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https://www.readbyqxmd.com/read/29343831/novel-hydrogenases-from-deep-sea-hydrothermal-vent-metagenomes-identified-by-a-recently-developed-activity-based-screen
#1
Nicole Adam, Mirjam Perner
Hydrogen is one of the most common elements on Earth. The enzymes converting molecular hydrogen into protons and electrons are the hydrogenases. Hydrogenases are ubiquitously distributed in all three domains of life where they play a central role in cell metabolism. So far, the recovery of hydrogenases has been restricted to culture-dependent and sequence-based approaches. We have recently developed the only activity-based screen for seeking H2-uptake enzymes from metagenomes without having to rely on enrichment and isolation of hydrogen-oxidizing microorganisms or prior metagenomic sequencing...
January 17, 2018: ISME Journal
https://www.readbyqxmd.com/read/29339971/terzyme-a-tool-for-identification-and-analysis-of-the-plant-terpenome
#2
Piyush Priya, Archana Yadav, Jyoti Chand, Gitanjali Yadav
Background: Terpenoid hydrocarbons represent the largest and most ancient group of phytochemicals, such that the entire chemical library of a plant is often referred to as its 'terpenome'. Besides having numerous pharmacological properties, terpenes contribute to the scent of the rose, the flavors of cinnamon and the yellow of sunflowers. Rapidly increasing -omics datasets provide an unprecedented opportunity for terpenome detection, paving the way for automated web resources dedicated to phytochemical predictions in genomic data...
2018: Plant Methods
https://www.readbyqxmd.com/read/29324054/bayesian-diagnostics-of-hidden-markov-structural-equation-models-with-missing-data
#3
Jingheng Cai, Ming Ouyang, Kai Kang, Xinyuan Song
Cocaine is a type of drug that functions to increase the availability of the neurotransmitter dopamine in the brain. However, cocaine dependence or abuse is highly related to an increased risk of psychiatric disorders and deficits in cognitive performance, attention, and decision-making abilities. Given the chronic and persistent features of drug addiction, the progression of abstaining from cocaine often evolves across several states, such as addiction to, moderate dependence on, and swearing off cocaine. Hidden Markov models (HMMs) are well suited to the characterization of longitudinal data in terms of a set of unobservable states, and have increasingly been used to uncover the dynamic heterogeneity in progressive diseases or activities...
January 11, 2018: Multivariate Behavioral Research
https://www.readbyqxmd.com/read/29322938/mdd-carb-a-combinatorial-model-for-the-identification-of-protein-carbonylation-sites-with-substrate-motifs
#4
Hui-Ju Kao, Shun-Long Weng, Kai-Yao Huang, Fergie Joanda Kaunang, Justin Bo-Kai Hsu, Chien-Hsun Huang, Tzong-Yi Lee
BACKGROUND: Carbonylation, which takes place through oxidation of reactive oxygen species (ROS) on specific residues, is an irreversibly oxidative modification of proteins. It has been reported that the carbonylation is related to a number of metabolic or aging diseases including diabetes, chronic lung disease, Parkinson's disease, and Alzheimer's disease. Due to the lack of computational methods dedicated to exploring motif signatures of protein carbonylation sites, we were motivated to exploit an iterative statistical method to characterize and identify carbonylated sites with motif signatures...
December 21, 2017: BMC Systems Biology
https://www.readbyqxmd.com/read/29321847/search-and-foraging-behaviors-from-movement-data-a-comparison-of-methods
#5
Ashley Bennison, Stuart Bearhop, Thomas W Bodey, Stephen C Votier, W James Grecian, Ewan D Wakefield, Keith C Hamer, Mark Jessopp
Search behavior is often used as a proxy for foraging effort within studies of animal movement, despite it being only one part of the foraging process, which also includes prey capture. While methods for validating prey capture exist, many studies rely solely on behavioral annotation of animal movement data to identify search and infer prey capture attempts. However, the degree to which search correlates with prey capture is largely untested. This study applied seven behavioral annotation methods to identify search behavior from GPS tracks of northern gannets (Morus bassanus), and compared outputs to the occurrence of dives recorded by simultaneously deployed time-depth recorders...
