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https://www.readbyqxmd.com/read/28092026/hidden-markov-models-for-protein-domain-homology-identification-and-analysis
#1
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
#2
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
#3
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
#4
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
#5
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...
December 30, 2016: European Biophysics Journal: EBJ
https://www.readbyqxmd.com/read/28011233/septic-shock-prediction-for-icu-patients-via-coupled-hmm-walking-on-sequential-contrast-patterns
#6
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
#7
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
#8
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
#9
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
#10
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
#11
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
#12
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
https://www.readbyqxmd.com/read/27916922/a-context-recognition-aided-pdr-localization-method-based-on-the-hidden-markov-model
#13
Yi Lu, Dongyan Wei, Qifeng Lai, Wen Li, Hong Yuan
Indoor positioning has recently become an important field of interest because global navigation satellite systems (GNSS) are usually unavailable in indoor environments. Pedestrian dead reckoning (PDR) is a promising localization technique for indoor environments since it can be implemented on widely used smartphones equipped with low cost inertial sensors. However, the PDR localization severely suffers from the accumulation of positioning errors, and other external calibration sources should be used. In this paper, a context-recognition-aided PDR localization model is proposed to calibrate PDR...
November 30, 2016: Sensors
https://www.readbyqxmd.com/read/27899595/panther-version-11-expanded-annotation-data-from-gene-ontology-and-reactome-pathways-and-data-analysis-tool-enhancements
#14
Huaiyu Mi, Xiaosong Huang, Anushya Muruganujan, Haiming Tang, Caitlin Mills, Diane Kang, Paul D Thomas
The PANTHER database (Protein ANalysis THrough Evolutionary Relationships, http://pantherdb.org) contains comprehensive information on the evolution and function of protein-coding genes from 104 completely sequenced genomes. PANTHER software tools allow users to classify new protein sequences, and to analyze gene lists obtained from large-scale genomics experiments. In the past year, major improvements include a large expansion of classification information available in PANTHER, as well as significant enhancements to the analysis tools...
January 4, 2017: Nucleic Acids Research
https://www.readbyqxmd.com/read/27898803/identification-and-expression-profiling-of-the-lectin-gene-superfamily-in-mulberry
#15
Bushra Saeed, Vinay K Baranwal, Paramjit Khurana
Lectins are a diverse group of ubiquitously present, highly specific sugar-binding proteins. Members of this large gene family have been assigned broad biological functions from defense to acting as storage proteins. Despite possessing several interesting characteristics, their functions remain essentially undefined. Mulberry ( spp.) known for its medicinal benefits is also a rich source of lectins. Using an exhaustive hidden Markov model (HMM)-based search, we identified the lectin gene complement in C.K. Schneid with around 197 members...
July 2016: Plant Genome
https://www.readbyqxmd.com/read/27895627/distribution-and-classification-of-serine-%C3%AE-lactamases-in-brazilian-hospital-sewage-and-other-environmental-metagenomes-deposited-in-public-databases
#16
Adriana M Fróes, Fábio F da Mota, Rafael R C Cuadrat, Alberto M R Dávila
β-lactam is the most used antibiotic class in the clinical area and it acts on blocking the bacteria cell wall synthesis, causing cell death. However, some bacteria have evolved resistance to these antibiotics mainly due the production of enzymes known as β-lactamases. Hospital sewage is an important source of dispersion of multidrug-resistant bacteria in rivers and oceans. In this work, we used next-generation DNA sequencing to explore the diversity and dissemination of serine β-lactamases in two hospital sewage from Rio de Janeiro, Brazil (South Zone, SZ and North Zone, NZ), presenting different profiles, and to compare them with public environmental data available...
2016: Frontiers in Microbiology
https://www.readbyqxmd.com/read/27875548/accelerating-information-retrieval-from-profile-hidden-markov-model-databases
#17
Ahmad Tamimi, Yaqoub Ashhab, Hashem Tamimi
Profile Hidden Markov Model (Profile-HMM) is an efficient statistical approach to represent protein families. Currently, several databases maintain valuable protein sequence information as profile-HMMs. There is an increasing interest to improve the efficiency of searching Profile-HMM databases to detect sequence-profile or profile-profile homology. However, most efforts to enhance searching efficiency have been focusing on improving the alignment algorithms. Although the performance of these algorithms is fairly acceptable, the growing size of these databases, as well as the increasing demand for using batch query searching approach, are strong motivations that call for further enhancement of information retrieval from profile-HMM databases...
2016: PloS One
https://www.readbyqxmd.com/read/27857059/hypomethylation-reduced-the-aggressive-potential-of-human-malignant-mesothelioma-cells
#18
N-Y Kim, M-C Kim, Y Kim
Epigenetic modifications have been implicated in the development of therapeutic resistance responsible for the poor prognosis of human malignant mesothelioma (HMM). To find a potential way to overcome this therapeutic resistance, this study investigated the anticancer effects of a DNA demethylating agent, 5-Aza-2'-Deoxycytidine (5-aza-dC), on HMM cells. The 5-aza-dC exhibited minimal detrimental effects on cell survival. However, treatment with 5-aza-dC significantly altered the biological characteristics associated with malignancy, such as cell migration and cell interaction, colony-forming capacity, and invasiveness...
December 2016: Cancer Gene Therapy
https://www.readbyqxmd.com/read/27851936/hidden-markov-modeling-with-detailed-balance-and-its-application-to-single-protein-folding
#19
Yongli Zhang, Junyi Jiao, Aleksander A Rebane
Hidden Markov modeling (HMM) has revolutionized kinetic studies of macromolecules. However, results from HMM often violate detailed balance when applied to the transitions under thermodynamic equilibrium, and the consequence of such violation has not been well understood. Here, to our knowledge, we developed a new HMM method that satisfies detailed balance (HMM-DB) and optimizes model parameters by gradient search. We used free energy of stable and transition states as independent fitting parameters and considered both normal and skew normal distributions of the measurement noise...
November 15, 2016: Biophysical Journal
https://www.readbyqxmd.com/read/27845655/a-hidden-markov-model-for-3d-catheter-tip-tracking-with-2d-x-ray-catheterization-sequence-and-3d-rotational-angiography
#20
Pierre Ambrosini, Ihor Smal, Daniel Ruijters, Wiro Niessen, Adriaan Moelker, Theo van Walsum
In minimal invasive image guided catheterization procedures, physicians require information of the catheter position with respect to the patient's vasculature. However, in fluoroscopic images, visualization of the vasculature requires toxic contrast agent. Static vasculature roadmapping, which can reduce the usage of iodine contrast, is hampered by the breathing motion in abdominal catheterization. In this paper, we propose a method to track the catheter tip inside the patient's 3D vessel tree using intra-operative single-plane 2D X-ray image sequences and a peri-operative 3D rotational angiography (3DRA)...
November 7, 2016: IEEE Transactions on Medical Imaging
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