bluuebunny/crossref_metadata_2025_split huggingface dataset:
Principals or puppets? Analysing variation in local political parties’ social policy positions
Authors: Broekema H. B. , Fenger H. J. M. , Van der Waal J. 
Published: May 2020

AbstractThe decentralisation of policy responsibilities from the national to the local level in the domain of social policies is meant to facilitate a better fit to local conditions, and, consequently, inspire local variation in social policy positions. This article examines two questions: (1) to what extent do Dutch local party branches’ social policy positions deviate from their national mother party and local peer parties and (2) do local conditions explain this deviation? To answer these questions, we developed a dataset including 168 local party manifestos from 27 strategically selected municipalities and 8 national party manifestos. Our analyses show limited deviation in local parties’ positions compared to their national mother party and other local branches of their national mother party. This suggests that the social policies addressed in the party manifestos of local parties seem to reflect a process of institutional isomorphism. Furthermore, the limited deviation that does exist in local parties’ social policy positions is not convincingly larger in municipalities (1) that are smaller, (2) that have higher social benefit dependency, or (3) that have high vote shares for local independent challengers. This is contrary to what can be expected based on the contingency theory.
Hearing faces and seeing accents?
Authors: Yu Chen-Wei Felix 
Published: May 2020

Abstract
In this paper, the McGurk effect displayed by native Mandarin Speakers is examined in the light of reaction time
(RT) and response types. Two within-subject factors, FACE and ACCENT, and one between-subject factor, English Proficiency, were
incorporated in the experiment. The results showed that FACE and ACCENT, but not English Proficiency, had effects on the participants’ RT and response types.
When a foreign ACCENT was dubbed onto a familiar FACE, the RT was the longest, and the McGurk effect was most likely to be found. Other kinds of McGurk stimuli composition did not receive different RT but induced different response types. When the FACE was
foreign, regardless of the ACCENT, the participants tended to respond with perceptive illusion. The author concluded that the
expectations of the perceiver influenced the use of multisensory integration and thus the longer RT and the appearance of the McGurk effect.
Have the social classes of yesterday vanished from Africanist issues or are African societies made up of new classes? A French anthropologist’s perspective
Authors: Copans Jean 
Published: May 2020

ABSTRACT
The concept of social class and how it relates to the African context was theorised in France during the 1960s and 1970s in Africanist sociology and anthropology. The author summarises the major contributions of these works as well as providing his own analysis. He concludes that the variety of empirical data and the abrupt shifts in societal evolution of the continent over the past century have unfortunately dictated a speculative and quasi-experimental use of the concept of class in much of the literature. He also comments on the interventions on class that were published in ROAPE and its blog, Roape.net, in recent years.
Generation of quantum coherence in two-qubit cavity system: qubit-dipole coupling and decoherence effects
Authors: Mohamed A-B A , Hessian H A , Eleuch H 
Published: May 2020

Abstract
The intrinsic decoherence effect for two qubits interacting with a coherent field, under the dipole-dipole interaction and two-photon resonance, is analytically described. We investigate numerically the population inversion and the quantum coherence. The results show that the generated mixture entropy and the entanglement negativity, can be enhanced and protected by the dipole-dipole interaction and by reducing the initial coherent field intensity. In particular, we find that, the collapses and revivals of the population inversion present high sensitivity to these physical parameters. The nonlinearity of the two-photon processes leads to a generation of a strong two-qubit entanglement. This generated entanglement depends on the initial coherent field intensity, the dipole-dipole interaction and the intrinsic decoherence.
Coulomb blocking of sequential tunnel ionization in complex systems
Authors: Bart G , Schubert I , Parks A M , Corkum P B , Brabec T 
Published: May 2020

Abstract
When atoms and molecules are exposed to intense low frequency laser fields, the dominant response is sequential tunnel ionization of charge states with increasing ionization potential. Sequential ionization is assumed to proceed as separate one electron processes. The theoretical analysis developed here reveals that in complex systems sequential tunnel ionization can be inhibited by Coulomb blocking. When ionization potentials of subsequent charge states are close to each other, multiple tunneling events can occur during a half cycle and in close proximity, so that a tunneled electron can block the next tunneling electron. In sub-nm clusters driven by near infrared single-cycle pulses, Coulomb blocking reduces two-electron sequential tunneling by up to 2-3 orders of magnitude.
Combinatorial and statistical prediction of gene expression from haplotype sequence
Authors: Alpay Berk A , Demetci Pinar , Istrail Sorin , Aguiar Derek 
Published: May 2020

