bluuebunny/crossref_metadata_2025_split huggingface dataset:
Using Data to Advance Educational Research, Policy, and Practice: Design, Content, and Research Potential of the Netherlands Cohort Study on Education
Authors: Haelermans Carla , Huijgen Timo , Jacobs Madelon , Levels Mark , van der Velden Rolf , van Vugt Lynn , van Wetten Sanne 
Published: May 2020

Abstract
In many countries, the quality of (large-scale quantitative) educational research is threatened by data challenges. In this article, we present an innovative data research project from the Netherlands in which many of the challenges that come forward in previous literature are addressed. The Netherlands Cohort Study on Education [in Dutch abbreviated as NCO (Nationaal Cohortonderzoek Onderwijs)] uses longitudinal register data on track placement of cohorts of pupils in primary and secondary education from Statistics Netherlands, which will be combined with school admin data on pupils’ performance and data from the major (inter)national surveys. NCO maps pupils’ pathways and performances through primary and secondary education and their trajectory into tertiary education. NCO so far covers more than 10 complete cohorts and is complemented with the newest data every year. These registers are made available at Statistics Netherlands. A major contribution of NCO is that data from school administrative systems and additional research projects are linked with administrative register data, thereby creating a unique data set that enriches not only research, but also policy and practice. This data brief elaborates on the possibilities of this database by exploring and following one of the cohorts over time.
Factors affecting the utilization of antenatal care services among women in Guinea: a population-based study
Authors: Shibre Gebretsadik , Zegeye Betregiorgis , Idriss-Wheeler Dina , Yaya Sanni 
Published: May 2020

Abstract

Introduction
Evidence suggests that a better understanding of determinants of antenatal care (ANC) utilization is crucial to reducing maternal and child deaths. Little is known about the utilization of ANC services in Guinea.

Objective
The aim of this study was to explore factors determining utilization of skilled ANC in Guinea.

Methods
This study focused on a sample of 7812 ever married women. Using multivariate logistic regression, factors associated with the utilization of ANC were identified. The output of the multivariate logistic regression was presented using adjusted odds ratio and the corresponding 95% confidence interval (CI).

Results
Several factors had significant association with utilization of skilled ANC service in Guinea: having decision-making power (2.21, 95% CI: 1.63, 3.00), employment status (1.86, 95% CI: 1.39, 2.48), media exposure (1.60, 95% CI: 1.26, 2.02), maternal education (2.68, 95% CI: 1.36, 5.28), husband/partner education status (1.66, 95% CI: 1.08, 2.55), household economic status (2.19, 95% CI: 1.40, 3.44), place of residence (0.29, 95% CI: 0.16, 0.50) and ethnicity (0.40, 95% CI: 0.23, 0.69).

Conclusions
These findings suggest a variety of socio-demographic and economic factors as well as media exposure are associated with women’s use of ANC. Policymakers should implement appropriate measures to address the existing variations and gaps in ANC services utilization among different subgroups of women in Guinea.
Genome-wide identification, characterization and expression analysis of lineage-specific genes within Hanseniaspora yeasts
Authors: Chen Kai , Tian Zhonghuan , Chen Ping , He Hua , Jiang Fatang , Long Chao-an 
Published: May 2020

ABSTRACT
Lineage-specific genes (LSGs) are defined as genes with sequences that are not significantly similar to those in any other lineage. LSGs have been proposed, and sometimes shown, to have significant effects in the evolution of biological function. In this study, two sets of Hanseniaspora spp. LSGs were identified by comparing the sequences of the Kloeckera apiculata genome and of 80 other yeast genomes. This study identified 344 Hanseniaspora-specific genes (HSGs) and 109 genes (‘orphan genes’) specific to K. apiculata. Three thousand three hundred thirty-one K. apiculata genes that showed significant similarity to at least one sequence outside the Hanseniaspora were classified into evolutionarily conserved genes. We analyzed their sequence features, functional categories, gene origin, gene structure and gene expression. We also investigated the predicted cellular roles and Gene Ontology categories of the LSGs using functional inference. The patterns of the functions of LSGs do not deviate significantly from genome-wide average. The results showed that a few LSGs were formed by gene duplication, followed by rapid sequence divergence. Many of the HSGs and orphan genes exhibited altered expression in response to abiotic stress. Studying these LSGs might be helpful for understanding the molecular mechanism of yeast adaption.
Rapid prediction of earthquake ground shaking intensity using raw waveform data and a convolutional neural network
Authors: Jozinović Dario , Lomax Anthony , Štajduhar Ivan , Michelini Alberto 
Published: May 2020

