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https://www.readbyqxmd.com/read/28508147/identification-of-beta-lactamases-and-beta-lactam-related-proteins-in-human-pathogenic-bacteria-using-a-computational-search-approach
#1
Aniel Jessica Leticia Brambila-Tapia, Ernesto Perez-Rueda, Humberto Barrios, Nory Omayra Dávalos-Rodríguez, Ingrid Patricia Dávalos-Rodríguez, Ernesto Germán Cardona-Muñoz, Mario Salazar-Páramo
A systematic analysis of beta-lactamases based on comparative proteomics has not been performed thus far. In this report, we searched for the presence of beta-lactam-related proteins in 591 bacterial proteomes belonging to 52 species that are pathogenic to humans. The amino acid sequences for 19 different types of beta-lactamases (ACT, CARB, CifA, CMY, CTX, FOX, GES, GOB, IMP, IND, KPC, LEN, OKP, OXA, OXY, SHV, TEM, NDM, and VIM) were obtained from the ARG-ANNOT database and were used to construct 19 HMM profiles, which were used to identify potential beta-lactamases in the completely sequenced bacterial proteomes...
May 16, 2017: Current Microbiology
https://www.readbyqxmd.com/read/28499350/transcription-factor-associated-combinatorial-epigenetic-pattern-reveals-higher-transcriptional-activity-of-tcf7l2-regulated-intragenic-enhancers
#2
Qi Liu, Russell Bonneville, Tianbao Li, Victor X Jin
BACKGROUND: Recent studies have suggested that combinations of multiple epigenetic modifications are essential for controlling gene expression. Despite numerous computational approaches have been developed to decipher the combinatorial epigenetic patterns or "epigenetic code", none of them has explicitly addressed the relationship between a specific transcription factor (TF) and the patterns. METHODS: Here, we developed a novel computational method, T-cep, for annotating chromatin states associated with a specific TF...
May 12, 2017: BMC Genomics
https://www.readbyqxmd.com/read/28497059/a-new-algorithm-for-identifying-cis-regulatory-modules-based-on-hidden-markov-model
#3
Haitao Guo, Hongwei Huo
The discovery of cis-regulatory modules (CRMs) is the key to understanding mechanisms of transcription regulation. Since CRMs have specific regulatory structures that are the basis for the regulation of gene expression, how to model the regulatory structure of CRMs has a considerable impact on the performance of CRM identification. The paper proposes a CRM discovery algorithm called ComSPS. ComSPS builds a regulatory structure model of CRMs based on HMM by exploring the rules of CRM transcriptional grammar that governs the internal motif site arrangement of CRMs...
2017: BioMed Research International
https://www.readbyqxmd.com/read/28486635/geseq%C3%A2-versatile-and-accurate-annotation-of-organelle-genomes
#4
Michael Tillich, Pascal Lehwark, Tommaso Pellizzer, Elena S Ulbricht-Jones, Axel Fischer, Ralph Bock, Stephan Greiner
We have developed the web application GeSeq (https://chlorobox.mpimp-golm.mpg.de/geseq.html) for the rapid and accurate annotation of organellar genome sequences, in particular chloroplast genomes. In contrast to existing tools, GeSeq combines batch processing with a fully customizable reference sequence selection of organellar genome records from NCBI and/or references uploaded by the user. For the annotation of chloroplast genomes, the application additionally provides an integrated database of manually curated reference sequences...
May 9, 2017: Nucleic Acids Research
https://www.readbyqxmd.com/read/28469382/performance-of-hidden-markov-models-in-recovering-the-standard-classification-of-glycoside-hydrolases
#5
Mariana Fonseca Rossi, Beatriz Mello, Carlos G Schrago
Glycoside hydrolases (GHs) are carbohydrate-active enzymes that assist the hydrolysis of glycoside bonds of complex sugars into carbohydrates. The current standard GH family classification is available in the CAZy database, which is based on the similarities of amino acid sequences and curated semi-automatically. However, with the exponential increase in data availability from genome sequences, automated classification methods are required for the fast annotation of coding sequences. Currently, the dbCAN database offers automatic annotations of signature domains from CAZy-defined classifications using a statistical approach, the hidden Markov models (HMMs)...
