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https://www.readbyqxmd.com/read/28178571/genome-wide-identification-and-analysis-of-biotic-and-abiotic-stress-regulation-of-small-heat-shock-protein-hsp20-family-genes-in-bread-wheat
#1
Senthilkumar K Muthusamy, Monika Dalal, Viswanathan Chinnusamy, Kailash C Bansal
Small Heat Shock Proteins (sHSPs)/HSP20 are molecular chaperones that protect plants by preventing protein aggregation during abiotic stress conditions, especially heat stress. Due to global climate change, high temperature is emerging as a major threat to wheat productivity. Thus, the identification of HSP20 and analysis of HSP transcriptional regulation under different abiotic stresses in wheat would help in understanding the role of these proteins in abiotic stress tolerance. We used sequences of known rice and Arabidopsis HSP20 HMM profiles as queries against publicly available wheat genome and wheat full length cDNA databases (TriFLDB) to identify the respective orthologues from wheat...
January 22, 2017: Journal of Plant Physiology
https://www.readbyqxmd.com/read/28155710/predicting-morfs-in-protein-sequences-using-hmm-profiles
#2
Ronesh Sharma, Shiu Kumar, Tatsuhiko Tsunoda, Ashwini Patil, Alok Sharma
BACKGROUND: Intrinsically Disordered Proteins (IDPs) lack an ordered three-dimensional structure and are enriched in various biological processes. The Molecular Recognition Features (MoRFs) are functional regions within IDPs that undergo a disorder-to-order transition on binding to a partner protein. Identifying MoRFs in IDPs using computational methods is a challenging task. METHODS: In this study, we introduce hidden Markov model (HMM) profiles to accurately identify the location of MoRFs in disordered protein sequences...
December 22, 2016: BMC Bioinformatics
https://www.readbyqxmd.com/read/28149522/incorporating-periodic-variability-in-hidden-markov-models-for-animal-movement
#3
Michael Li, Benjamin M Bolker
BACKGROUND: Clustering time-series data into discrete groups can improve prediction and provide insight into the nature of underlying, unobservable states of the system. However, temporal variation in probabilities of group occupancy, or the rates at which individuals move between groups, can obscure such signals. We use finite mixture and hidden Markov models (HMMs), two standard clustering techniques, to model long-term hourly movement data from Florida panthers (Puma concolor coryi)...
2017: Movement Ecology
https://www.readbyqxmd.com/read/28135296/genome-wide-association-of-copy-number-polymorphisms-and-kidney-function
#4
Man Li, Jacob Carey, Stephen Cristiano, Katalin Susztak, Josef Coresh, Eric Boerwinkle, Wen Hong L Kao, Terri H Beaty, Anna Köttgen, Robert B Scharpf
Genome-wide association studies (GWAS) using single nucleotide polymorphisms (SNPs) have identified more than 50 loci associated with estimated glomerular filtration rate (eGFR), a measure of kidney function. However, significant SNPs account for a small proportion of eGFR variability. Other forms of genetic variation have not been comprehensively evaluated for association with eGFR. In this study, we assess whether changes in germline DNA copy number are associated with GFR estimated from serum creatinine, eGFRcrea...
2017: PloS One
https://www.readbyqxmd.com/read/28122610/fast-and-simple-protein-alignment-guided-assembly-of-orthologous-gene-families-from-microbiome-sequencing-reads
#5
Daniel H Huson, Rewati Tappu, Adam L Bazinet, Chao Xie, Michael P Cummings, Kay Nieselt, Rohan Williams
BACKGROUND: Microbiome sequencing projects typically collect tens of millions of short reads per sample. Depending on the goals of the project, the short reads can either be subjected to direct sequence analysis or be assembled into longer contigs. The assembly of whole genomes from metagenomic sequencing reads is a very difficult problem. However, for some questions, only specific genes of interest need to be assembled. This is then a gene-centric assembly where the goal is to assemble reads into contigs for a family of orthologous genes...
