bluuebunny/crossref_metadata_2025_split huggingface dataset:
Endoprothetik bei Erwachsenen mit juveniler idiopathischer Arthritis
Authors: Haas J.-P. , Arbogast M. 
Published: August 2018

ZusammenfassungProgressive Verlaufsformen der JIA, die durch medikamentöse Behandlung wenig beeinflussbar sind, münden nicht selten in eine endoprothetische Versorgung vor dem fünften Lebensjahrzent. Durch den Beginn im Kindesoder Jugendalter werden Wachstum und physiologische Gelenkentwicklung verändert. Daraus resultierende Bewegungseinschränkungen und Gelenkfehlstellungen beeinflussen Implantatwahl und Weichteilbehand-lung. Schmerzlinderung und Verbesserung der Lebensqualität nach endoprothetischer Versorgung sind beeindruckend. Dennoch ist die Lebensplanung mit Endoprothesen unterschiedlich zu prognostizieren und abhängig vom Implantationsort.
Rationelles Screening bei Nebennierentumoren
Authors: Willenberg Holger , Kupfer Sophie 
Published: August 2018

AbstractThe characterization of adrenal tumors may become difficult for different reasons. Medical imaging is insufficient to establish a diagnosis, clinical symtoms may vary and medication interfers with lab analysis. Furthermore, hormonal measurements gain diagnostic power with endocrine function tests. This article reviews diagnostic and therapeutic strategies in the management of patients with adrenal tumors.
Mortalität und ihre Ursachen in einer deutschen Kohorte mit Typ-1-Diabetes mellitus in einer 20-jährigen Nachbeobachtung: Die JEVIN-Studie
Authors: Heller Tabitha , Kloos Christof , Lehmann Thomas , Schiel Ralf , Lorkowski Stefan , Wolf Gunter , Müller Ulrich , Müller Nicolle 
Published: August 2018

Zusammenfassung
Hintergrund und Ziel Die JEVIN-Studie begann 1989/90 als Querschnittsuntersuchung in Jena. Nach einer Nachbeobachtungszeit von über 20 Jahren erfolgte die Bestimmung der Mortalität in der Gruppe der an der JEVIN-Studie teilnehmenden Typ-1-Diabetes-Patienten.
Patienten und Methodik 103 (78,6 %) der 131 Patienten, die seit Beginn an der JEVIN-Studie teilnahmen, konnten untersucht werden. 38 Personen (36,9 %) waren zwischenzeitlich verstorben. Alle im Rahmen der JEVIN-Studie in der elektronischen Patientenakte EMIL® von überlebenden und verstorbenen Teilnehmern dokumentierten Erhebungsdaten sowie Routineuntersuchungen wurden in die Analysen einbezogen. Die Daten der überlebenden wurden mit denen der verstorbenen Teilnehmer verglichen (Nachbeobachtungsdauer: 2166 Personenjahre).
Ergebnisse Die Sterberate betrug 1,75/100 Personenjahre. Die mediane Beobachtungszeit für alle Patienten betrug 23,1 Jahre (Range 0,61 – 26,6 Jahre). Das mittlere Sterbealter lag bei 58,5 Jahren (34,2 – 78,4 Jahre) und die mittlere Diabetesdauer bei 35 Jahren (3,5 – 68,5 Jahre). Als häufigste Todesursachen fanden sich Herz-Kreislauf-Krankheiten (48,2 %, n = 13) und Infektionen (25,9 %, n = 7). Hinsichtlich Alter (p = 0,302), Diabetesdauer (p = 0,371), BMI (p = 0,535), Blutdruck (p = 0,622/0,820), Geschlecht (p = 0,566) und Raucherstatus (p = 0,709) ließen sich keine Unterschiede zwischen überlebenden und verstorbenen Personen nachweisen. Der mittlere HbA1c-Wert im letzten Jahr vor dem Tod oder der letzten Nachuntersuchung war bei den verstorbenen höher als bei den überlebenden Personen (7,5 vs. 7,0 %; p = 0,010). 57,4 % der überlebenden und 87,0 % der verstorbenen Teilnehmer hatten eine Nephropathie (p = 0,012), 79,7 vs. 89,7 % eine Retinopathie (p = 0,241) und 61,4 vs. 63,3 % eine Neuropathie (p = 0,860). Nur für die Nephropathie konnte eine signifikante Assoziation mit einem erhöhten Sterberisiko nachgewiesen werden (HR = 4,208; KI: 1,226 – 14,440; HR = 2,360, KI: 0,696 – 8,004; HR = 0,944, KI: 0,436 – 2,043).
Schlussfolgerung In der JEVIN-Studie war in der Gruppe der Patienten mit Typ-1-Diabetes mellitus nur die diabetische Nephropathie mit einem höheren Sterberisiko assoziiert.
Diversity of inference strategies can enhance the ‘wisdom-of-crowds’ effect
Authors: Fujisaki Itsuki , Honda Hidehito , Ueda Kazuhiro 
Published: August 2018

