265,236 results match your criteria Bioinformatics [Journal]


The Computational article format: Software as a research output.

Authors:
Greg Finak

Cytometry A 2018 Dec;93(12):1187-1188

Department of Biostatistics Bioinformatics and Epidemiology, Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Center, Seattle, Washington.

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December 2018
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CytoML for cross-platform cytometry data sharing.

Cytometry A 2018 Dec;93(12):1189-1196

Program in Biostatistics Bioinformatics and Epidemiology, Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Center, Seattle, Western Australia.

CytoML is an R/Bioconductor package that enables cross-platform import, export, and sharing of gated cytometry data. It currently supports Cytobank, FlowJo, Diva, and R, allowing users to import gated cytometry data from commercial platforms into R. Once data are available in R, the data can be further manipulated. Read More

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December 2018
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Novel endotypes in heart failure: effects on guideline-directed medical therapy.

Eur Heart J 2018 Dec 13. Epub 2018 Dec 13.

Department of Cardiology, University of Groningen, Hanzeplein 1, Groningen, the Netherlands.

Aims: We sought to determine subtypes of patients with heart failure (HF) with a distinct clinical profile and treatment response, using a wide range of biomarkers from various pathophysiological domains.

Methods And Results: We performed unsupervised cluster analysis using 92 established cardiovascular biomarkers to identify mutually exclusive subgroups (endotypes) of 1802 patients with HF and reduced ejection fraction (HFrEF) from the BIOSTAT-CHF project. We validated our findings in an independent cohort of 813 patients. Read More

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December 2018

MiR-23a-3p acts as an oncogene and potential prognostic biomarker by targeting PNRC2 in RCC.

Biomed Pharmacother 2018 Dec 11;110:656-666. Epub 2018 Dec 11.

Department of Urology, Peking University Shenzhen Hospital, Shenzhen, Guangdong 518036, P.R. China; Guangdong and Shenzhen Key Laboratory of Male Reproductive Medicine and Genetics, Institute of Urology, Peking University Shenzhen Hospital, Shenzhen PKU-HKUST Medical Center, Shenzhen, Guangdong 518036, P.R. China. Electronic address:

Background: Renal cell carcinoma (RCC) is a most common kidney malignancy, with atypical symptoms in the early stage and poor outcome in the late stage. Recently, emerging evidence revealed that some miRNAs play an essential role in the tumorigenesis and progression of RCC. Therefore, the aim of this study is that understand the detailed molecular mechanism of miR-23a-3p in RCC and identify its potential clinical value. Read More

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December 2018
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Immunosuppression, oxidative stress, and glycometabolism disorder caused by cadmium in common carp (Cyprinus carpio L.): Application of transcriptome analysis in risk assessment of environmental contaminant cadmium.

J Hazard Mater 2018 Dec 5;366:386-394. Epub 2018 Dec 5.

College of Animal Science and Technology, Northeast Agricultural University, Harbin, 150030, PR China. Electronic address:

Cadmium (Cd), a hazardous environmental contaminant with irreversible toxicity to fish, has been detected in aquatic environment of many countries. The common carp is one of the most widely distributed fish in the world, so we used common carp to assess environmental contaminant risk. In present study, we investigated effects of Cd on immune function, oxidative defense, and glycometabolism in the spleens of common carp by transcriptome analysis. Read More

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December 2018

Dissecting the Thermodynamic Contributions of the Charged Residues in the Membrane Anchoring of Bcl-xl C-Terminal Domain.

Chem Phys Lipids 2018 Dec 11. Epub 2018 Dec 11.

Bioinformatics Centre, Bose Institute, P-1/12 C.I.T. Scheme VII M, Kolkata, 700054, India. Electronic address:

The C-terminal helix of the Bcl-xl is known to initiate the membrane insertion of the protein by anchoring into the mitochondrial outer membrane. The C-terminal charged residues of that helix, R232, and K233, are reported to have an important structural role in the process of insertion. The present work provides a quantitative understanding of the thermodynamic contribution of these residues on the membrane insertion profile from Adaptive Biasing Force based MD simulations of 2. Read More

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December 2018

Reducing the Complexity of Mathematical Models for the Plant Circadian Clock by Distributed Delays.

J Theor Biol 2018 Dec 11. Epub 2018 Dec 11.

Sainsbury Laboratory, University of Cambridge, Bateman Street, Cambridge, CB2 1LR, UK. Electronic address:

A major bottleneck in the modelling of biological networks is the parameter explosion problem - the exponential increase in the number of parameters that need to be optimised to data as the size of the model increases. Here, we address this problem in the context of the plant circadian clock by applying the method of distributed delays. We show that using this approach, the system architecture can be simplified efficiently - reducing the number of parameters - whilst still preserving the core mechanistic dynamics of the gene regulatory network. Read More

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December 2018

Polyphyly in 16S rRNA-based LVTree Versus Monophyly in Whole-genome-based CVTree.

