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https://www.readbyqxmd.com/read/27920675/pyrcca-regularized-kernel-canonical-correlation-analysis-in-python-and-its-applications-to-neuroimaging
#1
Natalia Y Bilenko, Jack L Gallant
In this article we introduce Pyrcca, an open-source Python package for performing canonical correlation analysis (CCA). CCA is a multivariate analysis method for identifying relationships between sets of variables. Pyrcca supports CCA with or without regularization, and with or without linear, polynomial, or Gaussian kernelization. We first use an abstract example to describe Pyrcca functionality. We then demonstrate how Pyrcca can be used to analyze neuroimaging data. Specifically, we use Pyrcca to implement cross-subject comparison in a natural movie functional magnetic resonance imaging (fMRI) experiment by finding a data-driven set of functional response patterns that are similar across individuals...
2016: Frontiers in Neuroinformatics
https://www.readbyqxmd.com/read/27918599/hierarchical-bayesian-inference-for-ion-channel-screening-dose-response-data
#2
Ross H Johnstone, Rémi Bardenet, David J Gavaghan, Gary R Mirams
Dose-response (or 'concentration-effect') relationships commonly occur in biological and pharmacological systems and are well characterised by Hill curves. These curves are described by an equation with two parameters: the inhibitory concentration 50% (IC50); and the Hill coefficient. Typically just the 'best fit' parameter values are reported in the literature. Here we introduce a Python-based software tool, PyHillFit , and describe the underlying Bayesian inference methods that it uses, to infer probability distributions for these parameters as well as the level of experimental observation noise...
2016: Wellcome Open Res
https://www.readbyqxmd.com/read/27907142/ibisa_tools-a-computational-toolkit-for-ion-binding-state-analysis-in-molecular-dynamics-trajectories-of-ion-channels
#3
Kota Kasahara, Kengo Kinoshita
Ion conduction mechanisms of ion channels are a long-standing conundrum. Although the molecular dynamics (MD) method has been extensively used to simulate ion conduction dynamics at the atomic level, analysis and interpretation of MD results are not straightforward due to complexity of the dynamics. In our previous reports, we proposed an analytical method called ion-binding state analysis to scrutinize and summarize ion conduction mechanisms by taking advantage of a variety of analytical protocols, e.g., the complex network analysis, sequence alignment, and hierarchical clustering...
2016: PloS One
https://www.readbyqxmd.com/read/27905885/mefit-merging-and-filtering-tool-for-illumina-paired-end-reads-for-16s-rrna-amplicon-sequencing
#4
Hardik I Parikh, Vishal N Koparde, Steven P Bradley, Gregory A Buck, Nihar U Sheth
BACKGROUND: Recent advances in next-generation sequencing have revolutionized genomic research. 16S rRNA amplicon sequencing using paired-end sequencing on the MiSeq platform from Illumina, Inc., is being used to characterize the composition and dynamics of extremely complex/diverse microbial communities. For this analysis on the Illumina platform, merging and quality filtering of paired-end reads are essential first steps in data analysis to ensure the accuracy and reliability of downstream analysis...
December 1, 2016: BMC Bioinformatics
https://www.readbyqxmd.com/read/27899319/cost-effective-raspberry-pi-based-radio-frequency-identification-tagging-of-mice-suitable-for-automated-in-vivo-imaging
#5
Federico Bolaños, Jeff M LeDue, Timothy H Murphy
BACKGROUND: Automation of animal experimentation improves consistency, reduces potential for error while decreasing animal stress and increasing well-being. Radio frequency identification (RFID) tagging can identify individual mice in group housing environments enabling animal-specific tracking of physiological parameters. NEW METHOD: We describe a simple protocol to radio frequency identification (RFID) tag and detect mice. RFID tags were injected sub-cutaneously after brief isoflurane anesthesia and do not require surgical steps such as suturing or incisions...
