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https://www.readbyqxmd.com/read/27908084/a-robust-automatic-birdsong-phrase-classification-a-template-based-approach
#1
Kantapon Kaewtip, Abeer Alwan, Colm O'Reilly, Charles E Taylor
Automatic phrase detection systems of bird sounds are useful in several applications as they reduce the need for manual annotations. However, birdphrase detection is challenging due to limited training data and background noise. Limited data occur because of limited recordings or the existence of rare phrases. Background noise interference occurs because of the intrinsic nature of the recording environment such as wind or other animals. This paper presents a different approach to birdsong phrase classification using template-based techniques suitable even for limited training data and noisy environments...
November 2016: Journal of the Acoustical Society of America
https://www.readbyqxmd.com/read/27903912/the-complex-evolutionary-history-of-aminoacyl-trna-synthetases
#2
Anargyros Chaliotis, Panayotis Vlastaridis, Dimitris Mossialos, Michael Ibba, Hubert D Becker, Constantinos Stathopoulos, Grigorios D Amoutzias
Aminoacyl-tRNA synthetases (AARSs) are a superfamily of enzymes responsible for the faithful translation of the genetic code and have lately become a prominent target for synthetic biologists. Our large-scale analysis of >2500 prokaryotic genomes reveals the complex evolutionary history of these enzymes and their paralogs, in which horizontal gene transfer played an important role. These results show that a widespread belief in the evolutionary stability of this superfamily is misconceived. Although AlaRS, GlyRS, LeuRS, IleRS, ValRS are the most stable members of the family, GluRS, LysRS and CysRS often have paralogs, whereas AsnRS, GlnRS, PylRS and SepRS are often absent from many genomes...
November 29, 2016: Nucleic Acids Research
https://www.readbyqxmd.com/read/27899706/mixed-hidden-markov-quantile-regression-models-for-longitudinal-data-with-possibly-incomplete-sequences
#3
Maria Francesca Marino, Nikos Tzavidis, Marco Alfò
Quantile regression provides a detailed and robust picture of the distribution of a response variable, conditional on a set of observed covariates. Recently, it has be been extended to the analysis of longitudinal continuous outcomes using either time-constant or time-varying random parameters. However, in real-life data, we frequently observe both temporal shocks in the overall trend and individual-specific heterogeneity in model parameters. A benchmark dataset on HIV progression gives a clear example. Here, the evolution of the CD4 log counts exhibits both sudden temporal changes in the overall trend and heterogeneity in the effect of the time since seroconversion on the response dynamics...
November 28, 2016: Statistical Methods in Medical Research
https://www.readbyqxmd.com/read/27899595/panther-version-11-expanded-annotation-data-from-gene-ontology-and-reactome-pathways-and-data-analysis-tool-enhancements
#4
Huaiyu Mi, Xiaosong Huang, Anushya Muruganujan, Haiming Tang, Caitlin Mills, Diane Kang, Paul D Thomas
The PANTHER database (Protein ANalysis THrough Evolutionary Relationships, http://pantherdb.org) contains comprehensive information on the evolution and function of protein-coding genes from 104 completely sequenced genomes. PANTHER software tools allow users to classify new protein sequences, and to analyze gene lists obtained from large-scale genomics experiments. In the past year, major improvements include a large expansion of classification information available in PANTHER, as well as significant enhancements to the analysis tools...
November 29, 2016: Nucleic Acids Research
https://www.readbyqxmd.com/read/27898803/identification-and-expression-profiling-of-the-lectin-gene-superfamily-in-mulberry
#5
Bushra Saeed, Vinay K Baranwal, Paramjit Khurana
Lectins are a diverse group of ubiquitously present, highly specific sugar-binding proteins. Members of this large gene family have been assigned broad biological functions from defense to acting as storage proteins. Despite possessing several interesting characteristics, their functions remain essentially undefined. Mulberry ( spp.) known for its medicinal benefits is also a rich source of lectins. Using an exhaustive hidden Markov model (HMM)-based search, we identified the lectin gene complement in C.K. Schneid with around 197 members...
