bluuebunny/crossref_metadata_2025_split huggingface dataset:
Rapid Bayesian inference of heritability in animal models without convergence problems
Authors: Ahlinder Jon , Sillanpää Mikko J. 
Published: August 2013

Summary

The rapid advancement in genome sequencing techniques allows the dissection of complex traits of non‐model organisms of importance in evolutionary biology, conservation genetics, breeding and medicine. This advancement requires new statistical analysis tools that can handle large amount of sequencing data efficiently.

We propose an analytic Bayesian implementation of the mixed linear model which allows rapid and robust inferences of heritability. The two main features of the method are (i) breeding values and residual variance component are analytically integrated out of the model and (ii) the parameter space of the variance ratio parameter is discretized so that a Gibbs sampling distribution can be utilized. We propose further two separate methods to infer breeding values that acknowledge uncertainty of the learned heritability. The benefit of the method compared to a standard Markov Chain Monte Carlo (MCMC) method is visualized on public data sets: two simulated data sets and one Wheat (Triticum aestivum L.) pedigree.

Results show that while the accuracy of inferred heritability obtained by the proposed and standard methods are almost identical, the computational performance is very encouraging: up to hundred fold speed up and the possibility to make parallel implementation is particularly appealing here, which may further speed up computations.

The method allows analysis using a non‐invertible relationship matrix so that ad hoc manipulation is avoided which can be important as our results imply. We completely avoid convergence and mixing problems here: this is a well‐known problem of MCMC simulation, which sometimes can severely reduce the inferential power. Bayes factors for model comparisons can be conveniently calculated as a by‐product of the inference procedure. The source code will be available for download at http://www.rni.helsinki.fi/~mjs.
Precipitation of the warmest quarter and temperature of the warmest month are key to understanding the effect of climate change on plant species diversity in Southern African savannah
Authors: Gwitira Isaiah , Murwira Amon , Shekede Munyaradzi Davis , Masocha Mhosisi , Chapano Christopher 
Published: August 2013

AbstractIn this study, we test for the key bioclimatic variables that significantly explain the current distribution of plant species richness in a southern African ecosystem as a preamble to predicting plant species richness under a changed climate. We used 54,000 records of georeferenced plant species data to calculate species richness and spatially interpolated climate data to derive nineteen bioclimatic variables. Next, we determined the key bioclimatic variables explaining variation in species richness across Zimbabwe using regression analysis. Our results show that two bioclimatic variables, that is, precipitation of the warmest quarter (R2 = 0.92, P < 0.001) and temperature of the warmest month (R2 = 0.67, P < 0.001) significantly explain variation in plant species richness. In addition, results of bioclimatic modelling using future climate change projections show a reduction in the current bio‐climatically suitable area that supports high plant species richness. However, in high‐altitude areas, plant richness is less sensitive to climate change while low‐altitude areas show high sensitivity. Our results have important implications to biodiversity conservation in areas sensitive to climate change; for example, high‐altitude areas are likely to continue being biodiversity hotspots, as such future conservation efforts should be concentrated in these areas.
Association of maternal anti‐HLA class II antibodies with protection from allergy in offspring
Authors: Jones M. , Jeal H. , Harris J. M. , Smith J. D. , Rose M. L. , Taylor A. N. , Cullinan P. 
Published: August 2013

AbstractBackgroundRecent studies have suggested that the birth order effect in allergy may be established during the prenatal period and that the protective effect may originate in the mother. HLA class II disparity between mother and foetus has been associated with significantly increased Th1 production. In this study, we investigated whether production of HLA antibodies 4 years after pregnancy with index child is associated with allergic outcomes in offspring at 8 years.MethodsAnti‐HLA class I and II antibodies were measured in maternal serum (n = 284) and levels correlated to numbers of pregnancies and birth order, and allergic outcomes in offspring at 8 years of age.ResultsMaternal anti‐HLA class I and II antibodies were significantly higher when birth order, and the number of pregnancies were larger. Anti‐HLA class II, but not class I antibodies were associated with significantly less atopy and seasonal rhinitis in the offspring at age 8 years. Mothers with nonatopic (but not atopic) offspring had a significant increase in anti‐HLA class I and II antibodies with birth order.ConclusionThis study suggests that the ‘birth order’ effect in children may be due to parity‐related changes in the maternal immune response to foetal antigens. We have observed for the first time an association between maternal anti‐HLA class II antibodies and protection from allergy in the offspring. Further work is required to determine immunologically how HLA disparity between mother and father can protect against allergy.
Diagnosis of immediate hypersensitivity reactions to radiocontrast media
Authors: Salas M. , Gomez F. , Fernandez T. D. , Doña I. , Aranda A. , Ariza A. , Blanca‐López N. , Mayorga C. , Blanca M. , Torres M. J. 
Published: August 2013

