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https://www.readbyqxmd.com/read/28102867/a-systems-approach-for-the-elucidation-of-crucial-genes-and-network-constituents-of-cervical-intraepithelial-neoplasia-1-cin1
#1
Shikha Suman, Ashutosh Mishra, Anurag Kulshrestha
Cervical intra-epithelial neoplasia 1 (CIN1) is a pre-cancerous cervical cancer condition characterized by changes in the squamous cells of the cervix. Early detection may facilitate treatment as CIN1 may increase the risk of developing cervical cancer. An extensive system level analysis has been carried out to detect crucial network components of CIN1. Differential expression analysis was performed to identify genes that are differentially expressed in CIN1 in comparison to normal cells. Gene Ontology (GO) and pathway enrichment analyses of DEGs were followed by the construction of a protein-protein interaction (PPI) network...
January 19, 2017: Molecular BioSystems
https://www.readbyqxmd.com/read/28102292/integrated-molecular-analysis-reveals-complex-interactions-between-genomic-and-epigenomic-alterations-in-esophageal-adenocarcinomas
#2
DunFa Peng, Yan Guo, Heidi Chen, Shilin Zhao, Kay Washington, TianLing Hu, Yu Shyr, Wael El-Rifai
The incidence of esophageal adenocarcinoma (EAC) is rapidly rising in the United States and Western countries. In this study, we carried out an integrative molecular analysis to identify interactions between genomic and epigenomic alterations in regulating gene expression networks in EAC. We detected significant alterations in DNA copy numbers (CN), gene expression levels, and DNA methylation profiles. The integrative analysis demonstrated that altered expression of 1,755 genes was associated with changes in CN or methylation...
January 19, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28101863/lessons-from-animal-models-of-cytoplasmic-intermediate-filament-proteins
#3
Jamal-Eddine Bouameur, Thomas M Magin
Cytoplasmic intermediate filaments (IFs) represent a major cytoskeletal network contributing to cell shape, adhesion and migration as well as to tissue resilience and renewal in numerous bilaterians, including mammals. The observation that IFs are dispensable in cultured mammalian cells, but cause tissue-specific, life-threatening disorders, has pushed the need to investigate their function in vivo. In keeping with human disease, the deletion or mutation of murine IF genes resulted in highly specific pathologies...
2017: Sub-cellular Biochemistry
https://www.readbyqxmd.com/read/28101760/a-cad-of-fully-automated-colonic-polyp-detection-for-contrasted-and-non-contrasted-ct-scans
#4
Gökalp Tulum, Bülent Bolat, Onur Osman
PURPOSE: Computer-aided detection (CAD) systems are developed to help radiologists detect colonic polyps over CT scans. It is possible to reduce the detection time and increase the detection accuracy rates by using CAD systems. In this paper, we aimed to develop a fully integrated CAD system for automated detection of polyps that yields a high polyp detection rate with a reasonable number of false positives. METHODS: The proposed CAD system is a multistage implementation whose main components are: automatic colon segmentation, candidate detection, feature extraction and classification...
January 18, 2017: International Journal of Computer Assisted Radiology and Surgery
https://www.readbyqxmd.com/read/28101583/integrated-analysis-of-microrna-and-transcription-factor-reveals-important-regulators-and-regulatory-motifs-in-adult-b-cell-acute-lymphoblastic-leukemia
#5
Xiao-Cong Lin, Xin-Guang Liu, Yu-Ming Zhang, Ning Li, Zhi-Gang Yang, Wei-Yu Fu, Liu-Bo Lan, Hai-Tao Zhang, Yong Dai
B-cell acute lymphoblastic leukemia (B‑ALL) is an aggressive hematological malignancy and a leading cause of cancer-related mortality in children and young adults. The molecular mechanisms involved in the regulation of its gene expression has yet to be fully elucidated. In the present study, we performed large scale expression profiling of microRNA (miRNA) and transcription factor (TF) by Illumina deep‑sequencing and TF array technology, respectively, and identified 291 differentially expressed miRNAs and 201 differentially expressed TFs in adult B‑ALL samples relative to their controls...
February 2017: International Journal of Oncology
https://www.readbyqxmd.com/read/28101529/cortico-cortical-connections-of-primary-sensory-areas-and-associated-symptoms-in-migraine
#6
Duncan J Hodkinson, Rosanna Veggeberg, Aaron Kucyi, Koene R A van Dijk, Sophie L Wilcox, Steven J Scrivani, Rami Burstein, Lino Becerra, David Borsook
Migraine is a recurring, episodic neurological disorder characterized by headache, nausea, vomiting, and sensory disturbances. These events are thought to arise from the activation and sensitization of neurons along the trigemino-vascular pathway. From animal studies, it is known that thalamocortical projections play an important role in the transmission of nociceptive signals from the meninges to the cortex. However, little is currently known about the potential involvement of cortico-cortical feedback projections from higher-order multisensory areas and/or feedforward projections from principle primary sensory areas or subcortical structures...
