bluuebunny/crossref_metadata_2025_split huggingface dataset:
Selected papers from the 13th Annual Bio-Ontologies Special Interest Group Meeting
Authors: Soldatova Larisa N , Sansone Susanna-Assunta , Stephens Susie M , Shah Nigam H 
Published: May 2011

AbstractOver the years, the Bio-Ontologies SIG at ISMB has provided a forum for discussion of the latest and most innovative research in the application of ontologies and more generally the organisation, presentation and dissemination of knowledge in biomedicine and the life sciences. The ten papers selected for this supplement are extended versions of the original papers presented at the 2010 SIG. The papers span a wide range of topics including practical solutions for data and knowledge integration for translational medicine, hypothesis based querying , understanding kidney and urinary pathways, mining the pharmacogenomics literature; theoretical research into the orthogonality of biomedical ontologies, the representation of diseases, the representation of research hypotheses, the combination of ontologies and natural language processing for an annotation framework, the generation of textual definitions, and the discovery of gene interaction networks.
The Translational Medicine Ontology and Knowledge Base: driving personalized medicine by bridging the gap between bench and bedside
Authors: Luciano Joanne S , Andersson Bosse , Batchelor Colin , Bodenreider Olivier , Clark Tim , Denney Christine K , Domarew Christopher , Gambet Thomas , Harland Lee , Jentzsch Anja , Kashyap Vipul , Kos Peter , Kozlovsky Julia , Lebo Timothy , Marshall Scott M , McCusker Jamie P , McGuinness Deborah L , Ogbuji Chimezie , Pichler Elgar , Powers Robert L , Prud’hommeaux Eric , Samwald Matthias , Schriml Lynn , Tonellato Peter J , Whetzel Patricia L , Zhao Jun , Stephens Susie , Dumontier Michel 
Published: May 2011

Abstract
Background
Translational medicine requires the integration of knowledge using heterogeneous data from health care to the life sciences. Here, we describe a collaborative effort to produce a prototype Translational Medicine Knowledge Base (TMKB) capable of answering questions relating to clinical practice and pharmaceutical drug discovery.

Results
We developed the Translational Medicine Ontology (TMO) as a unifying ontology to integrate chemical, genomic and proteomic data with disease, treatment, and electronic health records. We demonstrate the use of Semantic Web technologies in the integration of patient and biomedical data, and reveal how such a knowledge base can aid physicians in providing tailored patient care and facilitate the recruitment of patients into active clinical trials. Thus, patients, physicians and researchers may explore the knowledge base to better understand therapeutic options, efficacy, and mechanisms of action.

Conclusions
This work takes an important step in using Semantic Web technologies to facilitate integration of relevant, distributed, external sources and progress towards a computational platform to support personalized medicine.

Availability
TMO can be downloaded from http://code.google.com/p/translationalmedicineontology and TMKB can be accessed at http://tm.semanticscience.org/sparql.
An open annotation ontology for science on web 3.0
Authors: Ciccarese Paolo , Ocana Marco , Garcia Castro Leyla Jael , Das Sudeshna , Clark Tim 
Published: May 2011

Abstract
Background
There is currently a gap between the rich and expressive collection of published biomedical ontologies, and the natural language expression of biomedical papers consumed on a daily basis by scientific researchers. The purpose of this paper is to provide an open, shareable structure for dynamic integration of biomedical domain ontologies with the scientific document, in the form of an Annotation Ontology (AO), thus closing this gap and enabling application of formal biomedical ontologies directly to the literature as it emerges.

Methods
Initial requirements for AO were elicited by analysis of integration needs between biomedical web communities, and of needs for representing and integrating results of biomedical text mining. Analysis of strengths and weaknesses of previous efforts in this area was also performed. A series of increasingly refined annotation tools were then developed along with a metadata model in OWL, and deployed for feedback and additional requirements the ontology to users at a major pharmaceutical company and a major academic center. Further requirements and critiques of the model were also elicited through discussions with many colleagues and incorporated into the work.

Results
This paper presents Annotation Ontology (AO), an open ontology in OWL-DL for annotating scientific documents on the web. AO supports both human and algorithmic content annotation. It enables “stand-off” or independent metadata anchored to specific positions in a web document by any one of several methods. In AO, the document may be annotated but is not required to be under update control of the annotator. AO contains a provenance model to support versioning, and a set model for specifying groups and containers of annotation. AO is freely available under open source license at http://purl.org/ao/, and extensive documentation including screencasts is available on AO’s Google Code page: http://code.google.com/p/annotation-ontology/ .

