bluuebunny/crossref_metadata_2025_split huggingface dataset:
Survival and course of lung function in the presence or absence of antifibrotic treatment in patients with idiopathic pulmonary fibrosis: long-term results of the INSIGHTS-IPF registry
Authors: Behr Jürgen , Prasse Antje , Wirtz Hubert , Koschel Dirk , Pittrow David , Held Matthias , Klotsche Jens , Andreas Stefan , Claussen Martin , Grohé Christian , Wilkens Henrike , Hagmeyer Lars , Skowasch Dirk , Meyer Joachim F. , Kirschner Joachim , Gläser Sven , Kahn Nicolas , Welte Tobias , Neurohr Claus , Schwaiblmair Martin , Bahmer Thomas , Oqueka Tim , Frankenberger Marion , Kreuter Michael 
Published: May 2020

ObjectiveThere is a paucity of observational data on antifibrotic therapy for idiopathic pulmonary fibrosis (IPF). We aimed to assess the course of disease of IPF patients with and without antifibrotic therapy under real-life conditions.MethodsWe analysed data from a non-interventional, prospective cohort study of consecutively enrolled IPF patients from 20 interstitial lung disease expert centres in Germany. Data quality was ensured by automated plausibility checks, on-site monitoring, and source data verification. Propensity scores were applied to account for known differences in baseline characteristics between patients with and without antifibrotic therapy.ResultsAmong the 588 patients suitable for analysis, the mean±sdage was 69.8±9.1 years, and 81.0% were male. The mean±sdduration of disease since diagnosis was 1.8±3.4 years. The mean±sdvalue at baseline for forced vital capacity (FVC) and diffusion capacity (DLCO) were 68.6±18.8% predicted and 37.8±18.5% predicted, respectively. During a mean±sdfollow-up of 1.2±0.7 years, 194 (33.0%) patients died. The 1-year and 2-year survival rates were 87%versus46% and 62%versus21%, respectively, for patients withversuswithout antifibrotic therapy. The risk of death was 37% lower in patients with antifibrotic therapy (hazard ratio 0.63, 95% CI 0.45; 0.87; p=0.005). The results were robust (and remained statistically significant) on multivariable analysis. Overall decline of FVC andDLCOwas slow and did not differ significantly between patients with or without antifibrotic therapy.ConclusionsSurvival was significantly higher in IPF patients with antifibrotic therapy, but the course of lung function parameters was similar in patients with and without antifibrotic therapy. This suggests that in clinical practice, premature mortality of IPF patients eventually occurs despite stable measurements for FVC andDLCO.
EEG-IP: an international infant EEG data integration platform for the study of risk and resilience in autism and related conditions
Authors: van Noordt Stefon , Desjardins James A. , Huberty Scott , Abou-Abbas Lina , Webb Sara Jane , Levin April R. , Segalowitz Sidney J. , Evans Alan C. , Elsabbagh Mayada 
Published: May 2020

Abstract
Background
Establishing reliable predictive and diganostic biomarkers of autism would enhance early identification and facilitate targeted intervention during periods of greatest plasticity in early brain development. High impact research on biomarkers is currently limited by relatively small sample sizes and the complexity of the autism phenotype.

Methods
EEG-IP is an International Infant EEG Data Integration Platform developed to advance biomarker discovery by enhancing the large scale integration of multi-site data. Currently, this is the largest multi-site standardized dataset of infant EEG data.

Results
First, multi-site data from longitudinal cohort studies of infants at risk for autism was pooled in a common repository with 1382 EEG longitudinal recordings, linked behavioral data, from 432 infants between 3- to 36-months of age. Second, to address challenges of limited comparability across independent recordings, EEG-IP applied the Brain Imaging Data Structure (BIDS)-EEG standard, resulting in a harmonized, extendable, and integrated data state. Finally, the pooled and harmonized raw data was preprocessed using a common signal processing pipeline that maximizes signal isolation and minimizes data reduction. With EEG-IP, we produced a fully standardized data set, of the pooled, harmonized, and pre-processed EEG data from multiple sites.