November 2016: ENeuro
https://www.readbyqxmd.com/read/28101157/functional-analysis-of-keratinocyte-and-fibroblast-gene-expression-in-skin-and-keloid-scar-tissue-based-on-deviation-analysis-of-dynamic-capabilities
#7
Mingming Li, Lei Wu
The aim of the present study was to select key genes that are associated with fibroblasts and keratinocytes during keloid scar progression and development. The gene expression profile of GSE44270, which includes 32 samples, was downloaded from the Gene Expression Omnibus database. Differentially expressed genes (DEGs) in case samples compared with control samples were screened using the Limma R package followed by hierarchical clustering analysis. Protein-protein interaction (PPI) networks of the total selected DEGs were constructed using Cytoscape...
December 2016: Experimental and Therapeutic Medicine
https://www.readbyqxmd.com/read/28100830/neural-bases-of-recommendations-differ-according-to-social-network-structure
#8
Matthew Brook O'Donnell, Joseph B Bayer, Christopher N Cascio, Emily B Falk
Ideas spread across social networks, but not everyone is equally positioned to be a successful recommender. Do individuals with more opportunities to connect otherwise unconnected others-high information brokers-use their brains differently than low information brokers when making recommendations? We test the hypothesis that those with more opportunities for information brokerage may use brain systems implicated in considering the thoughts, perspectives, and mental states of others (i.e. 'mentalizing') more when spreading ideas...
January 18, 2017: Social Cognitive and Affective Neuroscience
https://www.readbyqxmd.com/read/28100828/an-integrated-modelling-framework-for-neural-circuits-with-multiple-neuromodulators
#9
Alok Joshi, Vahab Youssofzadeh, Vinith Vemana, T M McGinnity, Girijesh Prasad, KongFatt Wong-Lin
Neuromodulators are endogenous neurochemicals that regulate biophysical and biochemical processes, which control brain function and behaviour, and are often the targets of neuropharmacological drugs. Neuromodulator effects are generally complex partly owing to the involvement of broad innervation, co-release of neuromodulators, complex intra- and extrasynaptic mechanism, existence of multiple receptor subtypes and high interconnectivity within the brain. In this work, we propose an efficient yet sufficiently realistic computational neural modelling framework to study some of these complex behaviours...
January 2017: Journal of the Royal Society, Interface
https://www.readbyqxmd.com/read/28100686/noncanonical-function-of-dgcr8-controls-mesc-exit-from-pluripotency
#10
Daniel Cirera-Salinas, Jian Yu, Maxime Bodak, Richard P Ngondo, Kristina M Herbert, Constance Ciaudo
Mouse embryonic stem cells (mESCs) deficient for DGCR8, a key component of the microprocessor complex, present strong differentiation defects. However, the exact reasons impairing their commitment remain elusive. The analysis of newly generated mutant mESCs revealed that DGCR8 is essential for the exit from the pluripotency state. To dissociate canonical versus noncanonical functions of DGCR8, we complemented the mutant mESCs with a phosphomutant DGCR8, which restored microRNA levels but did not rescue the exit from pluripotency defect...
January 18, 2017: Journal of Cell Biology
https://www.readbyqxmd.com/read/28100667/the-control-of-translational-accuracy-is-a-determinant-of-healthy-ageing-in-yeast
#11
Tobias von der Haar, Jane E Leadsham, Aimie Sauvadet, Daniel Tarrant, Ilectra S Adam, Kofo Saromi, Peter Laun, Mark Rinnerthaler, Hannelore Breitenbach-Koller, Michael Breitenbach, Mick F Tuite, Campbell W Gourlay
Life requires the maintenance of molecular function in the face of stochastic processes that tend to adversely affect macromolecular integrity. This is particularly relevant during ageing, as many cellular functions decline with age, including growth, mitochondrial function and energy metabolism. Protein synthesis must deliver functional proteins at all times, implying that the effects of protein synthesis errors like amino acid misincorporation and stop-codon read-through must be minimized during ageing. Here we show that loss of translational accuracy accelerates the loss of viability in stationary phase yeast...
