bluuebunny/crossref_metadata_2025_split huggingface dataset:
A tensed Tendyne
Authors: Grinberg Daniel , Pozzi Matteo , Bernard Chloé , Obadia Jean-Francois 
Published: March 2020

Abstract
We report a case of prosthesis dislodgement after transcatheter mitral valve replacement in an 85-year-old woman with chronic ischaemic heart failure. Two weeks after an initial successful implantation, she presented with a paravalvular leak associated with left ventricular outflow tract obstruction. Tether re-tensioning was performed and resolved the situation, but resulted in a deformation of the apical attachment zone into the left ventricle. Unfortunately, the patient finally expired from severe endocarditis. Proper anchoring is the main challenge for transcatheter mitral valve replacement techniques. Dislodgement of the prosthesis after transcatheter mitral valve replacement is an infrequent complication of the Tendyne® procedure. This case emphasizes the importance of assessing the quality of the myocardium at the implantation zone of the apical pad, and of prosthesis oversizing, especially if low-profile valves are chosen. .
Early Careers of Dropouts from Vocational Training: Signals, Human Capital Formation, and Training Firms
Authors: Patzina Alexander , Wydra-Somaggio Gabriele 
Published: March 2020

Abstract
Dropping out of post-secondary education has negative consequences for career progression. However, as human capital theory predicts and as previous studies have shown, having some training still pays off. For a large part of the European workforce who has attended vocational training, however, the theoretical predictions are less clear and empirical studies are scarce. In occupational labour markets, signalling and credentialism theories predict negative effects of dropping out. Furthermore, apprenticeship dropouts learn at different training firms, which differ in their influence on human capital development and the provision of job opportunities. Relying on a unique panel data set from Germany and estimating normalized fixed effects growth curve estimators, our study reveals the following results. First, the timing of dropping out structures career progression, as late dropouts have the highest employment rates and highest wages within the dropout population. However, in an occupational labour market setting, credentials and signals are still highly important for career progression, as the wage advantage of late dropouts within the dropout population is rather small, and late dropouts suffer a wage penalty when we compare their wage profiles to those of graduates. Second, our study emphasizes the importance of training firms, which influence the human capital development of individuals during the course of training and provide dropouts with connections to their first jobs. Thus, in occupational labour markets, the consequences of dropping out depend mainly on different mechanisms, as in other settings.
Can the State Accelerate the Secular Transition? Secularization in East and West Germany as a Natural Experiment
Authors: Stolz Jörg , Pollack Detlef , De Graaf Nan Dirk 
Published: March 2020

AbstractGermany was a divided country from 1949 until 1989. During this period, West Germany remained a rather religious country, while East Germany became, under socialist rule, one of the most secular regions in the world. We use this case of socialist state intervention as a natural experiment to test Voas’ model of secular transition, which states that all Western and Central European countries follow the same path and speed of secularization. We employ ESS, GSS, and KMU surveys, as well as church statistics, to show that Voas’ model holds for West Germany but not for the East. In East Germany, the state accelerated the secular transition substantially: through coercion, incentive structures, and education, it succeeded in triggering mass disaffiliations from the church irrespective of age, and in discouraging parents from socializing their children religiously. This led to a self-perpetuating process that resulted in a rapid increase in the number of people who were never socialized religiously at all.
HAMAP as SPARQL rules—A portable annotation pipeline for genomes and proteomes
Authors: Bolleman Jerven , de Castro Edouard , Baratin Delphine , Gehant Sebastien , Cuche Beatrice A , Auchincloss Andrea H , Coudert Elisabeth , Hulo Chantal , Masson Patrick , Pedruzzi Ivo , Rivoire Catherine , Xenarios Ioannis , Redaschi Nicole , Bridge Alan 
Published: March 2020

Abstract

Background
Genome and proteome annotation pipelines are generally custom built and not easily reusable by other groups. This leads to duplication of effort, increased costs, and suboptimal annotation quality. One way to address these issues is to encourage the adoption of annotation standards and technological solutions that enable the sharing of biological knowledge and tools for genome and proteome annotation.