AbstractStudies on inference have shown that people use a variety of inference strategies depending on the situation. Despite a great deal of discussion on the use of these strategies at an individual level, very little research has examined how the strategies people use affect group performance. To address this issue, we conducted two computer simulation studies on group decision-making. Our focus was primarily the diversity of strategies used in groups, as previous studies have suggested that diversity plays a critical role in the wisdom of crowds. Therefore, we systematically manipulated the diversity of inference strategies among group members and examined the effect on group performance. In Study 1, we conducted computer simulations using behavioural data from a previous study and found that diversity of strategies could improve group performance. That is, the group whose members used diverse strategies had higher accuracy than groups where all members used an identical strategy. We also investigated how such a phenomenon emerged. In Study 2, we created multiple hypothetical environmental settings and examined the effect. The environmental settings in Study 1 was limited to the ‘kind’ setting, in which correct inferences could be made for most problems by using a certain strategy, and the results of Study 2 showed that the findings of Study 1 could be generalized to other settings. For example, diversity could improve group performance in the ‘wicked’ environment where an inference strategy tends to lead an individual to the wrong answer. We also identified conditions in which the diversity enhanced group performance in each environment. Finally, for Study 1, we conducted additional simulations and discussed the conditions in which diversity would improve group performance more. The contributions to the research on the wisdom of crowds and human inference are discussed.
Convolutional neural networks automate detection for tracking of submicron-scale particles in 2D and 3D
Authors: Newby Jay M. , Schaefer Alison M. , Lee Phoebe T. , Forest M. Gregory , Lai Samuel K. 
Published: August 2018

Significance
The increasing availability of powerful light microscopes capable of collecting terabytes of high-resolution 2D and 3D videos in a single day has created a great demand for automated image analysis tools. Tracking the movement of nanometer-scale particles (e.g., virus, proteins, and synthetic drug particles) is critical for understanding how pathogens breach mucosal barriers and for the design of new drug therapies. Our advancement is to use an artificial neural network that provides, first and foremost, substantially improved automation. Additionally, our method improves accuracy compared with current methods and reproducibility across users and laboratories.
Radiative heating achieves the ultimate regime of thermal convection
Authors: Lepot Simon , Aumaître Sébastien , Gallet Basile 
Published: August 2018

Significance
Turbulent convection is ubiquitous in geophysical and astrophysical contexts: It drives winds in the atmosphere and currents in the ocean, it generates magnetic fields inside planets and stars, and it triggers supernova explosions inside collapsing stellar cores. In many such natural flows, convection is driven by the absorption of incoming radiation (light or neutrinos). We designed an experiment to reproduce such radiatively driven convection in the laboratory. In contrast with convection driven by heating and cooling plates, our radiative heating setup achieves the “ultimate” regime of turbulent convection, which is the one relevant to many natural flows. Such experiments can yield the constitutive laws of turbulent convection, to be implemented into geophysical and astrophysical models.
Adaptation Studies, Translation Studies, and Interdisciplinarity. Reflections on Siblings and Family Resemblance1
Authors: Cattrysse Patrick 
Published: August 2018

AbstractDefinitional issues are not new in translation and adaptation studies (TS and AS, respectively), and neither is the question of whether AS and TS should be seen as one discipline studying one object of study or rather as two disciplines studying two distinct sets of phenomena. This paper argues that an interdisciplinary view on the subject may offer some analytical tools that help advance this discussion. Since the issue is in part one of definition, Section one looks into theories of definitions and discusses four types of definition that could be of use to our debate. This leads to the paradoxical conclusion that to define translations and adaptations is at once easy and difficult. Words like ‘adaptation’ or ‘translation’ are common nouns, which point to sets of entities that share nonunique features. Hence to name is to categorize. Section two probes into theories of categorization and how they could help categorize translational and adaptational phenomena. It turns out that a study of categories and categorizing must involve categorizers. Consequently, one may study science as an epistemic practice, but also as a social one. This introduces section three, which looks into the emerging discipline of interdisciplinarity studies, that is, the study of the compartmentalization (e.g., disciplinarization) of academic knowledge. The conclusion that follows suggests that perhaps, instead of trying to absorb each other, AS and TS should consider themselves rather as siblings, that is, members of a larger family called intertextuality or influence studies.
Hypertension Prevalence Jointly Influenced by Acculturation and Gender in US Immigrant Groups
Authors: Divney A A , Echeverria S E , Thorpe L E , Trinh-Shevrin C , Islam N S 
Published: August 2018

