was reached in 69% on statements concerning the need for improvement of information provision, the need for DA development and that the DA should clarify patients' preferences. 3: DA development based on results from stage 1 and stage 2. 4 (N=10): Pros of the DA were clear information provision, systematic design and easy to read and re-read. A LUTS/BPH DA containing VCEs(**) was developed in cooperation with urologists and patients following a structured 4 stage method and was stated to be well accepted. This method can be adopted for the development of DAs to support other medical decision issues. Copyright © 2016 Elsevier Ireland Ltd. All rights reserved.

Pyélonéphrite Emphysémateuse Avec Une Issue Favorable Après ...

African Journals Online (AJOL)

28 août 2011 ... 1Service d'Urologie, 2Service de Radio Hôpital militaire Avicenne,. Marrakech, Maroc. RÉSUMÉ. Introduction: La pyélonéphrite emphysémateuse est une infection nécrotique du rein dont la sanction est le plus souvent radicale. Objectif: Notre propos est de montrer que le traitement conservateur pourrait ...

The specificity and flexibility of l1 reverse transcription priming at imperfect T-tracts.

Directory of Open Access Journals (Sweden)

Clément Monot

2013-05-01

Full Text Available L1 retrotransposons have a prominent role in reshaping mammalian genomes. To replicate, the L1 ribonucleoprotein particle (RNP first uses its endonuclease (EN to nick the genomic DNA. The newly generated DNA end is subsequently used as a primer to initiate reverse transcription within the L1 RNA poly(A tail, a process known as target-primed reverse transcription (TPRT. Prior studies demonstrated that most L1 insertions occur into sequences related to the L1 EN consensus sequence (degenerate 5'-TTTT/A-3' sites and frequently preceded by imperfect T-tracts. However, it is currently unclear whether--and to which degree--the liberated 3'-hydroxyl extremity on the genomic DNA needs to be accessible and complementary to the poly(A tail of the L1 RNA for efficient priming of reverse transcription. Here, we employed a direct assay for the initiation of L1 reverse transcription to define the molecular rules that guide this process. First, efficient priming is detected with as few as 4 matching nucleotides at the primer 3' end. Second, L1 RNP can tolerate terminal mismatches if they are compensated within the 10 last bases of the primer by an increased number of matching nucleotides. All terminal mismatches are not equally detrimental to DNA extension, a C being extended at higher levels than an A or a G. Third, efficient priming in the context of duplex DNA requires a 3' overhang. This suggests the possible existence of additional DNA processing steps, which generate a single-stranded 3' end to allow L1 reverse transcription. Based on these data we propose that the specificity of L1 reverse transcription initiation contributes, together with the specificity of the initial EN cleavage, to the distribution of new L1 insertions within the human genome.

The specificity and flexibility of l1 reverse transcription priming at imperfect T-tracts.

Science.gov (United States)

Monot, Clément; Kuciak, Monika; Viollet, Sébastien; Mir, Ashfaq Ali; Gabus, Caroline; Darlix, Jean-Luc; Cristofari, Gaël

2013-05-01

L1 retrotransposons have a prominent role in reshaping mammalian genomes. To replicate, the L1 ribonucleoprotein particle (RNP) first uses its endonuclease (EN) to nick the genomic DNA. The newly generated DNA end is subsequently used as a primer to initiate reverse transcription within the L1 RNA poly(A) tail, a process known as target-primed reverse transcription (TPRT). Prior studies demonstrated that most L1 insertions occur into sequences related to the L1 EN consensus sequence (degenerate 5'-TTTT/A-3' sites) and frequently preceded by imperfect T-tracts. However, it is currently unclear whether--and to which degree--the liberated 3'-hydroxyl extremity on the genomic DNA needs to be accessible and complementary to the poly(A) tail of the L1 RNA for efficient priming of reverse transcription. Here, we employed a direct assay for the initiation of L1 reverse transcription to define the molecular rules that guide this process. First, efficient priming is detected with as few as 4 matching nucleotides at the primer 3' end. Second, L1 RNP can tolerate terminal mismatches if they are compensated within the 10 last bases of the primer by an increased number of matching nucleotides. All terminal mismatches are not equally detrimental to DNA extension, a C being extended at higher levels than an A or a G. Third, efficient priming in the context of duplex DNA requires a 3' overhang. This suggests the possible existence of additional DNA processing steps, which generate a single-stranded 3' end to allow L1 reverse transcription. Based on these data we propose that the specificity of L1 reverse transcription initiation contributes, together with the specificity of the initial EN cleavage, to the distribution of new L1 insertions within the human genome.

Reconstruction of ancestral RNA sequences under multiple structural constraints

Directory of Open Access Journals (Sweden)

Olivier Tremblay-Savard

2016-11-01

Full Text Available Abstract Background Secondary structures form the scaffold of multiple sequence alignment of non-coding RNA (ncRNA families. An accurate reconstruction of ancestral ncRNAs must use this structural signal. However, the inference of ancestors of a single ncRNA family with a single consensus structure may bias the results towards sequences with high affinity to this structure, which are far from the true ancestors. Methods In this paper, we introduce achARNement, a maximum parsimony approach that, given two alignments of homologous ncRNA families with consensus secondary structures and a phylogenetic tree, simultaneously calculates ancestral RNA sequences for these two families. Results We test our methodology on simulated data sets, and show that achARNement outperforms classical maximum parsimony approaches in terms of accuracy, but also reduces by several orders of magnitude the number of candidate sequences. To conclude this study, we apply our algorithms on the Glm clan and the FinP-traJ clan from the Rfam database. Conclusions Our results show that our methods reconstruct small sets of high-quality candidate ancestors with better agreement to the two target structures than with classical approaches. Our program is freely available at: http://csb.cs.mcgill.ca/acharnement .

Basilea II y el crédito PyME en Colombia

Directory of Open Access Journals (Sweden)

Zulma Veloza Suárez

2009-04-01

Full Text Available El presente artículo muestra cuál es el impacto del Nuevo Acuerdo de Capitales de Basilea II, para el caso del sistema bancario en Colombia en la oferta crediticia para las pequeñasy medianas empresas. Para ello se aplicó el modelo de cálculo de la probabilidad de impago y requerimientos de capital de Basilea II. Los resultados indican que bajo las nuevas disposiciones del acuerdo la oferta de crédito total aumenta (PyME y Corporativo no obstante, el microcrédito se contrae.

Consensus coding sequence (CCDS) database: a standardized set of human and mouse protein-coding regions supported by expert curation.

Science.gov (United States)

Pujar, Shashikant; O'Leary, Nuala A; Farrell, Catherine M; Loveland, Jane E; Mudge, Jonathan M; Wallin, Craig; Girón, Carlos G; Diekhans, Mark; Barnes, If; Bennett, Ruth; Berry, Andrew E; Cox, Eric; Davidson, Claire; Goldfarb, Tamara; Gonzalez, Jose M; Hunt, Toby; Jackson, John; Joardar, Vinita; Kay, Mike P; Kodali, Vamsi K; Martin, Fergal J; McAndrews, Monica; McGarvey, Kelly M; Murphy, Michael; Rajput, Bhanu; Rangwala, Sanjida H; Riddick, Lillian D; Seal, Ruth L; Suner, Marie-Marthe; Webb, David; Zhu, Sophia; Aken, Bronwen L; Bruford, Elspeth A; Bult, Carol J; Frankish, Adam; Murphy, Terence; Pruitt, Kim D

2018-01-04

The Consensus Coding Sequence (CCDS) project provides a dataset of protein-coding regions that are identically annotated on the human and mouse reference genome assembly in genome annotations produced independently by NCBI and the Ensembl group at EMBL-EBI. This dataset is the product of an international collaboration that includes NCBI, Ensembl, HUGO Gene Nomenclature Committee, Mouse Genome Informatics and University of California, Santa Cruz. Identically annotated coding regions, which are generated using an automated pipeline and pass multiple quality assurance checks, are assigned a stable and tracked identifier (CCDS ID). Additionally, coordinated manual review by expert curators from the CCDS collaboration helps in maintaining the integrity and high quality of the dataset. The CCDS data are available through an interactive web page (https://www.ncbi.nlm.nih.gov/CCDS/CcdsBrowse.cgi) and an FTP site (ftp://ftp.ncbi.nlm.nih.gov/pub/CCDS/). In this paper, we outline the ongoing work, growth and stability of the CCDS dataset and provide updates on new collaboration members and new features added to the CCDS user interface. We also present expert curation scenarios, with specific examples highlighting the importance of an accurate reference genome assembly and the crucial role played by input from the research community. Published by Oxford University Press on behalf of Nucleic Acids Research 2017.

