602 results match your criteria BioData Mining [Journal]


Peptidylarginine deiminases 2 and 4 modulate innate and adaptive immune responses in TLR-7-dependent lupus.

JCI Insight 2018 Dec 6;3(23). Epub 2018 Dec 6.

Systemic Autoimmunity Branch, Intramural Research Program (IRP), National Institute of Arthritis and Musculoskeletal and Skin Diseases (NIAMS), and.

The peptidylarginine deiminases PAD2 and PAD4 are implicated in the pathogenesis of several autoimmune diseases. PAD4 may be pathogenic in systemic lupus erythematosus (SLE) through its role in neutrophil extracellular trap (NET) formation that promotes autoantigen externalization, immune dysregulation, and organ damage. The role of this enzyme in mouse models of autoimmunity remains unclear, as pan-PAD chemical inhibitors improve clinical phenotype, whereas PAD4-KO models have given conflicting results. Read More

View Article
December 2018
2 Reads

Effects of Wolbachia/Cardinium Infection on the Mitochondrial Phylogeny of Oligonychus castaneae (Acari: Tetranychidae).

J Econ Entomol 2018 Nov 28. Epub 2018 Nov 28.

Laboratory of Applied Entomology and Zoology, Faculty of Agriculture, Ibaraki University, Ami, Ibaraki, Japan.

A wide range of invertebrates harbor intracellular endosymbiotic bacteria. Within these endosymbionts, Wolbachia and Cardinium, have been attracting particular attention because these bacteria frequently affect the genetic structure and genetic diversity of their hosts. They cause various reproductive alterations such as cytoplasmic incompatibility, parthenogenesis induction, male-killing, and feminization. Read More

View Article
November 2018

Animal and management factors associated with weight gain in dairy calves and heifers on smallholder dairy farms in Kenya.

Prev Vet Med 2018 Dec 26;161:60-68. Epub 2018 Oct 26.

Ontario Veterinary College, University of Guelph, Canada.

Calf growth is an important determinant of dairy herd productivity, particularly in countries where the dairy industry is expanding, such as Kenya. Our objective was to determine factors associated with weight gain in randomly selected dairy calves and heifers in smallholder dairy farms (SDF) in Kenya. A cross-sectional study on a census of 321 calves and heifers (dairy calves and heifers up to 36 months of age), sampled from 200 randomly selected SDF in Naari, Kenya, formed the study population. Read More

View Article
December 2018
2 Reads

Distributed retrieval engine for the development of cloud-deployed biological databases.

BioData Min 2018 12;11:26. Epub 2018 Nov 12.

Neuro-biomorphic Engineering Lab, Faculty of Engineering, Jerusalem College of Technology, Jerusalem, Israel.

The integration of cloud resources with federated data retrieval has the potential of improving the maintenance, accessibility and performance of specialized databases in the biomedical field. However, such an integrative approach requires technical expertise in cloud computing, usage of a data retrieval engine and development of a unified data-model, which can encapsulate the heterogeneity of biological data. Here, a framework for the development of cloud-based biological specialized databases is proposed. Read More

View Article
November 2018
3 Reads

Knomics-Biota - a system for exploratory analysis of human gut microbiota data.

BioData Min 2018 6;11:25. Epub 2018 Nov 6.

Research and Development Department, Knomics LLC, Skolkovo Innovation Center, Moscow, Russian Federation.

Background: Metagenomic surveys of human microbiota are becoming increasingly widespread in academic research as well as in food and pharmaceutical industries and clinical context. Intuitive tools for investigating experimental data are of high interest to researchers.

Results: Knomics-Biota is a web-based resource for exploratory analysis of human gut metagenomes. Read More

View Article
November 2018

Molecular basis of Mitomycin C enhanced corneal sensory nerve repair after debridement wounding.

Sci Rep 2018 Nov 16;8(1):16960. Epub 2018 Nov 16.

Laboratory of Skin Biology, National Institute of Arthritis and Musculoskeletal and Skin Diseases, National Institutes of Health, Bethesda, MD, 20892, USA.

