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https://www.readbyqxmd.com/read/28719805/seizure-detection-from-eeg-signals-using-multivariate-empirical-mode-decomposition
#1
Asmat Zahra, Nadia Kanwal, Naveed Ur Rehman, Shoaib Ehsan, Klaus D McDonald-Maier
We present a data driven approach to classify ictal (epileptic seizure) and non-ictal EEG signals using the multivariate empirical mode decomposition (MEMD) algorithm. MEMD is a multivariate extension of empirical mode decomposition (EMD), which is an established method to perform the decomposition and time-frequency (T-F) analysis of non-stationary data sets. We select suitable feature sets based on the multiscale T-F representation of the EEG data via MEMD for the classification purposes. The classification is achieved using the artificial neural networks...
July 8, 2017: Computers in Biology and Medicine
https://www.readbyqxmd.com/read/28719651/link-prediction-on-twitter
#2
Sanda Martinčić-Ipšić, Edvin Močibob, Matjaž Perc
With over 300 million active users, Twitter is among the largest online news and social networking services in existence today. Open access to information on Twitter makes it a valuable source of data for research on social interactions, sentiment analysis, content diffusion, link prediction, and the dynamics behind human collective behaviour in general. Here we use Twitter data to construct co-occurrence language networks based on hashtags and based on all the words in tweets, and we use these networks to study link prediction by means of different methods and evaluation metrics...
2017: PloS One
https://www.readbyqxmd.com/read/28719614/beat-id-towards-a-computationally-low-cost-single-heartbeat-biometric-identity-check-system-based-on-electrocardiogram-wave-morphology
#3
Joana S Paiva, Duarte Dias, João P S Cunha
In recent years, safer and more reliable biometric methods have been developed. Apart from the need for enhanced security, the media and entertainment sectors have also been applying biometrics in the emerging market of user-adaptable objects/systems to make these systems more user-friendly. However, the complexity of some state-of-the-art biometric systems (e.g., iris recognition) or their high false rejection rate (e.g., fingerprint recognition) is neither compatible with the simple hardware architecture required by reduced-size devices nor the new trend of implementing smart objects within the dynamic market of the Internet of Things (IoT)...
2017: PloS One
https://www.readbyqxmd.com/read/28719601/clic-a-tool-for-expanding-biological-pathways-based-on-co-expression-across-thousands-of-datasets
#4
Yang Li, Alexis A Jourdain, Sarah E Calvo, Jun S Liu, Vamsi K Mootha
In recent years, there has been a huge rise in the number of publicly available transcriptional profiling datasets. These massive compendia comprise billions of measurements and provide a special opportunity to predict the function of unstudied genes based on co-expression to well-studied pathways. Such analyses can be very challenging, however, since biological pathways are modular and may exhibit co-expression only in specific contexts. To overcome these challenges we introduce CLIC, CLustering by Inferred Co-expression...
July 18, 2017: PLoS Computational Biology
https://www.readbyqxmd.com/read/28719033/identification-of-driver-copy-number-alterations-in-diverse-cancer-types-and-application-in-drug-repositioning
#5
Wenbin Zhou, Zhangxiang Zhao, Ruiping Wang, Yue Han, Chengyu Wang, Fan Yang, Ya Han, Haihai Liang, Lishuang Qi, Chenguang Wang, Zheng Guo, Yunyan Gu
Results from numerous studies suggest an important role for somatic copy number alterations (SCNAs) in cancer progression. Our work aimed to identify the drivers (oncogenes or tumor suppressor genes) that reside in recurrently aberrant genomic regions, including a large number of genes or non-coding genes, which remain a challenge for decoding the SCNAs involved in carcinogenesis. Here, we propose a new approach to comprehensively identify drivers, using 8740 cancer samples involving 18 cancer types from The Cancer Genome Atlas (TCGA)...
July 18, 2017: Molecular Oncology
https://www.readbyqxmd.com/read/28718849/an-efficient-method-to-transcription-factor-binding-sites-imputation-via-simultaneous-completion-of-multiple-matrices-with-positional-consistency
#6
Wei-Li Guo, De-Shuang Huang
Transcription factors (TFs) are DNA-binding proteins that have a central role in regulating gene expression. Identification of DNA-binding sites of TFs is a key task in understanding transcriptional regulation, cellular processes and disease. Chromatin immunoprecipitation followed by high-throughput sequencing (ChIP-seq) enables genome-wide identification of in vivo TF binding sites. However, it is still difficult to map every TF in every cell line owing to cost and biological material availability, which poses an enormous obstacle for integrated analysis of gene regulation...