January 25, 2017: Microbiome
https://www.readbyqxmd.com/read/28113739/one-shot-learning-of-human-activity-with-an-map-adapted-gmm-and-simplex-hmm
#6
Mario Rodriguez, Carlos Orrite, Carlos Medrano, Dimitrios Makris
This paper presents a novel activity class representation using a single sequence for training. The contribution of this representation lays on the ability to train an one-shot learning recognition system, useful in new scenarios where capturing and labeling sequences is expensive or impractical. The method uses a universal background model of local descriptors obtained from source databases available on-line and adapts it to a new sequence in the target scenario through a maximum a posteriori adaptation. Each activity sample is encoded in a sequence of normalized bag of features and modeled by a new hidden Markov model formulation, where the expectation-maximization algorithm for training is modified to deal with observations consisting in vectors in a unit simplex...
May 10, 2016: IEEE Transactions on Cybernetics
https://www.readbyqxmd.com/read/28113239/intsim-an-integrated-simulator-of-next-generation-sequencing-data
#7
Xiguo Yuan, Junying Zhang, Liying Yang
OBJECTIVE: Next-generation sequencing data has been widely used for DNA variant discovery and tumor study through computational tools. Effective simulation of such data with many realistic features is very necessary for testing existing tools and guiding the development of new tools. METHODS: We present an integrated simulation system, IntSIM, to simulate common DNA variants and to generate sequencing reads for mixture genomes. IntSIM has three novel features in comparison with other simulation programs: (1) it is able to simulate both germline and somatic variants in the same sequence, (2) it deals with tumor purity so as to generate reads corresponding to heterogeneous genomes and also produce tumor-normal matched samples, (3) it simulates correlations among SNPs, among CNVs/CNAs based on HMM models trained from real sequencing genomes, and can simulates broad and focal CNV/CNA events...
April 29, 2016: IEEE Transactions on Bio-medical Engineering
https://www.readbyqxmd.com/read/28113222/gait-event-based-synchronization-method-for-gait-rehabilitation-robots-via-a-bio-inspired-adaptive-oscillator
#8
Gong Chen, Peng Qi, Zhao Guo, Haoyong Yu
In the field of gait rehabilitation robotics, achieving human-robot synchronization is very important. In this paper, a novel human-robot synchronization method using gait event information is proposed. This method includes two steps. Firstly, seven gait events in one gait cycle are detected in real time with a hidden Markov model (HMM); secondly, an adaptive oscillator is utilized to estimate the stride percentage of human gait using any one of the gait events. Synchronous reference trajectories for the robot are then generated with the estimated stride percentage...
August 30, 2016: IEEE Transactions on Bio-medical Engineering
https://www.readbyqxmd.com/read/28092026/hidden-markov-models-for-protein-domain-homology-identification-and-analysis
#9
Karl Jablonowski
Protein domain identification and analysis are cornerstones of modern proteomics. The tools available to protein domain researchers avail a variety of approaches to understanding large protein domain families. Hidden Markov Models (HMM) form the basis for identifying and categorizing evolutionarily linked protein domains. Here I describe the use of HMM models for predicting and identifying Src Homology 2 (SH2) domains within the proteome.
2017: Methods in Molecular Biology
https://www.readbyqxmd.com/read/28086791/identification-of-functional-enolase-genes-of-the-silkworm-bombyx-mori-from-public-databases-with-a-combination-of-dry-and-wet-bench-processes
#10
Akira Kikuchi, Takeru Nakazato, Katsuhiko Ito, Yosui Nojima, Takeshi Yokoyama, Kikuo Iwabuchi, Hidemasa Bono, Atsushi Toyoda, Asao Fujiyama, Ryoichi Sato, Hiroko Tabunoki
BACKGROUND: Various insect species have been added to genomic databases over the years. Thus, researchers can easily obtain online genomic information on invertebrates and insects. However, many incorrectly annotated genes are included in these databases, which can prevent the correct interpretation of subsequent functional analyses. To address this problem, we used a combination of dry and wet bench processes to select functional genes from public databases. RESULTS: Enolase is an important glycolytic enzyme in all organisms...
