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Hidden markov

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https://www.readbyqxmd.com/read/28937668/complete-protein-protein-association-kinetics-in-atomic-detail-revealed-by-molecular-dynamics-simulations-and-markov-modelling
#1
Nuria Plattner, Stefan Doerr, Gianni De Fabritiis, Frank Noé
Protein-protein association is fundamental to many life processes. However, a microscopic model describing the structures and kinetics during association and dissociation is lacking on account of the long lifetimes of associated states, which have prevented efficient sampling by direct molecular dynamics (MD) simulations. Here we demonstrate protein-protein association and dissociation in atomistic resolution for the ribonuclease barnase and its inhibitor barstar by combining adaptive high-throughput MD simulations and hidden Markov modelling...
October 2017: Nature Chemistry
https://www.readbyqxmd.com/read/28923019/evolutionary-history-and-functional-divergence-of-the-cytochrome-p450-gene-superfamily-between-arabidopsis-thaliana-and-brassica-species-uncover-effects-of-whole-genome-and-tandem-duplications
#2
Jingyin Yu, Sadia Tehrim, Linhai Wang, Komivi Dossa, Xiurong Zhang, Tao Ke, Boshou Liao
BACKGROUND: The cytochrome P450 monooxygenase (P450) superfamily is involved in the biosynthesis of various primary and secondary metabolites. However, little is known about the effects of whole genome duplication (WGD) and tandem duplication (TD) events on the evolutionary history and functional divergence of P450s in Brassica after splitting from a common ancestor with Arabidopsis thaliana. RESULTS: Using Hidden Markov Model search and manual curation, we detected that Brassica species have nearly 1...
September 18, 2017: BMC Genomics
https://www.readbyqxmd.com/read/28920931/single-molecule-fret-reveals-the-energy-landscape-of-the-full-length-sam-i-riboswitch
#3
Christoph Manz, Andrei Yu Kobitski, Ayan Samanta, Bettina G Keller, Andres Jäschke, G Ulrich Nienhaus
S-adenosyl-L-methionine (SAM) ligand binding induces major structural changes in SAM-I riboswitches, through which gene expression is regulated via transcription termination. Little is known about the conformations and motions governing the function of the full-length Bacillus subtilis yitJ SAM-I riboswitch. Therefore, we have explored its conformational energy landscape as a function of Mg(2+) and SAM ligand concentrations using single-molecule Förster resonance energy transfer (smFRET) microscopy and hidden Markov modeling analysis...
September 18, 2017: Nature Chemical Biology
https://www.readbyqxmd.com/read/28916180/interpreting-temporal-fluctuations-in-resting-state-functional-connectivity-mri
#4
REVIEW
Raphaël Liégeois, Timothy O Laumann, Abraham Z Snyder, Juan Zhou, B T Thomas Yeo
Resting-state functional connectivity is a powerful tool for studying human functional brain networks. Temporal fluctuations in functional connectivity, i.e., dynamic functional connectivity (dFC), are thought to reflect dynamic changes in brain organization and non-stationary switching of discrete brain states. However, recent studies have suggested that dFC might be attributed to sampling variability of static FC. Despite this controversy, a detailed exposition of stationarity and statistical testing of dFC is lacking in the literature...
September 12, 2017: NeuroImage
https://www.readbyqxmd.com/read/28878807/distribution-and-functionality-of-copy-number-variation-across-european-cattle-populations
#5
Maulik Upadhyay, Vinicus H da Silva, Hendrik-Jan Megens, Marleen H P W Visker, Paolo Ajmone-Marsan, Valentin A Bâlteanu, Susana Dunner, Jose F Garcia, Catarina Ginja, Juha Kantanen, Martien A M Groenen, Richard P M A Crooijmans
Copy number variation (CNV), which is characterized by large-scale losses or gains of DNA fragments, contributes significantly to genetic and phenotypic variation. Assessing CNV across different European cattle populations might reveal genetic changes responsible for phenotypic differences, which have accumulated throughout the domestication history of cattle as consequences of evolutionary forces that act upon them. To explore pattern of CNVs across European cattle, we genotyped 149 individuals, that represent different European regions, using the Illumina Bovine HD Genotyping array...
