bluuebunny/crossref_metadata_2025_split huggingface dataset:
Comparison of Swiss and European risk algorithms for cardiovascular prevention in Switzerland
Authors: Beuret Hadrien , Hausler Nadine , Nanchen David , Méan Marie , Marques-Vidal Pedro , Vaucher Julien 
Published: February 2020

Abstract

Background
In Switzerland, two distinct algorithms are recommended for cardiovascular prevention: (a) Arbeitsgruppe Lipide und Atherosklerose (AGLA); and (b) European Society of Cardiology (ESC). We validated and determined which algorithm better predicts incident atherosclerotic cardiovascular disease and assessed statin eligibility in Switzerland.

Design
A prospective population-based cohort.

Methods
We employed longitudinal data of the CoLaus study involving 6733 individuals, aged 35–75 years, with a 10-year follow-up. Using discrimination and calibration, we evaluated the predictive performance of the AGLA and ESC algorithms for the prediction of atherosclerotic cardiovascular disease.

Results
From the 6733 initial participants, 5529 were analysed with complete baseline and follow-up data. Mean age (SD) was 52.4 (10.6) years and 54% were women. During an average follow-up (SD) of 10.2 years (1.7), 370 (6.7%) participants developed an incident atherosclerotic cardiovascular disease. The sensitivity of AGLA and ESC algorithms to predict atherosclerotic cardiovascular disease was 51.6% (95% confidence interval (CI) 46.4–56.8) and 58.6% (53.4–63.7), respectively. Discrimination and calibration were similar between the AGLA and ESC algorithms, with area under the receiver operating characteristic curve values of 0.78 (95% CI 0.76–0.80) and 0.79 (0.76–0.81), and Brier scores of 0.059 and 0.041, respectively. Among 370 individuals developing incident atherosclerotic cardiovascular disease, only 278 (75%) were eligible for statin therapy at baseline, including 210 (57%) according to both algorithms, 4 (1%) to AGLA only and 64 (17%) to ESC only.

Conclusion
AGLA and ESC algorithms presented similar accuracy to predict atherosclerotic cardiovascular disease in Switzerland. A quarter of adults developing atherosclerotic cardiovascular disease were not identified by preventive algorithms to be eligible for statin therapy.
Scaffolding Clinical Reasoning of Health Care Students: A Qualitative Exploration of Clinicians’ Perceptions on an Interprofessional Obstetric Ward
Authors: Visser Cora LF , Wouters Anouk , Croiset Gerda , Kusurkar Rashmi A 
Published: February 2020

Purpose: Interprofessional education (IPE) on a ward supports students to generate interprofessional patient care plans as a means to learn about the roles, responsibilities, and clinical reasoning of other professions. We investigated how clinicians guide the clinical reasoning of students from their own and other professions and whether clinicians from nursing, midwifery, and medicine could scaffold students from all professions, that is, by providing just-in-time and tailored support. Methods: Nine supervising clinicians from medicine, nursing, and midwifery were interviewed and a repeat interview held 3 to 15 weeks later; one nurse supervisor was interviewed only once. Using conventional content analysis, themes were identified inductively. Next, we applied an existing scaffolding framework to conceptualise how clinicians supported the clinical reasoning in an IPE setting. Results: Themes were clinicians’ interventions and intentions, results of interventions and of IPE, characteristics of students and clinicians, interactions between clinicians and students, and logistics. Clinicians applied various interventions and expressed several intentions to guide the learning of students from all professions. Clinicians stimulated students’ clinical reasoning by structuring meetings, asking students to explain their thoughts to each other and through giving group assignments. Thus, clinicians used peer-assisted learning for the students. By collaborating with other supervising clinicians regarding the form and amount of guidance to give to the students, clinicians applied peer-assisted learning for themselves as well. Conclusion: Clinicians can learn to scaffold the clinical reasoning of students from different professions, when they are provided with training, good examples, and structures. An existing scaffolding framework can serve as an overview of aims and interventions to provide just-in-time guidance to students from all professions. The scaffolding framework is useful for training clinicians and for depicting the pedagogical approach for IPE wards.
Challenges to the European automotive industry in securing critical raw materials for electric mobility: the case of rare earths
Authors: Schmid Marc 
Published: February 2020