Anatomy of extremely thin marine sequences landward of a passive-margin hinge zone: Neogene Calvert Cliffs succession, Maryland, U.S.A.

Energy Technology Data Exchange (ETDEWEB)

Kidwell, S.M. [Univ. of Chicago, IL (United States). Dept. of Geophysical Sciences

1997-03-01

Detailed examination of Neogene strata in cliffs 25--35 m high along the western shore of Chesapeake Bay, Maryland, reveals the complexity of the surviving record of siliciclastic sequences {approximately}150 km inland of the structural hinge zone of the Atlantic passive margin. Previous study of the lower to middle Miocene Calvert (Plum Point Member) and Choptank Formations documented a series of third-order sequences 7--10 m thick in which lowstand deposits are entirely lacking, transgressive tracts comprise a mosaic of condensed bioclastic facies, and regressive (highstand) tracts are present but partially truncated by the next sequence boundary; smaller-scale (fourth-order) cyclic units could not be resolved. Together, these sequences constitute the transgressive and early highstand tracts of a larger (second-order Miocene) composite sequence. The present paper documents stratigraphic relations higher in the Calvert Cliffs succession, including the upper Miocene St. Marys Formation, which represents late highstand marine deposits of the Miocene second-order sequence, and younger Neogene fluvial and tidal-inlet deposits representing incised-valley deposits of the succeeding second-order cycle. The St. Marys Formation consists of a series of tabular units 2--5 m thick, each with an exclusively transgressive array of facies and bounded by stranding surfaces of abrupt shallowing. These units, which are opposite to the flooding-surface-bounded regressive facies arrays of model parasequences, are best characterized as shaved sequences in which only the transgressive tract survives, and are stacked into larger transgressive, highstand, and forced-regression sets.

The complete genomic sequence of pepper yellow leaf curl virus (PYLCV and its implications for our understanding of evolution dynamics in the genus polerovirus.

Directory of Open Access Journals (Sweden)

Aviv Dombrovsky

Full Text Available We determined the complete sequence and organization of the genome of a putative member of the genus Polerovirus tentatively named Pepper yellow leaf curl virus (PYLCV. PYLCV has a wider host range than Tobacco vein-distorting virus (TVDV and has a close serological relationship with Cucurbit aphid-borne yellows virus (CABYV (both poleroviruses. The extracted viral RNA was subjected to SOLiD next-generation sequence analysis and used as a template for reverse transcription synthesis, which was followed by PCR amplification. The ssRNA genome of PYLCV includes 6,028 nucleotides encoding six open reading frames (ORFs, which is typical of the genus Polerovirus. Comparisons of the deduced amino acid sequences of the PYLCV ORFs 2-4 and ORF5, indicate that there are high levels of similarity between these sequences to ORFs 2-4 of TVDV (84-93% and to ORF5 of CABYV (87%. Both PYLCV and Pepper vein yellowing virus (PeVYV contain sequences that point to a common ancestral polerovirus. The recombination breakpoint which is located at CABYV ORF3, which encodes the viral coat protein (CP, may explain the CABYV-like sequences found in the genomes of the pepper infecting viruses PYLCV and PeVYV. Two additional regions unique to PYLCV (PY1 and PY2 were identified between nucleotides 4,962 and 5,061 (ORF 5 and between positions 5,866 and 6,028 in the 3' NCR. Sequence analysis of the pepper-infecting PeVYV revealed three unique regions (Pe1-Pe3 with no similarity to other members of the genus Polerovirus. Genomic analyses of PYLCV and PeVYV suggest that the speciation of these viruses occurred through putative recombination event(s between poleroviruses co-infecting a common host(s, resulting in the emergence of PYLCV, a novel pathogen with a wider host range.

The complete genomic sequence of pepper yellow leaf curl virus (PYLCV) and its implications for our understanding of evolution dynamics in the genus polerovirus.

Science.gov (United States)

Dombrovsky, Aviv; Glanz, Eyal; Lachman, Oded; Sela, Noa; Doron-Faigenboim, Adi; Antignus, Yehezkel

2013-01-01

We determined the complete sequence and organization of the genome of a putative member of the genus Polerovirus tentatively named Pepper yellow leaf curl virus (PYLCV). PYLCV has a wider host range than Tobacco vein-distorting virus (TVDV) and has a close serological relationship with Cucurbit aphid-borne yellows virus (CABYV) (both poleroviruses). The extracted viral RNA was subjected to SOLiD next-generation sequence analysis and used as a template for reverse transcription synthesis, which was followed by PCR amplification. The ssRNA genome of PYLCV includes 6,028 nucleotides encoding six open reading frames (ORFs), which is typical of the genus Polerovirus. Comparisons of the deduced amino acid sequences of the PYLCV ORFs 2-4 and ORF5, indicate that there are high levels of similarity between these sequences to ORFs 2-4 of TVDV (84-93%) and to ORF5 of CABYV (87%). Both PYLCV and Pepper vein yellowing virus (PeVYV) contain sequences that point to a common ancestral polerovirus. The recombination breakpoint which is located at CABYV ORF3, which encodes the viral coat protein (CP), may explain the CABYV-like sequences found in the genomes of the pepper infecting viruses PYLCV and PeVYV. Two additional regions unique to PYLCV (PY1 and PY2) were identified between nucleotides 4,962 and 5,061 (ORF 5) and between positions 5,866 and 6,028 in the 3' NCR. Sequence analysis of the pepper-infecting PeVYV revealed three unique regions (Pe1-Pe3) with no similarity to other members of the genus Polerovirus. Genomic analyses of PYLCV and PeVYV suggest that the speciation of these viruses occurred through putative recombination event(s) between poleroviruses co-infecting a common host(s), resulting in the emergence of PYLCV, a novel pathogen with a wider host range.

The nucleotide sequence of satellite RNA in grapevine fanleaf virus, strain F13.

Science.gov (United States)

Fuchs, M; Pinck, M; Serghini, M A; Ravelonandro, M; Walter, B; Pinck, L

1989-04-01

The nucleotide sequence of cDNA copies of grapevine fanleaf virus (strain F13) satellite RNA has been determined. The primary structure obtained was 1114 nucleotides in length, excluding the poly(A) tail, and contained only one long open reading frame encoding a 341 residue, highly hydrophilic polypeptide of Mr37275. The coding sequence was bordered by a leader of 14 nucleotides and a 3'-terminal non-coding region of 74 nucleotides. No homology has been found with small satellite RNAs associated with other nepoviruses. Two limited homologies of eight nucleotides have been detected between the satellite RNA in grapevine fanleaf virus and those in tomato black ring virus, and a consensus sequence U.G/UGAAAAU/AU/AU/A at the 5' end of nepovirus RNAs is reported. A less extended consensus exists in this region in comovirus and picornavirus RNA.