2017: Frontiers in Genetics
https://www.readbyqxmd.com/read/28878041/characteristics-of-29-novel-atypical-solute-carriers-of-major-facilitator-superfamily-type-evolutionary-conservation-predicted-structure-and-neuronal-co-expression
#6
Emelie Perland, Sonchita Bagchi, Axel Klaesson, Robert Fredriksson
Solute carriers (SLCs) are vital as they are responsible for a major part of the molecular transport over lipid bilayers. At present, there are 430 identified SLCs, of which 28 are called atypical SLCs of major facilitator superfamily (MFS) type. These are MFSD1, 2A, 2B, 3, 4A, 4B, 5, 6, 6 L, 7, 8, 9, 10, 11, 12, 13A, 14A and 14B; SV2A, SV2B and SV2C; SVOP and SVOPL; SPNS1, SPNS2 and SPNS3; and UNC93A and UNC93B1. We studied their fundamental properties, and we also included CLN3, an atypical SLC not yet belonging to any protein family (Pfam) clan, because its involvement in the same neuronal degenerative disorders as MFSD8...
September 2017: Open Biology
https://www.readbyqxmd.com/read/28873799/human-behavior-drift-detection-in-a-smart-home-environment
#7
Andrea Masciadri, Anna A Trofimova, Matteo Matteucci, Fabio Salice
The proposed system aims at elderly people independent living by providing an early indicator of habits changes which might be relevant for a diagnosis of diseases. It relies on Hidden Markov Model to describe the behavior observing sensors data, while Likelihood Ratio Test gives the variation within different time periods.
2017: Studies in Health Technology and Informatics
https://www.readbyqxmd.com/read/28873409/fine-scale-mapping-of-genomic-introgressions-within-the-drosophila-yakuba-clade
#8
David A Turissini, Daniel R Matute
The process of speciation involves populations diverging over time until they are genetically and reproductively isolated. Hybridization between nascent species was long thought to directly oppose speciation. However, the amount of interspecific genetic exchange (introgression) mediated by hybridization remains largely unknown, although recent progress in genome sequencing has made measuring introgression more tractable. A natural place to look for individuals with admixed ancestry (indicative of introgression) is in regions where species co-occur...
September 2017: PLoS Genetics
https://www.readbyqxmd.com/read/28869811/hidden-markov-model-analysis-reveals-the-advantage-of-analytic-eye-movement-patterns-in-face-recognition-across-cultures
#9
Tim Chuk, Kate Crookes, William G Hayward, Antoni B Chan, Janet H Hsiao
It remains controversial whether culture modulates eye movement behavior in face recognition. Inconsistent results have been reported regarding whether cultural differences in eye movement patterns exist, whether these differences affect recognition performance, and whether participants use similar eye movement patterns when viewing faces from different ethnicities. These inconsistencies may be due to substantial individual differences in eye movement patterns within a cultural group. Here we addressed this issue by conducting individual-level eye movement data analysis using hidden Markov models (HMMs)...
September 1, 2017: Cognition
https://www.readbyqxmd.com/read/28867956/meggasense-the-metagenome-genome-annotated-sequence-natural-language-search-engine-a-platform-for-%C3%A2-the-construction-of-sequence-data-warehouses
#10
Ranko Gacesa, Jurica Zucko, Solveig K Petursdottir, Elisabet Eik Gudmundsdottir, Olafur H Fridjonsson, Janko Diminic, Paul F Long, John Cullum, Daslav Hranueli, Gudmundur O Hreggvidsson, Antonio Starcevic
The MEGGASENSE platform constructs relational databases of DNA or protein sequences. The default functional analysis uses 14 106 hidden Markov model (HMM) profiles based on sequences in the KEGG database. The Solr search engine allows sophisticated queries and a BLAST search function is also incorporated. These standard capabilities were used to generate the SCATT database from the predicted proteome of Streptomyces cattleya. The implementation of a specialised metagenome database (AMYLOMICS) for bioprospecting of carbohydrate-modifying enzymes is described...
