bluuebunny/crossref_metadata_2025 huggingface dataset:
Stability, reliability, upscaling and possible technological applications of kesterite solar cells
Authors: Larramona G , Choné C , Meissner D , Ernits K , Bras P , Ren Y , Martín-Salinas R , Rodríguez-Villatoro J L , Vermang B , Brammertz G
Published: March 2020

We review the stability and reliability results of kesterite (Cu2ZnSn(S,Se)4, CZTSSe)-based solar cells and we complete the reviewed data with additional as yet unpublished data on these matters. We also review published and new data on upscaling and the possible technological applications for this material. Kesterite material is composed of mainly earth-abundant elements and is therefore very attractive for large-scale applications. Stability data are so far quite scarce and the main results are the accelerated aging tests carried out for CZTSSe monograin technology, as well as yet unpublished data on long indoor and outdoor irradiance tests carried out on thin-film CZTSSe technology deposited by a wet processing method. On upscaling and technological applications we point out the works on three main large-scale photovoltaic technologies (monograin, in-line vacuum thin film, and wet-deposited thin film), as well as some work on water-splitting applications.
Cryoprecipitate Utilization Patterns Observed With a Required Prospective Approval Process vs Electronic Dosing Guidance
Authors: Kruse Robert L , Neally Melissa , Cho Brian C , Bloch Evan M , Lokhandwala Parvez M , Ness Paul M , Frank Steven M , Tobian Aaron A R , Gehrie Eric A
Published: March 2020

Objectives

We evaluated the impact of electronic medical record (EMR)–guided pooled cryoprecipitate dosing vs our previous practice of requiring transfusion medicine (TM) resident approval for every cryoprecipitate transfusion.

Methods

At our hospital, cryoprecipitate pooled from five donors is dosed for adult patients, while single-donor cryoprecipitate is dosed for pediatric patients (defined as patients <50 kg in weight). EMR-based dosing guidance replaced a previously required TM consultation when cryoprecipitate pools were ordered, but a consultation remained required for single-unit orders. Usage was defined as thawed cryoprecipitate; wastage was defined as cryoprecipitate that expired prior to transfusion.

Results

In the 6 months prior to intervention, 178 ± 13 doses of pooled cryoprecipitate were used per month vs 187 ± 15 doses after the intervention (P = .68). Wastage of pooled cryoprecipitate increased from 7.7% ± 1.5% to 12.7% ± 1.4% (P = .038). There was no change in wastage of pediatric cryoprecipitate doses during the study period. These trends remained unchanged for a full year postimplementation.

Conclusions

Electronic dosing guidance resulted in similar cryoprecipitate usage as TM auditing. Increased wastage may result from reduced TM oversight. Product wastage should be balanced against the possibility that real-time audits could delay a lifesaving therapy.
Xylem anatomy needs to change, so that conductivity can stay the same: xylem adjustments across elevation and latitude in Nothofagus pumilio
Authors: García-Cervigón Ana I , Fajardo Alex , Caetano-Sánchez Cristina , Camarero J Julio , Olano José Miguel
Published: March 2020

Background and Aims

Plants have the potential to adjust the configuration of their hydraulic system to maintain its function across spatial and temporal gradients. Species with wide environmental niches provide an ideal framework to assess intraspecific xylem adjustments to contrasting climates. We aimed to assess how xylem structure in the widespread species Nothofagus pumilio varies across combined gradients of temperature and moisture, and to what extent within-individual variation contributes to population responses across environmental gradients.

Methods

We characterized xylem configuration in branches of N. pumilio trees at five sites across an 18° latitudinal gradient in the Chilean Andes, sampling at four elevations per site. We measured vessel area, vessel density and the degree of vessel grouping. We also obtained vessel diameter distributions and estimated the xylem-specific hydraulic conductivity. Xylem traits were studied in the last five growth rings to account for within-individual variation.

Key Results

Xylem traits responded to changes in temperature and moisture, but also to their combination. Reductions in vessel diameter and increases in vessel density suggested increased safety levels with lower temperatures at higher elevation. Vessel grouping also increased under cold and dry conditions, but changes in vessel diameter distributions across the elevational gradient were site-specific. Interestingly, the estimated xylem-specific hydraulic conductivity remained constant across elevation and latitude, and an overwhelming proportion of the variance of xylem traits was due to within-individual responses to year-to-year climatic fluctuations, rather than to site conditions.

