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Linh Tran, Tobias Hamp, Burkhard Rost
MOTIVATION: Protein-protein interactions (PPIs) play a key role in many cellular processes. Most annotations of PPIs mix experimental and computational data. The mix optimizes coverage, but obfuscates the annotation origin. Some resources excel at focusing on reliable experimental data. Here, we focused on new pairs of interacting proteins for several model organisms based solely on sequence-based prediction methods. RESULTS: We extracted reliable experimental data about which proteins interact (binary) for eight diverse model organisms from public databases, namely from Escherichia coli, Schizosaccharomyces pombe, Plasmodium falciparum, Drosophila melanogaster, Caenorhabditis elegans, Mus musculus, Rattus norvegicus, Arabidopsis thaliana, and for the previously used Homo sapiens and Saccharomyces cerevisiae...
2018: PloS One
Barbara E Ainsworth, Kathleen B Watson, Kate Ridley, Karin A Pfeiffer, Stephen D Herrmann, Scott E Crouter, Robert G McMurray, Nancy F Butte, David R Bassett, Stewart G Trost, David Berrigan, Janet E Fulton
PURPOSE: The purposes of this article are to: (a) describe the rationale and development of the Youth Compendium of Physical Activities (Youth Compendium); and (b) discuss the utility of the Youth Compendium for audiences in research, education, community, health care, public health, and the private sector. METHODS: The Youth Compendium provides a list of 196 physical activities (PA) categorized by activity types, specific activities, and metabolic costs (youth metabolic equivalents of task [METy ]) as measured by indirect calorimetry...
July 18, 2018: Research Quarterly for Exercise and Sport
Y Nichole Faller, Melissa Anne Wuerch, Mary Rucklos Hampton, Sylvia Barton, Cheryl Fraehlich, Darlene Juschka, Krista Milford, Pertice Moffitt, Jane Ursel, Alexis Zederayko
Intimate partner violence (IPV) has become a worldwide epidemic, yet little is known about the experiences of women survivors living in rural and Northern Canadian communities. Existing statistics suggest that women living in rural areas of the Canadian Prairie Provinces and Northwest Territories (NWT) are at a significantly higher risk of experiencing IPV. To better understand the experiences of IPV in these regions, qualitative interviews were conducted with service providers, including the Royal Canadian Mounted Police (RCMP), Victims Services, Shelter Services, counselors, and others (e...
July 1, 2018: Journal of Interpersonal Violence
Tania Samantha de Silva, Victoria Rose Russell, Francis Patrick Henry, Paul Thomas Ryan Thiruchelvam, Dimitri John Hadjiminas, Ragheed Al-Mufti, Roselyn Katy Hogben, Judith Hunter, Simon Wood, Navid Jallali, Daniel Richard Leff
INTRODUCTION: Patients with sporadic breast cancer (BC) have low contralateral breast cancer risk (CLBCR; approximately 0.7% per annum) and contralateral prophylactic mastectomy (CPM) offers no survival advantage. CPM with autologous reconstruction (AR) has major morbidity and resource implications. OBJECTIVE: The aim of this study was to review the impact of PREDICT survival estimates and lifetime CLBCR scores on decision making for CPM in patients with unilateral BC...
July 17, 2018: Annals of Surgical Oncology
Mursheda Begum, Grant Lewison, Mark Lawler, Richard Sullivan
BACKGROUND: Cancer research is among the most active biomedical research domains for the European Union (EU). However, little quantitative empirical evidence is available to guide the decisions on the choice of disease site to study, specific research domain focus or allocation of research resources. To inform national/supranational cancer research policy, high-resolution intelligence is needed. METHODS: We performed a bibliometric analysis of European cancer research papers in the Web of Science from 2002 to 2013 to quantify research activity in each of the 28 EU Member States, along with Iceland, Norway and Switzerland (EUR31), which cancer sites/research domains they addressed, and their sources of financial support (2009-2013)...
July 4, 2018: European Journal of Cancer
Selina Våge, Gunnar Bratbak, Jorun Egge, Mikal Heldal, Aud Larsen, Svein Norland, Maria Lund Paulsen, Bernadette Pree, Ruth-Anne Sandaa, Evy Foss Skjoldal, Tatiana M Tsagaraki, Lise Øvreås, T Frede Thingstad
In food webs, interactions between competition and defence control the partitioning of limiting resources. As a result, simple models of these interactions contain links between biogeochemistry, diversity, food web structure and ecosystem function. Working at hierarchical levels, these mechanisms also produce self-similarity and therefore suggest how complexity can be generated from repeated application of simple underlying principles. Reviewing theoretical and experimental literature relevant to the marine photic zone, we argue that there is a wide spectrum of phenomena, including single cell activity of prokaryotes, microbial biodiversity at different levels of resolution, ecosystem functioning, regional biogeochemical features and evolution at different timescales; that all can be understood as variations over a common principle, summarised in what has been termed the 'Killing-the-Winner' (KtW) motif...