The ocular surface is covered by stratified squamous corneal epithelial cells that are in cell:cell contact with the axonal membranes of a dense collection of sensory nerve fibers that act as sentinels to detect chemical and mechanical injuries which could lead to blindness. The sheerness of the cornea makes it susceptible to superficial abrasions and recurrent erosions which demand continuous regrowth of the axons throughout life. We showed previously that topical application of the antibiotic and anticancer drug Mitomycin C (MMC) enhances reinnervation of the corneal nerves and reduces recurrent erosions in mice via an unknown mechanism. Read More

View Article
November 2018
4 Reads

MAIA-A machine learning assisted image annotation method for environmental monitoring and exploration.

PLoS One 2018 16;13(11):e0207498. Epub 2018 Nov 16.

Biodata Mining Group, Faculty of Technology, Bielefeld University, Bielefeld, Germany.

Digital imaging has become one of the most important techniques in environmental monitoring and exploration. In the case of the marine environment, mobile platforms such as autonomous underwater vehicles (AUVs) are now equipped with high-resolution cameras to capture huge collections of images from the seabed. However, the timely evaluation of all these images presents a bottleneck problem as tens of thousands or more images can be collected during a single dive. Read More

View Article
November 2018
4 Reads

Diabetes and TelecommunicationS (DATES) study to support self-management for people with type 2 diabetes: a randomized controlled trial.

BMC Public Health 2018 Nov 12;18(1):1249. Epub 2018 Nov 12.

Institute of Psychiatry, Psychology and Neurosciences, King's College London Weston Education Centre, 10 Cutcombe Road, London, SE5 9RJ, UK.

Background: The increasing prevalence of type 2 diabetes and suboptimal glycaemic control in Kuwait requires novel, wide-reaching, low-cost interventions to motivate and mobilise individuals towards more effective self-management. More than 2 million people in Kuwait own mobile phones. We will test whether automated personalised health text messages based on principles of motivational interviewing and are responsive to biodata delivered remotely is potentially effective in improving glycaemic control compared to usual care. Read More

View Article
November 2018
6 Reads

A fast forward 3D connection algorithm for mitochondria and synapse segmentations from serial EM images.

BioData Min 2018 5;11:24. Epub 2018 Nov 5.

2Institute of Automation, Chinese Academy of Sciences, 95 Zhongguancun East Road, Beijing, 100190 China.

Background: It is becoming increasingly clear that the quantification of mitochondria and synapses is of great significance to understand the function of biological nervous systems. Electron microscopy (EM), with the necessary resolution in three directions, is the only available imaging method to look closely into these issues. Therefore, estimating the number of mitochondria and synapses from the serial EM images is coming into prominence. Read More

View Article
November 2018

Transition-transversion encoding and genetic relationship metric in ReliefF feature selection improves pathway enrichment in GWAS.

BioData Min 2018 3;11:23. Epub 2018 Nov 3.

1Tandy School of Computer Science, The University of Tulsa, 800 S. Tucker Dr, Tulsa, OK 74104 USA.

Background: ReliefF is a nearest-neighbor based feature selection algorithm that efficiently detects variants that are important due to statistical interactions or epistasis. For categorical predictors, like genotypes, the standard metric used in ReliefF has been a simple (binary) mismatch difference. In this study, we develop new metrics of varying complexity that incorporate allele sharing, adjustment for allele frequency heterogeneity via the genetic relationship matrix (GRM), and physicochemical differences of variants via a new transition/transversion encoding. Read More

View Article
November 2018

Human retinoic acid-regulated CD161 regulatory T cells support wound repair in intestinal mucosa.

Nat Immunol 2018 Dec 5;19(12):1403-1414. Epub 2018 Nov 5.

MRC, Centre for Transplantation, King's College London, London, UK.

Repair of tissue damaged during inflammatory processes is key to the return of local homeostasis and restoration of epithelial integrity. Here we describe CD161 regulatory T (T) cells as a distinct, highly suppressive population of T cells that mediate wound healing. These T cells were enriched in intestinal lamina propria, particularly in Crohn's disease. Read More

View Article
December 2018
17 Reads

Gender identities in adolescent population: Methodological issues and prevalence across age groups.

Eur Psychiatry 2018 Oct 31;55:61-66. Epub 2018 Oct 31.

Helsinki University and Helsinki University Hospital, Forensic Psychiatry, P O Box 590, 00029 HUS, Finland.

