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https://www.readbyqxmd.com/read/28647127/infrared-light-detection-by-the-haller-s-organ-of-adult-american-dog-ticks-dermacentor-variabilis-ixodida-ixodidae
#1
Robert D Mitchell, Jiwei Zhu, Ann L Carr, Anirudh Dhammi, Grayson Cave, Daniel E Sonenshine, R Michael Roe
The Haller's organ (HO), unique to ticks and mites, is found only on the first tarsus of the front pair of legs. The organ has an unusual morphology consisting of an anterior pit (AP) with protruding sensilla and a posterior capsule (Cp). The current thinking is that the HO's main function is chemosensation analogous to the insect antennae, but the functionality of its atypical structure (exclusive to the Acari) is unexplained. We provide the first evidence that the HO allows the American dog tick, Dermacentor variabilis, to respond to infrared (IR) light...
June 13, 2017: Ticks and Tick-borne Diseases
https://www.readbyqxmd.com/read/28646877/sbmlmod-a-python-based-web-application-and-web-service-for-efficient-data-integration-and-model-simulation
#2
Sascha Schäuble, Anne-Kristin Stavrum, Mathias Bockwoldt, Pål Puntervoll, Ines Heiland
BACKGROUND: Systems Biology Markup Language (SBML) is the standard model representation and description language in systems biology. Enriching and analysing systems biology models by integrating the multitude of available data, increases the predictive power of these models. This may be a daunting task, which commonly requires bioinformatic competence and scripting. RESULTS: We present SBMLmod, a Python-based web application and service, that automates integration of high throughput data into SBML models...
June 24, 2017: BMC Bioinformatics
https://www.readbyqxmd.com/read/28645842/opennft-an-open-source-python-matlab-framework-for-real-time-fmri-neurofeedback-training-based-on-activity-connectivity-and-multivariate-pattern-analysis
#3
Yury Koush, John Ashburner, Evgeny Prilepin, Ronald Sladky, Peter Zeidman, Sergei Bibikov, Frank Scharnowski, Artem Nikonorov, Dimitri Van De Ville
Neurofeedback based on real-time functional magnetic resonance imaging (rt-fMRI) is a novel and rapidly developing research field. It allows for training of voluntary control over localized brain activity and connectivity and has demonstrated promising clinical applications. Because of the rapid technical developments of MRI techniques and the availability of high-performance computing, new methodological advances in rt-fMRI neurofeedback become possible. Here we outline the core components of a novel open-source neurofeedback framework, termed Open NeuroFeedback Training (OpenNFT), which efficiently integrates these new developments...
June 20, 2017: NeuroImage
https://www.readbyqxmd.com/read/28645150/gfapy-a-flexible-and-extensible-software-library-for-handling-sequence-graphs-in-python
#4
Giorgio Gonnella, Stefan Kurtz
Summary: GFA 1 and GFA 2 are recently defined formats for representing sequence graphs, such as assembly, variation or splicing graphs. The formats are adopted by several software tools. Availability and Implementation: GfaPy is available open source at https://github.com/ggonnella/gfapy and installable via pip. Contact: gonnella@zbh.uni-hamburg.de. Supplementary information: Supplementary data are available at Bioinformatics online...
June 22, 2017: Bioinformatics
https://www.readbyqxmd.com/read/28644610/mzmine-2-data-preprocessing-to-enhance-molecular-networking-reliability
#5
Florent Olivon, Gwendal Grelier, Fanny Roussi, Marc Litaudon, David Touboul
Molecular networking is becoming more and more popular into the metabolomic community to organize tandem mass spectrometry (MS2) data. Even though this approach allows the treatment and comparison of large data sets, several drawbacks related to the MS-Cluster tool routinely used on the Global Natural Product Social Molecular Networking platform (GNPS) limit its potential. MS-Cluster cannot distinguish between chromatography well-resolved isomers as retention times are not taken into account. Annotation with predicted chemical formulas is also not implemented and semi-quantification is only based on the number of MS2 scans...
