bluuebunny/crossref_metadata_2025_split huggingface dataset:
Summary of the BioLINK SIG 2013 meeting at ISMB/ECCB 2013
Authors: Verspoor Karin , Shatkay Hagit , Hirschman Lynette , Blaschke Christian , Valencia Alfonso 
Published: July 2014

Abstract
The ISMB Special Interest Group on Linking Literature, Information and Knowledge for Biology (BioLINK) organized a one-day workshop at ISMB/ECCB 2013 in Berlin, Germany. The theme of the workshop was ‘Roles for text mining in biomedical knowledge discovery and translational medicine’. This summary reviews the outcomes of the workshop. Meeting themes included concept annotation methods and applications, extraction of biological relationships and the use of text-mined data for biological data analysis.
Availability and implementation: All articles are available at http://biolinksig.org/proceedings-online/ .
Contact: karin.verspoor@unimelb.edu.au
Using a weight-structured oyster population dynamic model to explore top-down control of coastal water quality in a subtropical embayment
Authors: Richards Russell G. , Chaloupka Milani 
Published: July 2014

AbstractThe natural filtering capacity of oysters and other suspension filter-feeders has seen them put forward as a potential water quality management option. However, the specifics of how many oysters would be required to clean a system are not necessarily straightforward to evaluate because of the size-dependence of oyster physiological rates along with the dynamic coupling that exists between the oysters and the environment. We use a weight-structured shellfish population model and a nutrient–phytoplankton–detritus model to answer the question of how many oysters it would take to clean a large estuary located in Queensland, Australia. Modelling results indicate that improvements in the water quality are not seen until the stocking density of oysters exceeds 0.09 ind. m−3 and that local water quality guidelines are not fully met until the density exceeds 1.80 ind. m−3. At these densities, the corresponding times to filter the entire volume of the study area are 52–38 d (0.09 ind. m−3) and 1.80–1.35 d (1.80 ind. m−3), respectively. This research highlights that regulatory feedback pathways exist between a shellfish population and the water quality constituents that they control through filtration. While the use of oysters and other filter-feeders may be an appealing approach to nutrient management and top-down control of phytoplankton, the practicalities of deploying oysters at a system-scale may be the greatest barrier to this option.
Cohort Profile: The Nicotine Dependence in Teens (NDIT) Study
Authors: O’Loughlin Jennifer , Dugas Erika N , Brunet Jennifer , DiFranza Joseph , Engert James C , Gervais Andre , Gray-Donald Katherine , Karp Igor , Low Nancy C , Sabiston Catherine , Sylvestre Marie-Pierre , Tyndale Rachel F , Auger Nathalie , Auger Nathalie , Mathieu Belanger , Tracie Barnett , Chaiton Michael , Chenoweth Meghan J , Constantin Evelyn , Contreras Gisèle , Kakinami Lisa , Labbe Aurelie , Maximova Katerina , McMillan Elizabeth , O’Loughlin Erin K , Pabayo Roman , Roy-Gagnon Marie-Hélène , Tremblay Michèle , Wellman Robert J , Hulst Andraeavan , Paradis Gilles 
Published: July 2014

Abstract
The Nicotine Dependence in Teens (NDIT) study is a prospective cohort investigation of 1294 students recruited in 1999–2000 from all grade 7 classes in a convenience sample of 10 high schools in Montreal, Canada. Its primary objectives were to study the natural course and determinants of cigarette smoking and nicotine dependence in novice smokers. The main source of data was self-report questionnaires administered in class at school every 3 months from grade 7 to grade 11 (1999–2005), for a total of 20 survey cycles during high school education. Questionnaires were also completed after graduation from high school in 2007–08 and 2011–12 (survey cycles 21 and 22, respectively) when participants were aged 20 and 24 years on average, respectively. In addition to its primary objectives, NDIT has embedded studies on obesity, blood pressure, physical activity, team sports, sedentary behaviour, diet, genetics, alcohol use, use of illicit drugs, second-hand smoke, gambling, sleep and mental health. Results to date are described in 58 publications, 20 manuscripts in preparation, 13 MSc and PhD theses and 111 conference presentations. Access to NDIT data is open to university-appointed or affiliated investigators and to masters, doctoral and postdoctoral students, through their primary supervisor ( www.nditstudy.ca ).
Comparison of Open Versus Percutaneous Pedicle Screw Fixation Using the Sextant System in the Treatment of Traumatic Thoracolumbar Fractures
Authors: Wang Hongwei , Zhou Yue , Li Changqing , Liu Jun , Xiang Liangbi 
Published: July 2014