Abstract

BACKGROUND
Latinos and Asians in the United States are disproportionately burdened by hypertension, a leading risk factor for cardiovascular disease. Few studies have used multicomponent measures of acculturation to compare cardiovascular risk factors across immigrant-origin groups. Additionally, little is known about how acculturation and gender shape hypertension risk among immigrants.

METHODS
We created an acculturation score composed of language use, nativity, and years in the United States and fit separate race/ethnicity log-binomial models examining associations with hypertension prevalence (≥130/80 mm Hg) among Latino (n = 4,267) and Asian (n = 2,142) National Health and Nutrition Examination Survey 2011–2016 participants aged 18+. Joint effect models tested the concept of “intersectionality” between acculturation and gender.

RESULTS
Adjusting for age, gender, and socioeconomic position, Latinos and Asians with high acculturation were 25% and 27% more likely to have hypertension, respectively, compared with low acculturation groups. Latino and Asian American men with high levels of acculturation were 74–79% more likely to have hypertension compared with women with low acculturation (adjusted prevalence ratios (aPR) for Latinos = 1.74, 95% confidence interval (CI): 1.49–2.03; aPR for Asians = 1.79, 95% CI: 1.42–2.25). The gradient of increasing hypertension with increasing acculturation was most apparent among Latino men (adjusted risk differences (aRD) = 12.0%, P &lt; 0.001) and Asian women (aRD = 14.0%, P = 0.003) and nonsignificant among Latino women and Asian men when comparing high vs. low acculturation categories.

CONCLUSIONS
Our results correspond with prior literature demonstrating increased morbidity among immigrants with increasing acculturation but also suggest differing patterns by race/ethnicity and gender. Future research should explore how migration processes differentially influence hypertension among men and women.
C3D: a tool to predict 3D genomic interactions between cis-regulatory elements
Authors: Mehdi Tahmid , Bailey Swneke D , Guilhamon Paul , Lupien Mathieu 
Published: August 2018

Abstract

Motivation
The 3D genome architecture influences the regulation of genes by facilitating chromatin interactions between distal cis-regulatory elements and gene promoters. We implement Cross Cell-type Correlation based on DNA accessibility (C3D), a customizable computational tool that predicts chromatin interactions using an unsupervised algorithm that utilizes correlations in chromatin measurements, such as DNaseI hypersensitivity signals.

Results
C3D accurately predicts 32.7%, 18.3% and 24.1% of interactions, validated by ChIA-PET assays, between promoters and distal regions that overlie DNaseI hypersensitive sites in K562, MCF-7 and GM12878 cells, respectively.

Availability and implementation
Source code is open-source and freely available on GitHub (https://github.com/LupienLabOrganization/C3D) under the GNU GPLv3 license. C3D is implemented in Bash and R; it runs on any platform with Bash (≥4.0), R (≥3.1.1) and BEDTools (≥2.19.0). It requires the following R packages: GenomicRanges, Sushi, data.table, preprocessCore and dynamicTreeCut.

Supplementary information
Supplementary data are available at Bioinformatics online.
A Bayesian model for single cell transcript expression analysis on MERFISH data
Authors: Köster Johannes , Brown Myles , Liu X Shirley 
Published: August 2018

Abstract

Motivation
Multiplexed error-robust fluorescence in-situ hybridization (MERFISH) is a recent technology to obtain spatially resolved gene or transcript expression profiles in single cells for hundreds to thousands of genes in parallel. So far, no statistical framework to analyze MERFISH data is available.

Results
We present a Bayesian model for single cell transcript expression analysis on MERFISH data. We show that the model successfully captures uncertainty in MERFISH data and eliminates systematic biases that can occur in raw RNA molecule counts obtained with MERFISH. Our model accurately estimates transcript expression and additionally provides the full probability distribution and credible intervals for each transcript. We further show how this enables MERFISH to scale towards the whole genome while being able to control the uncertainty in obtained results.