July 2016: Plant Genome
https://www.readbyqxmd.com/read/27895627/distribution-and-classification-of-serine-%C3%AE-lactamases-in-brazilian-hospital-sewage-and-other-environmental-metagenomes-deposited-in-public-databases
#6
Adriana M Fróes, Fábio F da Mota, Rafael R C Cuadrat, Alberto M R Dávila
β-lactam is the most used antibiotic class in the clinical area and it acts on blocking the bacteria cell wall synthesis, causing cell death. However, some bacteria have evolved resistance to these antibiotics mainly due the production of enzymes known as β-lactamases. Hospital sewage is an important source of dispersion of multidrug-resistant bacteria in rivers and oceans. In this work, we used next-generation DNA sequencing to explore the diversity and dissemination of serine β-lactamases in two hospital sewage from Rio de Janeiro, Brazil (South Zone, SZ and North Zone, NZ), presenting different profiles, and to compare them with public environmental data available...
2016: Frontiers in Microbiology
https://www.readbyqxmd.com/read/27894839/relationship-of-p3b-single-trial-latencies-and-response-times-in-one-two-and-three-stimulus-oddball-tasks
#7
Matthew M Walsh, Glenn Gunzelmann, John R Anderson
The P300 is one of the most widely studied components of the human event-related potential. According to a longstanding view, the P300, and particularly its posterior subcomponent (i.e., the P3b), is driven by stimulus categorization. Whether the P3b relates to tactical processes involved in immediate responding or strategic processes that affect future behavior remains controversial, however. It is difficult to determine whether variability in P3b latencies relates to variability in response times because of limitations in the methods currently available to quantify the latency of the P3b during single trials...
November 25, 2016: Biological Psychology
https://www.readbyqxmd.com/read/27893761/high-accuracy-human-activity-recognition-based-on-sparse-locality-preserving-projections
#8
Xiangbin Zhu, Huiling Qiu
Human activity recognition(HAR) from the temporal streams of sensory data has been applied to many fields, such as healthcare services, intelligent environments and cyber security. However, the classification accuracy of most existed methods is not enough in some applications, especially for healthcare services. In order to improving accuracy, it is necessary to develop a novel method which will take full account of the intrinsic sequential characteristics for time-series sensory data. Moreover, each human activity may has correlated feature relationship at different levels...
2016: PloS One
https://www.readbyqxmd.com/read/27891146/a-self-organizing-incremental-spatiotemporal-associative-memory-networks-model-for-problems-with-hidden-state
#9
Zuo-Wei Wang
Identifying the hidden state is important for solving problems with hidden state. We prove any deterministic partially observable Markov decision processes (POMDP) can be represented by a minimal, looping hidden state transition model and propose a heuristic state transition model constructing algorithm. A new spatiotemporal associative memory network (STAMN) is proposed to realize the minimal, looping hidden state transition model. STAMN utilizes the neuroactivity decay to realize the short-term memory, connection weights between different nodes to represent long-term memory, presynaptic potentials, and synchronized activation mechanism to complete identifying and recalling simultaneously...
2016: Computational Intelligence and Neuroscience
https://www.readbyqxmd.com/read/27882067/bioinformatic-identification-of-rare-codon-clusters-rccs-in-hbv-genome-and-evaluation-of-rccs-in-proteins-structure-of-hepatitis-b-virus
#10
Mojtaba Mortazavi, Mohammad Zarenezhad, Saeid Gholamzadeh, Seyed Moayed Alavian, Mohammad Ghorbani, Reza Dehghani, Abdorrasoul Malekpour, Mohammadhasan Meshkibaf, Ali Fakhrzad
BACKGROUND: Hepatitis B virus (HBV) as an infectious disease that has nine genotypes (A - I) and a 'putative' genotype J. OBJECTIVES: The aim of this study was to identify the rare codon clusters (RCC) in the HBV genome and to evaluate these RCCs in the HBV proteins structure. METHODS: For detection of protein family accession numbers (Pfam) in HBV proteins, the UniProt database and Pfam search tool were used. Protein family accession numbers is a comprehensive and accurate collection of protein domains and families...
