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https://www.readbyqxmd.com/read/28655153/the-ksea-app-a-web-based-tool-for-kinase-activity-inference-from-quantitative-phosphoproteomics
#1
Danica D Wiredja, Mehmet Koyutürk, Mark R Chance
Summary: Computational characterization of differential kinase activity from phosphoproteomics datasets is critical for correctly inferring cellular circuitry and how signaling cascades are altered in drug treatment and/or disease. Kinase-Substrate Enrichment Analysis (KSEA) offers a powerful approach to estimating changes in a kinase's activity based on the collective phosphorylation changes of its identified substrates. However, KSEA has been limited to programmers who are able to implement the algorithms...
June 26, 2017: Bioinformatics
https://www.readbyqxmd.com/read/28654057/murine-aortic-crush-injury-an-efficient-in-vivo-model-of-smooth-muscle-cell-proliferation-and-endothelial-function
#2
Dan Yu, George Makkar, Rajabrata Sarkar, Dudley K Strickland, Thomas S Monahan
Arterial reconstruction, whether angioplasty or bypass surgery, involves iatrogenic trauma causing endothelial disruption and vascular smooth muscle cell (VSMC) proliferation. Common murine models study small vessels such as the carotid and femoral arteries. Herein we describe an in vivo system in which both VSMC proliferation and endothelial barrier function can be simultaneously assessed in a large vessel. We studied the infrarenal aortic response to injury in C57BL/6 mice. The aorta was injured from the left renal vein to the aortic bifurcation by 30 transmural crushes of 5-seconds duration with a cotton-tipped applicator...
June 11, 2017: Journal of Visualized Experiments: JoVE
https://www.readbyqxmd.com/read/28653297/adherence-of-psychopharmacological-prescriptions-to-clinical-practice-guidelines-in-patients-with-eating-behavior-disorders
#3
María Del Mar Alañón Pardo, Mónica Ferrit Martín, Miguel Ángel Calleja Hernández, Francisco Morillas Márquez
PURPOSE: The purpose of this study was to analyze the adherence of psychopharmacological prescriptions to clinical practice guidelines (CPGs) for patients with eating behavior disorders (EDs) and to compare the effectiveness, safety, and cost of treatment according to adherence. METHODS: This retrospective observational study included ED patients admitted to the eating disorders unit (EDU) of Ciudad Real Hospital (Spain) between January 2006 and December 2009 and followed until December 2014...
June 26, 2017: European Journal of Clinical Pharmacology
https://www.readbyqxmd.com/read/28653025/proteomics-data-on-map-kinase-kinase-3-knock-out-bone-marrow-derived-macrophages-exposed-to-cigarette-smoke-extract
#4
Roshni Srivastava, Praveen Mannam, Navin Rauniyar, TuKiet T Lam, Ruiyan Luo, Patty J Lee, Anup Srivastava
This data article reports changes in the phosphoproteome and total proteome of cigarette smoke extract (CSE) exposed WT and MAP Kinase Kinase 3 knock out (MKK3(-/-)) bone marrow derived macrophages (BMDM). The dataset generated is helpful for understanding the mechanism of CSE induced inflammation and the role of MAP kinase signaling pathway. The cellular proteins were labeled with isobaric tags for relative and absolute quantitation (iTRAQ®) reagents and analyzed by LC-MS/MS. The standard workflow module for iTRAQ® quantification within the Proteome Discoverer was utilized for the data analysis...
August 2017: Data in Brief
https://www.readbyqxmd.com/read/28651860/fractional-fetal-thigh-volume-in-the-prediction-of-normal-and-abnormal-fetal-growth-during-the-third-trimester-of-pregnancy
#5
Louise E Simcox, Jenny E Myers, Tim J Cole, Edward D Johnstone
BACKGROUND: Currently 2D ultrasound (US) estimation of fetal size rather than fetal growth is used to define fetal growth restriction (FGR), but single estimates in late pregnancy lack sensitivity and may identify small for gestational age rather than growth restriction. Single or longitudinal measures of 3D fractional thigh volume may address this problem. OBJECTIVES: To derive normal values for 3D fractional thigh volume (TVol) in the third trimester, determine if TVol is superior to 2D ultrasound biometry alone for detecting FGR and whether individualised growth assessment parameters have the potential to identify FGR remote from term delivery...