Conclusions
The Annotation Ontology meets critical requirements for an open, freely shareable model in OWL, of annotation metadata created against scientific documents on the Web. We believe AO can become a very useful common model for annotation metadata on Web documents, and will enable biomedical domain ontologies to be used quite widely to annotate the scientific literature. Potential collaborators and those with new relevant use cases are invited to contact the authors.
Automating generation of textual class definitions from OWL to English
Authors: Stevens Robert , Malone James , Williams Sandra , Power Richard , Third Allan 
Published: May 2011

Abstract
Background
Text definitions for entities within bio-ontologies are a cornerstone of the effort to gain a consensus in understanding and usage of those ontologies. Writing these definitions is, however, a considerable effort and there is often a lag between specification of the main part of an ontology (logical descriptions and definitions of entities) and the development of the text-based definitions. The goal of natural language generation (NLG) from ontologies is to take the logical description of entities and generate fluent natural language. The application described here uses NLG to automatically provide text-based definitions from an ontology that has logical descriptions of its entities, so avoiding the bottleneck of authoring these definitions by hand.

Results
To produce the descriptions, the program collects all the axioms relating to a given entity, groups them according to common structure, realises each group through an English sentence, and assembles the resulting sentences into a paragraph, to form as ‘coherent’ a text as possible without human intervention. Sentence generation is accomplished using a generic grammar based on logical patterns in OWL, together with a lexicon for realising atomic entities. We have tested our output for the Experimental Factor Ontology (EFO) using a simple survey strategy to explore the fluency of the generated text and how well it conveys the underlying axiomatisation. Two rounds of survey and improvement show that overall the generated English definitions are found to convey the intended meaning of the axiomatisation in a satisfactory manner. The surveys also suggested that one form of generated English will not be universally liked; that intrusion of too much ‘formal ontology’ was not liked; and that too much explicit exposure of OWL semantics was also not liked.

Conclusions
Our prototype tools can generate reasonable paragraphs of English text that can act as definitions. The definitions were found acceptable by our survey and, as a result, the developers of EFO are sufficiently satisfied with the output that the generated definitions have been incorporated into EFO. Whilst not a substitute for hand-written textual definitions, our generated definitions are a useful starting point.

Availability
An on-line version of the NLG text definition tool can be found at http://swat.open.ac.uk/tools/. The questionaire and sample generated text definitions may be found at http://mcs.open.ac.uk/nlg/SWAT/bio-ontologies.html.
Nociceptive tolerance is improved by bradykinin receptor B1 antagonism and joint morphology is protected by both endothelin type A and bradykinin receptor B1 antagonism in a surgical model of osteoarthritis
Authors: Kaufman Gabriel N , Zaouter Charlotte , Valteau Barthélémy , Sirois Pierre , Moldovan Florina 
Published: May 2011

Abstract
Introduction
Endothelin-1, a vasoconstrictor peptide, influences cartilage metabolism mainly via endothelin receptor type A (ETA). Along with the inflammatory nonapeptide vasodilator bradykinin (BK), which acts via bradykinin receptor B1 (BKB1) in chronic inflammatory conditions, these vasoactive factors potentiate joint pain and inflammation. We describe a preclinical study of the efficacy of treatment of surgically induced osteoarthritis with ETA and/or BKB1 specific peptide antagonists. We hypothesize that antagonism of both receptors will diminish osteoarthritis progress and articular nociception in a synergistic manner.

Methods
Osteoarthritis was surgically induced in male rats by transection of the right anterior cruciate ligament. Animals were subsequently treated with weekly intra-articular injections of specific peptide antagonists of ETA and/or BKB1. Hind limb nociception was measured by static weight bearing biweekly for two months post-operatively. Post-mortem, right knee joints were analyzed radiologically by X-ray and magnetic resonance, and histologically by the OARSI histopathology assessment system.

Results
Single local BKB1 antagonist treatment diminished overall hind limb nociception, and accelerated post-operative recovery after disease induction. Both ETA and/or BKB1 antagonist treatments protected joint radiomorphology and histomorphology. Dual ETA/BKB1 antagonism was slightly more protective, as measured by radiology and histology.

