keyword
MENU ▼
Read by QxMD icon Read
search

Network function prediction

keyword
https://www.readbyqxmd.com/read/29791871/network-based-disease-module-discovery-by-a-novel-seed-connector-algorithm-with-pathobiological-implications
#1
Rui-Sheng Wang, Joseph Loscalzo
Understanding the genetic basis of complex diseases is challenging. Prior work shows that disease-related proteins do not typically function in isolation. Rather, they often interact with each other to form a network module that underlies dysfunctional mechanistic pathways. Identifying such disease modules will provide insights into a systems-level understanding of molecular mechanisms of diseases. Owing to the incompleteness of our knowledge of disease proteins and limited information on the biological mediators of pathobiological processes, the key proteins (seed proteins) for many diseases appear scattered over the human protein-protein interactome and form a few small branches, rather than coherent network modules...
May 20, 2018: Journal of Molecular Biology
https://www.readbyqxmd.com/read/29789577/long-non-coding-rna-gm2199-rescues-liver-injury-and-promotes-hepatocyte-proliferation-through-the-upregulation-of-erk1-2
#2
Qiang Gao, Yunyan Gu, Yanan Jiang, Li Fan, Zixiang Wei, Haobin Jin, Xirui Yang, Lijuan Wang, Xuguang Li, Sheng Tai, Baofeng Yang, Yan Liu
Long non-coding RNAs (lncRNAs) are a new class of regulators of various human diseases. This study was designed to explore the potential role of lncRNAs in experimental hepatic damage. In vivo hepatic damage in mice and in vitro hepatocyte damage in AML12 and NCTC1469 cells were induced by carbon tetrachloride (CCl4 ) treatments. Expression profiles of lncRNAs and mRNAs were analyzed by microarray. Bioinformatics analyses were conducted to predict the potential functions of differentially expressed lncRNAs with respect to hepatic damage...
May 22, 2018: Cell Death & Disease
https://www.readbyqxmd.com/read/29789405/the-mauthner-cell-in-a-fish-with-top-performance-and-yet-flexibly-tuned-c-starts-ii-physiology
#3
Peter Machnik, Kathrin Leupolz, Sabine Feyl, Wolfram Schulze, Stefan Schuster
The parallel occurrence in archerfish of fine-tuned and yet powerful predictive C-starts as well as of kinematically identical escape C-starts makes archerfish an interesting system to test hypotheses on the roles played by the Mauthner cells, a pair of giant reticulospinal neurons. In this study we show that the archerfish Mauthner cell shares all hallmark physiological properties with that of goldfish. Visual and acoustic inputs are received by the ventral and lateral dendrite, respectively, and cause complex postsynaptic potentials (PSPs) even in surgically anaesthetised fish...
May 22, 2018: Journal of Experimental Biology
https://www.readbyqxmd.com/read/29788092/cytokine-il9-triggers-the-pathogenesis-of-inflammatory-bowel-disease-through-the-mir21-cldn8-pathway
#4
Li Li, Shanshan Huang, Huiling Wang, Kang Chao, Li Ding, Rui Feng, Yun Qiu, Ting Feng, Gaoshi Zhou, Ji-Fan Hu, Minhu Chen, Shenghong Zhang
Background: Cytokine interleukin-9 (IL9) plays an essential role in the pathogenesis of inflammatory bowel disease. However, the molecular mechanism underlying the IL9 pathway remains unknown. Here, we initiate a series of studies to characterize the essential components of this pathway. Methods: The expression of IL9 in colon biopsies from Crohn's disease (CD) and controls were examined by quantitative polymerase chain reaction, immunoblot, and immunohistochemistry...
May 16, 2018: Inflammatory Bowel Diseases
https://www.readbyqxmd.com/read/29786489/determinants-of-cognitive-impairment-in-patients-with-multiple-sclerosis-with-and-without-atrophy
#5
Anand J C Eijlers, Kim A Meijer, Quinten van Geest, Jeroen J G Geurts, Menno M Schoonheim
Purpose To investigate the discrepancy between patients with multiple sclerosis (MS) without atrophy who have already developed cognitive impairment and patients with MS with atrophy who have preserved cognitive function. Materials and Methods This retrospective imaging study, with imaging acquired between 2008 and 2012, included 332 patients with MS (106 men and 226 women; mean age, 48.1 years; range, 23.0-72.5 years) and 96 healthy control participants. Cognitive impairment was defined as cognitive performance of z less than -1...
