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Hidden markov

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https://www.readbyqxmd.com/read/28734092/disentangling-the-role-of-seed-bank-and-dispersal-in-plant-metapopulation-dynamics-using-patch-occupancy-surveys
#1
F Manna, R Pradel, R Choquet, H Fréville, P-O Cheptou
In plants, the presence of a seed bank challenges the application of classical metapopulation models to above-ground presence surveys; ignoring seed bank leads to overestimated extinction and colonization rates. In this article, we explore the possibility to detect seed bank using hidden Markov models in the analysis of above-ground patch occupancy surveys of an annual plant with limited dispersal. Patch occupancy data were generated by simulation under two metapopulation sizes (N = 200 and N = 1000 patches) and different metapopulation scenarios, each scenario being a combination of the presence/absence of a one-year seed bank and the presence/absence of limited dispersal in a circular 1-dimension configuration of patches...
July 22, 2017: Ecology
https://www.readbyqxmd.com/read/28726751/an-adaptive-feature-learning-model-for-sequential-radar-high-resolution-range-profile-recognition
#2
Xuan Peng, Xunzhang Gao, Yifan Zhang, Xiang Li
This paper proposes a new feature learning method for the recognition of radar high resolution range profile (HRRP) sequences. HRRPs from a period of continuous changing aspect angles are jointly modeled and discriminated by a single model named the discriminative infinite restricted Boltzmann machine (Dis-iRBM). Compared with the commonly used hidden Markov model (HMM)-based recognition method for HRRP sequences, which requires efficient preprocessing of the HRRP signal, the proposed method is an end-to-end method of which the input is the raw HRRP sequence, and the output is the label of the target...
July 20, 2017: Sensors
https://www.readbyqxmd.com/read/28720084/sequence-based-identification-of-inositol-monophosphatase-like-histidinol-phosphate-phosphatases-hisn-in-corynebacterium-glutamicum-actinobacteria-and-beyond
#3
Robert Kasimir Kulis-Horn, Christian Rückert, Jörn Kalinowski, Marcus Persicke
BACKGROUND: The eighth step of L-histidine biosynthesis is carried out by an enzyme called histidinol-phosphate phosphatase (HolPase). Three unrelated HolPase families are known so far. Two of them are well studied: HAD-type HolPases known from Gammaproteobacteria like Escherichia coli or Salmonella enterica and PHP-type HolPases known from yeast and Firmicutes like Bacillus subtilis. However, the third family of HolPases, the inositol monophosphatase (IMPase)-like HolPases, present in Actinobacteria like Corynebacterium glutamicum (HisN) and plants, are poorly characterized...
July 18, 2017: BMC Microbiology
https://www.readbyqxmd.com/read/28715501/diversity-and-distribution-of-nuclease-bacteriocins-in-bacterial-genomes-revealed-using-hidden-markov-models
#4
Connor Sharp, James Bray, Nicholas G Housden, Martin C J Maiden, Colin Kleanthous
Bacteria exploit an arsenal of antimicrobial peptides and proteins to compete with each other. Three main competition systems have been described: type six secretion systems (T6SS); contact dependent inhibition (CDI); and bacteriocins. Unlike T6SS and CDI systems, bacteriocins do not require contact between bacteria but are diffusible toxins released into the environment. Identified almost a century ago, our understanding of bacteriocin distribution and prevalence in bacterial populations remains poor. In the case of protein bacteriocins, this is because of high levels of sequence diversity and difficulties in distinguishing their killing domains from those of other competition systems...
July 17, 2017: PLoS Computational Biology
https://www.readbyqxmd.com/read/28709213/when-memory-pays-discord-in-hidden-markov-models
#5
Emma Lathouwers, John Bechhoefer
When is keeping a memory of observations worthwhile? We use hidden Markov models to look at phase transitions that emerge when comparing state estimates in systems with discrete states and noisy observations. We infer the underlying state of the hidden Markov models from the observations in two ways: through naive observations, which take into account only the current observation, and through Bayesian filtering, which takes the history of observations into account. Defining a discord order parameter to distinguish between the different state estimates, we explore hidden Markov models with various numbers of states and symbols and varying transition-matrix symmetry...