Conclusions
BKB1 antagonism improves nociceptive tolerance, and both ETA and/or BKB1 antagonism prevents joint cartilage degradation in a surgical model of osteoarthritis. Therefore, they represent a novel therapeutic strategy: specific receptor antagonism may prove beneficial in disease management.
Feasibility of dual gradient-echo in-phase and opposed-phase magnetic resonance imaging for the evaluation of epicardial fat
Authors: Okayama Satoshi , Ayako Seno , Somekawa Satoshi , Uemura Shiro , Kubota Yasushi , Saito Yoshihiko 
Published: May 2011

Background Dual gradient-echo in-phase (IP) and opposed-phase (OP) magnetic resonance imaging (MRI) can evaluate small amounts of fat, and is widely used for imaging abdominal organs. Epicardial fat has recently been revealed as having an important role in the development of heart disease, but IPOP-MRI has not been widely applied in this field, probably because of cardiac motion artifacts. Purpose To demonstrate the feasibility of IPOP-MRI with electrocardiography (ECG)-gating for evaluation of epicardial fat in the normal human heart, compared to black-blood T1-weighted imaging (T1WI). Material and Methods Ten healthy volunteers were studied. Epicardial fat volume was quantitatively evaluated on OP-from-IP subtraction images and T1-weighted images. Results Epicardial fat was clearly visualized on the subtraction images as hyperintense areas that corresponded to regions identified as epicardial fat on the T1-weighted images. Epicardial fat volume correlated well between the two methods (r = 0.93, P <0.0001), and tended to be larger on the subtraction images than on the T1-weighted images (91.4 ± 30.1 vs. 84.1 ± 30.5 mL, P = 0.07). Conclusion IPOP-MRI with ECG-gating may be a useful alternative method to black-blood T1WI for evaluation of epicardial fat.
Diffusion tensor imaging of prostate at 3.0 Tesla
Authors: Li Chunmei , Chen Min , Li Saying , Zhao Xuna , Zhang Chen , Liu Ming , Zhou Cheng 
Published: May 2011

Background The feasibility of diffusion tensor imaging (DTI) of prostate has been confirmed by several studies. Apparent diffusion coefficient (ADC) and fractional anisotropy (FA) values of prostate with healthy or pathological changes remain controversial. Purpose To investigate the efficacy of DTI at 3.0 T in diagnosing prostate cancer in the peripheral zone and to determine the normative ADC and FA values of the normal prostate. Material and Methods T2-weighted imaging (T2WI) and DTI of the prostate was performed in 33 cases with diagnosis confirmed by biopsy at 3.0 T MR. ADC and FA values of cancerous and non-cancerous sextants were compared. Receiver-operating characteristic (ROC) curves were used to compare the ability of ADC, FA and the two values combined in diagnosing prostate cancer in the peripheral zone. DTI data of 20 healthy young volunteers were also acquired. ADC and FA values of the normal central gland and the peripheral zone were compared. Results ADC value (1.10 ± 0.09 × 10−3 mm2/s) was lower while FA value (0.37 ± 0.05) was higher in normal central gland, compared with that in normal peripheral zone (1.63 ± 0.15 × 10−3 mm2/s, 0.21 ± 0.07, respectively) ( P < 0.0001, P < 0.0001, respectively). Sixteen of 33 cases were confirmed to be malignant while 17 of 33 cases were benign. All the 198 sextants were confirmed by biopsy, including 136 non-cancerous sextants and 62 cancerous sextants. There were significant differences between cancerous sextants (1.02 ± 0.16 × 10−3 mm2/s, 0.38 ± 0.09) and non-cancerous sextants (1.22 ± 0.14 × 10−3 mm2/s, 0.31 ± 0.06) for both ADC and FA values ( P <0.0001, P <0.0001, respectively). Significant differences were noted between the AUC of DTI and FA alone (0.86 vs. 0.76, P = 0.0009), but no differences between the AUC of DTI and ADC alone (0.86 vs. 0.84, P = 0.1595). Conclusion ADC and FA values of normal prostate may be compatible with the microstructural organization of prostate. Furthermore, DTI may be a potential tool in diagnosing prostate cancer in the peripheral zone.
Risk factors associated with breast arterial calcifications
Authors: Ilica Ahmet Turan , Aydogan Umit , Guvenc Inanc , Cayci Tuncer , Oren Cem , Onar Tamer , Ugurel Sahin , Saglam Kenan 
Published: May 2011