May 18, 2018: Radiology
https://www.readbyqxmd.com/read/29786081/distinct-learning-induced-changes-in-stimulus-selectivity-and-interactions-of-gabaergic-interneuron-classes-in-visual-cortex
#6
Adil G Khan, Jasper Poort, Angus Chadwick, Antonin Blot, Maneesh Sahani, Thomas D Mrsic-Flogel, Sonja B Hofer
How learning enhances neural representations for behaviorally relevant stimuli via activity changes of cortical cell types remains unclear. We simultaneously imaged responses of pyramidal cells (PYR) along with parvalbumin (PV), somatostatin (SOM), and vasoactive intestinal peptide (VIP) inhibitory interneurons in primary visual cortex while mice learned to discriminate visual patterns. Learning increased selectivity for task-relevant stimuli of PYR, PV and SOM subsets but not VIP cells. Strikingly, PV neurons became as selective as PYR cells, and their functional interactions reorganized, leading to the emergence of stimulus-selective PYR-PV ensembles...
May 21, 2018: Nature Neuroscience
https://www.readbyqxmd.com/read/29785835/predicting-the-ecological-impacts-of-large-dam-removals-on-a-river-network-based-on-habitat-network-structure-and-flow-regimes
#7
Nobuo Ishiyama, Masahiro Ryo, Taiga Kataoka, Shigeya Nagayama, Masanao Sueyoshi, Akira Terui, Terutaka Mori, Takumi Akasaka, Futoshi Nakamura
Large dams have provided vital protection and services to human life and the economy. However, an increasing number of large dams worldwide have aged considerably and have thus become hazardous due to impaired functions. The removal of large dams has excellent potential to restore habitat connectivity and flow regimes; therefore, projecting the related ecological consequences is a key emerging need for water resource and ecosystem management. However, no modeling methods are currently available for such projections at the basin scale...
May 22, 2018: Conservation Biology: the Journal of the Society for Conservation Biology
https://www.readbyqxmd.com/read/29785561/reptb-a-gene-ontology-based-drug-repurposing-approach-for-tuberculosis
#8
Anurag Passi, Neeraj Kumar Rajput, David J Wild, Anshu Bhardwaj
Tuberculosis (TB) is the world's leading infectious killer with 1.8 million deaths in 2015 as reported by WHO. It is therefore imperative that alternate routes of identification of novel anti-TB compounds are explored given the time and costs involved in new drug discovery process. Towards this, we have developed RepTB. This is a unique drug repurposing approach for TB that uses molecular function correlations among known drug-target pairs to predict novel drug-target interactions. In this study, we have created a Gene Ontology based network containing 26,404 edges, 6630 drug and 4083 target nodes...
May 21, 2018: Journal of Cheminformatics
https://www.readbyqxmd.com/read/29784955/integration-of-large-scale-data-for-extraction-of-integrated-arabidopsis-root-cell-type-specific-models
#9
Michael Scheunemann, Siobhan M Brady, Zoran Nikoloski
Plant organs consist of multiple cell types that do not operate in isolation, but communicate with each other to maintain proper functions. Here, we extract models specific to three developmental stages of eight root cell types or tissue layers in Arabidopsis thaliana based on a state-of-the-art constraint-based modeling approach with all publicly available transcriptomics and metabolomics data from this system to date. We integrate these models into a multi-cell root model which we investigate with respect to network structure, distribution of fluxes, and concordance to transcriptomics and proteomics data...
May 21, 2018: Scientific Reports
https://www.readbyqxmd.com/read/29784056/biomarker-micrornas-for-prostate-cancer-metastasis-screened-with-a-network-vulnerability-analysis-model
#10
Yuxin Lin, Feifei Chen, Li Shen, Xiaoyu Tang, Cui Du, Zhandong Sun, Huijie Ding, Jiajia Chen, Bairong Shen
BACKGROUND: Prostate cancer (PCa) is a fatal malignant tumor among males in the world and the metastasis is a leading cause for PCa death. Biomarkers are therefore urgently needed to detect PCa metastatic signature at the early time. MicroRNAs are small non-coding RNAs with the potential to be biomarkers for disease prediction. In addition, computer-aided biomarker discovery is now becoming an attractive paradigm for precision diagnosis and prognosis of complex diseases. METHODS: In this study, we identified key microRNAs as biomarkers for predicting PCa metastasis based on network vulnerability analysis...