Conclusions
Implementing these integrated solutions for the first time with infant data has demonstrated success and challenges in generating a standardized multi-site data state. The challenges relate to annotation of signal sources, time, and ICA analysis during pre-processing. A number of future opportunities also emerge, including validation of analytic pipelines that can replicate existing findings and/or test novel hypotheses.
A WS2 Case Theoretical Study: Hydrogen Storage Performance Improved by Phase Altering
Authors: Zhou Jing , Cao Jiamu , Shi Jianing , Zhang Yufeng , Chen Junyu , Wang Weiqi , Liu Xiaowei 
Published: May 2020

AbstractHydrogen is a clean energy with high efficiency, while the storage and transport problems still prevent its extensive use. Because of the large specific surface area and unique electronic structure, two-dimensional materials have great potential in hydrogen storage. Particularly, monolayer 2H-WS2 has been proven to be suitable for hydrogen storage. But there are few studies concerning the other two phases of WS2 (1T, 1T′) in hydrogen storage. Here, we carried out first-principle calculations to investigate the hydrogen adsorption behaviors of all the three phases of WS2. Multiple hydrogen adsorption studies also evaluate the hydrogen storage abilities of these materials. Comprehensive analysis results show that the 1T′-WS2 has better hydrogen storage performance than the 2H-WS2, which means phase engineering could be an effective way to improve hydrogen storage performance. This paper provides a reference for the further study of hydrogen storage in two-dimensional materials.
The EMR-rural project: key techniques and devices development for rural environmental monitoring and remediation in China
Authors: Chen Zhongli , Shao Ying , He Miao , Liang Jialiang , Jiang Yanxue , Wang Yayi , Zhou Minghua , Gong Zongqiang , Zhou Xiaohong , Fang Fang , Guo Jinsong 
Published: May 2020

AbstractRural development, as one of the biggest challenges facing human beings recently, has attracted widely attention in the world, among which rural environment protection is essential for sustainable development. In response to the call to build “green livable villages”, the environmental monitoring and remediation in rural project (EMR-rural project) is launched. EMR-rural (2019 to 2022) is funded by the Ministry of Science and Technology of the People’s Republic of China (MOST). The project aims to develop key techniques and devices for contamination classification, risk assessment, pollution sources tracing and environmental remediation with regard to soil, underground and surface water quality in rural area. To this end, a new generation of physical, chemical and biological tools is integrated with intelligent management platform. The project follows a problem-oriented approach by in situ investigation, lab/pilot-scale mechanism exploration and field determination. EMR-rural takes advantage of the access to the applicable techniques and devices to investigate and to restore soil and water pollution in river network areas, mountainous areas as well as cold areas of China.
Natural and anthropogenic driving forces as key elements in the Lower Danube Basin–South-Eastern Carpathians–North-Western Black Sea coast area lakes: a broken stepping stones for fish in a climatic change scenario?
Authors: Bănăduc Doru , Joy Michael , Olosutean Horea , Afanasyev Sergey , Curtean-Bănăduc Angela 
Published: May 2020

Abstract
Background
Climate changes influence the ecosystems and induce potential risks regarding the natural products and services; the human society should predict and adapt in time to these coming global challenges. This research highlights a possible fragmentation of some of the Lower Danube River Basin lentic ecosystems fish populations in a climate change scenario.

Results
The studied climate change potential events will affect 18 fish species of economic interest and eight of conservation interest and will induce disorder in some of the Lower Danube specific type of fish communities. The studied area was identified as a significant hot spot regarding the fish fauna ecological status major hazard, in a possible climate change (heating–drought–water depth decreasing) sequence of potential future events. Primarily the southern lakes of the studied area can be negatively influenced by the decreasing of the lakes water quality and quantity, some of the spawning habitats will vanish, some habitats and species will disappear, suspended sediment and nutrient levels in water will increase, eutrophication phenomenon will increase, the hydrological connectivity will diminish, fish associations’ structure will significantly change, etc.