June 23, 2017: Analytical Chemistry
https://www.readbyqxmd.com/read/28643159/pymice-apython-library-for-analysis-of-intellicage-data
#6
Jakub M Dzik, Alicja Puścian, Zofia Mijakowska, Kasia Radwanska, Szymon Łęski
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...
June 22, 2017: Behavior Research Methods
https://www.readbyqxmd.com/read/28640810/lassim-a-network-inference-toolbox-for-genome-wide-mechanistic-modeling
#7
Rasmus Magnusson, Guido Pio Mariotti, Mattias Köpsén, William Lövfors, Danuta R Gawel, Rebecka Jörnsten, Jörg Linde, Torbjörn Nordling, Elin Nyman, Sylvie Schulze, Colm E Nestor, Huan Zhang, Gunnar Cedersund, Mikael Benson, Andreas Tjärnberg, Mika Gustafsson
Recent technological advancements have made time-resolved, quantitative, multi-omics data available for many model systems, which could be integrated for systems pharmacokinetic use. Here, we present large-scale simulation modeling (LASSIM), which is a novel mathematical tool for performing large-scale inference using mechanistically defined ordinary differential equations (ODE) for gene regulatory networks (GRNs). LASSIM integrates structural knowledge about regulatory interactions and non-linear equations with multiple steady state and dynamic response expression datasets...
June 22, 2017: PLoS Computational Biology
https://www.readbyqxmd.com/read/28637183/nuclitrack-an-integrated-nuclei-tracking-application
#8
Sam Cooper, Alexis R Barr, Robert Glen, Chris Bakal
Summary: Live imaging studies give unparalleled insight into dynamic single cell behaviours and fate decisions. However, the challenge of reliably tracking single cells over long periods of time limits both the throughput and ease with which such studies can be performed. Here, we present NucliTrack, a cross platform solution for automatically segmenting, tracking and extracting features from fluorescently-labelled nuclei. NucliTrack performs similarly to other state-of-the-art cell tracking algorithms, but NucliTrack's interactive, graphical interface makes it significantly more user friendly...
June 20, 2017: Bioinformatics
https://www.readbyqxmd.com/read/28635138/snake-spectacle-vessel-permeability-to-sodium-fluorescein
#9
Roy W Bellhorn, Ann R Strom, Monica J Motta, John Doval, Michelle G Hawkins, Joanne Paul-Murphy
OBJECTIVE: Assess vascular permeability of the snake spectacle to sodium fluorescein during resting and shedding phases of the ecdysis cycle. ANIMAL STUDIED: Ball python (Python regius). PROCEDURES: The snake was anesthetized, and spectral domain optic coherence tomography was performed prior to angiographic procedures. An electronically controlled digital single-lens reflex camera with a dual-head flash equipped with filters suitable for fluorescein angiography was used to make images...
June 20, 2017: Veterinary Ophthalmology
https://www.readbyqxmd.com/read/28633344/pheno4j-a-gene-to-phenotype-graph-database
#10
Sajid Mughal, Ismail Moghul, Jing Yu, Tristan Clark, David S Gregory, Nikolas Pontikos
Summary: Efficient storage and querying of large amounts of genetic and phenotypic data is crucial to contemporary clinical genetic research. This introduces computational challenges for classical relational databases, due to the sparsity and sheer volume of the data. Our Java based solution loads annotated genetic variants and well phenotyped patients into a graph database to allow fast efficient storage and querying of large volumes of structured genetic and phenotypic data. This abstracts technical problems away and lets researchers focus on the science rather than the implementation...
