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https://www.readbyqxmd.com/read/29236326/knockdown-of-ski-decreased-the-reactive-astrocytes-proliferation-in-vitro-induced-by-oxygen-glucose-deprivation-reoxygenation
#1
Xin Zhao, Kai-Sheng Zhou, Zhong-Hao Li, Wei Nan, Jing Wang, Ya-Yi Xia, Hai-Hong Zhang
Glia scar is a pathological marker in late phase of brain ischemia disease, which constitutes a major physical biochemical barrier to impede axonal regrowth. Astrocytes are known to be critically involved in the formation of glial scar. However, their response to ischemia and their role in neuroprotection after central nervous system (CNS) injury are not completely clear. Recently, we have demonstrated for the first time that Ski was up-regulated in reactive astrocytes after spinal cord injury in vivo and in vitro, which indicates Ski may be a new molecule that control astrocytes biologic properties after CNS injury...
December 13, 2017: Journal of Cellular Biochemistry
https://www.readbyqxmd.com/read/29235543/purification-of-replicating-pancreatic-%C3%AE-cells-for-gene-expression-studies
#2
Reyes Carballar, Maria de Lluc Canyelles, Claudia Fernández, Yasmina Martí, Sarah Bonnin, Esther Castaño, Eduard Montanya, Noèlia Téllez
β-cell proliferation is a rare event in adult pancreatic islets. To study the replication-related β-cell biology we designed a replicating β-cells sorting system for gene expression experiments. Replicating β-cells were identified by EdU incorporation and purified by flow cytometry. For β-cell separation islet cells were sorted by size, granularity and Newport Green fluorescence emission that was combined with emitted fluorescence for EdU-labelled replicating cells sorting. The purity of the resulting sorted populations was evaluated by insulin staining and EdU for β-cell identification and for replicating cells, respectively...
December 13, 2017: Scientific Reports
https://www.readbyqxmd.com/read/29233656/the-atypical-protein-kinase-riok3-contributes-to-glioma-cell-proliferation-survival-migration-invasion-and-the-akt-mtor-signaling-pathway
#3
Tong Zhang, Daofei Ji, Peng Wang, Liang Dong, Lei Jin, Hengliang Shi, Xuejiao Liu, Qingming Meng, Rutong Yu, Shangfeng Gao
The RIO (right open reading frame) protein kinases include RIOK1, RIOK2 and RIOK3. Emerging evidence has suggested an important role of RIO kinases in cancer cell proliferation, apoptosis, migration and invasion. However, the expression profile and specific roles of RIOK3 are largely unknown during glioma progression. In the current study, quantitative real-time PCR, Western blot, and immunohistochemical analysis showed that RIOK3 was upregulated in glioma tissues. Available database analysis revealed that higher levels of RIOK3 were associated with poorer survival outcome in glioma patients...
December 9, 2017: Cancer Letters
https://www.readbyqxmd.com/read/29233188/the-rio-protein-kinase-encoding-gene-sj-riok-2-is-involved-in-key-reproductive-processes-in-schistosoma-japonicum
#4
Lu Zhao, Xin He, Christoph G Grevelding, Qing Ye, Ying Li, Robin B Gasser, Colette Dissous, Mudassar N Mughal, Yan-Qin Zhou, Jun-Long Zhao, Min Hu
BACKGROUND: Schistosomiasis is one of the most prevalent parasitic diseases worldwide and is caused by parasitic trematodes of the genus Schistosoma. The pathogenesis of schistosomiasis is caused by eggs whose production is the consequence of the pairing of schistosomes and the subsequent sexual maturation of the female. Previous studies have demonstrated that protein kinases are involved in processes leading to the male-induced differentiation of the female gonads, ovary and vitellarium...