Results
Here we demonstrate one approach to generate portable genome and proteome annotation pipelines that users can run without recourse to custom software. This proof of concept uses our own rule-based annotation pipeline HAMAP, which provides functional annotation for protein sequences to the same depth and quality as UniProtKB/Swiss-Prot, and the World Wide Web Consortium (W3C) standards Resource Description Framework (RDF) and SPARQL (a recursive acronym for the SPARQL Protocol and RDF Query Language). We translate complex HAMAP rules into the W3C standard SPARQL 1.1 syntax, and then apply them to protein sequences in RDF format using freely available SPARQL engines. This approach supports the generation of annotation that is identical to that generated by our own in-house pipeline, using standard, off-the-shelf solutions, and is applicable to any genome or proteome annotation pipeline.

Conclusions
HAMAP SPARQL rules are freely available for download from the HAMAP FTP site, ftp://ftp.expasy.org/databases/hamap/sparql/, under the CC-BY-ND 4.0 license. The annotations generated by the rules are under the CC-BY 4.0 license. A tutorial and supplementary code to use HAMAP as SPARQL are available on GitHub at https://github.com/sib-swiss/HAMAP-SPARQL, and general documentation about HAMAP can be found on the HAMAP website at https://hamap.expasy.org.
Cumulative Histologic Inflammation Predicts Colorectal Neoplasia in Ulcerative Colitis: A Validation Study
Authors: Yvellez Olivia V , Rai Victoria , Sossenheimer Philip H , Hart John , Turner Jerrold R , Weber Christopher , El Jurdi Katia , Rubin David T 
Published: March 2020

Abstract

Background
Chronic inflammation in ulcerative colitis (UC) is associated with the development of colorectal neoplasia (CRN). A group at St. Mark’s Hospital reported a novel cumulative inflammatory index that predicted the development of CRN in UC patients that we validated with an independent, well-described, matched, case-controlled cohort from the University of Chicago.

Methods
Cumulative inflammatory burden (CIB) was calculated by summing each histological inflammatory activity (HIA) score and multiplying it by the length of the surveillance interval. Persistency was defined by the number of surveillance episodes (with a severity score &gt;2) divided by the total number of surveillance procedures. T tests compared the mean and maximum HIA scores, assessing mean and maximum severity, CIB, and persistency.

Results
Sixty-two UC patients (26 patients with CRN, 36 control patients without CRN) were analyzed. Fifty-five percent were men, mean disease duration was 20.6 years, and mean age at CRN diagnosis was 43.9. Of the CRN patients, 6 (23%) had colorectal cancer, 16 (62%) had low-grade dysplasia, and 4 (15%) had indefinite dysplasia. Using mean HIA scores, we found CIB to be statistically greater in CRN patients (P = 0.04). Using maximum HIA scores, we found CIB (P = 0.02), mean severity (P = 0.03), and persistency (P = 0.01) to be significantly greater in CRN patients. Maximum severity was numerically greater for mean and maximum HIA scores but did not reach significance.

Conclusion
Cumulative histologic inflammation is significantly associated with the development of CRN in UC patients. This suggests a management strategy of controlling inflammation to reduce the risk of CRN and may influence the selection of surveillance intervals.
Characterizing the historical role of parenteral antischistosomal therapy in hepatitis C virus transmission in Egypt
Authors: Ayoub Houssein H , Chemaitelly Hiam , Kouyoumjian Silva P , Abu-Raddad Laith J 
Published: March 2020

Abstract

Background
Egypt is the nation most affected by hepatitis C virus (HCV) infection, following an epidemic of historic proportions. We aimed to characterize the epidemic’s historical evolution and to delineate the role of parenteral antischistosomal therapy (PAT) campaigns in transmission.

Methods
A mathematical model was constructed and analysed in order to understand HCV-transmission dynamics. The model was fitted to Egypt’s Demographic and Health Survey data and to a systematic database of HCV-prevalence data.