AbstractMotivationGenome-wide association studies (GWAS) have discovered thousands of significant genetic effects on disease phenotypes. By considering gene expression as the intermediary between genotype and disease phenotype, expression quantitative trait loci studies have interpreted many of these variants by their regulatory effects on gene expression. However, there remains a considerable gap between genotype-to-gene expression association and genotype-to-gene expression prediction. Accurate prediction of gene expression enables gene-based association studies to be performed post hoc for existing GWAS, reduces multiple testing burden, and can prioritize genes for subsequent experimental investigation.ResultsIn this work, we develop gene expression prediction methods that relax the independence and additivity assumptions between genetic markers. First, we consider gene expression prediction from a regression perspective and develop the HAPLEXR algorithm which combines haplotype clusterings with allelic dosages. Second, we introduce the new gene expression classification problem, which focuses on identifying expression groups rather than continuous measurements; we formalize the selection of an appropriate number of expression groups using the principle of maximum entropy. Third, we develop the HAPLEXD algorithm that models haplotype sharing with a modified suffix tree data structure and computes expression groups by spectral clustering. In both models, we penalize model complexity by prioritizing genetic clusters that indicate significant effects on expression. We compare HAPLEXR and HAPLEXD with three state-of-the-art expression prediction methods and two novel logistic regression approaches across five GTEx v8 tissues. HAPLEXD exhibits significantly higher classification accuracy overall; HAPLEXR shows higher prediction accuracy on approximately half of the genes tested and the largest number of best predicted genes (r2&gt;0.1) among all methods. We show that variant and haplotype features selected by HAPLEXR are smaller in size than competing methods (and thus more interpretable) and are significantly enriched in functional annotations related to gene regulation. These results demonstrate the importance of explicitly modeling non-dosage dependent and intragenic epistatic effects when predicting expression.Availability and implementationSource code and binaries are freely available at https://github.com/rapturous/HAPLEX.Supplementary informationSupplementary data are available at Bioinformatics online.
GDASC: a GPU parallel-based web server for detecting hidden batch factors
Authors: Wang Xiao , Yi Haidong , Wang Jia , Liu Zhandong , Yin Yanbin , Zhang Han 
Published: May 2020

Abstract

Summary
We developed GDASC, a web version of our former DASC algorithm implemented with GPU. It provides a user-friendly web interface for detecting batch factors. Based on the good performance of DASC algorithm, it is able to give the most accurate results. For two steps of DASC, data-adaptive shrinkage and semi-non-negative matrix factorization, we designed parallelization strategies facing convex clustering solution and decomposition process. It runs more than 50 times faster than the original version on the representative RNA sequencing quality control dataset. With its accuracy and high speed, this server will be a useful tool for batch effects analysis.

Availability and implementation
http://bioinfo.nankai.edu.cn/gdasc.php.

Contact
zhanghan@nankai.edu.cn

Supplementary information
Supplementary data are available at Bioinformatics online.
Characteristics, management and outcomes of atypical haemolytic uraemic syndrome in kidney transplant patients: a retrospective national study
Authors: Portoles José , Huerta Ana , Arjona Emilia , Gavela Eva , Agüera Marisa , Jiménez Carlos , Cavero Teresa , Marrero Domingo , Rodríguez de Córdoba Santiago , Diekmann Fritz ,   Matrix Investigators, Portolés José , Huerta Ana , Arjona Emilia , Gavela Eva , Luisa Maria , Jiménez Carlos , Cavero Teresa , Marrero Domingo , Redondo Dolores , Ruiz Juan Carlos , Ferrero Maria Luisa Rodríguez , Carreño Agustín , de Córdoba Santiago Rodríguez , Diekmann Fritz 
Published: May 2020

Abstract

Background
Kidney transplantation (KTx) is a strong trigger for the development of either recurrent or de novo atypical haemolytic uraemic syndrome (aHUS). According to previous studies, eculizumab (ECU) is effective for prophylaxis and for treatment of recurrence.