July 18, 2017: Molecular BioSystems
https://www.readbyqxmd.com/read/28718820/a-transcriptomic-survey-of-ion-channel-based-conotoxins-in-the-chinese-tubular-cone-snail-conus-betulinus
#7
Yu Huang, Chao Peng, Yunhai Yi, Bingmiao Gao, Qiong Shi
Conotoxins in the venom of cone snails (Conus spp.) are a mixture of active peptides that work as blockers, agonists, antagonists, or inactivators of various ion channels. Recently we reported a high-throughput method to identify 215 conotoxin transcripts from the Chinese tubular cone snail, C. betulinus. Here, based on the previous datasets of four transcriptomes from three venom ducts and one venom bulb, we explored ion channel-based conotoxins and predicted their related ion channel receptors. Homologous analysis was also performed for the most abundant ion channel protein, voltage-gated potassium (Kv; with Kv1...
July 18, 2017: Marine Drugs
https://www.readbyqxmd.com/read/28718782/prediction-of-protein-hotspots-from-whole-protein-sequences-by-a-random-projection-ensemble-system
#8
Jinjian Jiang, Nian Wang, Peng Chen, Chunhou Zheng, Bing Wang
Hotspot residues are important in the determination of protein-protein interactions, and they always perform specific functions in biological processes. The determination of hotspot residues is by the commonly-used method of alanine scanning mutagenesis experiments, which is always costly and time consuming. To address this issue, computational methods have been developed. Most of them are structure based, i.e., using the information of solved protein structures. However, the number of solved protein structures is extremely less than that of sequences...
July 18, 2017: International Journal of Molecular Sciences
https://www.readbyqxmd.com/read/28718765/a-connectome-of-a-learning-and-memory-center-in-the-adult-drosophila-brain
#9
Shin-Ya Takemura, Yoshinori Aso, Toshihide Hige, Allan Wong, Zhiyuan Lu, C Shan Xu, Patricia K Rivlin, Harald F Hess, Ting Zhao, Toufiq Parag, Stuart Berg, Gary Huang, William Katz, Donald J Olbris, Stephen Plaza, Lowell Umayam, Roxanne Aniceto, Lei-Ann Chang, Shirley Lauchie, Omotara Ogundeyi, Christopher Ordish, Aya Shinomiya, Christopher Sigmund, Satoko Takemura, Julie Tran, Glenn C Turner, Gerald M Rubin, Louis K Scheffer
Understanding memory formation, storage and retrieval requires knowledge of the underlying neuronal circuits. In Drosophila, the mushroom body (MB) is the major site of associative learning. We reconstructed the morphologies and synaptic connections of all 983 neurons within the three functional units, or compartments, that compose the adult MB's α lobe, using a dataset of isotropic 8-nm voxels collected by focused ion-beam milling scanning electron microscopy. We found that Kenyon cells (KCs), whose sparse activity encodes sensory information, each make multiple en passant synapses to MB output neurons (MBONs) in each compartment...
July 18, 2017: ELife
https://www.readbyqxmd.com/read/28718392/efficient-body-fat-estimation-using-multistage-pair-ranked-set-sampling
#10
M Mahdizadeh, Ehsan Zamanzade
Rank-based sampling methods are applicable in settings where precise measurements are expensive, but small sets of units can be accurately ranked at negligible cost. This article introduces one such a design, called multistage pair ranked set sampling. It mitigates ranking burden associated with a competitor scheme, namely multistage ranked set sampling. The mean estimator in multistage pair ranked set sampling is unbiased, and under perfect rankings has variance no larger than its simple random sampling counterpart...
