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Megan J Huggett, Amy Apprill
Coral-associated microorganisms are thought to play a fundamental role in the health and ecology of corals, but understandings of specific coral-microbial interactions are lacking. In order to create a framework to examine coral-microbial specificity, we integrated and phylogenetically compared 21,100 SSU rRNA gene Sanger-produced sequences from bacteria and archaea associated with corals from previous studies, and accompanying host, location and publication metadata, to produce the Coral Microbiome Database...
August 9, 2018: Environmental Microbiology Reports
Josef Dolejs, Helena Homolkova, Petra Maresova
Background: In humans, the mortality rate dramatically decreases with age after birth, and the causes of death change significantly during childhood. In the present study, we attempted to explain age-associated decreases in mortality for congenital anomalies of the central nervous system (CACNS), as well as decreases in total mortality with age. We further investigated the age trajectory of mortality in the biologically related category "diseases of the nervous system" (DNS). Methods: The numbers of deaths were extracted from the mortality database of the World Health Organization (WHO) for the following nine countries: Denmark, Finland, Norway, Sweden, Austria, the Czech Republic, Hungary, Poland, and Slovakia...
2018: Frontiers in Neurology
Philip Heller, James Casaletto, Gregory Ruiz, Jonathan Geller
The Cytochrome C Oxidase subunit I gene ("COI") is the de facto standard for animal DNA barcoding. Organism identification based on COI requires an accurate and extensive annotated database of COI sequences. Such a database can also be of value in reconstructing evolutionary history and in diversity studies. Two COI databases are currently available: BOLD and Midori. BOLD's submissions conform to stringent sequence and metadata requirements; BOLD is specific to COI but makes no attempt to be comprehensive...
August 7, 2018: Scientific Data
Losasso Carmen, Di Cesare Andrea, Mastrorilli Eleonora, Patuzzi Ilaria, Cibin Veronica, Eckert Ester M, Fontaneto Diego, Vanzo Angiola, Ricci Antonia, Corno Gianluca
The massive use of antimicrobials in animal farming is considered as the greatest contributor to the phenomenon of antimicrobial resistant bacteria (ARB) presence in food of animal origin. Nevertheless, sewage from treated animals may impact on vegetables grown on fertilized fields, but it is largely unknown whether and to what extent ARB are transferred to vegetables and to human gut. It could be hypothesized that food of animal and vegetal origin have a different role into ARB transfer to human gut and that different diets could be characterized by different antimicrobial resistance genes (ARGs) load...
August 3, 2018: International Journal of Antimicrobial Agents
Kristopher D Parker, Shannon E Albeke, Jason P Gigley, Allan M Goldstein, Naomi L Ward
Murine models have become essential tools for understanding the complex interactions between gut microbes, their hosts, and disease. While many intra-facility factors are known to influence the structure of mouse microbiomes, the contribution of inter-facility variation to mouse microbiome composition, especially in the context of disease, remains under-investigated. We replicated microbiome experiments using identical mouse lines housed in two separate animal facilities and report drastic differences in composition of microbiomes based upon animal facility of origin...
2018: Frontiers in Microbiology
Jiangbo Pu, Xiangning Li
Electrical activity of developing dissociated neuronal networks is of immense significance for understanding the general properties of neural information processing and storage. In addition, the complexity and diversity of network activity patterns make them ideal candidates for developing novel computational models and evaluating algorithms. However, there are rare databases which focus on the changing network dynamics during development. Here, we describe the design and implementation of Neuroinformation Database for Developing Networks (NDDN), a repository for electrophysiological data collected from long-term cultured hippocampal networks...
2018: Journal of Healthcare Engineering
J Patrick Woolley, Emily Kirby, Josh Leslie, Francis Jeanson, Moran N Cabili, Gregory Rushton, James G Hazard, Vagelis Ladas, Colin D Veal, Spencer J Gibson, Anne-Marie Tassé, Stephanie O M Dyke, Clara Gaff, Adrian Thorogood, Bartha Maria Knoppers, John Wilbanks, Anthony J Brookes
Given the data-rich nature of modern biomedical research, there is a pressing need for a systematic, structured, computer-readable way to capture, communicate, and manage sharing rules that apply to biomedical resources. This is essential for responsible recording, versioning, communication, querying, and actioning of resource sharing plans. However, lack of a common "information model" for rules and conditions that govern the sharing of materials, methods, software, data, and knowledge creates a fundamental barrier...
