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Hidden markov

Fur-Hsing Wen, Jen-Shi Chen, Wen-Chi Chou, Chia-Hsun Hsieh, Wen-Cheng Chang, Ming-Mo Hou, Siew Tzuh Tang
CONTEXT/OBJECTIVES: Our study addressed important knowledge gaps about trajectories of distinct conjoint symptom-functional states, i.e., patterns for different levels of combined symptom distress and functional impairment, over cancer patients' last year and their ability to predict survival. METHODS: We identified distinct symptom-functional states and explored their changes over 317 terminally ill cancer patients' last year by a transition model using hidden Markov modeling...
March 12, 2018: Journal of Pain and Symptom Management
Neethu Mariam Joy, S Umesh
Assistive speech-based technologies can improve the quality of life for people affected with dysarthria, a motor speech disorder. In this paper, we explore multiple ways to improve Gaussian mixture model and deep neural network (DNN) based hidden Markov model (HMM) automatic speech recognition systems for TORGO dysarthric speech database. This work shows significant improvements over the previous attempts in building such systems in TORGO. We trained speaker-specific acoustic models by tuning various acoustic model parameters, using speaker normalized cepstral features and building complex DNN-HMM models with dropout and sequence-discrimination strategies...
March 2018: IEEE Transactions on Neural Systems and Rehabilitation Engineering
Surendra Neupane, Qin Ma, Febina M Mathew, Adam J Varenhorst, Ethan J Andersen, Madhav P Nepal
Disease-resistant genes (R genes) encode proteins that are involved in protecting plants from their pathogens and pests. Availability of complete genome sequences from soybean and common bean allowed us to perform a genome-wide identification and analysis of the Toll interleukin-1 receptor-like nucleotide-binding site leucine-rich repeat (TNL) proteins. Hidden Markov model (HMM) profiling of all protein sequences resulted in the identification of 117 and 77 regular TNL genes in soybean and common bean, respectively...
March 2, 2018: Biochemical Genetics
Youngjoo Suh, Hoirin Kim
The histogram equalization approach is an efficient feature normalization technique for noise robust automatic speech recognition. However, it suffers from performance degradation when some fundamental conditions are not satisfied in the test environment. To remedy these limitations of the original histogram equalization methods, class-based histogram equalization approach has been proposed. Although this approach showed substantial performance improvement under noise environments, it still suffers from performance degradation due to the overfitting problem when test data are insufficient...
February 2018: Journal of the Acoustical Society of America
Dickson Kinyanyi, George Obiero, George F O Obiero, Peris Amwayi, Stephen Mwaniki, Mark Wamalwa
African swine fever virus (ASFV) is the etiological agent of ASF, a fatal hemorrhagic fever that affects domestic pigs. There is currently no vaccine against ASFV, making it a significant threat to the pork industry. The ASFV genome sequence has been published; however, about half of ASFV open reading frames have not been characterized in terms of their structure and function despite being essential for our understanding of ASFV pathogenicity. The present study reports the three-dimensional structure and function of uncharacterized protein, pB263R (NP_042780...
2018: PeerJ
James S Steele, Keith Bush, Zachary N Stowe, George A James, Sonet Smitherman, Clint D Kilts, Josh Cisler
Numerous data demonstrate that distracting emotional stimuli cause behavioral slowing (i.e. emotional conflict) and that behavior dynamically adapts to such distractors. However, the cognitive and neural mechanisms that mediate these behavioral findings are poorly understood. Several theoretical models have been developed that attempt to explain these phenomena, but these models have not been directly tested on human behavior nor compared. A potential tool to overcome this limitation is Hidden Markov Modeling (HMM), which is a computational approach to modeling indirectly observed systems...
2018: PloS One
Timothy P Bilton, Matthew R Schofield, Michael A Black, David Chagné, Phillip L Wilcox, Ken G Dodds
Next generation sequencing is an efficient method that allows for substantially more markers than previous technologies, providing opportunities for building high density genetic linkage maps, which facilitate the development of non-model species' genomic assemblies and the investigation of their genes. However, constructing genetic maps using data generated via high-throughput sequencing technology (e.g., genotyping-by-sequencing) is complicated by the presence of sequencing errors and genotyping errors resulting from missing parental alleles due to low sequencing depth...
February 27, 2018: Genetics
Paul S Albert
Prediction of preterm birth as well as characterizing the etiological factors affecting both the recurrence and incidence of preterm birth (defined as gestational age at birth ≤ 37 wk) are important problems in obstetrics. The National Institute of Child Health and Human Development (NICHD) consecutive pregnancy study recently examined this question by collecting data on a cohort of women with at least 2 pregnancies over a fixed time interval. Unfortunately, measurement error due to the dating of conception may induce sizable error in computing gestational age at birth...