CoVaCS: a consensus variant calling system.

Science.gov (United States)

Chiara, Matteo; Gioiosa, Silvia; Chillemi, Giovanni; D'Antonio, Mattia; Flati, Tiziano; Picardi, Ernesto; Zambelli, Federico; Horner, David Stephen; Pesole, Graziano; Castrignanò, Tiziana

2018-02-05

The advent and ongoing development of next generation sequencing technologies (NGS) has led to a rapid increase in the rate of human genome re-sequencing data, paving the way for personalized genomics and precision medicine. The body of genome resequencing data is progressively increasing underlining the need for accurate and time-effective bioinformatics systems for genotyping - a crucial prerequisite for identification of candidate causal mutations in diagnostic screens. Here we present CoVaCS, a fully automated, highly accurate system with a web based graphical interface for genotyping and variant annotation. Extensive tests on a gold standard benchmark data-set -the NA12878 Illumina platinum genome- confirm that call-sets based on our consensus strategy are completely in line with those attained by similar command line based approaches, and far more accurate than call-sets from any individual tool. Importantly our system exhibits better sensitivity and higher specificity than equivalent commercial software. CoVaCS offers optimized pipelines integrating state of the art tools for variant calling and annotation for whole genome sequencing (WGS), whole-exome sequencing (WES) and target-gene sequencing (TGS) data. The system is currently hosted at Cineca, and offers the speed of a HPC computing facility, a crucial consideration when large numbers of samples must be analysed. Importantly, all the analyses are performed automatically allowing high reproducibility of the results. As such, we believe that CoVaCS can be a valuable tool for the analysis of human genome resequencing studies. CoVaCS is available at: https://bioinformatics.cineca.it/covacs .

Technical report: urinary tract infections in febrile infants and young children. The Urinary Tract Subcommittee of the American Academy of Pediatrics Committee on Quality Improvement.

Science.gov (United States)

Downs, S M

1999-04-01

The Urinary Tract Subcommittee of the American Academy of Pediatrics Committee on Quality Improvement has analyzed alternative strategies for the diagnosis and management of urinary tract infection (UTI) in children. The target population is limited to children between 2 months and 2 years of age who are examined because of fever without an obvious cause. Diagnosis and management of UTI in this group are especially challenging for these three reasons: 1) the manifestation of UTI tends to be nonspecific, and cases may be missed easily; 2) clean voided midstream urine specimens rarely can be obtained, leaving only urine collection methods that are invasive (transurethral catheterization or bladder tap) or result in nonspecific test results (bag urine); and 3) a substantial number of infants with UTI also may have structural or functional abnormalities of the urinary tract that put them at risk for ongoing renal damage, hypertension, and end-stage renal disease (ESRD). To examine alternative management strategies for UTI in infants, a conceptual model of the steps in diagnosis and management of UTI was developed. The model was expanded into a decision tree. Probabilities for branch points in the decision tree were obtained by review of the literature on childhood UTI. Data were extracted on standardized forms. Cost data were obtained by literature review and from hospital billing data. The data were collated into evidence tables. Analysis of the decision tree was used to produce risk tables and incremental cost-effectiveness ratios for alternative strategies. Based on the results of this analysis and, when necessary, consensus opinion, the Committee developed recommendations for the management of UTI in this population. This document provides the evidence the Subcommittee used in the development of its recommendations. The Subcommittee agreed that the objective of the practice parameter would be to minimize the risk of chronic renal damage within reasonable economic

Electronic Laboratory Notebook on Web2py Framework

Directory of Open Access Journals (Sweden)

2010-09-01

Full Text Available Proper experimental record-keeping is an important cornerstone in research and development for the purpose of auditing. The gold standard of record-keeping is based on the judicious use of physical, permanent notebooks. However, advances in technology had resulted in large amounts of electronic records making it virtually impossible to maintain a full set of records in physical notebooks. Electronic laboratory notebook systems aim to meet the stringency for keeping records electronically. This manuscript describes CyNote which is an electronic laboratory notebook system that is compliant with 21 CFP Part 11 controls on electronic records, requirements set by USA Food and Drug Administration for electronic records. CyNote is implemented on web2py framework and is adhering to the architectural paradigm of model-view-controller (MVC, allowing for extension modules to be built for CyNote. CyNote is available at http://cynote.sf.net.

The Python ARM Radar Toolkit (Py-ART, a Library for Working with Weather Radar Data in the Python Programming Language

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Jonathan J Helmus

2016-07-01

Full Text Available The Python ARM Radar Toolkit is a package for reading, visualizing, correcting and analysing data from weather radars. Development began to meet the needs of the Atmospheric Radiation Measurement Climate Research Facility and has since expanded to provide a general-purpose framework for working with data from weather radars in the Python programming language. The toolkit is built on top of libraries in the Scientific Python ecosystem including NumPy, SciPy, and matplotlib, and makes use of Cython for interfacing with existing radar libraries written in C and to speed up computationally demanding algorithms. The source code for the toolkit is available on GitHub and is distributed under a BSD license.

Distributed Optimal Consensus Control for Nonlinear Multiagent System With Unknown Dynamic.

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Zhang, Jilie; Zhang, Huaguang; Feng, Tao

2017-08-01

This paper focuses on the distributed optimal cooperative control for continuous-time nonlinear multiagent systems (MASs) with completely unknown dynamics via adaptive dynamic programming (ADP) technology. By introducing predesigned extra compensators, the augmented neighborhood error systems are derived, which successfully circumvents the system knowledge requirement for ADP. It is revealed that the optimal consensus protocols actually work as the solutions of the MAS differential game. Policy iteration algorithm is adopted, and it is theoretically proved that the iterative value function sequence strictly converges to the solution of the coupled Hamilton-Jacobi-Bellman equation. Based on this point, a novel online iterative scheme is proposed, which runs based on the data sampled from the augmented system and the gradient of the value function. Neural networks are employed to implement the algorithm and the weights are updated, in the least-square sense, to the ideal value, which yields approximated optimal consensus protocols. Finally, a numerical example is given to illustrate the effectiveness of the proposed scheme.

Characterizing leader sequences of CRISPR loci

DEFF Research Database (Denmark)

Alkhnbashi, Omer; Shah, Shiraz Ali; Garrett, Roger Antony

2016-01-01

The CRISPR-Cas system is an adaptive immune system in many archaea and bacteria, which provides resistance against invading genetic elements. The first phase of CRISPR-Cas immunity is called adaptation, in which small DNA fragments are excised from genetic elements and are inserted into a CRISPR...... array generally adjacent to its so called leader sequence at one end of the array. It has been shown that transcription initiation and adaptation signals of the CRISPR array are located within the leader. However, apart from promoters, there is very little knowledge of sequence or structural motifs...... sequences by focusing on the consensus repeat of the adjacent CRISPR array and weak upstream conservation signals. We applied our tool to the analysis of a comprehensive genomic database and identified several characteristic properties of leader sequences specific to archaea and bacteria, ranging from...

Compilation and analysis of Escherichia coli promoter DNA sequences.

OpenAIRE

Hawley, D K; McClure, W R

1983-01-01

The DNA sequence of 168 promoter regions (-50 to +10) for Escherichia coli RNA polymerase were compiled. The complete listing was divided into two groups depending upon whether or not the promoter had been defined by genetic (promoter mutations) or biochemical (5' end determination) criteria. A consensus promoter sequence based on homologies among 112 well-defined promoters was determined that was in substantial agreement with previous compilations. In addition, we have tabulated 98 promoter ...