Genomics Proteomics Bioinformatics 2018 Dec 11. Epub 2018 Dec 11.

T-Life Research Center, Department of Physics, Fudan University, Shanghai 200433, China.

We report an important but long-overlooked manifestation of low-resolution power of 16S rRNA sequence analysis at the species level, namely, in 16S rRNA-based phylogenetic trees polyphyletic placements of closely-related species are abundant compared to those in genome-based phylogeny. This phenomenon makes the demarcation of genera within many families ambiguous in the 16S rRNA-based taxonomy. In this study, we reconstructed phylogenetic relationship for more than ten thousand prokaryote genomes by using the CVTree method, which is based on whole-genome information. Read More

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December 2018

Identification of putative non-host essential genes and novel drug targets against Acinetobacter baumannii by in silico comparative genome analysis.

Microb Pathog 2018 Dec 11. Epub 2018 Dec 11.

Department of Biochemistry, Abdul Wali Khan University, Mardan, Pakistan.

Acinetobacter baumannii, the gram-negative bacteria emerged as an extremely critical pathogen causing nosocomial and different kinds of infections. A. baumannii exhibit resistivity towards various classes of antibiotics that shows that there is a dire need to search more drug targets by exploiting the full genome of the bacteria. Read More

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December 2018

Iron-associated protein interaction networks reveal the key functional modules related to survival and virulence of Pasteurella multocida.

Microb Pathog 2018 Dec 11. Epub 2018 Dec 11.

Department of Zoology, Faculty of Science, Kasetsart University, Bangkok, 10900, Thailand; Omics Center for Agriculture, Bioresources, Food, and Health, Faculty of Science, Kasetsart University (OmiKU), Bangkok, 10900, Thailand. Electronic address:

Pasteurella multocida causes respiratory infectious diseases in a multitude of birds and mammals. A number of virulence-associated genes were reported across different strains of P. multocida, including those involved in the iron transport and metabolism. Read More

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December 2018

Comparative Flavivirus-Host Protein Interaction Mapping Reveals Mechanisms of Dengue and Zika Virus Pathogenesis.

Cell 2018 Dec;175(7):1931-1945.e18

Department of Cellular and Molecular Pharmacology, University of California San Francisco, San Francisco, CA, USA; Quantitative Biosciences Institute (QBI), University of California San Francisco, San Francisco, CA, USA; The J. David Gladstone Institutes, San Francisco, CA, USA. Electronic address:

Mosquito-borne flaviviruses, including dengue virus (DENV) and Zika virus (ZIKV), are a growing public health concern. Systems-level analysis of how flaviviruses hijack cellular processes through virus-host protein-protein interactions (PPIs) provides information about their replication and pathogenic mechanisms. We used affinity purification-mass spectrometry (AP-MS) to compare flavivirus-host interactions for two viruses (DENV and ZIKV) in two hosts (human and mosquito). Read More

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December 2018

Deception through Mimicry: A Cellular Antiviral Strategy.

Cell 2018 Dec;175(7):1728-1729

Department of Integrative Structural and Computational Biology, the Scripps Research Institute, La Jolla, CA 92037, USA. Electronic address:

Viruses use mimicry to hijack cellular machinery, but can human cells use mimicry as an antiviral approach? Batra et al. identify a novel antiviral restriction factor, RBBP6, by characterizing the cellular interactome of Ebola virus. RBBP6 targets the Ebola virus transcription factor VP30 by mimicking the binding of Ebola virus nucleoprotein. Read More

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December 2018

Clinicopathological and molecular analysis of multinodular and vacuolating neuronal tumors of the cerebrum.

Hum Pathol 2018 Dec 11. Epub 2018 Dec 11.

Department of Pathology, Seoul National University Hospital and Seoul National University College of Medicine, Seoul, Republic of Korea; Institute of Neuroscience, Seoul National University College of Medicine, Seoul, Republic of Korea. Electronic address:

Multinodular and vacuolating neuronal tumor (MVNT) of the cerebrum is a recently recognized rare neuronal tumor, and its pathogenesis is unclear. We analyzed 7 cases of histologically typical MVNT: six were adults [mean age: 43.0years (range: 23-56)] and one was a child (10-year-old). Read More

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December 2018

The cytochrome b lysine 329 residue is critical for ubihydroquinone oxidation and proton release at the Q site of bacterial cytochrome bc.

Biochim Biophys Acta Bioenerg 2018 Dec 11. Epub 2018 Dec 11.

