keyword
MENU ▼
Read by QxMD icon Read
search

Network identification

keyword
https://www.readbyqxmd.com/read/28727829/functional-differentiation-and-spatial-temporal-co-expression-networks-of-the-nbs-encoding-gene-family-in-jilin-ginseng-panax-ginseng-c-a-meyer
#1
Rui Yin, Mingzhu Zhao, Kangyu Wang, Yanping Lin, Yanfang Wang, Chunyu Sun, Yi Wang, Meiping Zhang
Ginseng, Panax ginseng C.A. Meyer, is one of the most important medicinal plants for human health and medicine. It has been documented that over 80% of genes conferring resistance to bacteria, viruses, fungi and nematodes are contributed by the nucleotide binding site (NBS)-encoding gene family. Therefore, identification and characterization of NBS genes expressed in ginseng are paramount to its genetic improvement and breeding. However, little is known about the NBS-encoding genes in ginseng. Here we report genome-wide identification and systems analysis of the NBS genes actively expressed in ginseng (PgNBS genes)...
2017: PloS One
https://www.readbyqxmd.com/read/28727547/designing-and-implementation-of-stable-sinusoidal-rough-neural-identifier
#2
Ghasem Ahmadi, Mohammad Teshnehlab
A rough neuron is defined as a pair of conventional neurons that are called the upper and lower bound neurons. In this paper, the sinusoidal rough-neural networks (SR-NNs) are used to identify the discrete dynamic nonlinear systems (DDNSs) with or without noise in series-parallel configuration. In the identification of periodic nonlinear systems, sinusoidal activation functions provide more efficient neural networks than the sigmoidal activation functions. Based on the Lyapunov stability theory, an online learning algorithm is developed to train the SR-NNs...
August 2017: IEEE Transactions on Neural Networks and Learning Systems
https://www.readbyqxmd.com/read/28726754/identification-of-load-categories-in-rotor-system-based-on-vibration-analysis
#3
Kun Zhang, Zhaojian Yang
Rotating machinery is often subjected to variable loads during operation. Thus, monitoring and identifying different load types is important. Here, five typical load types have been qualitatively studied for a rotor system. A novel load category identification method for rotor system based on vibration signals is proposed. This method is a combination of ensemble empirical mode decomposition (EEMD), energy feature extraction, and back propagation (BP) neural network. A dedicated load identification test bench for rotor system was developed...
July 20, 2017: Sensors
https://www.readbyqxmd.com/read/28726130/transmission-network-characteristics-based-on-env-and-gag-sequences-from-msm-during-acute-hiv-1-infection-in-beijing-china
#4
Zhimin Zhang, Lili Dai, Yan Jiang, Kaidi Feng, Lifeng Liu, Wei Xia, Fengjiao Yu, Jun Yao, Wenge Xing, Lijun Sun, Tong Zhang, Hao Wu, Bin Su, Maofeng Qiu
Molecular epidemiology can be used to identify human immunodeficiency virus (HIV) transmission clusters, usually using pol sequence for analysis. In the present study, we explored appropriate parameters to construct a simple network using HIV env and gag sequences instead of pol sequences for constructing a phylogenetic tree and a genetic transmission subnetwork, which were used to identify individuals with many potential transmission links and to explore the evolutionary dynamics of the virus among men who have sex with men (MSM) in Beijing...
July 19, 2017: Archives of Virology
https://www.readbyqxmd.com/read/28725932/dna-methylation-in-elovl2-and-c1orf132-correctly-predicted-chronological-age-of-individuals-from-three-disease-groups
#5
M Spólnicka, E Pośpiech, B Pepłońska, R Zbieć-Piekarska, Ż Makowska, A Pięta, J Karłowska-Pik, B Ziemkiewicz, M Wężyk, P Gasperowicz, T Bednarczuk, M Barcikowska, C Żekanowski, R Płoski, Wojciech Branicki
Improving accuracy of the available predictive DNA methods is important for their wider use in routine forensic work. Information on age in the process of identification of an unknown individual may provide important hints that can speed up the process of investigation. DNA methylation markers have been demonstrated to provide accurate age estimation in forensics, but there is growing evidence that DNA methylation can be modified by various factors including diseases. We analyzed DNA methylation profile in five markers from five different genes (ELOVL2, C1orf132, KLF14, FHL2, and TRIM59) used for forensic age prediction in three groups of individuals with diagnosed medical conditions...
July 19, 2017: International Journal of Legal Medicine
https://www.readbyqxmd.com/read/28724991/benchmarking-selected-computational-gene-network-growing-tools-in-context-of-virus-host-interactions
#6
Biruhalem Taye, Candida Vaz, Vivek Tanavde, Vladimir A Kuznetsov, Frank Eisenhaber, Richard J Sugrue, Sebastian Maurer-Stroh