2018: NPJ Genomic Medicine
Yi Tan, Brett E Pickett, Susmita Shrivastava, Lionel Gresh, Angel Balmaseda, Paolo Amedeo, Lihui Hu, Vinita Puri, Nadia B Fedorova, Rebecca A Halpin, Matthew P LaPointe, Marshall R Cone, Lea Heberlein-Larson, Laura D Kramer, Alexander T Ciota, Aubree Gordon, Reed S Shabman, Suman R Das, Eva Harris
Chikungunya virus (CHIKV) has been detected sporadically since the 1950s and includes three distinct co-circulating genotypes. In late 2013, the Asian genotype of CHIKV was responsible for the Caribbean outbreak (CO) that rapidly became an epidemic throughout the Americas. There is a limited understanding of the molecular evolution of CHIKV in the Americas during this epidemic. We sequenced 185 complete CHIKV genomes collected mainly from Nicaragua in Central America and Florida in the United States during the 2014-2015 Caribbean/Americas epidemic...
July 2018: PLoS Neglected Tropical Diseases
Le Huang, Han Zhang, Peizhi Wu, Sarah Entwistle, Xueqiong Li, Tanner Yohe, Haidong Yi, Zhenglu Yang, Yanbin Yin
Carbohydrate-active enzyme (CAZymes) are not only the most important enzymes for bioenergy and agricultural industries, but also very important for human health, in that human gut microbiota encode hundreds of CAZyme genes in their genomes for degrading various dietary and host carbohydrates. We have built an online database dbCAN-seq ( to provide pre-computed CAZyme sequence and annotation data for 5,349 bacterial genomes. Compared to the other CAZyme resources, dbCAN-seq has the following new features: (i) a convenient download page to allow batch download of all the sequence and annotation data; (ii) an annotation page for every CAZyme to provide the most comprehensive annotation data; (iii) a metadata page to organize the bacterial genomes according to species metadata such as disease, habitat, oxygen requirement, temperature, metabolism; (iv) a very fast tool to identify physically linked CAZyme gene clusters (CGCs) and (v) a powerful search function to allow fast and efficient data query...
January 4, 2018: Nucleic Acids Research
Zhemin Zhou, Nabil-Fareed Alikhan, Martin J Sergeant, Nina Luhmann, Cátia Vaz, Alexandre P Francisco, João André Carriço, Mark Achtman
Current methods struggle to reconstruct and visualize the genomic relationships of large numbers of bacterial genomes. GrapeTree facilitates the analyses of large numbers of allelic profiles by a static "GrapeTree Layout" algorithm that supports interactive visualizations of large trees within a web browser window. GrapeTree also implements a novel minimum spanning tree algorithm (MSTree V2) to reconstruct genetic relationships despite high levels of missing data. GrapeTree is a stand-alone package for investigating phylogenetic trees plus associated metadata and is also integrated into EnteroBase to facilitate cutting edge navigation of genomic relationships among bacterial pathogens...
July 26, 2018: Genome Research
Joy Z Zhou, Benjamin T Lemelman, Nicolae Done, Macey L Henderson, Alexandra Macmillan, David H Song, Amir H Dorafshar
BACKGROUND: The purpose of this study is to quantify the relationship between social media use and the dissemination of research across nontraditional channels. METHODS: Between June and August of 2016, the authors identified 10 plastic surgery journals with the highest impact factor and their 10 most widely circulated articles. Article age; journal impact factor; "distinguished" article designation; and social media metadata of the first authors, last authors, and journals were incorporated into a multivariate regression model to predict the Altmetric Attention Score, a quantitative measure of popularity across Web-based media platforms...
August 2018: Plastic and Reconstructive Surgery
Yawen Zou, Manfred D Laubichler
Systems biology is a discipline that studies biological systems from a holistic and interdisciplinary perspective. It brings together biologists, mathematicians, computer scientists, physicists, and engineers, so it has both biology-oriented components and systems-oriented components. We applied several computational tools to analyze the bibliographic information of published articles in systems biology to answer the question: Did the research topics of systems biology become more biology-oriented or more systems-oriented from 1992 to 2013? We analyzed the metadata of 9923 articles on systems biology from the Web of Science database...
2018: PloS One
Jacquelynn Benjamino, Lidia Beka, Joerg Graf
Microbiomes can be thought of as the integration of biotic and abiotic factors, including the microbial communities and the distinct physio-chemical properties that are present in a habitat. The microbes within a microbiome can influence the chemical environment by degrading medications inside patients or contaminants in the environment, such as hydrocarbons released after the Deepwater Horizon oil spill. Identifying and monitoring the relative abundance of microbes can help to elucidate variations in their response to toxins and should be considered as a variable in statistical analyses...
