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https://www.readbyqxmd.com/read/29220076/the-hmmer-web-server-for-protein-sequence-similarity-search
#1
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/29206188/lightweight-biometric-sensing-for-walker-classification-using-narrowband-rf-links
#2
Tong Liu, Zhuo-Qian Liang
This article proposes a lightweight biometric sensing system using ubiquitous narrowband radio frequency (RF) links for path-dependent walker classification. The fluctuated received signal strength (RSS) sequence generated by human motion is used for feature representation. To capture the most discriminative characteristics of individuals, a three-layer RF sensing network is organized for building multiple sampling links at the most common heights of upper limbs, thighs, and lower legs. The optimal parameters of sensing configuration, such as the height of link location and number of fused links, are investigated to improve sensory data distinctions among subjects, and the experimental results suggest that the synergistic sensing by using multiple links can contribute a better performance...
December 5, 2017: Sensors
https://www.readbyqxmd.com/read/29127383/tunable-mid-ir-focusing-in-inas-based-semiconductor-hyperbolic-metamaterial
#3
Mai Desouky, Ahmed M Mahmoud, Mohamed A Swillam
Noble Metals such as Gold and Silver demonstrated for mid IR metamaterials have suffered many obstacles such as: high losses and lack of tunability. The application of doped semiconductors has allowed overcoming the tunability restriction, besides, possessing lower losses as compared to metals. In addition, doped semiconductors have small magnitude of negative real permittivity which is required to realize mid IR Hyperbolic Metamaterials (HMMs). We theoretically demonstrate super focusing based on an all Semiconductor planar HMM using InAs heterostructure...
November 10, 2017: Scientific Reports
https://www.readbyqxmd.com/read/29112715/refseq-an-update-on-prokaryotic-genome-annotation-and-curation
#4
Daniel H Haft, Michael DiCuccio, Azat Badretdin, Vyacheslav Brover, Vyacheslav Chetvernin, Kathleen O'Neill, Wenjun Li, Farideh Chitsaz, Myra K Derbyshire, Noreen R Gonzales, Marc Gwadz, Fu Lu, Gabriele H Marchler, James S Song, Narmada Thanki, Roxanne A Yamashita, Chanjuan Zheng, Françoise Thibaud-Nissen, Lewis Y Geer, Aron Marchler-Bauer, Kim D Pruitt
The Reference Sequence (RefSeq) project at the National Center for Biotechnology Information (NCBI) provides annotation for over 95 000 prokaryotic genomes that meet standards for sequence quality, completeness, and freedom from contamination. Genomes are annotated by a single Prokaryotic Genome Annotation Pipeline (PGAP) to provide users with a resource that is as consistent and accurate as possible. Notable recent changes include the development of a hierarchical evidence scheme, a new focus on curating annotation evidence sources, the addition and curation of protein profile hidden Markov models (HMMs), release of an updated pipeline (PGAP-4), and comprehensive re-annotation of RefSeq prokaryotic genomes...
November 3, 2017: Nucleic Acids Research
https://www.readbyqxmd.com/read/29082222/online-estimation-of-elbow-joint-angle-using-upper-arm-acceleration-a-movement-partitioning-approach
#5
M Farokhzadi, A Maleki, A Fallah, S Rashidi
Estimating the elbow angle using shoulder data is very important and valuable in Functional Electrical Stimulation (FES) systems which can be useful in assisting C5/C6 SCI patients. Much research has been conducted based on the elbow-shoulder synergies. The aim of this study was the online estimation of elbow flexion/extension angle from the upper arm acceleration signals during ADLs. For this, a three-level hierarchical structure was proposed based on a new approach, i.e. 'the movement phases'. These levels include Clustering, Recognition using HMMs and Angle estimation using neural networks...
September 2017: Journal of Biomedical Physics & Engineering
https://www.readbyqxmd.com/read/29060490/automated-analysis-of-in-meal-eating-behavior-using-a-commercial-wristband-imu-sensor
#6
Konstantinos Kyritsis, Christina Lefkothea Tatli, Christos Diou, Anastasios Delopoulos
Automatic objective monitoring of eating behavior using inertial sensors is a research problem that has received a lot of attention recently, mainly due to the mass availability of IMUs and the evidence on the importance of quantifying and monitoring eating patterns. In this paper we propose a method for detecting food intake cycles during the course of a meal using a commercially available wristband. We first model micro-movements that are part of the intake cycle and then use HMMs to model the sequences of micro-movements leading to mouthfuls...
