bluuebunny/crossref_metadata_2025_split huggingface dataset:
Efficient development of highly polymorphic microsatellite markers based on polymorphic repeats in transcriptome sequences of multiple individuals
Authors: Vukosavljev M. , Esselink G. D. , van ’t Westende W. P. C. , Cox P. , Visser R. G. F. , Arens P. , Smulders M. J. M. 
Published: June 2014

AbstractThe first hurdle in developing microsatellite markers, cloning, has been overcome by next‐generation sequencing. The second hurdle is testing to differentiate polymorphic from nonpolymorphic loci. The third hurdle, somewhat hidden, is that only polymorphic markers with a large effective number of alleles are sufficiently informative to be deployed in multiple studies. Both steps are laborious and still performed manually. We have developed a strategy in which we first screen reads from multiple genotypes for repeats that show the most length variants, and only these are subsequently developed into markers. We validated our strategy in tetraploid garden rose using Illumina paired‐end transcriptome sequences of 11 roses. Of 48 tested two markers failed to amplify, but all others were polymorphic. Ten loci amplified more than one locus, indicating duplicated genes or gene families. Completely avoiding duplicated loci will be difficult because the range of numbers of predicted alleles of highly polymorphic single‐ and multilocus markers largely overlapped. Of the remainder, half were replicate markers (i.e. multiple primer pairs for one locus), indicating the difficulty of correctly filtering short reads containing repeat sequences. We subsequently refined the approach to eliminate multiple primer sets to the same loci. The remaining 18 markers were all highly polymorphic, amplifying on average 11.7 alleles per marker (range = 6–20) in 11 tetraploid roses, exceeding the 8.2 alleles per marker of the 24 most polymorphic markers genotyped previously. This strategy therefore represents a major step forward in the development of highly polymorphic microsatellite markers.
Combination of blood tests for significant fibrosis and cirrhosis improves the assessment of liver‐prognosis in chronic hepatitis C
Authors: Boursier J. , Brochard C. , Bertrais S. , Michalak S. , Gallois Y. , Fouchard‐Hubert I. , Oberti F. , Rousselet M.‐C. , Calès P. 
Published: June 2014

SummaryBackgroundRecent longitudinal studies have emphasised the prognostic value of noninvasive tests of liver fibrosis and cross‐sectional studies have shown their combination significantly improves diagnostic accuracy.AimTo compare the prognostic accuracy of six blood fibrosis tests and liver biopsy, and evaluate if test combination improves the liver‐prognosis assessment in chronic hepatitis C (CHC).MethodsA total of 373 patients with compensated CHC, liver biopsy (Metavir F) and blood tests targeting fibrosis (APRI, FIB4, Fibrotest, Hepascore, FibroMeter) or cirrhosis (CirrhoMeter) were included. Significant liver‐related events (SLRE) and liver‐related deaths were recorded during follow‐up (started the day of biopsy).ResultsDuring the median follow‐up of 9.5 years (3508 person‐years), 47 patients had a SLRE and 23 patients died from liver‐related causes. For the prediction of first SLRE, most blood tests allowed higher prognostication than Metavir F [Harrell C‐index: 0.811 (95% CI: 0.751–0.868)] with a significant increase for FIB4: 0.879 [0.832–0.919] (P = 0.002), FibroMeter: 0.870 [0.812–0.922] (P = 0.005) and APRI: 0.861 [0.813–0.902] (P = 0.039). Multivariate analysis identified FibroMeter, CirrhoMeter and sustained viral response as independent predictors of first SLRE. CirrhoMeter was the only independent predictor of liver‐related death. The combination of FibroMeter and CirrhoMeter classifications into a new FM/CM classification improved the liver‐prognosis assessment compared to Metavir F staging or single tests by identifying five subgroups of patients with significantly different prognoses.ConclusionsSome blood fibrosis tests are more accurate than liver biopsy for determining liver prognosis in CHC. A new combination of two complementary blood tests, one targeted for fibrosis and the other for cirrhosis, optimises assessment of liver‐prognosis.
Review article: the management of portal hypertensive gastropathy and gastric antral vascular ectasia in cirrhosis
Authors: Patwardhan V. R. , Cardenas A. 
Published: June 2014

