bluuebunny/crossref_metadata_2025_split huggingface dataset:
Safety of intravenous push administration of beta-lactams within a healthcare system
Authors: Marsh Kassandra , Ahmed Nabeela , Decano Arnold , Dubrovskaya Yanina , Jen Shin-Pung (Polly) , Siegfried Justin , Chen Xian Jie (Cindy) , Merchan Cristian 
Published: April 2020

Abstract

Purpose
A critical shortage of small-volume parenteral solutions in late 2017 led hospitals to develop strategies to ensure availability for critical patients, including administration of antibiotics as intravenous push (IVP). Minimal literature has been published to date that assesses the safety of administration of beta-lactams via this route. Therefore, the purpose of this study was to evaluate the safety of IVP administration of select beta-lactam antibiotics.

Methods
We performed a retrospective review of IVP administrations of aztreonam, ceftriaxone, cefepime, and meropenem at two campuses of the New York University Langone Health system after October 2017. Patients receiving surgical prophylaxis or more than one IVP antibiotic simultaneously were excluded. The primary endpoint was adverse events (ADE) following IVP administration of antibiotics.

Results
We evaluated 1000 patients who received IVP aztreonam (n = 43), ceftriaxone (n = 544), cefepime (n = 368) or meropenem (n = 45). There were 10 (1%) ADE observed, 5 of which were allergic reactions. Four ADE were neurotoxicity related to IVP cefepime. Based on the Naranjo score, 1 adverse event was “probably” and 3 were “possibly” related to cefepime IVP administration. Lastly, only 1 report of phlebitis was observed with the use of IVP ceftriaxone.

Conclusions
The use of IVP as an alternative to intravenous piggyback (IVPB) during times of drug shortage for select beta-lactam antibiotics appears to be safe, and ADE are similar to those previously described for IVPB administration. Future studies evaluating clinical outcomes between IVP and IVPB administration may be of benefit.
Bayesian structural equation modeling in multiple omics data with application to circadian genes
Authors: Maity Arnab Kumar , Lee Sang Chan , Mallick Bani K , Sarkar Tapasree Roy 
Published: April 2020

Abstract

Motivation
It is well known that the integration among different data-sources is reliable because of its potential of unveiling new functionalities of the genomic expressions, which might be dormant in a single-source analysis. Moreover, different studies have justified the more powerful analyses of multi-platform data. Toward this, in this study, we consider the circadian genes’ omics profile, such as copy number changes and RNA-sequence data along with their survival response. We develop a Bayesian structural equation modeling coupled with linear regressions and log normal accelerated failure-time regression to integrate the information between these two platforms to predict the survival of the subjects. We place conjugate priors on the regression parameters and derive the Gibbs sampler using the conditional distributions of them.

Results
Our extensive simulation study shows that the integrative model provides a better fit to the data than its closest competitor. The analyses of glioblastoma cancer data and the breast cancer data from TCGA, the largest genomics and transcriptomics database, support our findings.

Availability and implementation
The developed method is wrapped in R package available at https://github.com/MAITYA02/semmcmc.

Supplementary information
Supplementary data are available at Bioinformatics online.
pepFunk: a tool for peptide-centric functional analysis of metaproteomic human gut microbiome studies
Authors: Simopoulos Caitlin M A , Ning Zhibin , Zhang Xu , Li Leyuan , Walker Krystal , Lavallée-Adam Mathieu , Figeys Daniel 
Published: April 2020

AbstractMotivationEnzymatic digestion of proteins before mass spectrometry analysis is a key process in metaproteomic workflows. Canonical metaproteomic data processing pipelines typically involve matching spectra produced by the mass spectrometer to a theoretical spectra database, followed by matching the identified peptides back to parent-proteins. However, the nature of enzymatic digestion produces peptides that can be found in multiple proteins due to conservation or chance, presenting difficulties with protein and functional assignment.ResultsTo combat this challenge, we developed pepFunk, a peptide-centric metaproteomic workflow focused on the analysis of human gut microbiome samples. Our workflow includes a curated peptide database annotated with Kyoto Encyclopedia of Genes and Genomes (KEGG) terms and a gene set variation analysis-inspired pathway enrichment adapted for peptide-level data. Analysis using our peptide-centric workflow is fast and highly correlated to a protein-centric analysis, and can identify more enriched KEGG pathways than analysis using protein-level data. Our workflow is open source and available as a web application or source code to be run locally.Availability and implementationpepFunk is available online as a web application at https://shiny.imetalab.ca/pepFunk/ with open-source code available from https://github.com/northomics/pepFunk.Contactdfigeys@uottawa.caSupplementary informationSupplementary data are available at Bioinformatics online.
GM-DockZn: a geometry matching-based docking algorithm for zinc proteins
Authors: Wang Kai , Lyu Nan , Diao Hongjuan , Jin Shujuan , Zeng Tao , Zhou Yaoqi , Wu Ruibo 
Published: April 2020

