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https://www.readbyqxmd.com/read/28453653/the-bologna-annotation-resource-bar-3-0-improving-protein-functional-annotation
#1
Giuseppe Profiti, Pier Luigi Martelli, Rita Casadio
BAR 3.0 updates our server BAR (Bologna Annotation Resource) for predicting protein structural and functional features from sequence. We increase data volume, query capabilities and information conveyed to the user. The core of BAR 3.0 is a graph-based clustering procedure of UniProtKB sequences, following strict pairwise similarity criteria (sequence identity ≥40% with alignment coverage ≥90%). Each cluster contains the available annotation downloaded from UniProtKB, GO, PFAM and PDB. After statistical validation, GO terms and PFAM domains are cluster-specific and annotate new sequences entering the cluster after satisfying similarity constraints...
April 27, 2017: Nucleic Acids Research
https://www.readbyqxmd.com/read/28443037/analyzing-dyadic-sequence-data-research-questions-and-implied-statistical-models
#2
Peter Fuchs, Fridtjof W Nussbeck, Nathalie Meuwly, Guy Bodenmann
The analysis of observational data is often seen as a key approach to understanding dynamics in romantic relationships but also in dyadic systems in general. Statistical models for the analysis of dyadic observational data are not commonly known or applied. In this contribution, selected approaches to dyadic sequence data will be presented with a focus on models that can be applied when sample sizes are of medium size (N = 100 couples or less). Each of the statistical models is motivated by an underlying potential research question, the most important model results are presented and linked to the research question...
2017: Frontiers in Psychology
https://www.readbyqxmd.com/read/28435123/is-having-similar-eye-movement-patterns-during-face-learning-and-recognition-beneficial-for-recognition-performance-evidence-from-hidden-markov-modeling
#3
Tim Chuk, Antoni B Chan, Janet Hsiao
The hidden Markov model (HMM)-based approach for eye movement analysis is able to reflect individual differences in both spatial and temporal aspects of eye movements. Here we used this approach to understand the relationship between eye movements during face learning and recognition, and its association with recognition performance. We discovered holistic (i.e., mainly looking at the face center) and analytic (i.e., specifically looking at the two eyes in addition to the face center) patterns during both learning and recognition...
April 20, 2017: Vision Research
https://www.readbyqxmd.com/read/28432981/hidden-markov-model-and-chapman-kolmogrov-for-protein-structures-prediction-from-images
#4
Md Sarwar Kamal, Linkon Chowdhury, Mohammad Ibrahim Khan, Amira S Ashour, João Manuel R S Tavares, Nilanjan Dey
Protein structure prediction and analysis are more significant for living organs to perfect asses the living organ functionalities. Several protein structure prediction methods use neural network (NN). However, the Hidden Markov model is more interpretable and effective for more biological data analysis compared to the NN. It employs statistical data analysis to enhance the prediction accuracy. The current work proposed a protein prediction approach from protein images based on Hidden Markov Model and Chapman Kolmogrov equation...
April 13, 2017: Computational Biology and Chemistry
https://www.readbyqxmd.com/read/28423795/multivariate-and-longitudinal-health-system-indicators
#5
Guido Antonio Powell, Yu T Luo, Aman Verma, David A Stephens, David L Buckeridge
Within population health information systems, indicators are commonly presented as independent, cross-sectional measures, neglecting the multivariate, longitudinal nature of disease progression, health care use, and profiles of performance. We use administrative claims data of Montreal, Canada to identify patterns across indicators and over time in chronic obstructive pulmonary disease patients. We first cluster regions based on four health service indicators. Our second approach discovers individual-level trajectories based on a hidden Markov model using the same four indicators...