AbstractCritical raw materials (CRMs) are crucial for the transformation towards low carbon mobility. However, their production is often highly concentrated in a few countries, which leads to supply risks. Exemplified by the case of rare earth elements (REEs) and based on in-depth interviews with corporate executives from companies along the automotive supply chain, this contribution provides insights into the strategies of the European automotive industry to cope with these supply risks. Results show a lack of awareness of REE criticality studies and their outcomes in the past, the decisive role of price competitiveness when pursuing mitigation strategies and a lack of willingness or ability to engage in rare earth (RE) projects to get access to production output and secure supply. Overall, affected companies struggle to pursue long-term oriented strategies to secure their need for REEs. These findings are discussed with regard to the new demand for CRMs due to the shift to electric mobility and the specific challenges that the automotive industry faces.
Prognostic factors for VTE and bleeding in hospitalized medical patients: a systematic review and meta-analysis
Authors: Darzi Andrea J. , Karam Samer G. , Charide Rana , Etxeandia-Ikobaltzeta Itziar , Cushman Mary , Gould Michael K. , Mbuagbaw Lawrence , Spencer Frederick A. , Spyropoulos Alex C. , Streiff Michael B. , Woller Scott , Zakai Neil A. , Germini Federico , Rigoni Marta , Agarwal Arnav , Morsi Rami Z. , Iorio Alfonso , Akl Elie A. , Schünemann Holger J. 
Published: February 2020

Abstract
There may be many predictors of venous thromboembolism (VTE) and bleeding in hospitalized medical patients, but until now, systematic reviews and assessments of the certainty of the evidence have not been published. We conducted a systematic review to identify prognostic factors for VTE and bleeding in hospitalized medical patients and searched Medline and EMBASE from inception through May 2018. We considered studies that identified potential prognostic factors for VTE and bleeding in hospitalized adult medical patients. Reviewers extracted data in duplicate and independently and assessed the certainty of the evidence using the Grading of Recommendations Assessment, Development, and Evaluation approach. Of 69 410 citations, we included 17 studies in our analysis: 14 that reported on VTE, and 3 that reported on bleeding. For VTE, moderate-certainty evidence showed a probable association with older age; elevated C-reactive protein (CRP), D-dimer, and fibrinogen levels; tachycardia; thrombocytosis; leukocytosis; fever; leg edema; lower Barthel Index (BI) score; immobility; paresis; previous history of VTE; thrombophilia; malignancy; critical illness; and infections. For bleeding, moderate-certainty evidence showed a probable association with older age, sex, anemia, obesity, low hemoglobin, gastroduodenal ulcers, rehospitalization, critical illness, thrombocytopenia, blood dyscrasias, hepatic disease, renal failure, antithrombotic medication, and presence of a central venous catheter. Elevated CRP, a lower BI, a history of malignancy, and elevated heart rate are not included in most VTE risk assessment models. This study informs risk prediction in the management of hospitalized medical patients for VTE and bleeding; it also informs guidelines for VTE prevention and future research.
proMAD: semiquantitative densitometric measurement of protein microarrays
Authors: Jaeschke Anna , Eckert Hagen , Bray Laura J. 
Published: February 2020

Abstract
Background
Protein microarrays are a versatile and widely used tool for analyzing complex protein mixtures. Membrane arrays utilize antibodies which are captured on a membrane to specifically immobilize several proteins of interest at once. Using detection antibodies, the bound protein-antibody-complex is converted into visual signals, which can be quantified using densitometry. The reliability of such densitometric assessments depends on a variety of factors, not only sample preparation and the choice of acquisition device but also the selected analysis software and the algorithms used for readout and processing data. Currently available software packages use a single image of a membrane at an optimal exposure time selected for that specific experimental framework. This selection is based on a user’s best guess and is subject to inter-user variability or the acquisition device algorithm. With modern image acquisition systems proving the capacity to collect signal development over time, this information can be used to improve densitometric measurements. Here we introduce proMAD, a toolkit for protein microarray analysis providing a novel systemic approach for the quantification of membrane arrays based on the kinetics of the analytical reaction.

