bluuebunny/crossref_metadata_2025_split huggingface dataset:
Widespread allelic heterogeneity in complex traits
Authors: Hormozdiari Farhad , Zhu Anthony , Kichaev Gleb , Segrè Ayellet V. , Ju Chelsea J.-T. , Joo Jong Wha J , Won Hyejung , Sankararaman Sriram , Pasaniuc Bogdan , Shifman Sagiv , Eskin Eleazar 
Published: September 2016

AbstractRecent successes in genome-wide association studies (GWASs) make it possible to address important questions about the genetic architecture of complex traits, such as allele frequency and effect size. One lesser-known aspect of complex traits is the extent of allelic heterogeneity (AH) arising from multiple causal variants at a locus. We developed a computational method to infer the probability of AH and applied it to three GWAS and four expression quantitative trait loci (eQTL) datasets. We identified a total of 4152 loci with strong evidence of AH. The proportion of all loci with identified AH is 4-23% in eQTLs, 35% in GWAS of High-Density Lipoprotein (HDL), and 23% in schizophrenia. For eQTLs, we observed a strong correlation between sample size and the proportion of loci with AH (R2=0.85, P = 2.2e-16), indicating that statistical power prevents identification of AH in other loci. Understanding the extent of AH may guide the development of new methods for fine mapping and association mapping of complex traits.
Occurrence and molecular characteristics of antimicrobial resistance of Escherichia coli from broilers, pigs and meat products in Thailand and Cambodia provinces
Authors: Trongjit Suthathip , Angkittitrakul Sunpetch , Chuanchuen Rungtip 
Published: September 2016

ABSTRACTNine hundred and forty‐one samples were collected in Sa Keao, Thailand (n = 554) and Banteay Meanchey, Cambodia (n = 387) from July 2014 to January 2015. A total of 667 Escherichia coli isolates (381 isolates from Sa Keao and 286 isolates from Banteay Meanchey) were obtained and examined for antimicrobial susceptibility, class 1 integrons, ESBL genes and horizontal transfer of resistance determinants. Prevalence of E. coli in pig and broiler carcass samples from slaughterhouses and fresh markets was 36–85% in Sa Keao and 11–69% in Banteay Meanchey. The majority of these isolates were multidrug resistant (75.3%). Class 1 integrons were common in both Thai (47%) and Cambodian (62%) isolates, of which four resistance gene cassette arrays including aadA1, dfrA1‐aadA1, dfrA12‐aadA2 and aadA2‐linF were identified. Class 1 integrons in two broiler isolates from Sa Keao (dfrA12‐aadA2) and one broiler isolate from Banteay Meanchey (dfrA1‐aadA1) were horizontally transferable. Sixteen isolates were confirmed to be ESBL‐producing strains with ESBL gene blaCTX‐M‐15, broad spectrum β‐lactamase gene blaTEM‐1 and the AmpC gene blaCMY‐2 being detected. The blaTEM‐1 gene was most prevalent and located on a conjugative plasmid.
A fast joint seismic data reconstruction by sparsity‐promoting inversion
Authors: Bai Lanshu , Lu Huiyi , Liu Yike , Khan Majid 
Published: September 2016

ABSTRACTSeismic field data are often irregularly or coarsely sampled in space due to acquisition limits. However, complete and regular data need to be acquired in most conventional seismic processing and imaging algorithms. We have developed a fast joint curvelet‐domain seismic data reconstruction method by sparsity‐promoting inversion based on compressive sensing. We have made an attempt to seek a sparse representation of incomplete seismic data by curvelet coefficients and solve sparsity‐promoting problems through an iterative thresholding process to reconstruct the missing data. In conventional iterative thresholding algorithms, the updated reconstruction result of each iteration is obtained by adding the gradient to the previous result and thresholding it. The algorithm is stable and accurate but always requires sufficient iterations. The linearised Bregman method can accelerate the convergence by replacing the previous result with that before thresholding, thus promoting the effective coefficients added to the result. The method is faster than conventional one, but it can cause artefacts near the missing traces while reconstructing small‐amplitude coefficients because some coefficients in the unthresholded results wrongly represent the residual of the data. The key process in the joint curvelet‐domain reconstruction method is that we use both the previous results of the conventional method and the linearised Bregman method to stabilise the reconstruction quality and accelerate the recovery for a while. The acceleration rate is controlled through weighting to adjust the contribution of the acceleration term and the stable term. A fierce acceleration could be performed for the recovery of comparatively small gaps, whereas a mild acceleration is more appropriate when the incomplete data has a large gap of high‐amplitude events. Finally, we carry out a fast and stable recovery using the trade‐off algorithm. Synthetic and field data tests verified that the joint curvelet‐domain reconstruction method can effectively and quickly reconstruct seismic data with missing traces.
Dietary rapamycin supplementation reverses age‐related vascular dysfunction and oxidative stress, while modulating nutrient‐sensing, cell cycle, and senescence pathways
Authors: Lesniewski Lisa A. , Seals Douglas R. , Walker Ashley E. , Henson Grant D. , Blimline Mark W. , Trott Daniel W. , Bosshardt Gary C. , LaRocca Thomas J. , Lawson Brooke R. , Zigler Melanie C. , Donato Anthony J. 
Published: September 2016