June 2017: Food Technology and Biotechnology
https://www.readbyqxmd.com/read/28861695/pharmacometrics-models-with-hidden-markovian-dynamics
#11
Marc Lavielle
The aim of this paper is to provide an overview of pharmacometric models that involve some latent process with Markovian dynamics. Such models include hidden Markov models which may be useful for describing the dynamics of a disease state that jumps from one state to another at discrete times. On the contrary, diffusion models are continuous-time and continuous-state Markov models that are relevant for modelling non observed phenomena that fluctuate continuously and randomly over time. We show that an extension of these models to mixed effects models is straightforward in a population context...
August 31, 2017: Journal of Pharmacokinetics and Pharmacodynamics
https://www.readbyqxmd.com/read/28858823/asynchronous-dissipative-control-for-fuzzy-markov-jump-systems
#12
Zheng-Guang Wu, Shanling Dong, Hongye Su, Chuandong Li
The problem of asynchronous dissipative control is investigated for Takagi-Sugeno fuzzy systems with Markov jump in this paper. Hidden Markov model is introduced to represent the nonsynchronization between the designed controller and the original system. By the fuzzy-basis-dependent and mode-dependent Lyapunov function, a sufficient condition is achieved such that the resulting closed-loop system is stochastically stable with a strictly (Q, S, R)-α-dissipative performance. The controller parameter is derived by applying MATLAB to solve a set of linear matrix inequalities...
August 25, 2017: IEEE Transactions on Cybernetics
https://www.readbyqxmd.com/read/28855724/uncovering-the-cognitive-processes-underlying-mental-rotation-an-eye-movement-study
#13
Jiguo Xue, Chunyong Li, Cheng Quan, Yiming Lu, Jingwei Yue, Chenggang Zhang
Mental rotation is an important paradigm for spatial ability. Mental-rotation tasks are assumed to involve five or three sequential cognitive-processing states, though this has not been demonstrated experimentally. Here, we investigated how processing states alternate during mental-rotation tasks. Inference was carried out using an advanced statistical modelling and data-driven approach - a discriminative hidden Markov model (dHMM) trained using eye-movement data obtained from an experiment consisting of two different strategies: (I) mentally rotate the right-side figure to be aligned with the left-side figure and (II) mentally rotate the left-side figure to be aligned with the right-side figure...
August 30, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28854235/brain-mr-image-segmentation-based-on-an-improved-active-contour-model
#14
Xiangrui Meng, Wenya Gu, Yunjie Chen, Jianwei Zhang
It is often a difficult task to accurately segment brain magnetic resonance (MR) images with intensity in-homogeneity and noise. This paper introduces a novel level set method for simultaneous brain MR image segmentation and intensity inhomogeneity correction. To reduce the effect of noise, novel anisotropic spatial information, which can preserve more details of edges and corners, is proposed by incorporating the inner relationships among the neighbor pixels. Then the proposed energy function uses the multivariate Student's t-distribution to fit the distribution of the intensities of each tissue...
2017: PloS One
https://www.readbyqxmd.com/read/28852755/intelligent-identification-of-multi-level-nanopore-signatures-for-accurate-detection-of-cancer-biomarkers
#15
Jian-Hua Zhang, Xiu-Ling Liu, Zheng-Li Hu, Yi-Lun Ying, Yi-Tao Long
To achieve accurate detection of cancer biomarkers with nanopore sensors, the precise recognition of multi-level current blockage events (signature) is a pivotal problem. However, it remains rather a challenge to identify the multi-level current blockages of target biomarkers in nanopore experiments, especially for the nanopore analysis of serum samples. In this work, we combined a modified DBSCAN (Density-Based Spatial Clustering of Applications with Noise) algorithm with the Viterbi training algorithm of the hidden Markov model (HMM) to achieve intelligent retrieval of multi-level current signatures from microRNA in serum samples...