June 23, 2017: American Journal of Obstetrics and Gynecology
https://www.readbyqxmd.com/read/28651329/high-speed-and-high-ratio-referential-genome-compression
#6
Yuansheng Liu, Hui Peng, Limsoon Wong, Jinyan Li
Motivation: The rapidly increasing number of genomes generated by high-throughput sequencing platforms and assembly algorithms is accompanied by problems in data storage, compression and communication. Traditional compression algorithms are unable to meet the demand of high compression ratio due to the intrinsic challenging features of DNA sequences such as small alphabet size, frequent repeats and palindromes. Reference-based lossless compression, by which only the differences between two similar genomes are stored, is a promising approach with high compression ratio...
June 23, 2017: Bioinformatics
https://www.readbyqxmd.com/read/28650382/hiv-drug-resistance-in-infants-increases-with-changing-pmtct-regimens
#7
Lisa K Poppe, Catherine Chunda-Liyoka, Eun Hee Kwon, Clement Gondwe, John T West, Chipepo Kankasa, Clement B Ndongmo, Charles Wood
OBJECTIVES: The objectives of this study were to determine HIV drug resistance prevalence in Zambian infants upon diagnosis, and to determine how changing prevention of mother-to-child transmission (PMTCT) regimens affect drug resistance. DESIGN: Dried blood spot (DBS) samples from infants in the Lusaka District of Zambia, obtained during routine diagnostic screening, were collected during four different years representing three different PMTCT treatment regimens...
June 23, 2017: AIDS
https://www.readbyqxmd.com/read/28646284/chd1l-expression-increases-tumor-progression-and-acts-as-a-predictive-biomarker-for-poor-prognosis-in-pancreatic-cancer
#8
Chuan Liu, Xiaowei Fu, Zhiwei Zhong, Jing Zhang, Haiyan Mou, Qiong Wu, Tianle Sheng, Bo Huang, Yeqing Zou
BACKGROUND: The chromodomain helicase/ATPase DNA binding protein 1-like gene (CHD1L) plays a key role in controlling various cellular phenomena, including immune-mediated inflammation, transformation, apoptosis, cell cycle progression, and proliferation. METHODS: This study investigated the function and clinical significance of CHD1L protein expression in pancreatic cancer (PC). We analyzed CHD1L expression in surgical specimens from 112 PC patients. The correlation between the clinical characteristics and prognosis was also determined...
June 23, 2017: Digestive Diseases and Sciences
https://www.readbyqxmd.com/read/28645171/upsetr-an-r-package-for-the-visualization-of-intersecting-sets-and-their-properties
#9
Jake R Conway, Alexander Lex, Nils Gehlenborg
Motivation: Venn and Euler diagrams are a popular yet inadequate solution for quantitative visualization of set intersections. A scalable alternative to Venn and Euler diagrams for visualizing intersecting sets and their properties is needed. Results: We developed UpSetR, an open source R package that employs a scalable matrix-based visualization to show intersections of sets, their size, and other properties. Availability: UpSetR is available at https://github...
June 22, 2017: Bioinformatics
https://www.readbyqxmd.com/read/28642276/dedifferentiation-proliferation-and-redifferentiation-of-adult-mammalian-cardiomyocytes-after-ischemic-injury
#10
Wei Eric Wang, Liangpeng Li, Xuewei Xia, Wenbin Fu, Qiao Liao, Cong Lan, Dezhong Yang, Hongmei Chen, Rongchuan Yue, Cindy S Zeng, Lin Zhou, Bin Zhou, Dayue D Duan, Xiongwen Chen, Steven R Houser, Chunyu Zeng
Background -Adult mammalian hearts have a limited ability to generate new cardiomyocytes. Proliferation of existing adult cardiomyocytes (ACM) is a potential source of new cardiomyocytes. Understanding the fundamental biology of ACM proliferation could be of great clinical significance for treating myocardial infarction (MI). We aim to understand the process and regulation of ACM proliferation and its role in new cardiomyocyte formation of post-MI mouse hearts. Methods -β-actin-GFP transgenic mice and fate-mapping Myh6-MerCreMer-tdTomato/lacZ mice were used to trace the fate of ACMs...
