bluuebunny/crossref_metadata_2025_split huggingface dataset:
A distributional multivariate approach for assessing performance of climate-hydrology models
Authors: Vezzoli Renata , Salvadori Gianfausto , De Michele Carlo 
Published: September 2017

AbstractOne of the ultimate goals of climate studies is to provide projections of future scenarios: for this purpose, sophisticated models are conceived, involving lots of parameters calibrated via observed data. The outputs of such models are used to investigate the impacts on related phenomena such as floods, droughts, etc. To evaluate the performance of such models, statistics like moments/quantiles are used, and comparisons with historical data are carried out. However, this may not be enough: correct estimates of some moments/quantiles do not imply that the probability distributions of observed and simulated data match. In this work, a distributional multivariate approach is outlined, also accounting for the fact that climate variables are often dependent. Suitable statistical tests are described, providing a non-parametric assessment exploiting the Copula Theory. These procedures allow to understand (i) whether the models are able to reproduce the distributional features of the observations, and (ii) how the models perform (e.g., in terms of future climate projections and changes). The proposed methodological approach is appropriate also in contexts different from climate studies, to evaluate the performance of any model of interest: methods to check a model per se are sketched out, investigating whether its outcomes are (statistically) consistent.
The crystal structure of the regulatory domain of the human sodium-driven chloride/bicarbonate exchanger
Authors: Alvadia Carolina M. , Sommer Theis , Bjerregaard-Andersen Kaare , Damkier Helle Hasager , Montrasio Michele , Aalkjaer Christian , Morth J. Preben 
Published: September 2017

AbstractThe sodium-driven chloride/bicarbonate exchanger (NDCBE) is essential for maintaining homeostatic pH in neurons. The crystal structure at 2.8 Å resolution of the regulatory N-terminal domain of human NDCBE represents the first crystal structure of an electroneutral sodium-bicarbonate cotransporter. The crystal structure forms an equivalent dimeric interface as observed for the cytoplasmic domain of Band 3, and thus establishes that the consensus motif VTVLP is the key minimal dimerization motif. The VTVLP motif is highly conserved and likely to be the physiologically relevant interface for all other members of the SLC4 family. A novel conserved Zn2+-binding motif present in the N-terminal domain of NDCBE is identified and characterized in vitro. Cellular studies confirm the Zn2+ dependent transport of two electroneutral bicarbonate transporters, NCBE and NBCn1. The Zn2+ site is mapped to a cluster of histidines close to the conserved ETARWLKFEE motif and likely plays a role in the regulation of this important motif. The combined structural and bioinformatics analysis provides a model that predicts with additional confidence the physiologically relevant interface between the cytoplasmic domain and the transmembrane domain.
Differential gene expression and SNP association between fast- and slow-growing turbot (Scophthalmus maximus)
Authors: Robledo Diego , Rubiolo Juan A. , Cabaleiro Santiago , Martínez Paulino , Bouza Carmen 
Published: September 2017

AbstractGrowth is among the most important traits for animal breeding. Understanding the mechanisms underlying growth differences between individuals can contribute to improving growth rates through more efficient breeding schemes. Here, we report a transcriptomic study in muscle and brain of fast- and slow-growing turbot (Scophthalmus maximus), a relevant flatfish in European and Asian aquaculture. Gene expression and allelic association between the two groups were explored. Up-regulation of the anaerobic glycolytic pathway in the muscle of fast-growing fish was observed, indicating a higher metabolic rate of white muscle. Brain expression differences were smaller and not associated with major growth-related genes, but with regulation of feeding-related sensory pathways. Further, SNP variants showing frequency differences between fast- and slow-growing fish pointed to genomic regions likely involved in growth regulation, and three of them were individually validated through SNP typing. Although different mechanisms appear to explain growth differences among families, general mechanisms seem also to be involved, and thus, results provide a set of useful candidate genes and markers to be evaluated for more efficient growth breeding programs and to perform comparative genomic studies of growth in fish and vertebrates.
Home and Community Language Proficiency in Spanish–English Early Bilingual University Students
Authors: Schmidtke Jens 
Published: September 2017

Purpose
This study assessed home and community language proficiency in Spanish–English bilingual university students to investigate whether the vocabulary gap reported in studies of bilingual children persists into adulthood.

