bluuebunny/crossref_metadata_2025_split huggingface dataset:
Latinx Health Disparities Research During COVID-19: Challenges and Innovations
Authors: Harkness Audrey , Gattamorta Karina A , Estrada Yannine , Jimenez Daniel , Kanamori Mariano , Prado Guillermo , Behar-Zusman Victoria 
Published: July 2020

Abstract

Background
The Center for Latino Health Research Opportunities (CLaRO) supports and facilitates research addressing substance abuse, violence/trauma, and HIV/AIDS among diverse and underserved Latinx populations. CLaRO runs a pilot awards program for early-stage investigators conducting Latinx health disparities research. This pilot awards program was impacted by the COVID-19 pandemic, necessitating innovative responses for research continuity.

Purpose
The purpose of this commentary is to describe the challenges and innovative research methods developed in response to COVID-19 to continue Latinx health disparities research in the context of COVID-19.

Methods/Results
This commentary provides a brief description of each CLaRO pilot project, the challenges introduced by COVID-19, and innovative research methods to continue Latinx health disparities research during and beyond COVID-19.

Conclusions
Despite the challenges COVID-19 presents to the continuity of health disparities research, it also presents unprecedented opportunities to innovate. Such innovation is essential for solving persistent scientific, public health, and clinical challenges underlying current and emerging health disparities.
Recurrent Autoimmune Hepatitis and De Novo Autoimmune Hepatitis in the Liver Allograft
Authors: González Iván A , Hartley Christopher P , Nalbantoglu ILKe 
Published: July 2020

Abstract

Objectives
Autoimmune hepatitis (AIH) is a form of severe hepatitis that can recur after orthotopic liver transplant (OLT). Presentation of AIH in patients with OLT who do not have a history of AIH is called de novo AIH (DNAIH). We evaluated the clinicopathologic characteristics of AIH and DNAIH.

Methods
Clinicopathologic and outcome measures of 11 patients with recurrent AIH (RAIH) and 22 with DNAIH identified between 2000 and 2017 were compared.

Results
Both cohorts showed female predominance. The mean clinical follow-up was 13 and 7.8 years in the in the RAIH and DNAIH groups, respectively (P = .1). Moderate portal inflammation was more common in patients with RAIH (64% vs 27%, P = .043). A trend was observed for more cases of DNAIH showing severe inflammation (36% vs 9%, P = .09) and submassive necrosis compared with RAIH (23% vs 0%, P = .086). A trend for more advanced fibrosis was also noted in the RAIH group (27% vs 5%, P = .059). Three patients with RAIH lost their grafts because of RAIH. Five-year disease-specific graft survival (GS) (P = .012) and overall GS (P = .015) were worse in patients with RAIH. Complement component 4d immunohistochemistry was positive in 2 patients with RAIH and 3 with DNAIH but showed no correlation with GS or other parameters.

Conclusions
RAIH seems to have a more aggressive clinical course than DNAIH and warrants closer clinical follow-up and aggressive treatment.
pyGenomeTracks: reproducible plots for multivariate genomic datasets
Authors: Lopez-Delisle Lucille , Rabbani Leily , Wolff Joachim , Bhardwaj Vivek , Backofen Rolf , Grüning Björn , Ramírez Fidel , Manke Thomas 
Published: July 2020

Abstract

Motivation
Generating publication ready plots to display multiple genomic tracks can pose a serious challenge. Making desirable and accurate figures requires considerable effort. This is usually done by hand or using a vector graphic software.

Results
pyGenomeTracks (PGT) is a modular plotting tool that easily combines multiple tracks. It enables a reproducible and standardized generation of highly customizable and publication ready images.

Availability and implementation
PGT is available through a graphical interface on https://usegalaxy.eu and through the command line. It is provided on conda via the bioconda channel, on pip and it is openly developed on github: https://github.com/deeptools/pyGenomeTracks.

