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Stefan Schulz, Martin Boeker, Catalina Martinez-Costa
BioTop is a domain upper level ontology for the life sciences, based on OWL DL, introduced ten years ago. This paper provides an update of the current state of this resource, with a special focus on BioTop's top level, BioTopLite, which currently contains 55 classes, 37 object properties and 247 description logics axioms. A bridging file allows harmonising BioTopLite with the classes of Basic Formal Ontology BFO2. The updated OWL resources are available at They build the core of several upper level ontological artefacts including bridging ontologies to other upper level resources...
2017: Studies in Health Technology and Informatics
Jennie B Jarrett, Sandra Sauereisen
Patients with a medial, degenerative meniscal tear and a minimal history of osteoarthritis make good candidates for physical therapy-- and there is an added benefit, too.
April 2017: Journal of Family Practice
William R Hogan, Josh Hanna, Amanda Hicks, Samira Amirova, Baxter Bramblett, Matthew Diller, Rodel Enderez, Timothy Modzelewski, Mirela Vasconcelos, Chris Delcher
BACKGROUND: The Drug Ontology (DrOn) is an OWL2-based representation of drug products and their ingredients, mechanisms of action, strengths, and dose forms. We originally created DrOn for use cases in comparative effectiveness research, primarily to identify historically complete sets of United States National Drug Codes (NDCs) that represent packaged drug products, by the ingredient(s), mechanism(s) of action, and so on contained in those products. Although we had designed DrOn from the outset to carefully distinguish those entities that have a therapeutic indication from those entities that have a molecular mechanism of action, we had not previously represented in DrOn any particular therapeutic indication...
March 3, 2017: Journal of Biomedical Semantics
Dustin K Smith, Deborah E Miller, Anne Mounsey
Counsel patients who want to quit smoking that doing so abruptly leads to higher cessation rates than does quitting gradually.
March 2017: Journal of Family Practice
Corey Lyon, Jennifer K Bello
Steroids--even when administered in the last leg of the late preterm period--still reduce the likelihood of respiratory complications in newborns.
February 2017: Journal of Family Practice
David Wyncott, Corey Lyon, Anne Mounsey
Sulfonylureas have been the preferred add-on therapy to metformin for T2DM, but a study finds that DPP-4s have lower risks of death, CV events, and hypoglycemia.
January 2017: Journal of Family Practice
Hirokazu Chiba, Ikuo Uchiyama
BACKGROUND: Toward improved interoperability of distributed biological databases, an increasing number of datasets have been published in the standardized Resource Description Framework (RDF). Although the powerful SPARQL Protocol and RDF Query Language (SPARQL) provides a basis for exploiting RDF databases, writing SPARQL code is burdensome for users including bioinformaticians. Thus, an easy-to-use interface is necessary. RESULTS: We developed SPANG, a SPARQL client that has unique features for querying RDF datasets...
February 8, 2017: BMC Bioinformatics
Carin E Reust, James J Stevermer, Jennie B Jarrett
Parents no longer need to struggle to get their kids to drink electrolyte solutions during episodes of mild gastroenteritis; apple juice works just as well.
December 2016: Journal of Family Practice
Keri Bergeson, Shailendra Prasad
While ACOG recommends delivery for all women with ruptured membranes after 34 weeks' gestation, a new study finds expectant management may be the way to go.
November 2016: Journal of Family Practice
Jeffrey B Vancouver, Justin D Purl
Self-efficacy, which is one's belief in one's capacity, has been found to both positively and negatively influence effort and performance. The reasons for these different effects have been a major topic of debate among social-cognitive and perceptual control theorists. In particular, the findings of various self-efficacy effects has been motivated by a perceptual control theory view of self-regulation that social-cognitive theorists' question. To provide more clarity to the theoretical arguments, a computational model of the multiple processes presumed to create the positive, negative, and null effects for self-efficacy is presented...
April 2017: Journal of Applied Psychology
Darren A Natale, Cecilia N Arighi, Judith A Blake, Jonathan Bona, Chuming Chen, Sheng-Chih Chen, Karen R Christie, Julie Cowart, Peter D'Eustachio, Alexander D Diehl, Harold J Drabkin, William D Duncan, Hongzhan Huang, Jia Ren, Karen Ross, Alan Ruttenberg, Veronica Shamovsky, Barry Smith, Qinghua Wang, Jian Zhang, Abdelrahman El-Sayed, Cathy H Wu
The Protein Ontology (PRO; formally defines and describes taxon-specific and taxon-neutral protein-related entities in three major areas: proteins related by evolution; proteins produced from a given gene; and protein-containing complexes. PRO thus serves as a tool for referencing protein entities at any level of specificity. To enhance this ability, and to facilitate the comparison of such entities described in different resources, we developed a standardized representation of proteoforms using UniProtKB as a sequence reference and PSI-MOD as a post-translational modification reference...