June 22, 2017: Circulation
https://www.readbyqxmd.com/read/28641268/newgoa-predicting-new-go-annotations-of-proteins-by-bi-random-walks-on-a-hybrid-graph
#11
Guoxian Yu, Guangyuan Fu, Jun Wang, Yingwen Zhao
A remaining key challenge of modern biology is annotating the functional roles of proteins. Various computational models have been proposed for this challenge. Most of them assume the annotations of annotated proteins are complete. But in fact, many of them are incomplete. We proposed a method called NewGOA to predict new Gene Ontology (GO) annotations for incompletely annotated proteins and for completely un-annotated ones. NewGOA employs a hybrid graph, composed of two types of nodes (proteins and GO terms), to encode interactions between proteins, hierarchical relationships between terms and available annotations of proteins...
June 15, 2017: IEEE/ACM Transactions on Computational Biology and Bioinformatics
https://www.readbyqxmd.com/read/28640617/5-methylhydantoin-from-isolated-molecules-in-a-low-temperature-argon-matrix-to-solid-state-polymorphs-characterization
#12
Bernardo A Nogueira, Gulce O Ildiz, João Canotilho, M Ermelinda S Eusébio, Marta Sofia C Henriques, José A Paixão, Rui Fausto
The molecular structure, vibrational spectra and photochemistry of 5-methylhydantoin (C4H6N2O2; 5-MH) were studied by matrix isolation infrared spectroscopy and theoretical calculations at the DFT(B3LYP)/6-311++G(d,p) theory level. The Natural Bond Orbital (NBO) analysis approach was used to study in detail the electronic structure of the minimum energy structure of 5-MH, namely the specific characteristics of the σ and π electronic systems of the molecule, and the stabilizing orbital interactions. UV irradiation of 5-MH isolated in argon matrix resulted in its photofragmentation through a single photochemical pathway, yielding isocyanic acid, ethanimine and carbon monoxide, thus following a pattern already observed before for the parent hydantoin and 1-methylhydantoin molecules...
June 22, 2017: Journal of Physical Chemistry. A
https://www.readbyqxmd.com/read/28640486/dendrimer-based-signal-amplification-of-click-labelled-dna-in-situ
#13
Nada Raddaoui, Samuele Stazzoni, Leonhard Möckl, Bastien Viverge, Florian Geiger, Hanna Engelke, Christoph Bräuchle, Thomas Carell
The in vivo incorporation of alkyne modified bases into the genome of cells is today the basis for efficient detection of cell proliferation. Cells are grown in the presence of ethinyl-dU (EdU), fixed and permeabilized. The incorporated alkynes are then efficiently detected using azide-containing fluorophores and the Cu(I) catalyzed alkyne-azide click reaction. In a world where constant improvement of the sensitivity of a given method is driving diagnostic advancement, we developed azide and alkyne modified dendrimers that allow to establish sandwich-type detection assays that show significantly improved signal intensities and signal to noise ratios far beyond of what is currently possible...
June 22, 2017: Chembiochem: a European Journal of Chemical Biology
https://www.readbyqxmd.com/read/28640224/nomegestrol-acetate-suppresses-human-endometrial-cancer-rl95-2-cells-proliferation-in-vitro-and-in-vivo-possibly-related-to-upregulating-expression-of-sufu-and-wnt7a
#14
A-Ying Ma, Shu-Wu Xie, Jie-Yun Zhou, Yan Zhu
Nomegestrol acetate (NOMAC) has been successfully used for the treatment of some gynecological disorders, and as a combined oral contraceptive with approval in many countries. In this study, we investigated the effects of NOMAC on human endometrial cancer cells in vitro and in vivo. The proliferation of human endometrial cancer cells (RL95-2 and KLE) were assessed using CCK-8 and EdU incorporation assays. Whole-genome cDNA microarray analysis was used to identify the effects of NOMAC on gene expression profiles in RL95-2 cells...
