bluuebunny/crossref_metadata_2025_split huggingface dataset:
Evaluation of genotype quality parameters for SowPro90, a new genotyping array for swine1
Authors: Wijesena Hiruni R , Rohrer Gary A , Nonneman Dan J , Keel Brittney N , Petersen Jessica L , Kachman Stephen D , Ciobanu Daniel C 
Published: May 2019

Abstract
Understanding early predictors of sow fertility has the potential to improve genomic predictions. A custom SNP array (SowPro90 produced by Affymetrix) was developed to include genetic variants overlapping quantitative trait loci for age at puberty, one of the earliest indicators of sow fertility, as well as variants related to innate and adaptive immunity. The polymorphisms included in the custom genotyping array were identified using multiple genomic approaches including deep genomic and transcriptomic sequencing and genome-wide associations. Animals from research and commercial populations (n = 2,586) were genotyped for 103,476 SNPs included in SowPro90. To assess the quality of data generated, genotype concordance was evaluated between the SowPro90 and Porcine SNP60 BeadArray using a subset of common SNP (n = 44,708) and animals (n = 277). The mean genotype concordance rate per SNP was 98.4%. Differences in distribution of data quality were observed between the platforms indicating the need for platform specific thresholds for quality parameters. The optimal thresholds for SowPro90 (≥97% SNP and ≥93% sample call rate) were obtained by analyzing the data quality distribution and genotype concordance per SNP across platforms. At ≥97% SNP call rate, there were 42,151 SNPs (94.3%) retained with a mean genotype concordance of 98.6% across platforms. Similarly, ≥94% SNPs and ≥85% sample call rates were established as thresholds for Porcine SNP60 BeadArray. At ≥94% SNPs call rate, there were 41,043 SNPs (91.8%) retained with a mean genotype concordance of 98.6% across platforms. Final evaluation of SowPro90 array content (n = 103,476) at ≥97% SNPs and ≥93% sample call rates allowed retention of 89,040 SNPs (86%) for downstream analysis. The findings and strategy for quality control could be helpful in identifying consistent, high-quality genotypes for genomic evaluations, especially when integrating genotype data from different platforms.
Delegation with a Reciprocal Agent
Authors: De Chiara Alessandro , Manna Ester 
Published: May 2019

Abstract
We consider a model in which a principal may delegate the choice of a project to a better informed agent. The preferences of the agent and the principal about which project should be undertaken may be discordant. Moreover, the agent benefits from being granted more discretion in the project choice and may be motivated by reciprocity. We find that the relationship between the agent’s reciprocity and discretion crucially depends on the conflict of interest with the principal. When preferences are more congruent (discordant), discretion is broader (more limited) if the agent is more reciprocal. Hence, reciprocity mitigates (exacerbates) a mild (severe) conflict of interest. We also present supportive evidence for the predictions of our model using the German Socio-Economic Panel dataset. (JEL D03, D82, D86)
Vegetation structure shapes small mammal communities in African savannas
Authors: Loggins Anne A , Monadjem Ara , Kruger Laurence M , Reichert Brian E , McCleery Robert A 
Published: May 2019

Abstract
Disturbance by large herbivores, fires, and humans shapes the structure of savannas, altering the amount of woody vegetation and grass. Due to change in the intensity and frequency of these disturbances, savannas are shifting toward grass-dominated or shrub-dominated systems, likely altering animal communities. Small mammals are critical components of savannas, and their distributions likely are affected by these ecosystem-wide changes in vegetative cover. We assessed the responses of small mammals to a gradient of woody cover in low-lying savannas of southeastern Africa. In Kruger National Park (South Africa) and in three nearby reserves (Eswatini), we livetrapped for over 2 years to build multispecies occupancy models that assessed the responses of the small mammal community to grass and woody cover. Overall, whole-community occupancy increased with grass biomass. More species responded positively to woody cover than to grass biomass, but woody cover was associated with reduced occurrence of one species (Mastomys natalensis). Our results suggest that an increase in grass biomass enhances whole-community occupancy of small mammals, but regional diversity is likely to be higher in areas that contain patches of high grass biomass as well as patches of woody cover.
Auto-regulatory feedback by RNA-binding proteins
Authors: Müller-McNicoll Michaela , Rossbach Oliver , Hui Jingyi , Medenbach Jan 
Published: May 2019