Availability and implementation
The presented model is implemented on top of Rust-Bio (Köster, 2016) and available open-source as MERFISHtools (https://merfishtools.github.io). It can be easily installed via Bioconda (Grüning et al., 2018). The entire analysis performed in this paper is provided as a fully reproducible Snakemake (Köster and Rahmann, 2012) workflow via Zenodo (https://doi.org/10.5281/zenodo.752340).

Supplementary information
Supplementary data are available at Bioinformatics online.
Batch effects correction for microbiome data with Dirichlet-multinomial regression
Authors: Dai Zhenwei , Wong Sunny H , Yu Jun , Wei Yingying 
Published: August 2018

Abstract

Motivation
Metagenomic sequencing techniques enable quantitative analyses of the microbiome. However, combining the microbial data from these experiments is challenging due to the variations between experiments. The existing methods for correcting batch effects do not consider the interactions between variables—microbial taxa in microbial studies—and the overdispersion of the microbiome data. Therefore, they are not applicable to microbiome data.

Results
We develop a new method, Bayesian Dirichlet-multinomial regression meta-analysis (BDMMA), to simultaneously model the batch effects and detect the microbial taxa associated with phenotypes. BDMMA automatically models the dependence among microbial taxa and is robust to the high dimensionality of the microbiome and their association sparsity. Simulation studies and real data analysis show that BDMMA can successfully adjust batch effects and substantially reduce false discoveries in microbial meta-analyses.

Availability and implementation
An R package” BDMMA” for Windows and Linux is available at https://github.com/DAIZHENWEI/BDMMA/BDMMA, and a version for MacOS is provided at https://github.com/DAIZHENWEI/BDMMA/BDMMA_MacOS.

Supplementary information
Supplementary data are available at Bioinformatics online.
PairedFB: a full hierarchical Bayesian model for paired RNA-seq data with heterogeneous treatment effects
Authors: Bian Yuanyuan , He Chong , Hou Jie , Cheng Jianlin , Qiu Jing 
Published: August 2018

Abstract

Motivation
Several methods have been proposed for the paired RNA-seq analysis. However, many of them do not consider the heterogeneity in treatment effect among pairs that can naturally arise in real data. In addition, it has been reported in literature that the false discovery rate (FDR) control of some popular methods has been problematic. In this paper, we present a full hierarchical Bayesian model for the paired RNA-seq count data that accounts for variation of treatment effects among pairs and controls the FDR through the posterior expected FDR.

Results
Our simulation studies show that most competing methods can have highly inflated FDR for small to moderate sample sizes while PairedFB is able to control FDR close to the nominal levels. Furthermore, PairedFB has overall better performance in ranking true differentially expressed genes (DEGs) on the top than others, especially when the sample size gets bigger or when the heterogeneity level of treatment effects is high. In addition, PairedFB can be applied to identify the biologically significant DEGs with controlled FDR. The real data analysis also indicates PairedFB tends to find more biologically relevant genes even when the sample size is small. PairedFB is also shown to be robust with respect to the model misspecification in terms of its relative performance compared to others.

Availability and implementation
Software to implement this method (PairedFB) can be downloaded at: https://sites.google.com/a/udel.edu/qiujing/publication.

Supplementary information
Supplementary data are available at Bioinformatics online.
QuantiNemo 2: a Swiss knife to simulate complex demographic and genetic scenarios, forward and backward in time
Authors: Neuenschwander Samuel , Michaud Frédéric , Goudet Jérôme 
Published: August 2018

Abstract

Summary
QuantiNemo 2 is a stochastic simulation program for quantitative population genetics. It was developed to investigate the effects of selection, mutation, recombination and drift on quantitative traits and neutral markers in structured populations connected by migration and located in heterogeneous habitats. A specific feature is that it allows to switch between an individual-based full-featured mode and a population-based faster mode. Several demographic, genetic and selective parameters can be fine-tuned in QuantiNemo 2: population, selection, trait(s) architecture, genetic map for QTL and/or markers, environment, demography and mating system are the main features.