Results
Briefly, our toolkit ensures an exact membrane alignment, utilizing basic computer vision techniques. It also provides a stable method to estimate the background light level. Finally, we model the light production over time, utilizing the knowledge about the reaction kinetics of the underlying horseradish peroxidase-based signal detection method.

Conclusion
proMAD incorporates the reaction kinetics of the enzyme to model the signal development over time for each membrane creating an individual, self-referencing concept. Variations of membranes within a given experimental set up can be accounted for, allowing for a better comparison of such. While the open-source library can be implemented in existing workflows and used for highly user-tailored analytic setups, the web application, on the other hand, provides easy platform-independent access to the core algorithm to a wide range of researchers. proMAD’s inherent flexibility has the potential to cover a wide range of use-cases and enables the automation of data analytic tasks.
Pre- and post-sequencing recommendations for functional annotation of human fecal metagenomes
Authors: Treiber Michelle L. , Taft Diana H. , Korf Ian , Mills David A. , Lemay Danielle G. 
Published: February 2020

Abstract
Background
Shotgun metagenomes are often assembled prior to annotation of genes which biases the functional capacity of a community towards its most abundant members. For an unbiased assessment of community function, short reads need to be mapped directly to a gene or protein database. The ability to detect genes in short read sequences is dependent on pre- and post-sequencing decisions. The objective of the current study was to determine how library size selection, read length and format, protein database, e-value threshold, and sequencing depth impact gene-centric analysis of human fecal microbiomes when using DIAMOND, an alignment tool that is up to 20,000 times faster than BLASTX.

Results
Using metagenomes simulated from a database of experimentally verified protein sequences, we find that read length, e-value threshold, and the choice of protein database dramatically impact detection of a known target, with best performance achieved with longer reads, stricter e-value thresholds, and a custom database. Using publicly available metagenomes, we evaluated library size selection, paired end read strategy, and sequencing depth. Longer read lengths were acheivable by merging paired ends when the sequencing library was size-selected to enable overlaps. When paired ends could not be merged, a congruent strategy in which both ends are independently mapped was acceptable. Sequencing depths of 5 million merged reads minimized the error of abundance estimates of specific target genes, including an antimicrobial resistance gene.

Conclusions
Shotgun metagenomes of DNA extracted from human fecal samples sequenced using the Illumina platform should be size-selected to enable merging of paired end reads and should be sequenced in the PE150 format with a minimum sequencing depth of 5 million merge-able reads to enable detection of specific target genes. Expecting the merged reads to be 180-250 bp in length, the appropriate e-value threshold for DIAMOND would then need to be more strict than the default. Accurate and interpretable results for specific hypotheses will be best obtained using small databases customized for the research question.
Assessing stationary distributions derived from chromatin contact maps
Authors: Segal Mark R. , Fletez-Brant Kipper 
Published: February 2020