Continuity and consensus

DEFF Research Database (Denmark)

Abrahamson, Peter

2010-01-01

maternal leave. These changes can be explained as adjustments to post-industrial conditions within a political culture relying on class compromises and a broad consensus informed by expert advice coming from civil servants and ad hoc policy commissions. The paper concludes that changes in Danish family...... policy reflect changing conditions for employment and the minding of children and that there has been a high degree of continuity and consensus about the change, as indicated by the strong increase in female labour market involvement....

An open source hydroeconomic model for California's water supply system: PyVIN

Science.gov (United States)

Dogan, M. S.; White, E.; Herman, J. D.; Hart, Q.; Merz, J.; Medellin-Azuara, J.; Lund, J. R.

2016-12-01

Models help operators and decision makers explore and compare different management and policy alternatives, better allocate scarce resources, and predict the future behavior of existing or proposed water systems. Hydroeconomic models are useful tools to increase benefits or decrease costs of managing water. Bringing hydrology and economics together, these models provide a framework for different disciplines that share similar objectives. This work proposes a new model to evaluate operation and adaptation strategies under existing and future hydrologic conditions for California's interconnected water system. This model combines the network structure of CALVIN, a statewide optimization model for California's water infrastructure, along with an open source solver written in the Python programming language. With the flexibilities of the model, reservoir operations, including water supply and hydropower, groundwater pumping, and the Delta water operations and requirements can now be better represented. Given time series of hydrologic inputs to the model, typical outputs include urban, agricultural and wildlife refuge water deliveries and shortage costs, conjunctive use of surface and groundwater systems, and insights into policy and management decisions, such as capacity expansion and groundwater management policies. Water market operations also represented in the model, allocating water from lower-valued users to higher-valued users. PyVIN serves as a cross-platform, extensible model to evaluate systemwide water operations. PyVIN separates data from the model structure, enabling model to be easily applied to other parts of the world where water is a scarce resource.

Multi-Optimisation Consensus Clustering

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Li, Jian; Swift, Stephen; Liu, Xiaohui

Ensemble Clustering has been developed to provide an alternative way of obtaining more stable and accurate clustering results. It aims to avoid the biases of individual clustering algorithms. However, it is still a challenge to develop an efficient and robust method for Ensemble Clustering. Based on an existing ensemble clustering method, Consensus Clustering (CC), this paper introduces an advanced Consensus Clustering algorithm called Multi-Optimisation Consensus Clustering (MOCC), which utilises an optimised Agreement Separation criterion and a Multi-Optimisation framework to improve the performance of CC. Fifteen different data sets are used for evaluating the performance of MOCC. The results reveal that MOCC can generate more accurate clustering results than the original CC algorithm.

Informed consent -- Building consensus

International Nuclear Information System (INIS)

Lovenheim, R.

1990-01-01

The author shares his observations and offers an approach to 'building consensus' for what he believes is the only environmentally sound option, i.e., safe, permanent disposal of low-level radioactive waste (LLRW). Consensus does not mean unanimity, acceptance, or harmony. The low-level radioactive waste disposal issue is fraught with fear and hysteria. The paper discusses major emotions that fracture public opinion regarding this issue. The author defines consensus as the informed consent of LLRW disposal strategies by a majority of citizens whose cooperation is required to achieve the goals of environmentally sound solution. The political aspects are reviewed. The need for US Department of Energy to fulfill its importance technical assistance role is discussed

AtomPy: A Cloud Atomic-data Service for Astrophysical Applications

Science.gov (United States)

Mendoza, Claudio; Boswell, J. S.; Bautista, M.

2013-06-01

Apart from our long-term commitment to the computing of accurate atomic data for astrophysical applications, we have also been interested in the problems of data access and dissemination. In this respect, one of us took part in the developments of TIPTOPbase [1, 2, 3], the astrophysical opacity server referred to as OPserver [4, 5], and, more recently, of the Virtual Atomic and Molecular Data Center [6, 7]. Our present effort is now with the establishment of a cloud atomic data web service, AtomPy, implemented by means of SOAP web services, Google Drive spreadsheets and Python modules. In the present poster we will describe the outline of this ambitious project, illustrated with some prototypes that are already operational.

A 1,681-locus consensus genetic map of cultivated cucumber including 67 NB-LRR resistance gene homolog and ten gene loci.

Science.gov (United States)

Yang, Luming; Li, Dawei; Li, Yuhong; Gu, Xingfang; Huang, Sanwen; Garcia-Mas, Jordi; Weng, Yiqun

2013-03-25

Cucumber is an important vegetable crop that is susceptible to many pathogens, but no disease resistance (R) genes have been cloned. The availability of whole genome sequences provides an excellent opportunity for systematic identification and characterization of the nucleotide binding and leucine-rich repeat (NB-LRR) type R gene homolog (RGH) sequences in the genome. Cucumber has a very narrow genetic base making it difficult to construct high-density genetic maps. Development of a consensus map by synthesizing information from multiple segregating populations is a method of choice to increase marker density. As such, the objectives of the present study were to identify and characterize NB-LRR type RGHs, and to develop a high-density, integrated cucumber genetic-physical map anchored with RGH loci. From the Gy14 draft genome, 70 NB-containing RGHs were identified and characterized. Most RGHs were in clusters with uneven distribution across seven chromosomes. In silico analysis indicated that all 70 RGHs had EST support for gene expression. Phylogenetic analysis classified 58 RGHs into two clades: CNL and TNL. Comparative analysis revealed high-degree sequence homology and synteny in chromosomal locations of these RGH members between the cucumber and melon genomes. Fifty-four molecular markers were developed to delimit 67 of the 70 RGHs, which were integrated into a genetic map through linkage analysis. A 1,681-locus cucumber consensus map including 10 gene loci and spanning 730.0 cM in seven linkage groups was developed by integrating three component maps with a bin-mapping strategy. Physically, 308 scaffolds with 193.2 Mbp total DNA sequences were anchored onto this consensus map that covered 52.6% of the 367 Mbp cucumber genome. Cucumber contains relatively few NB-LRR RGHs that are clustered and unevenly distributed in the genome. All RGHs seem to be transcribed and shared significant sequence homology and synteny with the melon genome suggesting conservation of

Production of a recombinant capsid protein VP1 from a newly described polyomavirus (RacPyV for downstream use in virus characterization

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Molly E. Church

2016-06-01

Full Text Available Here we describe the methods for production of a recombinant viral capsid protein and subsequent use in an indirect enzyme linked immunosorbent assay (ELISA, and for use in production of a rabbit polyclonal antibody. These reagents were utilized in development and optimization of an ELISA, which established the extent of exposure of free ranging raccoons to a newly described polyomavirus (RacPyV [1]. Production of a polyclonal antibody has allowed for further characterization of RacPyV, including immunohistochemistry and immunocytochemistry techniques, in order to answer questions about pathogenesis of this virus.

PyPWA: A partial-wave/amplitude analysis software framework

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Salgado, Carlos

2016-05-01

The PyPWA project aims to develop a software framework for Partial Wave and Amplitude Analysis of data; providing the user with software tools to identify resonances from multi-particle final states in photoproduction. Most of the code is written in Python. The software is divided into two main branches: one general-shell where amplitude's parameters (or any parametric model) are to be estimated from the data. This branch also includes software to produce simulated data-sets using the fitted amplitudes. A second branch contains a specific realization of the isobar model (with room to include Deck-type and other isobar model extensions) to perform PWA with an interface into the computer resources at Jefferson Lab. We are currently implementing parallelism and vectorization using the Intel's Xeon Phi family of coprocessors.