January 13, 2017: BMC Genomics
https://www.readbyqxmd.com/read/28065836/learning-effective-connectivity-from-fmri-using-autoregressive-hidden-markov-model-with-missing-data
#11
Shilpa Dang, Santanu Chaudhury, Brejesh Lall, Prasun Kumar Roy
BACKGROUND: Effective connectivity (EC) analysis of neuronal groups using fMRI delivers insights about functional-integration. However, fMRI signal has low-temporal resolution due to down-sampling and indirectly measures underlying neuronal activity. NEW METHOD: The aim is to address above issues for more reliable EC estimates. This paper proposes use of autoregressive hidden Markov model with missing data (AR-HMM-md) in dynamically multi-linked (DML) framework for learning EC using multiple fMRI time series...
January 5, 2017: Journal of Neuroscience Methods
https://www.readbyqxmd.com/read/28060703/a-dataset-and-benchmarks-for-segmentation-and-recognition-of-gestures-in-robotic-surgery
#12
Narges Ahmidi, Lingling Tao, Shahin Sefati, Yixin Gao, Colin Lea, Benjamin Bejar, Luca Zappella, Sanjeev Khudanpur, Rene Vidal, Gregory D Hager
OBJECTIVE: State-of-the-art techniques for surgical data analysis report promising results for automated skill assessment and action recognition. The contributions of many of these techniques, however, are limited to study-specific data and validation metrics, making assessment of progress across the field extremely challenging. METHODS: In this paper, we address two major problems for surgical data analysis: (1) lack of uniform shared datasets and benchmarks and (2) lack of consistent validation processes...
January 4, 2017: IEEE Transactions on Bio-medical Engineering
https://www.readbyqxmd.com/read/28039513/actomyosin-interaction-at-low-atp-concentrations
#13
Manuela Maffei, Emanuela Longa, Antonio Sabatini, Alberto Vacca, Stefano Iotti
In vitro motility assay (IVMA) experiments were performed to analyze the movement of actin filaments sliding on a pavement of myosin molecules at different [ATP] and [ADP]. In standard experimental conditions at [ATP] = 2 mM, about 80% of the actin filaments move in unloaded conditions with a constant velocity. However, a fraction of at least 20% static actin filaments is always present. The accepted explanation is the occurrence of damaged "rigor"-like myosin heads that do not undergo the normal ATP-dependent cycling motion...
March 2017: European Biophysics Journal: EBJ
https://www.readbyqxmd.com/read/28011233/septic-shock-prediction-for-icu-patients-via-coupled-hmm-walking-on-sequential-contrast-patterns
#14
Shameek Ghosh, Jinyan Li, Longbing Cao, Kotagiri Ramamohanarao
BACKGROUND AND OBJECTIVE: Critical care patient events like sepsis or septic shock in intensive care units (ICUs) are dangerous complications which can cause multiple organ failures and eventual death. Preventive prediction of such events will allow clinicians to stage effective interventions for averting these critical complications. METHODS: It is widely understood that physiological conditions of patients on variables such as blood pressure and heart rate are suggestive to gradual changes over a certain period of time, prior to the occurrence of a septic shock...
December 20, 2016: Journal of Biomedical Informatics
https://www.readbyqxmd.com/read/28009838/modeling-driver-behavior-near-intersections-in-hidden-markov-model
#15
Juan Li, Qinglian He, Hang Zhou, Yunlin Guan, Wei Dai
Intersections are one of the major locations where safety is a big concern to drivers. Inappropriate driver behaviors in response to frequent changes when approaching intersections often lead to intersection-related crashes or collisions. Thus to better understand driver behaviors at intersections, especially in the dilemma zone, a Hidden Markov Model (HMM) is utilized in this study. With the discrete data processing, the observed dynamic data of vehicles are used for the inference of the Hidden Markov Model...