June 2017: Physical Review. E
https://www.readbyqxmd.com/read/28696334/recent-advances-in-heart-sound-analysis
#6
Gari D Clifford, Chengyu Liu, Benjamin E Moody, José Millet Roig, Samuel E Schmidt, Qiao Li, Ikaro Silva, Roger G Mark
Heart sounds have been widely studied and have been demonstrated to have value for detecting pathologies in clinical applications. Over the last few decades, the use of heart sound signals has become increasingly uncommon and its practice in modern medicine somewhat diminished, although research into automated analysis has continued. Unfortunately, a comparative analyses of algorithms in the literature have been hindered by the lack of high-quality, rigorously validated, and standardized open databases of heart sound recordings...
July 11, 2017: Physiological Measurement
https://www.readbyqxmd.com/read/28682786/application-of-computational-methods-in-planaria-research-a-current-update
#7
Shyamasree Ghosh
Planaria is a member of the Phylum Platyhelminthes including flatworms. Planarians possess the unique ability of regeneration from adult stem cells or neoblasts and finds importance as a model organism for regeneration and developmental studies. Although research is being actively carried out globally through conventional methods to understand the process of regeneration from neoblasts, biology of development, neurobiology and immunology of Planaria, there are many thought provoking questions related to stem cell plasticity, and uniqueness of regenerative potential in Planarians amongst other members of Phylum Platyhelminthes...
July 6, 2017: Journal of Integrative Bioinformatics
https://www.readbyqxmd.com/read/28678716/learning-deep-generative-models-with-doubly-stochastic-gradient-mcmc
#8
Chao Du, Jun Zhu, Bo Zhang
Deep generative models (DGMs), which are often organized in a hierarchical manner, provide a principled framework of capturing the underlying causal factors of data. Recent work on DGMs focussed on the development of efficient and scalable variational inference methods that learn a single model under some mean-field or parameterization assumptions. However, little work has been done on extending Markov chain Monte Carlo (MCMC) methods to Bayesian DGMs, which enjoy many advantages compared with variational methods...
June 28, 2017: IEEE Transactions on Neural Networks and Learning Systems
https://www.readbyqxmd.com/read/28673234/genomic-variability-in-mexican-chicken-population-using-copy-number-variants
#9
E Gorla, M C Cozzi, S I Román-Ponce, F J Ruiz López, V E Vega-Murillo, S Cerolini, A Bagnato, M G Strillacci
BACKGROUND: Copy number variations are genome polymorphism that influence phenotypic variation and are an important source of genetic variation in populations. The aim of this study was to investigate genetic variability in the Mexican Creole chicken population using CNVs. RESULTS: The Hidden Markov Model of the PennCNV software detected a total of 1924 CNVs in the genome of the 256 samples processed with Axiom® Genome-Wide Chicken Genotyping Array (Affymetrix)...
July 3, 2017: BMC Genetics
https://www.readbyqxmd.com/read/28667599/identification-of-protein-secretion-systems-in-bacterial-genomes-using-macsyfinder
#10
Sophie S Abby, Eduardo P C Rocha
Protein secretion systems are complex molecular machineries that translocate proteins through the outer membrane, and sometimes through multiple other barriers. They have evolved by co-option of components from other envelope-associated cellular machineries, making them sometimes difficult to identify and discriminate. Here, we describe how to identify protein secretion systems in bacterial genomes using MacSyFinder. This flexible computational tool uses the knowledge stemming from experimental studies to identify homologous systems in genome data...