June 22, 2017: International Journal of Molecular Sciences
https://www.readbyqxmd.com/read/28637337/matrix-completion-with-side-information-and-its-applications-in-predicting-the-antigenicity-of-influenza-viruses
#15
Li Huang, Xianhong Li, Pengfei Guo, Yuhua Yao, Bo Liao, Weiwei Zhang, Fayou Wang, Jiasheng Yang, Yulong Zhao, Hailiang Sun, Pingan He, Jialiang Yang
Motivation: Low-rank matrix completion has been demonstrated to be powerful in predicting antigenic distances among influenza viruses and vaccines from partially revealed hemagglutination inhibition (HI) table. Meanwhile, influenza hemagglutinin (HA) protein sequences are also effective in inferring antigenic distances. Thus, it is natural to integrate HA protein sequence information into low-rank matrix completion model to help infer influenza antigenicity, which is critical to influenza vaccine development...
June 16, 2017: Bioinformatics
https://www.readbyqxmd.com/read/28636545/reversal-effect-of-jagged1-signaling-inhibition-on-ccl4-induced-hepatic-fibrosis-in-rats
#16
Guiju Tang, Zhihong Weng, Jun Song, Yixiong Chen
The role of the Notch ligand Jagged1 in hepatic fibrosis remains to be elucidated. In the current study, we investigated the role of Jagged1 in the activation of hepatic stellate cells (HSCs) and development of hepatic fibrosis in rats. In vitro, Jagged1 in HSCs was downregulated and upregulated by Jagged1 siRNA and pcDNA3.1 Jagged1, respectively. The levels of epithelial-mesenchymal transition (EMT) markers and HSC activation markers were assessed using western blot analysis. The proliferation and migration capacity of HSCs were assessed using 5-ethynyl-2'-deoxyuridine (EdU) incorporation and Transwell migration assays...
June 15, 2017: Oncotarget
https://www.readbyqxmd.com/read/28634344/omniga-optimized-omnivariate-decision-trees-for-generalizable-classification-models
#17
Arturo Magana-Mora, Vladimir B Bajic
Classification problems from different domains vary in complexity, size, and imbalance of the number of samples from different classes. Although several classification models have been proposed, selecting the right model and parameters for a given classification task to achieve good performance is not trivial. Therefore, there is a constant interest in developing novel robust and efficient models suitable for a great variety of data. Here, we propose OmniGA, a framework for the optimization of omnivariate decision trees based on a parallel genetic algorithm, coupled with deep learning structure and ensemble learning methods...
June 20, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28633445/bpp-a-sequence-based-algorithm-for-branch-point-prediction
#18
Qing Zhang, Xiaodan Fan, Yejun Wang, Mingan Sun, Jianlin Shao, Dianjing Guo
Motivation: Although high-throughput sequencing methods have been proposed to identify splicing branch points in the human genome, these methods can only detect a small fraction of the branch points subject to the sequencing depth, experimental cost and the expression level of the mRNA. An accurate computational model for branch point prediction is therefore an ongoing objective in human genome research. Results: We here propose a novel branch point prediction algorithm that utilises information on the branch point sequence and the polypyrimidine tract...
June 19, 2017: Bioinformatics
https://www.readbyqxmd.com/read/28633441/bioqueue-a-novel-pipeline-framework-to-accelerate-bioinformatics-analysis
#19
Li Yao, Heming Wang, Yuanyuan Song, Guangchao Sui
Motivation: With the rapid development of Next-Generation Sequencing, a large amount of data is now available for bioinformatics research. Meanwhile, the presence of many pipeline frameworks makes it possible to analyse these data. However, these tools concentrate mainly on their syntax and design paradigms, and dispatch jobs based on users' experience about the resources needed by the execution of a certain step in a protocol. As a result, it is difficult for these tools to maximize the potential of computing resources, and avoid errors caused by overload, such as memory overflow...
June 19, 2017: Bioinformatics
https://www.readbyqxmd.com/read/28633438/sandpuma-ensemble-predictions-of-nonribosomal-peptide-chemistry-reveals-biosynthetic-diversity-across-actinobacteria
#20
Marc G Chevrette, Fabian Aicheler, Oliver Kohlbacher, Cameron R Currie, Marnix H Medema
Summary: Nonribosomally synthesized peptides (NRPs) are natural products with widespread applications in medicine and biotechnology. Many algorithms have been developed to predict the substrate specificities of nonribosomal peptide synthetase adenylation (A) domains from DNA sequences, which enables prioritization and dereplication, and integration with other data types in discovery efforts. However, insufficient training data and a lack of clarity regarding prediction quality have impeded optimal use...
June 19, 2017: Bioinformatics
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