July 17, 2018: Ecology Letters
R A K Kennedy, C M E Reynolds, S Cawley, E O'Malley, D M McCartney, M J Turner
Background: Maternal nutrition is a determinant of pregnancy outcomes. Few studies have evaluated the potential of online nutrition resources to modify behaviour. This randomized controlled trial aimed to determine whether access to a customized evidence-based nutrition website in pregnancy improved neonatal outcomes. Methods: Women <18 weeks gestation were recruited at their convenience. The control group received standard care. In addition to standard care, the intervention group received access to an evidence-based nutrition website, customized to the preferences of pregnant women...
July 13, 2018: Journal of Public Health
Lu Zhou, Qingyu Xiao, Jie Bi, Zhen Wang, Yixue Li
The rabbit is a very important species for both biomedical research and agriculture animal breeding. They are not only the most-used experimental animals for the production of antibodies, but also widely used for studying a variety of human diseases. Here we developed RabGTD, the first comprehensive rabbit database containing both genome and transcriptome data generated by next-generation sequencing. Genomic variations coming from 79 samples were identified and annotated, including 33 samples of wild rabbits and 46 samples of domestic rabbits with diverse populations...
January 1, 2018: Database: the Journal of Biological Databases and Curation
E A Ivanov, I N Mordvintsev, N G Platonov, S V Naidenko, A V Tiunov, V V Rozhnov
The data on the content of carbon and nitrogen isotopes in the blood samples of polar bears obtained in the present study confirm that polar bears in the Taimyr region (and the Kara-Barents sea population in general) are partly dependent on the resources of terrestrial origin. However the "terrestrial carbon" evidently reaches bears' tissues indirectly, via marine food webs utilizing organic carbon brought into the polar basin by Siberian rivers.
May 2018: Doklady Biological Sciences: Proceedings of the Academy of Sciences of the USSR, Biological Sciences Sections
Sanja Abbott, Andrii Iudin, Paul K Korir, Sriram Somasundharam, Ardan Patwardhan
The Electron Microscopy Data Bank (EMDB; is a global openly-accessible archive of biomolecular and cellular 3D reconstructions derived from electron microscopy (EM) data. EMBL-EBI develops web-based resources to facilitate the reuse of EMDB data. Here we provide protocols for how these resources can be used for searching EMDB, visualising EMDB structures, statistically analysing EMDB content and checking the validity of EMDB structures. Protocols for searching include quick link categories from the main page, links to latest entries released during the weekly cycle, filtered browsing of the entire archive and a form-based search...
March 2018: Current Protocols in Bioinformatics
Stephanie Ho, Elizabeth Janiak
OBJECTIVE: The Massachusetts Access Program is a statewide, centralised referral and case management program created to address barriers to later second-trimester abortions. This study outlines the scope of, describes provider experiences with, and evaluates provider acceptability of the Program. STUDY DESIGN: We invited physicians, nurses and staff working in hospitals within the later abortion provider referral network to participate in a mixed-methods study that included a web-based quantitative survey and/or a semi-structured qualitative interview...
July 14, 2018: BMJ sexual & reproductive health
Kurt G Schilling, Yurui Gao, Matthew Christian, Vaibhav Janve, Iwona Stepniewska, Bennett A Landman, Adam W Anderson
The squirrel monkey (Saimiri sciureus) is a commonly-used surrogate for humans in biomedical research. In the neuroimaging community, MRI and histological atlases serve as valuable resources for anatomical, physiological, and functional studies of the brain; however, no digital MRI/histology atlas is currently available for the squirrel monkey. This paper describes the construction of a web-based multi-modal atlas of the squirrel monkey brain. The MRI-derived information includes anatomical MRI contrast (i...
July 13, 2018: Neuroinformatics
Rymon Rofaiel, Nilesh Chande
Background/Aims: Many patients currently seek the Internet for health-related information without discerning the quality or bias of the evidence presented. Biologic agents have become the mainstay of therapy in inflammatory bowel disease (IBD), and it is important that patients have access to high-quality information when exploring the various available agents to make informed decisions about their therapy. The primary aim of this study was to evaluate the quality of patient-searched Internet websites that describe the biologic agents used as treatment options for IBD...
July 6, 2018: Saudi Journal of Gastroenterology: Official Journal of the Saudi Gastroenterology Association
Sara Simblett, Ben Greer, Faith Matcham, Hannah Curtis, Ashley Polhemus, José Ferrão, Peter Gamble, Til Wykes
BACKGROUND: Remote measurement technology refers to the use of mobile health technology to track and measure change in health status in real time as part of a person's everyday life. With accurate measurement, remote measurement technology offers the opportunity to augment health care by providing personalized, precise, and preemptive interventions that support insight into patterns of health-related behavior and self-management. However, for successful implementation, users need to be engaged in its use...