January 2018: Ecology and Evolution
https://www.readbyqxmd.com/read/29316636/segmentation-of-gait-sequences-in-sensor-based-movement-analysis-a-comparison-of-methods-in-parkinson-s-disease
#6
Nooshin Haji Ghassemi, Julius Hannink, Christine F Martindale, Heiko Gaßner, Meinard Müller, Jochen Klucken, Björn M Eskofier
Robust gait segmentation is the basis for mobile gait analysis. A range of methods have been applied and evaluated for gait segmentation of healthy and pathological gait bouts. However, a unified evaluation of gait segmentation methods in Parkinson's disease (PD) is missing. In this paper, we compare four prevalent gait segmentation methods in order to reveal their strengths and drawbacks in gait processing. We considered peak detection from event-based methods, two variations of dynamic time warping from template matching methods, and hierarchical hidden Markov models (hHMMs) from machine learning methods...
January 6, 2018: Sensors
https://www.readbyqxmd.com/read/29314736/development-of-a-chlamydia-suis-specific-antibody-enzyme-linked-immunosorbent-assay-based-on-the-use-of-a-b-cell-epitope-of-the-polymorphic-membrane-protein-c
#7
K De Puysseleyr, E Kieckens, L De Puysseleyr, H Van den Wyngaert, B Ahmed, S Van Lent, H H Creasy, G S A Myers, D Vanrompay
Chlamydia suis infections lead to economic loss in the pork industry. Chlamydia suis infections could be successfully treated with tetracyclines until the appearance of a tetracycline resistant phenotype, which was acquired via horizontal gene transfer of the tet(C) gene. Given the importance of C. suis as a swine pathogen and as a recently emerged tetracycline resistant pathogen with zoonotic potential, our aim was to develop a sensitive C. suis-specific antibody ELISA based on the polymorphic membrane proteins (Pmps)...
January 4, 2018: Transboundary and Emerging Diseases
https://www.readbyqxmd.com/read/29313315/eye-movement-patterns-in-face-recognition-are-associated-with-cognitive-decline-in-older-adults
#8
Cynthia Y H Chan, Antoni B Chan, Tatia M C Lee, Janet H Hsiao
The Hidden Markov Modeling approach for eye-movement data analysis is able to quantitatively assess differences and similarities among individual patterns. Here we applied this approach to examine the relationships between eye-movement patterns in face recognition and age-related cognitive decline. We found that significantly more older than young adults adopted "holistic" patterns, in which most eye fixations landed around the face center, as opposed to "analytic" patterns, in which eye movements switched among the two eyes and the face center...
January 8, 2018: Psychonomic Bulletin & Review
https://www.readbyqxmd.com/read/29297699/on-the-search-for-retrotransposons-alternative-protocols-to-obtain-sequences-to-learn-profile-hidden-markov-models
#9
Carlos N Fischer, Victor De A Campos, Victor H Barella
Profile hidden Markov models (pHMMs) have been used to search for transposable elements (TEs) in genomes. For the learning of pHMMs aimed to search for TEs of the retrotransposon class, the conventional protocol is to use the whole internal nucleotide portions of these elements as representative sequences. To further explore the potential of pHMMs in such a search, we propose five alternative ways to obtain the sets of representative sequences of TEs other than the conventional protocol. In this study, we are interested in Bel-PAO, Copia, Gypsy, and DIRS superfamilies from the retrotransposon class...
January 3, 2018: Journal of Computational Biology: a Journal of Computational Molecular Cell Biology
https://www.readbyqxmd.com/read/29284540/pureclip-capturing-target-specific-protein-rna-interaction-footprints-from-single-nucleotide-clip-seq-data
#10
Sabrina Krakau, Hugues Richard, Annalisa Marsico
The iCLIP and eCLIP techniques facilitate the detection of protein-RNA interaction sites at high resolution, based on diagnostic events at crosslink sites. However, previous methods do not explicitly model the specifics of iCLIP and eCLIP truncation patterns and possible biases. We developed PureCLIP ( https://github.com/skrakau/PureCLIP ), a hidden Markov model based approach, which simultaneously performs peak-calling and individual crosslink site detection. It explicitly incorporates a non-specific background signal and, for the first time, non-specific sequence biases...