Results
The incidence rate peaked in 1966 at 15.7 infections per 1000 person-years—a period of time that coincides with the PAT campaigns—and rapidly declined thereafter, beginning the mid-1990s. The annual number of new infections peaked in 1993 at 581 200 (with rapid demographic growth), leading to a high-incidence-cohort effect, and declined to 67 800 by 2018. The number of individuals ever infected (1950–2018) was 16.4 million, with HCV prevalence peaking in 1979. The number of individuals ever exposed to PAT was 8.3 million; however, of these individuals, 7.3 million were alive in 1980 and only 3.5 million alive in 2018. The number of individuals ever infected due to PAT exposure was 963 900, with 850 200 individuals alive in 1980 and only 389 800 alive in 2018. The proportion of PAT-attributed prevalent infections peaked at 19.9% in 1972, declining to 5.5% by 2018.

Conclusions
PAT campaigns played an important role in HCV transmission, yet explain only 6% of infections—they appear to be a manifestation, rather than a cause, of the epidemic. A possible driver of the epidemic could be the mass expansion of inadequate-quality healthcare during PAT campaigns and subsequent decades. Despite a historic toll, the epidemic has been rapidly diminishing since the mid-1990s.
High-contrast approximation for penetrable wedge diffraction
Authors: Nethercote M A , Assier R C , Abrahams I D 
Published: March 2020

Abstract
The important open canonical problem of wave diffraction by a penetrable wedge is considered in the high-contrast limit. Mathematically, this means that the contrast parameter, the ratio of a specific material property of the host and the wedge scatterer, is assumed small. The relevant material property depends on the physical context and is different for acoustic and electromagnetic waves for example. Based on this assumption, a new asymptotic iterative scheme is constructed. The solution to the penetrable wedge is written in terms of infinitely many solutions to (possibly inhomogeneous) impenetrable wedge problems. Each impenetrable problem is solved using a combination of the Sommerfeld–Malyuzhinets and Wiener–Hopf techniques. The resulting approximated solution to the penetrable wedge involves a large number of nested complex integrals and is hence difficult to evaluate numerically. In order to address this issue, a subtle method (combining asymptotics, interpolation and complex analysis) is developed and implemented, leading to a fast and efficient numerical evaluation. This asymptotic scheme is shown to have excellent convergent properties and leads to a clear improvement on extant approaches.
Hyperbolic Groups That Are Not Commensurably Co-Hopfian
Authors: Stark Emily , Woodhouse Daniel J 
Published: March 2020

Abstract
Sela proved that every torsion-free one-ended hyperbolic group is co-Hopfian. We prove that there exist torsion-free one-ended hyperbolic groups that are not commensurably co-Hopfian. In particular, we show that the fundamental group of every simple surface amalgam is not commensurably co-Hopfian.
Toxicological Assessment of the Role of Alcohol and Drugs in Drug-Facilitated Sexual Assault Cases in New Zealand
Authors: Poulsen Helen , McCarthy Mary-Jane , Baker Jessica , Verma Avnish , Moir Hannah J , Brodie Tara , Thatti Baljit , Trotter Gavin , Rooney Brian 
Published: March 2020

Abstract
This report details the toxicology profile of victims of drug-facilitated sexual assault (DFSA) in New Zealand from 2015 to 2018. This study represents all of the toxicology results for DFSA cases in New Zealand during this time period, of which there were 161 cases. Blood and urine samples were screened for legal and illicit drugs in addition to testing for alcohol and correlating alcohol concentration with sampling delay. Our results indicate that increased delay in sampling time resulted in a corresponding decrease in alcohol concentration. In victims who had declared alcohol use but of which none was detected, the average sampling time was 14 hours for blood and 17 hours for urine, which is in excess of the average sampling delay for even the lowest alcohol-positive samples. The most frequently detected alcohol concentration was in the range of 51–80 mg/100 mL for blood and 121–200 mg/100 mL for urine with an average sampling time of 8.5 and 6.5 hours, respectively. We also examined acetone concentrations in alcohol-positive samples, and our results indicate that 82% of blood alcohol-positive samples contained acetone at concentrations between 5 and 10 mg/L and 68% of alcohol-positive urine samples contained acetone at a concentration &gt;20 mg/L. It may be that the nature of sexual assault affects an individual’s metabolism of alcohol and results in increased acetone production. Cannabis was the most commonly detected illicit drug, followed by methamphetamine. In relation to medicinal drugs, there was a high usage of antidepressants and antipsychotics, suggesting the victims may have been people of vulnerable personality. Based on case information, it does not appear there are many cases where stupefaction by unknown administration of a drug has occurred, instead loss of consent through voluntary alcohol and drug consumption is more common and poses a greater risk than surreptitious drug administration.
MicroRNA-760 inhibits cell viability and migration through down-regulating BST2 in gastric cancer
Authors: Liu Weiyu , Li Yan , Feng Shuting , Guan Yadi , Cao Yong 
Published: March 2020