July 12, 2018: Journal of Medical Internet Research
Kathryn Fletcher, Fiona Foley, Neil Thomas, Erin Michalak, Lesley Berk, Michael Berk, Steve Bowe, Sue Cotton, Lidia Engel, Sheri L Johnson, Steven Jones, Michael Kyrios, Sara Lapsley, Cathrine Mihalopoulos, Tania Perich, Greg Murray
BACKGROUND: The primary objective of this randomised controlled trial (RCT) is to establish the effectiveness of a novel online quality of life (QoL) intervention tailored for people with late stage (≥ 10 episodes) bipolar disorder (BD) compared with psychoeducation. Relative to early stage individuals, this late stage group may not benefit as much from existing psychosocial treatments. The intervention is a guided self-help, mindfulness based intervention (MBI) developed in consultation with consumers, designed specifically for web-based delivery, with email coaching support...
July 13, 2018: BMC Psychiatry
Debasree Sarkar, Tanmoy Jana, Sudipto Saha
Protein-peptide interactions form an important subset of the total protein interaction network in the cell and play key roles in signaling and regulatory networks, and in major biological processes like cellular localization, protein degradation, and immune response. In this work, we have described the LMDIPred web server, an online resource for generalized prediction of linear peptide sequences that may bind to three most prevalent and well-studied peptide recognition modules (PRMs)-SH3, WW and PDZ. We have developed support vector machine (SVM)-based prediction models that achieved maximum Matthews Correlation Coefficient (MCC) of 0...
2018: PloS One
Maria Teresa Ruiz Tsukazan, Ricardo Mingarini Terra, Frank Detterbeck, Ilka Lopes Santoro, Bruno Hochhegger, Gustavo de Souza Portes Meirelles, Gustavo Fortunato, Gustavo Faibischew Prado
Background: Pulmonary nodules are common; some are inconsequential while others are malignant. Management of solitary pulmonary nodule (SPN) in Brazil appears to be highly variable, potentially leading to suboptimal outcomes. Assessment of the variability and the association with the degree of availability of resources can provide a foundation for development of clinical guidelines for management of SPN specific for the Brazilian setting. Methods: A web-based survey was developed by thoracic surgeons, pulmonologists and radiologists to evaluate SPN perception and management...
May 2018: Journal of Thoracic Disease
Elton J R Vasconcelos, Vinícius C Mesel, Lucas F daSilva, David S Pires, Guilherme M Lavezzo, Adriana S A Pereira, Murilo S Amaral, Sergio Verjovski-Almeida
Long non-coding RNAs (lncRNAs) have been widely discovered in several organisms with the help of high-throughput RNA sequencing. LncRNAs are over 200 nt-long transcripts that do not have protein-coding (PC) potential, having been reported in model organisms to act mainly on the overall control of PC gene expression. Little is known about the functionality of lncRNAs in evolutionarily ancient non-model metazoan organisms, like Schistosoma mansoni, the parasite that causes schistosomiasis, one of the most prevalent infectious-parasitic diseases worldwide...
January 1, 2018: Database: the Journal of Biological Databases and Curation
Tatiana M Tsagaraki, Bernadette Pree, Øystein Leiknes, Aud Larsen, Gunnar Bratbak, Lise Øvreås, Jorun K Egge, Roman Spanek, Maria L Paulsen, Yngvar Olsen, Olav Vadstein, T F Thingstad
Combining a minimum food web model with Arctic microbial community dynamics, we have suggested that top-down control by copepods can affect the food web down to bacterial consumption of organic carbon. Pursuing this hypothesis further, we used the minimum model to design and analyse a mesocosm experiment, studying the effect of high (+Z) and low (-Z) copepod density on resource allocation, along an organic-C addition gradient. In the Arctic, both effects are plausible due to changes in advection patterns (affecting copepods) and meltwater inputs (affecting carbon)...
July 10, 2018: ISME Journal
Rachel Maczis Shahan, Christopher Zawora, Haley Melissa Wight, John Sittmann, Wanpeng Wang, Stephen M Mount, Zhongchi Liu
Fragaria vesca, a diploid strawberry, is a developing model system for the economically important Rosaceae family. Unlike tomato, the traditional model for fleshy fruit development, strawberry fleshy fruit develops from the floral receptacle and its ripening is non-climacteric. Additionally, the external seed configuration of strawberry fruit facilitates the study of seed-to-fruit cross-tissue communication, particularly phytohormone biosynthesis and transport. Insight gained from strawberry fruit development broadens our understanding of general developmental processes...
July 10, 2018: Plant Physiology
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