Department of Biology, University of Pennsylvania, Philadelphia, PA 19104, USA. Electronic address:

The ubihydroquinone:cytochrome (cyt) c oxidoreductase (or cyt bc) is an important enzyme for photosynthesis and respiration. In bacteria like Rhodobacter capsulatus, this membrane complex has three subunits, the iron‑sulfur protein (ISP) with its FeS cluster, cyt c and cyt b, forming two catalytic domains, the Q (hydroquinone (QH) oxidation) and Q (quinone (Q) reduction) sites. At the Q site, the electron transfer pathways originating from QH oxidation are known, but their associated proton release routes are less well defined. Read More

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December 2018

Stochastic resonance improves visuomotor temporal integration in healthy young adults.

PLoS One 2018 14;13(12):e0209382. Epub 2018 Dec 14.

Neurorehabilitation Research Center, Kio University, Nara, Japan.

Mechanical and electrical noise stimulation to the body is known to improve the sensorimotor system. This improvement is related to stochastic resonance (SR), a phenomenon described as a "noise benefit" to various sensory and motor systems. The current study investigated the influence of SR on visuomotor temporal integration and hand motor function under delayed visual feedback in healthy young adults. Read More

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December 2018
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Prediction of antibiotic resistance in Escherichia coli from large-scale pan-genome data.

PLoS Comput Biol 2018 Dec 14;14(12):e1006258. Epub 2018 Dec 14.

Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridgeshire, United Kingdom.

The emergence of microbial antibiotic resistance is a global health threat. In clinical settings, the key to controlling spread of resistant strains is accurate and rapid detection. As traditional culture-based methods are time consuming, genetic approaches have recently been developed for this task. Read More

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December 2018
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Influence of pathway topology and functional class on the molecular evolution of human metabolic genes.

PLoS One 2018 14;13(12):e0208782. Epub 2018 Dec 14.

Institute of Systems Biology, Department of Biochemistry and Molecular Biology, University of Valencia, Valencia, Spain.

Metabolic networks comprise thousands of enzymatic reactions functioning in a controlled manner and have been shaped by natural selection. Thanks to the genome data, the footprints of adaptive (positive) selection are detectable, and the strength of purifying selection can be measured. This has made possible to know where, in the metabolic network, adaptive selection has acted and where purifying selection is more or less strong and efficient. Read More

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December 2018

Distinction of sporadic and familial forms of ALS based on mitochondrial characteristics.

FASEB J 2018 Dec 14:fj201801843R. Epub 2018 Dec 14.

Laboratory of Bioenergetics and Biomembranes, Nencki Institute of Experimental Biology, Polish Academy of Sciences, Warsaw, Poland.

Bioenergetic failure, oxidative stress, and changes in mitochondrial morphology are common pathologic hallmarks of amyotrophic lateral sclerosis (ALS) in several cellular and animal models. Disturbed mitochondrial physiology has serious consequences for proper functioning of the cell, leading to the chronic mitochondrial stress. Mitochondria, being in the center of cellular metabolism, play a pivotal role in adaptation to stress conditions. Read More

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December 2018

Modular Nanoparticulate Prodrug Design Enables Efficient Treatment of Solid Tumors Using Bioorthogonal Activation.

ACS Nano 2018 Dec 14. Epub 2018 Dec 14.

Center for Systems Biology , Massachusetts General Hospital , Boston , Massachusetts 02114 , United States.

Prodrug strategies that facilitate localized and controlled activity of small-molecule therapeutics can reduce systemic exposure and improve pharmacokinetics, yet limitations in activation chemistry have made it difficult to assign tunable multifunctionality to prodrugs. Here, we present the design and application of a modular small-molecule caging strategy that couples bioorthogonal cleavage with a self-immolative linker and an aliphatic anchor. This strategy leverages recently discovered in vivo catalysis by a nanoencapsulated palladium compound (Pd-NP), which mediates alloxylcarbamate cleavage and triggers release of the activated drug. Read More

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December 2018

[Gene expression profile analysis involved in pathogenesis of allergic rhinitis by using bioinformatics method as a novel way of drug screening].

Lin Chung Er Bi Yan Hou Tou Jing Wai Ke Za Zhi 2018 Oct;32(19):1464-1468

Department of Otorhinolaryngology, Beijing Shijitan Hospital, Affiliated to Capital Medical University.

To analyze the dynamic changes of the clinical features of chronic rhinosinusitis in recent 10 years, so as to deeply understand the characteristics of chronic rhinosinusitis, and to provide new ideas for treatment of chronic rhinosinusitis. This retrospective study was performed in patients who were diagnosed as chronic rhinosinusitis and enrolled. General information, clinical examination and pathological results were all collected, then patients' age, gender, the incidence of asthma and allergic rhinitis, peripheral eosinophil percentage, olfactory dysfunction and pathological results were statistically analyzed. Read More

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October 2018

Acupuncture for Treatment of Persistent Disturbed Sleep: A Randomized Clinical Trial in Veterans With Mild Traumatic Brain Injury and Posttraumatic Stress Disorder.