Conclusions

Despite conspicuous adjustments, xylem traits were coordinated to maintain a constant hydraulic function under a wide range of conditions. This, combined with the within-individual capacity for responding to year-to-year climatic variations, may have the potential to increase forest resilience against future environmental changes.
Sources of Multidrug Resistance in Patients With Previous Isoniazid-Resistant Tuberculosis Identified Using Whole Genome Sequencing: A Longitudinal Cohort Study
Authors: Srinivasan Vijay , Ha Vu T N , Vinh Dao N , Thai Phan V K , Ha Dang T M , Lan Nguyen H , Hai Hoang T , Walker Timothy M , Thu Do D A , Dunstan Sarah J , Thwaites Guy E , Ashton Philip M , Caws Maxine , Thuong Nguyen T T
Published: March 2020

Background

Meta-analysis of patients with isoniazid-resistant tuberculosis (TB) given standard first-line anti-TB treatment indicated an increased risk of multidrug-resistant TB (MDR-TB) emerging (8%), compared to drug-sensitive TB (0.3%). Here we use whole genome sequencing (WGS) to investigate whether treatment of patients with preexisting isoniazid-resistant disease with first-line anti-TB therapy risks selecting for rifampicin resistance, and hence MDR-TB.

Methods

Patients with isoniazid-resistant pulmonary TB were recruited and followed up for 24 months. Drug susceptibility testing was performed by microscopic observation drug susceptibility assay, mycobacterial growth indicator tube, and by WGS on isolates at first presentation and in the case of re-presentation. Where MDR-TB was diagnosed, WGS was used to determine the genomic relatedness between initial and subsequent isolates. De novo emergence of MDR-TB was assumed where the genomic distance was 5 or fewer single-nucleotide polymorphisms (SNPs), whereas reinfection with a different MDR-TB strain was assumed where the distance was 10 or more SNPs.

Results

Two hundred thirty-nine patients with isoniazid-resistant pulmonary TB were recruited. Fourteen (14/239 [5.9%]) patients were diagnosed with a second episode of TB that was multidrug resistant. Six (6/239 [2.5%]) were identified as having evolved MDR-TB de novo and 6 as having been reinfected with a different strain. In 2 cases, the genomic distance was between 5 and 10 SNPs and therefore indeterminate.

Conclusions

In isoniazid-resistant TB, de novo emergence and reinfection of MDR-TB strains equally contributed to MDR development. Early diagnosis and optimal treatment of isoniazid-resistant TB are urgently needed to avert the de novo emergence of MDR-TB during treatment.
Hierarchical Identity-Based Signature in Polynomial Rings
Authors: Yang Zhichao , Duong Dung H , Susilo Willy , Yang Guomin , Li Chao , Chen Rongmao
Published: March 2020

Hierarchical identity-based signature (HIBS) plays a core role in a large community as it significantly reduces the workload of the root private key generator. To make HIBS still available and secure in post-quantum era, constructing lattice-based schemes is a promising option. In this paper, we present an efficient HIBS scheme in polynomial rings. Although there are many lattice-based signatures proposed in recent years, to the best of our knowledge, our HIBS scheme is the first ring-based construction. In the center of our construction are two new algorithms to extend lattice trapdoors to higher dimensions, which are non-trivial and of independent interest. With these techniques, the security of the new scheme can be proved, assuming the hardness of the Ring-SIS problem. Since operations in the ring setting are much faster than those over integers and the new construction is the first ring-base HIBS scheme, our scheme is more efficient and practical in terms of computation and storage cost when comparing to the previous constructions.
A tensed Tendyne
Authors: Grinberg Daniel , Pozzi Matteo , Bernard Chloé , Obadia Jean-Francois
Published: March 2020

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

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

Germany 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

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

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 >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

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

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

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

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 >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

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

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

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

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

The 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.
PR3-ANCAs predict relapses in ANCA-associated vasculitis patients after rituximab
Authors: van Dam Laura S , Dirikgil Ebru , Bredewold Edwin W , Ray Argho , Bakker Jaap A , van Kooten Cees , Rabelink Ton J , Teng Yoe K Onno
Published: March 2020

Background. The primary challenge of anti-neutrophil cytoplasmic antibody (ANCA)-associated vasculitis (AAV) patient care is the early detection of relapses to prevent organ damage and increase survival. Potential biomarkers for relapses are ANCA and B cells, but their predictive value is a matter of debate. Therefore this study investigated how ANCA and B-cell status related to relapses in AAV patients treated with rituximab (RTX) as remission induction (RI).