SummaryInhibition of mammalian target of rapamycin, mTOR, extends lifespan and reduces age‐related disease. It is not known what role mTOR plays in the arterial aging phenotype or if mTOR inhibition by dietary rapamycin ameliorates age‐related arterial dysfunction. To explore this, young (3.8 ± 0.6 months) and old (30.3 ± 0.2 months) male B6D2F1 mice were fed a rapamycin supplemented or control diet for 6–8 weeks. Although there were few other notable changes in animal characteristics after rapamycin treatment, we found that glucose tolerance improved in old mice, but was impaired in young mice, after rapamycin supplementation (both P < 0.05). Aging increased mTOR activation in arteries evidenced by elevated S6K phosphorylation (P < 0.01), and this was reversed after rapamycin treatment in old mice (P < 0.05). Aging was also associated with impaired endothelium‐dependent dilation (EDD) in the carotid artery (P < 0.05). Rapamycin improved EDD in old mice (P < 0.05). Superoxide production and NADPH oxidase expression were higher in arteries from old compared to young mice (P < 0.05), and rapamycin normalized these (P < 0.05) to levels not different from young mice. Scavenging superoxide improved carotid artery EDD in untreated (P < 0.05), but not rapamycin‐treated, old mice. While aging increased large artery stiffness evidenced by increased aortic pulse‐wave velocity (PWV) (P < 0.01), rapamycin treatment reduced aortic PWV (P < 0.05) and collagen content (P < 0.05) in old mice. Aortic adenosine monophosphate‐activated protein kinase (AMPK) phosphorylation and expression of the cell cycle‐related proteins PTEN and p27kip were increased with rapamycin treatment in old mice (all P < 0.05). Lastly, aging resulted in augmentation of the arterial senescence marker, p19 (P < 0.05), and this was ameliorated by rapamycin treatment (P < 0.05). These results demonstrate beneficial effects of rapamycin treatment on arterial function in old mice and suggest these improvements are associated with reduced oxidative stress, AMPK activation and increased expression of proteins involved in the control of the cell cycle.
Body‐mass index is associated with fibrosis regression during long‐term nucleoside analogue therapy in chronic hepatitis B
Authors: Seto W.‐K. , Fung J. , Cheung K.‐S. , Mak L.‐Y. , Hui R. W. H. , Liu K. S. H. , Lai C.‐L. , Yuen M.‐F. 
Published: September 2016

SummaryBackgroundFactors influencing changes in liver stiffness measurements during long‐term nucleoside analogue therapy for chronic hepatitis B (CHB) have not been thoroughly investigated.AimTo identify determinants of on‐treatment fibrosis regression in CHB.MethodsWe performed follow‐up liver stiffness and controlled attenuation parameter measurements on nucleoside analogue‐treated CHB patients with severe liver fibrosis, according to EASL‐ALEH criteria, diagnosed by transient elastography in 2006–2008. Anthropometric measurements and different metabolic parameters were recorded.ResultsAmong 257 patients with severe liver fibrosis by initial transient elastography, 123 (47.9%) were recruited for reassessment. Median treatment duration was 87.5 (interquartile range 75.3–102.2) months; 97.5% had undetectable HBV DNA. There was a significant reduction in median liver stiffness from 14.6 to 8.3 kPa (P < 0.001). A total of 29.3% had fibrosis regression, with lower rates of 17.9%, 14.9% and 11.5% noted in patients with body‐mass index (BMI) ≥25 kg/m2, metabolic syndrome and diabetes, respectively. Absence of BMI ≥25 kg/m2, diabetes and metabolic syndrome, when compared with presence of any one of these three factors, was associated with increased fibrosis regression (43.1% vs. 16.9%, P = 0.001). Multivariate analysis found a lower BMI to be the only factor independently associated with fibrosis regression (P = 0.034, odds ratio 0.68, 95% CI 0.48–0.97). No association was noted between controlled attenuation parameter measurements and fibrosis regression (P > 0.05).ConclusionAn increased BMI hindered fibrosis regression in patients with chronic hepatitis B during nucleoside analogue treatment, suggesting that control of metabolic risk factors, in addition to virologic suppression via antiviral therapy, might be needed to halt the fibrogenic process in chronic hepatitis B.
Feasibility of BAALC gene expression for detection of minimal residual disease and risk stratification in normal karyotype acute myeloid leukaemia
Authors: Weber Simone , Haferlach Torsten , Alpermann Tamara , Perglerová Karolína , Schnittger Susanne , Haferlach Claudia , Kern Wolfgang 
Published: September 2016