J Clin Psychiatry 2018 Dec 11;80(1). Epub 2018 Dec 11.

Department of Neurology, Emory Sleep Center, Department of Psychiatry and Behavioral Sciences, Emory University School of Medicine, Atlanta, Georgia, USA.

Objective: To evaluate real, as compared with sham, acupuncture in improving persistent sleep disturbance in veterans with mild traumatic brain injury (mTBI) and posttraumatic stress disorder (PTSD).

Methods: This sham-controlled randomized clinical trial at a US Department of Veterans Affairs Medical Center (2010-2015) included 60 veterans aged 24-55 years (mean of 40 years) with history of mTBI of at least 3 months and refractory sleep disturbance. Most of these participants (66. Read More

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December 2018

Quantitative multi-locus metabarcoding and waggle dance interpretation reveal honey bee spring foraging patterns in Midwest agroecosystems.

Mol Ecol 2018 Dec 14. Epub 2018 Dec 14.

Department of Entomology, The Ohio State University.

We explored the pollen foraging behavior of honey bee colonies situated in the corn and soybean dominated agroecosystems of central Ohio over a month-long period using both pollen metabarcoding and waggle dance inference of spatial foraging patterns. For molecular pollen analysis we developed simple and cost-effective laboratory and bioinformatics methods. Targeting four plant barcode loci (ITS2, rbcL, trnL and trnH), we implemented metabarcoding library preparation and dual-indexing protocols designed to minimize amplification biases and index mis-tagging events. Read More

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December 2018

Identification of potential prognostic TF-associated lncRNAs for predicting survival in ovarian cancer.

J Cell Mol Med 2018 Dec 13. Epub 2018 Dec 13.

The First Affiliated Hospital, Harbin Medical University, Harbin, China.

The pathophysiology of ovarian cancer (OV) is complex and depends on multiple biological processes and pathways. Therefore, there is an urgent need to identify reliable prognostic biomarkers for predicting clinical outcomes and helping personalize treatment of OV. A long non-coding RNA (lncRNA)-based risk score model was constructed to infer the prognostic efficacy of transcription factors (TFs) based on the OV dataset from The Cancer Genome Atlas. Read More

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December 2018

MicroRNA-1204 promotes cell proliferation by regulating PITX1 in non-small cell lung cancer.

Cell Biol Int 2018 Dec 14. Epub 2018 Dec 14.

Department of Thoracic and Cardiovascular Surgery, The First Affiliated Hospital of Nanjing Medical University, Nanjing, China.

MicroRNA-1204 (miR-1204), a member of the PVT1 region, may improve B cell differentiation and metastasis in breast cancer. However, the role of miR-1204 in NSCLC (non-small cell lung cancer) and its mechanism remain unclear. The GEO public database was first employed to find differentially expressed genes. Read More

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December 2018

HER2 mCRC patients with exon 20 R784G substitution mutation do not respond to the cetuximab therapy.

J Cell Physiol 2018 Dec 13. Epub 2018 Dec 13.

Gastroenterology and Liver Diseases Research Center, Research Institute for Gastroenterology and Liver Diseases, Shahid Beheshti University of Medical Sciences, Tehran, Iran.

The human epidermal growth factor 2 (HER2) gene undergoes various mutations that could alter its activity or respond to the antibody therapies. Cetuximab, a known anti-EGFR monoclonal antibody (mAB), is widely administered in metastatic colorectal cancer (mCRC) cases. Here we identified mCRC patients who did not respond to cetuximab (500 mg/m , q2w) after fluoropyrimidine/oxaliplatin regimen failure. Read More

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December 2018

Metabolic Profiling of High Egg Consumption and the Associated Lower Risk of Type 2 Diabetes in Middle-Aged Finnish Men.

Mol Nutr Food Res 2018 Dec 12:e1800605. Epub 2018 Dec 12.

S. Noerman, Dr. O. Kärkkäinen, Prof. T. Nurmi, Prof. T.-P. Tuomainen, Prof. S. Voutilainen, Dr. K. Hanhineva, Dr. J. K. Virtanen, Institute of Public Health and Clinical Nutrition, University of Eastern Finland, Kuopio, Finland.

Scope: Higher egg intake was previously associated with a lower risk of developing type 2 diabetes (T2D) in the prospective, population-based Kuopio Ischaemic Heart Disease Risk Factor Study (KIHD) in eastern Finland. We explored potential compounds that could explain this association using non-targeted LC-MS-based metabolic profiling.