Background: Increasing numbers of adolescents are seeking treatment from gender identity services, particularly natal girls. It is known from survey studies some adolescents exaggerate their belonging to minorities, thereby distorting prevalence estimates and findings on related problems. The aim of the present study was to explore the susceptibility of gender identity to mischievous responding, and prevalences of cis-gender, opposite-sex and other/ non-binary gender identities as corrected for likely mischievous responding among Finnish adolescents. Read More

View Article
October 2018
3 Reads

Hyperglycaemic Emergencies in a Tertiary Health Facility in South-Eastern Nigeria.

West Afr J Med 2018 Sep-Dec;35(3):137-143

Endocrine, Diabetes & Metabolism Unit, Department of Medicine, Federal Medical Centre, Umuahia, Abia State.

Background: Patterns of hyperglycaemic emergencies (HE) include diabetic ketoacidosis, (DKA), hyperglycaemic hypero-smolar state, (HHS), normo-osmolar non-ketotic hyper-glycaemic state, (NONKHS), or the mixed/indeterminate form. Certain factors are predictive of adverse HE outcome. There is a paucity of literature on the patterns and poor prognostic factors of HE in the South East (SE) region of Nigeria, hence, the need for this study. Read More

View Article
November 2018
3 Reads

Combining DNA methylation and RNA sequencing data of cancer for supervised knowledge extraction.

BioData Min 2018 25;11:22. Epub 2018 Oct 25.

3Department of Engineering, Uninettuno University, Corso Vittorio Emanuele II, 39, Rome, 00186 Italy.

Background: In the Next Generation Sequencing (NGS) era a large amount of biological data is being sequenced, analyzed, and stored in many public databases, whose interoperability is often required to allow an enhanced accessibility. The combination of heterogeneous NGS genomic data is an open challenge: the analysis of data from different experiments is a fundamental practice for the study of diseases. In this work, we propose to combine DNA methylation and RNA sequencing NGS experiments at gene level for supervised knowledge extraction in cancer. Read More

View Article
October 2018
6 Reads

SeeVis - 3D space-time cube rendering for visualization of microfluidics image data.

Bioinformatics 2018 Oct 22. Epub 2018 Oct 22.

Biodata Mining Group, Faculty of Technology, Bielefeld University, Germany.

Motivation: Live cell imaging plays a pivotal role in understanding cell growth. Yet, there is a lack of visualization alternatives for quick qualitative characterization of colonies.

Results: SeeVis is a Python workflow for automated and qualitative visualization of time-lapse microscopy data. Read More

View Article
October 2018
9 Reads

To know the objective is not (necessarily) to know the objective function.

BioData Min 2018 4;11:21. Epub 2018 Oct 4.

1Institute for Biomedical Informatics, University of Pennsylvania, Philadelphia, 19104-6021 PA USA.

View Article
October 2018

Haplosaurus computes protein haplotypes for use in precision drug design.

Nat Commun 2018 10 8;9(1):4128. Epub 2018 Oct 8.

MedImmune Ltd., Granta Park, Cambridge, CB21 4QR, UK.

Selecting the most appropriate protein sequences is critical for precision drug design. Here we describe Haplosaurus, a bioinformatic tool for computation of protein haplotypes. Haplosaurus computes protein haplotypes from pre-existing chromosomally-phased genomic variation data. Read More

View Article
October 2018
1 Read

Determinants of Timing of Presentation of Neurotrauma Patients to a Neurosurgical Center in a Developing Country.

J Neurosci Rural Pract 2018 Oct-Dec;9(4):545-550

Department of Neurological Surgery, University College Hospital, Ibadan, Nigeria.

Background: A major goal in neurotrauma management is the prevention of secondary neuronal injuries. This goal is time bound as neurological deficits once established are usually irreversible. Late presentation is the norm in most neurotrauma patients in developing countries. Read More

View Article
October 2018
1 Read

A biomarker feasibility study in the South East Asia Community Observatory health and demographic surveillance system.

Glob Health Epidemiol Genom 2018 22;3:e14. Epub 2018 Aug 22.

Jeffrey Cheah School of Medicine and Health Sciences, Monash University Malaysia, Selangor, Malaysia.