SUMMARY
This study describes a deep convolutional neural network (CNN) based technique to predict intensity measurements (IMs) of earthquake ground shaking. The input data to the CNN model consists of multistation, 3C acceleration waveforms recorded during the 2016 Central Italy earthquake sequence for M ≥ 3.0 events. Using a 10 s window starting at the earthquake origin time, we find that the CNN is capable of accurately predicting IMs at stations far from the epicentre which have not yet recorded the maximum ground shaking. The CNN IM predictions do not require previous knowledge of the earthquake source (location and magnitude). Comparison between the CNN model predictions and those obtained with the Bindi et al. GMPE (which requires location and magnitude) shows that the CNN model features similar error variance but smaller bias. Although the technique is not strictly designed for earthquake early warning, we find that it can provide useful estimates of ground motions within 15–20 s after earthquake origin time depending on various setup elements (e.g. times for data transmission, computation, latencies). The technique has been tested on raw data without any initial data pre-selection in order to closely replicate real-time data streaming. When noise examples were included with the earthquake data the CNN was found to be stable, accurately predicting the ground shaking intensity corresponding to the noise amplitude.
Structure of the Ecuadorian forearc from the joint inversion of receiver functions and ambient noise surface waves
Authors: Koch Clinton D , Lynner Colton , Delph Jonathan , Beck Susan L , Meltzer Anne , Font Yvonne , Soto-Cordero Lillian , Hoskins Mariah , Stachnik Josh C , Ruiz Mario , Alvarado Alexandra , Agurto-Detzel Hans , Charvis Philippe , Regnier Marc , Rietbrock Andreas 
Published: May 2020

SUMMARYThe Ecuadorian forearc is a complex region of accreted terranes with a history of large megathrust earthquakes. Most recently, a Mw 7.8 megathrust earthquake ruptured the plate boundary offshore of Pedernales, Ecuador on 16 April 2016. Following this event, an international collaboration arranged by the Instituto Geofisico at the Escuela Politécnica Nacional mobilized a rapid deployment of 65 seismic instruments along the Ecuadorian forearc. We combine this new seismic data set with 14 permanent stations from the Ecuadorian national network to better understand how variations in crustal structure relate to regional seismic hazards along the margin. Here, we present receiver function adaptive common conversion point stacks and a shear velocity model derived from the joint inversion of receiver functions and surface wave dispersion data obtained through ambient noise cross-correlations for the upper 50 km of the forearc. Beneath the forearc crust, we observe an eastward dipping slow velocity anomaly we interpret as subducting oceanic crust, which shallows near the projected centre of the subducting Carnegie Ridge. We also observe a strong shallow positive conversion in the Ecuadorian forearc near the Borbon Basin indicating a major discontinuity at a depth of ∼7 km. This conversion is not ubiquitous and may be the top of the accreted terranes. We also observe significant north–south changes in shear wave velocity. The velocity changes indicate variations in the accreted terranes and may indicate an increased amount of hydration beneath the Manabí Basin. This change in structure also correlates geographically with the southern rupture limit of multiple high magnitude megathrust earthquakes. The earthquake record along the Ecuadorian trench shows that no event with a Mw &gt;7.4 has ruptured south of ∼0.5°S in southern Ecuador or northern Peru. Our observations, along with previous studies, suggest that variations in the forearc crustal structure and subducting oceanic crust may influance the occurrence and spatial distribution of high magnitude seismicity in the region.
Genome editing strategies for fetal hemoglobin induction in beta-hemoglobinopathies
Authors: Demirci Selami , Leonard Alexis , Tisdale John F 
Published: May 2020

AbstractGenome editing to correct a defective β-globin gene or induce fetal globin (HbF) for patients with beta-hemoglobinopathies has the potential to be a curative strategy available to all. HbF reactivation has long been an area of intense interest given the HbF inhibition of sickle hemoglobin (HbS) polymerization. Patients with HbS who also have high HbF tend to have less severe or even minimal clinical manifestations. Approaches to genetically engineer high HbF include de novo generation of naturally occurring hereditary persistence of fetal hemoglobin (HPFH) mutations, editing of transcriptional HbF repressors or their binding sites and/or regulating epigenetic intermediates controlling HbF expression. Recent preclinical and early clinical trial data show encouraging results; however, long-term follow-up is lacking, and the safety and efficacy concerns of genome editing remain.
Recent advances in Wilms’ tumor predisposition
Authors: Maciaszek Jamie L , Oak Ninad , Nichols Kim E 
Published: May 2020