Methods. This single-centre cohort study identified 110 ANCA-positive AAV patients treated with RTX between 2006 and 2018. Serial ANCA, CD19+ B-cell status and relapses were assessed >2 years.

Results. Patients (31/110) relapsed within 2 years after RTX RI treatment. Patients who achieved and maintained PR3-ANCA negativity (n = 29) had few relapses (3%), while persistent proteinase 3 (PR3)-ANCA positivity (n = 49) and reappearance of PR3-ANCAs (n = 10) associated significantly with more relapses (37%, P = 0.002 and 50%, P = 0.002). Patients with incomplete B-cell depletion (n = 11) had significantly more relapses (54%) as compared with patients with B-cell depletion [n = 76 (26%), P = 0.02]. Also, patients with repopulation of B cells (n = 58) had significantly more relapses (41%) as compared with patients without B-cell repopulation [n = 27 (15%), P = 0.03]. Overall, the absence of PR3- or myeloperoxidase (MPO)-ANCA positivity was highly predictive for remaining relapse-free. In PR3-ANCA-positive patients, 96% of the relapses occurred with persistent or reappearance of PR3-ANCAs and 81% with B-cell repopulation. In MPO-ANCA-positive patients, all relapses were restricted to patients with persistent MPO-ANCAs and B-cell repopulation.

Conclusions. Upon RI treatment with RTX in AAV patients, ANCA and B-cell status were predictive of the majority of relapses and specifically their absence strongly predicted a relapse-free status. Therefore the implementation of ANCA and B-cell monitoring could guide therapeutic decision-making to prevent relapses in AAV patients treated with RTX.
Embracing at arm’s length: Ronald Coase’s uneasy relationship with the Chicago school
Authors: Medema Steven G
Published: March 2020

This paper takes up Ronald Coase’s views on the Chicago school, as found in his published and, especially, unpublished writings. Coase’s personal and professional papers, recently opened for examination in the University of Chicago’s Regenstein Library, reveal that his commentaries on the Chicago Economics Department and the Chicago school began already in the early 1960s, prior to his appointment at Chicago. These and later commentaries at once reveal a measure of kinship and significant differences of viewpoint, particularly as respects economic method. Pulling back the lens a bit further, the paper provides additional evidence for the heterogeneity of views on fundamental questions that existed even among ostensibly cornerstone members of the so-called ‘Chicago school’.
Modern and Traditional Descriptive Approaches
Authors: Huddleston Rodney , Pullum Geoffrey K.
Published: March 2020

Theoretical linguists of the twentieth century made many discoveries about English grammar motivating abandonment of central assumptions of traditional grammars—assumptions often unquestioned for 300 years. This chapter surveys some of the central ways in which The Cambridge Grammar of the English Language (CGEL) (Huddleston and Pullum 2002) rejects the tradition. CGEL carefully distinguishes categories from functions; thus, for example, the category ‘adjective’ is not defined by reference to the function of noun modification. Pronouns are treated as syntactically special nouns, and auxiliaries as a special subclass of verbs. The category of prepositions is redefined to include many items traditionally misanalysed as adverbs or ‘subordinating conjunctions’. Subordinate clauses are classified by their internal structure. Both syntactic and pragmatic constraints on discourse-sensitive constructions are acknowledged. The chapter also briefly relates the implicit formal machinery of the CGEL description to that of certain other contemporary theoretical frameworks.
Clause Types and Speech Act Functions
Authors: König Ekkehard
Published: March 2020

The differentiation of clause types in this chapter (declarative, interrogative, imperative, exclamative) is primarily based on morpho-syntactic criteria, but is also motivated by the use of these types for the performance of speech acts, i.e. acts resulting in a change of social situations. Instead of relating the different types directly to a list of speech acts typically performed by them, an attempt is made to characterize their illocutionary potential in terms of a basic meaning. On the basis of this approach the subtypes of the functional clause types and their possible use in specific contexts are characterized in detail. This systematization of the relationship between clause type and possible illocutionary acts is additionally based on the well-known distinction between ‘direct’ and ‘indirect(ly performed)’ speech acts. The chapter concludes with some comparative remarks characterizing the specific properties of English within the Germanic languages family and within a general typology of clause types.
Clause Structure, Complements, and Adjuncts
Authors: Duffley Patrick
Published: March 2020