Background A number of studies have linked the presence of breast arterial calcifications (BACs) with an increased risk of diabetes, hypertension, coronary artery disease (CAD), and cardiovascular mortality. Because there is a well-established screening system for breast cancer, it has been proposed that the presence of BACs can be used as a warning sign indicating an increased risk of metabolic and vascular diseases. Purpose To determine the relation between BAC and early renal dysfunction. Material and Methods A retrospective review of 6118 mammograms identified 701 cases with BACs. Women with BACs were compared to a random selection of 362 women without BACs based on available laboratory data. Univariate analysis was conducted according to age groups. Results The prevalence of BACs was 11.5% in our study. Hyperglycemia increased the odds of BACs by 8.1 (95% CI 3.0–22.1, P < 0.001) in the 50–59-year age group. The presence of an elevated blood urea nitrogen (BUN) and serum creatinine increased the odds of BACs by 2.6 (95% CI 1.2–6.0, P = 0.016) and 2.3 (95% CI 1.0–5.2, P = 0.045) in women ≥70 years of age. Hyperlipidemia was not a significant risk factor for BACs in any age group. Conclusion Our results support the view that the presence of BACs on mammography may be indicative of diabetes in middle-aged women. On the other hand, BACs are not very useful for predicting early renal dysfunction in women <70 years of age.
Cognitive Development and Down Syndrome: Age-Related Change on the Stanford-Binet Test (Fourth Edition)
Authors: Couzens Donna , Cuskelly Monica , Haynes Michele 
Published: May 2011

Abstract
Growth models for subtests of the Stanford-Binet Intelligence Scale, 4th edition (R. L. Thorndike, E. P. Hagen, & J. M. Sattler, 1986a, 1986b) were developed for individuals with Down syndrome. Models were based on the assessments of 208 individuals who participated in longitudinal and cross-sectional research between 1987 and 2004. Variation in performance among individuals was large and significant across all subtests except Memory for Sentences. Scores on the Memory for Sentences subtest remained low between ages 4 to 30 years. Greatest variation was found on the Pattern Analysis subtest, where scores continued to rise into adulthood. Turning points for scores on the Vocabulary and Comprehension subtests appeared premature relative to normative patterns of development. The authors discuss development at the subdomain level and analyze both individual and group trajectories.
Physical Activity Benefits and Needs in Adults With Intellectual Disabilities: Systematic Review of the Literature
Authors: Bartlo Pamela , Klein Penelope J. 
Published: May 2011

Abstract
Regular physical activity is vital for adult individuals with intellectual disabilities. The purpose of this review was to assess critically the evidence on effectiveness of physical activity interventions for adults with intellectual disability. An electronic database search was conducted. Research was then assessed for methodological rigor, and strength of the evidence was determined. Eleven clinical studies met inclusion criteria. Interventions studied included a variety of physical activity modes. Critical review revealed moderate to strong evidence that physical activity positively affected balance, muscle strength, and quality of life in individuals with intellectual disability. The authors also found that the research in this area needs to be translated into practice, specifically the development of physical activity programs that are adaptable to the needs of individuals with intellectual disability.
Contrasting Roles for Dopamine D1 and D2 Receptor Subtypes in the Dorsomedial Striatum but Not the Nucleus Accumbens Core during Behavioral Inhibition in the Stop-Signal Task in Rats
Authors: Eagle Dawn M. , Wong Jacky C. K. , Allan Michelle E. , Mar Adam C. , Theobald David E. , Robbins Trevor W. 
Published: May 2011

Dopamine and dopamine-receptor function are often implicated in behavioral inhibition, and deficiencies within behavioral inhibition processes linked to attention deficit/hyperactivity disorder (ADHD), schizophrenia, obsessive-compulsive disorder, and drug addiction. In the stop-signal task, which measures the speed of the process of inhibition [stop-signal reaction time (SSRT)], psychostimulant-related improvement of SSRT in ADHD is linked with dopamine function. However, the precise nature of dopaminergic control over SSRT remains unclear.This study examined region- and receptor-specific modulation of SSRT in the rat using direct infusions of the dopamine D1 receptor (DRD1) antagonist SCH 23390 or dopamine D2 receptor (DRD2) antagonist sulpiride into the dorsomedial striatum (DMStr) or nucleus accumbens core (NAcbC). DRD1 and DRD2 antagonists had contrasting effects on SSRT that were specific to the DMStr. SCH 23390 decreased SSRT with little effect on the go response. Conversely, sulpiride increased SSRT but also increased go-trial reaction time and reduced trial completion at the highest doses. These results suggest that DRD1 and DRD2 function within the DMStr, but not the NAcbC, may act to balance behavioral inhibition in a manner that is independent of behavioral activation.
“Focus pronouns” in Old Latin reflexive constructions
Authors: Lühr Rosemarie 
Published: May 2011