July 25, 2018: Current Protocols in Toxicology
David Cibula, Richard Pötter, François Planchamp, Elisabeth Avall-Lundqvist, Daniela Fischerova, Christine Haie-Meder, Christhardt Köhler, Fabio Landoni, Sigurd Lax, Jacob Christian Lindegaard, Umesh Mahantshetty, Patrice Mathevet, W Glenn McCluggage, Mary McCormack, Raj Naik, Remi Nout, Sandro Pignata, Jordi Ponce, Denis Querleu, Francesco Raspagliesi, Alexandros Rodolakis, Karl Tamussino, Pauline Wimberger, Maria Rosaria Raspollini
Regrettably, the author metadata used for the previous correction (doi: ) contained an error in the tagging of W. Glenn McCluggage's name; this has been corrected. No further adjustments have been made to the Correction, or the original Guideline paper (doi: ).
July 25, 2018: Virchows Archiv: An International Journal of Pathology
Julie Bergeron, Dany Doiron, Yannick Marcon, Vincent Ferretti, Isabel Fortier
BACKGROUND: The lack of accessible and structured documentation creates major barriers for investigators interested in understanding, properly interpreting and analyzing cohort data and biological samples. Providing the scientific community with open information is essential to optimize usage of these resources. A cataloguing toolkit is proposed by Maelstrom Research to answer these needs and support the creation of comprehensive and user-friendly study- and network-specific web-based metadata catalogues...
2018: PloS One
Su Bin Lim, Swee Jin Tan, Wan-Teck Lim, Chwee Teck Lim
The Gene Expression Omnibus (GEO) database is an excellent public source of whole transcriptomic profiles of multiple cancers. The main challenge is the limited accessibility of such large-scale genomic data to people without a background in bioinformatics or computer science. This presents difficulties in data analysis, sharing and visualization. Here, we present an integrated bioinformatics pipeline and a normalized dataset that has been preprocessed using a robust statistical methodology; allowing others to perform large-scale meta-analysis, without having to conduct time-consuming data mining and statistical correction...
July 24, 2018: Scientific Data
Jean F Power, Carlo R Carere, Charles K Lee, Georgia L J Wakerley, David W Evans, Mathew Button, Duncan White, Melissa D Climo, Annika M Hinze, Xochitl C Morgan, Ian R McDonald, S Craig Cary, Matthew B Stott
Geothermal springs are model ecosystems to investigate microbial biogeography as they represent discrete, relatively homogenous habitats, are distributed across multiple geographical scales, span broad geochemical gradients, and have reduced metazoan interactions. Here, we report the largest known consolidated study of geothermal ecosystems to determine factors that influence biogeographical patterns. We measured bacterial and archaeal community composition, 46 physicochemical parameters, and metadata from 925 geothermal springs across New Zealand (13...
July 23, 2018: Nature Communications
Timm B Poeppl, Maximilian R Donges, Andreas Mokros, Rainer Rupprecht, Peter T Fox, Angela R Laird, Danilo Bzdok, Berthold Langguth, Simon B Eickhoff
Psychopathy is a disorder of high public concern because it predicts violence and offense recidivism. Recent brain imaging studies suggest abnormal brain activity underlying psychopathic behavior. No reliable pattern of altered neural activity has been disclosed so far. This study sought to identify consistent changes of brain activity in psychopaths and to investigate whether these could explain known psychopathology. First, we used activation likelihood estimation (p < 0.05, corrected) to meta-analyze brain activation changes associated with psychopathy across 28 functional magnetic resonance imaging studies reporting 753 foci from 155 experiments...
July 23, 2018: Molecular Psychiatry
MiHyun Jang, Tejal Patted, Yolanda Gil, Daniel Garijo, Varun Ratnakar, Jie Ji, Prince Wang, Aggie McMahon, Paul M Thompson, Neda Jahanshad
Scientific collaborations involving multiple institutions are increasingly commonplace. It is not unusual for publications to have dozens or hundreds of authors, in some cases even a few thousands. Gathering the information for such papers may be very time consuming, since the author list must include authors who made different kinds of contributions and whose affiliations are hard to track. Similarly, when datasets are contributed by multiple institutions, the collection and processing details may also be hard to assemble due to the many individuals involved...
October 2017: CEUR Workshop Proceedings
John Zulueta, Andrea Piscitello, Mladen Rasic, Rebecca Easter, Pallavi Babu, Scott A Langenecker, Melvin McInnis, Olusola Ajilore, Peter C Nelson, Kelly Ryan, Alex Leow
BACKGROUND: Mood disorders are common and associated with significant morbidity and mortality. Better tools are needed for their diagnosis and treatment. Deeper phenotypic understanding of these disorders is integral to the development of such tools. This study is the first effort to use passively collected mobile phone keyboard activity to build deep digital phenotypes of depression and mania. OBJECTIVE: The objective of our study was to investigate the relationship between mobile phone keyboard activity and mood disturbance in subjects with bipolar disorders and to demonstrate the feasibility of using passively collected mobile phone keyboard metadata features to predict manic and depressive signs and symptoms as measured via clinician-administered rating scales...
July 20, 2018: Journal of Medical Internet Research
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