2017: Studies in Health Technology and Informatics
https://www.readbyqxmd.com/read/28423752/a-decision-support-system-for-cardiac-disease-diagnosis-based-on-machine-learning-methods
#6
Arash Gharehbaghi, Maria Lindén, Ankica Babic
This paper proposes a decision support system for screening pediatric cardiac disease in primary healthcare centres relying on the heart sound time series analysis. The proposed system employs our processing method which is based on the hidden Markov model for extracting appropriate information from the time series. The binary output resulting from the method is discriminative for the two classes of time series existing in our databank, corresponding to the children with heart disease and the healthy ones. A total 90 children referrals to a university hospital, constituting of 55 healthy and 35 children with congenital heart disease, were enrolled into the study after obtaining the informed consent...
2017: Studies in Health Technology and Informatics
https://www.readbyqxmd.com/read/28419748/the-known-genetic-potential-for-microbial-communities-to-degrade-organic-phosphorus-is-reduced-in-low-ph-soils
#7
Ian D E A Lidbury, Tandra Fraser, Andrew R J Murphy, David J Scanlan, Gary D Bending, Alexandra M E Jones, Jonathan D Moore, Andrew Goodall, Mark Tibbett, John P Hammond, Elizabeth M H Wellington
In soil, bioavailable inorganic orthophosphate is found at low concentrations and thus limits biological growth. To overcome this phosphorus scarcity, plants and bacteria secrete numerous enzymes, namely acid and alkaline phosphatases, which cleave orthophosphate from various organic phosphorus substrates. Using profile hidden Markov modeling approaches, we investigated the abundance of various non specific phosphatases, both acid and alkaline, in metagenomes retrieved from soils with contrasting pH regimes...
April 16, 2017: MicrobiologyOpen
https://www.readbyqxmd.com/read/28417113/temporal-registration-in-in-utero-volumetric-mri-time-series
#8
Ruizhi Liao, Esra A Turk, Miaomiao Zhang, Jie Luo, P Ellen Grant, Elfar Adalsteinsson, Polina Golland
We present a robust method to correct for motion and deformations in in-utero volumetric MRI time series. Spatio-temporal analysis of dynamic MRI requires robust alignment across time in the presence of substantial and unpredictable motion. We make a Markov assumption on the nature of deformations to take advantage of the temporal structure in the image data. Forward message passing in the corresponding hidden Markov model (HMM) yields an estimation algorithm that only has to account for relatively small motion between consecutive frames...
October 2016: Medical Image Computing and Computer-assisted Intervention: MICCAI ..
https://www.readbyqxmd.com/read/28409487/scanpath-modeling-and-classification-with-hidden-markov-models
#9
Antoine Coutrot, Janet H Hsiao, Antoni B Chan
How people look at visual information reveals fundamental information about them; their interests and their states of mind. Previous studies showed that scanpath, i.e., the sequence of eye movements made by an observer exploring a visual stimulus, can be used to infer observer-related (e.g., task at hand) and stimuli-related (e.g., image semantic category) information. However, eye movements are complex signals and many of these studies rely on limited gaze descriptors and bespoke datasets. Here, we provide a turnkey method for scanpath modeling and classification...
April 13, 2017: Behavior Research Methods
https://www.readbyqxmd.com/read/28408921/phase-segmentation-methods-for-an-automatic-surgical-workflow-analysis
#10
Dinh Tuan Tran, Ryuhei Sakurai, Hirotake Yamazoe, Joo-Ho Lee
In this paper, we present robust methods for automatically segmenting phases in a specified surgical workflow by using latent Dirichlet allocation (LDA) and hidden Markov model (HMM) approaches. More specifically, our goal is to output an appropriate phase label for each given time point of a surgical workflow in an operating room. The fundamental idea behind our work lies in constructing an HMM based on observed values obtained via an LDA topic model covering optical flow motion features of general working contexts, including medical staff, equipment, and materials...
2017: International Journal of Biomedical Imaging
https://www.readbyqxmd.com/read/28405277/a-hidden-markov-movement-model-for-rapidly-identifying-behavioral-states-from-animal-tracks
#11
Kim Whoriskey, Marie Auger-Méthé, Christoffer M Albertsen, Frederick G Whoriskey, Thomas R Binder, Charles C Krueger, Joanna Mills Flemming
Electronic telemetry is frequently used to document animal movement through time. Methods that can identify underlying behaviors driving specific movement patterns can help us understand how and why animals use available space, thereby aiding conservation and management efforts. For aquatic animal tracking data with significant measurement error, a Bayesian state-space model called the first-Difference Correlated Random Walk with Switching (DCRWS) has often been used for this purpose. However, for aquatic animals, highly accurate tracking data are now becoming more common...