SummaryBackgroundPortal hypertensive gastropathy (PHG) and gastric antral vascular ectasia (GAVE) are important causes of both acute and chronic gastrointestinal bleeding in patients with cirrhosis.AimTo review the current management of PHG and GAVE.MethodsPubMed was searched for English language articles using the key words ‘GAVE’, ‘gastric antral vascular ectasia’, ‘cirrhosis’, ‘gastrointestinal bleeding’, ‘acute’, ‘chronic’, ‘portal hypertensive gastropathy’, ‘watermelon stomach’, ‘radiofrequency ablation’, ‘band ligation’, ‘thermoablation’ and ‘TIPSS’.ResultsGAVE and PHG are both encountered in patients with cirrhosis. They can be seen in asymptomatic patients and in those with either acute or chronic gastrointestinal bleeding. PHG, by definition, requires the presence of portal hypertension, with or without cirrhosis, whereas GAVE requires neither cirrhosis nor portal hypertension. They can often be diagnosed on endoscopic appearance alone, but may require biopsy in certain cases. The treatment of PHG is aimed at reducing hepatic venous pressure gradients, most often by pharmacologic means, but may require shunt procedures in severe cases. Management of GAVE on the other hand is predominantly endoscopic, focusing on various ablative techniques.ConclusionsGastric antral vascular ectasia and portal hypertensive gastropathy are distinct entities and are both encountered in cirrhotic patients. Management of portal hypertensive gastropathy is centred on reduction in portal pressures, whereas treatment of gastric antral vascular ectasia is predominantly endoscopic.
Suppression of blastogenesis and proliferation of activated CD4+ T cells: intravenous immunoglobulin (IVIg)versusnovel anti-human leucocyte antigen (HLA)-E monoclonal antibodies mimicking HLA-I reactivity of IVIg
Authors: Ravindranath M H , Terasaki P I , Pham T , Jucaud V , Kawakita S 
Published: June 2014

SummaryActivated CD4+ T cells undergo blastogenesis and proliferation and they express several surface receptors, including β2-microglobulin-free human leucocyte antigen (HLA) heavy chains (open conformers). Intravenous immunoglobulin (IVIg) suppresses activated T cells, but the mechanism is unclear. IVIg reacts with HLA-Ia/Ib antigens but its reactivity is lost when the anti-HLA-E Ab is adsorbed out. Anti-HLA-E antibodies may bind to the peptides shared by HLA-E and the HLA-I alleles. These shared peptides are cryptic in intact HLA, but exposed in open conformers. The hypothesis that anti-HLA-E monoclonal antibodies (mAbs) that mimic HLA-I reactivity of IVIg may suppress activated T cells by binding to the shared peptides of the open conformers on the T cell surface was tested by examining the relative binding affinity of those mAbs for open conformers coated on regular beads and for intact HLA coated on iBeads, and by comparing the effects on the suppression of phytohaemagglutinin (PHA)-activated T cells of three entities: IVIg, anti-HLA-E mAbs that mimic IVIg [Terasaki Foundation Laboratory (TFL)-006 and (TFL)-007]; and anti-HLA-E antibodies that do not mimic IVIg (TFL-033 and TFL-037). Suppression of blastogenesis and proliferation of those T cells by both IVIg and the anti-HLA-E mAbs was dose-dependent, the dose required with mAbs 50–150-fold lower than with IVIg. TFL-006 and TFL-007 significantly suppressed blastogenesis and proliferation of activated CD4+ T cells, but neither the non-IVIg-mimicking mAbs nor control antibodies did so. The suppression may be mediated by Fab-binding of TFL-006/TFL-007 to the exposed shared peptides. The mAb binding to the open conformer may signal T cell deactivation because the open conformers have an elongated cytoplasmic tail with phosphorylation sites (tryosine320/serine335).
Genetic polymorphism related to exfoliative glaucoma is also associated with primary open‐angle glaucoma risk
Authors: Zanon‐Moreno Vicente , Zanon‐Moreno Laura , Ortega‐Azorin Carolina , Asensio‐Marquez Eva M , Garcia‐Medina Jose Javier , Sanz Pedro , Pinazo‐Duran Maria D , Ordovás Jose M , Corella Dolores 
Published: June 2014

AbstractBackgroundTo investigate the possible association of the rs2165241 polymorphism (C > T) in LOXL1 gene with the risk of primary open‐angle glaucoma in a Mediterranean population.MethodsThe analysis of genetic polymorphisms was performed by standard TaqMan allelic discrimination technique, using a 7900HT Sequence Detection System (Applied Biosystems).ResultsIn a recessive genetic model, the T allele of the rs2165241 polymorphism was significantly associated with the risk of primary open‐angle glaucoma (TT vs. CC: odds ratios = 2.19, 95% confidence interval = [1.33–3.62]). After multivariate logistic regression model adjusted by age and weight, the magnitude of the association decreased but remained statistically significant (TT vs. CC: odds ratios = 2.07, 95% confidence interval = [1.20–3.57]).ConclusionThis polymorphism seems to be associated with high risk for primary open‐angle glaucoma in a Mediterranean population.
Enhancing Research Ethics Review Systems in Egypt: The Focus of an International Training Program Informed by an Ecological Developmental Approach to Enhancing Research Ethics Capacity
Authors: Edwards Hillary Anne , Hifnawy Tamer , Silverman Henry 
Published: June 2014