October 2016: Hepatitis Monthly
https://www.readbyqxmd.com/read/27875548/accelerating-information-retrieval-from-profile-hidden-markov-model-databases
#11
Ahmad Tamimi, Yaqoub Ashhab, Hashem Tamimi
Profile Hidden Markov Model (Profile-HMM) is an efficient statistical approach to represent protein families. Currently, several databases maintain valuable protein sequence information as profile-HMMs. There is an increasing interest to improve the efficiency of searching Profile-HMM databases to detect sequence-profile or profile-profile homology. However, most efforts to enhance searching efficiency have been focusing on improving the alignment algorithms. Although the performance of these algorithms is fairly acceptable, the growing size of these databases, as well as the increasing demand for using batch query searching approach, are strong motivations that call for further enhancement of information retrieval from profile-HMM databases...
2016: PloS One
https://www.readbyqxmd.com/read/27851936/hidden-markov-modeling-with-detailed-balance-and-its-application-to-single-protein-folding
#12
Yongli Zhang, Junyi Jiao, Aleksander A Rebane
Hidden Markov modeling (HMM) has revolutionized kinetic studies of macromolecules. However, results from HMM often violate detailed balance when applied to the transitions under thermodynamic equilibrium, and the consequence of such violation has not been well understood. Here, to our knowledge, we developed a new HMM method that satisfies detailed balance (HMM-DB) and optimizes model parameters by gradient search. We used free energy of stable and transition states as independent fitting parameters and considered both normal and skew normal distributions of the measurement noise...
November 15, 2016: Biophysical Journal
https://www.readbyqxmd.com/read/27845655/a-hidden-markov-model-for-3d-catheter-tip-tracking-with-2d-x-ray-catheterization-sequence-and-3d-rotational-angiography
#13
Pierre Ambrosini, Ihor Smal, Daniel Ruijters, Wiro Niessen, Adriaan Moelker, Theo van Walsum
In minimal invasive image guided catheterization procedures, physicians require information of the catheter position with respect to the patient's vasculature. However, in fluoroscopic images, visualization of the vasculature requires toxic contrast agent. Static vasculature roadmapping, which can reduce the usage of iodine contrast, is hampered by the breathing motion in abdominal catheterization. In this paper, we propose a method to track the catheter tip inside the patient's 3D vessel tree using intra-operative single-plane 2D X-ray image sequences and a peri-operative 3D rotational angiography (3DRA)...
November 7, 2016: IEEE Transactions on Medical Imaging
https://www.readbyqxmd.com/read/27833120/backward-transfer-entropy-informational-measure-for-detecting-hidden-markov-models-and-its-interpretations-in-thermodynamics-gambling-and-causality
#14
Sosuke Ito
The transfer entropy is a well-established measure of information flow, which quantifies directed influence between two stochastic time series and has been shown to be useful in a variety fields of science. Here we introduce the transfer entropy of the backward time series called the backward transfer entropy, and show that the backward transfer entropy quantifies how far it is from dynamics to a hidden Markov model. Furthermore, we discuss physical interpretations of the backward transfer entropy in completely different settings of thermodynamics for information processing and the gambling with side information...
November 11, 2016: Scientific Reports
https://www.readbyqxmd.com/read/27828094/detection-and-removal-of-fence-occlusions-in-an-image-using-a-video-of-the-static-dynamic-scene
#15
Sankaraganesh Jonna, Krishna K Nakka, Vrushali S Khasare, Rajiv R Sahay, Mohan S Kankanhalli
The advent of inexpensive smartphones/tablets/phablets equipped with cameras has resulted in the average person capturing cherished moments as images/videos and sharing them on the internet. However, at several locations, an amateur photographer may be frustrated with the captured images. For example, the object of interest to the photographer might be occluded or fenced. Currently available image de-fencing methods in the literature are limited by non-robust fence detection and can handle only static occluded scenes whose video is captured by constrained camera motion...