June 15, 2017: Bioinformatics
https://www.readbyqxmd.com/read/28632436/development-of-computer-algorithm-for-editing-of-next-generation-sequencing-metagenome-data
#11
Radhika Khanna, Sangeeta Mittal, Sujata Mohanty
The successful implementation of the advanced sequencing technology, the next generation sequencing (NGS) motivates scientists from diverse fields of biological research especially from genomics and transcriptomics in generating large genomic data set to make their analysis more robust and come up with strong inference. However, exploiting this huge genomic data set becomes a challenge for the molecular biologists. To corroborate this problem, computational software and hardware are being developed in parallel and become an integral part of life science...
June 20, 2017: Journal of Computational Biology: a Journal of Computational Molecular Cell Biology
https://www.readbyqxmd.com/read/28632399/prokaryotic-contig-annotation-pipeline-server-web-application-for-a-prokaryotic-genome-annotation-pipeline-based-on-the-shiny-app-package
#12
Byeonghyeok Park, Min-Jeong Baek, Byoungnam Min, In-Geol Choi
Genome annotation is a primary step in genomic research. To establish a light and portable prokaryotic genome annotation pipeline for use in individual laboratories, we developed a Shiny app package designated as "P-CAPS" (Prokaryotic Contig Annotation Pipeline Server). The package is composed of R and Python scripts that integrate publicly available annotation programs into a server application. P-CAPS is not only a browser-based interactive application but also a distributable Shiny app package that can be installed on any personal computer...
June 20, 2017: Journal of Computational Biology: a Journal of Computational Molecular Cell Biology
https://www.readbyqxmd.com/read/28630948/near-theoretical-gigabit-link-efficiency-for-distributed-data-acquisition-systems
#13
Faisal T Abu-Nimeh, Woon-Seng Choong
Link efficiency, data integrity, and continuity for high-throughput and real-time systems is crucial. Most of these applications require specialized hardware and operating systems as well as extensive tuning in order to achieve high efficiency. Here, we present an implementation of gigabit Ethernet data streaming which can achieve 99.26% link efficiency while maintaining no packet losses. The design and implementation are built on OpenPET, an opensource data acquisition platform for nuclear medical imaging, where (a) a crate hosting multiple OpenPET detector boards uses a User Datagram Protocol over Internet Protocol (UDP/IP) Ethernet soft-core, that is capable of understanding PAUSE frames, to stream data out to a computer workstation; (b) the receiving computer uses Netmap to allow the processing software (i...
March 2017: IEEE transactions on radiation and plasma medical sciences
https://www.readbyqxmd.com/read/28630944/clinvar-data-parsing
#14
Xiaolei Zhang, Eric V Minikel, Anne H O'Donnell-Luria, Daniel G MacArthur, James S Ware, Ben Weisburd
This software repository provides a pipeline for converting raw ClinVar data files into analysis-friendly tab-delimited tables, and also provides these tables for the most recent ClinVar release. Separate tables are generated for genome builds GRCh37 and GRCh38 as well as for mono-allelic variants and complex multi-allelic variants. Additionally, the tables are augmented with allele frequencies from the ExAC and gnomAD datasets as these are often consulted when analyzing ClinVar variants. Overall, this work provides ClinVar data in a format that is easier to work with and can be directly loaded into a variety of popular analysis tools such as R, python pandas, and SQL databases...
2017: Wellcome Open Research
https://www.readbyqxmd.com/read/28630888/gillespy-a-python-package-for-stochastic-model-building-and-simulation
#15
John H Abel, Brian Drawert, Andreas Hellander, Linda R Petzold
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...
September 2016: IEEE Life Sciences Letters
https://www.readbyqxmd.com/read/28630199/genome-wide-analysis-of-the-antimicrobial-peptides-in-python-bivittatus-and-characterization-of-cathelicidins-with-potent-antimicrobial-activity-and-low-cytotoxicity
#16
Dayeong Kim, Nagasundarapandian Soundrarajan, Juyeon Lee, Hye-Sun Cho, Minkyeung Choi, Se-Yeoun Cha, Byeongyong Ahn, Hyoim Jeon, Minh Thong Le, Hyuk Song, Jin-Hoi Kim, Chankyu Park
In this study, we sought to identify novel antimicrobial peptides (AMPs) in Python bivittatus through bioinformatic analyses of publicly available genome information and experimental validation. In our analysis of the python genome, we identified 29 AMP-related candidate sequences. Of these, we selected five cathelicidin-like sequences and subjected them to further in silico analyses. The results showed that these sequences likely have antimicrobial activity. The sequences were named Pb-CATH1-Pb-CATH5 according to their sequence similarity to previously reported snake cathelicidins...