Methods And Results: We analyzed 239 baseline serum samples from the KIHD in 4 groups: subjects with higher (mean intake 1 egg/d) or lower (mean intake 2 eggs/wk) egg intake who developed T2D (cases) or remained heatlhy (controls) during the mean follow-up of 19. Read More

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December 2018

Etiology of acute viral respiratory infections common in Pakistan: A review.

Rev Med Virol 2018 Dec 12:e2024. Epub 2018 Dec 12.

Department of Bioinformatics and Biotechnology, International Islamic University, Islamabad, Pakistan.

Respiratory infections, especially those of the lower respiratory tract, remain a foremost cause of mortality and morbidity of children greater than 5 years in developing countries including Pakistan. Ignoring these acute-level infections may lead to complications. Particularly in Pakistan, respiratory infections account for 20% to 30% of all deaths of children. Read More

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December 2018

Long noncoding RNA CCAT2 functions as a competitive endogenous RNA to regulate FOXC1 expression by sponging miR-23b-5p in lung adenocarcinoma.

J Cell Biochem 2018 Dec 12. Epub 2018 Dec 12.

Department of Thoracic Surgery, Huai'an Second People's Hospital and The Affiliated Huai'an Hospital of Xuzhou Medical University, Huai'an, China.

Long noncoding RNA (lncRNA) may regulate the process of tumor formation. Although lncRNA CCAT2 has been identified as a key point in many diseases, its pathophysiological mechanism in lung adenocarcinoma remains unknown. We measured the expression level of CCAT2 in lung adenocarcinoma cells and normal lung epithelial cell line BEAS-2B by quantitative real-time polymerase chain reaction (qRT-PCR). Read More

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December 2018

Computational investigation into the fluorescence of luciferin analogues.

J Comput Chem 2019 Jan;40(2):527-531

Department of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School, Worcester, Massachusetts.

Luciferin analogues that display bioluminescence at specific wavelengths can broaden the scope of imaging and biological assays, but the need to design and synthesize many new analogues can be time-consuming. Employing a collection of previously synthesized and characterized aminoluciferin analogues, we demonstrate that computational TD-DFT methods can accurately reproduce and further explain the experimentally measured fluorescence wavelengths. The best computational approach yields a correlation with experiment of r = 0. Read More

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January 2019

Integrating molecular networks with genetic variant interpretation for precision medicine.

Wiley Interdiscip Rev Syst Biol Med 2018 Dec 12:e1443. Epub 2018 Dec 12.

Department of Medicine and Institute for Genomic Medicine, University of California, San Diego, La Jolla, California.

More reliable and cheaper sequencing technologies have revealed the vast mutational landscapes characteristic of many phenotypes. The analysis of such genetic variants has led to successful identification of altered proteins underlying many Mendelian disorders. Nevertheless the simple one-variant one-phenotype model valid for many monogenic diseases does not capture the complexity of polygenic traits and disorders. Read More

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December 2018

Deconstructing Retinal Organoids: Single cell RNA-Seq reveals the cellular components of human pluripotent stem cell-derived retina.

Stem Cells 2018 Dec 12. Epub 2018 Dec 12.

Institute of Genetic Medicine, Newcastle University, Newcastle, UK.

The rapid improvements in single cell sequencing technologies and analyses afford greater scope for dissecting organoid cultures composed of multiple cell types and create an opportunity to interrogate these models to understand tissue biology, cellular behaviour and interactions. To this end, retinal organoids generated from human embryonic stem cells (hESCs) were analysed by single cell RNA-sequencing (scRNA-Seq) at three time points of differentiation. Combinatorial data from all time points revealed the presence of nine clusters, five of which corresponded to key retinal cell types: retinal pigment epithelium (RPE), retinal ganglion cells (RGCs), cone and rod photoreceptors and Müller glia. Read More

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December 2018

PI3K-AKT-FOXO1 pathway targeted by skeletal muscle microRNA to suppress proteolytic gene expression in response to carbohydrate intake during aerobic exercise.

Physiol Rep 2018 Dec;6(23):e13931

Military Nutrition Division, U.S. Army Research Institute of Environmental Medicine, Natick, Massachusetts.

Ingesting protein and carbohydrate together during aerobic exercise suppresses the expression of specific skeletal muscle microRNA and promotes muscle hypertrophy. Determining whether there are independent effects of carbohydrate and protein on microRNA will allow for a clearer understanding of the mechanistic role microRNA serve in regulating skeletal muscle protein synthetic and proteolytic responses to nutrition and exercise. This study determined skeletal muscle microRNA responses to aerobic exercise with or without carbohydrate, and recovery whey protein (WP). Read More

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December 2018

Smoking, age, nodal disease, T stage, p16 status, and risk of distant metastases in patients with squamous cell cancer of the oropharynx.