The microbiota continuum along the female reproductive tract and its relation to uterine-related diseases

DEFF Research Database (Denmark)

Chen, Chen; Song, Xiaolei; Wei, Weixia

2017-01-01

Reports on bacteria detected in maternal fluids during pregnancy are typically associated with adverse consequences, and whether the female reproductive tract harbours distinct microbial communities beyond the vagina has been a matter of debate. Here we systematically sample the microbiota within...... the female reproductive tract in 110 women of reproductive age, and examine the nature of colonisation by 16S rRNA gene amplicon sequencing and cultivation. We find distinct microbial communities in cervical canal, uterus, fallopian tubes and peritoneal fluid, differing from that of the vagina. The results...

Chlamydiae in febrile children with respiratory tract symptoms and age-matched controls, Ghana

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H. Bühl

2018-03-01

Full Text Available Members of the Chlamydiales order are obligate intracellular pathogens causing acute and chronic infectious diseases. Chlamydiaceae are established agents of community- and zoonotically acquired respiratory tract infections, and emerging pathogens among the Chlamydia-related bacteria have been implicated in airway infections. The role of both in airway infections in Africa is underexplored. We performed a case -control study on the prevalence of Chlamydiaceae and Chlamydia-related emerging pathogens in children with febrile respiratory tract infections in West Africa, Ghana. Using a pan-Chlamydiales broad-range real-time PCR, we detected chlamydial DNA in 11 (1.9% of 572 hospitalized febrile children with respiratory tract symptoms and in 24 (4.3% of 560 asymptomatic age-matched controls (p 0.03. Chlamydiaceae were found to be common among both symptomatic and healthy Ghanaian children, with Chlamydia pneumoniae being the most prevalent species. Parachlamydiaceae were detected in two children without symptoms but not in the symptomatic group. We identified neither Chlamydia psittaci nor Simkania negevensis but a member of a new chlamydial family that shared 90.2% sequence identity with the 16S rRNA gene of the zoonotic pathogen Chlamydia pecorum. In addition, we found a new Chlamydia-related species that belonged to a novel family sharing 91.3% 16S rRNA sequence identity with Candidatus Syngnamydia venezia. The prevalence and spectrum of chlamydial species differed from previous results obtained from children of other geographic regions and our study indicates that both, Chlamydiaceae and Chlamydia-related bacteria, are not clearly linked to clinical symptoms in Ghanaian children. Keywords: Children, Chlamydia, Chlamydia-related bacteria, febrile respiratory tract infection, Ghana

The Consensus String Problem and the Complexity of Comparing Hidden Markov Models

DEFF Research Database (Denmark)

Lyngsø, Rune Bang; Pedersen, Christian Nørgaard Storm

2002-01-01

The basic theory of hidden Markov models was developed and applied to problems in speech recognition in the late 1960s, and has since then been applied to numerous problems, e.g. biological sequence analysis. Most applications of hidden Markov models are based on efficient algorithms for computing...... the probability of generating a given string, or computing the most likely path generating a given string. In this paper we consider the problem of computing the most likely string, or consensus string, generated by a given model, and its implications on the complexity of comparing hidden Markov models. We show...... that computing the consensus string, and approximating its probability within any constant factor, is NP-hard, and that the same holds for the closely related labeling problem for class hidden Markov models. Furthermore, we establish the NP-hardness of comparing two hidden Markov models under the L∞- and L1...

Adaptation of PyFlag to Efficient Analysis of Overtaken Computer Data Storage

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Aleksander Byrski

2010-03-01

Full Text Available Based on existing software aimed at investigation support in the analysis of computer data storage overtaken during investigation (PyFlag, an extension is proposed involving the introduction of dedicated components for data identification and filtering. Hash codes for popular software contained in NIST/NSRL database are considered in order to avoid unwanted files while searching and to classify them into several categories. The extension allows for further analysis, e.g. using artificial intelligence methods. The considerations are illustrated by the overview of the system's design.

Genital and Urinary Tract Defects

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... conditions > Genital and urinary tract defects Genital and urinary tract defects E-mail to a friend Please fill ... and extra fluids. What problems can genital and urinary tract defects cause? Genital and urinary tract defects affect ...

The diploid genome sequence of an Asian individual

DEFF Research Database (Denmark)

Wang, Jun; Wang, Wei; Li, Ruiqiang

2008-01-01

Here we present the first diploid genome sequence of an Asian individual. The genome was sequenced to 36-fold average coverage using massively parallel sequencing technology. We aligned the short reads onto the NCBI human reference genome to 99.97% coverage, and guided by the reference genome, we...... used uniquely mapped reads to assemble a high-quality consensus sequence for 92% of the Asian individual's genome. We identified approximately 3 million single-nucleotide polymorphisms (SNPs) inside this region, of which 13.6% were not in the dbSNP database. Genotyping analysis showed that SNP...... identification had high accuracy and consistency, indicating the high sequence quality of this assembly. We also carried out heterozygote phasing and haplotype prediction against HapMap CHB and JPT haplotypes (Chinese and Japanese, respectively), sequence comparison with the two available individual genomes (J...

A molecular phylogeny of the bladed Bangiales (Rhodophyta) in China provides insights into biodiversity and biogeography of the genus Pyropia.

Science.gov (United States)

Yang, Li-En; Zhou, Wei; Hu, Chuan-Ming; Deng, Yin-Yin; Xu, Guang-Ping; Zhang, Tao; Russell, Stephen; Zhu, Jian-Yi; Lu, Qin-Qin; Brodie, Juliet

2018-03-01

A molecular taxonomic study was undertaken for the first time of the bladed Bangiales of the mainland coast of China (Northwest Pacific) based on sequence data of 201 plastid rbcL and 148 nuclear 18S sequences of historical and contemporary specimens. The results revealed that only one genus of bladed Bangiales, Pyropia, was present along Chinese coast. Species delimitation was determined using two empirical methods: the Automatic Barcode Gap Discovery (ABGD) and General Mixed Yule Coalescence (GMYC) coupled with detection of monophyly in tree reconstruction. At least fourteen species of Pyropia were recovered. Six species were confirmed that had been recorded previously based on morphology (Py. suborbiculata, Py. yezoensis, Py. haitanensis, Py. katadae, Py. tenera and Py. acanthophora), three species were recorded from China for the first time (Py. kinositae, Py. pseudolinearis and Py. tanegashimensis), and five cryptic species that did not match any molecular sequences were also discovered. The phylogeny of the concatenated rbcL and 18S dataset resolved three singletons and four clades. Each clades has a strong trend towards occupying a biogeographic region, but they are not confined to them. A transoceanic and antitropical pattern of distribution was found for Pyropia at both the subgeneric and species level. This together with high biodiversity (ca. 30% of all known Pyropia species) indicates that the Northwest Pacific might act as a centre of origin for modern distribution of Pyropia since the early Cenozoic. Copyright © 2017 Elsevier Inc. All rights reserved.