This chapter discusses central concepts in clause structure such as the notion of ‘head’ and the distinction between ‘complements’ and ‘adjuncts’. The different ways in which constituency and dependency grammars approach clausal heads are examined, and modern analyses are juxtaposed with the grammatical tradition. Regarding the distinction between complements and adjuncts, two important issues are discussed: its relevance to the clause’s semantic structure and how to determine obligatoriness, the defining characteristic of complements. The use of the term ‘complement’ to refer to clauses construed as core arguments of main predicates is also explored, particularly the challenge of explaining complement choice with individual verbs, either by means of a general complement binding hierarchy or particular subcategorization features attached to each verb.
Executive Politics in Spain
Authors: Rodríguez-Teruel Juan
Published: March 2020

The chapter offers an overview of the main features of executive politics in democratic Spain. Adopting a core executive approach, it focuses on the actors and the processes defining the interaction and the power relationship between the prime minister, the ministers, and the cabinet at the national level. The main argument discusses the ‘presidentialization’ thesis in Spain. Instead, it proposes a more complex dynamics based in the exchange of power resources among actors within the government. Although institutional and political factors – like party politics and the personalization of politics – have favoured the prime minister’s predominance, other factors help to counterbalance this trend with elements of ministerial government. The chapter also discusses the (limited) role of political parties within governments, and the multilevel trend reshaping the nature of the executive in Spain.
Barth and Liberal Protestantism
Authors: Chalamet Christophe
Published: March 2020

Karl Barth has often been seen as the arch-enemy of liberal theology. Closer attention, however, reveals a constant concern to nuance his understanding of key liberal thinkers—even to the point where Barth claimed, towards the end of his life, to be himself a liberal theologian. But what does it mean to be a liberal theologian? What are the key markers of theological liberalism, and is that tradition homogeneous? This chapter addresses these questions and considers the ways that Barth cannot be said to have been either simply ‘anti-liberal’ or straight-forwardly a direct heir of modern liberal theology.
Liberation Theology’s Spiritual Legacy for the Latin American Church
Authors: Segura Harold
Published: March 2020

Spirituality has increasingly become an important interpretive key to understand the develop of theologies in Latin America over the last 50 years, particularly Latin America Liberation Theology. This chapter presents some of the most important background of Liberation Theology by describing its theological emphasis and its implications for the pastoral work. This theological work has been consequential not only for the Catholic Church, but also for evangelical churches and other Christian communities. The argument is that the Liberation Theology is not new, but is rather a new way of doing theology, and therefore, a new way of understanding Christian spirituality and following Jesus.
Time and Christianity in Early Latin America
Authors: O'Hara Matthew
Published: March 2020

The arrival of Christianity in the Americas and its long-term development throughout the colonial era were closely connected to questions of time—whether the human experience and manipulation of time, the crafting of historical memory, or the imagining of potential futures. Exploring classic and recent scholarship on the colonial era, this chapter considers some of the ways that the history of Christianity in early Latin America is also a history of time. This chapter focuses on the viceroyalty of New Spain—Central Mexico in particular—but also makes some references to scholarship from other parts of Spanish America. The centering of attention on time starts a productive dialogue within the historiography on early Latin American Christianity—a conversation that steps beyond a tired debate about the relative “Europeanness” or “indigeneity” of post-conquest cultures, focusing, instead, on unique ways of being that emerged out of the remarkable convergence of intellectual traditions and cultural practices in the colonial world.
Mary, Mother of Jesus
Authors: Rodriguez Jeanette
Published: March 2020

Throughout the history of Christianity in Latin America, Mary has been portrayed in multiple manifestations (e.g. Our Lady of Charity in Cuba, Nuestra Señora de la Altagracia in the Dominican Republic, and Nossa Senhora Aparecida in Brazil). She is the official patron of countries, cities, and neighborhoods, known by many names in devotional practices, and central to the region’s religio-social history. Given Latin America’s rich, varied, and complex expressions of both Christianity and Marian Devotions, this chapter focuses on three separate understandings of Mary as presented by Richard Nebel: (1) the person of Mary, (2) the deep affective bond that encompasses millions of her devotees, and (3) the genuine evangelization of the people devoted to her. As an example of these three theological trajectories, the chapter offers a reflection on the Guadalupe Event and its continued broad impact on the faith life of her devotees.
Evidence of Neural Microstructure Abnormalities in Type I Chiari Malformation: Associations Among Fiber Tract Integrity, Pain, and Cognitive Dysfunction
Authors: Houston James R , Hughes Michelle L , Bennett Ilana J , Allen Philip A , Rogers Jeffrey M , Lien Mei-Ching , Stoltz Haylie , Sakaie Ken , Loth Francis , Maleki Jahangir , Vorster Sarel J , Luciano Mark G
Published: March 2020

Background

Previous case–control investigations of type I Chiari malformation (CMI) have reported cognitive deficits and microstructural white matter abnormalities, as measured by diffusion tensor imaging (DTI). CMI is also typically associated with pain, including occipital headache, but the relationship between pain symptoms and microstructure is not known.

