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https://www.readbyqxmd.com/read/29444233/betaserpentine-a-bioinformatics-tool-for-reconstruction-of-amyloid-structures
#1
Stanislav A Bondarev, Olga V Bondareva, Galina A Zhouravleva, Andrey V Kajava, Alfonso Valencia
Motivation: Numerous experimental studies have suggested that polypeptide chains of large amyloidogenic regions zig-zag in β-serpentine arrangements. These β-serpentines are stacked axially and form the superpleated β-structure. Despite this progress in the understanding of amyloid folds, the determination of their 3D structure at the atomic level is still a problem due to the polymorphism of these fibrils and incompleteness of experimental structural data. Today, the way to get insight into the atomic structure of amyloids is a combination of experimental studies with bioinformatics...
February 15, 2018: Bioinformatics
https://www.readbyqxmd.com/read/29444182/towards-phenotyping-stroke-leveraging-data-from-a-large-scale-epidemiological-study-to-detect-stroke-diagnosis
#2
Yizhao Ni, Kathleen Alwell, Charles J Moomaw, Daniel Woo, Opeolu Adeoye, Matthew L Flaherty, Simona Ferioli, Jason Mackey, Felipe De Los Rios La Rosa, Sharyl Martini, Pooja Khatri, Dawn Kleindorfer, Brett M Kissela
OBJECTIVE: 1) To develop a machine learning approach for detecting stroke cases and subtypes from hospitalization data, 2) to assess algorithm performance and predictors on real-world data collected by a large-scale epidemiology study in the US; and 3) to identify directions for future development of high-precision stroke phenotypic signatures. MATERIALS AND METHODS: We utilized 8,131 hospitalization events (ICD-9 codes 430-438) collected from the Greater Cincinnati/Northern Kentucky Stroke Study in 2005 and 2010...
2018: PloS One
https://www.readbyqxmd.com/read/29444145/waggawagga-cli-a-command-line-tool-for-predicting-stable-single-%C3%AE-helices-sah-domains-and-the-sah-domain-distribution-across-eukaryotes
#3
Dominic Simm, Martin Kollmar
Stable single-alpha helices (SAH-domains) function as rigid connectors and constant force springs between structural domains, and can provide contact surfaces for protein-protein and protein-RNA interactions. SAH-domains mainly consist of charged amino acids and are monomeric and stable in polar solutions, characteristics which distinguish them from coiled-coil domains and intrinsically disordered regions. Although the number of reported SAH-domains is steadily increasing, genome-wide analyses of SAH-domains in eukaryotic genomes are still missing...
2018: PloS One
https://www.readbyqxmd.com/read/29440670/characterization-of-conserved-and-novel-micrornas-in-lilium-lancifolium-thunb-by-high-throughput-sequencing
#4
Xiangfeng He, Awraris Getachew Shenkute, Wenhe Wang, Shufa Xu
MicroRNAs (miRNAs) are among the class of noncoding small RNA molecules and play a crucial role in post-transcriptional regulation in plants. Although Lilium is one of the most popular ornamental flowers worldwide, however, there is no report on miRNAs identification. In the present study, therefore, miRNAs and their targets were identified from flower, leaf, bulblet and bulb of Lilium lancifolium Thunb. by high-throughput sequencing and bioinformatics analysis. In this study, a total of 38 conserved miRNAs belonging to 17 miRNA families and 44 novel miRNAs were identified...
February 13, 2018: Scientific Reports
https://www.readbyqxmd.com/read/29440596/multi-omics-driven-assembly-and-annotation-of-the-sandalwood-santalum-album-genome
#5
H B Mahesh, Pratigya Subba, Jayshree Advani, Meghana Deepak Shirke, Ramya Malarini Loganathan, S Chandana, S Shilpa, Oishi Chatterjee, Sneha M Pinto, Keshava Prasad, Malali Gowda
Santalum album (Indian sandalwood) is an important tropical evergreen tree, known for its fragrant heartwood-derived essential oil and its valuable carving wood. Here, we applied an integrated genomic, transcriptomic, and proteomic approach to assemble and annotate the Indian sandalwood genome. Our genome sequencing resulted in the establishment of a draft map of the smallest genome for any woody tree species to date (221 Mb). The genome annotation predicted 38,119 protein-coding genes and 27.42% repetitive DNA elements...