May 21, 2018: Journal of Translational Medicine
https://www.readbyqxmd.com/read/29783642/a-novel-locating-system-for-cereal-plant-stem-emerging-points-detection-using-a-convolutional-neural-network
#11
Hadi Karimi, Søren Skovsen, Mads Dyrmann, Rasmus Nyholm Jørgensen
Determining the individual location of a plant, besides evaluating sowing performance, would make subsequent treatment for each plant across a field possible. In this study, a system for locating cereal plant stem emerging points (PSEPs) has been developed. In total, 5719 images were gathered from several cereal fields. In 212 of these images, the PSEPs of the cereal plants were marked manually and used to train a fully-convolutional neural network. In the training process, a cost function was made, which incorporates predefined penalty regions and PSEPs...
May 18, 2018: Sensors
https://www.readbyqxmd.com/read/29783076/disrupted-reward-and-cognitive-control-networks-contribute-to-anhedonia-in-depression
#12
Liang Gong, Cancan He, Haisan Zhang, Hongxing Zhang, Zhijun Zhang, Chunming Xie
Neuroimaging studies have identified that anhedonia, a core feature of major depressive disorder (MDD), is associated with dysfunction in reward and cognitive control processing. However, it is still not clear how the reward network (β-network) and the cognitive control network (δ-network) are linked to biased anhedonia in MDD patients. Sixty-eight MDD patients and 64 cognitively normal (CN) subjects underwent a resting-state functional magnetic resonance imaging scan. A 2*2 ANCOVA analysis was used to explore the differences in the nucleus accumbens-based, voxelwise functional connectivity (FC) between the groups...
May 12, 2018: Journal of Psychiatric Research
https://www.readbyqxmd.com/read/29781401/screening-of-prognostic-risk-micrornas-for-acute-myeloid-leukemia
#13
Hai-Yan Gao, Wei Wang, Xin-Guo Luo, Yong-Fang Jiang, Xin He, Ping Xu, Xi Chen, Xiao-Yun Li
OBJECTIVES: This study aimed to investigate the risk miRNAs (microRNAs) for AML (acute myeloid leukemia) prognosis and related regulatory mechanisms. METHODS: MiRNA and gene expression data, as well as clinical data of 176 patients were first downloaded from TCGA. Then miRNAs and genes significantly affecting the survival time based on KM survival curve were identified using Log Rank test. Next, COX proportional-hazard regression analysis was performed to screen the risk miRNAs (P-value < 0...
May 19, 2018: Hematology (Amsterdam, Netherlands)
https://www.readbyqxmd.com/read/29780993/ideal-reversible-polymer-networks
#14
German Alberto Parada, Xuanhe Zhao
In this article we introduce the concept of ideal reversible polymer networks, which have well-controlled polymer network structures similar to ideal covalent polymer networks but exhibit viscoelastic behaviors due to the presence of reversible crosslinks. We first present a theory to describe the mechanical properties of ideal reversible polymer networks. Because short polymer chains of equal length are used to construct the network, there are no chain entanglements and the chains' Rouse relaxation time is much shorter than the reversible crosslinks' characteristic time...
May 21, 2018: Soft Matter
https://www.readbyqxmd.com/read/29780313/network-dynamics-of-attention-during-a-naturalistic-behavioral-paradigm
#15
René Weber, Bradly Alicea, Richard Huskey, Klaus Mathiak
This study investigates the dynamics of attention during continuous, naturalistic interactions in a video game. Specifically, the effect of repeated distraction on a continuous primary task is related to a functional model of network connectivity. We introduce the Non-linear Attentional Saturation Hypothesis (NASH), which predicts that effective connectivity within attentional networks increases non-linearly with decreasing distraction over time, and exhibits dampening at critical parameter values. Functional magnetic resonance imaging (fMRI) data collected using a naturalistic behavioral paradigm coupled with an interactive video game is used to test the hypothesis...