February 21, 2018: Statistics in Medicine
Eric Duchaud, Tatiana Rochat, Christophe Habib, Paul Barbier, Valentin Loux, Cyprien Guérin, Inger Dalsgaard, Lone Madsen, Hanne Nilsen, Krister Sundell, Tom Wiklund, Nicole Strepparava, Thomas Wahli, Greta Caburlotto, Amedeo Manfrin, Gregory D Wiens, Erina Fujiwara-Nagata, Ruben Avendaño-Herrera, Jean-François Bernardet, Pierre Nicolas
Flavobacterium psychrophilum , the etiological agent of rainbow trout fry syndrome and bacterial cold-water disease in salmonid fish, is currently one of the main bacterial pathogens hampering the productivity of salmonid farming worldwide. In this study, the genomic diversity of the F. psychrophilum species is analyzed using a set of 41 genomes, including 30 newly sequenced isolates. These were selected on the basis of available MLST data with the two-fold objective of maximizing the coverage of the species diversity and of allowing a focus on the main clonal complex (CC-ST10) infecting farmed rainbow trout ( Oncorhynchus mykiss ) worldwide...
2018: Frontiers in Microbiology
Markus Götz, Philipp Wortmann, Sonja Schmid, Thorsten Hugel
Single-molecule Förster resonance energy transfer (smFRET) has become a widely used biophysical technique to study the dynamics of biomolecules. For many molecular machines in a cell proteins have to act together with interaction partners in a functional cycle to fulfill their task. The extension of two-color to multi-color smFRET makes it possible to simultaneously probe more than one interaction or conformational change. This not only adds a new dimension to smFRET experiments but it also offers the unique possibility to directly study the sequence of events and to detect correlated interactions when using an immobilized sample and a total internal reflection fluorescence microscope (TIRFM)...
January 30, 2018: Journal of Visualized Experiments: JoVE
Qi Huang, Dwayne Cohen, Sandra Komarzynski, Xiao-Mei Li, Pasquale Innominato, Francis Lévi, Bärbel Finkenstädt
Wearable computing devices allow collection of densely sampled real-time information on movement enabling researchers and medical experts to obtain objective and non-obtrusive records of actual activity of a subject in the real world over many days. Our interest here is motivated by the use of activity data for evaluating and monitoring the circadian rhythmicity of subjects for research in chronobiology and chronotherapeutic healthcare. In order to translate the information from such high-volume data arising we propose the use of a Markov modelling approach which (i) naturally captures the notable square wave form observed in activity data along with heterogeneous ultradian variances over the circadian cycle of human activity, (ii) thresholds activity into different states in a probabilistic way while respecting time dependence and (iii) gives rise to circadian rhythm parameter estimates, based on probabilities of transitions between rest and activity, that are interpretable and of interest to circadian research...
February 2018: Journal of the Royal Society, Interface
Fuming Fang, Takahiro Shinozaki
Human-computer interface systems whose input is based on eye movements can serve as a means of communication for patients with locked-in syndrome. Eye-writing is one such system; users can input characters by moving their eyes to follow the lines of the strokes corresponding to characters. Although this input method makes it easy for patients to get started because of their familiarity with handwriting, existing eye-writing systems suffer from slow input rates because they require a pause between input characters to simplify the automatic recognition process...
2018: PloS One
Thao Thi Nguyen, Hyun-Hee Lee, Inmyoung Park, Young-Su Seo
Type VI secretion system (T6SS) has been discovered in a variety of gram-negative bacteria as a versatile weapon to stimulate the killing of eukaryotic cells or prokaryotic competitors. Type VI secretion effectors (T6SEs) are well known as key virulence factors for important pathogenic bacteria. In many Burkholderia species, T6SS has evolved as the most complicated secretion pathway with distinguished types to translocate diverse T6SEs, suggesting their essential roles in this genus. Here we attempted to detect and characterize T6SSs and potential T6SEs in target genomes of plant-associated and environmental Burkholderia species based on computational analyses...
February 2018: Plant Pathology Journal
Mariam Lami, Harsimrat Singh, James H Dilley, Hajra Ashraf, Matthew Edmondon, Felipe Orihuela-Espina, Jonathan Hoare, Ara Darzi, Mikael H Sodergren
BACKGROUND:  The adenoma detection rate (ADR) is an important quality indicator in colonoscopy. The aim of this study was to evaluate the changes in visual gaze patterns (VGPs) with increasing polyp detection rate (PDR), a surrogate marker of ADR. METHODS:  18 endoscopists participated in the study. VGPs were measured using eye-tracking technology during the withdrawal phase of colonoscopy. VGPs were characterized using two analyses - screen and anatomy. Eye-tracking parameters were used to characterize performance, which was further substantiated using hidden Markov model (HMM) analysis...