February 12, 2018: Plant Physiology
https://www.readbyqxmd.com/read/29440217/using-big-data-to-improve-cardiovascular-care-and-outcomes-in-china-a-protocol-for-the-chinese-electronic-health-records-research-in-yinzhou-cherry-study
#6
Hongbo Lin, Xun Tang, Peng Shen, Dudan Zhang, Jinguo Wu, Jingyi Zhang, Ping Lu, Yaqin Si, Pei Gao
INTRODUCTION: Data based on electronic health records (EHRs) are rich with individual-level longitudinal measurement information and are becoming an increasingly common data source for clinical risk prediction worldwide. However, few EHR-based cohort studies are available in China. Harnessing EHRs for research requires a full understanding of data linkages, management, and data quality in large data sets, which presents unique analytical opportunities and challenges. The purpose of this study is to provide a framework to establish a uniquely integrated EHR database in China for scientific research...
February 12, 2018: BMJ Open
https://www.readbyqxmd.com/read/29439669/a-novel-mir-375-hoxb3-cdca3-dnmt3b-regulatory-circuitry-contributes-to-leukemogenesis-in-acute-myeloid-leukemia
#7
Laixi Bi, Bin Zhou, Haiying Li, Licai He, Chunjing Wang, Zhonggai Wang, Liqing Zhu, Mengqian Chen, Shenmeng Gao
BACKGROUND: Acute myeloid leukemia (AML) is a heterogeneous group of hematopoietic malignancies due to sophisticated genetic mutations and epigenetic dysregulation. MicroRNAs (miRNAs), a class of small non-coding RNAs, are important regulators of gene expression in all biological processes, including leukemogenesis. Recently, miR-375 has been reported to be a suppressive miRNA in multiple types of cancers, but its underlying anti-leukemia activity in AML is largely unknown. METHODS: Quantitative reverse transcriptase PCR (qRT-PCR) was used to measure the expression of miR-375 and HOXB3 in leukemic cells and normal controls...
February 13, 2018: BMC Cancer
https://www.readbyqxmd.com/read/29439149/pediatric-dog-bites-a-population-based-profile
#8
Jackson Fein, David Bogumil, Jeffrey S Upperman, Rita V Burke
BACKGROUND: Previous studies have identified risk factors for dog bites in children, but use data from individual trauma centers, with limited generalizability. This study identifies a population risk profile for pediatric dog bites using the National Trauma Data Bank. We hypothesized that the population at risk was younger boys, that such bites occur at home, are moderately severe, and are on the face or neck. METHODS: For this retrospective cross-sectional study, a sample of 7912 children 17 years old and younger with International Classification of Diseases (ICD)-9 event code E906...
February 8, 2018: Injury Prevention: Journal of the International Society for Child and Adolescent Injury Prevention
https://www.readbyqxmd.com/read/29438560/hiite-hiv-1-incidence-and-infection-time-estimator
#9
Sung Yong Park, Tanzy M T Love, Shivankur Kapoor, Ha Youn Lee, John Hancock
Motivation: Around 2.1 million new HIV-1 infections were reported in 2015, alerting that the HIV-1 epidemic remains a significant global health challenge. Precise incidence assessment strengthens epidemic monitoring efforts and guides strategy optimization for prevention programs. Estimating the onset time of HIV-1 infection can facilitate optimal clinical management and identify key populations largely responsible for epidemic spread and thereby infer HIV-1 transmission chains. Our goal is to develop a genomic assay estimating the incidence and infection time in a single cross-sectional survey setting...
February 9, 2018: Bioinformatics
https://www.readbyqxmd.com/read/29438049/oncoprotein-aeg-1-is-an-endoplasmic-reticulum-rna-binding-protein-whose-interactome-is-enriched-in-organelle-resident-protein-encoding-mrnas
#10
Jack C-C Hsu, David W Reid, Alyson M Hoffman, Devanand Sarkar, Christopher V Nicchitta
Astrocyte elevated gene-1 (AEG-1), an oncogene whose overexpression promotes tumor cell proliferation, angiogenesis, invasion, and enhanced chemoresistance, is thought to function primarily as a scaffolding protein, regulating PI3K/Akt and Wnt/β-catenin signaling pathways. Here we report that AEG-1 is an endoplasmic reticulum (ER) resident integral membrane RNA-binding protein (RBP). Examination of the AEG-1 RNA interactome by HITS-CLIP and PAR-CLIP methodologies revealed a high enrichment for endomembrane organelle-encoding transcripts, most prominently those encoding ER resident proteins, and within this cohort, for integral membrane protein-encoding RNAs...