April 2017: Ecology and Evolution
https://www.readbyqxmd.com/read/28395282/expanding-genetic-and-functional-diagnoses-of-igf1r-haploinsufficiencies
#12
Paula Ocaranza, Marjorie C Golekoh, Shayne F Andrew, Michael H Guo, Paul Kaplowitz, Howard Saal, Ron G Rosenfeld, Andrew Dauber, Fernando Cassorla, Philippe F Backeljauw, Vivian Hwa
BACKGROUND: The growth-promoting effects of IGF-I is mediated through the IGF-I receptor (IGF1R), a widely expressed cell-surface tyrosine kinase receptor. IGF1R copy number variants (CNV) can cause pre- and postnatal growth restriction or overgrowth. METHODS: Whole exome sequence (WES), chromosomal microarray, and targeted IGF1R gene analyses were performed on 3 unrelated children who share features of small for gestational age, short stature, and elevated serum IGF-I, but otherwise had clinical heterogeneity...
April 10, 2017: Hormone Research in Pædiatrics
https://www.readbyqxmd.com/read/28394163/longitudinal-profiles-of-eudaimonic-well-being-in-asian-american-adolescents
#13
Lisa Kiang, Edward Ip
OBJECTIVE: The current study explores whether a well-known model (i.e., Ryff's, 1989, conceptualization of psychological functioning) can be used to examine patterns of eudaimonic well-being among Asian Americans, who are rarely the focus of systematic investigations in positive psychology. METHOD: Hidden Markov modeling, a form of latent transition analysis, was used to analyze longitudinal data from adolescents (N = 180; 49% female; 75% U.S.-born). RESULTS: After establishing measurement validity, analyses revealed 4 profiles of well-being: Flourishing (consistently high on all well-being dimensions), Functioning (consistently moderate), Hindered (consistently low), and Self-Driven Success (high on most dimensions, but moderate levels of positive relationships)...
April 10, 2017: Cultural Diversity & Ethnic Minority Psychology
https://www.readbyqxmd.com/read/28391203/a-spatial-temporal-method-to-detect-global-influenza-epidemics-using-heterogeneous-data-collected-from-the-internet
#14
Xichuan Zhou, Fan Yang, Yujie Feng, Qin Li, Fang Tang, Shengdong Hu, Zhi Lin, Lei Zhang
The 2009 influenza pandemic teaches us how fast the influenza virus could spread globally within a short period of time. To address the challenge of timely global influenza surveillance, this paper presents a spatial-temporal method that incorporates heterogeneous data collected from the Internet to detect influenza epidemics in real time. Specifically, the influenza morbidity data, the influenza-related Google query data and news data, and the international air transportation data are integrated in a multivariate hidden Markov model, which is designed to describe the intrinsic temporal-geographical correlation of influenza transmission for surveillance purpose...
April 4, 2017: IEEE/ACM Transactions on Computational Biology and Bioinformatics
https://www.readbyqxmd.com/read/28387747/stroboscope-based-synchronization-of-full-frame-ccd-sensors
#15
Liang Shen, Xiaobing Feng, Yuan Zhang, Min Shi, Dengming Zhu, Zhaoqi Wang
The key obstacle to the use of consumer cameras in computer vision and computer graphics applications is the lack of synchronization hardware. We present a stroboscope based synchronization approach for the charge-coupled device (CCD) consumer cameras. The synchronization is realized by first aligning the frames from different video sequences based on the smear dots of the stroboscope, and then matching the sequences using a hidden Markov model. Compared with current synchronized capture equipment, the proposed approach greatly reduces the cost by using inexpensive CCD cameras and one stroboscope...