Method
Sixty-five early bilinguals (mean age = 21 years) were assessed in English and Spanish vocabulary and verbal reasoning ability using subtests of the Woodcock-Muñoz Language Survey–Revised (Schrank & Woodcock, 2009). Their English scores were compared to 74 monolinguals matched in age and level of education. Participants also completed a background questionnaire.

Results
Bilinguals scored below the monolingual control group on both subtests, and the difference was larger for vocabulary compared to verbal reasoning. However, bilinguals were close to the population mean for verbal reasoning. Spanish scores were on average lower than English scores, but participants differed widely in their degree of balance. Participants with an earlier age of acquisition of English and more current exposure to English tended to be more dominant in English.

Conclusions
Vocabulary tests in the home or community language may underestimate bilingual university students' true verbal ability and should be interpreted with caution in high-stakes situations. Verbal reasoning ability may be more indicative of a bilingual's verbal ability.
Wideband RCS reduction of slot‐coupled patch antenna by AMC structure
Authors: Xue Jingjing , Jiang Wen , Gong Shuxi 
Published: September 2017

A novel approach to realise the wideband and polarisation‐independent radar cross‐section (RCS) reduction of a slot‐coupled patch antenna is proposed. The RCS reduction is based on the unique reflection phase properties of artificial magnetic conductor (AMC) and perfect electric conductor (PEC) cell. By using the quasi‐fractal structure in AMC design, 180° ± 37° reflection phase difference between AMC and PEC cells is obtained over 109% (6.4–21.7 GHz) frequency range. Then, the two different unit cells are applied properly to a slot‐coupled patch antenna for wideband RCS reduction. The simulated and measured results indicate that the proposed antenna realises a remarkable RCS reduction between 6.0 and 30.0 GHz for both phi‐ and theta‐polarised waves. Moreover, the radiation characteristics of the antenna are well kept simultaneously.
Design of highly efficient broadband harmonic‐optimised GaN power amplifier via modified simplified real frequency technique
Authors: Hu Xingwei , Meng Xiangyu , Yu Cuiping , Liu Yuanan 
Published: September 2017

A design of broadband power amplifier (PA) which uses harmonic‐optimised matching network (MN) is designed to maintain high efficiency. The load–pull data is used to construct the optimal impedance areas in fundamental and harmonic parts. Then, the modified simplified real frequency technique algorithm is employed to design output‐MN through constructing the defined harmonic‐error functions. A 10 W Cree gallium nitride high‐electron‐mobility transistor device CGH40010F is used to validate this method. The proposed PA has a 40% bandwidth (1.8–2.7 GHz) and a 64–81% drain efficiency. The digital pre‐distortion process shows the adjacent channel leakage ratio (ACLR) is <−52 dBc at 2.25 GHz.
Physical modelling and experimental characterisation of InAlAs/InGaAs avalanche photodiode for 10 Gb/s data rates and higher
Authors: Abdulwahid Omar S. , Sexton James , Kostakis Ioannis , Ian Kawa , Missous Mohamed 
Published: September 2017

InAlAs/InGaAs avalanche photodiodes (APD) were simulated using physical device models, then designed and fabricated to detect light in the wavelength range from 1.3 to 1.55 µm. DC characterisation under dark and light conditions were performed at room temperature to measure and investigate the performance of the APD. High‐frequency characterisation was carried out on the device to extract the diode intrinsic and extrinsic parameters. The work reported here focuses on the dark and light physical device simulations (both under DC and AC conditions) which were accomplished using Atlas SILVACO tool. The effect of electron velocity overshoot was considered for accurate bandwidth modelling. All measured data are in excellent agreement with the modelled ones. The internal device gain of the APD is 45 at −23.5 V leading to a ∼220 GHz gain–bandwidth product. This successful APD model can be exploited to further improve the diode structure for higher data rate applications beyond 10 Gb/s.
Impact of Elevated Donor Troponin I as Predictor of Adverse Outcome in Adult Heart Transplantation: A Single-center Experience
Authors: Freundt Miriam , Philipp Alois , Kolat Philipp , Rupprecht Leopold , Friedrich Christine , Hirt Stephan , Haneya Assad 
Published: September 2017