2017: Evolutionary Bioinformatics Online
https://www.readbyqxmd.com/read/28466793/seqping-gene-prediction-pipeline-for-plant-genomes-using-self-training-gene-models-and-transcriptomic-data
#6
Kuang-Lim Chan, Rozana Rosli, Tatiana V Tatarinova, Michael Hogan, Mohd Firdaus-Raih, Eng-Ti Leslie Low
BACKGROUND: Gene prediction is one of the most important steps in the genome annotation process. A large number of software tools and pipelines developed by various computing techniques are available for gene prediction. However, these systems have yet to accurately predict all or even most of the protein-coding regions. Furthermore, none of the currently available gene-finders has a universal Hidden Markov Model (HMM) that can perform gene prediction for all organisms equally well in an automatic fashion...
January 27, 2017: BMC Bioinformatics
https://www.readbyqxmd.com/read/28462208/diagnosis-of-the-ocd-patients-using-drawing-features-of-the-bender-gestalt-shapes
#7
R Boostani, F Asadi, N Mohammadi
BACKGROUND: Since psychological tests such as questionnaire or drawing tests are almost qualitative, their results carry a degree of uncertainty and sometimes subjectivity. The deficiency of all drawing tests is that the assessment is carried out after drawing the objects and lots of information such as pen angle, speed, curvature and pressure are missed through the test. In other words, the psychologists cannot assess their patients while running the tests. One of the famous drawing tests to measure the degree of Obsession Compulsion Disorder (OCD) is the Bender Gestalt, though its reliability is not promising...
March 2017: Journal of Biomedical Physics & Engineering
https://www.readbyqxmd.com/read/28462050/a-profile-hidden-markov-model-to-investigate-the-distribution-and-frequency-of-lanb-encoding-lantibiotic-modification-genes-in-the-human-oral-and-gut-microbiome
#8
Calum J Walsh, Caitriona M Guinane, Paul W O' Toole, Paul D Cotter
BACKGROUND: The human microbiota plays a key role in health and disease, and bacteriocins, which are small, bacterially produced, antimicrobial peptides, are likely to have an important function in the stability and dynamics of this community. Here we examined the density and distribution of the subclass I lantibiotic modification protein, LanB, in human oral and stool microbiome datasets using a specially constructed profile Hidden Markov Model (HMM). METHODS: The model was validated by correctly identifying known lanB genes in the genomes of known bacteriocin producers more effectively than other methods, while being sensitive enough to differentiate between different subclasses of lantibiotic modification proteins...
2017: PeerJ
https://www.readbyqxmd.com/read/28460065/sbspksv2-structure-based-sequence-analysis-of-polyketide-synthases-and-non-ribosomal-peptide-synthetases
#9
Shradha Khater, Money Gupta, Priyesh Agrawal, Neetu Sain, Jyoti Prava, Priya Gupta, Mansi Grover, Narendra Kumar, Debasisa Mohanty
Genome guided discovery of novel natural products has been a promising approach for identification of new bioactive compounds. SBSPKS web-server has been a valuable resource for analysis of polyketide synthase (PKS) and non-ribosomal peptide synthetase (NRPS) gene clusters. We have developed an updated version - SBSPKSv2 which is based on comprehensive analysis of sequence, structure and secondary metabolite chemical structure data from 311 experimentally characterized PKS/NRPS gene clusters with known biosynthetic products...
April 29, 2017: Nucleic Acids Research
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
#10
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/28433414/diffusion-tensor-imaging-findings-and-cognitive-function-following-hospitalised-mixed-mechanism-mild-traumatic-brain-injury-a-systematic-review-and-meta-analysis
#11
REVIEW
Lucy Oehr, Jacqueline Anderson
OBJECTIVE: To undertake a systematic review and meta-analysis of the relationship between microstructural damage and cognitive function following hospitalised mixed-mechanism (HMM) mild traumatic brain injury (mTBI). DATA SOURCES: PsycInfo, Embase, and Medline were used to find relevant empirical papers published between January 2002 to January 2016. STUDY SELECTION: Studies that examined the specific relationship between diffusion tensor imaging (DTI) and cognitive test performance were included...