Cancer 2018 Dec 11. Epub 2018 Dec 11.

NRG Oncology.

Background: With an expectation of excellent locoregional control, ongoing efforts to de-intensify therapy for patients with human papillomavirus-associated squamous cell oropharyngeal cancer necessitate a better understanding of the metastatic risk for patients with this disease. The objective of this study was to determine what factors affect the risk of metastases in patients with squamous cell cancers of the oropharynx.

Methods: Under a shared use agreement, 547 patients from Radiation Therapy Oncology Group 0129 and 0522 with nonmetastatic oropharyngeal squamous cell cancers who had a known p16 status and smoking status were analyzed to assess the association of clinical features with the development of distant metastases. Read More

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December 2018

PTP1B markedly promotes breast cancer progression and is regulated by miR-193a-3p.

FEBS J 2018 Dec 7. Epub 2018 Dec 7.

State Key Laboratory of Pharmaceutical Biotechnology, Collaborative Innovation Center of Chemistry for Life Sciences, Jiangsu Engineering Research Center for MicroRNA Biology and Biotechnology, NJU Advanced Institute for Life Sciences (NAILS), School of life sciences, Nanjing University, 163 Xianlin Road, Nanjing, Jiangsu, 210023, China.

The protein tyrosine phosphatase PTP1B, which is encoded by PTPN1, is a ubiquitously expressed non-receptor protein tyrosine phosphatase. PTP1B has long been known to negatively regulate insulin and leptin receptor signalling. Recently, it was reported to be aberrantly expressed in cancer cells and to function as an important oncogene. Read More

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December 2018

Proteomic Analysis of the initial Oral Pellicle in Caries-Active and Caries-Free Individuals.

Proteomics Clin Appl 2018 Dec 8:e1800143. Epub 2018 Dec 8.

Clinic of Operative Dentistry, Periodontology and Preventive Dentistry, University Hospital, Saarland University, Homburg/Saar, Germany.

Purpose: To 1) elucidate individual proteomic profiles of the 3-min biofilm of caries-active and caries-free individuals and 2) compare these proteomic profiles against the background of caries.

Experimental Design: The initial oral pellicle of 12 caries-active and 12 caries-free individuals was generated in situ on ceramics specimens. The individual, host-specific proteomic profiles of this basic pellicle layer were analyzed by a chemical elution protocol combined with an elaborate mass spectrometry and evaluated bioinformatically. Read More

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December 2018

Local Genomic Features Predict the Distinct and Overlapping Binding Patterns of the bHLH-Zip Family Oncoproteins MITF and MYC-MAX.

Pigment Cell Melanoma Res 2018 Dec 7. Epub 2018 Dec 7.

Department of Physics, University of Illinois at Urbana-Champaign, IL.

MITF and MYC are well-known oncoproteins and members of the basic helix-loop-helix leucine zipper (bHLH-Zip) family of transcription factors (TFs) recognizing hexamer E-box motifs. MITF and MYC not only share the core binding motif, but are also the two most highly expressed bHLH-Zip transcription factors in melanocytes, raising the possibility that they may compete for the same binding sites in select oncogenic targets. Mechanisms determining the distinct and potentially overlapping binding modes of these critical oncoproteins remain uncharacterized. Read More

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December 2018

Co-expression of long non-coding RNAs and autism risk genes in the developing human brain.

BMC Syst Biol 2018 Dec 14;12(Suppl 7):91. Epub 2018 Dec 14.

Department of Genetics and Biochemistry, Clemson University, Clemson, SC, 29646, USA.

Background: Autism Spectrum Disorder (ASD) is the umbrella term for a group of neurodevelopmental disorders convergent on behavioral phenotypes. While many genes have been implicated in the disorder, the predominant focus of previous research has been on protein coding genes. This leaves a vast number of long non-coding RNAs (lncRNAs) not characterized for their role in the disorder although lncRNAs have been shown to play important roles in development and are highly represented in the brain. Read More

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December 2018

Association of serum levels of fibrosis-related biomarkers with disease activity in patients with IgG4-related disease.

Arthritis Res Ther 2018 Dec 14;20(1):277. Epub 2018 Dec 14.

Immunology and Rheumatology, Nagasaki University Graduate School of Biomedical Sciences, Nagasaki, Japan.

Background: The aim of this study was to identify fibrosis-related serological surrogate outcome measures in patients with immunoglobulin G4-related disease (IgG4-RD).