Abstract
This paper deals with a Latin reflexivization strategy distinct from other reflexive constructions. It consists of first and second person pronouns which are used to emphasize the first and second person referents in Old Latin comedy by certain emphasizing elements like ‑met in egomet or ‑te in tūte. The form and function of these emphasizing personal pronouns has not been observed and described yet. Moreover, the grammatical, semantic and pragmatic status of this reflexivization strategy has hitherto been unknown. The elements ‑met and ‑te are likely to be derived from suffixes which have an identifying and emphasizing function similar to German selbst ‘self’. Reflexivization here obviously is connected to focalization, a typologically well-known relationship.
An Effective Quarantine Measure Reduced the Total Incidence of Influenza A H1N1 in the Workplace: Another Way to Control the H1N1 Flu Pandemic
Authors: Miyaki Koichi , Sakurazawa Hirofumi , Mikurube Hajime , Nishizaka Mika , Ando Hidehiko , Song Yixuan , Shimbo Takuro 
Published: May 2011

An Effective Quarantine Measure Reduced the Total Incidence of Influenza A H1N1 in the Workplace: Another Way to Control the H1N1 Flu Pandemic: Koichi Miyaki, et al. Department of Clinical Research and Informatics, National Center for Global Health and Medicine—ObjectivesTo evaluate the effectiveness of a non‐vaccine quarantine measure against pandemic influenza A H1N1 in workplaces.MethodsDesign was quasi‐cluster randomized controlled trial in two sibling companies (Cohort 1 n=6,634, Cohort 2 n=8,500). The follow‐up period was from July 1st, 2009 to February 19th, 2010 (233 days). Intervention was voluntary waiting at home on full pay if the family became Influenza like Illness (ILI). The incidences of influenza A H1N1 and those of the subgroups whose families got ILI in both cohorts were compared by a Cox regression model and log‐rank test.ResultsThere were 189 and 270 workers who got H1N1 infection during the follow‐up period in each cohort. In this period 317 workers in Cohort 1 were asked to wait at home for several days (100% obeyed). The intervention group (Cohort 1) showed a statistically significant lower risk (p for log‐rank test=0.033) compared with the control (Cohort 2), and the hazard ratio of the intervention was 0.799 [0.658–0.970] after adjusting for age, sex, BMI and smoking status. The workers who were asked to wait at home showed H1N1 infection more frequently (49 out of 317) compared with the workers whose family got ILI but were not asked to wait and work regularly (77 out of 990, RR=2.17 [1.48– 3.18]).ConclusionsThe waiting on full pay policy in the workplace reduced the overall risk of influenza A H1N1 by about 20% in one lu season in Japan. This kind of non‐vaccine measure will be a promising option in workplaces to control the next lu pandemic.
The Effect of Redox Potential and Metal Solubility on Oxidative Polymer Degradation
Authors: Levitt David B. , Slaughter Will , Pope Gary A. , Jouenne Stephane 
Published: May 2011

Summary
Oxidative degradation of polymers is a serious concern in their field application for enhanced oil recovery (EOR). This study is an attempt to resolve some of the discrepancies in the literature regarding the occurrence and extent of this degradation, as well as to present a coherent framework for discussing the multitude of possible radical reactions. Sodium carbonate and bicarbonate are demonstrated to play a key role in stabilizing polymer against multiple reported sources of degradation, and it seems likely that this is caused by their effect on iron solubility. Brines containing iron in the reduced state are often obtained from aquifers for use in polymer hydration. These brines are shown to be prone to causing immediate degradation if exposed to air during or after polymer hydration because of the oxidation of soluble iron. If this cannot be avoided, preaeration may be a feasible strategy to minimize degradation during hydration. However, care must be taken to ensure subsequent degradation is not caused by the injection of a polymer solution containing oxygen into a formation containing iron. For instance, sodium dithionite can be added downstream of the last exposure to oxygen. The use of sodium carbonate may also mitigate degradation caused by the oxidation of iron (II) during polymer hydration.