AbstractWilms’ tumor (WT), the most common childhood kidney cancer, develops in association with an underlying germline predisposition in up to 15% of cases. Germline alterations affecting the WT1 gene and epigenetic alterations affecting the 11p15 locus are associated with a selective increase in WT risk. Nevertheless, WT also occurs in the context of more pleiotropic cancer predispositions, such as DICER1, Li-Fraumeni and Bloom syndrome, as well as Fanconi anemia. Recent germline genomic investigations have increased our understanding of the host genetic factors that influence WT risk, with sequencing of rare familial cases and large WT cohorts revealing an expanding array of predisposition genes and associated genetic conditions. Here, we describe evidence implicating WT1, the 11p15 locus, and the recently identified genes CTR9, REST and TRIM28 in WT predisposition. We discuss the clinical features, mode of inheritance and biological aspects of tumorigenesis, when known. Despite these described associations, many cases of familial WT remain unexplained. Continued investigations are needed to fully elucidate the landscape of germline genetic alterations in children with WT. Establishing a genetic diagnosis is imperative for WT families so that individuals harboring a predisposing germline variant can undergo surveillance, which should enable the early detection of tumors and use of less intensive treatments, thereby leading to improved overall outcomes.
Pharmacological Augmentation in Unipolar Depression: A Guide to the Guidelines
Authors: Taylor Rachael W , Marwood Lindsey , Oprea Emanuella , DeAngel Valeria , Mather Sarah , Valentini Beatrice , Zahn Roland , Young Allan H , Cleare Anthony J 
Published: May 2020

AbstractBackgroundPharmacological augmentation is a recommended strategy for patients with treatment-resistant depression. A range of guidelines provide advice on treatment selection, prescription, monitoring and discontinuation, but variation in the content and quality of guidelines may limit the provision of objective, evidence-based care. This is of importance given the side effect burden and poorer long-term outcomes associated with polypharmacy and treatment-resistant depression. This review provides a definitive overview of pharmacological augmentation recommendations by assessing the quality of guidelines for depression and comparing the recommendations made.MethodsA systematic literature search identified current treatment guidelines for depression published in English. Guidelines were quality assessed using the Appraisal of Guidelines for Research and Evaluation II tool. Data relating to the prescription of pharmacological augmenters were extracted from those developed with sufficient rigor, and the included recommendations compared.ResultsTotal of 1696 records were identified, 19 guidelines were assessed for quality, and 10 were included. Guidelines differed in their quality, the stage at which augmentation was recommended, the agents included, and the evidence base cited. Lithium and atypical antipsychotics were recommended by all 10, though the specific advice was not consistent. Of the 15 augmenters identified, no others were universally recommended.ConclusionsThis review provides a comprehensive overview of current pharmacological augmentation recommendations for major depression and will support clinicians in selecting appropriate treatment guidance. Although some variation can be accounted for by date of guideline publication, and limited evidence from clinical trials, there is a clear need for greater consistency across guidelines to ensure patients receive consistent evidence-based care.
Quasi-Affineness and the 1-Resolution Property
Authors: Deshmukh Neeraj , Hogadi Amit , Mathur Siddharth 
Published: May 2020

Abstract
We prove that, under mild hypothesis, every normal algebraic space that satisfies the $1$-resolution property is quasi-affine. More generally, we show that for algebraic stacks satisfying similar hypotheses, the 1-resolution property guarantees the existence of a finite flat cover by a quasi-affine scheme.
Chikungunya-Induced Arthritis in Reunion Island: A Long-Term Observational Follow-Up Study Showing Frequently Persistent Joint Symptoms, Some Cases of Persistent Chikungunya Immunoglobulin M Positivity, and No Anticyclic Citrullinated Peptide Seroconversion After 13 Years
Authors: Guillot Xavier , Ribera Anne , Gasque Philippe 
Published: May 2020

Abstract

Background
Reunion Island was struck by a massive Chikungunya outbreak in 2005–2006. Chikungunya infection is characterized by inflammatory joint symptoms, which may evolve into chronic arthritis.