AbstractRNA-binding proteins (RBPs) are key regulators in post-transcriptional control of gene expression. Mutations that alter their activity or abundance have been implicated in numerous diseases such as neurodegenerative disorders and various types of cancer. This highlights the importance of RBP proteostasis and the necessity to tightly control the expression levels and activities of RBPs. In many cases, RBPs engage in an auto-regulatory feedback by directly binding to and influencing the fate of their own mRNAs, exerting control over their own expression. For this feedback control, RBPs employ a variety of mechanisms operating at all levels of post-transcriptional regulation of gene expression. Here we review RBP-mediated autogenous feedback regulation that either serves to maintain protein abundance within a physiological range (by negative feedback) or generates binary, genetic on/off switches important for e.g. cell fate decisions (by positive feedback).
Physical Activity and the Risk of Liver Cancer: A Systematic Review and Meta-Analysis of Prospective Studies and a Bias Analysis
Authors: Baumeister Sebastian E , Leitzmann Michael F , Linseisen Jakob , Schlesinger Sabrina 
Published: May 2019

Abstract

Background
Physical inactivity is an established risk factor for several cancers of the digestive system and female reproductive organs, but the evidence for liver cancers is less conclusive.

Methods
The aim of this study was to synthesize prospective observational studies on the association of physical activity and liver cancer risk by means of a systematic review and meta-analysis. We searched Medline, Embase, and Scopus from inception to January 2019 for prospective studies investigating the association of physical activity and liver cancer risk. We calculated mean hazard ratios (HRs) and 95% confidence intervals (CIs) using a random-effects model. We quantified the extent to which an unmeasured confounder or an unaccounted selection variable could shift the mean hazard ratio to the null.

Results
Fourteen prospective studies, including 6,440 liver cancers, were included in the systematic review and meta-analysis. The mean hazard ratio for high compared with low physical activity was 0.75 (95% CI = 0.63 to 0.89; 95% prediction interval = 0.52 to 1.07; I² = 64.2%). We estimated that 67.6% (95% CI = 56.6% to 78.5%) of all true effect estimates would have a hazard ratio less than 0.8. Bias analysis suggested than an unobserved confounder would have to be associated with a 1.99-fold increase in the risk of physical activity or liver cancer to explain away the observed mean hazard ratio. An unaccounted for selection variable would have to be related to exposure and endpoint with a relative risk of 1.58 to explain away the mean hazard ratio.

Conclusions
Physical activity is inversely related to the risk of liver cancer. Further studies with objectively measured physical activity and quasi-experimental designs addressing confounding are needed.
The Relationship Between Insomnia and Cognitive Impairment in Breast Cancer Survivors
Authors: Liou Kevin T , Ahles Tim A , Garland Sheila N , Li Q Susan , Bao Ting , Li Yuelin , Root James C , Mao Jun J 
Published: May 2019

Abstract

Background
Cancer-related cognitive impairment is an emerging public health burden. Growing research suggests that sleep disturbances contribute to poor cognition. Our study aimed to evaluate the association between insomnia and cognitive impairment in breast cancer survivors.

Methods
We analyzed cross-sectional data from a cohort study of postmenopausal women with stage 0–III hormone receptor-positive breast cancer on aromatase inhibitor therapy. The study was conducted between November 2011 and April 2015 at an academic cancer center (Philadelphia, PA). Insomnia was assessed with the Insomnia Severity Index. Perceived cognitive impairment was assessed with the cognitive subscale of the Breast Cancer Prevention Trial Symptom Checklist. We used linear regression to evaluate the association between insomnia and perceived cognitive impairment.

Results
Among 1072 patients, 556 (51.9%) reported insomnia and 847 (79.0%) were bothered by cognitive symptoms (forgetfulness, difficulty concentrating, distractibility). Greater perceived cognitive impairment was reported by patients with mild insomnia (regression coefficient [β] = 0.35, 95% confidence interval [CI] = 0.23 to 0.46, P &lt; .001), moderate insomnia (β = 0.51, 95% CI = 0.36 to 0.65, P &lt; .001), and severe insomnia (β = 0.94, 95% CI = 0.67 to 1.21, P &lt; .001), compared with those without insomnia. Greater perceived cognitive impairment was also associated with patients younger than 55 years (β = 0.30, 95% CI = 0.15 to 0.45, P &lt; .001), taxane-based chemotherapy (β = 0.11, 95% CI = 0.004 to 0.22, P = .04), anxiety (β = 0.47, 95% CI = 0.30 to 0.64, P &lt; .001), and depression (β = 0.65, 95% CI = 0.35 to 0.94, P &lt; .001).