Supplementary information
Supplementary data are available at Bioinformatics online.
GeoMine: interactive pattern mining of protein–ligand interfaces in the Protein Data Bank
Authors: Diedrich Konrad , Graef Joel , Schöning-Stierand Katrin , Rarey Matthias 
Published: July 2020

Abstract

Summary
The searching of user-defined 3D queries in molecular interfaces is a computationally challenging problem that is not satisfactorily solved so far. Most of the few existing tools focused on that purpose are desktop based and not openly available. Besides that, they show a lack of query versatility, search efficiency and user-friendliness. We address this issue with GeoMine, a publicly available web application that provides textual, numerical and geometrical search functionality for protein–ligand binding sites derived from structural data contained in the Protein Data Bank (PDB). The query generation is supported by a 3D representation of a start structure that provides interactively selectable elements like atoms, bonds and interactions. GeoMine gives full control over geometric variability in the query while performing a deterministic, precise search. Reasonably selective queries are processed on the entire set of protein–ligand complexes in the PDB within a few minutes. GeoMine offers an interactive and iterative search process of successive result analyses and query adaptations. From the numerous potential applications, we picked two from the field of side-effect analyze showcasing the usefulness of GeoMine.

Availability and implementation
GeoMine is part of the ProteinsPlus web application suite and freely available at https://proteins.plus.

Supplementary information
Supplementary data are available at Bioinformatics online.
VRmol: an integrative web-based virtual reality system to explore macromolecular structure
Authors: Xu Kui , Liu Nan , Xu Jingle , Guo Chunlong , Zhao Lingyun , Wang Hong-Wei , Zhang Qiangfeng Cliff 
Published: July 2020

Abstract

Summary
Structural visualization and analysis are fundamental to explore macromolecular functions. Here, we present a novel integrative web-based virtual reality (VR) system—VRmol, to visualize and study molecular structures in an immersive virtual environment. Importantly, it is integrated with multiple online databases and is able to couple structure studies with associated genomic variations and drug information in a visual interface by cloud-based drug docking. VRmol thus can serve as an integrative platform to aid structure-based translational research and drug design.

Availability and implementation
VRmol is freely available (https://VRmol.net), with detailed manual and tutorial (https://VRmol.net/docs). The code of VRmol is available as open source under the MIT license at http://github.com/kuixu/VRmol.

Supplementary information
Supplementary data are available at Bioinformatics online.
Poisson reduced-rank models with an application to political text data
Authors: Jentsch Carsten , Lee Eun Ryung , Mammen Enno 
Published: July 2020

Summary
We discuss Poisson reduced-rank models for low-dimensional summaries of high-dimensional Poisson vectors that allow inference on the location of individuals in a low-dimensional space. We show that under weak dependence conditions, which allow for certain correlations between the Poisson random variables, the locations can be consistently estimated using Poisson maximum likelihood estimation. Moreover, we develop consistent rules for determining the dimension of the location from the discrete data. Our main motivation for studying Poisson reduced-rank models arises from applications to political text data, where word counts in a political document are modelled by Poisson random variables. We apply our method to party manifesto data taken from German political parties across seven federal elections following German reunification, to make statistical inferences on the multi-dimensional evolution of party positions.
Anti-inflammatories in Alzheimer’s disease—potential therapy or spurious correlate?
Authors: Rivers-Auty Jack , Mather Alison E , Peters Ruth , Lawrence Catherine B , Brough David 
Published: July 2020

Abstract
Epidemiological evidence suggests non-steroidal anti-inflammatory drugs reduce the risk of Alzheimer’s disease. However, clinical trials have found no evidence of non-steroidal anti-inflammatory drug efficacy. This incongruence may be due to the wrong non-steroidal anti-inflammatory drugs being tested in robust clinical trials or the epidemiological findings being caused by confounding factors. Therefore, this study used logistic regression and the innovative approach of negative binomial generalized linear mixed modelling to investigate both prevalence and cognitive decline, respectively, in the Alzheimer’s Disease Neuroimaging dataset for each commonly used non-steroidal anti-inflammatory drug and paracetamol. Use of most non-steroidal anti-inflammatories was associated with reduced Alzheimer’s disease prevalence yet no effect on cognitive decline was observed. Paracetamol had a similar effect on prevalence to these non-steroidal anti-inflammatory drugs suggesting this association is independent of the anti-inflammatory effects and that previous results may be due to spurious associations. Interestingly, diclofenac use was significantly associated with both reduce incidence and slower cognitive decline warranting further research into the potential therapeutic effects of diclofenac in Alzheimer’s disease.
Rapid MSPD-LC–MS/MS Procedure for Determination of Pesticides in Potato Tubers
Authors: Danek Magdalena , Sajdak Marcin , Płonka Joanna , Barchańska Hanna 
Published: July 2020