Study Design:We retrospectively reviewed 100 patients who were posterior stabilized without graft fusion. Using the Sextant system, 22 patients underwent minimally invasive short-segment 4-pedicle screw fixation (MIF4) and 39 patients underwent minimally invasive short-segment combined with intermediate screws fixation, that is, 6-pedicle screw fixation (MIF6). The conventional open posterior short-segment 4-pedicle screw fixation (OPF4) technique was used in 39 patients.Objective:To evaluate the feasibility, safety, and efficacy of percutaneous pedicle screw fixation using the Sextant system in the treatment of traumatic thoracolumbar fractures compared with the conventional open posterior short-segment pedicle screw fixation technique.Summary of Background Data:To the best of our knowledge, the clinical and radiographic outcomes of MIF4, MIF6 with polyaxial pedicle screws, and OPF4 with monoaxial pedicle screws have not been compared in the treatment of thoracolumbar fractures.Methods:Visual analogue scores (VAS), Oswestry disability index (ODI) scores, clinical outcomes including surgical blood loss, operation time, and postoperative hospital stay, sagittal Cobb angle, vertebral body angle, and anterior height of the fractured vertebrae were compared among the 3 groups.Results:Significant postoperative improvements, relative to baseline, were observed in the VAS and ODI scores (P<0.05 each). There were no significant differences between the MIF4 and MIF6 groups in clinical outcomes, including surgical blood loss, operation time, postoperative hospital stay, VAS, and ODI scores (P>0.05 each). However, there were significant differences between both MIF groups and the OPF group (P<0.05 each). Significant improvements were observed in the sagittal Cobb angle, vertebral body angle, and anterior height of the fractured vertebrae (P<0.05 each). During follow-up, however, the correction loss of the sagittal Cobb angle was smallest in the MIF6 group (P<0.05).Conclusions:Minimally invasive posterior stabilization using the Sextant system resulted in reduced injury compared with the open surgery, during both the internal fixation surgery and the implant removal surgery. Percutaneous screw fixation through the pedicle of the fractured vertebra is superior to the conventional OPF4 technique in correcting kyphotic deformities, and can be performed without any extra procedures.
Using Natural Language Processing to Extract Abnormal Results From Cancer Screening Reports
Authors: Moore Carlton R. , Farrag Ashraf , Ashkin Evan 
Published: July 2014

Objectives
Numerous studies show that follow-up of abnormal cancer screening results, such as mammography and Papanicolaou (Pap) smears, is frequently not performed in a timely manner. A contributing factor is that abnormal results may go unrecognized because they are buried in free-text documents in electronic medical records (EMRs), and, as a result, patients are lost to follow-up. By identifying abnormal results from free-text reports in EMRs and generating alerts to clinicians, natural language processing (NLP) technology has the potential for improving patient care. The goal of the current study was to evaluate the performance of NLP software for extracting abnormal results from free-text mammography and Pap smear reports stored in an EMR.

Methods
A sample of 421 and 500 free-text mammography and Pap reports, respectively, were manually reviewed by a physician, and the results were categorized for each report. We tested the performance of NLP to extract results from the reports. The 2 assessments (criterion standard versus NLP) were compared to determine the precision, recall, and accuracy of NLP.

Results
When NLP was compared with manual review for mammography reports, the results were as follows: precision, 98% (96%–99%); recall, 100% (98%–100%); and accuracy, 98% (96%–99%). For Pap smear reports, the precision, recall, and accuracy of NLP were all 100%.