SummaryHigh BAALC gene expression has been associated with poor prognosis in cytogenetically normal acute myeloid leukaemia (CN‐AML) and has been suggested as a suitable marker for assessing minimal residual disease (MRD). The purpose of this study was to substantiate these findings by the analysis of a large data set of 632 diagnostic and follow‐up samples in 142 intensively treated CN‐AML patients. Paired diagnostic/relapse samples of 35 patients revealed stable high BAALC expression in 89%, irrespective of a high proportion of clonal evolution found in 49% of these cases. High BAALC expression, both directly after induction chemotherapy and within 3–6 months after induction chemotherapy, correlated significantly with shorter event‐free survival and overall survival. Moreover, 8 of 10 patients displaying high BAALC expression levels after completion of induction therapy as well as 5 of 5 patients exhibiting high BAALC expression levels within 3–6 months after induction chemotherapy experienced relapse with a median of 197 and 101 days, respectively, from sampling to relapse. Thus, BAALC expression‐based MRD detection during therapy may be considered a strategy to identify patients at high risk of relapse.
Numerical and experimental investigation of the mesoscale fracture behaviour of quenched steels
Authors: Said Schicchi D , Hoffmann F , Hunkel M , Lübben T 
Published: September 2016

AbstractDuring heat treatment processes, especially during quenching, cracks may form because of the presence of high thermal and mechanical stresses and strains. Notwithstanding the fact that increasingly detailed modelling for heat treatment is being performed (considering, i.a., grain size, creep and transformation plasticity), homogeneous microstructures are still normally assumed. Chemical and hence structural inhomogeneities are not commonly explicitly considered, which is especially accentuated in the case of real parts simulation because of the resulting numerical problem's size. Intensive quenching on a cylindrical specimen of 100Cr6 (SAE) steel is proposed here to experimentally investigate the microcrack generation. A finite element based model is proposed to numerically evaluate the fracture behaviour in a two‐step simulation. First, by solving the quenching problem in direct correspondance with the experimental test performed, and second, by studying the mesoscale response taking into account the influence of second phase particles in a representative volume element based approach. The maximum principal stress criterion is used to trigger the fracture by means of the extended finite element method at the mesoscale. The trend to form cracks in the surface region, experimentally observed, has been well captured by the model. The influence of carbides sizes and content on the mesoscale fracture response has been numerically analysed as well. A good agreement has been reached between the simulations and the experimental results, exhibiting the potential of the introduced approach to be used as a failure prediction methodology.
Numerical model of pore‐pressure diffusion associated with the initiation of the 2010–2011 Guy–Greenbrier, Arkansas earthquakes
Authors: Ogwari P. O. , Horton S. P. 
Published: September 2016