AbstractThe program of potato protection recommended by the producers of agrochemicals requires application: thiamethoxam, lambda-cyhalothrin, deltamethrin, rimsulfuron and metalaxyl. Therefore, there is a risk that these pesticides are present in tubers, thus posing a toxicological risk to the consumer. In this respect, it is necessary to monitor the presence of these compounds in edible plants. Therefore, the aim of this paper was to develop a novel, simple and robust analytical procedure for simultaneous determination of above-mentioned pesticides in potato tubers. To develop an analytical procedure that fulfills SANTE demands, quick, easy, cheap, effective, rugged and safe method and matrix solid phase dispersion technique were investigated. The final determination was conducted by liquid chromatography with tandem mass spectrometry. The obtained experimental data were analyzed by analysis of variance. For the extraction of analytes, matrix solid phase dispersion with octadecyl sorbent and methanol as eluent was chosen, since it provides the validation parameters according to SANTE requirements (recovery: 77–111%, relative standard deviation: 1–10%, limit of quantification: 0.9–5.0 μg/kg). This innovative analytical procedure is a practical analytical tool, which was successfully proven by applying it for target pesticides determination in potato tuber samples of different varieties randomly chosen at local markets.
Scalar postpolitics, inclusive growth and inclusive economies: challenging the Greater Manchester agglomeration model
Authors: Deas Iain , Haughton Graham , Ward Kevin 
Published: July 2020

Abstract
This article examines the changing scalar political relations underpinning English city-regional governance. Drawing on case study research in Greater Manchester, the article demonstrates how locally rooted discourses around inclusive growth and inclusive economies have been deployed to challenge the city-region’s historically dominant agglomeration-based model. Using the analytical lens of scalar postpolitics, the article shows how the earlier technocratic approach adopted by national and city-region leaders attracted criticism in the face of continuing socio-spatial inequalities within Greater Manchester. We highlight the contrasting experiences of Oldham and Trafford, two boroughs of Greater Manchester, to reveal how local geographies were central to challenging the previously dominant model and promoting new thinking around inclusive growth and inclusive economies.
Increased incidence and improved prognosis of glomerulonephritis: a national 30-year study
Authors: Heaf James G , Sørensen Søren S , Hansen Alastair 
Published: July 2020

Abstract

Background
While there are many cross-sectional studies of glomerulonephritis (GN) incidence, changes in incidence over time, particularly in the 21st century have received less attention. Similarly, little is known about temporal changes in GN prognosis. The presence in Denmark of comprehensive registries for renal biopsy results, end-stage renal disease (ESRD), comorbidity and mortality permit these questions to be addressed.

Methods
Data for all renal biopsies in Denmark between 1985 and 2014 were extracted from the Danish Renal Biopsy Registry and Patobank registries. The date of first dialysis or transplantation was extracted from the Danish Nephrology Registry for those patients developing ESRD. Dates of death and presence of chronic comorbid conditions at date of biopsy were extracted from the National Patient Registry. The incidence of GN, adjusted to the 2013 European standard population, was calculated. ESRD incidence and mortality were calculated, both in absolute terms and after correction for age, comorbidity and presence of renal tubulointerstitial fibrosis.

Results
The incidence rose from 33.3 patients per million (ppm)/year in 1985–94 to 46.5 ppm in 2005–14. The increase could in part be related to changes in renal biopsy policy. Large increases in Anti-neutropil cytoplasmic antibody (ANCA) vasculitis (ANCAV) (3.1–7.7 ppm/year) and focal segmental glomerulosclerosis (FSGS) (1.5–5.7 ppm/year) incidence were noted. The biopsy-proven prevalence of GN in 2014 was 748 ppm of which 155 ppm were being treated with dialysis or transplantation. Adjusted ESRD incidence fell by 25% during the study period, mortality by 62% and combined ESRD/mortality by 46%. The fall in ESRD incidence was limited to minimal change GN, FSGS, membranous GN and lupus nephritis, while reductions in mortality, and the combination of ESRD and/or death, were seen for nearly all GN diagnoses.