Abstract
Gastric cancer is one of the most common types of carcinoma with a threat to global health. MicroRNA-760 (miR-760) was significantly down-regulated in the primary tumour of patients with advanced gastric cancer. However, the role of miR-760 in gastric cancer is still unclear. Herein, miR-760 was down-regulated in gastric cancer tissues. Moreover, miR-760 overexpression and knockdown were conducted in gastric cancer cells (MGC-803 and SGC-7901) in vitro. The in vitro functional assays proved that miR-760 overexpression reduced cell viability, cell cycle, migration and invasion, promoted apoptosis and suppressed MMP activity in MGC-803 cells. Conversely, miR-760 knockdown led to the opposite in SGC-7901 cells. Notably, bone marrow stromal antigen 2 (BST2) was verified as a target gene of miR-760. MiR-760 mimics down-regulated BST2 level in gastric cancer tissues and in MGC-803 cells, whereas miR-760 inhibitor up-regulated its level in SGC-7901 cells. MiR-760-regulated cell properties through reduction of BST2. In addition, miR-760 inhibited tumourigenesis in a nude mouse xenograft model in vivo. In conclusion, our results demonstrated that miR-760 exhibited a suppressive role in gastric cancer via inhibiting BST2, indicating that miR-760/BST2 axis may provide promising therapeutic target for gastric cancer.
Home range size and resource use by swift foxes in northeastern Montana
Authors: Butler Andrew R , Bly Kristy L S , Harris Heather , Inman Robert M , Moehrenschlager Axel , Schwalm Donelle , Jachowski David S 
Published: March 2020

Abstract
Swift foxes (Vulpes velox) are endemic to the Great Plains of North America, but were extirpated from the northern portion of their range by the mid-1900s. Despite several reintroductions to the Northern Great Plains, there remains a ~350 km range gap between the swift fox population along the Montana and Canada border and that in northeastern Wyoming and northwestern South Dakota. A better understanding of what resources swift foxes use along the Montana and Canada border region will assist managers to facilitate connectivity among populations. From 2016 to 2018, we estimated the home range size and evaluated resource use within the home ranges of 22 swift foxes equipped with Global Positioning System tracking collars in northeastern Montana. Swift fox home ranges in our study were some of the largest ever recorded, averaging (± SE) 42.0 km2 ± 4.7. Our results indicate that both environmental and anthropogenic factors influenced resource use. At the population level, resource use increased by 3.3% for every 5.0% increase in percent grasslands. Relative probability of use decreased by 7.9% and 7.4% for every kilometer away from unpaved roads and gas well sites, respectively, and decreased by 3.0% and 11.3% for every one-unit increase in topographic roughness and every 0.05 increase in normalized difference vegetation index (NDVI), respectively. Our study suggests that, to reestablish connectivity among swift fox populations in Montana, managers should aim to maintain large corridors of contiguous grasslands at a landscape scale, a process that likely will require having to work with multiple property owners.
Cryptococcal arthritis in an immunocompetent migrant
Authors: Mokrzycki Alexandra , Meyssonnier Vanina , Heym Beate , Aubert Thomas , Mouton Antoine , Marmor Simon , Zeller Valérie 
Published: March 2020

Cryptococcosis is a rare infection in immunocompetent patients. While the lungs and the central nervous system are most often involved, skeletal cryptococcosis is uncommon.
We report a case of isolated osteoarthritis of the ankle due to Cryptococcus neoformans in a 24-year-old immunocompetent patient, who underwent surgical and medical treatment with total recovery at 6 months.
Multiple Genetic Trajectories to Extreme Abiotic Stress Adaptation in Arctic Brassicaceae
Authors: Birkeland Siri , Gustafsson A Lovisa S , Brysting Anne K , Brochmann Christian , Nowak Michael D 
Published: March 2020