AbstractBackgroundNo consensus exists on the diagnostic approach for immediate hypersensitivity reactions (IHR) to radiocontrast media (RCM). We analyzed the diagnostic value of a skin test (ST), drug provocation test (DPT) and basophil activation test (BAT) in patients with symptoms compatible with IHR to RCM.MethodsNinety patients with symptoms suggestive of IHR to RCM were evaluated. ST with a panel of RCM was performed, and if negative, DPT was carried out with the culprit RCM. If ST or DPT were positive, tolerance was assessed with an alternative RCM and BAT was carried out with the same panel used for ST.ResultsEight (8.9%) cases were confirmed as having IHR, 5 (62.5%) by ST and 3 (37.5%) by DPT. Five from those confirmed as IHR (62.5%) had a positive BAT.ConclusionsHypersensitivity to RCM was confirmed in 9%, by ST or DPT. BAT proved a valuable method for diagnosis.
Increased risk of developing dementia in patients with bipolar disorder: a nested matched case–control study
Authors: Wu Kuan‐Yi , Chang Chia‐Ming , Liang Hsin‐Yi , Wu Chi‐Shin , Chia‐Hsuan Wu Erin , Chen Chia‐Hsiang , Chau Yeuk‐Lun , Tsai Hui‐Ju 
Published: August 2013

ObjectiveThe association between bipolar disorder and subsequent dementia risk is not well established. The objective of this study was to investigate whether patients with bipolar disorder were at an increased risk for developing dementia.MethodsA conditional logistic regression model was performed using data from the National Health Insurance Research Database, a nationwide dataset in Taiwan. The study sample included 9,304 patients with incident dementia first diagnosed between 2000 and 2009, and 55,500 gender‐, age‐, and index date‐matched subjects without dementia. Cerebrovascular disease, diabetes, hypertension, head injury, chronic pulmonary disease, alcohol‐related disorders, substance use disorders, and health system utilization were treated as covariates in the analyses.ResultsAfter controlling for the covariates, bipolar disorder was significantly associated with an increased risk of subsequent dementia [adjusted odds ratio (aOR) = 4.32, 95% confidence interval (CI): 3.21–5.82]. An increased risk of developing dementia was observed in males and females alike (aOR = 4.01, 95% CI: 2.53–6.35 in males; aOR = 4.55, 95% CI: 3.07–6.73 in females). Moreover, a significantly increased risk was observed in subjects diagnosed with dementia before the age of 65 years (aOR = 3.77, 95% CI: 1.78–8.01).ConclusionsFindings from this study suggest a positive association between the presence of a lifetime history of bipolar disorder and an increased risk of developing dementia. Furthermore, our results also suggest that subjects with bipolar disorder tend to develop dementia in middle age. Going forward, it will be of importance to confirm our findings in different populations.
An investigation into the public health roles of community learning disability nurses
Authors: Mafuba Kay , Gates Bob 
Published: August 2013

Accessible summary

People with learning disabilities find it difficult to get their health checked and to get information about their health.

Community learning disability nurses play an important role in supporting people with learning disabilities to stay healthy.

Community learning disability nurses support people with learning disabilities to get their health checked and to get information about their health.

SummaryInternational studies have shown poor uptake of public health initiatives by people with learning disabilities. In addition, studies have shown that people with learning disabilities experience poor access to public health services. The contribution of community learning disability nurses in meeting the public health needs of people with learning disabilities has evolved differently across the UK resulting in conflicting understanding of this role. This paper reports on a study that explored and explained the contribution of community learning disability nurses in the implementation of public health policies for people with learning disabilities. The study demonstrates that community learning disability nurses are involved in health surveillance, health promotion, health facilitation, health prevention and protection, health education, and healthcare delivery.
Measuring and decomposing oral health inequalities in an UK population
Authors: Shen Jing , Wildman John , Steele Jimmy 
Published: August 2013