December 21, 2016: International Journal of Environmental Research and Public Health
https://www.readbyqxmd.com/read/28000118/smart-sensor-based-motion-detection-system-for-hand-movement-training-in-open-surgery
#16
Xinyao Sun, Simon Byrns, Irene Cheng, Bin Zheng, Anup Basu
We introduce a smart sensor-based motion detection technique for objective measurement and assessment of surgical dexterity among users at different experience levels. The goal is to allow trainees to evaluate their performance based on a reference model shared through communication technology, e.g., the Internet, without the physical presence of an evaluating surgeon. While in the current implementation we used a Leap Motion Controller to obtain motion data for analysis, our technique can be applied to motion data captured by other smart sensors, e...
February 2017: Journal of Medical Systems
https://www.readbyqxmd.com/read/27992342/representation-learning-based-assistive-system-for-persons-with-dysarthria
#17
S Chandrakala, N Rajeswari
An assistive system for persons with vocal impairment due to dysarthria converts dysarthric speech to normal speech or text. Because of the articulatory deficits, dysarthric speech recognition needs a robust learning technique. Representation learning is significant for complex tasks such as dysarthric speech recognition. We focus on robust representation for dysarthric speech recognition that involves recognizing sequential patterns of varying length utterances. We propose a hybrid framework that uses a generative learning based data representation with a discriminative learning based classifier...
December 13, 2016: IEEE Transactions on Neural Systems and Rehabilitation Engineering
https://www.readbyqxmd.com/read/27965558/visualization-of-whole-night-sleep-eeg-from-2-channel-mobile-recording-device-reveals-distinct-deep-sleep-stages-with-differential-electrodermal-activity
#18
Julie A Onton, Dae Y Kang, Todd P Coleman
Brain activity during sleep is a powerful marker of overall health, but sleep lab testing is prohibitively expensive and only indicated for major sleep disorders. This report demonstrates that mobile 2-channel in-home electroencephalogram (EEG) recording devices provided sufficient information to detect and visualize sleep EEG. Displaying whole-night sleep EEG in a spectral display allowed for quick assessment of general sleep stability, cycle lengths, stage lengths, dominant frequencies and other indices of sleep quality...
2016: Frontiers in Human Neuroscience
https://www.readbyqxmd.com/read/27959921/temporal-dynamics-and-developmental-maturation-of-salience-default-and-central-executive-network-interactions-revealed-by-variational-bayes-hidden-markov-modeling
#19
Srikanth Ryali, Kaustubh Supekar, Tianwen Chen, John Kochalka, Weidong Cai, Jonathan Nicholas, Aarthi Padmanabhan, Vinod Menon
Little is currently known about dynamic brain networks involved in high-level cognition and their ontological basis. Here we develop a novel Variational Bayesian Hidden Markov Model (VB-HMM) to investigate dynamic temporal properties of interactions between salience (SN), default mode (DMN), and central executive (CEN) networks-three brain systems that play a critical role in human cognition. In contrast to conventional models, VB-HMM revealed multiple short-lived states characterized by rapid switching and transient connectivity between SN, CEN, and DMN...
December 2016: PLoS Computational Biology
https://www.readbyqxmd.com/read/27923999/query-seeded-iterative-sequence-similarity-searching-improves-selectivity-5-20-fold
#20
William R Pearson, Weizhong Li, Rodrigo Lopez
Iterative similarity search programs, like psiblast, jackhmmer, and psisearch, are much more sensitive than pairwise similarity search methods like blast and ssearch because they build a position specific scoring model (a PSSM or HMM) that captures the pattern of sequence conservation characteristic to a protein family. But models are subject to contamination; once an unrelated sequence has been added to the model, homologs of the unrelated sequence will also produce high scores, and the model can diverge from the original protein family...
December 6, 2016: Nucleic Acids Research
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