AbstractRecently, training programs in research ethics have been established to enhance individual and institutional capacity in research ethics in the developing world. However, commentators have expressed concern that the efforts of these training programs have placed ‘too great an emphasis on guidelines and research ethics review’, which will have limited effect on ensuring ethical conduct in research. What is needed instead is a culture of ethical conduct supported by national and institutional commitment to ethical practices that are reinforced by upstream enabling conditions (strong civil society, public accountability, and trust in basic transactional processes), which are in turn influenced by developmental conditions (basic freedoms of political freedoms, economic facilities, social opportunities, transparency guarantees, and protective security). Examining this more inclusive understanding of the determinants of ethical conduct enhances at once both an appreciation of the limitations of current efforts of training programs in research ethics and an understanding of what additional training elements are needed to enable trainees to facilitate national and institutional policy changes that enhance research practices. We apply this developmental model to a training program focused in Egypt to describe examples of such additional training activities.
Impact of rosiglitazone on body composition, hepatic fat, fatty acids, adipokines and glucose in persons with impaired fasting glucose or impaired glucose tolerance: a sub‐study of the DREAM trial
Authors: Punthakee Z. , Alméras N. , Després J.‐P. , Dagenais G. R. , Anand S. S. , Hunt D. L. , Sharma A. M. , Jung H. , Yusuf S. , Gerstein H. C. 
Published: June 2014

AbstractAimsThiazolidinediones reduce ectopic fat, increase adiponectin and reduce inflammatory adipokines, fatty acids and glucose in people with Type 2 diabetes. We aimed to measure these effects in people with impaired fasting glucose and/or impaired glucose tolerance.MethodsAfter approximately 3.5 years of exposure to rosiglitazone 8 mg (n = 88) or placebo (n = 102), 190 DREAM trial participants underwent abdominal computed tomography and dual‐energy X‐ray absorptiometry scans. Visceral and subcutaneous adipose tissue areas, estimated hepatic fat content, total fat and lean mass were calculated and changes in levels of fasting adipokines, free fatty acids, glucose and post‐load glucose were assessed.ResultsCompared with the placebo, participants on rosiglitazone had no difference in lean mass, had 4.1 kg more body fat (P < 0.0001) and 31 cm2 more subcutaneous abdominal adipose tissue area (P = 0.007). Only after adjusting for total fat, participants on rosiglitazone had 23 cm² less visceral adipose tissue area (P = 0.01) and an 0.08‐unit higher liver:spleen attenuation ratio (i.e. less hepatic fat; P = 0.02) than those on the placebo. Adiponectin increased by 15.0 μg/ml with rosiglitazone and by 0.4 μg/ml with placebo (P < 0.0001). Rosiglitazone's effect on fat distribution was not independent of changes in adiponectin. Rosiglitazone's effects on fasting (–0.36 mmol/l; P = 0.0004) and 2‐h post‐load glucose (–1.21 mmol/l; P = 0.0008) were not affected by adjustment for fat distribution or changes in adiponectin or free fatty acids.ConclusionsIn people with impaired fasting glucose/impaired glucose tolerance, rosiglitazone is associated with relatively less hepatic and visceral fat, increased subcutaneous fat and increased adiponectin levels. These effects do not appear to explain the glucose‐lowering effect of rosiglitazone.
Effects of fasting blood glucose levels and blood pressure and treatment of diabetes and hypertension on the incidence of cardiovascular disease: a study of 740 patients with incident Type 2 diabetes with up to 30 years' follow‐up
Authors: Jansson S. P. O. , Svärdsudd K. , Andersson D. K. G. 
Published: June 2014