AbstractObjectivesWith health inequalities high on the policy agenda, this study measures oral health inequalities in the UK.MethodsWe compare an objective clinical measure of oral health (number of natural teeth) with a self‐reported measure of the impact of oral health (the Oral Health Impact Profile, OHIP) to establish whether the type of measure affects the scale of inequality measured. Gini coefficients and Concentration Indices (CIs) are calculated with subsequent decompositions using data from the 1998 UK Adult Dental Health Survey. Because the information on OHIP is only available on dentate individuals, analyses on the number of natural teeth are conducted for two samples – the entire sample and the sample with dentate individuals only, the latter to allow direct comparison with OHIP.ResultsWe find considerable overall pure oral health inequalities (number of teeth: Gini = 0.68 (including edentate), Gini = 0.40 (excluding edentate); OHIP: Gini = 0.33) and income‐related inequalities for both measures (number of teeth: CI = 0.35 (including edentate), CI = 0.15 (excluding edentate); OHIP: CI = 0.03), and the CI is generally higher for the number of teeth than for OHIP. There are differences across age groups, with CI increasing with age for the number of teeth (excluding edentate: 16–30 years: CI = 0.01, 65 + years: CI = 0.11; including edentate: 16–30 years: CI = 0.01, 65 + years: CI = 0.19). However, inequalities for OHIP were highest in the youngest age group (CI = 0.05). Number of teeth reflects the accumulation of damage over a lifetime, while OHIP records more immediate concerns.ConclusionsThere are considerable pure oral health inequalities and income‐related oral health inequalities in the UK. Using sophisticated methods to measure oral health inequality, we have been able to compare inequality in oral health with inequality in general health. The results provide a benchmark for future comparisons but also indicate that the type of health measure may be of considerable significance in how we think about and measure oral health inequalities.
Women with high early pregnancy urinary iodine levels have an increased risk of hyperthyroid newborns: the population‐based Generation R Study
Authors: Medici Marco , Ghassabian Akhgar , Visser Willy , de Muinck Keizer‐Schrama Sabine M. P. F. , Jaddoe Vincent W. V. , Visser W. Edward , Hooijkaas Herbert , Hofman Albert , Steegers Eric A. P. , Bongers‐Schokking Jacoba J. , Ross H. Alec , Tiemeier Henning , Visser Theo J. , de Rijke Yolanda B. , Peeters Robin P. 
Published: August 2013

AbstractObjectiveIodine deficiency during pregnancy results in thyroid dysfunction and has been associated with adverse obstetric and foetal effects, leading to worldwide salt iodization programmes.As nowadays 69% of the world's population lives in iodine‐sufficient regions, we investigated the effects of variation in iodine status on maternal and foetal thyroid (dys)function in an iodine‐sufficient population.Design, Participants and MeasurementsUrinary iodine, serum TSH, free T4 (FT4) and TPO‐antibody levels were determined in early pregnancy (13·3 (1·9) week; mean (SD)) in 1098 women from the population‐based Generation R Study. Newborn cord serum TSH and FT4 levels were determined at birth.ResultsThe median urinary iodine level was 222·5 μg/l, indicating an iodine‐sufficient population. 30·8% and 11·5% had urinary iodine levels <150 and >500 μg/l, respectively.When comparing mothers with urinary iodine levels <150 vs ≥150 μg/l, and >500 vs ≤500 μg/l, there were no differences in the risk of maternal increased or decreased TSH, hypothyroxinaemia or hyperthyroidism. Mothers with urinary iodine levels >500 μg/l had a higher risk of a newborn with decreased cord TSH levels (5·6 ± 1·4 (mean ± SE) vs 2·1 ± 0·5%, P = 0·04), as well as a higher risk of a hyperthyroid newborn (3·1 ± 0·9 vs 0·6 ± 0·3%, P = 0·02). These mothers had newborns with higher cord FT4 levels (21·7 ± 0·3 vs 21·0 ± 0·1 pm, P = 0·04).Maternal urinary iodine levels <150 μg/l were not associated with newborn thyroid dysfunction.ConclusionsIn an iodine‐sufficient population, higher maternal urinary iodine levels are associated with an increased risk of a hyperthyroid newborn.
Non‐Oriented MLS Gradient Fields
Authors: Chen Jiazhou , Guennebaud Gaël , Barla Pascal , Granier Xavier 
Published: August 2013