July 2017: Conference Proceedings: Annual International Conference of the IEEE Engineering in Medicine and Biology Society
https://www.readbyqxmd.com/read/29060101/recognizing-cigarette-smoke-inhalations-using-hidden-markov-models
#7
Raul I Ramos-Garcia, Edward Sazonov, Stephen Tiffany
Previous studies with the Personal Automatic Cigarette Tracker (PACT) wearable system have found that smoking presents a distinct temporal breathing pattern, which might be well-suited for recognition by hidden Markov models (HMMs). In this work, we explored the feasibility of using HMMs to characterize the temporal information of smoking inhalations contained in the respiratory signals such as tidal volume, airflow, and the signal from the hand-to-mouth proximity sensor. Left-to-right HMMs were built to classify smoking and non-smoking inhalations using either only the respiratory signals, or both respiratory and hand proximity signals...
July 2017: Conference Proceedings: Annual International Conference of the IEEE Engineering in Medicine and Biology Society
https://www.readbyqxmd.com/read/28974026/joint-toxicity-of-different-heavy-metal-mixtures-after-a-short-term-oral-repeated-administration-in-rats
#8
Hong Su, Zhou Li, Samuel Selorm Fiati Kenston, Hongbo Shi, Yafei Wang, Xin Song, Yuanliang Gu, Tabatha Barber, Joni Aldinger, Baobo Zou, Min Ding, Jinshun Zhao, Xialu Lin
The systemic toxicity of different combinations of heavy metal mixtures (HMMs) was studied according to equivalent proportions of the eight most common detectable heavy metals found in fish consumption in the Ningbo area of China. The ion mass proportions of Zn, Cu, Mn, Cr, Ni, Cd, Pb, and Hg were 1070.0, 312.6, 173.1, 82.6, 30.0, 13.3, 6.6, and 1.0, respectively. In this study, 10 experimental groups were set as follows: M8 (Pb + Cd + Hg + Ni + Cu + Zn + Mn + Cr); M5 (Pb + Cd + Hg + Ni + Cr); M4A (Pb + Cd + Hg + Ni); M4B (Cu + Zn + Mn + Cr); M3 (Cu + Zn + Mn); Cr; Cu; Zn; Mn; and control...
October 1, 2017: International Journal of Environmental Research and Public Health
https://www.readbyqxmd.com/read/28970740/maximum-likelihood-estimation-for-stochastic-volatility-in-mean-models-with-heavy-tailed-distributions
#9
Carlos A Abanto-Valle, Roland Langrock, Ming-Hui Chen, Michel V Cardoso
In this article, we introduce a likelihood-based estimation method for the stochastic volatility in mean (SVM) model with scale mixtures of normal (SMN) distributions (Abanto-Valle et al., 2012). Our estimation method is based on the fact that the powerful hidden Markov model (HMM) machinery can be applied in order to evaluate an arbitrarily accurate approximation of the likelihood of an SVM model with SMN distributions. The method is based on the proposal of Langrock et al. (2012) and makes explicit the useful link between HMMs and SVM models with SMN distributions...
July 2017: Applied Stochastic Models in Business and Industry
https://www.readbyqxmd.com/read/28964073/a-fully-automated-approach-for-baby-cry-signal-segmentation-and-boundary-detection-of-expiratory-and-inspiratory-episodes
#10
Lina Abou-Abbas, Chakib Tadj, Hesam Alaie Fersaie
The detection of cry sounds is generally an important pre-processing step for various applications involving cry analysis such as diagnostic systems, electronic monitoring systems, emotion detection, and robotics for baby caregivers. Given its complexity, an automatic cry segmentation system is a rather challenging topic. In this paper, a framework for automatic cry sound segmentation for application in a cry-based diagnostic system has been proposed. The contribution of various additional time- and frequency-domain features to increase the robustness of a Gaussian mixture model/hidden Markov model (GMM/HMM)-based cry segmentation system in noisy environments is studied...
September 2017: Journal of the Acoustical Society of America
https://www.readbyqxmd.com/read/28961686/sequence2vec-a-novel-embedding-approach-for-modeling-transcription-factor-binding-affinity-landscape
#11
Hanjun Dai, Ramzan Umarov, Hiroyuki Kuwahara, Yu Li, Le Song, Xin Gao
Motivation: An accurate characterization of transcription factor (TF)-DNA affinity landscape is crucial to a quantitative understanding of the molecular mechanisms underpinning endogenous gene regulation. While recent advances in biotechnology have brought the opportunity for building binding affinity prediction methods, the accurate characterization of TF-DNA binding affinity landscape still remains a challenging problem. Results: Here we propose a novel sequence embedding approach for modeling the transcription factor binding affinity landscape...
November 15, 2017: Bioinformatics
https://www.readbyqxmd.com/read/28952936/dual-sticky-hierarchical-dirichlet-process-hidden-markov-model-and-its-application-to-natural-language-description-of-motions
#12
Weiming Hu, Guodong Tian, Yongxin Kang, Chunfeng Yuan, Stephen Maybank
In this paper, a new nonparametric Bayesian model called the dual sticky hierarchical Dirichlet process hidden Markov model (HDP-HMM) is proposed for mining activities from a collection of time series data such as trajectories. All the time series data are clustered. Each cluster of time series data, corresponding to a motion pattern, is modeled by an HMM. Our model postulates a set of HMMs that share a common set of states (topics in an analogy with topic models for document processing), but have unique transition distributions...