Background: Integration of biomarker data with information on health and lifestyle provides a powerful tool to enhance the scientific value of health research. Existing health and demographic surveillance systems (HDSSs) present an opportunity to create novel biodata resources for this purpose, but data and biological sample collection often presents challenges. We outline some of the challenges in developing these resources and present the outcomes of a biomarker feasibility study embedded within the South East Asia Community Observatory (SEACO) HDSS. Read More

View Article
August 2018
1 Read

A Single Pheromone Receptor Gene Conserved across 400 My of Vertebrate Evolution.

Mol Biol Evol 2018 Dec;35(12):2928-2939

School of Life Science and Technology, Tokyo Institute of Technology, Meguro-ku, Tokyo, Japan.

Pheromones are crucial for eliciting social and sexual behaviors in diverse animal species. The vomeronasal receptor type-1 (V1R) genes, encoding members of a pheromone receptor family, are highly variable in number and repertoire among mammals due to extensive gene gain and loss. Here, we report a novel pheromone receptor gene belonging to the V1R family, named ancient V1R (ancV1R), which is shared among most Osteichthyes (bony vertebrates) from the basal lineage of ray-finned fishes to mammals. Read More

View Article
December 2018
9 Reads

A cross-sectional study of the welfare of calves raised in smallholder dairy farms in Meru, Kenya, 2017.

Vet World 2018 Aug 10;11(8):1094-1101. Epub 2018 Aug 10.

Department of Health Management, Atlantic Veterinary College, University of Prince Edward Island, Canada.

Aim: This study was aimed at describing calf comfort and determining the individual and pen level factors that affect comfort status (in particular, calf leg hygiene scores) of smallholder dairy farms in Meru County, Kenya.

Materials And Methods: A cross-sectional study was carried out on 52 calves that were up to 1 year old in 38 dairy farms (mean±standard deviation: Herd size=1.71±0. Read More

View Article
August 2018
1 Read

Grasping frequent subgraph mining for bioinformatics applications.

BioData Min 2018 3;11:20. Epub 2018 Sep 3.

1Department of Mathematics and Computer Science, University of Antwerp, Antwerp, Belgium.

Searching for interesting common subgraphs in graph data is a well-studied problem in data mining. Subgraph mining techniques focus on the discovery of patterns in graphs that exhibit a specific network structure that is deemed interesting within these data sets. The definition of which subgraphs are interesting and which are not is highly dependent on the application. Read More

View Article
September 2018
1 Read

Phylogeny of the spider mite sub-family Tetranychinae (Acari: Tetranychidae) inferred from RNA-Seq data.

PLoS One 2018 7;13(9):e0203136. Epub 2018 Sep 7.

Faculty of Agriculture, Ibaraki University, Ami, Ibaraki, Japan.

Phylogenetic trees of spider mites were previously obtained using 18S and 28S rRNA genes. Because some of the bootstrap values were relatively low, these trees were unable to completely resolve the phylogeny. Here, we obtained RNA-Seq data for the 72 known species (73 strains) of spider mites to analyze the phylogeny of the sub-family Tetranychinae. Read More

View Article
September 2018
2 Reads

Distinct Clinical and Pathological Features of Melorheostosis Associated With Somatic MAP2K1 Mutations.

J Bone Miner Res 2018 Aug 23. Epub 2018 Aug 23.

Clinical and Investigative Orthopedics Surgery Unit, National Institute of Arthritis and Musculoskeletal and Skin Diseases (NIAMS), National Institutes of Health (NIH), Bethesda, MD, USA.

Melorheostosis is a rare hyperostotic disease of the long bones classically characterized by a "dripping candle-wax" radiographic appearance. We recently described somatic activating mutations in MAP2K1 as a cause of melorheostosis. Here, we report distinguishing characteristics of patients with MAP2K1-positive melorheostosis. Read More

View Article
August 2018
17 Reads
6.830 Impact Factor

Dysregulated neutrophil responses and neutrophil extracellular trap formation and degradation in PAPA syndrome.

Ann Rheum Dis 2018 Dec 21;77(12):1825-1833. Epub 2018 Aug 21.

Systemic Autoimmunity Branch, National Institute of Arthritis and Musculoskeletal and Skin Diseases (NIAMS), National Institutes of Health (NIH), Bethesda, Maryland, USA.

Objectives: Pyogenic arthritis, pyoderma gangrenosum and acne (PAPA) syndrome is characterised by flares of sterile arthritis with neutrophil infiltrate and the overproduction of interleukin (IL)-1β. The purpose of this study was to elucidate the potential role of neutrophil subsets and neutrophil extracellular traps (NET) in the pathogenesis of PAPA.