Methods
We evaluated the experiences of Spanish patients with recurrent and de novo aHUS associated with KTx, treated or not treated with ECU. In the de novo group, we classified patients as having early de novo (during the first month) or late de novo aHUS (subsequent onset).

Results
We analysed 36 cases of aHUS associated with KTx. All of the 14 patients with pre-KTx diagnosis of aHUS were considered to have high or moderate risk of recurrence. Despite receiving grafts from suboptimal donors, prophylactic ECU was effective for avoiding recurrence. The drug was stopped only in two cases with low–moderate risk of recurrence and was maintained in high-risk patients with no single relapse. There were 22 de novo aHUS cases and 16 belonged to the early de novo group. The median time of onset in the late group was 3.4 years. The early group had a better response to ECU than the late group, probably due to earlier diagnosis and use of the drug. No genetic pathogenic variant was detected in de novo aHUS cases, suggesting a secondary profile of the disease. ECU was stopped in all de novo patients with no relapses. ECU was well tolerated in all cases.

Conclusions
Both groups (pre-aHUS and de novo) presented different clinical profiles, management approaches and outcomes. One should consider aHUS regardless of time after KTx. Genetic studies are crucial to stratify risks of relapse and to determine necessary lengths of treatment. We suggest short ECU treatment for de novo cases without pathogenic mutation and that ECU treatment be considered pre-emptively for patients with moderate or high risk of recurrence.
Annual adult survival drives trends in Arctic-breeding shorebirds but knowledge gaps in other vital rates remain
Authors: Weiser Emily L , Lanctot Richard B , Brown Stephen C , Gates H River , Bêty Joël , Boldenow Megan L , Brook Rodney W , Brown Glen S , English Willow B , Flemming Scott A , Franks Samantha E , Gilchrist H Grant , Giroux Marie-Andrée , Johnson Andrew , Kendall Steve , Kennedy Lisa V , Koloski Laura , Kwon Eunbi , Lamarre Jean-François , Lank David B , Latty Christopher J , Lecomte Nicolas , Liebezeit Joseph R , McGuire Rebecca L , McKinnon Laura , Nol Erica , Payer David , Perz Johanna , Rausch Jennie , Robards Martin , Saalfeld Sarah T , Senner Nathan R , Smith Paul A , Soloviev Mikhail , Solovyeva Diana , Ward David H , Woodard Paul F , Sandercock Brett K 
Published: May 2020

AbstractConservation status and management priorities are often informed by population trends. Trend estimates can be derived from population surveys or models, but both methods are associated with sources of uncertainty. Many Arctic-breeding shorebirds are thought to be declining based on migration and/or overwintering population surveys, but data are lacking to estimate the trends of some shorebird species. In addition, for most species, little is known about the stage(s) at which population bottlenecks occur, such as breeding vs. nonbreeding periods. We used previously published and unpublished estimates of vital rates to develop the first large-scale population models for 6 species of Arctic-breeding shorebirds in North America, including separate estimates for 3 subspecies of Dunlin. We used the models to estimate population trends and identify life stages at which population growth may be limited. Our model for the arcticola subspecies of Dunlin agreed with previously published information that the subspecies is severely declining. Our results also linked the decline to the subspecies’ low annual adult survival rate, thus potentially implicating factors during the nonbreeding period in the East Asian–Australasian Flyway. However, our trend estimates for all species showed high uncertainty, highlighting the need for more accurate and precise estimates of vital rates. Of the vital rates, annual adult survival had the strongest influence on population trend in all taxa. Improving the accuracy, precision, and spatial and temporal coverage of estimates of vital rates, especially annual adult survival, would improve demographic model-based estimates of population trends and help direct management to regions or seasons where birds are subject to higher mortality.
Electrophysiological effects of non-vitamin K antagonist oral anticoagulants on atrial repolarizing potassium channels
Authors: Wiedmann Felix , Schlund Daniel , Kraft Manuel , Nietfeld Jendrik , Katus Hugo A , Schmidt Constanze , Thomas Dierk 
Published: May 2020

Abstract

Aims
Non-vitamin K antagonist oral anticoagulants (NOACs) are widely used in the prevention of stroke and systemic embolism in patients with non-valvular atrial fibrillation (AF). The efficacy of NOACs has been attributed in part to pleiotropic effects that are mediated through effects on thrombin, factor Xa, and their respective receptors. Direct pharmacological effects of NOACs and cardiac ion channels have not been addressed to date. We hypothesized that the favourable clinical outcome of NOAC use may be associated with previously unrecognized effects on atrial repolarizing potassium channels.