Methods

Eighteen CMI patients and 18 adult age- and education-matched control participants underwent DTI, were tested using digit symbol coding and digit span tasks, and completed a self-report measure of chronic pain. Tissue microstructure indices were used to examine microstructural abnormalities in CMI as compared with healthy controls. Group differences in DTI parameters were then reassessed after controlling for self-reported pain. Finally, DTI parameters were correlated with performance on the digit symbol coding and digit span tasks within each group.

Results

CMI patients exhibited greater fractional anisotropy (FA), lower radial diffusivity, and lower mean diffusivity in multiple brain regions compared with controls in diffuse white matter regions. Group differences no longer existed after controlling for self-reported pain. A significant correlation between FA and the Repeatable Battery for the Assessment of Neuropsychological Status coding performance was observed for controls but not for the CMI group.

Conclusions

Diffuse microstructural abnormalities appear to be a feature of CMI, manifesting predominantly as greater FA and less diffusivity on DTI sequences. These white matter changes are associated with the subjective pain experience of CMI patients and may reflect reactivity to neuroinflammatory responses. However, this hypothesis will require further deliberate testing in future studies.
INVESTIGATION AND ANALYSIS OF ENVIRONMENTAL RADIOACTIVITY LEVELS AT TYPICAL URANIUM MINES IN THE SOUTH OF CHINA
Authors: Qin Guoxiu , Liu Yujuan , Wang Qimin , Li Fan , Li Weizhe , Wu Hexi
Published: March 2020

The environmental radioactivity levels of two typical uranium mines in the south of China were investigated and analysed. According to the characteristics of uranium mines, the relevant parameters, including the surface gamma ray dose rate, concentration of radon in the air and concentration of radionuclides in the soil and surface water, of two uranium mines were evaluated and analysed. The results show that residents in the mining area were exposed to average maximum annual effective doses of 1.69 and 1.58 mSv due to the inhalation of radon and its daughters, while the employees received 2.59 and 1.87 mSv, respectively. Residents in the mining area were exposed to average maximum annual effective doses of 0.77 and 0.69 mSv due to gamma ray, while the employees received 1.64 and 1.33 mSv, respectively.
Economic and cultural determinants of elite attitudes toward redistribution
Authors: López Matias , Moraes Silva Graziella , Teeger Chana , Marques Pedro
Published: March 2020

Previous studies have posited that elites are willing to advance the redistribution of income and social goods when the negative effects of inequality, such as crime and conflict, threaten their own interests. Although elites acknowledge these negative effects, their support for redistributive policies remains low throughout the Global South. We address this paradox using a multi-method research design. Drawing on 56 in-depth interviews with Brazilian political and economic elites, we document how, when discussing the negative effects of inequality, interviewees consistently characterized the poor as ignorant, irrational and politically incompetent. We use these findings to theorize about the negative impact of such perceptions of the poor on elite support for redistribution. We then test this relationship using survey data gathered from random samples of political and economic elites in Brazil, South Africa and Uruguay (N = 544). We find the relationship to be robust.
Teen Parents’ Cumulative Inequality in Job Achievement: Mediation Effect of Educational Achievement
Authors: Bae Junghee
Published: March 2020

Teen pregnancy remains an important societal concern in the United States because teen pregnancy tremendously influences teen parents in terms of opportunities for education and employment. However, little is known about the long-term dynamic relationship between the trajectory of educational attainment and trajectory of  job achievement among teen parents. This study examined the sample of National Longitudinal Survey of Youth 1997, which comprises representative American youths born between 1980 and 1984 (N = 7,771). Latent growth models revealed that teen parents had not only lower initial educational levels, hourly compensation, and annual wages, but also lower increases in educational level, hourly compensation, and annual wages over 10 years. Also, the latent growth mediation model found that initial educational level and changes in educational level mediated the negative association between teen parents and job achievement. These findings suggest that social work intervention for teen parents should focus on supporting academic success in the long term and providing appropriate employment training programs for better job achievement. Future research may contribute by examining the long-term effect of being a teen parent beyond 10 years and investigating differences between teen mothers and teen fathers.