AbstractAimsTo analyse the effects of hyperglycaemia and hypertension and treatment of diabetes and hypertension on cardiovascular disease incidence in patients with Type 2 diabetes with up to 30 years of follow‐up.MethodsA total of 740 patients with incident Type 2 diabetes were registered at the Laxå Primary Health Care Centre, Sweden between 1972 and 2001. Annual data on mean fasting blood glucose, systolic, diastolic and mean arterial blood pressure, and type of diabetes and hypertension treatment were obtained from patient records, and information on cardiovascular disease, myocardial infarction and stroke events was obtained from national registers.ResultsDuring the follow‐up period, cumulative cardiovascular disease incidence increased significantly with male sex (hazard ratio 1.48, 95% CI 1.21–1.82), number of previous cardiovascular disease events (hazard ratio 1.13, 95% CI 1.08–1.18), age, per year (HR 1.05, 95% CI 1.04–1.07), mean fasting blood glucose, per mmol/l (hazard ratio 1.05, 95% CI 1.00–1.10) BMI (hazard ratio 1.04, 95% CI 1.01–1.06), mean arterial blood pressure, per mmHg (hazard ratio 1.02, 95% CI 1.01–1.03), and decreased significantly with metformin treatment (hazard ratio 0.58, 95% CI 0.38–0.90) and sulfonylurea (hazard ratio 0.73, 95% CI 0.55–0.97). Cumulative myocardial infarction incidence increased significantly with male sex, number of previous myocardial infarction events, mean fasting blood glucose level, BMI, age and mean arterial blood pressure, and decreased with metformin treatment. Cumulative stroke incidence increased with number of previous stroke events, age and mean arterial blood pressure.ConclusionsThe cumulative incidence of cardiovascular disease and myocardial infarction increased with number of previous events and presence of hyperglycaemia and hypertension and decreased with pharmacological treatment of diabetes. A higher number of previous stroke events increased the cumulative incidence of stroke but no protective effect of pharmacological treatment was observed.
Rural Economies in the ‘Age of Migration’: Perspectives from OECD Countries
Authors: Dufty‐Jones Rae 
Published: June 2014

AbstractAn important feature of globalisation processes has been the increased level of immigration. For the most part, this has been considered an urban phenomenon. As a consequence, a less well‐known feature of contemporary global immigration patterns is that an increasing proportion of immigrants are now settling in rural locations. Over the last decade, however, there has been a burgeoning of research into the political‐economic processes that have produced an increased level of immigration into rural regions in many OECD nation‐states. This paper begins by reviewing some of the reasons why this dimension of rural demographic change has gone under the radar of both researchers and policy makers. It then examines how immigration into rural regions is both an important feature of the multifunctional rural transition and a product of the ‘regionalisation’ of immigration policy as a distinct regional development strategy employed regarding rural areas.
An Urban Political Ecology of Climate Change Governance
Authors: Rice Jennifer L. 
Published: June 2014

AbstractThis paper utilizes insights from urban political ecology (UPE) to highlight the importance of carbon in urban climate politics. Through an emphasis on the socio‐material politics of urban climate governance, this analysis provides an explicit account of the performance of power within and over the urban landscape. Two specific efforts are reviewed here, including local greenhouse gas inventorying practices and urban educational and outreach efforts to create carbon conscious citizens. By considering these social and political processes in relation to ecological aspects of urban carbon cycling, it becomes evident that urban interventions into climate change do little to disrupt or restructure the ways in which carbon flows into or out of cities and instead operate at the level of carbon representation (via measurement) and subjection (via educational outreach). A UPE framework also helps highlight the ways in which urban carbon governance erases importance aspects of social and spatial difference among carbon emitters and how efforts to change individual behavior direct attention away from carbon intensive urban development. The review concludes with some thoughts on why social scientists should pay closer attention to the myriad ways that carbon is modeled, measured, and monitored as an ecological, technical, and political project in the world's cities.
The development and initial validation of a questionnaire to measure help‐seeking behaviour in patients with new onset rheumatoid arthritis
Authors: Stack Rebecca J. , Mallen Christian D. , Deighton Chris , Kiely Patrick , Shaw Karen L. , Booth Alison , Kumar Kanta , Thomas Susan , Rowan Ian , Horne Rob , Nightingale Peter , Herron‐Marx Sandy , Jinks Clare ,   DELAY Study Syndicate, Raza Karim 
Published: June 2014