AbstractBackgroundThe spatial configuration of chromosomes is essential to various cellular processes, notably gene regulation, while architecture related alterations, such as translocations and gene fusions, are often cancer drivers. Thus, eliciting chromatin conformation is important, yet challenging due to compaction, dynamics and scale. However, a variety of recent assays, in particular Hi-C, have generated new details of chromatin structure, spawning a number of novel biological findings. Many findings have resulted from analyses on the level of native contact data as generated by the assays. Alternatively, reconstruction based approaches often proceed by first converting contact frequencies into distances, then generating a three dimensional (3D) chromatin configuration that best recapitulates these distances. Subsequent analyses can enrich contact level analyses via superposition of genomic attributes on the reconstruction. But, such advantages depend on the accuracy of the reconstruction which, absent gold standards, is inherently difficult to assess. Attempts at accuracy evaluation have relied on simulation and/or FISH imaging that typically features a handful of low resolution probes. While newly advanced multiplexed FISH imaging offers possibilities for refined 3D reconstruction accuracy evaluation, availability of such data is limited due to assay complexity and the resolution thereof is appreciably lower than the reconstructions being assessed. Accordingly, there is demand for new methods of reconstruction accuracy appraisal.ResultsHere we explore the potential of recently proposed stationary distributions, hereafter StatDns, derived from Hi-C contact matrices, to serve as a basis for reconstruction accuracy assessment. Current usage of such StatDns has focussed on the identification of highly interactive regions (HIRs): computationally defined regions of the genome purportedly involved in numerous long-range intra-chromosomal contacts. Consistent identification of HIRs would be informative with respect to inferred 3D architecture since the corresponding regions of the reconstruction would have an elevated number ofknearest neighbors (kNNs). More generally, we anticipate a monotone decreasing relationship between StatDn values andkNN distances. After initially evaluating the reproducibility of StatDns across replicate Hi-C data sets, we use this implied StatDn -kNN relationship to gauge the utility of StatDns for reconstruction validation, making recourse to both real and simulated examples.ConclusionsOur analyses demonstrate that, as constructed, StatDns donotprovide a suitable measure for assessing the accuracy of 3D genome reconstructions. Whether this is attributable to specific choices surrounding normalization in defining StatDns or to the logic underlying their very formulation remains to be determined.
Macroevolutionary bursts and constraints generate a rainbow in a clade of tropical birds
Authors: Merwin Jon T. , Seeholzer Glenn F. , Smith Brian Tilston 
Published: February 2020

AbstractBackgroundBird plumage exhibits a diversity of colors that serve functional roles ranging from signaling to camouflage and thermoregulation. However, birds must maintain a balance between evolving colorful signals to attract mates, minimizing conspicuousness to predators, and optimizing adaptation to climate conditions. Examining plumage color macroevolution provides a framework for understanding this dynamic interplay over phylogenetic scales. Plumage evolution due to a single overarching process, such as selection, may generate the same macroevolutionary pattern of color variation across all body regions. In contrast, independent processes may partition plumage and produce region-specific patterns. To test these alternative scenarios, we collected color data from museum specimens of an ornate clade of birds, the Australasian lorikeets, using visible-light and UV-light photography, and comparative methods. We predicted that the diversification of homologous feather regions, i.e., patches, known to be involved in sexual signaling (e.g., face) would be less constrained than patches on the back and wings, where new color states may come at the cost of crypsis. Because environmental adaptation may drive evolution towards or away from color states, we tested whether climate more strongly covaried with plumage regions under greater or weaker macroevolutionary constraint.ResultsWe found that alternative macroevolutionary models and varying rates best describe color evolution, a pattern consistent with our prediction that different plumage regions evolved in response to independent processes. Modeling plumage regions independently, in functional groups, and all together showed that patches with similar macroevolutionary models clustered together into distinct regions (e.g., head, wing, belly), which suggests that plumage does not evolve as a single trait in this group. Wing patches, which were conserved on a macroevolutionary scale, covaried with climate more strongly than plumage regions (e.g., head), which diversified in a burst.ConclusionsOverall, our results support the hypothesis that the extraordinary color diversity in the lorikeets was generated by a mosaic of evolutionary processes acting on plumage region subsets. Partitioning of plumage regions in different parts of the body provides a mechanism that allows birds to evolve bright colors for signaling and remain hidden from predators or adapt to local climatic conditions.
GSAlign: an efficient sequence alignment tool for intra-species genomes
Authors: Lin Hsin-Nan , Hsu Wen-Lian 
Published: February 2020