Several available online tools provide network growing functions where an algorithm utilizing different data sources suggests additional genes/proteins that should connect an input gene set into functionally meaningful networks. Using the well-studied system of influenza host interactions, we compare the network growing function of two free tools GeneMANIA and STRING and the commercial IPA for their performance of recovering known influenza A virus host factors previously identified from siRNA screens. The result showed that given small (~30 genes) or medium (~150 genes) input sets all three network growing tools detect significantly more known host factors than random human genes with STRING overall performing strongest...
July 19, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28724903/co-expression-network-analysis-of-toxin-antitoxin-loci-in-mycobacterium-tuberculosis-reveals-key-modulators-of-cellular-stress
#7
Amita Gupta, Balaji Venkataraman, Madavan Vasudevan, Kiran Gopinath Bankar
Research on toxin-antitoxin loci (TA loci) is gaining impetus due to their ubiquitous presence in bacterial genomes and their observed roles in stress survival, persistence and drug tolerance. The present study investigates the expression profile of all the seventy-nine TA loci found in Mycobacterium tuberculosis. The bacterium was subjected to multiple stress conditions to identify key players of cellular stress response and elucidate a TA-coexpression network. This study provides direct experimental evidence for transcriptional activation of each of the seventy-nine TA loci following mycobacterial exposure to growth-limiting environments clearly establishing TA loci as stress-responsive modules in M...
July 19, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28724775/n-degradomic-analysis-reveals-a-proteolytic-network-processing-the-podocyte-cytoskeleton
#8
Markus M Rinschen, Ann-Kathrin Hoppe, Florian Grahammer, Martin Kann, Linus A Völker, Eva-Maria Schurek, Julie Binz, Martin Höhne, Fatih Demir, Milena Malisic, Tobias B Huber, Christine Kurschat, Jayachandran N Kizhakkedathu, Bernhard Schermer, Pitter F Huesgen, Thomas Benzing
Regulated intracellular proteostasis, controlled in part by proteolysis, is essential in maintaining the integrity of podocytes and the glomerular filtration barrier of the kidney. We applied a novel proteomics technology that enables proteome-wide identification, mapping, and quantification of protein N-termini to comprehensively characterize cleaved podocyte proteins in the glomerulus in vivo We found evidence that defined proteolytic cleavage results in various proteoforms of important podocyte proteins, including those of podocin, nephrin, neph1, α-actinin-4, and vimentin...
July 19, 2017: Journal of the American Society of Nephrology: JASN
https://www.readbyqxmd.com/read/28724751/tomo-seq-identifies-sox9-as-a-key-regulator-of-cardiac-fibrosis-during-ischemic-injury
#9
Grégory P A Lacraz, Jan Philipp Junker, Monika M Gladka, Bas Molenaar, Koen T Scholman, Marta Vigil-Garcia, Danielle Versteeg, Hesther de Ruiter, Marit W Vermunt, Menno P Creyghton, Manon M H Huibers, Nicolaas de Jonge, Alexander van Oudenaarden, Eva van Rooij
Background -Cardiac ischemic injury induces a pathological remodeling response, which can ultimately lead to heart failure. Detailed mechanistic insights into molecular signaling pathways relevant for different aspects of cardiac remodeling will support the identification of novel therapeutic targets. Methods -While genome-wide transcriptome analysis on diseased tissues has greatly advanced our understanding of the regulatory networks that drive pathological changes in the heart, this approach has been disadvantaged by the fact that the signals are derived from tissue homogenates...
July 19, 2017: Circulation
https://www.readbyqxmd.com/read/28724614/nuclear-mtor-acts-as-a-transcriptional-integrator-of-the-androgen-signaling-pathway-in-prostate-cancer
#10
Étienne Audet-Walsh, Catherine R Dufour, Tracey Yee, Fatima Z Zouanat, Ming Yan, Georges Kalloghlian, Mathieu Vernier, Maxime Caron, Guillaume Bourque, Eleonora Scarlata, Lucie Hamel, Fadi Brimo, Armen G Aprikian, Jacques Lapointe, Simone Chevalier, Vincent Giguère
Androgen receptor (AR) signaling reprograms cellular metabolism to support prostate cancer (PCa) growth and survival. Another key regulator of cellular metabolism is mTOR, a kinase found in diverse protein complexes and cellular localizations, including the nucleus. However, whether nuclear mTOR plays a role in PCa progression and participates in direct transcriptional cross-talk with the AR is unknown. Here, via the intersection of gene expression, genomic, and metabolic studies, we reveal the existence of a nuclear mTOR-AR transcriptional axis integral to the metabolic rewiring of PCa cells...