Methods
In this long-term longitudinal observational monocentric study, after the 2005–2006 outbreak in Reunion Island, 159 patients were first referred to a rheumatologist for post-Chikungunya chronic musculoskeletal pain, 73 of them were diagnosed with classifiable Chikungunya-related chronic inflammatory rheumatic diseases (&gt;3 month symptom duration from the initial viral infection). Thirty of these 73 patients were clinically evaluated by a second rheumatologist in 2018–2019. The main objective of this second examination was to estimate the proportion of patients with persistent Chikungunya-related inflammatory joint symptoms after 13 years.

Results
Inflammatory joint symptoms persisted in 17/30 patients after 13 years (therefore in at least 23.3% of the 73 patients initially diagnosed with Chikungunya-related inflammatory joint symptoms and 10.7% of the 159 patients referred for post-Chikungunya chronic musculoskeletal pain). In the symptom persistence subgroup, the prevalence of positive autoantibodies (antinuclear or ACPA) was significantly higher – without any seroconversion, Chikungunya IgG and IgM levels were higher, long-term IgM positivity and radiographic damage were more frequent. Overall, after 13 years, pain and fatigue levels remained significant, 5 patients were still treated by methotrexate, 3 by TNF-blockers, highlighting long-term Chikungunya-related patient burden.

Conclusions
Such a long-term persistence of Chikungunya-related chronic inflammatory rheumatic diseases had not been reported so far. Furthermore, the long-term Chikungunya IgM positivity we observed in some cases might corroborate the hypothesis of residual viral antigen-driven chronic arthritis.
Pivotal role of the carbohydrate recognition domain in self-interaction of CLEC4A to elicit the ITIM-mediated inhibitory function in murine conventional dendritic cellsin vitro
Authors: Nasu Junta , Uto Tomofumi , Fukaya Tomohiro , Takagi Hideaki , Fukui Takehito , Miyanaga Noriaki , Nishikawa Yotaro , Yamasaki Sho , Yamashita Yoshihiro , Sato Katsuaki 
Published: May 2020

AbstractC-type lectin receptors (CLRs), pattern recognition receptors (PRRs) with a characteristic carbohydrate recognition domain (CRD) in the extracellular portion, mediate crucial cellular functions upon recognition of glycosylated pathogens and self-glycoproteins. CLEC4A is the only classical CLR that possesses an intracellular immunoreceptor tyrosine-based inhibitory motif (ITIM), which possibly transduces negative signals. However, how CLEC4A exerts cellular inhibition remains unclear. Here, we report that the self-interaction of CLEC4A through the CRD is required for the ITIM-mediated suppressive function in conventional dendritic cells (cDCs). Human type 2 cDCs (cDC2) and monocytes display a higher expression of CLEC4A than cDC1 and plasmacytoid DCs (pDCs) as well as B cells. The extracellular portion of CLEC4A specifically binds to a murine cDC cell line expressing CLEC4A, while its extracellular portion lacking the N-glycosylation site or the EPS motif within the CRD reduces their association. Furthermore, the deletion of the EPS motif within the CRD or ITIM in CLEC4A almost completely impairs its suppressive effect on the activation of the murine cDC cell line, whereas the absence of the N-glycosylation site within the CRD exhibits partial inhibition on their activation. On the other hand, antagonistic monoclonal antibody (mAb) to CLEC4A, which inhibits the self-interaction of CLEC4A and its downstream signaling in murine transfectants, enhances the activation of monocytes and monocyte-derived immature DCs upon stimulation with a Toll-like receptor (TLR) ligand. Thus, our findings suggest a pivotal role of the CRD in self-interaction of CLEC4A to elicit the ITIM-mediated inhibitory signal for the control of the function of cDCs.
Revision of EUCAST breakpoints: consequences for susceptibility of contemporary Danish mould isolates to isavuconazole and comparators
Authors: Jørgensen Karin Meinike , Guinea Jesus , Meletiadis Joseph , Hare Rasmus Krøger , Arendrup Maiken Cavling 
Published: May 2020

Abstract

Background
EUCAST recently revised the definition of the ‘I’ category from ‘intermediate’ to ‘susceptible, increased exposure’. Consequently, all current antifungal breakpoints have been reviewed and revised breakpoints (v 10.0) have been released.