Conclusions
Our study developed NLP models that accurately extract abnormal results from mammography and Pap smear reports. Plans include using NLP technology to generate real-time alerts and reminders for providers to facilitate timely follow-up of abnormal results.
Benchmark Analysis of Algorithms for Determining and Quantifying Full-length mRNA Splice Forms from RNA-Seq Data
Authors: Hayer K. , Pizzaro A. , Lahens N. L. , Hogenesch J. B. , Grant G. R. 
Published: July 2014

AbstractThe advantages of RNA sequencing (RNA-Seq) suggest it will replace microarrays for highly parallel gene expression analysis. For example, in contrast to arrays, RNA-Seq is expected to be able to provide accurate identification and quantification of full-length transcripts. A number of methods have been developed for this purpose, but short error prone reads makes it a difficult problem in practice. It is essential to determine which algorithms perform best, and where and why they fail. However, there is a dearth of independent and unbiased benchmarking studies of these algorithms. Here we take an approach using both simulated and experimental benchmark data to evaluate their accuracy. We conclude that most methods are inaccurate even using idealized data, and that no is method sufficiently accurate once complicating factors such as polymorphisms, intron signal, sequencing error, and multiple splice forms are present. These results point to the pressing need for further algorithm development.
Does Intra‐African Trade Reduce Youth Unemployment in Africa?
Authors: Anyanwu John C. 
Published: July 2014

AbstractThis study empirically estimates the effect of Africa's intra‐regional trade on the burgeoning youth unemployment in the continent. This is necessary since very few studies have been undertaken in the particular context of African countries. To the best of our knowledge there are no studies exploring the intra‐African trade–youth unemployment nexus in Africa. We investigate both the aggregate and gender‐specific impacts. Our empirical estimates, using available cross‐sectional time series data over the period 1980 to 2010, suggest that higher levels of intra‐African trade reduce both the aggregate, female and male youth unemployment in Africa. In addition, our results show that domestic investment rate, institutionalized democracy, secondary education, inflation, economic growth, and higher urbanization tend to reduce youth unemployment both on the aggregate and gender‐differentiated and therefore are good for youth unemployment reduction in the continent. On the other hand, higher real per capita GDP and to a lesser extent credit to the private sector have a significant positive effect on youth unemployment in Africa. Government consumption expenditure and foreign direct investment have an insignificant effect on both the aggregate level and the gendered level of youth unemployment in Africa. Based on these results, some policy recommendations are proffered.
Biraderi, Bloc Votes and Bradford: Investigating the Respect Party's Campaign Strategy
Authors: Peace Timothy , Akhtar Parveen 
Published: July 2014

Research Highlights and Abstract This article Contributes to theoretical debates on minority political participation in the UK, with specific reference to inter-generational variations within the South Asian Muslim community; Contributes to the scholarly literature on the impact and effectiveness of new political parties within the British political system, through a case study of the Respect Party; Adds to empirical primary data on strategies adopted by political parties in courting specific sections of the ethnic minority vote in the UK; Offers an empirically-led demonstration of the changes taking place within the political sphere of South Asian Muslim diasporas in Britain. In March 2012, the Respect Party won an unexpected by-election in the British city of Bradford, previously regarded as a safe Labour seat. This article examines the party's campaign strategy and in particular how it courted South Asian Muslim voters. A dominant feature of South Asian Muslim politics in the UK has been community bloc voting along lines of kinship (biraderi). The use of kinship networks for political gain effectively disenfranchised many young people and women. We demonstrate how Respect used their experience of campaigning in constituencies with significant numbers of South Asian Muslim voters to achieve an unlikely victory in Bradford. A key strategy was to mobilise otherwise politically marginalised sections of the South Asian Muslim community by offering an alternative to the culture of patronage in Bradford whilst at the same time utilising certain community structures in order to gain their own bloc votes.
The Early Effects of Medicare's Mandatory Hospital Pay‐for‐Performance Program
Authors: Ryan Andrew M. , Burgess James F. , Pesko Michael F. , Borden William B. , Dimick Justin B. 
Published: July 2014