November 27, 2016: Journal of Neuroscience Methods
https://www.readbyqxmd.com/read/27896969/reproducible-drug-repurposing-when-similarity-does-not-suffice
#6
Emre Guney
Repurposing existing drugs for new uses has attracted considerable attention over the past years. To identify potential candidates that could be repositioned for a new indication, many studies make use of chemical, target, and side effect similarity between drugs to train classifiers. Despite promising prediction accuracies of these supervised computational models, their use in practice, such as for rare diseases, is hindered by the assumption that there are already known and similar drugs for a given condition of interest...
2016: Pacific Symposium on Biocomputing
https://www.readbyqxmd.com/read/27896026/jicbioimage-a-tool-for-automated-and-reproducible-bioimage-analysis
#7
Tjelvar S G Olsson, Matthew Hartley
There has been steady improvement in methods for capturing bioimages. However analysing these images still remains a challenge. The Python programming language provides a powerful and flexible environment for scientific computation. It has a wide range of supporting libraries for image processing but lacks native support for common bioimage formats, and requires specific code to be written to ensure that suitable audit trails are generated and analyses are reproducible. Here we describe the development of a Python tool that: (1) allows users to quickly view and explore microscopy data; (2) generate reproducible analyses, encoding a complete history of image transformations from raw data to final result; and (3) scale up analyses from initial exploration to high throughput processing pipelines, with a minimal amount of extra effort...
2016: PeerJ
https://www.readbyqxmd.com/read/27887642/rapid-scoring-of-genes-in-microbial-pan-genome-wide-association-studies-with-scoary
#8
Ola Brynildsrud, Jon Bohlin, Lonneke Scheffer, Vegard Eldholm
Genome-wide association studies (GWAS) have become indispensable in human medicine and genomics, but very few have been carried out on bacteria. Here we introduce Scoary, an ultra-fast, easy-to-use, and widely applicable software tool that scores the components of the pan-genome for associations to observed phenotypic traits while accounting for population stratification, with minimal assumptions about evolutionary processes. We call our approach pan-GWAS to distinguish it from traditional, single nucleotide polymorphism (SNP)-based GWAS...
November 25, 2016: Genome Biology
https://www.readbyqxmd.com/read/27884103/amplimethprofiler-a-pipeline-for-the-analysis-of-cpg-methylation-profiles-of-targeted-deep-bisulfite-sequenced-amplicons
#9
Giovanni Scala, Ornella Affinito, Domenico Palumbo, Ermanno Florio, Antonella Monticelli, Gennaro Miele, Lorenzo Chiariotti, Sergio Cocozza
BACKGROUND: CpG sites in an individual molecule may exist in a binary state (methylated or unmethylated) and each individual DNA molecule, containing a certain number of CpGs, is a combination of these states defining an epihaplotype. Classic quantification based approaches to study DNA methylation are intrinsically unable to fully represent the complexity of the underlying methylation substrate. Epihaplotype based approaches, on the other hand, allow methylation profiles of cell populations to be studied at the single molecule level...
November 25, 2016: BMC Bioinformatics
https://www.readbyqxmd.com/read/27876400/a-dynamic-regression-analysis-tool-for-quantitative-assessment-of-bacterial-growth-written-in-python
#10
Jennifer L Hoeflinger, Daniel E Hoeflinger, Michael J Miller
Herein, an open-source method to generate quantitative bacterial growth data from high-throughput microplate assays is described. The bacterial lag time, maximum specific growth rate, doubling time and delta OD are reported. Our method was validated by carbohydrate utilization of lactobacilli, and visual inspection revealed 94% of regressions were deemed excellent.