April 19, 2017: Archives of Physical Medicine and Rehabilitation
https://www.readbyqxmd.com/read/28417113/temporal-registration-in-in-utero-volumetric-mri-time-series
#12
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
#13
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
#14
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
#15
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/28403817/homology-to-peptide-pattern-for-annotation-of-carbohydrate-active-enzymes-and-prediction-of-function
#16
P K Busk, B Pilgaard, M J Lezyk, A S Meyer, L Lange
BACKGROUND: Carbohydrate-active enzymes are found in all organisms and participate in key biological processes. These enzymes are classified in 274 families in the CAZy database but the sequence diversity within each family makes it a major task to identify new family members and to provide basis for prediction of enzyme function. A fast and reliable method for de novo annotation of genes encoding carbohydrate-active enzymes is to identify conserved peptides in the curated enzyme families followed by matching of the conserved peptides to the sequence of interest as demonstrated for the glycosyl hydrolase and the lytic polysaccharide monooxygenase families...
April 12, 2017: BMC Bioinformatics
https://www.readbyqxmd.com/read/28401336/genome-wide-identification-and-characterization-of-nb-arc-resistant-genes-in-wheat-triticum-aestivum-l-and-their-expression-during-leaf-rust-infection
#17
Saket Chandra, Andaleeb Z Kazmi, Zainab Ahmed, Gargi Roychowdhury, Veena Kumari, Manish Kumar, Kunal Mukhopadhyay
NB-ARC domain-containing resistance genes from the wheat genome were identified, characterized and localized on chromosome arms that displayed differential yet positive response during incompatible and compatible leaf rust interactions. Wheat (Triticum aestivum L.) is an important cereal crop; however, its production is affected severely by numerous diseases including rusts. An efficient, cost-effective and ecologically viable approach to control pathogens is through host resistance. In wheat, high numbers of resistance loci are present but only few have been identified and cloned...
April 11, 2017: Plant Cell Reports
https://www.readbyqxmd.com/read/28373668/double-stacked-hyperbolic-metamaterial-waveguide-arrays-for-efficient-and-broadband-terahertz-quarter-wave-plates
#18
Xianmin Ke, Hua Zhu, Junhao Li, Lin Chen, Xun Li
We demonstrate how it is possible to achieve weak dispersion in the phase delay between two orthogonal polarization states by using double-stacked hyperbolic metamaterial (HMM) waveguide arrays. The weak dispersion in the phase delay originates from the different signs of phase delay from the two different HMM waveguide arrays. The condition of dispersion-free phase delay for the transmitted waves has been theoretically derived from the transmission matrix as the propagation characteristic of the HMM waveguide is involved...
April 3, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28361954/hidden-markov-models-reveal-complexity-in-the-diving-behaviour-of-short-finned-pilot-whales
#19
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
https://www.readbyqxmd.com/read/28361708/sequoia-significance-enhanced-network-querying-through-context-sensitive-random-walk-and-minimization-of-network-conductance
#20
Hyundoo Jeong, Byung-Jun Yoon
BACKGROUND: Network querying algorithms provide computational means to identify conserved network modules in large-scale biological networks that are similar to known functional modules, such as pathways or molecular complexes. Two main challenges for network querying algorithms are the high computational complexity of detecting potential isomorphism between the query and the target graphs and ensuring the biological significance of the query results. RESULTS: In this paper, we propose SEQUOIA, a novel network querying algorithm that effectively addresses these issues by utilizing a context-sensitive random walk (CSRW) model for network comparison and minimizing the network conductance of potential matches in the target network...
March 14, 2017: BMC Systems Biology
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