Methods and results
This study was designed to elucidate acute pharmacological effects of NOACs on cloned ion channels Kv11.1, Kv1.5, Kv4.3, Kir2.1, Kir2.2, and K2P2.1 contributing to IKr, IKur, Ito, IK1, and IK2P K+ currents. Human genes, KCNH2, KCNA5, KCND3, KCNJ2, KCNJ12, and KCNK2, were heterologously expressed in Xenopus laevis oocytes, and currents were recorded using voltage-clamp electrophysiology. Apixaban, dabigatran, edoxaban, and rivaroxaban applied at 1 µM did not significantly affect peak current amplitudes of Kv11.1, Kv1.5, Kv4.3, Kir2.1, Kir2.2, or K2P2.1 K+ channels. Furthermore, biophysical characterization did not reveal significant effects of NOACs on current–voltage relationships of study channels.

Conclusion
Apixaban, dabigatran, edoxaban, and rivaroxaban did not exhibit direct functional interactions with human atrial K+ channels underlying IKr, IKur, Ito, IK1, and IK2P currents that could account for beneficial clinical outcome associated with the drugs. Indirect or chronic effects and potential underlying signalling mechanisms remain to be investigated.
Quality of clinical assessment and child mortality: a three-country cross-sectional study
Authors: Perales Nicole A , Wei Dorothy , Khadka Aayush , Leslie Hannah H , Hamadou Saïdou , Yama Gervais Chamberlin , Robyn Paul Jacob , Shapira Gil , Kruk Margaret E , Fink Günther 
Published: May 2020

Abstract
This analysis describes specific gaps in the quality of health care in Central Africa and assesses the association between quality of clinical care and mortality at age 2–59 months. Regionally representative facility and household surveys for the Democratic Republic of the Congo, Cameroon and Central African Republic were collected between 2012 and 2016. These data are novel in linking facilities with households in their catchment area. Compliance with diagnostic and danger sign protocols during sick-child visits was observed by trained assessors. We computed facility- and district-level compliance indicators for patients aged 2–59 months and used multivariate multi-level logistic regression models to estimate the association between clinical assessment quality and mortality at age 2–59 months in the catchment areas of the observed facilities. A total of 13 618 live births were analysed and 1818 sick-child visits were directly observed and used to rate 643 facilities. Eight percent of observed visits complied with 80% of basic diagnostic protocols, and 13% of visits fully adhered to select general danger sign protocols. A 10% greater compliance with diagnostic protocols was associated with a 14.1% (adjusted odds ratio (aOR) 95% CI: 0.025–0.244) reduction in the odds of mortality at age 2–59 months; a 10% greater compliance with select general danger sign protocols was associated with a 15.3% (aOR 95% CI: 0.058–0.237) reduction in the same odds. The results of this article suggest that compliance with recommended clinical protocols remains poor in many settings and improvements in mortality at age 2–59 months could be possible if compliance were improved.
An Evaluation of Baseline Kidney Function in the REPRIEVE Trial of Pitavastatin in Human Immunodeficiency Virus
Authors: Overton Edgar T , Kantor Amy , Fitch Kathleen V , Muntner Paul , Supparatpinyo Khuanchai , Mosepele Mosepele , Mohapi Lerato , Cardoso Sandra Wagner , Patil Sandesh , de Lacerda Marcus V G , McComsey Grace , Aberg Judith A , Douglas Pamela S , Grinspoon Steven K , Ribaudo Heather , Wyatt Christina M 
Published: May 2020