Conclusions
Among postmenopausal breast cancer survivors receiving aromatase inhibitor therapy, insomnia and cognitive impairment are prevalent and characterized by a graded association, in which severity of perceived cognitive impairment increases as insomnia severity increases. Our findings warrant further research to determine whether addressing sleep is a strategy to improve management of cancer-related cognitive impairment.
Robust velocity dispersion and binary population modelling of the ultrafaint dwarf galaxy Reticulum II
Authors: Minor Quinn E , Pace Andrew B , Marshall Jennifer L , Strigari Louis E 
Published: May 2019

AbstractWe apply a Bayesian method to model multi-epoch radial velocity measurements in the ultrafaint dwarf galaxy Reticulum II, fully accounting for the effects of binary orbital motion and systematic offsets between different spectroscopic data sets. We find that the binary fraction of Ret II is higher than 0.5 at the 90 per cent confidence level, if the mean orbital period is assumed to be 30 yr or longer. Despite this high-binary fraction, we infer a best-fitting intrinsic dispersion of 2.8$_{-1.2}^{+0.7}$ km s−1, which is smaller than the previous estimates but still indicates Ret II is a dark matter dominated galaxy. We likewise infer a ≲ 1 per cent probability that Ret II’s dispersion is due to binaries rather than dark matter (which would correspond to the regime $M/L \lesssim 2\, \mathrm{M}_\odot /\mathrm{L}_\odot$). Our inference of a high-close binary fraction in Ret II echoes previous results for the Segue 1 ultrafaint dwarf and is consistent with studies of Milky Way halo stars that indicate a high-close binary fraction tends to exist in metal-poor environments.
Evolution of the AGN UV luminosity function from redshift 7.5
Authors: Kulkarni Girish , Worseck Gábor , Hennawi Joseph F 
Published: May 2019

ABSTRACTDeterminations of the ultraviolet (UV) luminosity function of active galactic nuclei (AGN) at high redshifts are important for constraining the AGN contribution to reionization and understanding the growth of supermassive black holes. Recent inferences of the luminosity function suffer from inconsistencies arising from inhomogeneous selection and analysis of data. We address this problem by constructing a sample of more than 80 000 colour-selected AGN from redshift $z$ = 0 to 7.5 using multiple data sets homogenized to identical cosmologies, intrinsic AGN spectra, and magnitude systems. Using this sample, we derive the AGN UV luminosity function from redshift $z$ = 0 to 7.5. The luminosity function has a double power-law form at all redshifts. The break magnitude M* shows a steep brightening from M* ∼ −24 at $z$ = 0.7 to M* ∼ −29 at $z$ = 6. The faint-end slope β significantly steepens from −1.9 at $z$ < 2.2 to −2.4 at $z$ ≃ 6. In spite of this steepening, the contribution of AGN to the hydrogen photoionization rate at $z$ ∼ 6 is subdominant (<3 per cent), although it can be non-negligible (∼10 per cent) if these luminosity functions hold down to M1450 = −18. Under reasonable assumptions, AGN can reionize He ii by redshift $z$ = 2.9. At low redshifts ($z$ < 0.5), AGN can produce about half of the hydrogen photoionization rate inferred from the statistics of H i absorption lines in the intergalactic medium. Our analysis also reveals important systematic errors in the data, which need to be addressed and incorporated in the AGN selection function in future in order to improve our results. We make various fitting functions, codes, and data publicly available.
Differences in spatial distribution between WHO 2016 low-grade glioma molecular subgroups
Authors: Wijnenga Maarten M J , van der Voort Sebastian R , French Pim J , Klein Stefan , Dubbink Hendrikus J , Dinjens Winand N M , Atmodimedjo Peggy N , de Groot Marius , Kros Johan M , Schouten Joost W , Dirven Clemens M F , Vincent Arnaud J P E , Smits Marion , van den Bent Martin J 
Published: May 2019

Abstract

Background
Several studies reported a correlation between anatomic location and genetic background of low-grade gliomas (LGGs). As such, tumor location may contribute to presurgical clinical decision-making. Our purpose was to visualize and compare the spatial distribution of different WHO 2016 gliomas, frequently aberrated single genes and DNA copy number alterations within subgroups, and groups of postoperative tumor volume.