July 19, 2017: Genes & Development
https://www.readbyqxmd.com/read/28724354/novel-plasmodium-falciparum-metabolic-network-reconstruction-identifies-shifts-associated-with-clinical-antimalarial-resistance
#11
Maureen A Carey, Jason A Papin, Jennifer L Guler
BACKGROUND: Malaria remains a major public health burden and resistance has emerged to every antimalarial on the market, including the frontline drug, artemisinin. Our limited understanding of Plasmodium biology hinders the elucidation of resistance mechanisms. In this regard, systems biology approaches can facilitate the integration of existing experimental knowledge and further understanding of these mechanisms. RESULTS: Here, we developed a novel genome-scale metabolic network reconstruction, iPfal17, of the asexual blood-stage P...
July 19, 2017: BMC Genomics
https://www.readbyqxmd.com/read/28723200/flexible-transparent-and-free-standing-silicon-nanowire-sers-platform-for-in-situ-food-inspection
#12
Hao Cui, Shuoyu Li, Shaozhi Deng, Huanjun Chen, Chengxin Wang
We demonstrated a flexible transparent and free-standing Si nanowire paper (SiNWP) as a surface enhanced Raman scattering (SERS) platform for in situ chemical sensing on warping surfaces with high sensitivity. The SERS activity has originated from the three-dimension interconnected nanowire network structure and electromagnetic coupling between closely separated nanowires in the SiNWP. In addition, the SERS activity can be highly improved by functionalizing the SiNWP with plasmonic Au nanoparticles. The hybrid substrate not only showed excellent reproducibility and stability of the SERS signal, but also maintained the flexibility and transparency of the pristine SiNWP...
March 24, 2017: ACS Sensors
https://www.readbyqxmd.com/read/28721172/contact-tracing-following-outbreak-of-ebola-virus-disease-in-urban-settings-in-nigeria
#13
Olufunmilayo Ibitola Fawole, Mahmood Muazu Dalhat, Meeyoung Park, Casey Daniel Hall, Patrick Mboya Nguku, Peter Adebayo Adewuyi
An outbreak of Ebola virus disease occurred in Nigeria between July and September 2014. Contact tracing commenced in Lagos, and extended to Port Harcourt and Enugu as the outbreak continued to spread. A total of 899 contacts were traced. Contact tracing enhanced immediate identification of symptomatic contacts, some of whom eventually became cases. Contact tracing could be challenging in urban cities. However, use of electronic technology, adequate logistics, and highly skilled personnel enhanced the tracing of contacts to facilitate the successful containment of the outbreak...
2017: Pan African Medical Journal
https://www.readbyqxmd.com/read/28721073/exploration-of-the-molecular-mechanism-of-prostate-cancer-based-on-mrna-and-mirna-expression-profiles
#14
Xing Zhang, YuYan Sun, Peng Wang, Changfu Yang, Shengwei Li
Prostate cancer, the second most common cancer in men, has been rarely explored by integrating mRNA and miRNA expression profiles. In this study, we combined two mRNA expression datasets and six documented miRNAs to uncover the comprehensive molecular mechanism of prostate cancer. Results showed that a total of 30 genes were significantly differentially expressed in 49 tumor samples by comparing with 22 normal samples. Importantly, all samples from the two datasets can be clearly classified into two groups, tumor group and normal group, based on the selected differentially expressed genes (DEGs)...
2017: OncoTargets and Therapy
https://www.readbyqxmd.com/read/28720584/protein-kinase-n2-regulates-amp-kinase-signaling-and-insulin-responsiveness-of-glucose-metabolism-in-skeletal-muscle
#15
Maxwell A Ruby, Isabelle Riedl, Julie Massart, Marcus Åhlin, Juleen R Zierath
Insulin resistance is central to the development of type 2 diabetes and related metabolic disorders. As skeletal muscle is responsible for the majority of whole body insulin-stimulated glucose uptake, regulation of glucose metabolism in this tissue is of particular importance. While Rho GTPases and many of their affecters influence skeletal muscle metabolism, there is a paucity of information on the protein kinase N (PKN) family of serine/threonine protein kinases. We investigated the impact of PKN2 on insulin signaling and glucose metabolism in primary human skeletal muscle cells in vitro and mouse tibialis anterior muscle in vivo...
July 18, 2017: American Journal of Physiology. Endocrinology and Metabolism
https://www.readbyqxmd.com/read/28719228/successful-use-of-noninvasive-ventilation-in-chronic-obstructive-pulmonary-disease-how-do-high-performing-hospitals-do-it
#16
Kimberly A Fisher, Kathleen M Mazor, Sarah Goff, Mihaela S Stefan, Penelope S Pekow, Lauren A Williams, Vida Rastegar, Michael B Rothberg, Nicholas S Hill, Peter K Lindenauer