AbstractMotivationMolecular docking is a widely used technique for large-scale virtual screening of the interactions between small-molecule ligands and their target proteins. However, docking methods often perform poorly for metalloproteins due to additional complexity from the three-way interactions among amino-acid residues, metal ions and ligands. This is a significant problem because zinc proteins alone comprise about 10% of all available protein structures in the protein databank. Here, we developed GM-DockZn that is dedicated for ligand docking to zinc proteins. Unlike the existing docking methods developed specifically for zinc proteins, GM-DockZn samples ligand conformations directly using a geometric grid around the ideal zinc-coordination positions of seven discovered coordination motifs, which were found from the survey of known zinc proteins complexed with a single ligand.ResultsGM-DockZn has the best performance in sampling near-native poses with correct coordination atoms and numbers within the top 50 and top 10 predictions when compared to several state-of-the-art techniques. This is true not only for a non-redundant dataset of zinc proteins but also for a homolog set of different ligand and zinc-coordination systems for the same zinc proteins. Similar superior performance of GM-DockZn for near-native-pose sampling was also observed for docking to apo-structures and cross-docking between different ligand complex structures of the same protein. The highest success rate for sampling nearest near-native poses within top 5 and top 1 was achieved by combining GM-DockZn for conformational sampling with GOLD for ranking. The proposed geometry-based sampling technique will be useful for ligand docking to other metalloproteins.Availability and implementationGM-DockZn is freely available at www.qmclab.com/ for academic users.Supplementary informationSupplementary data are available at Bioinformatics online.
The Current Status of Enteric Fever Diagnostics and Implications for Disease Control
Authors: Baker Stephen , Blohmke Christoph J , Maes Mailis , Johnston Peter I , Darton Thomas C 
Published: April 2020

AbstractEnteric (typhoid) fever remains a problem in low- and middle-income countries that lack the infrastructure to maintain sanitation and where inadequate diagnostic methods have restricted our ability to identify and control the disease more effectively. As we move into a period of potential disease elimination through the introduction of typhoid conjugate vaccine (TCV), we again need to reconsider the role of typhoid diagnostics in how they can aid in facilitating disease control. Recent technological advances, including serology, transcriptomics, and metabolomics, have provided new insights into how we can detect signatures of invasive Salmonella organisms interacting with the host during infection. Many of these new techniques exhibit potential that could be further explored with the aim of creating a new enteric fever diagnostic to work in conjunction with TCV. We need a sustained effort within the enteric fever field to accelerate, validate, and ultimately introduce 1 (or more) of these methods to facilitate the disease control initiative. The window of opportunity is still open, but we need to recognize the need for communication with other research areas and commercial organizations to assist in the progression of these diagnostic approaches. The elimination of enteric fever is now becoming a real possibility, but new diagnostics need to be part of the equation and factored into future calculations for disease control.
Predictors of Discordant Tuberculin Skin Test and QuantiFERON-TB Gold In-tube Results in Eastern China: A Population-based, Cohort Study
Authors: Lu Peng , Liu Qiao , Zhou Yang , Martinez Leonardo , Kong Wen , Ding Xiaoyan , Peng Hong , Zhu Tao , Zhu Limei , Lu Wei 
Published: April 2020