Methods
Adult grade II glioma patients (WHO 2016 classified) diagnosed between 2003 and 2016 were included. Tumor volume and location were assessed with semi-automatic software. All volumes of interest were mapped to a standard reference brain. Location heatmaps were created for each WHO 2016 glioma subgroup, frequently aberrated single genes and copy numbers (CNVs), as well as heatmaps according to groups of postoperative tumor volume. Differences between subgroups were determined using voxelwise permutation testing.

Results
A total of 110 IDH mutated astrocytoma patients, 92 IDH mutated and 1p19q co-deleted oligodendroglioma patients, and 22 IDH wild-type astrocytoma patients were included. We identified small regions in which specific molecular subtypes occurred more frequently. IDH-mutated LGGs were more frequently located in the frontal lobes and IDH wild-type tumors more frequently in the basal ganglia of the right hemisphere. We found no localizations of significant difference for single genes/CNVs in subgroups, except for loss of 9p in oligodendrogliomas with a predilection for the left parietal lobes. More extensive resections in LGG were associated with frontal locations.

Conclusions
WHO low-grade glioma subgroups show differences in spatial distribution. Our data may contribute to presurgical clinical decision-making in LGG patients.
Poor work ability increases sickness absence over 10 years
Authors: Palmlöf L , Skillgate E , Talbäck M , Josephson M , Vingård E , Holm L W 
Published: May 2019

AbstractBackgroundLittle is known about the predictive value of single items from the work ability index (WAI) on the risk of sickness absence over several years, and whether such risk varies across age groups.AimsThe aim of the study was to investigate whether poor self-perceived physical and mental work ability among employees in the public sector are associated with long-term sickness absence over a 10-year period.MethodsThe study was based on a prospective cohort of employees within the public sector in Sweden reporting ‘good health for working’. Baseline information was collected with questionnaires from 2000 to 2003. Poor physical and mental work ability in relation to work demands were assessed with two items from the WAI. The outcome was the number of years of long-term sickness absence between 2003 and 2012. Long-term sickness absence was defined as ≥28 days of sickness and this information was retrieved from Swedish National Registers. Crude and adjusted incidence rate ratios were calculated with analyses stratified by age.ResultsCompared with those reporting very good physical work ability, employees reporting any lower grade of physical work ability had a higher risk of long-term sickness absence across all age strata, with higher risk estimates in the highest age groups and 6-fold increased risk in the oldest age group. Similar results were found for mental work ability with an almost 4-fold increased risk in the highest age group.ConclusionsSelf-reported physical and mental poor work ability are associated with long-term sickness absence during the subsequent 10 years. The risk increases with age.
A regularization approach to the minimum distance estimation: application to structural macroeconomic estimation using IRFs
Authors: Sokullu Senay 
Published: May 2019

AbstractThis article considers the invertibility problem of the optimal weighting matrix encountered during Impulse Response Function Matching Estimation (IRFME) of Dynamic Stochastic General Equilibrium (DSGE) Models. We propose to use a regularized inverse and derive the asymptotic properties of the estimator. We show that the asymptotic distribution of our estimator converges to that of the optimal estimator which has important implications for testing the fit of the model. We demonstrate the small sample properties of the estimator by Monte Carlo simulation exercises. Finally, we use our estimator to estimate the model in Altig et al.
Opinions et positions de médecins à l’endroit de la punition corporelle comme pratique parentale disciplinaire
Authors: Clément Marie-Ève , Gagné Marie-Hélène , Dufour Sarah , Frappier Jean-Yves 
Published: May 2019