ObjectiveTo evaluate the impact of hospital value‐based purchasing (HVBP) on clinical quality and patient experience during its initial implementation period (July 2011–March 2012).Data SourcesHospital‐level clinical quality and patient experience data from Hospital Compare from up to 5 years before and three quarters after HVBP was initiated.Study DesignAcute care hospitals were exposed to HVBP by mandate while critical access hospitals and hospitals located in Maryland were not exposed. We performed a difference‐in‐differences analysis, comparing performance on 12 incentivized clinical process and 8 incentivized patient experience measures between hospitals exposed to the program and a matched comparison group of nonexposed hospitals. We also evaluated whether hospitals that were ultimately exposed to HVBP may have anticipated the program by improving quality in advance of its introduction.Principal FindingsDifference‐in‐differences estimates indicated that hospitals that were exposed to HVBP did not show greater improvement for either the clinical process or patient experience measures during the program's first implementation period. Estimates from our preferred specification showed that HVBP was associated with a 0.51 percentage point reduction in composite quality for the clinical process measures (p > .10, 95 percent CI: −1.37, 0.34) and a 0.30 percentage point reduction in composite quality for the patient experience measures (p > .10, 95 percent CI: −0.79, 0.19). We found some evidence that hospitals improved performance on clinical process measures prior to the start of HVBP, but no evidence of this phenomenon for the patient experience measures.ConclusionsThe timing of the financial incentives in HVBP was not associated with improved quality of care. It is unclear whether improvement for the clinical process measures prior to the start of HVBP was driven by the expectation of the program or was the result of other factors.
Busted! Management of paediatric upper limb fractures: Not all that it's cracked up to be
Authors: Mills Erin , Craig Simon , Oakley Ed 
Published: July 2014

AbstractObjectiveThe primary objective was to assess use of splinting prior to X‐ray in paediatric ED patients with deformed upper limb fractures. Secondary objectives were to evaluate pharmaceutical analgesia use and the impact of demographic, hospital and clinical variables on splint and analgesia provision.MethodsA retrospective study of 1407 paediatric ED patients who received upper limb X‐rays. The records of those with fractures requiring manipulation were identified, and reviewed for data on demographics, mode of arrival, triage category, site of fracture, clinician seniority, pain scoring, splint application and analgesic use.ResultsTwo hundred and twelve patients had fractures requiring manipulation. Of these, 47 (22%) had a splint applied prior to X‐ray and 161 (76%) of patients were prescribed analgesia in the first hour after presentation. A triage category 1 or 2 and arrival by ambulance predicted for splint application. Children with higher recorded pain scores were more likely to receive any analgesia in the first hour (91% with a pain score ≥7 compared with 62% with pain score of ≤6, P < 0.001), and more likely to receive strong analgesia (59% vs 13%, P < 0.001). Those triaged to category 1 or 2 were more likely to receive analgesia in the first hour (P < 0.001).ConclusionsThis study identified significant shortcomings in ED management of children with deformed upper limb fractures. Only a minority were splinted prior to X‐ray, and a quarter did not receive any analgesia in the first hour after presentation. Future study should investigate methods to improve ED management of these patients.
Fucosylated Chondroitin Sulfate from Sea Cucumber Improves Insulin Sensitivity via Activation of PI3K/PKB Pathway
Authors: Hu Shiwei , Chang Yaoguang , He Min , Wang Jingfeng , Wang Yuming , Xue Changhu 
Published: July 2014