AbstractBackgroundDiscordance between the QuantiFERON-TB Gold In-tube (QFT) and tuberculin skin test (TST) is not well understood. We aimed to identify the factors that determine discordance between the TST and QFT when compared to either TST+QFT+ or TST-QFT- results in a medium tuberculosis (TB) burden setting.MethodsWe conducted a population-based study in Eastern China and administered TSTs and QFTs to participants. We calculated kappa values while constructing multivariable logistic regression models to evaluate predictors of test discordance. We analyzed the predictive value of discordant and concordant test results for progression to TB over 6 years of follow-up.ResultsOverall, 5405 participants were enrolled; 2043 (37.8%) and 1104 (20.4%) were TST and QFT positive, respectively. There was fair agreement between the TST and the QFT (kappa values between 0.30–0.39 at different TST cutoffs). Agreement was lower among participants vaccinated with Bacillus Calmette-Guerin (BCG; κ, 0.17 versus 0.47 in nonvaccinated participants). TST+QFT- results were associated with decreasing age, smoking, undiagnosed diabetes, and BCG vaccination (adjusted odds ratio, 1.45; 95% confidence interval [CI], 1.11–1.90). TST-QFT+ results were associated with increasing age, male sex, smoking, and diagnosed diabetes. Compared to participants with TST-QFT- results, QFT+ and TST+QFT+ participants were 6.3 (95% CI, 1.9–20.4) and 7.5 (95%CI, 2.3–25.1) times more likely to progress to TB, respectively.ConclusionsIn this population-based study of over 5000 participants from a medium TB burden region, the test agreement between QFT and TST was fair overall and we found multiple novel predictors of discordant QFT/TST results. QFT provides a substantial improvement to the TST among these populations and was multi-fold better at predicting progression to TB.
Are current accounts driven by cost competitiveness or asset prices? A synthetic model and an empirical test
Authors: Guschanski Alexander , Stockhammer Engelbert 
Published: April 2020

Abstract
While current account imbalances have widened in recent decades, their causes are still debated. Trade-centred approaches highlight the role of cost competitiveness, in particular unit labour costs, and aggregate demand. In contrast, finance-centred approaches focus on gross financial flows, driven by expectations and the return on assets, that impact demand and the exchange rate. This article, first, builds a simple model of the current account that provides a synthesis between the two approaches. Unit labour costs impact the current account via the real exchange rate and income distribution, while financial inflows drive up asset prices, which leads to nominal appreciation and an increase in domestic demand. Second, we estimate a reduced form of this model for 28 OECD countries from 1972 to 2014, controlling for both trade- and finance-centred channels and a wide range of control variables. Our results indicate that finance-centred channels, via equity and residential property prices, drove current account divergence in the OECD, while unit labour costs were less important. They suggest that the effects of gross financial flows deserve more attention in theoretical and empirical models of the current account.
Clinical outcomes of hemodialysis patients infected with severe acute respiratory syndrome coronavirus 2 and impact of proactive chest computed tomography scans
Authors: Wang Rui , He Hong , Liao Cong , Hu Hongtao , Hu Chun , Zhang Juan , Gao Ping , Wu Xiaoyan , Cheng Zhenshun , Liao Meiyan , Shui Hua 
Published: April 2020

Abstract

Background
Coronavirus disease 2019 (COVID-19) is an emerging infectious disease that first manifested in humans in Wuhan, Hubei Province, China, in December 2019, and has subsequently spread worldwide.

Methods
We conducted a retrospective, single-center case series of the seven maintenance hemodialysis (HD) patients infected with COVID-19 at Zhongnan Hospital of Wuhan University from 13 January to 7 April 2020 and a proactive search of potential cases by chest computed tomography (CT) scans.

Results
Of 202 HD patients, 7 (3.5%) were diagnosed with COVID-19. Five were diagnosed by reverse transcription polymerase chain reaction (RT-PCR) because of compatible symptoms, while two were diagnosed by RT-PCR as a result of screening 197 HD patients without respiratory symptoms by chest CT. Thirteen of 197 patients had positive chest CT features and, of these, 2 (15%) were confirmed to have COVID-19. In COVID-19 patients, the most common features at admission were fatigue, fever and diarrhea [5/7 (71%) had all these]. Common laboratory features included lymphocytopenia [6/7 (86%)], elevated lactate dehydrogenase [3/4 (75%)], D-dimer [5/6 (83%)], high-sensitivity C-reactive protein [4/4 (100%)] and procalcitonin [5/5 (100%)]. Chest CT showed bilateral patchy shadows or ground-glass opacity in the lungs of all patients. Four of seven (57%) received oxygen therapy, one (14%) received noninvasive and invasive mechanical ventilation, five (71%) received antiviral and antibacterial drugs, three (43%) recieved glucocorticoid therapy and one (14%) received continuous renal replacement therapy. As the last follow-up, four of the seven patients (57%) had been discharged and three patients were dead.