September 25, 2017: IEEE Transactions on Pattern Analysis and Machine Intelligence
https://www.readbyqxmd.com/read/28948473/buccal-micronucleus-cytome-assay-of-populations-under-chronic-heavy-metal-and-other-metal-exposure-along-the-santiago-river-mexico
#13
B C Gómez-Meda, G M Zúñiga-González, L V Sánchez-Orozco, A L Zamora-Perez, J P Rojas-Ramírez, A D Rocha-Muñoz, A A Sobrevilla-Navarro, M A Arellano-Avelar, A A Guerrero-de León, J S Armendáriz-Borunda, M G Sánchez-Parada
The Santiago River is one of the most contaminated rivers in Mexico, with heavy metal levels above the allowed limits. Scientific evidence indicates that chronic heavy metal exposure leads to cytogenotoxic effects. The aims of this study were to evaluate the genotoxic and cytotoxic effects of such exposure in buccal mucosa cells by micronucleus (MN) assay and to identify other nuclear abnormalities (NAs), such as nuclear buds (NBUDs), binucleated cells (BNs), pyknotic nuclei (PNs), karyorrhexis (KX), karyolysis (KL), and abnormally condensed chromatin (CC)...
September 26, 2017: Environmental Monitoring and Assessment
https://www.readbyqxmd.com/read/28945590/interactions-between-large-scale-functional-brain-networks-are-captured-by-sparse-coupled-hmms
#14
Thomas Aw Bolton, Anjali Tarun, Virginie Sterpenich, Sophie Schwartz, Dimitri Van De Ville
Functional magnetic resonance imaging (fMRI) provides a window on the human brain at work. Spontaneous brain activity measured during resting-state has already provided many insights into brain function. In particular, recent interest in dynamic interactions between brain regions has increased the need for more advanced modeling tools. Here, we deploy a recent fMRI deconvolution technique to express resting-state temporal fluctuations as a combination of large-scale functional network activity profiles. Then, building upon a novel sparse coupled hidden Markov model (SCHMM) framework, we parameterised their temporal evolution as a mix between intrinsic dynamics, and a restricted set of cross-network modulatory couplings extracted in data-driven manner...
September 21, 2017: IEEE Transactions on Medical Imaging
https://www.readbyqxmd.com/read/28944062/coupling-spectral-analysis-and-hidden-markov-models-for-the-segmentation-of-behavioural-patterns
#15
Karine Heerah, Mathieu Woillez, Ronan Fablet, François Garren, Stéphane Martin, Hélène De Pontual
BACKGROUND: Movement pattern variations are reflective of behavioural switches, likely associated with different life history traits in response to the animals' abiotic and biotic environment. Detecting these can provide rich information on the underlying processes driving animal movement patterns. However, extracting these signals from movement time series, requires tools that objectively extract, describe and quantify these behaviours. The inference of behavioural modes from movement patterns has been mainly addressed through hidden Markov models...
2017: Movement Ecology
https://www.readbyqxmd.com/read/28869811/hidden-markov-model-analysis-reveals-the-advantage-of-analytic-eye-movement-patterns-in-face-recognition-across-cultures
#16
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)...
December 2017: Cognition
https://www.readbyqxmd.com/read/28841506/parkinsonian-rest-tremor-can-be-detected-accurately-based-on-neuronal-oscillations-recorded-from-the-subthalamic-nucleus
#17
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...
October 2017: Clinical Neurophysiology: Official Journal of the International Federation of Clinical Neurophysiology
https://www.readbyqxmd.com/read/28720084/sequence-based-identification-of-inositol-monophosphatase-like-histidinol-phosphate-phosphatases-hisn-in-corynebacterium-glutamicum-actinobacteria-and-beyond
#18
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/28682786/application-of-computational-methods-in-planaria-research-a-current-update
#19
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/28639636/hyperbolic-metamaterials-for-dispersion-assisted-directional-light-emission
#20
Lorenzo Ferrari, Joseph Stephen Thomas Smalley, Yeshaiahu Fainman, Zhaowei Liu
A novel method is presented to outcouple high spatial frequency (large-k) waves from hyperbolic metamaterials (HMMs) without the use of a grating. This approach relies exclusively on dispersion engineering, and enables preferential power extraction from the top or from the side of a HMM. Multilayer (ML) HMMs are shown to be better suited for lateral outcoupling, while nanowire HMMs are the most convenient choice for top outcoupling. A 6-fold increase in laterally extracted power is predicted for a dipole-HMM system with a Ag/Si ML operating at λ = 530 nm, when metallic filling ratio is changed from an unoptimized to the optimized one...
July 6, 2017: Nanoscale
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