SEDIMENTATION AND BASIN-FILL HISTORY OF THE PLIOCENE SUCCESSION EXPOSED IN THE NORTHERN SIENA-RADICOFANI BASIN (TUSCANY, ITALY: A SEQUENCE-STRATIGRAPHIC APPROACH

Directory of Open Access Journals (Sweden)

IVAN MARTINI

2017-08-01

Full Text Available Basin-margin paralic deposits are sensitive indicators of relative sea-level changes and typically show complex stratigraphic architectures that only a facies-based sequence-stratigraphic approach, supported by detailed biostratigraphic data, can help unravel, thus providing constraints for the tectono-stratigraphic reconstructions of ancient basins. This paper presents a detailed facies analysis of Pliocene strata exposed in a marginal key-area of the northern Siena-Radicofani Basin (Tuscany, Italy, which is used as a ground for a new sequence-stratigraphic scheme of the studied area. The study reveals a more complex sedimentary history than that inferred from the recent geological maps produced as part of the Regional Cartographic Project (CARG, which are based on lithostratigraphic principles. Specifically, four sequences (S1 to S4, in upward stratigraphic order have been recognised, each bounded by erosional unconformities and deposited within the Zanclean-early Gelasian time span. Each sequence typically comprises fluvial to open marine facies, with deposits of different sequences that show striking lithological similarities.The architecture and internal variability shown by the studied depositional sequences are typical of low-accommodation basin-margin settings, that shows: i a poorly-developed to missing record of the falling-stage systems tract; ii a lowstand system tract predominantly made of fluvio-deltaic deposits; iii a highstand system tract with substantial thickness variation between different sequences due to erosional processes associated with the overlying unconformity; iv a highly variable transgressive system tract, ranging from elementary to parasequential organization.

The microbiota continuum along the female reproductive tract and its relation to uterine-related diseases.

Science.gov (United States)

Chen, Chen; Song, Xiaolei; Wei, Weixia; Zhong, Huanzi; Dai, Juanjuan; Lan, Zhou; Li, Fei; Yu, Xinlei; Feng, Qiang; Wang, Zirong; Xie, Hailiang; Chen, Xiaomin; Zeng, Chunwei; Wen, Bo; Zeng, Liping; Du, Hui; Tang, Huiru; Xu, Changlu; Xia, Yan; Xia, Huihua; Yang, Huanming; Wang, Jian; Wang, Jun; Madsen, Lise; Brix, Susanne; Kristiansen, Karsten; Xu, Xun; Li, Junhua; Wu, Ruifang; Jia, Huijue

2017-10-17

Reports on bacteria detected in maternal fluids during pregnancy are typically associated with adverse consequences, and whether the female reproductive tract harbours distinct microbial communities beyond the vagina has been a matter of debate. Here we systematically sample the microbiota within the female reproductive tract in 110 women of reproductive age, and examine the nature of colonisation by 16S rRNA gene amplicon sequencing and cultivation. We find distinct microbial communities in cervical canal, uterus, fallopian tubes and peritoneal fluid, differing from that of the vagina. The results reflect a microbiota continuum along the female reproductive tract, indicative of a non-sterile environment. We also identify microbial taxa and potential functions that correlate with the menstrual cycle or are over-represented in subjects with adenomyosis or infertility due to endometriosis. The study provides insight into the nature of the vagino-uterine microbiome, and suggests that surveying the vaginal or cervical microbiota might be useful for detection of common diseases in the upper reproductive tract.Whether the female reproductive tract harbours distinct microbiomes beyond the vagina has been a matter of debate. Here, the authors show a subject-specific continuity in microbial communities at six sites along the female reproductive tract, indicative of a non-sterile environment.

Characterization of short interspersed elements (SINEs) in a red alga, Porphyra yezoensis.

Science.gov (United States)

Zhang, Wenbo; Lin, Xiaofei; Peddigari, Suresh; Takechi, Katsuaki; Takano, Hiroyoshi; Takio, Susumu

2007-02-01

Short interspersed element (SINE)-like sequences referred to as PySN1 and PySN2 were identified in a red alga, Porphyra yezoensis. Both elements contained an internal promoter with motifs (A box and B box) recognized by RNA polymerase III, and target site duplications at both ends. Genomic Southern blot analysis revealed that both elements were widely and abundantly distributed on the genome. 3' and 5' RACE suggested that PySN1 was expressed as a chimera transcript with flanking SINE-unrelated sequences and possessed the poly-A tail at the same position near the 3' end of PySN1.

Kidneys and Urinary Tract

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... Videos for Educators Search English Español Kidneys and Urinary Tract KidsHealth / For Teens / Kidneys and Urinary Tract What's ... a sign of diabetes . What the Kidneys and Urinary Tract Do Although the two kidneys work together to ...

PY-GC-MS applied to the identification of synthetic resins in Brazilian painting

International Nuclear Information System (INIS)

Redigolo, Marcelo M.; Amaral, Priscila O.; Leao, Claudio; Crepaldi, Caike; Munita, Casimiro S.; Bustillos, Oscar V.; Russo, Tatiana; Mendonca, Valeria de

2015-01-01

Works of art are appreciated for their material and immaterial value. Restoring objects of art is a delicate procedure, mostly due to the irreversibility of the interventions. Hence, it is recommended to study the chemical composition of the object to avoid errors. The premise for restoring or conserving these objects is their physical preservation, i.e., it is advisable to avoid sampling and, when necessary, samples must be minute. The analytical techniques that fulfill these requirements are limited. Mass spectrometry (MS) is a versatile technique due to its hyphenation possibilities. Recently, it has being employed in the identification of natural and synthetic resins in works of art. Electron ionization (EI) is a powerful method of molecular fragmentation employed in the detection of volatile organic compounds by mass spectrometry. In this work, two micrograms (μg) of sample from a Brazilian contemporary painting were analyzed by pyrolysis-gas chromatography/mass spectrometry (Py-GC/MS) technique. A microfurnace-type pyrolyzer was coupled to a gas chromatograph, using a non-polar capillary column. The electron ionization was achieved applying 70 eV electron energy. This technique is suitable for the analysis of material from objects of art, being specific, accurate and requiring minimal sampling. The synthetic resin diallyl phthalate (DAP) was identified by the Py-GC/MS technique. (author)

PY-GC-MS applied to the identification of synthetic resins in Brazilian painting

Energy Technology Data Exchange (ETDEWEB)

Redigolo, Marcelo M.; Amaral, Priscila O.; Leao, Claudio; Crepaldi, Caike; Munita, Casimiro S.; Bustillos, Oscar V., E-mail: marcelo.redigolo@usp.br [Instituto de Pesquisas Energeticas e Nucleares (IPEN/CNEN-SP), Sao Paulo, SP (Brazil); Russo, Tatiana; Mendonca, Valeria de [Pinacoteca do Estado de Sao Paulo, SP (Brazil)

2015-07-01

Works of art are appreciated for their material and immaterial value. Restoring objects of art is a delicate procedure, mostly due to the irreversibility of the interventions. Hence, it is recommended to study the chemical composition of the object to avoid errors. The premise for restoring or conserving these objects is their physical preservation, i.e., it is advisable to avoid sampling and, when necessary, samples must be minute. The analytical techniques that fulfill these requirements are limited. Mass spectrometry (MS) is a versatile technique due to its hyphenation possibilities. Recently, it has being employed in the identification of natural and synthetic resins in works of art. Electron ionization (EI) is a powerful method of molecular fragmentation employed in the detection of volatile organic compounds by mass spectrometry. In this work, two micrograms (μg) of sample from a Brazilian contemporary painting were analyzed by pyrolysis-gas chromatography/mass spectrometry (Py-GC/MS) technique. A microfurnace-type pyrolyzer was coupled to a gas chromatograph, using a non-polar capillary column. The electron ionization was achieved applying 70 eV electron energy. This technique is suitable for the analysis of material from objects of art, being specific, accurate and requiring minimal sampling. The synthetic resin diallyl phthalate (DAP) was identified by the Py-GC/MS technique. (author)

Urinary Tract Infections (For Kids)

Science.gov (United States)

... Staying Safe Videos for Educators Search English Español Urinary Tract Infections (UTIs) KidsHealth / For Kids / Urinary Tract Infections ( ... Let's find out more. What Exactly Is a Urinary Tract? Your urinary tract is actually a system made ...

Democracy-based consensus in medicine.