December 12, 2017: Parasites & Vectors
https://www.readbyqxmd.com/read/29230839/prevalence-estimation-when-disease-status-is-verified-only-among-test-positives-applications-in-hiv-screening-programs
#5
Emma G Thomas, Sarah B Peskoe, Donna Spiegelman
The first goal of the United Nations' 90-90-90 HIV/AIDS elimination strategy is to ensure that, by 2020, 90% of HIV-positive people know their HIV status. Estimating the prevalence of HIV among people eligible for screening allows assessment of the number of additional cases that might be diagnosed through continued screening efforts in this group. Here, we present methods for estimating prevalence when HIV status is verified by a gold standard only among those who test positive on an initial, imperfect screening test with known sensitivity and specificity...
December 11, 2017: Statistics in Medicine
https://www.readbyqxmd.com/read/29228417/mir-155-affects-renal-carcinoma-cell-proliferation-invasion-and-apoptosis-through-regulating-gsk-3%C3%AE-%C3%AE-catenin-signaling-pathway
#6
R-J Wei, C-H Zhang, W-Z Yang
OBJECTIVE: Glycogen Synthase Kinase-3β (GSK-3β) negatively regulates Wnt/β-catenin signaling pathway through degrading β-catenin protein. It plays an inhibitory role in various tumors, while the influence in the pathogenesis of renal carcinoma has not been elucidated. MicroRNA-155 (MiR-155) was found to be upregulated in renal carcinoma tissue. Bioinformatics analysis revealed the complementary binding site between miR-155 and 3'-UTR of GSK-3β. This study investigated the influence of miR-155 in regulating GSK-3β expression, Wnt/β-catenin signaling pathway activity, and renal carcinoma cell proliferation, invasion, and apoptosis...
November 2017: European Review for Medical and Pharmacological Sciences
https://www.readbyqxmd.com/read/29228285/matrix-factorization-based-data-fusion-for-the-prediction-of-lncrna-disease-associations
#7
Guangyuan Fu, Jun Wang, Carlotta Domeniconi, Guoxian Yu
Motivation: Long non-coding RNAs (lncRNAs) play crucial roles in complex disease diagnosis, prognosis, prevention, and treatment, but only a small portion of lncRNA-disease associations have been experimentally verified. Various computational models have been proposed to identify lncRNA-disease associations by integrating heterogeneous data sources. However, existing models generally ignore the intrinsic structure of data sources or treat them as equally relevant, while they may not be...
December 7, 2017: Bioinformatics
https://www.readbyqxmd.com/read/29228193/deepsf-deep-convolutional-neural-network-for-mapping-protein-sequences-to-folds
#8
Jie Hou, Badri Adhikari, Jianlin Cheng
Motivation: Protein fold recognition is an important problem in structural bioinformatics. Almost all traditional fold recognition methods use sequence (homology) comparison to indirectly predict the fold of a target protein based on the fold of a template protein with known structure, which cannot explain the relationship between sequence and fold. Only a few methods had been developed to classify protein sequences into a small number of folds due to methodological limitations, which are not generally useful in practice...
December 8, 2017: Bioinformatics
https://www.readbyqxmd.com/read/29228186/aether-leveraging-linear-programming-for-optimal-cloud-computing-in-genomics
#9
Jacob M Luber, Braden T Tierney, Evan M Cofer, Chirag J Patel, Aleksandar D Kostic
Motivation: Across biology we are seeing rapid developments in scale of data production without a corresponding increase in data analysis capabilities. Results: Here, we present Aether (http://aether.kosticlab.org), an intuitive, easy-to-use, cost-effective, and scalable framework that uses linear programming (LP) to optimally bid on and deploy combinations of underutilized cloud computing resources. Our approach simultaneously minimizes the cost of data analysis and provides an easy transition from users' existing HPC pipelines...
December 8, 2017: Bioinformatics
https://www.readbyqxmd.com/read/29228185/dncon2-improved-protein-contact-prediction-using-two-level-deep-convolutional-neural-networks
#10
Badri Adhikari, Jie Hou, Jianlin Cheng
Motivation: Significant improvements in the prediction of protein residue-residue contacts are observed in the recent years. These contacts, predicted using a variety of coevolution-based and machine learning methods, are the key contributors to the recent progress in ab initio protein structure prediction, as demonstrated in the recent CASP experiments. Continuing the development of new methods to reliably predict contact maps is essential to further improve ab initio structure prediction...