Objectives
We investigated isavuconazole and comparator MICs (mg/L) against contemporary moulds and the consequences of the breakpoint revision for susceptibility classification.

Methods
Six hundred and ninety-six Aspergillus and 46 other moulds were included. EUCAST E.Def 10.1 azole resistance screening was performed for Aspergillus fumigatus and E.Def 9.3.1 testing of non-susceptible A. fumigatus and other moulds. Most non-wildtype/resistant isolates underwent cyp51A sequencing.

Results
Isavuconazole MIC50/MIC90s were ≤1/≤2 mg/L for Aspergillus flavus, A. fumigatus and Aspergillus nidulans versus 2/4 mg/L for Aspergillus niger and 2/16 mg/L for Aspergillus terreus. For the remaining moulds, MICs were highest for Fusarium (16 to &gt;16 mg/L), lowest for dermatophytes (0.06–0.5 mg/L) and in between for Mucorales and others (1 to &gt;16 mg/L). A very strong isavuconazole–voriconazole MIC correlation was found for A. fumigatus (Pearson r = 0.888) and itraconazole–posaconazole correlation for A. fumigatus (r = 0.905) and A. terreus (r = 0.848). For A. fumigatus, the revised breakpoints lowered isavuconazole resistance (22.6% to 7.7%, P &lt; 0.0001) and increased voriconazole resistance (3.8% to 6.7%, P = 0.025), resulting in similar resistance rates across the four azoles (range: 6.7%–7.7%). For A. terreus, isavuconazole resistance remained unchanged (81.3%) and higher than itraconazole (43.8%, P = 0.004) and posaconazole (53.1%, P = 0.03) resistance. Azole cross-resistance was found in 24/24, 13/20 and 4/90 isolates, and Cyp51A alterations in 16/18, 1/7 and 2/4 sequenced isolates with isavuconazole MICs of &gt;4, 4 and 2 mg/L, respectively.

Conclusions
Isavuconazole displays broad anti-mould activity. The revised breakpoints result in fewer misclassifications of wildtype isolates without compromising detection of resistant mutants.
PheMap: a multi-resource knowledge base for high-throughput phenotyping within electronic health records
Authors: Zheng Neil S , Feng QiPing , Kerchberger V Eric , Zhao Juan , Edwards Todd L , Cox Nancy J , Stein C Michael , Roden Dan M , Denny Joshua C , Wei Wei-Qi 
Published: May 2020

Abstract

Objective
Developing algorithms to extract phenotypes from electronic health records (EHRs) can be challenging and time-consuming. We developed PheMap, a high-throughput phenotyping approach that leverages multiple independent, online resources to streamline the phenotyping process within EHRs.

Materials and Methods
PheMap is a knowledge base of medical concepts with quantified relationships to phenotypes that have been extracted by natural language processing from publicly available resources. PheMap searches EHRs for each phenotype’s quantified concepts and uses them to calculate an individual’s probability of having this phenotype. We compared PheMap to clinician-validated phenotyping algorithms from the Electronic Medical Records and Genomics (eMERGE) network for type 2 diabetes mellitus (T2DM), dementia, and hypothyroidism using 84 821 individuals from Vanderbilt Univeresity Medical Center's BioVU DNA Biobank. We implemented PheMap-based phenotypes for genome-wide association studies (GWAS) for T2DM, dementia, and hypothyroidism, and phenome-wide association studies (PheWAS) for variants in FTO, HLA-DRB1, and TCF7L2.

Results
In this initial iteration, the PheMap knowledge base contains quantified concepts for 841 disease phenotypes. For T2DM, dementia, and hypothyroidism, the accuracy of the PheMap phenotypes were &gt;97% using a 50% threshold and eMERGE case-control status as a reference standard. In the GWAS analyses, PheMap-derived phenotype probabilities replicated 43 of 51 previously reported disease-associated variants for the 3 phenotypes. For 9 of the 11 top associations, PheMap provided an equivalent or more significant P value than eMERGE-based phenotypes. The PheMap-based PheWAS showed comparable or better performance to a traditional phecode-based PheWAS. PheMap is publicly available online.

Conclusions
PheMap significantly streamlines the process of extracting research-quality phenotype information from EHRs, with comparable or better performance to current phenotyping approaches.