Science.gov (United States)

Greco, Massimiliano; Zangrillo, Alberto; Mucchetti, Marta; Nobile, Leda; Landoni, Paolo; Bellomo, Rinaldo; Landoni, Giovanni

2015-04-01

High-quality evidence and derived guidelines, as typically published in major academic journals, are a major process that shapes physician decision-making worldwide. However, for many aspects of medical practice, there is a lack of High-quality evidence or an overload of somewhat contradictory low-quality information, which makes decision-making a difficult, uncertain, and unpredictable process. When the issues in question are important and evidence limited or controversial, the medical community seeks to establish common ground for "best practice" through consensus conferences and consensus statements or guidelines. Such consensus statements are seen as a useful tool to establish expert agreement, define the boundaries of acceptable practice, provide priorities for the research agenda, and obtain opinions from different countries and healthcare systems. This standard approach, however, can be criticized for being elitist, noninclusive, and poorly representative of the community of clinicians who will have to make decisions about the implementation of such recommendations. Accordingly, the authors propose a new model based on a combination of a local core meeting (detailed review and expert input) followed by a worldwide web-based network assessment (democracy-based consensus). The authors already have applied this approach to develop consensus on all nonsurgical interventions that increase or reduce perioperative mortality in critically ill patients and in those with acute kidney injury. The methodology was based on 5 sequential local and web-based steps. Both a panel of experts and a large number of professionals from all over the world were involved, giving birth to a new type of "democracy-based consensus." This new type of "democracy-based consensus" has the potential to increase grass-root clinician involvement, expand the reach to less-developed countries, provide a more global perspective on proposed interventions, and perhaps more importantly, increase

The effect of subject measurement error on joint kinematics in the conventional gait model: Insights from the open-source pyCGM tool using high performance computing methods.

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Schwartz, Mathew; Dixon, Philippe C

2018-01-01

The conventional gait model (CGM) is a widely used biomechanical model which has been validated over many years. The CGM relies on retro-reflective markers placed along anatomical landmarks, a static calibration pose, and subject measurements as inputs for joint angle calculations. While past literature has shown the possible errors caused by improper marker placement, studies on the effects of inaccurate subject measurements are lacking. Moreover, as many laboratories rely on the commercial version of the CGM, released as the Plug-in Gait (Vicon Motion Systems Ltd, Oxford, UK), integrating improvements into the CGM code is not easily accomplished. This paper introduces a Python implementation for the CGM, referred to as pyCGM, which is an open-source, easily modifiable, cross platform, and high performance computational implementation. The aims of pyCGM are to (1) reproduce joint kinematic outputs from the Vicon CGM and (2) be implemented in a parallel approach to allow integration on a high performance computer. The aims of this paper are to (1) demonstrate that pyCGM can systematically and efficiently examine the effect of subject measurements on joint angles and (2) be updated to include new calculation methods suggested in the literature. The results show that the calculated joint angles from pyCGM agree with Vicon CGM outputs, with a maximum lower body joint angle difference of less than 10-5 degrees. Through the hierarchical system, the ankle joint is the most vulnerable to subject measurement error. Leg length has the greatest effect on all joints as a percentage of measurement error. When compared to the errors previously found through inter-laboratory measurements, the impact of subject measurements is minimal, and researchers should rather focus on marker placement. Finally, we showed that code modifications can be performed to include improved hip, knee, and ankle joint centre estimations suggested in the existing literature. The pyCGM code is provided

Urinary Tract Infections (For Teens)

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... Staying Safe Videos for Educators Search English Español Urinary Tract Infections KidsHealth / For Teens / Urinary Tract Infections What's ... especially girls — visit a doctor. What Is a Urinary Tract Infection? A bacterial urinary tract infection (UTI) is ...

Near-infrared neuroimaging with NinPy

Directory of Open Access Journals (Sweden)

Gary E Strangman

2009-05-01

Full Text Available There has been substantial recent growth in the use of non-invasive optical brain imaging in studies of human brain function in health and disease. Near-infrared neuroimaging (NIN is one of the most promising of these techniques and, although NIN hardware continues to evolve at a rapid pace, software tools supporting optical data acquisition, image processing, statistical modeling and visualization remain less refined. Python, a modular and computationally efficient development language, can support functional neuroimaging studies of diverse design and implementation. In particular, Python's easily readable syntax and modular architecture allow swift prototyping followed by efficient transition to stable production systems. As an introduction to our ongoing efforts to develop Python software tools for structural and functional neuroimaging, we discuss: (i the role of noninvasive diffuse optical imaging in measuring brain function, (ii the key computational requirements to support NIN experiments, (iii our collection of software tools to support near-infrared neuroimaging, called NinPy, and (iv future extensions of these tools that will allow integration of optical with other structural and functional neuroimaging data sources. Source code for the software discussed here will be made available at www.nmr.mgh.harvard.edu/Neural_SystemsGroup/software.html.

A Python package for parsing, validating, mapping and formatting sequence variants using HGVS nomenclature.

Science.gov (United States)

Hart, Reece K; Rico, Rudolph; Hare, Emily; Garcia, John; Westbrook, Jody; Fusaro, Vincent A

2015-01-15

Biological sequence variants are commonly represented in scientific literature, clinical reports and databases of variation using the mutation nomenclature guidelines endorsed by the Human Genome Variation Society (HGVS). Despite the widespread use of the standard, no freely available and comprehensive programming libraries are available. Here we report an open-source and easy-to-use Python library that facilitates the parsing, manipulation, formatting and validation of variants according to the HGVS specification. The current implementation focuses on the subset of the HGVS recommendations that precisely describe sequence-level variation relevant to the application of high-throughput sequencing to clinical diagnostics. The package is released under the Apache 2.0 open-source license. Source code, documentation and issue tracking are available at http://bitbucket.org/hgvs/hgvs/. Python packages are available at PyPI (https://pypi.python.org/pypi/hgvs). Supplementary data are available at Bioinformatics online. © The Author 2014. Published by Oxford University Press.

Reconstruction of ancestral RNA sequences under multiple structural constraints

OpenAIRE

Tremblay-Savard, Olivier; Reinharz, Vladimir; Waldisp?hl, J?r?me

2016-01-01

Background Secondary structures form the scaffold of multiple sequence alignment of non-coding RNA (ncRNA) families. An accurate reconstruction of ancestral ncRNAs must use this structural signal. However, the inference of ancestors of a single ncRNA family with a single consensus structure may bias the results towards sequences with high affinity to this structure, which are far from the true ancestors. Methods In this paper, we introduce achARNement, a maximum parsimony approach that, given...

Urinary Tract Infections (For Kids)

Medline Plus

Full Text Available ... Staying Safe Videos for Educators Search English Español Urinary Tract Infections (UTIs) KidsHealth / For Kids / Urinary Tract Infections ( ... Let's find out more. What Exactly Is a Urinary Tract? Your urinary tract is actually a system made ...

Rapid development of image analysis research tools: Bridging the gap between researcher and clinician with pyOsiriX.