June 19, 2017: Antimicrobial Agents and Chemotherapy
https://www.readbyqxmd.com/read/28629175/the-instrumentation-of-a-microfluidic-analyzer-enabling-the-characterization-of-the-specific-membrane-capacitance-cytoplasm-conductivity-and-instantaneous-young-s-modulus-of-single-cells
#17
Ke Wang, Yang Zhao, Deyong Chen, Chengjun Huang, Beiyuan Fan, Rong Long, Chia-Hsun Hsieh, Junbo Wang, Min-Hsien Wu, Jian Chen
This paper presents the instrumentation of a microfluidic analyzer enabling the characterization of single-cell biophysical properties, which includes seven key components: a microfluidic module, a pressure module, an imaging module, an impedance module, two LabVIEW platforms for instrument operation and raw data processing, respectively, and a Python code for data translation. Under the control of the LabVIEW platform for instrument operation, the pressure module flushes single cells into the microfluidic module with raw biophysical parameters sampled by the imaging and impedance modules and processed by the LabVIEW platform for raw data processing, which were further translated into intrinsic cellular biophysical parameters using the code developed in Python...
June 19, 2017: International Journal of Molecular Sciences
https://www.readbyqxmd.com/read/28628201/designing-drug-response-experiments-and-quantifying-their-results
#18
Marc Hafner, Mario Niepel, Kartik Subramanian, Peter K Sorger
We developed a Python package to help in performing drug-response experiments at medium and high throughput and evaluating sensitivity metrics from the resulting data. In this article, we describe the steps involved in (1) generating files necessary for treating cells with the HP D300 drug dispenser, by pin transfer or by manual pipetting; (2) merging the data generated by high-throughput slide scanners, such as the Perkin Elmer Operetta, with treatment annotations; and (3) analyzing the results to obtain data normalized to untreated controls and sensitivity metrics such as IC50 or GR50 ...
June 19, 2017: Current Protocols in Chemical Biology
https://www.readbyqxmd.com/read/28620282/a-reward-based-behavioral-platform-to-measure-neural-activity-during-head-fixed-behavior
#19
Andrew H Micallef, Naoya Takahashi, Matthew E Larkum, Lucy M Palmer
Understanding the neural computations that contribute to behavior requires recording from neurons while an animal is behaving. This is not an easy task as most subcellular recording techniques require absolute head stability. The Go/No-Go sensory task is a powerful decision-driven task that enables an animal to report a binary decision during head-fixation. Here we discuss how to set up an Ardunio and Python based platform system to control a Go/No-Go sensory behavior paradigm. Using an Arduino micro-controller and Python-based custom written program, a reward can be delivered to the animal depending on the decision reported...
2017: Frontiers in Cellular Neuroscience
https://www.readbyqxmd.com/read/28608704/a-numerical-framework-for-computing-steady-states-of-structured-population-models-and-their-stability
#20
Inom Mirzaev, David M Bortz
Structured population models are a class of general evolution equations which are widely used in the study of biological systems. Many theoretical methods are available for establishing existence and stability of steady states of general evolution equations. However, except for very special cases, finding an analytical form of stationary solutions for evolution equations is a challenging task. In the present paper, we develop a numerical framework for computing approximations to stationary solutions of general evolution equations, which can also be used to produce approximate existence and stability regions for steady states...
August 1, 2017: Mathematical Biosciences and Engineering: MBE
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