Methods: Neutrophils and low-density granulocytes (LDG) were quantified by flow cytometry. Read More

View Article
December 2018
14 Reads

Functional relevance for central cornea thickness-associated genetic variants by using integrative analyses.

BioData Min 2018 15;11:19. Epub 2018 Aug 15.

Department of Ophthalmology and Visual Science, Eye Institute, Eye & ENT Hospital, Shanghai Medical College of Fudan University, NHC Key Laboratory of myopia (Fudan University), Shanghai, China.

Background: The genetic architecture underlying central cornea thickness (CCT) is far from understood. Most of the CCT-associated variants are located in the non-coding regions, raising the difficulty of following functional characterizations. Thus, integrative functional analyses on CCT-associated loci might benefit in overcoming these issues by prioritizing the hub genes that are located in the center of CCT genetic network. Read More

View Article
August 2018
1 Read

Evolutionary methods for variable selection in the epidemiological modeling of cardiovascular diseases.

BioData Min 2018 14;11:18. Epub 2018 Aug 14.

1Department of Environmental and Biological Sciences, University of Eastern Finland, Yliopistonranta 1 E, 70211 Kuopio, Finland.

Background: The redundancy of information is becoming a critical issue for epidemiologists. High-dimensional datasets require new effective variable selection methods to be developed. This study implements an advanced evolutionary variable selection method which is applied for cardiovascular predictive modeling. Read More

View Article
August 2018
1 Read

TRIQ: a new method to evaluate triclusters.

BioData Min 2018 6;11:15. Epub 2018 Aug 6.

2Department of computer Science, University of Seville, Seville, Spain.

Background: Triclustering has shown to be a valuable tool for the analysis of microarray data since its appearance as an improvement of classical clustering and biclustering techniques. The standard for validation of triclustering is based on three different measures: correlation, graphic similarity of the patterns and functional annotations for the genes extracted from the Gene Ontology project (GO).

Results: We propose , a single evaluation measure that combines the three measures previously described: correlation, graphic validation and functional annotation, providing a single value as result of the validation of a tricluster solution and therefore simplifying the steps inherent to research of comparison and selection of solutions. Read More

View Article
August 2018
1 Read

Protein folding prediction in the HP model using ions motion optimization with a greedy algorithm.

BioData Min 2018 8;11:17. Epub 2018 Aug 8.

5Department of Biomedical Science and Environmental Biology, Kaohsiung Medical University, Kaohsiung, Taiwan.

Background: The function of a protein is determined by its native protein structure. Among many protein prediction methods, the Hydrophobic-Polar (HP) model, an ab initio method, simplifies the protein folding prediction process in order to reduce the prediction complexity.

Results: In this study, the ions motion optimization (IMO) algorithm was combined with the greedy algorithm (namely IMOG) and implemented to the HP model for the protein folding prediction based on the 2D-triangular-lattice model. Read More

View Article
August 2018
1 Read

A multi-objective gene clustering algorithm guided by apriori biological knowledge with intensification and diversification strategies.

BioData Min 2018 7;11:16. Epub 2018 Aug 7.

1Centre for Biotechnology and Bioengineering (CeBiB), Departamento de Ingeniería Informática, Universidad de Santiago de Chile, Av. Ecuador 3659, Santiago, Chile.

Background: Biologists aim to understand the genetic background of diseases, metabolic disorders or any other genetic condition. Microarrays are one of the main high-throughput technologies for collecting information about the behaviour of genetic information on different conditions. In order to analyse this data, clustering arises as one of the main techniques used, and it aims at finding groups of genes that have some criterion in common, like similar expression profile. Read More

View Article
August 2018
9 Reads

Adaptation of CARE (CAse REport) guidelines on published case reports in the Saudi Journal of Anesthesia.

Saudi J Anaesth 2018 Jul-Sep;12(3):446-449

Department of Surgery, Lahore General Hospital, Lahore, Pakistan.

Background: Toward improving the reporting quality of clinical case reports in the Saudi Journal of Anesthesia, we conducted this audit. The aim of this paper is to provide an overview of the different objectives for clinical case reports and to identify those subordinate items which seem most relevant from the CAse REport (CARE) checklist.