December 8, 2017: Bioinformatics
https://www.readbyqxmd.com/read/29228175/sana-netgo-a-combinatorial-approach-to-using-gene-ontology-go-terms-to-score-network-alignments
#11
Wayne B Hayes, Nil Mamano
Motivation: Gene Ontology (GO) terms are frequently used to score alignments between protein-protein interaction (PPI) networks. Methods exist to measure GO similarity between proteins in isolation, but proteins in a network alignment are not isolated: each pairing is dependent on every other via the alignment itself. Existing measures fail to take into account the frequency of GO terms across networks, instead imposing arbitrary rules on when to allow GO terms. Results: Here we develop NetGO, a new measure that naturally weighs infrequent, informative GO terms more heavily than frequent, less informative GO terms, without arbitrary cutoffs, instead downweighting GO terms according to their frequency in the networks being aligned...
December 7, 2017: Bioinformatics
https://www.readbyqxmd.com/read/29228172/spring-a-kinetic-interface-for-visualizing-high-dimensional-single-cell-expression-data
#12
Caleb Weinreb, Samuel Wolock, Allon Klein
Motivation: Single-cell gene expression profiling technologies can map the cell states in a tissue or organism. As these technologies become more common, there is a need for computational tools to explore the data they produce. In particular, visualizing continuous gene expression topologies can be improved, since current tools tend to fragment gene expression continua or capture only limited features of complex population topologies. Results: Force-directed layouts of k-nearest-neighbor graphs can visualize continuous gene expression topologies in a manner that preserves high-dimensional relationships and captures complex population topologies...
December 7, 2017: Bioinformatics
https://www.readbyqxmd.com/read/29228171/gene-graphics-a-genomic-neighborhood-data-visualization-web-application
#13
Katherine J Harrison, Valérie de Crécy-Lagard, Rémi Zallot
Summary: The examination of gene neighborhood is an integral part of comparative genomics but no tools to produce publication quality graphics of gene clusters are available. Gene Graphics is a straightforward web application for creating such visuals. Supported inputs include National Center for Biotechnology Information (NCBI) gene and protein identifiers with automatic fetching of neighboring information, GenBank files and data extracted from the SEED database. Gene representations can be customized for many parameters including gene and genome names, colors and sizes...
December 7, 2017: Bioinformatics
https://www.readbyqxmd.com/read/29227745/florida-state-university-s-institute-for-family-violence-studies
#14
Karen Oehme
This article outlines the role of the Institute for Family Violence Studies (IFVS) within the Florida State University College of Social Work in navigating issues intersecting social work and the law ( http://familyvio.csw.fsu.edu/ ). By developing comprehensive state and national trainings for unique populations and conducting interdisciplinary research, the IFVS promotes public policy that benefits healthy families and decreases family and intimate partner violence. The crucial role of staff and students, the IFVS's collaborative alliances, and funding sources are highlighted...
December 11, 2017: Journal of Evidence-informed Social Work
https://www.readbyqxmd.com/read/29227052/laparoscopy-or-clinical-follow-up-to-detect-occult-diaphragm-injuries-following-left-sided-thoracoabdominal-stab-wounds-a-pilot-randomized-controlled-trial
#15
G F Malherbe, P H Navsaria, A J Nicol, S Edu, S Chowdhury
BACKGROUND: The purpose of this study was to determine whether patients with left-sided thoracoabdominal (TA) stab wounds can be safely treated with clinical and chest X-ray follow up. METHOD: A prospective, randomized control study was conducted at Groote Schuur Hospital from September 2009 through to November 2014. Patients with asymptomatic left TA stab wounds included in the trial were randomized into two groups. Group A underwent diagnostic laparoscopy and Group B underwent clinical and radiological follow-up...