AbstractBackgroundChronic kidney disease is a common comorbid condition among persons living with human immunodeficiency virus (PWH). We characterized baseline kidney function in the REPRIEVE (Randomized Trial to Prevent Vascular Events in HIV) trial cohort.MethodsREPRIEVE enrolled PWH with low to moderate cardiovascular risk based on traditional risk factors to evaluate the effect of statin therapy on cardiovascular events. We determined baseline estimated glomerular filtration rate (eGFR) with the Chronic Kidney Disease Epidemiology Collaboration (CKD-EPI), Modification of Diet in Renal Disease, and Cockcroft-Gault equations, and we evaluated baseline factors associated with eGFR &lt;90 mL/min/1.73 m2 by logistic regression. We performed Bland-Altman plots and scatterplots to assess agreement between equations.ResultsAmong 7770 participants enrolled, the median age was 50 years, 31% were female (natal sex), 43% black or African American and 15% Asian, the median body mass index (calculated as calculated as weight in kilograms divided by height in meters squared) was 25.8, and the median CD4 cell count 620/µL. The median CKD-EPI eGFR was 97 mL/min/1.73 m2, and 38% had an eGFR &lt;90 mL/min/1.73 m2. In the adjusted model, factors associated with eGFR &lt;90 mL/min/1.73 m2 included white race, older age, higher body mass index, high-income region of enrollment, hypertension, and tenofovir disoproxil fumarate. The CKD-EPI and Modification of Diet in Renal Disease equations demonstrated strong agreement, particularly at lower eGFR values. Overall, there was 56% concordance between the 3 equations (categories &lt;60, 60 to &lt;90, ≥90 mL/min), improving to 73% after accounting for individual body surface area.ConclusionsREPRIEVE enrolled a diverse cohort including a substantial number of PWH with reduced kidney function. Factors associated with reduced eGFR included traditional risk factors and tenofovir disoproxil fumarate exposure. Three commonly used equations have only fair agreement, with potential implications for both clinical care and epidemiologic studies.Clinical Trials RegistrationNCT02344290.
Adenovirus Viral Kinetics and Mortality in Ex Vivo T Cell-Depleted Hematopoietic Cell Transplant Recipients With Adenovirus Infection From a Single Center
Authors: Lee Yeon Joo , Fang Jiaqi , Zavras Phaedon D , Prockop Susan E , Boulad Farid , Tamari Roni , Perales Miguel Angel , Papadopoulos Esperanza B , Jakubowski Ann A , Giralt Sergio A , Papanicolaou Genovefa A 
Published: May 2020

Abstract

Background
We report on predictors of adenovirus (ADV) viremia and correlation of ADV viral kinetics with mortality in ex vivo T-cell depleted (TCD) hematopoietic cell transplant (HCT).

Methods
T cell-depleted HCT recipients from January 1, 2012 through September 30, 2018 were prospectively monitored for ADV in the plasma through Day (D) +100 posttransplant or for 16 weeks after the onset of ADV viremia. Adenovirus viremia was defined as ≥2 consecutive viral loads (VLs) ≥1000 copies/mL through D +100. Time-averaged area under the curve (AAUC) or peak ADV VL through 16 weeks after onset of ADV viremia were explored as predictors of mortality in Cox models.

Results
Of 586 patients (adult 81.7%), 51 (8.7%) developed ADV viremia by D +100. Age &lt;18 years, recipient cytomegalovirus seropositivity, absolute lymphocyte count &lt;300 cells/µL at D +30, and acute graft-versus-host disease were predictors of ADV viremia in multivariate models. Fifteen (29%) patients with ADV viremia died by D +180; 8 of 15 (53%) died from ADV. Peak ADV VL (hazard ratio [HR], 2.25; 95% confidence interval [CI], 1.52–3.33) and increasing AAUC (HR, 2.95; 95% CI, 1.83–4.75) correlated with mortality at D +180.

Conclusions
In TCD HCT, peak ADV VL and ADV AAUC correlated with mortality at D +180. Our data support the potential utility of ADV viral kinetics as endpoints in clinical trials of ADV therapies.
Recent progress in synchrotron radiation 3D–4D nano-imaging based on X-ray full-field microscopy
Authors: Takeuchi Akihisa , Suzuki Yoshio 
Published: May 2020

Abstract
The advent of high-flux, high-brilliance synchrotron radiation (SR) has prompted the development of high-resolution X-ray imaging techniques such as full-field microscopy, holography, coherent diffraction imaging and ptychography. These techniques have strong potential to establish non-destructive three- and four-dimensional nano-imaging when combined with computed tomography (CT), called nano-tomography (nano-CT). X-ray nano-CTs based on full-field microscopy are now routinely available and widely used. Here we discuss the current status and some applications of nano-CT using a Fresnel zone plate as an objective. Optical properties of full-field microscopy, such as spatial resolution and off-axis aberration, which determine the effective field of view, are also discussed, especially in relation to 3D tomographic imaging.