January 1, 2017: Statistical Methods in Medical Research
https://www.readbyqxmd.com/read/28718365/tmem88-ccl14-and-clec3b-as-prognostic-biomarkers-for-prognosis-and-palindromia-of-human-hepatocellular-carcinoma
#11
Xin Zhang, Jin-Xiang Wan, Zun-Ping Ke, Feng Wang, Hai-Xia Chai, Jia-Qiang Liu
Hepatocellular carcinoma is one of the most mortal and prevalent cancers with increasing incidence worldwide. Elucidating genetic driver genes for prognosis and palindromia of hepatocellular carcinoma helps managing clinical decisions for patients. In this study, the high-throughput RNA sequencing data on platform IlluminaHiSeq of hepatocellular carcinoma were downloaded from The Cancer Genome Atlas with 330 primary hepatocellular carcinoma patient samples. Stable key genes with differential expressions were identified with which Kaplan-Meier survival analysis was performed using Cox proportional hazards test in R language...
July 2017: Tumour Biology: the Journal of the International Society for Oncodevelopmental Biology and Medicine
https://www.readbyqxmd.com/read/28717996/patterns-of-oribatid-mite-species-diversity-testing-the-effects-of-elevation-area-and-sampling-effort
#12
Levan Mumladze, Maka Murvanidze, Mark Maraun
Elevational gradients in species diversity and species area relationships are two well established patterns that are not mutually exclusive in space and time. Elevation and area are both considered as good proxies to detect and characterize the patterns of species diversity distribution. However, such studies are hampered by the incomplete biodiversity data available for ecologists, which may affect the pattern perceptions. Using the large dataset of oribatid mite communities sampled in Georgia, we tested the effects of altitude and area on species distribution using various approaches, while explicitly considering the biases from sampling effort...
July 17, 2017: Experimental & Applied Acarology
https://www.readbyqxmd.com/read/28717971/subnetwork-mining-on-functional-connectivity-network-for-classification-of-minimal-hepatic-encephalopathy
#13
Daoqiang Zhang, Liyang Tu, Long-Jiang Zhang, Biao Jie, Guang-Ming Lu
Hepatic encephalopathy (HE), as a complication of cirrhosis, is a serious brain disease, which may lead to death. Accurate diagnosis of HE and its intermediate stage, i.e., minimal HE (MHE), is very important for possibly early diagnosis and treatment. Brain connectivity network, as a simple representation of brain interaction, has been widely used for the brain disease (e.g., HE and MHE) analysis. However, those studies mainly focus on finding disease-related abnormal connectivity between brain regions, although a large number of studies have indicated that some brain diseases are usually related to local structure of brain connectivity network (i...
July 17, 2017: Brain Imaging and Behavior
https://www.readbyqxmd.com/read/28717847/exploring-the-genomic-diversity-and-cariogenic-differences-of-streptococcus-mutans-strains-through-pan-genome-and-comparative-genome-analysis
#14
Peiqi Meng, Chang Lu, Qian Zhang, Jiuxiang Lin, Feng Chen
Pan-genome refers to the sum of genes that can be found in a given bacterial species, including the core-genome and the dispensable genome. In this study, the genomes from 183 Streptococcus mutans (S. mutans) isolates were analyzed from the pan-genome perspective. This analysis revealed that S. mutans has an "open" pan-genome, implying that there are plenty of new genes to be found as more genomes are sequenced. Additionally, S. mutans has a limited core-genome, which is composed of genes related to vital activities within the bacterium, such as metabolism and hereditary information storage or processing, occupying 35...
July 17, 2017: Current Microbiology
https://www.readbyqxmd.com/read/28717596/phenotypic-and-microrna-transcriptomic-profiling-of-the-mda-mb-231-spheroid-enriched-cscs-with-comparison-of-mcf-7-microrna-profiling-dataset
#15
Lily Boo, Wan Yong Ho, Norlaily Mohd Ali, Swee Keong Yeap, Huynh Ky, Kok Gan Chan, Wai Fong Yin, Dilan Amila Satharasinghe, Woan Charn Liew, Sheau Wei Tan, Soon Keng Cheong, Han Kiat Ong
Breast cancer spheroids have been widely used as in vitro models of cancer stem cells (CSCs), yet little is known about their phenotypic characteristics and microRNAs (miRNAs) expression profiles. The objectives of this research were to evaluate the phenotypic characteristics of MDA-MB-231 spheroid-enriched cells for their CSCs properties and also to determine their miRNAs expression profile. Similar to our previously published MCF-7 spheroid, MDA-MB-231 spheroid also showed typical CSCs characteristics namely self-renewability, expression of putative CSCs-related surface markers and enhancement of drug resistance...