August 30, 2017: Chemical Communications: Chem Comm
https://www.readbyqxmd.com/read/28845485/emphysema-quantification-on-cardiac-ct-scans-using-hidden-markov-measure-field-model-the-mesa-lung-study
#16
Jie Yang, Elsa D Angelini, Pallavi P Balte, Eric A Hoffman, Colin O Wu, Bharath A Venkatesh, R Graham Barr, Andrew F Laine
Cardiac computed tomography (CT) scans include approximately 2/3 of the lung and can be obtained with low radiation exposure. Large cohorts of population-based research studies reported high correlations of emphysema quantification between full-lung (FL) and cardiac CT scans, using thresholding-based measurements. This work extends a hidden Markov measure field (HMMF) model-based segmentation method for automated emphysema quantification on cardiac CT scans. We show that the HMMF-based method, when compared with several types of thresholding, provides more reproducible emphysema segmentation on repeated cardiac scans, and more consistent measurements between longitudinal cardiac and FL scans from a diverse pool of scanner types and thousands of subjects with ten thousands of scans...
October 2016: Medical Image Computing and Computer-assisted Intervention: MICCAI ..
https://www.readbyqxmd.com/read/28842677/gschx19-3-a-member-of-cation-h-exchanger-superfamily-from-wild-soybean-contributes-to-high-salinity-and-carbonate-alkaline-tolerance
#17
Bowei Jia, Mingzhe Sun, Huizi DuanMu, Xiaodong Ding, Beidong Liu, Yanming Zhu, Xiaoli Sun
Cation/H(+) exchangers (CHX) are characterized to be involved in plant growth, development and stress responses. Although soybean genome sequencing has been completed, the CHX family hasn't yet been systematically analyzed, especially in wild soybean. Here, through Hidden Markov Model search against Glycine soja proteome, 34 GsCHXs were identified and phylogenetically clustered into five groups. Members within each group showed high conservation in motif architecture. Interestingly, according to our previous RNA-seq data, only Group IVa members exhibited highly induced expression under carbonate alkaline stress...
August 25, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28841506/parkinsonian-rest-tremor-can-be-detected-accurately-based-on-neuronal-oscillations-recorded-from-the-subthalamic-nucleus
#18
J Hirschmann, J M Schoffelen, A Schnitzler, M A J van Gerven
OBJECTIVE: To investigate the possibility of tremor detection based on deep brain activity. METHODS: We re-analyzed recordings of local field potentials (LFPs) from the subthalamic nucleus in 10 PD patients (12 body sides) with spontaneously fluctuating rest tremor. Power in several frequency bands was estimated and used as input to Hidden Markov Models (HMMs) which classified short data segments as either tremor-free rest or rest tremor. HMMs were compared to direct threshold application to individual power features...
August 9, 2017: Clinical Neurophysiology: Official Journal of the International Federation of Clinical Neurophysiology
https://www.readbyqxmd.com/read/28840939/viruses-in-cancers-among-the-immunosuppressed
#19
Laila Sara Arroyo Mühr, Zurab Bzhalava, Maria Hortlund, Camilla Lagheden, Sara Nordqvist Kleppe, Davit Bzhalava, Emilie Hultin, Joakim Dillner
Most cancer forms known to be caused by viruses are increased among the immunosuppressed, but several cancer forms without established viral etiology are also increased, notably non-melanoma skin carcinoma (NMSC). We followed all 13429 solid organ transplantation patients in Sweden for cancer occurrence after transplantation. We requested these tumor specimens and sequenced the first 89 specimens received (62 NMSCs, 27 other cancers). The sequences were analyzed for viruses based on two bioinformatics algorithms (paracel-blast (sensitive for detection of known viruses) and hidden Markov model (HMM; sensitive for distantly related viruses))...
August 25, 2017: International Journal of Cancer. Journal International du Cancer
https://www.readbyqxmd.com/read/28837580/driving-style-recognition-method-using-braking-characteristics-based-on-hidden-markov-model
#20
Chao Deng, Chaozhong Wu, Nengchao Lyu, Zhen Huang
Since the advantage of hidden Markov model in dealing with time series data and for the sake of identifying driving style, three driving style (aggressive, moderate and mild) are modeled reasonably through hidden Markov model based on driver braking characteristics to achieve efficient driving style. Firstly, braking impulse and the maximum braking unit area of vacuum booster within a certain time are collected from braking operation, and then general braking and emergency braking characteristics are extracted to code the braking characteristics...
2017: PloS One
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