AbstractThis study was to investigate the effects of fucosylated chondroitin sulfate (CHS) from sea cucumber on insulin sensitivity in skeletal muscle of type 2 diabetic mice induced by a high‐fat high‐sucrose diet (HFSD). CHS supplementation for 19 wk significantly improved insulin sensitivity by 20%, and reduced blood glucose and insulin levels. Western blotting assay showed that CHS significantly increased insulin‐stimulated glucose transporter 4 (GLUT4) translocation to 1.7‐fold, phosphorylation of phosphoinositide 3‐kinase (PI3K) at p85 to 5.0‐fold, protein kinase B (PKB) at Ser473 to 1.5‐fold, and Thr308 to 1.6‐fold in skeletal muscle. However, PI3K, PKB, and GLUT4 total proteins expression were unchangeable. In addition, qRT‐PCR analysis proved that the insulin signaling was activated by CHS treatment, showing the increased mRNA expressions of glucose uptake‐related key genes. It indicated that CHS improved insulin sensitivity by activation of PI3K/PKB signaling in skeletal muscle of type 2 diabetic mice. Identification of potential mechanism by which CHS increased insulin sensitivity might provide a new functional food or pharmaceutical application of sea cucumber.
Sensory Characterization of Young South American Red Wines Classified by Varietal and Origin
Authors: Llobodanin Laura Garcia , Barroso Lucia Pereira , Castro Inar Alves 
Published: July 2014

AbstractTypicality is the set of sensory characteristics that identify a distinctive type of wine. Thus, the aim of this research was to identify the sensory characteristics that contribute to define typicality of young South American red wines based on their varietal and origin, and to evaluate the effect of the vintage on this identification. To achieve this objective, visual appearance, odor, and taste of 138 wines from 2 vintages were submitted to a sensory evaluation using a descriptive analysis complemented with the frequency of citation method, performed by wine experts. The intensity of 17 odor and taste attributes was evaluated using a 5 points rating structured scale. The panel performance evaluation demonstrated its high level of expertise and reproducibility. The wines were separated into 3 clusters by multivariate analyses. Cluster 1 was primarily composed of Carménère, Malbec, and Syrah wines from Chile. Cluster 2 was predominantly composed of Tannat wines from Uruguay and Brazil, while Cluster 3 contained a higher proportion of Malbec and Merlot wines from Argentina and Brazil. Cabernet Sauvignon was equally distributed into all clusters. Wine experts were able to identify the wines according to their varietal and origin, suggesting that there is typicality in young South American red wines. The combination of descriptive analysis with the frequency of citation was useful in characterizing most of the wines, but the typicality perceived by the panelists was not achieved by multivariate analysis. Vintage did not alter the sensory characterization of the wines, and this result could be due the new viticulture or oenological practices used by the winemakers to compensate the environmental variation.
Towards consistency, rigour and compatibility of risk assessments for ecosystems and ecological communities
Authors: Nicholson Emily , Regan Tracey J. , Auld Tony D. , Burns Emma L. , Chisholm Laurie A. , English Valerie , Harris Stephen , Harrison Peter , Kingsford Richard T. , Leishman Michelle R. , Metcalfe Daniel J. , Pisanu Phil , Watson Christopher J. , White Matthew , White Matt D. , Williams Richard J. , Wilson Bruce , Keith David A. 
Published: July 2014

AbstractEcosystem‐level conservation is increasingly important at global, national and local levels. Many jurisdictions have developed and apply their own protocols for assessing the threat status of ecosystems, often independently, leading to inconsistencies between and within countries which are problematic for cross‐jurisdictional environmental reporting. Australia is a good example of these historic legacies, with different risk assessment methods applied nationally and in most states. The newly developed criteria for the International Union for the Conservation of Nature (IUCN) Red List of Ecosystems (RLE) provide a framework to compare and contrast apparently divergent protocols. We critically reviewed the Australian protocols and compared them with the IUCN RLE, based on the following components of a risk assessment protocol: (i) categories of threat; (ii) assessment units; (iii) underlying concepts and definitions; (iv) assessment criteria; (v) uncertainty methods; and (vi) assessment outcomes. Despite some differences in specific objectives, criteria and their expression, the protocols were structurally similar, included broadly similar types of criteria, and produced assessment outcomes that were generally concordant. Alignment with the IUCN RLE would not require extensive changes to existing protocols, but would improve consistency, rigour and robustness in ecosystem risk assessment across jurisdictions. To achieve this, we recommend: (i) more quantitative assessments of functional change; (ii) separation of management and policy considerations from risk assessment; and (iii) cross‐referencing of assessment units in different jurisdictions. We argue that the focus on processes and ecological function, rather than only patterns, is key to robust risk assessment.