Conclusions
Chest CT may identify COVID-19 patients without clear symptoms, but the specificity is low. The mortality of COVID-19 patients on HD was high.
Are we curing one evil with another? A translational approach targeting the role of neoatherosclerosis in late stent failure
Authors: Lenz Tobias , Nicol Philipp , Castellanos Maria Isabel , Abdelgalil Ayat Aboutaleb Abdellah , Hoppmann Petra , Kempf Wolfgang , Koppara Tobias , Lahmann Anna Lena , Rüscher Alena , Kessler Horst , Joner Michael 
Published: April 2020

Abstract
Neoatherosclerosis is defined as foamy macrophage infiltration into the peri-strut or neointimal area after stent implantation, potentially leading to late stent failure through progressive atherosclerotic changes including calcification, fibroatheroma, thin-cap fibroatheroma, and rupture with stent thrombosis (ST) in advanced stages. Human autopsy as well as intravascular imaging studies have led to the understanding of neoatherosclerosis formation as a similar but significantly accelerated pathophysiology as compared to native atherosclerosis. This acceleration is mainly based on disrupted endothelial integrity with insufficient barrier function and augmented transmigration of lipids following vascular injury after coronary intervention and especially after implantation of drug-eluting stents. In this review, we summarize translational insights into disease pathophysiology and discuss therapeutic approaches to tackle this novel disease entity. We introduce a novel animal model of neoatherosclerosis alongside accompanying in vitro experiments, which show impaired endothelial integrity causing increased permeability for low-density lipoprotein cholesterol resulting in foam cell transformation of human monocytes. In addition, we discuss novel intravascular imaging surrogates to improve reliable diagnosis of early stage neoatherosclerosis. Finally, a therapeutic approach to prevent in-stent neoatherosclerosis with magnesium-based bioresorbable scaffolds and systemic statin treatment demonstrated the potential to improve arterial healing and re-endothelialization, leading to significantly mitigated neoatherosclerosis formation in an animal model of neoatherosclerosis.
Parental mortality following the loss of a child to a drug-related death
Authors: Christiansen Solveig Glestad , Reneflot Anne , Stene-Larsen Kim , Johan Hauge Lars 
Published: April 2020

Abstract

Background
The drug-related death of a child has been linked to higher prevalence of complicated grief and mental health problems than bereavement by other causes of death. Whether this leads to an increased risk of mortality following the loss has not yet been examined.

Methods
Employing register data covering the years 1986–2015 and encompassing the entire Norwegian population, parents with at least one child aged 15 or older were analyzed using Cox regression. Drug-death bereaved parents were compared with both non-bereaved parents and parents bereaved by other causes of death.

Results
Parents bereaved by a drug-related death generally had a higher natural cause mortality throughout the follow-up. Drug-death bereaved parents had a particularly high external cause mortality in the first 2 years subsequent to bereavement when compared with non-bereaved parents (mothers: hazard ratio 4.82, 95% CI = 3.11–7.47; fathers: hazard ratio 2.50, 95% CI = 1.57–3.97). There was also an elevated, but significantly lower mortality risk from external causes 2 to 10 years subsequent to bereavement. This indicates that the associations observed are not solely due to selection.