RATIONALE: Noninvasive ventilation (NIV) is a cornerstone of treatment for patients with severe exacerbations of chronic obstructive pulmonary disease (COPD) where it has been shown to reduce the need for intubation, hospital length of stay, and mortality. Despite high quality evidence and strong recommendations in clinical guidelines, use of NIV varies widely across hospitals. OBJECTIVE: To identify approaches used by hospitals which have been successful in implementing NIV to treat patients with severe exacerbations of COPD...
July 18, 2017: Annals of the American Thoracic Society
https://www.readbyqxmd.com/read/28717181/discovery-of-novel-human-gene-regulatory-modules-from-gene-co-expression-and-promoter-motif-analysis
#17
Shisong Ma, Michael Snyder, Savithramma P Dinesh-Kumar
Deciphering gene regulatory networks requires identification of gene expression modules. We describe a novel bottom-up approach to identify gene modules regulated by cis-regulatory motifs from a human gene co-expression network. Target genes of a cis-regulatory motif were identified from the network via the motif's enrichment or biased distribution towards transcription start sites in the promoters of co-expressed genes. A gene sub-network containing the target genes was extracted and used to derive gene modules...
July 17, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28716154/new-insights-from-gorongosa-national-park-and-niassa-national-reserve-of-mozambique-increasing-the-genetic-diversity-of-trypanosoma-vivax-and-trypanosoma-vivax-like-in-tsetse-flies-wild-ungulates-and-livestock-from-east-africa
#18
Carla Mf Rodrigues, Herakles A Garcia, Adriana C Rodrigues, André G Costa-Martins, Carlos L Pereira, Dagmar L Pereira, Zakaria Bengaly, Luis Neves, Erney P Camargo, Patrick B Hamilton, Marta Mg Teixeira
BACKGROUND: Trypanosoma (Duttonella) vivax is a major pathogen of livestock in Africa and South America (SA), and genetic studies limited to small sampling suggest greater diversity in East Africa (EA) compared to both West Africa (WA) and SA. METHODS: Multidimensional scaling and phylogenetic analyses of 112 sequences of the glycosomal glyceraldehyde phosphate dehydrogenase (gGAPDH) gene and 263 sequences of the internal transcribed spacer of rDNA (ITS rDNA) were performed to compare trypanosomes from tsetse flies from Gorongosa National Park and Niassa National Reserve of Mozambique (MZ), wild ungulates and livestock from EA, and livestock isolates from WA and SA...
July 17, 2017: Parasites & Vectors
https://www.readbyqxmd.com/read/28716001/variant-ranker-a-web-tool-to-rank-genomic-data-according-to-functional-significance
#19
John Alexander, Dimitris Mantzaris, Marianthi Georgitsi, Petros Drineas, Peristera Paschou
BACKGROUND: The increasing volume and complexity of high-throughput genomic data make analysis and prioritization of variants difficult for researchers with limited bioinformatics skills. Variant Ranker allows researchers to rank identified variants and determine the most confident variants for experimental validation. RESULTS: We describe Variant Ranker, a user-friendly simple web-based tool for ranking, filtering and annotation of coding and non-coding variants...
July 17, 2017: BMC Bioinformatics
https://www.readbyqxmd.com/read/28715501/diversity-and-distribution-of-nuclease-bacteriocins-in-bacterial-genomes-revealed-using-hidden-markov-models
#20
Connor Sharp, James Bray, Nicholas G Housden, Martin C J Maiden, Colin Kleanthous
Bacteria exploit an arsenal of antimicrobial peptides and proteins to compete with each other. Three main competition systems have been described: type six secretion systems (T6SS); contact dependent inhibition (CDI); and bacteriocins. Unlike T6SS and CDI systems, bacteriocins do not require contact between bacteria but are diffusible toxins released into the environment. Identified almost a century ago, our understanding of bacteriocin distribution and prevalence in bacterial populations remains poor. In the case of protein bacteriocins, this is because of high levels of sequence diversity and difficulties in distinguishing their killing domains from those of other competition systems...
July 17, 2017: PLoS Computational Biology
keyword
keyword
61631
1
2
Fetch more papers »
Fetching more papers... Fetching...
Read by QxMD. Sign in or create an account to discover new knowledge that matter to you.
Remove bar
Read by QxMD icon Read
×

Search Tips

Use Boolean operators: AND/OR

diabetic AND foot
diabetes OR diabetic

Exclude a word using the 'minus' sign

Virchow -triad

Use Parentheses

water AND (cup OR glass)

Add an asterisk (*) at end of a word to include word stems

Neuro* will search for Neurology, Neuroscientist, Neurological, and so on

Use quotes to search for an exact phrase

"primary prevention of cancer"
(heart or cardiac or cardio*) AND arrest -"American Heart Association"