2017: PeerJ
https://www.readbyqxmd.com/read/28717159/the-essential-genomic-landscape-of-the-commensal-bifidobacterium-breve-ucc2003
#16
Lorena Ruiz, Francesca Bottacini, Christine J Boinett, Amy K Cain, Mary O'Connell-Motherway, Trevor D Lawley, Douwe van Sinderen
Bifidobacteria are common gut commensals with purported health-promoting effects. This has encouraged scientific research into bifidobacteria, though recalcitrance to genetic manipulation and scarcity of molecular tools has hampered our knowledge on the precise molecular determinants of their health-promoting attributes and gut adaptation. To overcome this problem and facilitate functional genomic analyses in bifidobacteria, we created a large Tn5 transposon mutant library of the commensal Bifidobacterium breve UCC2003 that was further characterized by means of a Transposon Directed Insertion Sequencing (TraDIS) approach...
July 17, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28716740/multilocus-analysis-of-the-catfish-family-trichomycteridae-teleostei-ostariophysi-siluriformes-supporting-a-monophyletic-trichomycterinae
#17
Luz E Ochoa, Fabio F Roxo, Carlos DoNascimiento, Mark H Sabaj, Aléssio Datovo, Michael Alfaro, Claudio Oliveira
Trichomycteridae is the second most diverse family of the order Siluriformes, its members are widely distributed through the freshwaters of Central and South America, exhibiting an exceptional ecological and phenotypic disparity. The most diverse subfamily, Trichomycterinae, represented mainly by the genus Trichomycterus, historically has been recognized as non-monophyletic and various characters used to unite or divide its constituents are repeatedly called into question. No comprehensive molecular phylogenetic hypothesis regarding relationships of trichomycterids has been produced, and the present study is the first extensive phylogeny for the family Trichomycteridae, based on a multilocus dataset of three mitochondrial loci and two nuclear markers (3284 bp total)...
July 14, 2017: Molecular Phylogenetics and Evolution
https://www.readbyqxmd.com/read/28716683/trimmed-autocalibrating-k-space-estimation-based-on-structured-matrix-completion
#18
Mark Bydder, Stanislas Rapacchi, Olivier Girard, Maxime Guye, Jean-Philippe Ranjeva
PURPOSE: Parallel imaging allows the reconstruction of undersampled data from multiple coils. This provides a means to reject and regenerate corrupt data (e.g. from motion artefact). The purpose of this work is to approach this problem using the SAKE parallel imaging method. THEORY AND METHODS: Parallel imaging methods typically require calibration by fully sampling the center of k-space. This is a challenge in the presence of corrupted data, since the calibration data may be corrupted which leads to an errors-in-variables problem that cannot be solved by least squares or even iteratively reweighted least squares...
July 14, 2017: Magnetic Resonance Imaging
https://www.readbyqxmd.com/read/28716561/influence-of-renal-biopsy-results-on-the-management-of-small-kidney-cancers-in-older-patients-results-from-a-population-based-cohort
#19
Marc A Bjurlin, Elena B Elkin, Coral L Atoria, Paul Russo, Samir S Taneja, William C Huang
BACKGROUND AND OBJECTIVE: Small kidney cancers are a heterogeneous group with varying malignant potential. Pathologic information obtained from a renal biopsy may guide decision-making for small kidney cancers. We sought to assess the effect of pathologic information from renal biopsy on the nonsurgical management of small kidney cancers in a population-based cohort of patients over 65 years of age. METHODS: In the Surveillance, Epidemiology and End Results-Medicare dataset, we identified patients ≥66 years diagnosed with a kidney cancer<4cm between 2002 and 2011...
July 14, 2017: Urologic Oncology
https://www.readbyqxmd.com/read/28716520/modeling-color-preference-using-color-space-metrics
#20
Karen B Schloss, Laurent Lessard, Chris Racey, Anya C Hurlbert
Studying color preferences provides a means to discover how perceptual experiences map onto cognitive and affective judgments. A challenge is finding a parsimonious way to describe and predict patterns of color preferences, which are complex with rich individual differences. One approach has been to model color preferences using factors from metric color spaces to establish direct correspondences between dimensions of color and preference. Prior work established that substantial, but not all, variance in color preferences could be captured by weights on color space dimensions using multiple linear regression...
July 14, 2017: Vision Research
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