February 7, 2018: RNA
https://www.readbyqxmd.com/read/29436887/machine-learning-in-autistic-spectrum-disorder-behavioral-research-a-review-and-ways-forward
#11
Fadi Thabtah
Autistic Spectrum Disorder (ASD) is a mental disorder that retards acquisition of linguistic, communication, cognitive, and social skills and abilities. Despite being diagnosed with ASD, some individuals exhibit outstanding scholastic, non-academic, and artistic capabilities, in such cases posing a challenging task for scientists to provide answers. In the last few years, ASD has been investigated by social and computational intelligence scientists utilizing advanced technologies such as machine learning to improve diagnostic timing, precision, and quality...
February 13, 2018: Informatics for Health & Social Care
https://www.readbyqxmd.com/read/29436874/the-influence-of-fiber-dispersion-on-the-mechanical-response-of-aortic-tissues-in-health-and-disease-a-computational-study
#12
Justyna A Niestrawska, Daniel Ch Haspinger, Gerhard A Holzapfel
Changes in the structural components of aortic tissues have been shown to play a significant role in the pathogenesis of aortic degeneration. Therefore, reliable stress analyses require a suitable and meaningful constitutive model that captures micro-structural changes. As recent data show, in-plane and out-of-plane collagen fiber dispersions vary significantly between healthy and aneurysmatic aortic walls. The aim of this study is to computationally investigate the influence of fiber dispersion on the mechanical response of aortic tissues in health and disease...
February 13, 2018: Computer Methods in Biomechanics and Biomedical Engineering
https://www.readbyqxmd.com/read/29436619/a-six-long-non-coding-rna-signature-predicts-prognosis-in-melanoma-patients
#13
Shuocheng Yang, Jianguo Xu, Xuan Zeng
The aim of this study was to identify long non-coding RNAs (lncRNAs) which may prove useful for risk-classifying patients with melanoma. For this purpose, based on a dataset from The Cancer Genome Atlas (TCGA), we selected and analyzed samples from melanoma stages I, II, III and IV, from which differentially expressed lncRNAs were identified. The lncRNAs were classified using two-way hierarchical clustering analysis and analysis of support vector machine (SVM), followed by Kaplan-Meier survival analysis. The prognostic capacity of the signature was verified on an independent dataset...
February 7, 2018: International Journal of Oncology
https://www.readbyqxmd.com/read/29435866/diagnostic-accuracy-of-icd-9-code-780-2-for-the-identification-of-patients-with-syncope-in-the-emergency-department
#14
Ludovico Furlan, Monica Solbiati, Veronica Pacetti, Franca Dipaola, Martino Meda, Mattia Bonzi, Elisa Fiorelli, Giulia Cernuschi, Daniele Alberio, Giovanni Casazza, Nicola Montano, Raffaello Furlan, Giorgio Costantino
PURPOSE: Syncope is a common condition that affects individuals of all ages and is responsible for 1-3% of all emergency department (ED) visits. Prospective studies on syncope are often limited by the exiguous number of subjects enrolled. A possible alternative approach would be to use of hospital discharge diagnoses from administrative databases to identify syncope subjects in epidemiological observational studies. We assessed the accuracy of the International Classification of Diseases, Ninth Revision (ICD-9) code 780...
February 12, 2018: Clinical Autonomic Research: Official Journal of the Clinical Autonomic Research Society
https://www.readbyqxmd.com/read/29435780/protein-ligand-interfaces-are-polarized-discovery-of-a-strong-trend-for-intermolecular-hydrogen-bonds-to-favor-donors-on-the-protein-side-with-implications-for-predicting-and-designing-ligand-complexes
#15
Sebastian Raschka, Alex J Wolf, Joseph Bemister-Buffington, Leslie A Kuhn
Understanding how proteins encode ligand specificity is fascinating and similar in importance to deciphering the genetic code. For protein-ligand recognition, the combination of an almost infinite variety of interfacial shapes and patterns of chemical groups makes the problem especially challenging. Here we analyze data across non-homologous proteins in complex with small biological ligands to address observations made in our inhibitor discovery projects: that proteins favor donating H-bonds to ligands and avoid using groups with both H-bond donor and acceptor capacity...