February 7, 2018: Endoscopy
Yi-Han Lin, María Lucas, Timothy R Evans, Guillermo Abascal-Palacios, Alexandra G Doms, Nicole A Beauchene, Adriana L Rojas, Aitor Hierro, Matthias P Machner
The eukaryotic ubiquitylation machinery catalyzes the covalent attachment of the small protein modifier ubiquitin to cellular target proteins in order to alter their fate. Microbial pathogens exploit this post-translational modification process by encoding molecular mimics of E3 ubiquitin ligases, eukaryotic enzymes that catalyze the final step in the ubiquitylation cascade. Here, we show that the Legionella pneumophila effector protein RavN belongs to a growing class of bacterial proteins that mimic host cell E3 ligases to exploit the ubiquitylation pathway...
February 7, 2018: PLoS Pathogens
Xiaole Yin, Xiao-Tao Jiang, Benli Chai, Liguan Li, Ying Yang, James R Cole, James M Tiedje, Tong Zhang
Motivation: Much global attention has been paid to antibiotic resistance in monitoring its emergence, accumulation and dissemination. For rapid characterization and quantification of antibiotic resistance genes (ARGs) in metagenomic datasets, an online analysis pipeline, ARGs-OAP has been developed consisting of a database termed Structured Antibiotic Resistance Genes (the SARG) with a hierarchical structure (ARGs type-subtype-reference sequence). Results: The new release of the database, termed SARG version 2...
February 2, 2018: Bioinformatics
Imane Saif, Yassine Kasmi, Karam Allali, Moulay Mustapha Ennaji
The epigenetics methylation of cytosine is the most common epigenetic form in DNA sequences. It is highly concentrated in the promoter regions of the genes, leading to an inactivation of tumor suppressors regardless of their initial function. In this work, we aim to identify the highly methylated regions; the cytosine-phosphate-guanine (CpG) island located on the promoters and/or the first exon gene known for their key roles in the cell cycle, hence the need to study gene-gene interactions. The Frommer and hidden Markov model algorithms are used as computational methods to identify CpG islands with specificity and sensitivity up to 76% and 80%, respectively...
February 2, 2018: Gene
Kirubin Pillay, Anneleen Dereymaeker, Katrien Jansen, Gunnar Naulaers, Sabine Van Huffel, Maarten De Vos
<i>Objective</i>. We develop a method for automated four-state sleep classification of preterm and term-born babies at term-age of 38-40 weeks postmenstrual age (the age since the last menstrual cycle of the mother) using multichannel Electroencephalogram (EEG) recordings. At this critical age, EEG differentiates from broader Quiet Sleep (QS) and Active Sleep (AS) stages to four, more complex states, and the quality and timing of this differentiation is indicative of the level of brain development...
January 30, 2018: Journal of Neural Engineering
Joel Smith, Graham Coop, Matthew Stephens, John Novembre
The haplotypes of a beneficial allele carry information about its history that can shed light on its age and the putative cause for its increase in frequency. Specifically, the signature of an allele's age is contained in the pattern of variation that mutation and recombination impose on its haplotypic background. We provide a method to exploit this pattern and infer the time to the common ancestor of a positively selected allele following a rapid increase in frequency. We do so using a hidden Markov model which leverages the length distribution of the shared ancestral haplotype, the accumulation of derived mutations on the ancestral background, and the surrounding background haplotype diversity...
January 18, 2018: Molecular Biology and Evolution
Maurizio Righini, Antony Lee, Cristhian Cañari-Chumpitaz, Troy Lionberger, Ronen Gabizon, Yves Coello, Ignacio Tinoco, Carlos Bustamante
In recent years, highly stable optical tweezers systems have enabled the characterization of the dynamics of molecular motors at very high resolution. However, the motion of many motors with angstrom-scale dynamics cannot be consistently resolved due to poor signal-to-noise ratio. Using an acousto-optic deflector to generate a "time-shared" dual-optical trap, we decreased low-frequency noise by more than one order of magnitude compared with conventional dual-trap optical tweezers. Using this instrument, we implemented a protocol that synthesizes single base-pair trajectories, which are used to test a Large State Space Hidden Markov Model algorithm to recover their individual steps...
January 19, 2018: Proceedings of the National Academy of Sciences of the United States of America
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