Conclusions
This study suggests that the incidence of GN has generally increased between 1985 and 2014, but some of the increase may be related to changes in renal biopsy policy. Major increases in FSGS and ANCAV incidence have occurred. The prognosis of GN, both as regards ESRD and mortality, has improved.
The use of novel oral anticoagulants compared to vitamin K antagonists (warfarin) in patients with left ventricular thrombus after acute myocardial infarction
Authors: Jones Daniel A , Wright Paul , Alizadeh Momin A , Fhadil Sadeer , Rathod Krishnaraj S , Guttmann Oliver , Knight Charles , Timmis Adam , Baumbach Andreas , Wragg Andrew , Mathur Anthony , Antoniou Sotiris 
Published: July 2020

Abstract

Aim
Current guidelines recommend the use of vitamin K antagonist (VKA) for up to 3–6 months for treatment of left ventricular (LV) thrombus post-acute myocardial infarction (AMI). However, based on evidence supporting non-inferiority of novel oral anticoagulants (NOAC) compared to VKA for other indications such as deep vein thrombosis, pulmonary embolism (PE), and thromboembolic prevention in atrial fibrillation, NOACs are being increasingly used off licence for the treatment of LV thrombus post-AMI. In this study, we investigated the safety and effect of NOACs compared to VKA on LV thrombus resolution in patients presenting with AMI.

Methods and results
This was an observational study of 2328 consecutive patients undergoing coronary angiography ± percutaneous coronary intervention (PCI) for AMI between May 2015 and December 2018, at a UK cardiac centre. Patients’ details were collected from the hospital electronic database. The primary endpoint was rate of LV thrombus resolution with bleeding rates a secondary outcome. Left ventricular thrombus was diagnosed in 101 (4.3%) patients. Sixty patients (59.4%) were started on VKA and 41 patients (40.6%) on NOAC therapy (rivaroxaban: 58.5%, apixaban: 36.5%, and edoxaban: 5.0%). Both groups were well matched in terms of baseline characteristics including age, previous cardiac history (previous myocardial infarction, PCI, coronary artery bypass grafting), and cardiovascular risk factors (hypertension, diabetes, hypercholesterolaemia). Over the follow-up period (median 2.2 years), overall rates of LV thrombus resolution were 86.1%. There was greater and earlier LV thrombus resolution in the NOAC group compared to patients treated with warfarin (82% vs. 64.4%, P = 0.0018, at 1 year), which persisted after adjusting for baseline variables (odds ratio 1.8, 95% confidence interval 1.2–2.9). Major bleeding events during the follow-up period were lower in the NOAC group, compared with VKA group (0% vs. 6.7%, P = 0.030) with no difference in rates of systemic thromboembolism (5% vs. 2.4%, P = 0.388).

Conclusion
These data suggest improved thrombus resolution in post-acute coronary syndrome (ACS) LV thrombosis in patients treated with NOACs compared to VKAs. This improvement in thrombus resolution was accompanied with a better safety profile for NOAC patients vs. VKA-treated patients. Thus, provides data to support a randomized trial to answer this question.
Improved cardiovascular risk prediction using targeted plasma proteomics in primary prevention
Authors: Hoogeveen Renate M , Pereira João P Belo , Nurmohamed Nick S , Zampoleri Veronica , Bom Michiel J , Baragetti Andrea , Boekholdt S Matthijs , Knaapen Paul , Khaw Kay-Tee , Wareham Nicholas J , Groen Albert K , Catapano Alberico L , Koenig Wolfgang , Levin Evgeni , Stroes Erik S G 
Published: July 2020

Abstract

Aims
In the era of personalized medicine, it is of utmost importance to be able to identify subjects at the highest cardiovascular (CV) risk. To date, single biomarkers have failed to markedly improve the estimation of CV risk. Using novel technology, simultaneous assessment of large numbers of biomarkers may hold promise to improve prediction. In the present study, we compared a protein-based risk model with a model using traditional risk factors in predicting CV events in the primary prevention setting of the European Prospective Investigation (EPIC)-Norfolk study, followed by validation in the Progressione della Lesione Intimale Carotidea (PLIC) cohort.