AbstractWe model pore‐pressure diffusion caused by pressurized waste‐fluid injection at two nearby wells and then compare the buildup of pressure with the observed initiation and migration of earthquakes during the early part of the 2010–2011 Guy–Greenbrier earthquake swarm. Pore‐pressure diffusion is calculated using MODFLOW 2005 that allows the actual injection histories (volume/day) at the two wells to diffuse through a fractured and faulted 3D aquifer system representing the eastern Arkoma basin. The aquifer system is calibrated using the observed water‐level recovery following well shut‐in at three wells. We estimate that the hydraulic conductivities of the Boone Formation and Arbuckle Group are 2.2 × 10−2 and 2.03 × 10−3 m day−1, respectively, with a hydraulic conductivity of 1.92 × 10−2 m day−1 in the Hunton Group when considering 1.72 × 10−3 m day−1 in the Chattanooga Shale. Based on the simulated pressure field, injection near the relatively conductive Enders and Guy–Greenbrier faults (that hydraulically connect the Arbuckle Group with the underlying basement) permits pressure diffusion into the crystalline basement, but the effective radius of influence is limited in depth by the vertical anisotropy of the hydraulic diffusivity. Comparing spatial/temporal changes in the simulated pore‐pressure field to the observed seismicity suggests that minimum pore‐pressure changes of approximately 0.009 and 0.035 MPa are sufficient to initiate seismic activity within the basement and sedimentary sections of the Guy–Greenbrier fault, respectively. Further, the migration of a second front of seismicity appears to follow the approximately 0.012 MPa and 0.055 MPa pore‐pressure fronts within the basement and sedimentary sections, respectively.
La dinámica manufacturas‐servicios y el desarrollo económico
Authors: KUCERA David , RONCOLATO Leanne 
Published: September 2016

ResumenEste artículo se enmarca en el debate sobre el crecimiento impulsado por los servicios, que trata de determinar si estos son sustitutos o complementos, ex‐ante o ex‐post, de las manufacturas. Tras una revisión de la bibliografía empírica, los autores aplican métodos de descomposición del crecimiento a datos de 18 países asiáticos y latinoamericanos de 1980–2005, centrándose en las manufacturas y en los servicios más intensivos en TIC. Después tratan de ver si los países con más o menos crecimiento de la productividad del trabajo y del empleo tienen características estructurales comunes. También analizan la viabilidad del crecimiento impulsado por los servicios, en particular en la India.
Intensidad en empleo a largo plazo del crecimiento del producto sectorial en Túnez
Authors: SASSI Seifallah , GOAIED Mohamed 
Published: September 2016

ResumenSe examina la capacidad a largo plazo de Túnez de generar empleo. Con datos de panel de 15 sectores económicos de 1983–2010, los autores estiman sus elasticidades producto‐empleo a largo plazo utilizando el estimador de media grupal. Según sus resultados, la política económica debería orientarse a los sectores más intensivos en empleo: servicios y manufacturas exportadoras. Destaca la incapacidad del sector minero de absorber mano de obra, por lo que la inversión en el mismo no será productiva; asimismo, el crecimiento sin empleo a largo plazo de la hotelería y restauración induce a pensar que deberían fomentarse más las actividades paraturísticas que las turísticas.
Derechos de los trabajadores migrantes. Aspectos económicos, políticos y éticos
Authors: RUHS Martin 
Published: September 2016

ResumenLas políticas de inmigración laboral de los países de altos ingresos establecen una relación inversa entre el grado de apertura y algunos de los derechos concedidos a los migrantes admitidos. Esta observación empírica es la base del libro The price of rights: Regulating international labor migration, que el autor de este artículo escribió en 2013. Aquí resume sus principales conclusiones, argumentos e implicaciones políticas, y responde a una reseña publicada por la Revista Internacional del Trabajo en 2015. Concluye exhortando a un debate más abierto sobre los vínculos entre derechos, migración laboral y desarrollo entre las organizaciones nacionales e internacionales interesadas en estas cuestiones.
Use of molecular markers to improve relationship information in the genetic evaluation of beef cattle tick resistance under pedigree‐based models
Authors: Junqueira V.S. , Cardoso F.F. , Oliveira M.M. , Sollero B.P. , Silva F.F. , Lopes P.S. 
Published: September 2016