October 1, 2016: Journal of the Optical Society of America. A, Optics, Image Science, and Vision
https://www.readbyqxmd.com/read/27819220/genomic-and-genetic-variability-of-six-chicken-populations-using-single-nucleotide-polymorphism-and-copy-number-variants-as-markers
#16
M G Strillacci, M C Cozzi, E Gorla, F Mosca, F Schiavini, S I Román-Ponce, F J Ruiz López, A Schiavone, M Marzoni, S Cerolini, A Bagnato
Genomic and genetic variation among six Italian chicken native breeds (Livornese, Mericanel della Brianza, Milanino, Bionda Piemontese, Bianca di Saluzzo and Siciliana) were studied using single nucleotide polymorphism (SNP) and copy number variants (CNV) as markers. A total of 94 DNA samples genotyped with Axiom® Genome-Wide Chicken Genotyping Array (Affymetrix) were used in the analyses. The results showed the genetic and genomic variability occurring among the six Italian chicken breeds. The genetic relationship among animals was established with a principal component analysis...
November 7, 2016: Animal: An International Journal of Animal Bioscience
https://www.readbyqxmd.com/read/27818677/enhancing-interacting-residue-prediction-with-integrated-contact-matrix-prediction-in-protein-protein-interaction
#17
Tianchuan Du, Li Liao, Cathy H Wu
Identifying the residues in a protein that are involved in protein-protein interaction and identifying the contact matrix for a pair of interacting proteins are two computational tasks at different levels of an in-depth analysis of protein-protein interaction. Various methods for solving these two problems have been reported in the literature. However, the interacting residue prediction and contact matrix prediction were handled by and large independently in those existing methods, though intuitively good prediction of interacting residues will help with predicting the contact matrix...
December 2016: EURASIP Journal on Bioinformatics & Systems Biology
https://www.readbyqxmd.com/read/27810917/subdiffractional-tracking-of-internalized-molecules-reveals-heterogeneous-motion-states-of-synaptic-vesicles
#18
Merja Joensuu, Pranesh Padmanabhan, Nela Durisic, Adekunle T D Bademosi, Elizabeth Cooper-Williams, Isabel C Morrow, Callista B Harper, WooRam Jung, Robert G Parton, Geoffrey J Goodhill, Andreas Papadopulos, Frédéric A Meunier
Our understanding of endocytic pathway dynamics is severely restricted by the diffraction limit of light microscopy. To address this, we implemented a novel technique based on the subdiffractional tracking of internalized molecules (sdTIM). This allowed us to image anti-green fluorescent protein Atto647N-tagged nanobodies trapped in synaptic vesicles (SVs) from live hippocampal nerve terminals expressing vesicle-associated membrane protein 2 (VAMP2)-pHluorin with 36-nm localization precision. Our results showed that, once internalized, VAMP2-pHluorin/Atto647N-tagged nanobodies exhibited a markedly lower mobility than on the plasma membrane, an effect that was reversed upon restimulation in presynapses but not in neighboring axons...
October 24, 2016: Journal of Cell Biology
https://www.readbyqxmd.com/read/27809781/pse-hmm-genome-wide-cnv-detection-from-ngs-data-using-an-hmm-with-position-specific-emission-probabilities
#19
Seyed Amir Malekpour, Hamid Pezeshk, Mehdi Sadeghi
BACKGROUND: Copy Number Variation (CNV) is envisaged to be a major source of large structural variations in the human genome. In recent years, many studies apply Next Generation Sequencing (NGS) data for the CNV detection. However, still there is a necessity to invent more accurate computational tools. RESULTS: In this study, mate pair NGS data are used for the CNV detection in a Hidden Markov Model (HMM). The proposed HMM has position specific emission probabilities, i...
November 3, 2016: BMC Bioinformatics
https://www.readbyqxmd.com/read/27802791/an-ensemble-approach-for-cognitive-fault-detection-and-isolation-in-sensor-networks
#20
Manuel Roveri, Francesco Trovò
Cognitive fault detection and diagnosis systems are systems able to provide timely information about possibly occurring faults without requiring any a priori knowledge about the process generating the data or the possible faults. This ability is crucial in sensor network scenarios where a priori information about the data generating process, the noise level or the dictionary of the possibly occurring faults is generally hard to obtain. We here present a novel cognitive fault detection and isolation system for sensor networks...
June 26, 2016: International Journal of Neural Systems
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