Methods and results
Using the proximity extension assay, 368 proteins were measured in a nested case–control sample of 822 individuals from the EPIC-Norfolk prospective cohort study and 702 individuals from the PLIC cohort. Using tree-based ensemble and boosting methods, we constructed a protein-based prediction model, an optimized clinical risk model, and a model combining both. In the derivation cohort (EPIC-Norfolk), we defined a panel of 50 proteins, which outperformed the clinical risk model in the prediction of myocardial infarction [area under the curve (AUC) 0.754 vs. 0.730; P &lt; 0.001] during a median follow-up of 20 years. The clinically more relevant prediction of events occurring within 3 years showed an AUC of 0.732 using the clinical risk model and an AUC of 0.803 for the protein model (P &lt; 0.001). The predictive value of the protein panel was confirmed to be superior to the clinical risk model in the validation cohort (AUC 0.705 vs. 0.609; P &lt; 0.001).

Conclusion
In a primary prevention setting, a proteome-based model outperforms a model comprising clinical risk factors in predicting the risk of CV events. Validation in a large prospective primary prevention cohort is required to address the value for future clinical implementation in CV prevention.
Lefschetz Theory for Exterior Algebras and Fermionic Diagonal Coinvariants
Authors: Kim Jongwon , Rhoades Brendon 
Published: July 2020

Abstract
Let $W$ be an irreducible complex reflection group acting on its reflection representation $V$. We consider the doubly graded action of $W$ on the exterior algebra $\wedge (V \oplus V^*)$ as well as its quotient $DR_W:= \wedge (V \oplus V^*)/ \langle \wedge (V \oplus V^*)^{W}_+ \rangle $ by the ideal generated by its homogeneous $W$-invariants with vanishing constant term. We describe the bigraded isomorphism type of $DR_W$; when $W = {{\mathfrak{S}}}_n$ is the symmetric group, the answer is a difference of Kronecker products of hook-shaped ${{\mathfrak{S}}}_n$-modules. We relate the Hilbert series of $DR_W$ to the (type A) Catalan and Narayana numbers and describe a standard monomial basis of $DR_W$ using a variant of Motzkin paths. Our methods are type-uniform and involve a Lefschetz-like theory, which applies to the exterior algebra $\wedge (V \oplus V^*)$.
The efficiency–thoroughness trade-off after implementation of electronic medication management: a qualitative study in paediatric oncology
Authors: Baysari Melissa T , van Dort Bethany A , Prgomet Mirela , Zheng Wu Yi , Raban Magdalena Z , Dalla-Pozza Luciano , Mccullagh Cheryl , Westbrook Johanna 
Published: July 2020

Abstract

Objective
The efficiency–thoroughness trade-off (ETTO) principle proposes that people and organizations are often required to make a trade-off between being efficient and being thorough, as it is difficult to be both efficient and thorough at the same time. This study aimed to compare pre- electronic medication management system (EMMS) expectation of how an EMMS is likely to impact on efficiency and thoroughness to post-EMM experiences of an EMMS and the ETTO.

Design
Qualitative interview study.

Setting
A paediatric oncology cancer centre in a large paediatric tertiary teaching hospital in Sydney, Australia.

Participants
Forty-four semi-structured interviews with doctors, nurses and pharmacists six months prior to and two years following implementation of an EMMS.

Results
Prior to EMM implementation, staff identified a number of areas of work where both efficiency and thoroughness were expected to improve with EMM. These included ease of accessibility of the medication record, and organization and legibility of medication information. Following EMMS implementation, staff reported improvements in these areas. However, the EMMS was perceived to drive thoroughness (safety) benefits at the expense of efficiency (time). Measures to improve safety in the EMMS enforced processes that required time, such as medication double-checking procedures.

Conclusions
Overall, staff were aware of the competitive interplay between thoroughness and efficiency and reported that introduction of an EMMS had imposed processes that favoured improvements in thoroughness at the expense of efficiency.