Background Due to globally increasing donor organ shortage, investigation of previously described risk factors for utilizing marginal donor hearts is needed. The aim of this study was to determine the impact of elevated donor serum troponin I (TnI) levels on outcome after heart transplantation (HTx).
Methods Between January 1996 and August 2013, 161 patients were reviewed for donor TnI serum levels (>0.3 ng/mL was considered elevated), postoperative outcome parameters, 30-day mortality, and 1-, 3-, and 5-year survival.
Results TnI levels were elevated in 45 (28.0%) donors. Recipients of hearts with elevated TnI had higher incidence of postoperative systolic dysfunction, prolonged inotropic support, prolonged mechanical ventilation, and longer intensive care unit (ICU) stay (p < 0.001). This group had higher 30-day mortality (22.2% vs 8.6%, p = 0.03) and lower 1-, 3-, and 5-year survival (56%, 53%, and 50% versus 82%, 76%, and 69%, p = 0.032). Elevated TnI was the only independent risk factor for 30-day mortality (odds ratio [OR] 3.63, 95% confidence interval [CI] 1.28–10.27, p = 0.015).
Conclusions Elevated donor TnI serum concentration seems to be a marker for adverse outcome and increased short- and long-term mortality after HTx. Nevertheless, many other perioperative variables and parameters can be associated with outcome.
French Connection between Specialized and Routine Pediatric Surgical Care
Authors: Peycelon Matthieu , Faraj Sebastien , Leclair Marc , Bonnard Arnaud 
Published: September 2017

Introduction The success of modern pediatric surgery (PS) management has led to the recommendation of regional organization and coordination of PS departments. Although small units may obtain excellent results, there is evidence that a concentration to larger units is advantageous. In France, the centralization of PS has been discussed for the past 15 years. A new organization was finally achieved in 2010. The intent was to assure children prompt access to the level of care appropriate to the degree of their pathologies to improve the outcomes and reduce morbidity and mortality.
Methods One of the first pertinent governmental measures was an attempt to centralize the PS departments and encourage the development of connection between specialized PS care and routine PS unit. In this review, we report this coordination through the analysis inside two regional French areas.
Results Paris is the first example that illustrates the network between four specialized PS departments and eight local hospitals. The aim of this connection was to improve the safety and quality of pediatric surgical management during the night for emergency issues and in the case of neonatology. The second example is the network that coexists in the west part of France through monthly video conferencing sessions and subspecialization (pediatric urology, pediatric oncology, and pediatric liver surgery). Moreover, a national program aimed at improving the management of patients with rare diseases since 2005. For instance, biliary atresia and anorectal malformation centers are located in two academic centers in Paris and the esophageal atresia center is in Lille. These expert centers allowed performing numerous studies along with international publications, thereby offering a better vision of the natural story of diseases to improve care. Finally, this network is emphasized during medical education from PS residency to the fellowship when trainees have to spend at least 1 year in a local hospital.
Conclusion The European legislation calls for multidisciplinary centers treating children with rare diseases and proposes clear and demanding quality criteria. The French experience illustrates some interesting and encouraging aspects of the current trends in PS care. Our results strongly suggest that centralization, specialization, and connections between specialized and routine PS departments can greatly improve management of and outcomes in children treated in our units.
Einfluss des Disease-Management-Programms auf den HbA1c-Wert bei Typ-2-Diabetes-mellitus-Patienten: Ein retrospektiver Vergleich zwischen Disease Management Programm und Regelversorgung
Authors: Wiefarn Stefan , Kostev Karel , Heumann Christian , Rettelbach Anja 
Published: September 2017