April 7, 2017: Sensors
https://www.readbyqxmd.com/read/28387224/multi-scale-chromatin-state-annotation-using-a-hierarchical-hidden-markov-model
#16
Eugenio Marco, Wouter Meuleman, Jialiang Huang, Kimberly Glass, Luca Pinello, Jianrong Wang, Manolis Kellis, Guo-Cheng Yuan
Chromatin-state analysis is widely applied in the studies of development and diseases. However, existing methods operate at a single length scale, and therefore cannot distinguish large domains from isolated elements of the same type. To overcome this limitation, we present a hierarchical hidden Markov model, diHMM, to systematically annotate chromatin states at multiple length scales. We apply diHMM to analyse a public ChIP-seq data set. diHMM not only accurately captures nucleosome-level information, but identifies domain-level states that vary in nucleosome-level state composition, spatial distribution and functionality...
April 7, 2017: Nature Communications
https://www.readbyqxmd.com/read/28386434/repeatability-of-circadian-behavioural-variation-revealed-in-free-ranging-marine-fish
#17
Josep Alós, Martina Martorell-Barceló, Andrea Campos-Candela
Repeatable between-individual differences in the behavioural manifestation of underlying circadian rhythms determine chronotypes in humans and terrestrial animals. Here, we have repeatedly measured three circadian behaviours, awakening time, rest onset and rest duration, in the free-ranging pearly razorfish, Xyrithchys novacula, facilitated by acoustic tracking technology and hidden Markov models. In addition, daily travelled distance, a standard measure of daily activity as fish personality trait, was repeatedly assessed using a State-Space Model...
February 2017: Royal Society Open Science
https://www.readbyqxmd.com/read/28379490/dambe6-new-tools-for-microbial-genomics-phylogenetics-and-molecular-evolution
#18
Xuhua Xia
DAMBE is a comprehensive software workbench for data analysis in molecular biology, phylogenetics and evolution. Several important new functions have been added since version 5 of DAMBE: 1) comprehensive genomic profiling of translation initiation efficiency of different genes in different prokaryotic species, 2) a new index of translation elongation (ITE) that takes into account both tRNA-mediated selection and background mutation on codon-anticodon adaptation, 3) a new and accurate phylogenetic approach based on pairwise alignment only, which is useful for highly divergent sequences from which a reliable multiple sequence alignment is difficult to obtain...
April 4, 2017: Journal of Heredity
https://www.readbyqxmd.com/read/28376731/ad-libs-inferring-ancestry-across-hybrid-genomes-using-low-coverage-sequence-data
#19
Nathan K Schaefer, Beth Shapiro, Richard E Green
BACKGROUND: Inferring the ancestry of each region of admixed individuals' genomes is useful in studies ranging from disease gene mapping to speciation genetics. Current methods require high-coverage genotype data and phased reference panels, and are therefore inappropriate for many data sets. We present a software application, AD-LIBS, that uses a hidden Markov model to infer ancestry across hybrid genomes without requiring variant calling or phasing. This approach is useful for non-model organisms and in cases of low-coverage data, such as ancient DNA...
April 4, 2017: BMC Bioinformatics
https://www.readbyqxmd.com/read/28361954/hidden-markov-models-reveal-complexity-in-the-diving-behaviour-of-short-finned-pilot-whales
#20
Nicola J Quick, Saana Isojunno, Dina Sadykova, Matthew Bowers, Douglas P Nowacek, Andrew J Read
Diving behaviour of short-finned pilot whales is often described by two states; deep foraging and shallow, non-foraging dives. However, this simple classification system ignores much of the variation that occurs during subsurface periods. We used multi-state hidden Markov models (HMM) to characterize states of diving behaviour and the transitions between states in short-finned pilot whales. We used three parameters (number of buzzes, maximum dive depth and duration) measured in 259 dives by digital acoustic recording tags (DTAGs) deployed on 20 individual whales off Cape Hatteras, North Carolina, USA...
March 31, 2017: Scientific Reports
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