January 2017: Open Biology
https://www.readbyqxmd.com/read/28100492/dynamic-assembly-of-ultrasoft-colloidal-networks-enables-cell-invasion-within-restrictive-fibrillar-polymers
#12
Alison M Douglas, Alexandros A Fragkopoulos, Michelle K Gaines, L Andrew Lyon, Alberto Fernandez-Nieves, Thomas H Barker
In regenerative medicine, natural protein-based polymers offer enhanced endogenous bioactivity and potential for seamless integration with tissue, yet form weak hydrogels that lack the physical robustness required for surgical manipulation, making them difficult to apply in practice. The use of higher concentrations of protein, exogenous cross-linkers, and blending synthetic polymers has all been applied to form more mechanically robust networks. Each relies on generating a smaller network mesh size, which increases the elastic modulus and robustness, but critically inhibits cell spreading and migration, hampering tissue regeneration...
January 18, 2017: Proceedings of the National Academy of Sciences of the United States of America
https://www.readbyqxmd.com/read/28100277/stress-echo-2020-the-international-stress-echo-study-in-ischemic-and-non-ischemic-heart-disease
#13
Eugenio Picano, Quirino Ciampi, Rodolfo Citro, Antonello D'Andrea, Maria Chiara Scali, Lauro Cortigiani, Iacopo Olivotto, Fabio Mori, Maurizio Galderisi, Marco Fabio Costantino, Lorenza Pratali, Giovanni Di Salvo, Eduardo Bossone, Francesco Ferrara, Luna Gargani, Fausto Rigo, Nicola Gaibazzi, Giuseppe Limongelli, Giuseppe Pacileo, Maria Grazia Andreassi, Bruno Pinamonti, Laura Massa, Marco A R Torres, Marcelo H Miglioranza, Clarissa Borguezan Daros, José Luis de Castro E Silva Pretto, Branko Beleslin, Ana Djordjevic-Dikic, Albert Varga, Attila Palinkas, Gergely Agoston, Dario Gregori, Paolo Trambaiolo, Sergio Severino, Ayana Arystan, Marco Paterni, Clara Carpeggiani, Paolo Colonna
BACKGROUND: Stress echocardiography (SE) has an established role in evidence-based guidelines, but recently its breadth and variety of applications have extended well beyond coronary artery disease (CAD). We lack a prospective research study of SE applications, in and beyond CAD, also considering a variety of signs in addition to regional wall motion abnormalities. METHODS: In a prospective, multicenter, international, observational study design, > 100 certified high-volume SE labs (initially from Italy, Brazil, Hungary, and Serbia) will be networked with an organized system of clinical, laboratory and imaging data collection at the time of physical or pharmacological SE, with structured follow-up information...
January 18, 2017: Cardiovascular Ultrasound
https://www.readbyqxmd.com/read/28100260/iregnet3d-three-dimensional-integrated-regulatory-network-for-the-genomic-analysis-of-coding-and-non-coding-disease-mutations
#14
Siqi Liang, Nathaniel D Tippens, Yaoda Zhou, Matthew Mort, Peter D Stenson, David N Cooper, Haiyuan Yu
The mechanistic details of most disease-causing mutations remain poorly explored within the context of regulatory networks. We present a high-resolution three-dimensional integrated regulatory network (iRegNet3D) in the form of a web tool, where we resolve the interfaces of all known transcription factor (TF)-TF, TF-DNA and chromatin-chromatin interactions for the analysis of both coding and non-coding disease-associated mutations to obtain mechanistic insights into their functional impact. Using iRegNet3D, we find that disease-associated mutations may perturb the regulatory network through diverse mechanisms including chromatin looping...
January 18, 2017: Genome Biology
https://www.readbyqxmd.com/read/28100246/genetic-effect-of-interleukin-1-beta-c-511t-polymorphism-on-the-structural-covariance-network-and-white-matter-integrity-in-alzheimer-s-disease
#15
Chi-Wei Huang, Shih-Wei Hsu, Shih-Jen Tsai, Nai-Ching Chen, Mu-En Liu, Chen-Chang Lee, Shu-Hua Huang, Weng-Neng Chang, Ya-Ting Chang, Wan-Chen Tsai, Chiung-Chih Chang
BACKGROUND: Inflammatory processes play a pivotal role in the degenerative process of Alzheimer's disease. In humans, a biallelic (C/T) polymorphism in the promoter region (position-511) (rs16944) of the interleukin-1 beta gene has been significantly associated with differences in the secretory capacity of interleukin-1 beta. In this study, we investigated whether this functional polymorphism mediates the brain networks in patients with Alzheimer's disease. METHODS: We enrolled a total of 135 patients with Alzheimer's disease (65 males, 70 females), and investigated their gray matter structural covariance networks using 3D T1 magnetic resonance imaging and their white matter macro-structural integrities using fractional anisotropy...