December 28, 2017: Genome Biology
https://www.readbyqxmd.com/read/29283467/characterizing-synchrony-patterns-across-cognitive-task-stages-of-associative-recognition-memory
#11
Oscar Portoles, Jelmer P Borst, Marieke K van Vugt
Numerous studies seek to understand the role of oscillatory synchronization in cognition. This problem is particularly challenging in the context of complex cognitive behavior, which consists of a sequence of processing steps with uncertain duration. In this study, we analyzed oscillatory connectivity measures in time windows that previous computational models had associated with a specific sequence of processing steps in an associative memory recognition task (visual encoding, familiarity, memory retrieval, decision making, and motor response)...
December 28, 2017: European Journal of Neuroscience
https://www.readbyqxmd.com/read/29282542/using-hidden-markov-models-to-characterise-intermittent-social-behaviour-in-fish-shoals
#12
Nikolai W F Bode, Michael J Seitz
The movement of animals in groups is widespread in nature. Understanding this phenomenon presents an important problem in ecology with many applications that range from conservation to robotics. Underlying all group movements are interactions between individual animals and it is therefore crucial to understand the mechanisms of this social behaviour. To date, despite promising methodological developments, there are few applications to data of practical statistical techniques that inferentially investigate the extent and nature of social interactions in group movement...
December 27, 2017: Die Naturwissenschaften
https://www.readbyqxmd.com/read/29278101/bayesian-hidden-markov-models-for-delineating-the-pathology-of-alzheimer-s-disease
#13
Kai Kang, Jingheng Cai, Xinyuan Song, Hongtu Zhu
Alzheimer's disease is a firmly incurable and progressive disease. The pathology of Alzheimer's disease usually evolves from cognitive normal, to mild cognitive impairment, to Alzheimer's disease. The aim of this paper is to develop a Bayesian hidden Markov model to characterize disease pathology, identify hidden states corresponding to the diagnosed stages of cognitive decline, and examine the dynamic changes of potential risk factors associated with the cognitive normal-mild cognitive impairment-Alzheimer's disease transition...
January 1, 2017: Statistical Methods in Medical Research
https://www.readbyqxmd.com/read/29277330/a-hidden-semi-markov-model-based-approach-for-rehabilitation-exercise-assessment
#14
Marianna Capecci, Maria Gabriella Ceravolo, Francesco Ferracuti, Sabrina Iarlori, Ville Kyrki, Andrea Monteriù, Luca Romeo, Federica Verdini
In this paper, a Hidden Semi-Markov Model (HSMM) based approach is proposed to evaluate and monitor body motion during a rehabilitation training program. The approach extracts clinically relevant motion features from skeleton joint trajectories, acquired by the RGB-D camera, and provides a score for the subject's performance. The approach combines different aspects of rule and template based methods. The features have been defined by clinicians as exercise descriptors and are then assessed by a HSMM, trained upon an exemplar motion sequence...
December 22, 2017: Journal of Biomedical Informatics
https://www.readbyqxmd.com/read/29277075/gaze-gesture-based-human-robot-interaction-for-laparoscopic-surgery
#15
Kenko Fujii, Gauthier Gras, Antonino Salerno, Guang-Zhong Yang
While minimally invasive surgery offers great benefits in terms of reduced patient trauma, bleeding, as well as faster recovery time, it still presents surgeons with major ergonomic challenges. Laparoscopic surgery requires the surgeon to bimanually control surgical instruments during the operation. A dedicated assistant is thus required to manoeuvre the camera, which is often difficult to synchronise with the surgeon's movements. This article introduces a robotic system in which a rigid endoscope held by a robotic arm is controlled via the surgeon's eye movement, thus forgoing the need for a camera assistant...