Methods: We performed this pilot study on clinical case reports published in the Saudi Journal of Anesthesia (SJA) in the past 5 years from 2013 to 2017. Read More

View Article
August 2018
9 Reads

Transcriptional signature primes human oral mucosa for rapid wound healing.

Sci Transl Med 2018 07;10(451)

Laboratory of Skin Biology, National Institute of Arthritis and Musculoskeletal and Skin Diseases, Bethesda, MD 20892, USA.

Oral mucosal wound healing has long been regarded as an ideal system of wound resolution. However, the intrinsic characteristics that mediate optimal healing at mucosal surfaces are poorly understood, particularly in humans. We present a unique comparative analysis between human oral and cutaneous wound healing using paired and sequential biopsies during the repair process. Read More

View Article
July 2018
11 Reads

Soft document clustering using a novel graph covering approach.

BioData Min 2018 14;11:11. Epub 2018 Jun 14.

Fraunhofer Institute for Algorithms and Scientific Computing, Sankt Augustin, Schloss Birlinghoven, Sankt Augustin, Germany.

Background: In text mining, document clustering describes the efforts to assign unstructured documents to clusters, which in turn usually refer to topics. Clustering is widely used in science for data retrieval and organisation.

Results: In this paper we present and discuss a novel graph-theoretical approach for document clustering and its application on a real-world data set. Read More

View Article
June 2018
2 Reads

Feature selection for gene prediction in metagenomic fragments.

BioData Min 2018 7;11. Epub 2018 Jun 7.

College of Computer and Information Sciences, Computer Science Department, King Saud University, Riyadh, Saudi Arabia.

Background: Computational approaches, specifically machine-learning techniques, play an important role in many metagenomic analysis algorithms, such as gene prediction. Due to the large feature space, current de novo gene prediction algorithms use different combinations of classification algorithms to distinguish between coding and non-coding sequences.

Results: In this study, we apply a filter method to select relevant features from a large set of known features instead of combining them using linear classifiers or ignoring their individual coding potential. Read More

View Article
June 2018
2 Reads

PathCORE-T: identifying and visualizing globally co-occurring pathways in large transcriptomic compendia.

BioData Min 2018 3;11:14. Epub 2018 Jul 3.

1Department of Systems Pharmacology and Translational Therapeutics. Perelman School of Medicine, University of Pennsylvania, 3400 Civic Center Blvd., Philadelphia, PA 19104 USA.

Background: Investigators often interpret genome-wide data by analyzing the expression levels of genes within pathways. While this within-pathway analysis is routine, the products of any one pathway can affect the activity of other pathways. Past efforts to identify relationships between biological processes have evaluated overlap in knowledge bases or evaluated changes that occur after specific treatments. Read More

View Article
July 2018
2 Reads

Audit of ophthalmology discharge summaries in a Nigerian Teaching Hospital.

Niger J Clin Pract 2018 Jul;21(7):901-906

Department of Ophthalmology, University of Nigeria Teaching Hospital, Ituku Ozalla, Enugu, Nigeria.

Background: Discharge summaries are important components of hospital-care transitions in ensuring continuity of care.

Aim: We assessed the adequacy and accuracy of discharge summaries written by junior doctors.

Methods: An instrument, adapted largely from the current hospital discharge summary template and recommendations regarding content from the Joint Commission International, was used to study 420 discharge summaries written in 2012 from the ophthalmology service of a Rural Teaching Hospital in Nigeria. Read More

View Article
July 2018
2 Reads

Integrative analysis of gene expression and methylation data for breast cancer cell lines.

BioData Min 2018 25;11:13. Epub 2018 Jun 25.

4Department of Mathematics, Texas State University, San Marcos, TX USA.

Background: The deadly costs of cancer and necessity for an accurate method of early cancer detection have demanded the identification of genetic and epigenetic factors associated with cancer. DNA methylation, an epigenetic event, plays an important role in cancer susceptibility. In this paper, we use DNA methylation and gene expression data integration and pathway analysis to further explore and understand the complex relationship between methylation and gene expression. Read More

View Article
June 2018
4 Reads

Measuring associations between the microbiota and repeated measures of continuous clinical variables using a lasso-penalized generalized linear mixed model.