Conclusions
The climate changes trend in the Lower Danube Basin will affect the studied lakes ecological state and associated fish communities; mitigating measures are urgently needed. The future potential relative isolation of researched lakes by the surrounding hydrographical nets, for safety reasons of human communities or to convert inland areas should be banned specially for the lakes: Balta Domnească, Razelm, Tăbăcărie, Siutghiol, Taşaul, Tatlageac, Sinoe, Potcoava, Snagov, Comana, Victoria Gheormane, Dunărea Veche, Oltina, and Bugeac. Some of the researched lakes should be managed as wetlands of international importance and as important stepping stone areas for the fish fauna of the Danube Basin: Snagov, Comana, Victoria Gheormane, Dunărea Veche, Oltina, and Bugeac.
Prevalence and factors associated with pedestrian fatalities and serious injuries: case Finland
Authors: Malin Fanny , Silla Anne , Mladenović Miloš N. 
Published: May 2020

AbstractThe aim of the study was to examine the prevalence of pedestrian fatalities and serious injuries (MAIS3+) in traffic, and to identify differences in the factors associated with the injury severities. The study included all motor vehicle-pedestrian accidents in Finland in 2014–2017 and exposure data from the national travel survey of 2016. The results showed a heightened fatality and serious injury rate specifically for pedestrians aged over 75 years and in rural heartland areas. Furthermore, differences were identified in the current speed limit, municipality type, lighting conditions, vehicle type, area type, accident location, and road conditions between pedestrian fatalities and serious injuries. The main implications of the study are that traffic safety measures should be tailored to local conditions and amended and redirected to account for both fatalities and serious injuries. In order to conduct comparative studies between countries and support the achievement of transport policy objectives, further harmonisation of definitions and data collection procedures for traffic accidents is needed.
Identifying novel associations in GWAS by hierarchical Bayesian latent variable detection of differentially misclassified phenotypes
Authors: Shafquat Afrah , Crystal Ronald G. , Mezey Jason G. 
Published: May 2020

Abstract
Background
Heterogeneity in the definition and measurement of complex diseases in Genome-Wide Association Studies (GWAS) may lead to misdiagnoses and misclassification errors that can significantly impact discovery of disease loci. While well appreciated, almost all analyses of GWAS data consider reported disease phenotype values as is without accounting for potential misclassification.

Results
Here, we introduce Phenotype Latent variable Extraction of disease misdiagnosis (PheLEx), a GWAS analysis framework that learns and corrects misclassified phenotypes using structured genotype associations within a dataset. PheLEx consists of a hierarchical Bayesian latent variable model, where inference of differential misclassification is accomplished using filtered genotypes while implementing a full mixed model to account for population structure and genetic relatedness in study populations. Through simulations, we show that the PheLEx framework dramatically improves recovery of the correct disease state when considering realistic allele effect sizes compared to existing methodologies designed for Bayesian recovery of disease phenotypes. We also demonstrate the potential of PheLEx for extracting new potential loci from existing GWAS data by analyzing bipolar disorder and epilepsy phenotypes available from the UK Biobank. From the PheLEx analysis of these data, we identified new candidate disease loci not previously reported for these datasets that have value for supplemental hypothesis generation.

Conclusion
PheLEx shows promise in reanalyzing GWAS datasets to provide supplemental candidate loci that are ignored by traditional GWAS analysis methodologies.
A method for obtaining flexible broccoli varieties for sustainable agriculture
Authors: Ciancaleoni Simona , Negri Valeria 
Published: May 2020

Abstract
Background
The use of high inputs in agriculture resulted in few varieties (hybrids and pure lines) used in all agricultural systems. Also varieties of vegetables, including broccoli, for organic and low-input agriculture, are almost exclusively hybrids, since there are very few specific breeding programs and varieties for sustainable agriculture systems.
A strategy to overcome this issue is the adoption of specific breeding programs for developing heterogeneous varieties (i.e. synthetics, open pollinated varieties, composite cross populations and mixtures). In fact, heterogeneous varieties are able to evolve and adapt to specific agro-climatic conditions.
The aim of this study was to develop a method (an Evolutionary Breeding Program, EBP) for obtaining heterogeneous varieties of broccoli and test its efficiency in developing highly diverse varieties, as needed in sustainable agriculture.
A synthetic variety originated from a landrace was multiplied in different environments for 3 cycles and morpho-phenological and genetic diversity of the derived populations were assessed.