Zusammenfassung
Hintergrund Diese retrospektive Studie hat das Ziel, den Einfluss des Disease-Management-Programms (DMP) für Typ-2-Diabetes-mellitus-Patienten (T2DM) auf den HbA1c-Wert innerhalb Deutschlands zu messen.
Methoden Die Studie basiert auf retrospektiven Patientendaten aus dem Disease Analyzer Panel (IMS Health). Mittels 2:1 Propensity Score Matching wurde eine adäquate Kontrollgruppe gebildet. Nach dem Matching umfasste die Analyse 14 759 Patienten. Davon nahmen 5875 Patienten an einem DMP teil und 8884 erhielten die Regelversorgung. Auf Basis der gematchten Daten wurde der DMP-Effekt mittels unverbundenem t-Test geschätzt. Darüber hinaus erfolgte unter dem Gesichtspunkt der personalisierten Medizin die Betrachtung von Subgruppen.
Ergebnisse Die Senkung des HbA1c-Wertes in der DMP-Gruppe lag bei durchschnittlich 1,0 Prozentpunkten (Baseline HbA1c = 8,1 vs. HbA1c-Endwert = 7,1), wohingegen die RV-Gruppe den HbA1c-Wert im Mittel um 0,9 Prozentpunkte senken konnte (Baseline HbA1c = 8,1 vs. HbA1c-Endwert = 7,2). Somit konnte die DMP-Gruppe eine nur um 0,1 Prozentpunkte höhere Senkung des HbA1c-Wertes erreichen [95 %-KI: 0,04 – 0,16]. Deskriptiv zeigte sich zudem, dass Patienten aus der DMP-Gruppe durchschnittlich mehr Verordnungen und HbA1c-Messungen pro Jahr aufwiesen. In der Subgruppenanalyse konnten Gruppen von Patienten identifiziert werden, welche mehr von einem DMP profitieren als andere. So können junge Patienten oder Patienten in Behandlung bei einem Diabetologen den größten Nutzen aus einem DMP ziehen. Des Weiteren hat der Baseline-HbA1c-Wert einen Einfluss auf die Höhe des DMP-Effekts.
Folgerung T2DM-Patienten im DMP weisen zwar eine signifikant höhere Senkung des HbA1c-Wertes auf, jedoch ist fraglich, ob der Effekt als klinisch relevant anzusehen ist. Allerdings gibt es Gruppen von Patienten, welche mehr von einem DMP profitieren als andere. Um jedoch den Einfluss des DMPs und die Gründe für die vorhandenen Subgruppeneffekte besser zu verstehen, bedarf es weiterer Studien, welche in einem randomisierten kontrollierten Design durchgeführt werden sollten.
Mouthguard Use and Cardiopulmonary Capacity – A Systematic Review and Meta-Analysis
Authors: Caneppele Taciana , Borges Alessandra , Pereira Daniele , Fagundes Alessandra , Fidalgo Tatiane , Maia Luciane 
Published: September 2017

AbstractThis study aimed to perform a systematic review and meta-analysis of the literature to determine the effects of the use of mouthguards (MGs) on cardiopulmonary capacity in athletes (oxygen uptake: VO2 max, and minute ventilation: VE max). Seven electronic databases and reference lists of relevant papers were searched for randomized clinical trials (RCTs) that compared the cardiopulmonary capacity in athletes with and without the use of an MG. The risk of bias tool of the Cochrane Collaboration was used for quality assessment. Fourteen studies were included. For both the overall VO2 max and VE max analyses, significant differences were observed between the MG and no MG conditions, favoring no MG, which presented the highest VO2 max values (p=0.0001; 95% CI; –2.638 to –1.728) and the highest VE max values (p=0.0001; 95% CI; –4.103 to –1.354). When the results were analyzed separately for each subgroup (type of MG and place of use), the meta-analysis showed that the effect of the use of an MG on VO2 max and VE max was not significant when custom-made MGs were used. The use of an MG overall decreased VO2 max and VE max compared to the control. Nevertheless, custom-made MGs seem to have no effect on these parameters.
Diverse p53/DNA binding modes expand the repertoire of p53 response elements
Authors: Vyas Pratik , Beno Itai , Xi Zhiqun , Stein Yan , Golovenko Dmitrij , Kessler Naama , Rotter Varda , Shakked Zippora , Haran Tali E. 
Published: September 2017

Significance
The tumor suppressor protein p53 acts as a transcription factor by binding as a tetramer to response elements made of two DNA half-sites separated by a variable spacer, leading to diverse cellular outcomes. Fifty percent of all p53 response elements contain spacers, but their significance is unclear at present. Here, we show that p53 binds to response elements containing long spacers in two different modes: fully specific and hemispecific. In the latter, only one p53 dimer is specifically bound to a DNA half-site, whereas the other dimer is bound to the spacer DNA. Nonetheless, the two modes have comparable binding affinity and specificity. Our findings expand and diversify the p53 regulatory network.
SNP genotyping and parameter estimation in polyploids using low-coverage sequencing data
Authors: Blischak Paul D , Kubatko Laura S , Wolfe Andrea D 
Published: September 2017