November 28, 2017: Medical Image Analysis
https://www.readbyqxmd.com/read/29273000/age-based-partitioning-of-individual-genomic-inbreeding-levels-in-belgian-blue-cattle
#16
Marina Solé, Ann-Stephan Gori, Pierre Faux, Amandine Bertrand, Frédéric Farnir, Mathieu Gautier, Tom Druet
BACKGROUND: Inbreeding coefficients can be estimated either from pedigree data or from genomic data, and with genomic data, they are either global or local (when the linkage map is used). Recently, we developed a new hidden Markov model (HMM) that estimates probabilities of homozygosity-by-descent (HBD) at each marker position and automatically partitions autozygosity in multiple age-related classes (based on the length of HBD segments). Our objectives were to: (1) characterize inbreeding with our model in an intensively selected population such as the Belgian Blue Beef (BBB) cattle breed; (2) compare the properties of the model at different marker densities; and (3) compare our model with other methods...
December 22, 2017: Genetics, Selection, Evolution: GSE
https://www.readbyqxmd.com/read/29250805/innovative-modeling-of-naturalistic-driving-data-inference-and-prediction
#17
Paul S Albert
Naturalistic driving studies provide opportunities for investigating the effects of key driving exposures on risky driving performance and accidents. New technology provides a realistic assessment of risky driving through the intensive monitoring of kinematic behavior while driving. These studies with their complex data structures provide opportunities for statisticians to develop needed modeling techniques for statistical inference. This article discusses new statistical modeling procedures that were developed to specifically answer important analytical questions for naturalistic driving studies...
December 18, 2017: Statistics in Medicine
https://www.readbyqxmd.com/read/29229523/inference-in-population-genetics-using-forward-and-backward-discrete-and-continuous-time-processes
#18
Juraj Bergman, Dominik Schrempf, Carolin Kosiol, Claus Vogl
A central aim of population genetics is the inference of the evolutionary history of a population. To this end, the underlying process can be represented by a model of the evolution of allele frequencies parametrized by e.g., the population size, mutation rates and selection coefficients. A large class of models use forward-in-time models, such as the discrete Wright-Fisher and Moran models and the continuous forward diffusion, to obtain distributions of population allele frequencies, conditional on an ancestral initial allele frequency distribution...
December 8, 2017: Journal of Theoretical Biology
https://www.readbyqxmd.com/read/29220076/the-hmmer-web-server-for-protein-sequence-similarity-search
#19
Ananth Prakash, Matt Jeffryes, Alex Bateman, Robert D Finn
Protein sequence similarity search is one of the most commonly used bioinformatics methods for identifying evolutionarily related proteins. In general, sequences that are evolutionarily related share some degree of similarity, and sequence-search algorithms use this principle to identify homologs. The requirement for a fast and sensitive sequence search method led to the development of the HMMER software, which in the latest version (v3.1) uses a combination of sophisticated acceleration heuristics and mathematical and computational optimizations to enable the use of profile hidden Markov models (HMMs) for sequence analysis...
December 8, 2017: Current Protocols in Bioinformatics
https://www.readbyqxmd.com/read/29209194/a-heavy-tailed-expectation-maximization-hidden-markov-random-field-model-with-applications-to-segmentation-of-mri
#20
Diego Castillo-Barnes, Ignacio Peis, Francisco J Martínez-Murcia, Fermín Segovia, Ignacio A Illán, Juan M Górriz, Javier Ramírez, Diego Salas-Gonzalez
A wide range of segmentation approaches assumes that intensity histograms extracted from magnetic resonance images (MRI) have a distribution for each brain tissue that can be modeled by a Gaussian distribution or a mixture of them. Nevertheless, intensity histograms of White Matter and Gray Matter are not symmetric and they exhibit heavy tails. In this work, we present a hidden Markov random field model with expectation maximization (EM-HMRF) modeling the components using the α-stable distribution. The proposed model is a generalization of the widely used EM-HMRF algorithm with Gaussian distributions...
2017: Frontiers in Neuroinformatics
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