November 20, 2016: Journal of Microbiological Methods
https://www.readbyqxmd.com/read/27876174/artificial-neural-networks-predicting-head-ct-findings-in-elderly-patients-presenting-with-minor-head-injury-after-a-fall
#11
Michael W Dusenberry, Charles K Brown, Kori L Brewer
OBJECTIVES: To construct an artificial neural network (ANN) model that can predict the presence of acute CT findings with both high sensitivity and high specificity when applied to the population of patients≥age 65years who have incurred minor head injury after a fall. METHODS: An ANN was created in the Python programming language using a population of 514 patients ≥ age 65 years presenting to the ED with minor head injury after a fall. The patient dataset was divided into three parts: 60% for "training", 20% for "cross validation", and 20% for "testing"...
November 3, 2016: American Journal of Emergency Medicine
https://www.readbyqxmd.com/read/27875984/plastid-nucleotide-resolution-analysis-of-next-generation-sequencing-and-genomics-data
#12
Joshua G Dunn, Jonathan S Weissman
BACKGROUND: Next-generation sequencing (NGS) informs many biological questions with unprecedented depth and nucleotide resolution. These assays have created a need for analytical tools that enable users to manipulate data nucleotide-by-nucleotide robustly and easily. Furthermore, because many NGS assays encode information jointly within multiple properties of read alignments - for example, in ribosome profiling, the locations of ribosomes are jointly encoded in alignment coordinates and length - analytical tools are often required to extract the biological meaning from the alignments before analysis...
November 22, 2016: BMC Genomics
https://www.readbyqxmd.com/read/27873420/and-you-try-and-tell-the-medical-students-of-today-that%C3%A2-and-they-won-t-believe-ya
#13
Benjamin H L Harris, David J Wilson
Older clinicians typically engage in reflections on their own early careers and indeed whichever generation of clinician you talk to, their medical school and early career experiences were more challenging than the last. We draw on inspiration from Monty Python and specifically the Four Yorkshiremen to illustrate this point. However, as we strive to lay the foundations of learning that avoids the adage 'whatever doesn't kill you, makes you stronger', we must remember that medics are competitive… even at complaining...
December 2016: Medical Education
https://www.readbyqxmd.com/read/27863339/classifying-injury-narratives-of-large-administrative-databases-for-surveillance-a-practical-approach-combining-machine-learning-ensembles-and-human-review
#14
Helen R Marucci-Wellman, Helen L Corns, Mark R Lehto
Injury narratives are now available real time and include useful information for injury surveillance and prevention. However, manual classification of the cause or events leading to injury found in large batches of narratives, such as workers compensation claims databases, can be prohibitive. In this study we compare the utility of four machine learning algorithms (Naïve Bayes, Single word and Bi-gram models, Support Vector Machine and Logistic Regression) for classifying narratives into Bureau of Labor Statistics Occupational Injury and Illness event leading to injury classifications for a large workers compensation database...
November 15, 2016: Accident; Analysis and Prevention
https://www.readbyqxmd.com/read/27860095/a-statistical-framework-for-neuroimaging-data-analysis-based-on-mutual-information-estimated-via-a-gaussian-copula
#15
Robin A A Ince, Bruno L Giordano, Christoph Kayser, Guillaume A Rousselet, Joachim Gross, Philippe G Schyns
We begin by reviewing the statistical framework of information theory as applicable to neuroimaging data analysis. A major factor hindering wider adoption of this framework in neuroimaging is the difficulty of estimating information theoretic quantities in practice. We present a novel estimation technique that combines the statistical theory of copulas with the closed form solution for the entropy of Gaussian variables. This results in a general, computationally efficient, flexible, and robust multivariate statistical framework that provides effect sizes on a common meaningful scale, allows for unified treatment of discrete, continuous, unidimensional and multidimensional variables, and enables direct comparisons of representations from behavioral and brain responses across any recording modality...