2017: Methods in Molecular Biology
https://www.readbyqxmd.com/read/28664514/comparative-and-bioinformatics-analyses-of-pathogenic-bacterial-secretomes-identified-by-mass-spectrometry-in-burkholderia-species
#11
Thao Thi Nguyen, Tae-Soo Chon, Jaehan Kim, Young-Su Seo, Muyoung Heo
Secreted proteins (secretomes) play crucial roles during bacterial pathogenesis in both plant and human hosts. The identification and characterization of secretomes in the two plant pathogens Burkholderia glumae BGR1 and B. gladioli BSR3, which cause diseases in rice such as seedling blight, panicle blight, and grain rot, are important steps to not only understand the disease-causing mechanisms but also find remedies for the diseases. Here, we identified two datasets of secretomes in B. glumae BGR1 and B. gladioli BSR3, which consist of 118 and 111 proteins, respectively, using mass spectrometry approach and literature curation...
July 2017: Journal of Microbiology / the Microbiological Society of Korea
https://www.readbyqxmd.com/read/28649598/an-analysis-of-two-common-reference-points-for-eegs
#12
S López, A Gross, S Yang, M Golmohammadi, I Obeid, J Picone
Clinical electroencephalographic (EEG) data varies significantly depending on a number of operational conditions (e.g., the type and placement of electrodes, the type of electrical grounding used). This investigation explores the statistical differences present in two different referential montages: Linked Ear (LE) and Averaged Reference (AR). Each of these accounts for approximately 45% of the data in the TUH EEG Corpus. In this study, we explore the impact this variability has on machine learning performance...
December 2016: ... IEEE Signal Processing in Medicine and Biology Symposium. IEEE Signal Processing in Medicine and Biology Symposium
https://www.readbyqxmd.com/read/28645261/genome-wide-analysis-of-udp-glycosyltransferase-super-family-in-brassica-rapa-and-brassica-oleracea-reveals-its-evolutionary-history-and-functional-characterization
#13
Jingyin Yu, Fan Hu, Komivi Dossa, Zhaokai Wang, Tao Ke
BACKGROUND: Glycosyltransferases comprise a highly divergent and polyphyletic multigene family that is involved in widespread modification of plant secondary metabolites in a process called glycosylation. According to conserved domains identified in their amino acid sequences, these glycosyltransferases can be classified into a single UDP-glycosyltransferase (UGT) 1 superfamily. RESULTS: We performed genome-wide comparative analysis of UGT genes to trace evolutionary history in algae, bryophytes, pteridophytes, and angiosperms; then, we further investigated the expansion mechanisms and function characterization of UGT gene families in Brassica rapa and Brassica oleracea...
June 23, 2017: BMC Genomics
https://www.readbyqxmd.com/read/28641078/signal-dimensionality-and-the-emergence-of-combinatorial-structure
#14
Hannah Little, Kerem Eryılmaz, Bart de Boer
In language, a small number of meaningless building blocks can be combined into an unlimited set of meaningful utterances. This is known as combinatorial structure. One hypothesis for the initial emergence of combinatorial structure in language is that recombining elements of signals solves the problem of overcrowding in a signal space. Another hypothesis is that iconicity may impede the emergence of combinatorial structure. However, how these two hypotheses relate to each other is not often discussed. In this paper, we explore how signal space dimensionality relates to both overcrowding in the signal space and iconicity...
June 19, 2017: Cognition
https://www.readbyqxmd.com/read/28630425/reconstructing-cell-cycle-pseudo-time-series-via-single-cell-transcriptome-data
#15
Zehua Liu, Huazhe Lou, Kaikun Xie, Hao Wang, Ning Chen, Oscar M Aparicio, Michael Q Zhang, Rui Jiang, Ting Chen
Single-cell mRNA sequencing, which permits whole transcriptional profiling of individual cells, has been widely applied to study growth and development of tissues and tumors. Resolving cell cycle for such groups of cells is significant, but may not be adequately achieved by commonly used approaches. Here we develop a traveling salesman problem and hidden Markov model-based computational method named reCAT, to recover cell cycle along time for unsynchronized single-cell transcriptome data. We independently test reCAT for accuracy and reliability using several data sets...