Results
The presented results are the first and unique indication about the efficiency of a short-time EBP for an allogamous species like broccoli.
Few morphological changes were observed among varieties multiplied in different environments with different agro-climatic conditions. This could be probably due to the initial genetic diversity of the landrace from which the populations were selected and also to the great plasticity of the crop. However, SSR data highlighted a genetic differentiation among populations multiplied for two/three years across Europe and in Central Italy, that was not so evident when considering morphological data only.

Conclusions
Few years of multiplication in different environments resulted in genetically differentiated broccoli populations that nonetheless preserved the original genetic diversity and productivity level and appear to evolve in relationship to different environments: the applied EBP is useful for developing heterogeneous materials for sustainable agriculture.
The tapeworm interactome: inferring confidence scored protein-protein interactions from the proteome of Hymenolepis microstoma
Authors: James Katherine , Olson Peter D. 
Published: May 2020

Abstract
Background
Reference genome and transcriptome assemblies of helminths have reached a level of completion whereby secondary analyses that rely on accurate gene estimation or syntenic relationships can be now conducted with a high level of confidence. Recent public release of the v.3 assembly of the mouse bile-duct tapeworm, Hymenolepis microstoma, provides chromosome-level characterisation of the genome and a stabilised set of protein coding gene models underpinned by bioinformatic and empirical data. However, interactome data have not been produced. Conserved protein-protein interactions in other organisms, termed interologs, can be used to transfer interactions between species, allowing systems-level analysis in non-model organisms.

Results
Here, we describe a probabilistic, integrated network of interologs for the H. microstoma proteome, based on conserved protein interactions found in eukaryote model species. Almost a third of the 10,139 gene models in the v.3 assembly could be assigned interaction data and assessment of the resulting network indicates that topologically-important proteins are related to essential cellular pathways, and that the network clusters into biologically meaningful components. Moreover, network parameters are similar to those of single-species interaction networks that we constructed in the same way for S. cerevisiae, C. elegans and H. sapiens, demonstrating that information-rich, system-level analyses can be conducted even on species separated by a large phylogenetic distance from the major model organisms from which most protein interaction evidence is based. Using the interolog network, we then focused on sub-networks of interactions assigned to discrete suites of genes of interest, including signalling components and transcription factors, germline multipotency genes, and genes differentially-expressed between larval and adult worms. Results show not only an expected bias toward highly-conserved proteins, such as components of intracellular signal transduction, but in some cases predicted interactions with transcription factors that aid in identifying their target genes.

Conclusions
With key helminth genomes now complete, systems-level analyses can provide an important predictive framework to guide basic and applied research on helminths and will become increasingly informative as new protein-protein interaction data accumulate.
Genome-wide association analyses identify known and novel loci for teat number in Duroc pigs using single-locus and multi-locus models
Authors: Zhuang Zhanwei , Ding Rongrong , Peng Longlong , Wu Jie , Ye Yong , Zhou Shenping , Wang Xingwang , Quan Jianping , Zheng Enqin , Cai Gengyuan , Huang Wen , Yang Jie , Wu Zhenfang 
Published: May 2020