January 18, 2017: Journal of Neuroinflammation
https://www.readbyqxmd.com/read/28100172/integrated-genomics-based-mapping-reveals-the-genetics-underlying-maize-flavonoid-biosynthesis
#16
Min Jin, Xuehai Zhang, Mingchao Zhao, Min Deng, Yuanhao Du, Yang Zhou, Shouchuang Wang, Takayuki Tohge, Alisdair R Fernie, Lothar Willmitzer, Yariv Brotman, Jianbing Yan, Weiwei Wen
BACKGROUND: Flavonoids constitute a diverse class of secondary metabolites which exhibit potent bioactivities for human health and have been indicated to play an important role in plant development and defense. However, accumulation and variation of flavonoid content in diverse maize lines and the genes responsible for their biosynthesis in this important crop remain largely unknown. In this study, we combine genetic mapping, metabolite profiling and gene regulatory network analysis to further enhance understanding of the maize flavonoid pathway...
January 18, 2017: BMC Plant Biology
https://www.readbyqxmd.com/read/28100166/smite-an-r-bioconductor-package-that-identifies-network-modules-by-integrating-genomic-and-epigenomic-information
#17
N Ari Wijetunga, Andrew D Johnston, Ryo Maekawa, Fabien Delahaye, Netha Ulahannan, Kami Kim, John M Greally
BACKGROUND: The molecular assays that test gene expression, transcriptional, and epigenetic regulation are increasingly diverse and numerous. The information generated by each type of assay individually gives an insight into the state of the cells tested. What should be possible is to add the information derived from separate, complementary assays to gain higher-confidence insights into cellular states. At present, the analysis of multi-dimensional, massive genome-wide data requires an initial pruning step to create manageable subsets of observations that are then used for integration, which decreases the sizes of the intersecting data sets and the potential for biological insights...
January 18, 2017: BMC Bioinformatics
https://www.readbyqxmd.com/read/28100070/exploring-relationships-among-social-integration-social-isolation-self-rated-health-and-demographics-among-latino-day-laborers
#18
Kenneth C Steel, Maria Eugenia Fernandez-Esquer, John S Atkinson, Wendell C Taylor
OBJECTIVES: Research indicates social integration and social isolation are related to health, and Latino day laborers (LDLs) tend to be socially isolated and, thus, at high risk for adverse health consequences. relationships among social isolation, social integration, self-rated health (SRH), and demographics were examined in a sample of LDLs to contribute to the literature on social networks and health in this and other migrant populations. DESIGN: We analyzed data from 324 LDLs who participated in Proyecto SHILOS (Salud del Hombre Inmigrante Latino), a Houston-based survey of Latino immigrant men's health...
January 19, 2017: Ethnicity & Health
https://www.readbyqxmd.com/read/28099516/clinical-practice-guidelines-for-rare-diseases-the-orphanet-database
#19
Sonia Pavan, Kathrin Rommel, María Elena Mateo Marquina, Sophie Höhn, Valérie Lanneau, Ana Rath
Clinical practice guidelines (CPGs) for rare diseases (RDs) are scarce, may be difficult to identify through Internet searches and may vary in quality depending on the source and methodology used. In order to contribute to the improvement of the diagnosis, treatment and care of patients, Orphanet (www.orpha.net) has set up a procedure for the selection, quality evaluation and dissemination of CPGs, with the aim to provide easy access to relevant, accurate and specific recommendations for the management of RDs...
2017: PloS One
https://www.readbyqxmd.com/read/28098904/identification-of-biomarkers-of-intrahepatic-cholangiocarcinoma-via-integrated-analysis-of-mrna-and-mirna-microarray-data
#20
Yaqing Chen, Dan Liu, Pengfei Liu, Yajing Chen, Huiling Yu, Quan Zhang
The present study aimed to identify potential therapeutic targets of intrahepatic cholangiocarcinoma (ICC) via integrated analysis of gene (transcript version) and microRNA (miRNA/miR) expression. The miRNA microarray dataset GSE32957 contained miRNA expression data from 16 ICC, 7 mixed type of combined hepatocellular‑cholangiocarcinoma (CHC), 2 hepatic adenoma, 3 focal nodular hyperplasia (FNH) and 5 healthy liver tissue samples, and 2 cholangiocarcinoma cell lines. In addition, the mRNA microarray dataset GSE32879 contained mRNA expression data from 16 ICC, 7 CHC, 2 hepatic adenoma, 5 FNH and 7 healthy liver tissue samples...
January 16, 2017: Molecular Medicine Reports
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