November 17, 2016: Human Brain Mapping
https://www.readbyqxmd.com/read/27852256/health-conditions-of-inmates-in-italy
#16
Fabio Voller, Caterina Silvestri, Gianrocco Martino, Eleonora Fanti, Giorgio Bazzerla, Fabio Ferrari, Marco Grignani, Sandro Libianchi, Antonio Maria Pagano, Franco Scarpa, Cristina Stasi, Teresa Di Fiandra
BACKGROUND: Several studies have shown that prison is characterized by a higher prevalence of chronic diseases than unconfined settings. The aim of this study was to describe the characteristics and health of inmates, focusing on internal diseases. METHODS: We designed a specific clinical record using the Python programming language. We considered all of the diagnoses according to the ICD-9-CM. RESULTS: Of a total of 17,086 inmates, 15,751 were enrolled in our study (M = 14,835; F = 869), corresponding to 92...
November 16, 2016: BMC Public Health
https://www.readbyqxmd.com/read/27851906/magpy-a-python-toolbox-for-controlling-magstim-transcranial-magnetic-stimulators
#17
Nicolas A McNair
BACKGROUND: 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. NEW METHOD: This manuscript presents the MagPy toolbox, a Python software package that provides full control over Magstim stimulators via the serial port...
November 13, 2016: Journal of Neuroscience Methods
https://www.readbyqxmd.com/read/27847299/an-mrspec-database-query-and-visualization-engine-with-applications-as-a-clinical-diagnostic-and-research-tool
#18
Filip Miscevic, Justin Foong, Benjamin Schmitt, Susan Blaser, Michael Brudno, Andreas Schulze
PURPOSE: Proton magnetic resonance spectroscopy (MRspec), one of the very few techniques for in vivo assessment of neuro-metabolic profiles, is often complicated by lack of standard population norms and paucity of computational tools. METHODS: 7035 scans and clinical information from 4430 pediatric patients were collected from 2008 to 2014. Scans were conducted using a 1.5T (n=3664) or 3T scanner (n=3371), and with either a long (144ms, n=5559) or short echo time (35ms, n=1476)...
November 9, 2016: Molecular Genetics and Metabolism
https://www.readbyqxmd.com/read/27837108/characterization-and-transcriptomic-analysis-of-porcine-blood-conventional-and-plasmacytoid-dendritic-cells-reveals-striking-species-specific-differences
#19
Gael Auray, Irene Keller, Sylvie Python, Markus Gerber, Remy Bruggmann, Nicolas Ruggli, Artur Summerfield
Porcine dendritic cells (DCs) are relatively well characterized, but a clear-cut identification of all DC subsets combined with full transcriptional profiling was lacking, preventing an unbiased insight into the functional specializations of DC subsets. Using a large panel of Abs in multicolor flow cytometry, cell sorting, and RNA sequencing we identified and characterized the porcine equivalent of conventional DCs (cDC) 1 and cDC2 as well as plasmacytoid DCs (pDCs) in the peripheral blood of pigs. We demonstrate that cDC1 are CD135(+)CD14(-)CD172a(low)CADM1(+)wCD11R1(+) cells, cDC2 are CD135(+)CD14(-)CD172a(+)CADM1(+)CD115(+)wCD11R1(+)CD1(+) cells and pDCs are CD4(+)CD135(+)CD172a(+)CD123(+)CD303(+) cells...
December 15, 2016: Journal of Immunology: Official Journal of the American Association of Immunologists
https://www.readbyqxmd.com/read/27835690/vidjil-a-web-platform-for-analysis-of-high-throughput-repertoire-sequencing
#20
Marc Duez, Mathieu Giraud, Ryan Herbert, Tatiana Rocher, Mikaël Salson, Florian Thonier
BACKGROUND: The B and T lymphocytes are white blood cells playing a key role in the adaptive immunity. A part of their DNA, called the V(D)J recombinations, is specific to each lymphocyte, and enables recognition of specific antigenes. Today, with new sequencing techniques, one can get billions of DNA sequences from these regions. With dedicated Repertoire Sequencing (RepSeq) methods, it is now possible to picture population of lymphocytes, and to monitor more accurately the immune response as well as pathologies such as leukemia...
2016: PloS One
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