2018: Frontiers in Human Neuroscience
https://www.readbyqxmd.com/read/29778237/prevalence-temporal-evolution-and-impact-on-survival-of-ventricular-conduction-blocks-in-patients-with-acute-coronary-syndrome-and-cardiogenic-shock
#16
Heli Tolppanen, Tuija Javanainen, Jordi Sans-Rosello, Jiri Parenica, Tuomo Nieminen, Marie Pavlusova, Josep Masip, Lars Köber, Marek Banaszewski, Alessandro Sionis, Jindrich Spinar, Veli-Pekka Harjola, Raija Jurkko, Johan Lassus
Changes in QRS duration and pattern are regarded to reflect severe ischemia in acute coronary syndromes (ACS), and ventricular conduction blocks (VCBs) are recognized high-risk markers in both ACS and acute heart failure. Our aim was to evaluate the prevalence, temporal evolution, association with clinical and angiographic parameters, and impact on mortality of VCBs in ACS-related cardiogenic shock (CS). Data of 199 patients with ACS-related CS from a prospective multinational cohort were evaluated with electrocardiogram data from baseline and day 3...
April 20, 2018: American Journal of Cardiology
https://www.readbyqxmd.com/read/29775159/bioinformatics-functional-analysis-of-let-7a-mir-34a-and-mir-199a-b-reveals-novel-insights-into-immune-system-pathways-and-cancer-hallmarks-for-hepatocellular-carcinoma
#17
Bangly Soliman, Ahmed Salem, Mohamed Ghazy, Nourhan Abu-Shahba, Mahmoud El Hefnawi
Let-7a, miR-34a, and miR-199 a/b have gained a great attention as master regulators for cellular processes. In particular, these three micro-RNAs act as potential onco-suppressors for hepatocellular carcinoma. Bioinformatics can reveal the functionality of these micro-RNAs through target prediction and functional annotation analysis. In the current study, in silico analysis using innovative servers (miRror Suite, DAVID, miRGator V3.0, GeneTrail) has demonstrated the combinatorial and the individual target genes of these micro-RNAs and further explored their roles in hepatocellular carcinoma progression...
May 2018: Tumour Biology: the Journal of the International Society for Oncodevelopmental Biology and Medicine
https://www.readbyqxmd.com/read/29773793/dynamically-induced-cascading-failures-in-power-grids
#18
Benjamin Schäfer, Dirk Witthaut, Marc Timme, Vito Latora
Reliable functioning of infrastructure networks is essential for our modern society. Cascading failures are the cause of most large-scale network outages. Although cascading failures often exhibit dynamical transients, the modeling of cascades has so far mainly focused on the analysis of sequences of steady states. In this article, we focus on electrical transmission networks and introduce a framework that takes into account both the event-based nature of cascades and the essentials of the network dynamics...
May 17, 2018: Nature Communications
https://www.readbyqxmd.com/read/29772236/identification-and-characterization-of-circular-rnas-in-rapid-atrial-pacing-dog-atrial-tissue
#19
Wenfeng Shangguan, Xue Liang, Wen Shi, Tong Liu, Manman Wang, Guangping Li
Circular RNAs (circRNAs) have emerged as novel molecules of interest in gene regulation as other noncoding RNAs, and participating in the process of many diseases. However, the expression and functions of circRNAs in Rapid atrial pacing (RAP) dog atrial tissue still unknown. 12 canines were randomly assigned to control and pacing group. RAP at 500 beats per minute was maintained 14 days in the pacing group. The expression characterization of circRNAs were revealed by high-throughput sequencing. We totally predicted 15,990 circRNAs in dog atrial tissues...
May 14, 2018: Biochemical and Biophysical Research Communications
https://www.readbyqxmd.com/read/29772009/ptra-a-reporter-system-for-monitoring-the-intracellular-dynamics-of-gene-expression
#20
Sabine G Wagner, Martin Ziegler, Hannes Löwe, Andreas Kremling, Katharina Pflüger-Grau
The presence of standardised tools and methods to measure and represent accurately biological parts and functions is a prerequisite for successful metabolic engineering and crucial to understand and predict the behaviour of synthetic genetic circuits. Many synthetic gene networks are based on transcriptional circuits, thus information on transcriptional and translational activity is important for understanding and fine-tuning the synthetic function. To this end, we have developed a toolkit to analyse systematically the transcriptional and translational activity of a specific synthetic part in vivo...
2018: PloS One
keyword
keyword
6569
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"