AbstractMotivationGenotyping and parameter estimation using high throughput sequencing data are everyday tasks for population geneticists, but methods developed for diploids are typically not applicable to polyploid taxa. This is due to their duplicated chromosomes, as well as the complex patterns of allelic exchange that often accompany whole genome duplication (WGD) events. For WGDs within a single lineage (autopolyploids), inbreeding can result from mixed mating and/or double reduction. For WGDs that involve hybridization (allopolyploids), alleles are typically inherited through independently segregating subgenomes.ResultsWe present two new models for estimating genotypes and population genetic parameters from genotype likelihoods for auto- and allopolyploids. We then use simulations to compare these models to existing approaches at varying depths of sequencing coverage and ploidy levels. These simulations show that our models typically have lower levels of estimation error for genotype and parameter estimates, especially when sequencing coverage is low. Finally, we also apply these models to two empirical datasets from the literature. Overall, we show that the use of genotype likelihoods to model non-standard inheritance patterns is a promising approach for conducting population genomic inferences in polyploids.Availability and implementationA C ++ program, EBG, is provided to perform inference using the models we describe. It is available under the GNU GPLv3 on GitHub: https://github.com/pblischak/polyploid-genotyping.Supplementary informationSupplementary data are available at Bioinformatics online.
Mobi 2.0: an improved method to define intrinsic disorder, mobility and linear binding regions in protein structures
Authors: Piovesan Damiano , Tosatto Silvio C E 
Published: September 2017

Abstract

Motivation
The structures contained in the Protein Data Bank (PDB) database are of paramount importance to define our knowledge of folded proteins. While providing mainly circumstantial evidence, PDB data is also increasingly used to define the lack of unique structure, represented by mobile regions and even intrinsic disorder (ID). However, alternative definitions are used by different authors and potentially limit the generality of the analyses being carried out.

Results
Here we present Mobi 2.0, a completely re-written version of the Mobi software for the determination of mobile and potentially disordered regions from PDB structures. Mobi 2.0 provides robust definitions of mobility based on four main sources of information: (i) missing residues, (ii) residues with high temperature factors, (iii) mobility between different models of the same structure and (iv) binding to another protein or nucleotide chain. Mobi 2.0 is well suited to aggregate information across different PDB structures for the same UniProt protein sequence, providing consensus annotations. The software is expected to standardize the treatment of mobility, allowing an easier comparison across different studies related to ID.

Availability
Mobi 2.0 provides the structure-based annotation for the MobiDB database. The software is available from URL http://protein.bio.unipd.it/mobi2/.
Monoidal Categories Enriched in Braided Monoidal Categories
Authors: Morrison Scott , Penneys David 
Published: September 2017

AbstractWe introduce the notion of a monoidal category enriched in a braided monoidal category $\mathcal{V}$. We set up the basic theory, and prove a classification result in terms of braided oplax monoidal functors to the Drinfeld centre of some monoidal category $\mathcal{T}$.Even the basic theory is interesting; it shares many characteristics with the theory of monoidal categories enriched in a symmetric monoidal category, but lacks some features. Of particular note, there is no cartesian product of braided-enriched categories, and the natural transformations do not form a 2-category, but rather satisfy a braided interchange relation.Strikingly, our classification is slightly more general than what one might have anticipated in terms of strong monoidal functors $\mathcal{V}\to Z(\mathcal{T})$. We would like to understand this further; in a future article, we show that the functor is strong if and only if the enriched category is ‘complete’ in a certain sense. Nevertheless it remains to understand what non-complete enriched categories may look like.One should think of our construction as a generalization of de-equivariantization, which takes a strong monoidal functor ${\mathsf {Rep}}(G) \to Z(\mathcal{T})$ for some finite group $G$ and a monoidal category $\mathcal{T}$, and produces a new monoidal category $\mathcal{T} _{{/\hspace{-2px}/}G}$. In our setting, given any braided oplax monoidal functor $\mathcal{V} \to Z(\mathcal{T})$, for any braided $\mathcal{V}$, we produce $\mathcal{T} _{{/\hspace{-2px}/}\mathcal{V}}$: this is not usually an ‘honest’ monoidal category, but is instead $\mathcal{V}$-enriched. If $\mathcal{V}$ has a braided lax monoidal functor to ${\mathsf {Vec}}$, we can use this to reduce the enrichment to ${\mathsf {Vec}}$, and this recovers de-equivariantization as a special case. This is the published version of arXiv:1701.00567.