February 12, 2018: Journal of Computer-aided Molecular Design
https://www.readbyqxmd.com/read/29435649/genome-sequence-and-description-of-haloferax-massiliense-sp-nov-a-new-halophilic-archaeon-isolated-from-the-human-gut
#16
Saber Khelaifia, Aurelia Caputo, Claudia Andrieu, Frederique Cadoret, Nicholas Armstrong, Caroline Michelle, Jean-Christophe Lagier, Felix Djossou, Pierre-Edouard Fournier, Didier Raoult
By applying the culturomics concept and using culture conditions containing a high salt concentration, we herein isolated the first known halophilic archaeon colonizing the human gut. Here we described its phenotypic and biochemical characterization as well as its genome annotation. Strain Arc-HrT (= CSUR P0974 = CECT 9307) was mesophile and grew optimally at 37 °C and pH 7. Strain Arc-HrT was also extremely halophilic with an optimal growth observed at 15% NaCl. It showed gram-negative cocci, was strictly aerobic, non-motile and non-spore-forming, and exhibited catalase and oxidase activities...
February 12, 2018: Extremophiles: Life Under Extreme Conditions
https://www.readbyqxmd.com/read/29435179/identifying-characteristic-mirnas-genes-and-risk-pathways-of-multiple-sclerosis-based-on-bioinformatics-analysis
#17
Deling Luo, Jin Fu
Multiple sclerosis is a chronic autoimmune disorder of the central nervous system. In MS, the genetic susceptibility is high and currently there is no effective treatment. MicroRNA, a small non-coding RNA, plays a vital role in immune responses. Aberrant or dysfunctional miRNAs may cause several diseases, including MS, thus miRNAs and miRNA related genes may be therapeutic weapons against MS. Here, we identified 21 miRNAs in peripheral blood mono-nuclear cells from over 600 persons, including healthy controls...
January 12, 2018: Oncotarget
https://www.readbyqxmd.com/read/29434722/analysis-of-long-non-coding-rna-expression-profiles-identifies-functional-lncrnas-associated-with-the-progression-of-acute-coronary-syndromes
#18
Yingjie Lu, Xiangwei Meng, Lifeng Wang, Xiaoyun Wang
It has been demonstrated that long non-coding RNAs (lncRNAs) are important in the gene regulatory network and their dysregulated expression has been implicated in cardiovascular disease. However, little is known regarding lncRNA expression patterns and their function in the progression of acute coronary syndromes (ACSs). In the present study, the expression profiles of lncRNAs from 52 patients with ACS were analyzed by re-annotating existing microarray data. The lncRNA expression profiles in the two distinct clinical entities of ACS, myocardial infarction (MI) and unstable angina (UA), were examined...
February 2018: Experimental and Therapeutic Medicine
https://www.readbyqxmd.com/read/29434705/identification-of-a-progression-associated-long-non-coding-rna-signature-for-predicting-the-prognosis-of-lung-squamous-cell-carcinoma
#19
Yanyan Wang, Fang Yang, Yongzhi Zhuang
Long non-coding RNAs (lncRNAs) have been indicated to have prognostic roles in various cancer types. However, the association between lncRNAs and lung squamous cell carcinoma (LSCC) progression, and the prognostic value of lncRNAs as a marker for early detection of LSCC have not been systematically investigated. The present study performed a genome-wide comparative analysis in order to determine the expression profiles of 10,207 lncRNAs to investigate the expression patterns between patients with early stages of LSCC (stage I-II) and those with late-stage disease (stage III-IV)...
February 2018: Experimental and Therapeutic Medicine
https://www.readbyqxmd.com/read/29434344/identification-of-micrornas-differentially-expressed-in-glioblastoma-stem-like-cells-and-their-association-with-patient-survival
#20
Jiri Sana, Petr Busek, Pavel Fadrus, Andrej Besse, Lenka Radova, Marek Vecera, Stefan Reguli, Lucie Stollinova Sromova, Marek Hilser, Radim Lipina, Radek Lakomy, Leos Kren, Martin Smrcka, Aleksi Sedo, Ondrej Slaby
Glioblastoma stem-like cells (GSCs) are critical for the aggressiveness and progression of glioblastoma (GBM) and contribute to its resistance to adjuvant treatment. MicroRNAs (miRNAs) are small, non-coding RNAs controlling gene expression at the post-transcriptional level, which are known to be important regulators of the stem-like features. Moreover, miRNAs have been previously proved to be promising diagnostic biomarkers in several cancers including GBM. Using global expression analysis of miRNAs in 10 paired in-vitro as well as in-vivo characterized primary GSC and non-stem glioblastoma cultures, we identified a miRNA signature associated with the stem-like phenotype in GBM...
February 12, 2018: Scientific Reports
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