AbstractWe introduce a new approach for defining continuous non‐oriented gradient fields from discrete inputs, a fundamental stage for a variety of computer graphics applications such as surface or curve reconstruction, and image stylization. Our approach builds on a moving least square formalism that computes higher‐order local approximations of non‐oriented input gradients. In particular, we show that our novel isotropic linear approximation outperforms its lower‐order alternative: surface or image structures are much better preserved, and instabilities are significantly reduced. Thanks to its ease of implementation (on both CPU and GPU) and small performance overhead, we believe our approach will find a widespread use in graphics applications, as demonstrated by the variety of our results.
Systematic review of methods to predict and detect anastomotic leakage in colorectal surgery
Authors: Hirst N. A. , Tiernan J. P. , Millner P. A. , Jayne D. G. 
Published: August 2013

AbstractAimAnastomotic leakage is a serious complication of gastrointestinal surgery resulting in increased morbidity and mortality, poor function and predisposing to cancer recurrence. Earlier diagnosis and intervention can minimize systemic complications but is hindered by current diagnostic methods that are non‐specific and often uninformative. The purpose of this paper is to review current developments in the field and to identify strategies for early detection and treatment of anastomotic leakage.MethodA systematic literature search was performed using theMEDLINE, Embase, PubMed and Cochrane Library databases. Search terms included ‘anastomosis’ and ‘leak’ and ‘diagnosis’ or ‘detection’ and ‘gastrointestinal’ or ‘colorectal’. Papers concentrating on the diagnosis of gastrointestinal anastomotic leak were identified and further searches were performed by cross‐referencing.ResultsComputerized tomographyCTscanning and water‐soluble contrast studies are the current preferred techniques for diagnosing anastomotic leakage but suffer from variable sensitivity and specificity, have logistical constraints and may delay timely intervention. Intra‐operative endoscopy and imaging may offer certain advantages, but the ability to predict anastomotic leakage is unproven. Newer techniques involve measurement of biomarkers for anastomotic leakage and have the potential advantage of providing cheap real‐time monitoring for postoperative complications.ConclusionCurrent diagnostic tests often fail to diagnose anastomotic leak at an early stage that enables timely intervention and minimizes serious morbidity and mortality. Emerging technologies, based on detection of local biomarkers, have achieved proof of concept status but require further evaluation to determine whether they translate into improved patient outcomes. Further research is needed to address this important, yet relatively unrecognized, area of unmet clinical need.
Mucocutaneous disorders in renal transplant recipients receiving sirolimus‐based immunosuppressive therapy: a prospective, case–control study
Authors: Özcan Deren , Seçkin Deniz , Ada Simin , Haberal Mehmet 
Published: August 2013

AbstractBackgroundSirolimus (SRL) has some dermatologic complications including acneiform eruptions, edema, aphthous ulceration, and onychopathy. However, controlled studies reporting the prevalence and clinical characteristics of mucocutaneous disorders are scarce.ObjectiveTo investigate the prevalence and clinical spectrum of mucocutaneous disorders in renal transplant recipients (RTRs) receiving SRL and to compare the findings with those in RTRs not receiving SRL.MethodsFifty RTRs (35 men, 15 women; mean age, 34.6 ± 11.6 yr) receiving SRL, 50 RTRs (36 men, 14 women; mean age, 34.4 ± 11.3 yr) not on SRL were screened for mucocutaneous disorders.ResultsIn RTRs receiving SRL, skin infection (78%) was the most common dermatologic disorder followed by facial hyperpigmentation (50%) and acneiform eruption (46%). Herpes simplex virus infections (14%) and seborrheic dermatitis (38%) were significantly more common in RTRs on SRL (p < 0.05); the frequencies of edema, aphthous ulceration, acne, and longitudinal nail ridging were similar in both groups (p > 0.05).LimitationsThis study had a small sample size. The investigator was not blinded to immunosuppressive treatment protocols.ConclusionRenal transplant recipients receiving SRL are more likely to develop seborrheic dermatitis and herpes simplex virus infections than those not taking SRL. Whereas, they are not more prone to edema, aphthous ulceration, acne, or longitudinal nail ridging.
The potential role of transient receptor potential type A1 as a mechanoreceptor in human periodontal ligament cells
Authors: Tsutsumi Takashi , Kajiya Hiroshi , Fukawa Teruhisa , Sasaki Mina , Nemoto Tetsuomi , Tsuzuki Takashi , Takahashi Yutaka , Fujii Shinsuke , Maeda Hidefumi , Okabe Koji 
Published: August 2013