June 19, 2017: Nature Communications
https://www.readbyqxmd.com/read/28625764/genome-wide-identification-and-expression-profiling-of-eil-gene-family-in-woody-plant-representative-poplar-populus-trichocarpa
#16
Ertugrul Filiz, Recep Vatansever, Ibrahim Ilker Ozyigit, Mehmet Emin Uras, Ugur Sen, Naser A Anjum, Eduarda Pereira
This study aimed to improve current understanding on ethylene-insensitive 3-like (EIL) members, least explored in woody plants such as poplar (Populus trichocarpa Torr. & Grey). Herein, seven putative EIL members were identified in P. trichocarpa genome and were roughly annotated either as EIN3-like sequence associated with ethylene pathway or EIL3-like sequences related with sulfur (S)-pathway. Motif-distribution pattern of proteins also corroborated this annotation. They were distributed on six chromosomes (chr1, 3, 4 and 8-10), and were revealed to encode a protein of 509-662 residues with nuclear localization...
August 1, 2017: Archives of Biochemistry and Biophysics
https://www.readbyqxmd.com/read/28606054/variable-order-sequence-modeling-improves-bacterial-strain-discrimination-for-ion-torrent-dna-reads
#17
Thomas M Poulsen, Martin Frith
BACKGROUND: Genome sequencing provides a powerful tool for pathogen detection and can help resolve outbreaks that pose public safety and health risks. Mapping of DNA reads to genomes plays a fundamental role in this approach, where accurate alignment and classification of sequencing data is crucial. Standard mapping methods crudely treat bases as independent from their neighbors. Accuracy might be improved by using higher order paired hidden Markov models (HMMs), which model neighbor effects, but introduce design and implementation issues that have typically made them impractical for read mapping applications...
June 12, 2017: BMC Bioinformatics
https://www.readbyqxmd.com/read/28603402/hidden-parameter-markov-decision-processes-a-semiparametric-regression-approach-for-discovering-latent-task-parametrizations
#18
Finale Doshi-Velez, George Konidaris
Control applications often feature tasks with similar, but not identical, dynamics. We introduce the Hidden Parameter Markov Decision Process (HiP-MDP), a framework that parametrizes a family of related dynamical systems with a low-dimensional set of latent factors, and introduce a semiparametric regression approach for learning its structure from data. We show that a learned HiP-MDP rapidly identifies the dynamics of new task instances in several settings, flexibly adapting to task variation.
July 2016: IJCAI: Proceedings of the Conference
https://www.readbyqxmd.com/read/28587299/remote-sensing-image-change-detection-based-on-nsct-hmt-model-and-its-application
#19
Pengyun Chen, Yichen Zhang, Zhenhong Jia, Jie Yang, Nikola Kasabov
Traditional image change detection based on a non-subsampled contourlet transform always ignores the neighborhood information's relationship to the non-subsampled contourlet coefficients, and the detection results are susceptible to noise interference. To address these disadvantages, we propose a denoising method based on the non-subsampled contourlet transform domain that uses the Hidden Markov Tree model (NSCT-HMT) for change detection of remote sensing images. First, the ENVI software is used to calibrate the original remote sensing images...
June 6, 2017: Sensors
https://www.readbyqxmd.com/read/28587095/comparative-study-of-lectin-domains-in-model-species-new-insights-into-evolutionary-dynamics
#20
Sofie Van Holle, Kristof De Schutter, Lore Eggermont, Mariya Tsaneva, Liuyi Dang, Els J M Van Damme
Lectins are present throughout the plant kingdom and are reported to be involved in diverse biological processes. In this study, we provide a comparative analysis of the lectin families from model species in a phylogenetic framework. The analysis focuses on the different plant lectin domains identified in five representative core angiosperm genomes (Arabidopsisthaliana, Glycine max, Cucumis sativus, Oryza sativa ssp. japonica and Oryza sativa ssp. indica). The genomes were screened for genes encoding lectin domains using a combination of Basic Local Alignment Search Tool (BLAST), hidden Markov models, and InterProScan analysis...
May 25, 2017: International Journal of Molecular Sciences
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