Conclusions
Parents bereaved by the drug-related death of a child had a higher mortality than both non-bereaved parents and parents bereaved by other causes of death. Drug-death bereaved parents had particularly high external cause mortality. Our results indicate that losing a child to a drug-related death is associated with adverse health outcomes and that these might be more severe than bereavement due to other causes of death.
Napoleonic Latin inscriptions
Authors: Turk Thomas N 
Published: April 2020

Abstract
Even though Napoleon Bonaparte was a mediocre Latin student, he made more extensive public use of that language throughout the French Empire than any secular ruler since Roman times. While Napoleon’s use of the images of imperial Rome to promote himself and his vision for France has been amply discussed elsewhere, the Latin inscriptions that accompanied this imperial imagery on medals and monuments have been largely overlooked. This article explores how Napoleon made use of these inscriptions for self-promotion and considers why Latin rather than French often appeared in public spaces. It also assesses who was responsible for the language and imagery of the inscriptions, where they appeared and who could read them and how.
Gross Negligence Manslaughter in Healthcare: Time for a Restorative Justice Approach?
Authors: Farrell Anne-Maree , Alghrani Amel , Kazarian Melinee 
Published: April 2020

Abstract
This article explores the merits of employing a restorative justice approach in cases of gross negligence manslaughter involving healthcare professionals, in line with the recent policy turn towards developing a just culture in addressing episodes of healthcare malpractice within the National Health Service in England. It is argued that redress for victims and rehabilitation of offenders should operate as key values, underpinning the adoption of a restorative justice approach in such cases. It would also be vital that a structured pathway was designed that established suitable protocols and safeguards for both victims and offenders taking account of problematic issues such as the informality of the process, power asymmetries between parties, and the context in which the offence took place. Taking all such matters into account, we propose that consideration be given to establishing a pilot involving the use of restorative justice in cases of gross negligence manslaughter involving healthcare professionals, which would be subject to judicial and stakeholder oversight to ensure transparency and accountability, which in turn could inform future policy options.
Electromagnetic transients and gravitational waves from white dwarf disruptions by stellar black holes in triple systems
Authors: Fragione Giacomo , Metzger Brian D , Perna Rosalba , Leigh Nathan W C , Kocsis Bence 
Published: April 2020

ABSTRACT
Mergers of binaries comprising compact objects can give rise to explosive transient events, heralding the birth of exotic objects that cannot be formed through single-star evolution. Using a large number of direct N-body simulations, we explore the possibility that a white dwarf (WD) is dynamically driven to tidal disruption by a stellar-mass black hole (BH) as a consequence of the joint effects of gravitational wave (GW) emission and Lidov–Kozai oscillations imposed by the tidal field of an outer tertiary companion orbiting the inner BH–WD binary. We explore the sensitivity of our results to the distributions of natal kick velocities imparted to the BH and WD upon formation, adiabatic mass loss, semimajor axes and eccentricities of the triples, and stellar-mass ratios. We find rates of WD–tidal disruption events (TDEs) in the range 1.2 × 10−3 − 1.4 Gpc−3 yr−1 for z ≤ 0.1, rarer than stellar TDEs in triples by a factor of ∼3–30. The uncertainty in the TDE rates may be greatly reduced in the future using GW observations of Galactic binaries and triples with LISA. WD–TDEs may give rise to high-energy X-ray or gamma-ray transients of duration similar to long gamma-ray bursts but lacking the signatures of a core-collapse supernova, while being accompanied by a supernova-like optical transient that lasts for only days. WD–BH and WD–NS binaries will also emit GWs in the LISA band before the TDE. The discovery and identification of triple-induced WD–TDE events by future time domain surveys and/or GWs could enable the study of the demographics of BHs in nearby galaxies.
Conscientious Objection and the Politics of Cake-Making
Authors: Moon Richard 
Published: April 2020

Abstract
In two recent cases, one in the USA and the other in the UK, courts have considered conscientious objection claims made by cake bakers who objected to providing a cake for the celebration/advocacy of same-sex marriage. I will argue that the issue in these cases is not the reasonable balance between the individual’s religious interests and the interests or rights of others in the community but is instead whether the individual’s religiously based objection should be viewed as an expression of personal religious conscience or as a (religiously grounded) civic position or action that falls outside the scope of religious freedom protection. In determining whether a conscientious objection should be viewed as a personal/spiritual matter or instead as a civic/political position, two factors are relevant. The first is whether the individual is being required to perform the particular act (to which she/he objects) because she/he holds a special position not held by others. The other factor is the relative remoteness/proximity of the act that the objector is required to perform from the act that she/he considers to be inherently immoral. The more remote the legally required action, the more likely we are to regard the objection as a political position.