AbstractBackgroundPersonal genomics and comparative genomics are becoming more important in clinical practice and genome research. Both fields require sequence alignment to discover sequence conservation and variation. Though many methods have been developed, some are designed for small genome comparison while some are not efficient for large genome comparison. Moreover, most existing genome comparison tools have not been evaluated the correctness of sequence alignments systematically. A wrong sequence alignment would produce false sequence variants.ResultsIn this study, we present GSAlign that handles large genome sequence alignment efficiently and identifies sequence variants from the alignment result. GSAlign is an efficient sequence alignment tool for intra-species genomes. It identifies sequence variations from the sequence alignments. We estimate performance by measuring the correctness of predicted sequence variations. The experiment results demonstrated that GSAlign is not only faster than most existing state-of-the-art methods, but also identifies sequence variants with high accuracy.ConclusionsAs more genome sequences become available, the demand for genome comparison is increasing. Therefore an efficient and robust algorithm is most desirable. We believe GSAlign can be a useful tool. It exhibits the abilities of ultra-fast alignment as well as high accuracy and sensitivity for detecting sequence variations.
The Oxidoreductase DsbA1 negatively influences 2,4-diacetylphloroglucinol biosynthesis by interfering the function of Gcd in Pseudomonas fluorescens 2P24
Authors: Zhang Bo , Zhao Hui , Wu Xiaogang , Zhang Li-Qun 
Published: February 2020

Abstract
Background
The polyketide antibiotic 2,4-diacetylphloroglucinol (2,4-DAPG), produced by Pseudomonas fluorescens 2P24, is positively regulated by the GacS-GacA two-component system.

Results
Here we reported on the characterization of DsbA1 (disulfide oxidoreductase) as novel regulator of biocontrol activity in P. fluorescens. Our data showed that mutation of dsbA1 caused the accumulation of 2,4-DAPG in a GacA-independent manner. Further analysis indicated that DsbA1 interacts with membrane-bound glucose dehydrogenase Gcd, which positively regulates the production of 2,4-DAPG. Mutation of cysteine (C)-235, C275, and C578 of Gcd, significantly reduced the interaction with DsbA1, enhanced the activity of Gcd and increased 2,4-DAPG production.

Conclusions
Our results suggest that DsbA1 regulates the 2,4-DAPG concentration via fine-tuning the function of Gcd in P. fluorescens 2P24.
A simulation study to compare different estimation approaches for network meta-analysis and corresponding methods to evaluate the consistency assumption
Authors: Kiefer Corinna , Sturtz Sibylle , Bender Ralf 
Published: February 2020

AbstractBackgroundNetwork meta-analysis (NMA) is becoming increasingly popular in systematic reviews and health technology assessments. However, there is still ambiguity concerning the properties of the estimation approaches as well as for the methods to evaluate the consistency assumption.MethodsWe conducted a simulation study for networks with up to 5 interventions. We investigated the properties of different methods and give recommendations for practical application. We evaluated the performance of 3 different models for complex networks as well as corresponding global methods to evaluate the consistency assumption. The models are the frequentist graph-theoretical approach netmeta, the Bayesian mixed treatment comparisons (MTC) consistency model, and the MTC consistency model with stepwise removal of studies contributing to inconsistency identified in a leverage plot.ResultsWe found that with a high degree of inconsistency none of the evaluated effect estimators produced reliable results, whereas with moderate or no inconsistency the estimator from the MTC consistency model and the netmeta estimator showed acceptable properties. We also saw a dependency on the amount of heterogeneity. Concerning the evaluated methods to evaluate the consistency assumption, none was shown to be suitable.ConclusionsBased on our results we recommend a pragmatic approach for practical application in NMA. The estimator from the netmeta approach or the estimator from the Bayesian MTC consistency model should be preferred. Since none of the methods to evaluate the consistency assumption showed satisfactory results, users should have a strong focus on the similarity as well as the homogeneity assumption.