Availability and implementation
QuantiNemo 2 is a C++ program with a source code available under the GNU General Public License version 3. Executables are provided for Windows, MacOS and Linux platforms, together with a comprehensive manual and tutorials illustrating its flexibility. The executable, manual and tutorial can be found on the website www2.unil.ch/popgen/softwares/quantinemo/, while the source code and user support are given through GitHub: github.com/jgx65/quantinemo.

Supplementary information
Supplementary data are available at Bioinformatics online.
Choline ameliorates cardiac hypertrophy by regulating metabolic remodelling and UPRmt through SIRT3-AMPK pathway
Authors: Xu Man , Xue Run-Qing , Lu Yi , Yong Su-Yun , Wu Qing , Cui Yan-Ling , Zuo Xiao-Ting , Yu Xiao-Jiang , Zhao Ming , Zang Wei-Jin 
Published: August 2018

Abstract

Aims
Cardiac hypertrophy is characterized by a shift in metabolic substrate utilization, but the molecular events underlying the metabolic remodelling remain poorly understood. We explored metabolic remodelling and mitochondrial dysfunction in cardiac hypertrophy and investigated the cardioprotective effects of choline.

Methods and results
The experiments were conducted using a model of ventricular hypertrophy by partially banding the abdominal aorta of Sprague Dawley rats. Cardiomyocyte size and cardiac fibrosis were significantly increased in hypertrophic hearts. In vitro cardiomyocyte hypertrophy was induced by exposing neonatal rat cardiomyocytes to angiotensin II (Ang II) (10−6 M, 24 h). Choline attenuated the mito-nuclear protein imbalance and activated the mitochondrial-unfolded protein response (UPRmt) in the heart, thereby preserving the ultrastructure and function of mitochondria in the context of cardiac hypertrophy. Moreover, choline inhibited myocardial metabolic dysfunction by promoting the expression of proteins involved in ketone body and fatty acid metabolism in response to pressure overload, accompanied by the activation of sirtuin 3/AMP-activated protein kinase (SIRT3-AMPK) signalling. In vitro analyses demonstrated that SIRT3 siRNA diminished choline-mediated activation of ketone body metabolism and UPRmt, as well as inhibition of hypertrophic signals. Intriguingly, serum from choline-treated abdominal aorta banding models (where β-hydroxybutyrate was increased) attenuated Ang II-induced myocyte hypertrophy, which indicates that β-hydroxybutyrate is important for the cardioprotective effects of choline.

Conclusion
Choline attenuated cardiac dysfunction by modulating the expression of proteins involved in ketone body and fatty acid metabolism, and induction of UPRmt; this was likely mediated by activation of the SIRT3-AMPK pathway. Taken together, these results identify SIRT3-AMPK as a key cardiac transcriptional regulator that helps orchestrate an adaptive metabolic response to cardiac stress. Choline treatment may represent a new therapeutic strategy for optimizing myocardial metabolism in the context of hypertrophy and heart failure.
How Protestant was the Elizabethan Regime?
Authors: Younger Neil 
Published: August 2018

Abstract
Recent historiography on the Elizabethan regime has argued that it was strongly dominated by convinced Protestants, most prominently Lord Burghley, the earl of Leicester and Sir Francis Walsingham. This article argues that this consensus glosses over many important political figures whose religion was much more conservative, who were often sympathetic to Catholics and in several cases were probably essentially Catholic themselves. These individuals, although prominent at the time, have been seriously neglected by historians, often because of the nature of the archival record. The article surveys the prominence of such men throughout the reign, examining their religious inclinations. It goes on to assess the extent of their influence on the politics of the period, arguing that they were capable of mounting major political initiatives, and indeed scored several important successes against more strongly Protestant policies. Likewise, it argues that very often forward Protestant policies met with failure, in which the conservatives’ influence can often be detected. Finally, it discusses some of the consequences of these findings, proposing a more complex picture of Elizabethan politics, in which religious division and indeed conflict was a significant factor, and arguing that the Elizabethan regime should therefore be seen as a much less united and univocal entity than is often assumed.
Crystalline Cohomology of Towers of Curves
Authors: Vonk Jan 
Published: August 2018

AbstractWe investigate the geometry of finite maps and correspondences between curves, and construct canonical trace and pullback maps between Hyodo–Kato integral structures on de Rham cohomology of curves, which are functorial for finite morphisms of the generic fibres. This leads to a crystalline version of the étale cohomology of towers of modular curves considered by Hida and Ohta, whose ordinary part satisfies $\Lambda $-adic control and Eichler–Shimura theorems.