Methods: This was a clinical observational study of 72 patients with untreated IgG4-RD from four institutions in Japan. The serum concentrations of growth differentiation factor 15 (GDF-15), CCL2, hyaluronic acid (HA), amino-terminal propeptide of type III procollagen (PIIINP), and tissue inhibitor of metalloproteinases 1 (TIMP-1) were measured by enzyme-linked immunosorbent assays. Read More

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December 2018

Systems biology analysis reveals new insights into invasive lung cancer.

BMC Syst Biol 2018 Dec 14;12(Suppl 7):117. Epub 2018 Dec 14.

MidSouth Bioinformatics Center and Joint Bioinformatics Ph.D. Program, University of Arkansas at Little Rock and University of Arkansas for Medical Sciences, 2801 S. University Avenue, Little Rock, AR, 72204, USA.

Background: Adenocarcinoma in situ (AIS) is a pre-invasive lesion in the lung and a subtype of lung adenocarcinoma. The patients with AIS can be cured by resecting the lesion completely. In contrast, the patients with invasive lung adenocarcinoma have very poor 5-year survival rate. Read More

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December 2018

A hotspots analysis-relation discovery representation model for revealing diabetes mellitus and obesity.

BMC Syst Biol 2018 Dec 14;12(Suppl 7):116. Epub 2018 Dec 14.

Key Laboratory of Symbolic Computation and Knowledge Engineering of Ministry of Education, College of Computer Science and Technology, Jilin University, Changchun, 130012, China.

Background: Nowadays, because of the huge economic burden on society causing by obesity and diabetes, they turn into the most serious public health challenges in the world. To reveal the close and complex relationships between diabetes, obesity and other diseases, search the effective treatment for them, a novel model named as representative latent Dirichlet allocation (RLDA) topic model is presented.

Results: RLDA was applied to a corpus of more than 337,000 literatures of diabetes and obesity which were published from 2007 to 2016. Read More

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December 2018

Comparative toxicogenomics of three insensitive munitions constituents 2,4-dinitroanisole, nitroguanidine and nitrotriazolone in the soil nematode Caenorhabditis elegans.

BMC Syst Biol 2018 Dec 14;12(Suppl 7):92. Epub 2018 Dec 14.

Environmental Laboratory, U.S. Army Engineer Research and Development Center, 3909 Halls Ferry Road, Vicksburg, MS, 39180, USA.

Background: Ecotoxicological studies on the insensitive munitions formulation IMX-101 and its components 2,4-dinitroanisole (DNAN), nitroguanidine (NQ) and nitrotriazolone (NTO) in various organisms showed that DNAN was the main contributor to the overall toxicity of IMX-101 and suggested that the three compounds acted independently. These results motivated this toxicogenomics study to discern toxicological mechanisms for these compounds at the molecular level.

Methods: Here we used the soil nematode Caenorhabditis elegans, a well-characterized genomics model, as the test organism and a species-specific, transcriptome-wide 44 K-oligo probe microarray for gene expression analysis. Read More

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December 2018

MISC: missing imputation for single-cell RNA sequencing data.

BMC Syst Biol 2018 Dec 14;12(Suppl 7):114. Epub 2018 Dec 14.

Joint Bioinformatics Program, University of Arkansas Little Rock George Washington Donaghey College of Engineering & IT and University of Arkansas for Medical Sciences, Little Rock, AR, 72204, USA.

Background: Single-cell RNA sequencing (scRNA-seq) technology provides an effective way to study cell heterogeneity. However, due to the low capture efficiency and stochastic gene expression, scRNA-seq data often contains a high percentage of missing values. It has been showed that the missing rate can reach approximately 30% even after noise reduction. Read More

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December 2018

Genomics of lipid-laden human hepatocyte cultures enables drug target screening for the treatment of non-alcoholic fatty liver disease.

BMC Med Genomics 2018 Dec 14;11(1):111. Epub 2018 Dec 14.

Centre for Pharmacology and Toxicology, Hannover Medical School, Carl-Neuberg-Str. 1, 30625, Hannover, Germany.

Background: Non-alcoholic fatty liver disease (NAFLD) is a major health burden in need for new medication. To identify potential drug targets a genomic study was performed in lipid-laden primary human hepatocyte (PHH) and human hepatoma cell cultures.

Methods: PHH, HuH7 and HepG2 hepatoma cell cultures were treated with lipids and/or TNFα. Read More

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December 2018

Increased AURKA promotes cell proliferation and predicts poor prognosis in bladder cancer.

BMC Syst Biol 2018 Dec 14;12(Suppl 7):118. Epub 2018 Dec 14.

National Medical Centre of Colorectal Disease, The Third Affiliated Hospital of Nanjing University of Chinese Medicine, Nanjing, 210001, China.