November 2017: South African Journal of Surgery. Suid-Afrikaanse Tydskrif Vir Chirurgie
https://www.readbyqxmd.com/read/29226803/quantitative-missense-variant-effect-prediction-using-large-scale-mutagenesis-data
#16
Vanessa E Gray, Ronald J Hause, Jens Luebeck, Jay Shendure, Douglas M Fowler
Large datasets describing the quantitative effects of mutations on protein function are becoming increasingly available. Here, we leverage these datasets to develop Envision, which predicts the magnitude of a missense variant's molecular effect. Envision combines 21,026 variant effect measurements from nine large-scale experimental mutagenesis datasets, a hitherto untapped training resource, with a supervised, stochastic gradient boosting learning algorithm. Envision outperforms other missense variant effect predictors both on large-scale mutagenesis data and on an independent test dataset comprising 2,312 TP53 variants whose effects were measured using a low-throughput approach...
December 1, 2017: Cell Systems
https://www.readbyqxmd.com/read/29226381/a-robust-and-powerful-two-step-testing-procedure-for-local-ancestry-adjusted-allelic-association-analysis-in-admixed-populations
#17
Qing Duan, Zheng Xu, Laura M Raffield, Suhua Chang, Di Wu, Ethan M Lange, Alex P Reiner, Yun Li
Genetic association studies in admixed populations allow us to gain deeper understanding of the genetic architecture of human diseases and traits. However, population stratification, complicated linkage disequilibrium (LD) patterns, and the complex interplay of allelic and ancestry effects on phenotypic traits pose challenges in such analyses. These issues may lead to detecting spurious associations and/or result in reduced statistical power. Fortunately, if handled appropriately, these same challenges provide unique opportunities for gene mapping...
December 10, 2017: Genetic Epidemiology
https://www.readbyqxmd.com/read/29226322/mir-1290-promotes-proliferation-migration-and-invasion-of-glioma-cells-by-targeting-lhx6
#18
Lei Yan, Kai Sun, Yang Liu, Jun Liang, Kerui Cai, Jinqiu Gui
OBJECTIVE: To investigate the interaction of miR-1290 and LHX6 in gliomas, and their influence on the propagation and metastasis of glioma cells. METHODS: The differential expression of miR-1290 in glioma cells was identified by chip screening. The expression level of miR-1290 and LHX6 were determined by qRT-PCR and western blot. The influence of miR-1290 on propagation of glioma cells were analyzed by MTT assay, EdU incorporation and colony formation, while the impact of miR-1290 on metastasis was assessed by transwell assay...
December 11, 2017: Journal of Cellular Physiology
https://www.readbyqxmd.com/read/29224730/a-validated-calculator-to-estimate-risk-of-cesarean-after-an-induction-of-labor-with-an-unfavorable-cervix
#19
Lisa D Levine, Katheryne L Downes, Samuel Parry, Michal A Elovitz, Mary D Sammel, Sindhu K Srinivas
BACKGROUND: Induction of labor occurs in more than 20% of pregnancies, which equates to approximately 1 million women undergoing an induction in the United States annually. Regardless of how common inductions are, our ability to predict induction success is limited. Although multiple risk factors for a failed induction have been identified, risk factors alone are not enough to quantify an actual risk of cesarean for an individual woman undergoing a cesarean. OBJECTIVE: The objective of this study was to derive and validate a prediction model for cesarean after induction with an unfavorable cervix and to create a web-based calculator to assist in patient counseling...
December 7, 2017: American Journal of Obstetrics and Gynecology
https://www.readbyqxmd.com/read/29222504/rnastructuromedb-a-genome-wide-database-for-rna-structural-inference
#20
Ryan J Andrews, Levi Baber, Walter N Moss
RNA plays important roles in almost every aspect of biology, and every aspect of RNA biology is influenced by its folding. This is a particularly important consideration in the era of high-throughput sequencing, when the discovery of novel transcripts far outpaces our knowledge of their functions. To gain a comprehensive picture of biology requires a structural framework for making functional inferences on RNA. To this end we have developed the RNA Structurome Database ( https://structurome.bb.iastate.edu ), a comprehensive repository of RNA secondary structural information that spans the entire human genome...
December 8, 2017: Scientific Reports
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