RésuméContexte de l’étudeLes médecins sont parmi les professionnels les plus sollicités par les parents pour obtenir des conseils sur l’exercice du rôle parental. Pourtant, ils sont rarement formés pour informer les parents, et particulièrement en ce qui concerne la légitimité des pratiques disciplinaires comme la punition corporelle (PC).ObjectifsCette étude vise à documenter les attitudes de médecins québécois en faveur de la PC ainsi que leur pratique de soutien auprès des parents.MéthodesAu total 113 médecins œuvrant au moins 20% du temps avec des enfants mineurs ou leurs parents ont complété un sondage en ligne sur leurs caractéristiques personnelles et professionnelles, leurs connaissances et attitudes face à la PC et leurs pratiques de soutien.RésultatsLes résultats montrent que les répondants connaissent bien les balises légales de l’article 43 du Code criminel canadien qui encadrent le recours aux PC et qu’ils sont en désaccord avec cette méthode disciplinaire. Lorsqu’ils soupçonnent une situation de PC envers un enfant, les médecins répondants offrent diverses modalités de soutien aux parent (ex.: aborder le sujet, proposer d’autres pratiques disciplinaires), ce qui est moins souvent le cas lorsque la situation implique un adolescent. Enfin, les résultats montrent que certains facteurs sont associés aux pratiques de soutien des répondants, dont les attitudes face aux PC et le sentiment d’être suffisamment formé pour aborder les pratiques disciplinaires avec les parents.ConclusionsCes résultats soulignent l’importance d’outiller et de soutenir les médecins dans leurs interventions auprès des parents en difficulté.
The Alkaline Lamprophyres of the Dolomitic Area (Southern Alps, Italy): Markers of the Late Triassic Change from Orogenic-like to Anorogenic Magmatism
Authors: Casetta Federico , Ickert Ryan B , Mark Darren F , Bonadiman Costanza , Giacomoni Pier Paolo , Ntaflos Theodoros , Coltorti Massimo 
Published: May 2019

AbstractWe present the first complete petrological, geochemical and geochronological characterization of the oldest lamprophyric rocks in Italy, which crop out around Predazzo (Dolomitic Area), with the aim of deciphering their relationship with Triassic magmatic events across the whole of the Southern Alps. Their Mg# of between 37 and 70, together with their trace element contents, suggests that fractional crystallization was the main process responsible for their differentiation, together with small-scale mixing, as evidenced by some complex amphibole textures. Moreover, the occurrence of primary carbonate ocelli suggests an intimate association between the alkaline lamprophyric magmas and a carbonatitic melt. 40Ar/39Ar data show that the lamprophyres were emplaced at 219·22 ± 0·73 Ma (2σ; full systematic uncertainties), around 20 Myr after the high-K calc-alkaline to shoshonitic, short-lived, Ladinian (237–238 Ma) magmatic event of the Dolomitic Area. Their trace element and Sr–Nd isotopic signatures (87Sr/86Sri = 0·7033–0·7040; 143Nd/144Ndi = 0·51260–0·51265) are probably related to a garnet–amphibole-bearing lithosphere interacting with an asthenospheric component, significantly more depleted than the mantle source of the high-K calc-alkaline to shoshonitic magmas. These features suggest that the Predazzo lamprophyres belong to the same alkaline–carbonatitic magmatic event that intruded the mantle beneath the Southern Alps (e.g. Finero peridotite) between 190 and 225 Ma. In this scenario, the Predazzo lamprophyres cannot be considered as a late-stage pulse of the orogenic-like Ladinian magmatism of the Dolomitic Area, but most probably represent a petrological bridge to the opening of the Alpine Tethys.
Exploring the Meaning of Cognitive Behavioral Therapy for Insomnia for Patients with Chronic Pain
Authors: Koffel Erin , Amundson Erin , Wisdom Jennifer P 
Published: May 2019

AbstractObjectiveInsomnia is one of the most common, persistent, and distressing symptoms associated with chronic pain. Cognitive behavioral therapy for insomnia (CBT-I) is the firstline treatment for insomnia, but patient preferences and perspectives about CBT-I within the context of chronic pain are unknown. The current qualitative study sought to understand the experience of CBT-I among patients with chronic pain, including aspects of CBT-I that were found to be difficult (e.g., pain as a specific barrier to adherence/dropout), changes in sleep and pain functioning after CBT-I, and aspects of CBT-I that were appreciated.DesignQualitative semistructured interviews.MethodsWe conducted individual semistructured interviews with 17 veterans with chronic pain and insomnia who had recently participated in CBT-I, as well as their CBT-I therapists, and used thematic analysis to identify conceptual themes.ResultsResults revealed that patients and CBT-I therapists found changing sleep habits during CBT-I challenging due to anxiety and temporary increases in fatigue, but did not identify major pain-related barriers to adhering to CBT-I recommendations; patients experienced better sleep, mood, energy, and socialization after CBT-I despite minimal changes in pain intensity; and patients highly valued CBT-I as a personalized treatment for sleep and strongly recommended it for other patients with chronic pain.ConclusionsFindings of improved sleep and functional outcomes support efforts to incorporate CBT-I into chronic pain treatment, including educating patients and providers about the strong feasibility of improving sleep and quality of life despite ongoing pain.