BioData Min 2018 15;11:12. Epub 2018 Jun 15.

1Department of Computational & Systems Biology, University of Pittsburgh School of Medicine, Pittsburgh, PA 15261 USA.

Background: Human microbiome studies in clinical settings generally focus on distinguishing the microbiota in health from that in disease at a specific point in time. However, microbiome samples may be associated with disease severity or continuous clinical health indicators that are often assessed at multiple time points. While the temporal data from clinical and microbiome samples may be informative, analysis of this type of data can be problematic for standard statistical methods. Read More

View Article
June 2018
7 Reads

A Muscle-Specific Enhancer RNA Mediates Cohesin Recruitment and Regulates Transcription In trans.

Mol Cell 2018 Jul;71(1):129-141.e8

Laboratory of Muscle Stem Cells and Gene Regulation, National Institute of Arthritis and Musculoskeletal and Skin Diseases (NIAMS), NIH, Bethesda, MD 20892, USA. Electronic address:

The enhancer regions of the myogenic master regulator MyoD give rise to at least two enhancer RNAs. Core enhancer eRNA (eRNA) regulates transcription of the adjacent MyoD gene, whereas eRNA affects expression of Myogenin in trans. We found that eRNA is recruited at the Myogenin locus, where it colocalizes with Myogenin nascent transcripts. Read More

View Article
July 2018
1 Read

Evaluation of Vocal Cord Function Before Thyroidectomy: Experience from a Developing Country.

Indian J Surg 2018 Jun 23;80(3):211-215. Epub 2016 Dec 23.

2Department of Otorhinolaryngology, University of Nigeria Teaching Hospital, Ituku/Ozalla, Enugu, Nigeria.

Vocal cord palsy (VCP) is a major complication of thyroidectomy. Some patients have preexisting VCP prompting the need for routine or selective preoperative evaluation of the vocal cords. The study aims at ascertaining the prevalence of preoperative VCP and making appropriate recommendations. Read More

View Article

Burnout in Indian Psychiatrists.

Indian J Psychol Med 2018 Mar-Apr;40(2):156-160

Department of Psychiatry, Yashoda Hospital, Hyderabad, Telangana, India.

Background: Individuals associated with service providing and decision-taking are prone for stress leading to burnout.

Aim: The aim of this study is to find out the details of burnout among Psychiatrists in India.

Materials And Methods: Copenhagen Burnout Inventory (CBI) with structured biodata sheet was sent to the representative sample of psychiatrists by e-mail. Read More

View Article
July 2018
14 Reads

Genomic Variability among Field Isolates and Laboratory-Adapted Strains of Serovar Hardjo.

Int J Microbiol 2018 22;2018:2137036. Epub 2018 May 22.

School of Veterinary Medicine, Ross University, Basseterre, Saint Kitts and Nevis.

serovar Hardjo colonizes cattle kidneys and may occasionally infect humans and other mammals. Strains belonging to two clonal subtypes (types A and B) with marked differences in their pathogenicity in the hamster experimental model have been described for this serovar. Such differences have been attributed to point mutations in individual genes, although those genes have not yet been characterized. Read More

View Article

Characterizing the effects of missing data and evaluating imputation methods for chemical prioritization applications using ToxPi.

BioData Min 2018 13;11:10. Epub 2018 Jun 13.

1Bioinformatics Research Center, North Carolina State University, 1 Lampe Dr, Raleigh, 27695 NC USA.

Background: The Toxicological Priority Index (ToxPi) is a method for prioritization and profiling of chemicals that integrates data from diverse sources. However, individual data sources ("assays"), such as in vitro bioassays or in vivo study endpoints, often feature sections of missing data, wherein subsets of chemicals have not been tested in all assays. In order to investigate the effects of missing data and recommend solutions, we designed simulation studies around high-throughput screening data generated by the ToxCast and Tox21 programs on chemicals highlighted by the Agency for Toxic Substances and Disease Registry's (ATSDR) Substance Priority List (SPL), which helps prioritize environmental research and remediation resources. Read More

View Article
June 2018
6 Reads

The Reprimo Gene Family: A Novel Gene Lineage in Gastric Cancer with Tumor Suppressive Properties.

Int J Mol Sci 2018 Jun 25;19(7). Epub 2018 Jun 25.