Background: Bladder cancer (BC) is the most common cancer of the urinary bladder and upper tract, in which the clinical management is limited. AURKA (aurora kinase A) has been identified as an oncogene in cancer development; however, its potential role and underlying mechanisms in the progression of BC remain unknown.

Results: In this study, we evaluated Aurora kinase A (AURKA) expression in patient samples by performing gene expression profiling, and found that AURKA expression levels were significantly higher in BC tissues than in normal tissues. Read More

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December 2018
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The emerging role of microRNA-4487/6845-3p in Alzheimer's disease pathologies is induced by Aβ25-35 triggered in SH-SY5Y cell.

BMC Syst Biol 2018 Dec 14;12(Suppl 7):119. Epub 2018 Dec 14.

Department of Pharmacy, Shanghai University of Medicine & Health Sciences, Shanghai, 201318, China.

Background: Accumulation of amyloid β-peptide (Aβ) is implicated in the pathogenesis and development of Alzheimer's disease (AD). Neuron-enriched miRNA was aberrantly regulated and may be associated with the pathogenesis of AD. However, regarding whether miRNA is involved in the accumulation of Aβ in AD, the underlying molecule mechanism remains unclear. Read More

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December 2018

Analysis of the differential urinary protein profile in IgA nephropathy patients of Uygur ethnicity.

BMC Nephrol 2018 Dec 14;19(1):358. Epub 2018 Dec 14.

Nephrology department, The Xinjiang Uygur Autonomous Region People's Hospital, 91 Tianchi Road, Urumqi, Xinjiang, China.

Background: IgA nephropathy (IgAN) is one of the most common forms of idiopathic glomerular diseases and might lead to end-stage kidney disease. Accurate and non-invasive biomarkers for early diagnosis are required for early intervention and consequent therapy for IgAN patients. Because variance in the disease incidence and predisposing genes of IgAN has been detected among different ethnicities, the ethnicity factor should be considered in IgAN biomarker discovery. Read More

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December 2018

Association of Klotho gene polymorphism with hypertension and coronary artery disease in an Iranian population.

BMC Cardiovasc Disord 2018 Dec 14;18(1):237. Epub 2018 Dec 14.

Cardiovascular Research Center, Institute of Basic and Clinical Physiology Sciences, Kerman University of Medical Sciences, Kerman, Iran.

Background: Klotho, possibly an age-regulating protein, is considered an important factor contributing to the lifespan and pathophysiology of hypertension and coronary artery disease (CAD). The present study was carried out aiming to investigate the association of Klotho-rs564481 (C1818T) gene polymorphism with hypertension and CAD.

Methods: A total of 286 CAD-suspicious subjects were entered into this case-control study. Read More

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December 2018

Mind the gaps: overlooking inaccessible regions confounds statistical testing in genome analysis.

BMC Bioinformatics 2018 Dec 14;19(1):481. Epub 2018 Dec 14.

Department of Informatics, University of Oslo, Oslo, Norway.

Background: The current versions of reference genome assemblies still contain gaps represented by stretches of Ns. Since high throughput sequencing reads cannot be mapped to those gap regions, the regions are depleted of experimental data. Moreover, several technology platforms assay a targeted portion of the genomic sequence, meaning that regions from the unassayed portion of the genomic sequence cannot be detected in those experiments. Read More

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December 2018

In Silico Characterization of B Cell and T Cell Epitopes for Subunit Vaccine Design of Salmonella typhi PgtE: A Molecular Dynamics Simulation Approach.

J Comput Biol 2018 Dec 14. Epub 2018 Dec 14.

4 Data Mining and Text Mining Laboratory, Department of Bioinformatics, Bharathiar University , Coimbatore, India .

Typhoid fever is an acute illness in humans, caused by Salmonella typhi, a gram-negative bacterium. Outer membrane proteins of S. typhi have strong potential for its use in the development of subunit vaccine against typhoid. Read More

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December 2018

Conformational Shift of a β-Hairpin Peptide upon Complex Formation with an Oligo-proline Peptide Studied by Mass Spectrometry.

ChemistrySelect 2016 Aug 19;1(13):3651-3656. Epub 2016 Aug 19.

Department of Pharmaceutical Chemistry and Bioanalytics, Institute for Pharmacy, Martin-Luther-Universit t Halle-Wittenberg W.-Langenbeck-Straße 4, 06120 Halle (Germany).

So-called super-secondary structures such as the β-hairpin, studied here, form an intermediate hierarchy between secondary and tertiary structures of proteins. Their sequence-derived 'pure' peptide backbone conformation is combined with 'remote' interstrand or interresidue contacts reminiscent of the 3D-structure of full-length proteins. This renders them ideally suited for studying potential nucleation sites of protein folding reactions as well as intermolecular interactions. Read More

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