AbstractBackgroundMore teats are necessary for sows to nurse larger litters to provide immunity and nutrient for piglets prior to weaning. Previous studies have reported the strong effect of an insertion mutation in the Vertebrae Development Associated (VRTN) gene onSus scrofachromosome 7 (SSC7) that increased the number of thoracic vertebrae and teat number in pigs. We used genome-wide association studies (GWAS) to map genetic markers and genes associated with teat number in two Duroc pig populations with different genetic backgrounds. A single marker method and several multi-locus methods were utilized. A meta-analysis that combined the effects andP-values of 34,681 single nucleotide polymorphisms (SNPs) that were common in the results of single marker GWAS of American and Canadian Duroc pigs was conducted. We also performed association tests between theVRTNinsertion and teat number in the same populations.ResultsA total of 97 SNPs were found to be associated with teat number. Among these, six, eight and seven SNPs were consistently detected with two, three and four multi-locus methods, respectively. Seven SNPs were concordantly identified between single marker and multi-locus methods. Moreover, 26 SNPs were newly found by multi-locus methods to be associated with teat number. Notably, we detected one consistent quantitative trait locus (QTL) on SSC7 for teat number using single-locus and meta-analysis of GWAS and the top SNP (rs692640845) explained 8.68% phenotypic variance of teat number in the Canadian Duroc pigs. The associations between theVRTNinsertion and teat number in two Duroc pig populations were substantially weaker. Further analysis revealed that the effect ofVRTNon teat number may be mediated by its LD with the true causal mutation.ConclusionsOur study suggested thatVRTNinsertion may not be a strong or the only candidate causal mutation for the QTL on SSC7 for teat number in the analyzed Duroc pig populations. The combination of single-locus and multi-locus GWAS detected additional SNPs that were absent using only one model. The identified SNPs will be useful for the genetic improvement of teat number in pigs by assigning higher weights to associated SNPs in genomic selection.
Chromosomal instability in untreated primary prostate cancer as an indicator of metastatic potential
Authors: Miller Eric T. , You Sungyong , Cadaneanu Radu M. , Kim Minhyung , Yoon Junhee , Liu Sandy T. , Li Xinmin , Kwan Lorna , Hodge Jennelle , Quist Michael J. , Grasso Catherine S. , Lewis Michael S. , Knudsen Beatrice S. , Freeman Michael R. , Garraway Isla P. 
Published: May 2020

Abstract
Background
Metastatic prostate cancer (PC) is highly lethal. The ability to identify primary tumors capable of dissemination is an unmet need in the quest to understand lethal biology and improve patient outcomes. Previous studies have linked chromosomal instability (CIN), which generates aneuploidy following chromosomal missegregation during mitosis, to PC progression. Evidence of CIN includes broad copy number alterations (CNAs) spanning > 300 base pairs of DNA, which may also be measured via RNA expression signatures associated with CNA frequency. Signatures of CIN in metastatic PC, however, have not been interrogated or well defined. We examined a published 70-gene CIN signature (CIN70) in untreated and castration-resistant prostate cancer (CRPC) cohorts from The Cancer Genome Atlas (TCGA) and previously published reports. We also performed transcriptome and CNA analysis in a unique cohort of untreated primary tumors collected from diagnostic prostate needle biopsies (PNBX) of localized (M0) and metastatic (M1) cases to determine if CIN was linked to clinical stage and outcome.

Methods
PNBX were collected from 99 patients treated in the VA Greater Los Angeles (GLA-VA) Healthcare System between 2000 and 2016. Total RNA was extracted from high-grade cancer areas in PNBX cores, followed by RNA sequencing and/or copy number analysis using OncoScan. Multivariate logistic regression analyses permitted calculation of odds ratios for CIN status (high versus low) in an expanded GLA-VA PNBX cohort (n = 121).

Results
The CIN70 signature was significantly enriched in primary tumors and CRPC metastases from M1 PC cases. An intersection of gene signatures comprised of differentially expressed genes (DEGs) generated through comparison of M1 versus M0 PNBX and primary CRPC tumors versus metastases revealed a 157-gene “metastasis” signature that was further distilled to 7-genes (PC-CIN) regulating centrosomes, chromosomal segregation, and mitotic spindle assembly. High PC-CIN scores correlated with CRPC, PC-death and all-cause mortality in the expanded GLA-VA PNBX cohort. Interestingly, approximately 1/3 of M1 PNBX cases exhibited low CIN, illuminating differential pathways of lethal PC progression.

Conclusions
Measuring CIN in PNBX by transcriptome profiling is feasible, and the PC-CIN signature may identify patients with a high risk of lethal progression at the time of diagnosis.