Laboratory of Oncology, Facultad de Medicina, Pontificia Universidad Católica de Chile, 8330034 Santiago, Chile.

The reprimo () gene family is a group of single exon genes present exclusively within the vertebrate lineage. Two out of three members of this family are present in humans: and (). induces cell cycle arrest at G2/M in response to p53 expression. Read More

View Article
June 2018
1 Read

Risks associated with overcontrolled behavior in police officer recruits.

Psychol Assess 2018 Dec 11;30(12):1691-1702. Epub 2018 Jun 11.

Department of Psychology, Kent State University.

Potential externalizing tendencies have long been a focus of research in police candidates. Early studies often reported positive correlations between Minnesota Multiphasic Personality Inventory (MMPI) externalizing scales and problem behaviors in law enforcement officers. However, more recent investigations reveal mixed findings, with some showing either no significant correlations between externalizing measures and police performance problems or negative associations. Read More

View Article
December 2018
1 Read

Gene set analysis methods: a systematic comparison.

BioData Min 2018 31;11. Epub 2018 May 31.

1Bioinformatics Research Center, North Carolina State University, Raleigh, NC USA.

Background: Gene set analysis is a valuable tool to summarize high-dimensional gene expression data in terms of biologically relevant sets. This is an active area of research and numerous gene set analysis methods have been developed. Despite this popularity, systematic comparative studies have been limited in scope. Read More

View Article
May 2018
5 Reads

Connecting genetics and gene expression data for target prioritisation and drug repositioning.

BioData Min 2018 31;11. Epub 2018 May 31.

2Computational Biology, Target Sciences, GSK, 1250 S. Collegeville Road, UP12-100, Collegeville, PA 19426-0989 USA.

Developing new drugs continues to be a highly inefficient and costly business. By repurposing an existing compound for a different indication, drug repositioning offers an attractive alternative to traditional drug discovery. Most of these approaches work by matching transcriptional disease signatures to anti-correlated gene expression profiles of drug perturbations. Read More

View Article
May 2018
2 Reads

A 5-year audit of major maxillofacial surgeries at Usmanu Danfodiyo university teaching hospital, Nigeria.

BMC Health Serv Res 2018 06 7;18(1):416. Epub 2018 Jun 7.

Department of Dental and Maxillofacial Surgery, Usmanu Danfodiyo University Teaching Hospital Sokoto, PMB, Sokoto, 12003, Nigeria.

Background: There is a paucity of data on the pattern of oral and maxillofacial surgeries done in Nigeria. Despite the rising prominence of oral and maxillofacial surgery as a specialty in our immediate environment, no published audit of the surgeries performed exist. This study aims to present the pattern and types of major surgeries done by oral and maxillofacial surgeons in our hospital as well as the indications for such surgeries. Read More

View Article
June 2018
1.660 Impact Factor

Impact of zinc on sexual maturation of female sickle cell anemia (SCA) children in Enugu, Southeast Nigeria.

Pediatr Hematol Oncol 2018 Mar 5;35(2):145-155. Epub 2018 Jun 5.

a Department of Pediatrics, College of Medicine , University of Nigeria , Ituku, Ozalla, Enugu.

Adolescence is an important developmental period of childhood. Good health and adequate nutrition consisting major food constituents and trace elements like zinc are fundamental for optimal sexual maturation. To determine the relationship between zinc levels and pattern of breast and pubic hair development, as well as menarcheal age of female SCA children aged 6-18 years and their matched controls with hemoglobin genotype AA. Read More

View Article
March 2018
9 Reads

Variation of Carotid Intima Media Thickness With Body Mass Index in Healthy Adults of Black African Descent.

J Ultrasound Med 2018 May 15. Epub 2018 May 15.

Department of Radiology, Obafemi Awolowo University/Obafemi Awolowo University Teaching Hospitals Complex, Ile-Ife, Osun State, Nigeria.

Objectives: Studies have shown that common carotid intima media thickness (CIMT) measured by B-mode sonography increases with body mass index (BMI) among subjects with cardiovascular diseases in different populations. However, association of body fat and subclinical atherosclerosis in the absence of these cardiovascular diseases is understudied. We aimed to evaluate the correlation between BMI and CIMT in a healthy adult population of black African ancestry. Read More

View Article
May 2018
5 Reads