Abstract
Extreme environments offer powerful opportunities to study how different organisms have adapted to similar selection pressures at the molecular level. Arctic plants have adapted to some of the coldest and driest biomes on Earth and typically possess suites of similar morphological and physiological adaptations to extremes in light and temperature. Here, we compare patterns of molecular evolution in three Brassicaceae species that have independently colonized the Arctic and present some of the first genetic evidence for plant adaptations to the Arctic environment. By testing for positive selection and identifying convergent substitutions in orthologous gene alignments for a total of 15 Brassicaceae species, we find that positive selection has been acting on different genes, but similar functional pathways in the three Arctic lineages. The positively selected gene sets identified in the three Arctic species showed convergent functional profiles associated with extreme abiotic stress characteristic of the Arctic. However, there was little evidence for independently fixed mutations at the same sites and for positive selection acting on the same genes. The three species appear to have evolved similar suites of adaptations by modifying different components in similar stress response pathways, implying that there could be many genetic trajectories for adaptation to the Arctic environment. By identifying candidate genes and functional pathways potentially involved in Arctic adaptation, our results provide a framework for future studies aimed at testing for the existence of a functional syndrome of Arctic adaptation in the Brassicaceae and perhaps flowering plants in general.
Computational identification of cell-specific variable regions in ChIP-seq data
Authors: Andreani Tommaso , Albrecht Steffen , Fontaine Jean-Fred , Andrade-Navarro Miguel A 
Published: March 2020

Abstract
Chromatin immunoprecipitation followed by sequencing (ChIP-seq) is used to identify genome-wide DNA regions bound by proteins. Given one ChIP-seq experiment with replicates, binding sites not observed in all the replicates will usually be interpreted as noise and discarded. However, the recent discovery of high-occupancy target (HOT) regions suggests that there are regions where binding of multiple transcription factors can be identified. To investigate ChIP-seq variability, we developed a reproducibility score and a method that identifies cell-specific variable regions in ChIP-seq data by integrating replicated ChIP-seq experiments for multiple protein targets on a particular cell type. Using our method, we found variable regions in human cell lines K562, GM12878, HepG2, MCF-7 and in mouse embryonic stem cells (mESCs). These variable-occupancy target regions (VOTs) are CG dinucleotide rich, and show enrichment at promoters and R-loops. They overlap significantly with HOT regions, but are not blacklisted regions producing non-specific binding ChIP-seq peaks. Furthermore, in mESCs, VOTs are conserved among placental species suggesting that they could have a function important for this taxon. Our method can be useful to point to such regions along the genome in a given cell type of interest, to improve the downstream interpretative analysis before follow-up experiments.
A Snu114–GTP–Prp8 module forms a relay station for efficient splicing in yeast
Authors: Jia Junqiao , Ganichkin Oleg M , Preußner Marco , Absmeier Eva , Alings Claudia , Loll Bernhard , Heyd Florian , Wahl Markus C 
Published: March 2020

AbstractThe single G protein of the spliceosome, Snu114, has been proposed to facilitate splicing as a molecular motor or as a regulatory G protein. However, available structures of spliceosomal complexes show Snu114 in the same GTP-bound state, and presently no Snu114 GTPase-regulatory protein is known. We determined a crystal structure of Snu114 with a Snu114-binding region of the Prp8 protein, in which Snu114 again adopts the same GTP-bound conformation seen in spliceosomes. Snu114 and the Snu114–Prp8 complex co-purified with endogenous GTP. Snu114 exhibited weak, intrinsic GTPase activity that was abolished by the Prp8 Snu114-binding region. Exchange of GTP-contacting residues in Snu114, or of Prp8 residues lining the Snu114 GTP-binding pocket, led to temperature-sensitive yeast growth and affected the same set of splicing events in vivo. Consistent with dynamic Snu114-mediated protein interactions during splicing, our results suggest that the Snu114–GTP–Prp8 module serves as a relay station during spliceosome activation and disassembly, but that GTPase activity may be dispensable for splicing.