Science.gov (United States)

Blackledge, Matthew D; Collins, David J; Koh, Dow-Mu; Leach, Martin O

2016-02-01

We present pyOsiriX, a plugin built for the already popular dicom viewer OsiriX that provides users the ability to extend the functionality of OsiriX through simple Python scripts. This approach allows users to integrate the many cutting-edge scientific/image-processing libraries created for Python into a powerful DICOM visualisation package that is intuitive to use and already familiar to many clinical researchers. Using pyOsiriX we hope to bridge the apparent gap between basic imaging scientists and clinical practice in a research setting and thus accelerate the development of advanced clinical image processing. We provide arguments for the use of Python as a robust scripting language for incorporation into larger software solutions, outline the structure of pyOsiriX and how it may be used to extend the functionality of OsiriX, and we provide three case studies that exemplify its utility. For our first case study we use pyOsiriX to provide a tool for smooth histogram display of voxel values within a user-defined region of interest (ROI) in OsiriX. We used a kernel density estimation (KDE) method available in Python using the scikit-learn library, where the total number of lines of Python code required to generate this tool was 22. Our second example presents a scheme for segmentation of the skeleton from CT datasets. We have demonstrated that good segmentation can be achieved for two example CT studies by using a combination of Python libraries including scikit-learn, scikit-image, SimpleITK and matplotlib. Furthermore, this segmentation method was incorporated into an automatic analysis of quantitative PET-CT in a patient with bone metastases from primary prostate cancer. This enabled repeatable statistical evaluation of PET uptake values for each lesion, before and after treatment, providing estaimes maximum and median standardised uptake values (SUVmax and SUVmed respectively). Following treatment we observed a reduction in lesion volume, SUVmax and SUVmed for

Prevalence and incidence of urinary tract and genital infections among patients with and without type 2 diabetes.

Science.gov (United States)

Nichols, Gregory A; Brodovicz, Kimberly G; Kimes, Teresa M; Déruaz-Luyet, Anouk; Bartels, Dorothee B

2017-11-01

Epidemiological data on genitourinary infections (GUIs) comparing patients with and without type 2 diabetes (T2DM) is scant. We aimed to estimate the incidence of urinary tract infections (UTIs), genital infections (GIs), or any GUI in total and stratified by history of GUI and sex. We identified 39,295 patients in the Kaiser Permanente Northwest health plan with T2DM and an equal number of age and sex matched patients without diabetes. The cohort was followed for up to 9years (2006-2014). We calculated incidence rates and corresponding 95% confidence intervals (CI) of any GUI, UTIs and GIs adjusting for age, sex, race, BMI, presence of chronic kidney disease, annual number of outpatient visits, and diuretic use. Adjusted incidence of any GUI was 97.2/1000person-years (p-y) (95% CI 95.5-98.8) among the T2DM cohort vs. 79.7/1000 p-y (78.3-81.2) among those without diabetes. T2DM was associated with an adjusted 25% increased risk of UTI (rate ratio 1.25, 95% CI 1.22-1.29), a 26% increased risk of GI (1.26, 1.22-1.31) and a 22% increased risk of any GUI (1.22, 1.19-1.25). Incidence rates were lower among those with no GUI history, but the relative risks were similar. Women in both groups had higher incidence rates of GUIs than men. T2DM was associated with increased risks of any GUI, UTIs and GIs. Incidence rates of UTIs were higher than rates of GIs, but the relative risk of GIs was essentially identical. A similar pattern was observed when stratifying by sex. RESEARCH QUESTIONS. Copyright © 2017 Elsevier Inc. All rights reserved.

Ultra-deep sequencing of intra-host rabies virus populations during cross-species transmission.

Directory of Open Access Journals (Sweden)

Monica K Borucki

2013-11-01

Full Text Available One of the hurdles to understanding the role of viral quasispecies in RNA virus cross-species transmission (CST events is the need to analyze a densely sampled outbreak using deep sequencing in order to measure the amount of mutation occurring on a small time scale. In 2009, the California Department of Public Health reported a dramatic increase (350 in the number of gray foxes infected with a rabies virus variant for which striped skunks serve as a reservoir host in Humboldt County. To better understand the evolution of rabies, deep-sequencing was applied to 40 unpassaged rabies virus samples from the Humboldt outbreak. For each sample, approximately 11 kb of the 12 kb genome was amplified and sequenced using the Illumina platform. Average coverage was 17,448 and this allowed characterization of the rabies virus population present in each sample at unprecedented depths. Phylogenetic analysis of the consensus sequence data demonstrated that samples clustered according to date (1995 vs. 2009 and geographic location (northern vs. southern. A single amino acid change in the G protein distinguished a subset of northern foxes from a haplotype present in both foxes and skunks, suggesting this mutation may have played a role in the observed increased transmission among foxes in this region. Deep-sequencing data indicated that many genetic changes associated with the CST event occurred prior to 2009 since several nonsynonymous mutations that were present in the consensus sequences of skunk and fox rabies samples obtained from 20032010 were present at the sub-consensus level (as rare variants in the viral population in skunk and fox samples from 1995. These results suggest that analysis of rare variants within a viral population may yield clues to ancestral genomes and identify rare variants that have the potential to be selected for if environment conditions change.

43 CFR 46.110 - Incorporating consensus-based management.

Science.gov (United States)

2010-10-01

... 43 Public Lands: Interior 1 2010-10-01 2010-10-01 false Incorporating consensus-based management... § 46.110 Incorporating consensus-based management. (a) Consensus-based management incorporates direct... carry out those plans and activities. For the purposes of this Part, consensus-based management involves...

Consensus statement on panic disorder from the International Consensus Group on Depression and Anxiety.

Science.gov (United States)

Ballenger, J C; Davidson, J R; Lecrubier, Y; Nutt, D J; Baldwin, D S; den Boer, J A; Kasper, S; Shear, M K

1998-01-01

To provide primary care clinicians with a better understanding of management issues in panic disorder and guide clinical practice with recommendations for appropriate pharmacotherapy. The 4 members of the International Consensus Group on Depression and Anxiety were James C. Ballenger (chair), Jonathan R. T. Davidson, Yves Lecrubier, and David J. Nutt. Four faculty invited by the chairman also participated: David S. Baldwin, Johan A. den Boer, Siegfried Kasper, and M. Katherine Shear. The consensus statement is based on the 6 review papers that are published in this supplement and on the scientific literature relevant to these issues. There were group meetings held during a 2-day period. On day 1, the group discussed each review paper and the chairman and discussant (Dr. Kasper) identified key issues for further debate. On day 2, the group discussed these key issues to arrive at a consensus view. After the group meetings, the consensus statement was drafted by the chairman and approved by all attendees. The consensus statement provides standard definitions for response and remission and identifies appropriate strategy for the management of panic disorder in a primary care setting. Serotonin selective reuptake inhibitors are recommended as drugs of first choice with a treatment period of 12 to 24 months. Pharmacotherapy should be discontinued slowly over a period of 4 to 6 months.

``Urania - Postępy Astronomii'' as magazine and internet portal

Science.gov (United States)

Czart, Krzysztof; Mikołajewski, Maciej

2016-06-01

We describe examples of the activities of the ``Urania - Postępy Astronomii'' magazine undertaken in 2014-2015. These tasks included the special project for schools of a "Sponsored subscription" in cooperation with the Ministry of Science and Higher Education, support for the Astronomy Olimpiad, further development of the internet portal, extension of the digital archive and making the archive available for smartphones and tablets in the Google Play system. ``Urania'' is a popular science journal devoted to astronomy and space research. It is the main Polish magazine of this kind, and one of the oldest in the world. ``Urania'' was awarded the Special Prize in the contest Popularyzator Nauki 2014, which is the main contest for science communicators in Poland.

Building consensus in developing radioactive waste management systems

International Nuclear Information System (INIS)

Terrell, R.; Philpott, R.; Smith, S.L.; Gibson, J.

1991-01-01

To successfully develop radioactive waste management systems, national authorities must work to establish consensus on numerous complex issues among many affected and interested parties. This paper explores the meaning of consensus in waste management, with special attention to the different arenas in which consensus is established and how DOE can respond if consensus is withheld. Highlights of other national waste management programs are introduced to provide a broader perspective on consensus. It is suggested that the US waste management program has reached a point where Congress needs to act to reaffirm consensus on the direction of the US program

Prevalence of urinary tract infection and vesicoureteral reflux in children with lower urinary tract dysfunction.