SummaryThe selection of genetically superior individuals is conditional upon accurate breeding value predictions which, in turn, are highly depend on how precisely relationship is represented by pedigree. For that purpose, the numerator relationship matrix is essential asa prioriinformation in mixed model equations. The presence of pedigree errors and/or the lack of relationship information affect the genetic gain because it reduces the correlation between the true and estimated breeding values. Thus, this study aimed to evaluate the effects of correcting the pedigree relationships using single‐nucleotide polymorphism (SNP) markers on genetic evaluation accuracies for resistance of beef cattle to ticks. Tick count data from Hereford and Braford cattle breeds were used as phenotype. Genotyping was carried out using a high‐density panel (BovineHD ‐ Illumina®bead chip with 777 962 SNPs) for sires and the Illumina BovineSNP50 panel (54 609 SNPs) for their progenies. The relationship between the parents and progenies of genotyped animals was evaluated, and mismatches were based on the Mendelian conflicts counts. Variance components and genetic parameters estimates were obtained using a Bayesian approach via Gibbs sampling, and the breeding values were predicted assuming a repeatability model. A total of 460 corrections in relationship definitions were made (Table 1) corresponding to 1018 (9.5%) tick count records. Among these changes, 97.17% (447) were related to the sire's information, and 2.8% (13) were related to the dam's information. We observed 27.2% (236/868) of Mendelian conflicts for sire–progeny genotyped pairs and 14.3% (13/91) for dam–progeny genotyped pairs. We performed 2174 new definitions of half‐siblings according to the correlation coefficient between the coancestry and molecular coancestry matrices. It was observed that higher‐quality genetic relationships did not result in significant differences of variance components estimates; however, they resulted in more accurate breeding values predictions. Using SNPs to assess conflicts between parents and progenies increases certainty in relationships and consequently the accuracy of breeding value predictions of candidate animals for selection. Thus, higher genetic gains are expected when compared to the traditional non‐corrected relationship matrix.
An innovative masticatory efficiency test using odour intensity in the mouth as a target marker: a feasibility study
Authors: Goto T. , Higaki N. , Yagi K. , Ishida Y. , Watanabe M. , Nagao K. , Ichikawa T. 
Published: September 2016

SummaryA large number of studies have reported the findings for masticatory efficiency tests; however, some objective masticatory efficiency tests have a drawback, in that subjects are required to spit out the test material. This study examined the possibility of a masticatory efficiency test that evaluates the intensity of odours released when chewing an odour compound‐containing material. A total of 20 volunteers were used in this study. The odour intensity in the breath after chewing a gum was measured by portable odour sensor device. The odour intensity after chewing the gum was measured over four chewing durations and at four intervals between spitting out and measurement of the odour intensity. The volume of stimulated saliva was measured by calculating the difference in the weight of the gauze before and after chewing to examine the effect of saliva flow. With an increase in chewing duration, odour intensity reduced. The odour intensity was the highest immediately after chewing. There was a positive correlation between odour intensity and gummy jelly‐related masticatory efficiency test value (G‐METV), which was significant for 10‐s chewing. The regression equation was calculated from three objective variables of odour intensity and G‐METV as dependent variable. Pearson's correlation coefficient between G‐METV and the odour intensity‐related masticatory efficiency value (O‐METV) was 0·68. The coefficient of variation of O‐METV was significantly lower than that of G‐METV. These results suggest that the masticatory performance can be estimated by measuring the odour intensity immediately after chewing food containing odour compounds for 10 s.
Children's medicine: What do consumers really want to know?
Authors: Crunkhorn Clara , van Driel Mieke , Nguyen Van , McGuire Treasure 
Published: September 2016

AimThis study explored consumer knowledge gaps and concerns regarding medication use in children.MethodsCalls concerning or made by people under 18 to the pharmacist‐operated, national consumer medicines call centre National Prescribing Service Medicines Line (2002 to June 2010) were analysed. Calls were classified and narratively explored by age group: <1, 1–4, 5–14 and 15–17 years. Consumer Medication Information (CMI) and evidence‐based resources were examined to determine information concordance for common questions.ResultsThere were 14 753 paediatric‐related calls (mean age 4.1 years). Callers were predominantly female (91.5%), mean age was 35.8 years. Most (89.4%) phoned for a child and 2.2% for themselves. Main enquiry types were: lactation (22.1%), treatment/prophylaxis (11.1%), dose (10.2%), adverse reaction (10.0%), interaction (8.4%) and vaccination (8.4%). However, the primary enquiry differed by age group: lactation (<1 year), dosing (1–4, 5–14 years) and interactions (15–17 years). Global concerns were medication safety, with breastfeeding for infants <1 year and age/weight dose clarification for children 1–4 and 5–14 years. In contrast, interaction questions from adolescents concerned nervous system medicines, cold/flu products, contraceptives and recreational drugs. While paracetamol was the primary medication of interest across age groups, the remaining ‘top two’ differed significantly. Inconsistencies identified between CMI and evidence‐based resources contribute to consumer uncertainty.ConclusionsCare givers and older children use a call centre to address their information needs about frequently used and highly accessible medicines, and their concerns vary across paediatric age groups. Inconsistent information provided by CMI on medication use in children contributes to consumer uncertainty and help‐seeking behaviour.