AbstractBackgroundEarly treatment for rheumatoid arthritis (RA) is vital. However, people often delay in seeking help at symptom onset. An assessment of the reasons behind patient delay is necessary to develop interventions to promote rapid consultation.ObjectiveUsing a mixed methods design, we aimed to develop and test a questionnaire to assess the barriers to help seeking at RA onset.DesignQuestionnaire items were extracted from previous qualitative studies. Fifteen people with a lived experience of arthritis participated in focus groups to enhance the questionnaire's face validity. The questionnaire was also reviewed by groups of multidisciplinary health‐care professionals. A test–retest survey of 41 patients with newly presenting RA or unclassified arthritis assessed the questionnaire items' intraclass correlations.ResultsDuring focus groups, participants rephrased questions, added questions and deleted items not relevant to the questionnaire's aims. Participants organized items into themes: early symptom experience, initial reactions to symptoms, self‐management behaviours, causal beliefs, involvement of significant others, pre‐diagnosis knowledge about RA, direct barriers to seeking help and relationship with GP. The test–retest survey identified seven items (out of 79) with low intraclass correlations which were removed from the final questionnaire.ConclusionThe involvement of people with a lived experience of arthritis and multidisciplinary health‐care professionals in the preliminary validation of the DELAY (delays in evaluating arthritis early) questionnaire has enriched its development. Preliminary assessment established its reliability. The DELAY questionnaire provides a tool for researchers to evaluate individual, cultural and health service barriers to help‐seeking behaviour at RA onset.
Incidence of upper gastrointestinal haemorrhage in Maori and New Zealand European ethnic groups, 2001–2010
Authors: Irwin J. , Ferguson R. , Weilert F. , Smith A. 
Published: June 2014

AbstractBackgroundTo date no incidence figures for upper gastrointestinal haemorrhage (UGIH) in New Zealand have been published.AimsTo determine the incidence of UGIH in a demographically defined population, and to assess variation in incidence associated with demographic parameters.MethodsBetween 17 March 2001 and 12 October 2010, all patients presenting to Waikato Hospital with UGIH were prospectively ascertained, and clinical, epidemiological and laboratory data were collected. Incidence rates were calculated, and were age adjusted to the World Health Organization world standard population. Parameters associated with trends in incidence were examined.ResultsThere were 1360 UGIH events, yielding a crude incidence of 59.2 per 100 000 adults (age ≥ 15 years) per year (all quoted incidence figures per 100 000 adults per year), and an age‐adjusted incidence (AAI) of 46.4. AAI was higher for Maori compared with New Zealand Europeans (91.3 vs 37.0, rate ratio (RR) = 2.47, P < 0.001). Maori were more likely to have a gastric ulcer at endoscopy (odds ratio (OR) = 2.21, P < 0.001). For those tested for Helicobacter pylori (n = 702), Maori were more likely to be infected (OR = 2.12, P < 0.001). AAI was higher for males (61.1 vs 33.6, RR = 1.82, P < 0.001). Males were more likely to have a duodenal ulcer at endoscopy (OR = 1.79, P < 0.001). AAI incidence decreased from the first to the second half of the study period (53.6 vs 45.8, RR = 1.17, P < 0.001).ConclusionAAI of UGIH in the Waikato region was 46.4. This was significantly higher in Maori and in males, and decreased over the study period. These data will provide a comparison for future assessment of trends in UGIH.
The Positive and Negative Magnetodielectric Effects in Double Perovskite Pr2CoMnO6
Authors: Wang Liao Yu , Li Qian , Gong Yuan Yuan , Wang Dun Hui , Cao Qing Qi , Du You Wei 
Published: June 2014

The magnetic, electric, and dielectric properties of a B‐site ordered double perovskite Pr2CoMnO6 were investigated. A charge localization state and a negative magnetoresistance effect were observed below 250 K. Different from other double perovskites, one negative and two positive magnetodielectric effects were simultaneously observed in this sample. The physical origins of these interesting magnetodielectric properties were discussed.
The Adaptation of a School‐based Health Promotion Programme for Youth with Intellectual and Developmental Disabilities: A Community‐Engaged Research Process
Authors: Hubbard Kristie L. , Bandini Linda G. , Folta Sara C. , Wansink Brian , Must Aviva 
Published: June 2014

BackgroundEvidenced‐based health promotion programmes for youth with intellectual and developmental disabilities (I/DD) are notably absent. Barriers include a lack of understanding of how to adapt existing evidence‐based programmes to their needs, maximize inclusion and support mutual goals of health and autonomy.MethodsWe undertook a community‐engaged process to adapt a school‐based nutrition intervention in a residential school for youth with I/DD. Focus groups and interviews with school staff elicited recommendations for adaptation strategies; these were then reviewed by an expert panel.ResultsAdaptations were developed to address needs in three categories: food‐related challenges among students, adjusting to change and transition and social environment factors. Choice and heterogeneity were overarching themes across the adaptation categories.ConclusionsFuture research should consider community‐engaged approaches for adaptation so that youth with I/DD can participate and benefit from evidence‐based health promotion programmes to their maximum potential.