January 4, 2017: Nucleic Acids Research
Jennie B Jarrett, Linda Hogan, Corey Lyon, Kate Rowland
This novel method of identifying patients with uncontrolled hypertension correlates well with ambulatory BP monitoring.
October 2016: Journal of Family Practice
Biplab Ghosh, Venuka Durani Goyal
Histidine is ubiquitous in enzyme active sites but its role is often difficult to ascribe due to ambiguity of protonation state and complex electrostatic and dynamic effects involved. In this study the role of His 72 in TmPurL, a glutamine amidotransferase (GAT) enzyme, is investigated. TmPurL is a large 66kDa enzyme that works as part of an even larger (>100kDa) multi-protein complex. This enzyme complex performs an essential step in the purine biosynthesis pathway by abstracting ammonia from a glutamine molecule and channeling it 30Å away into the active site of TmPurL, incorporating it into a purine biosynthesis intermediate...
October 25, 2016: Bioorganic & Medicinal Chemistry Letters
Amir Barzin, Anne Mounsey
This study's findings regarding the risk of miscarriage may mean it's time to forego fluconazole in favor of topical azoles as first-line treatment.
September 2016: Journal of Family Practice
Pier Luigi Buttigieg, Evangelos Pafilis, Suzanna E Lewis, Mark P Schildhauer, Ramona L Walls, Christopher J Mungall
BACKGROUND: The Environment Ontology (ENVO; ), first described in 2013, is a resource and research target for the semantically controlled description of environmental entities. The ontology's initial aim was the representation of the biomes, environmental features, and environmental materials pertinent to genomic and microbiome-related investigations. However, the need for environmental semantics is common to a multitude of fields, and ENVO's use has steadily grown since its initial description...
September 23, 2016: Journal of Biomedical Semantics
Kathryn Justesen, Shailendra Prasad
Finally, there's an effective prevention strategy--other than condoms--that can be used, as needed, by patients at high risk for HIV infection.
August 2016: Journal of Family Practice
Kehinde Eniola, Angela Bacigalupo, Anne Mounsey
While bright light therapy already has a place in the treatment of seasonal affective disorder, a recent trial spotlights its utility beyond the winter months.
July 2016: Journal of Family Practice
William R Hogan, Michael M Wagner, Mathias Brochhausen, John Levander, Shawn T Brown, Nicholas Millett, Jay DePasse, Josh Hanna
BACKGROUND: We developed the Apollo Structured Vocabulary (Apollo-SV)-an OWL2 ontology of phenomena in infectious disease epidemiology and population biology-as part of a project whose goal is to increase the use of epidemic simulators in public health practice. Apollo-SV defines a terminology for use in simulator configuration. Apollo-SV is the product of an ontological analysis of the domain of infectious disease epidemiology, with particular attention to the inputs and outputs of nine simulators...
August 18, 2016: Journal of Biomedical Semantics
Yuzo Watanabe, Hisaaki Yanai, Mayumi Kanagawa, Sakiko Suzuki, Satoko Tamura, Kiyoshi Okada, Seiki Baba, Takashi Kumasaka, Yoshihiro Agari, Lirong Chen, Zheng Qing Fu, John Chrzas, Bi Cheng Wang, Noriko Nakagawa, Akio Ebihara, Ryoji Masui, Seiki Kuramitsu, Shigeyuki Yokoyama, Gen Ichi Sampei, Gota Kawai
The crystal structures of a subunit of the formylglycinamide ribonucleotide amidotransferase, PurS, from Thermus thermophilus, Sulfolobus tokodaii and Methanocaldococcus jannaschii were determined and their structural characteristics were analyzed. For PurS from T. thermophilus, two structures were determined using two crystals that were grown in different conditions. The four structures in the dimeric form were almost identical to one another despite their relatively low sequence identities. This is also true for all PurS structures determined to date...
August 2016: Acta Crystallographica. Section F, Structural Biology Communications
Kevin Frazer, James J Stevermer
Adding cyclobenzaprine or oxycodone/acetaminophen to naproxen for the treatment of acute low back pain does nothing more than increase adverse effects.
June 2016: Journal of Family Practice
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