Transient receptor potential type A1 (TRPA1) is reported to be a Ca2+‐permeable channel and is activated by cold temperatures and mechanical stimuli in the hair cells and in dorsal root ganglion. Using a DNA microarray, we found that TRPA1 was significantly up‐regulated in human periodontal ligament (hPDL) cells 2 d after intermittent mechanical stimulation (iMS) loading compared with unloaded cells. Although hPDL cells are known to respond to mechanical stimulation induced by occlusal force, little is known about the expression and functional role of TRPA1 in these cells. Therefore, we investigated the effects of iMS on TRPA1 expression and its signaling pathway in hPDL cells. Intermittent mechanical stimulation loading up‐regulated TRPA1 expression in hPDL cells in a time‐dependent manner, but had no effect on other mechanoreceptors. Furthermore, iMS significantly increased the phosphorylation of mitogen‐activated protein kinases (MAPKs), especially extracellular signal‐regulated kinase 1/2 (ERK1/2) and p38, and the expression of C‐C chemokine ligand 2 (CCL2). Transient receptor potential type A1 agonists also increased MAPK phosphorylation and the intracellular Ca2+ concentration. By contrast, inhibition or silencing of TRPA1 partially suppressed iMS‐induced MAPK phosphorylation. In summary, iMS during occlusion activates TRPA1 and MAPK signaling in periodontal ligament tissues, suggesting that TRPA1 regulates the mechanosensitivity of occlusal force via activation of MAPKs in hPDL cells.
Investigating the genetics of Bti resistance using mRNA tag sequencing: application on laboratory strains and natural populations of the dengue vector Aedes aegypti
Authors: Paris Margot , Marcombe Sebastien , Coissac Eric , Corbel Vincent , David Jean‐Philippe , Després Laurence 
Published: August 2013

AbstractMosquito control is often the main method used to reduce mosquito‐transmitted diseases. In order to investigate the genetic basis of resistance to the bio‐insecticide Bacillus thuringiensis subsp. israelensis (Bti), we used information on polymorphism obtained from cDNA tag sequences from pooled larvae of laboratory Bti‐resistant and susceptible Aedes aegypti mosquito strains to identify and analyse 1520 single nucleotide polymorphisms (SNPs). Of the 372 SNPs tested, 99.2% were validated using DNA Illumina GoldenGate® array, with a strong correlation between the allelic frequencies inferred from the pooled and individual data (r = 0.85). A total of 11 genomic regions and five candidate genes were detected using a genome scan approach. One of these candidate genes showed significant departures from neutrality in the resistant strain at sequence level. Six natural populations from Martinique Island were sequenced for the 372 tested SNPs with a high transferability (87%), and association mapping analyses detected 14 loci associated with Bti resistance, including one located in a putative receptor for Cry11 toxins. Three of these loci were also significantly differentiated between the laboratory strains, suggesting that most of the genes associated with resistance might differ between the two environments. It also suggests that common selected regions might harbour key genes for Bti resistance.
Bahiagrass response and N loss from selected N fertilizer sources
Authors: Silveira M. L. , Vendramini J. M. B. , Sellers B. , Monteiro F. A. , Artur A. G. , Dupas E. 
Published: August 2013

AbstractThe increasing cost of commercial fertilizers and environmental problems associated with improper fertilization management have prompted the need to re‐examine commercial N sources that can effectively supply N to pastures while minimizing N losses. This 3‐year study evaluated the effects of selected N sources on bahiagrass (Paspalum notatum Flügge) responses, soil properties and N losses. Treatments consisted of a factorial combination of 6 N sources [(i) ammonium nitrate (AN), (ii) ammonium sulphate (AS), (iii) urea (U), (iv) urea treated with Agrotain (U + Agrotain), (v) SuperU and (vi) ammonium sulphate nitrate] and 3 N levels (0, 60 or 120 kg ha−1 year−1), replicated three times. Bahiagrass dry‐matter yield (DMY), crude protein (CP) concentration, N uptake and recovery were not affected by N source, with the exception of AN that resulted in reduced DMY in 2010 compared with the other sources. Bahiagrass DMY, CP concentration, N uptake and recovery increased linearly as N levels increased. Nitrogen fertilization showed no effect on soil pH or soil N accumulation. Soil pore‐water N concentrations from treatments fertilized with N were similar to the control plots indicating no threat to the environment. At the N levels evaluated in this study, selection of N source should be based on the fertilizer cost.