bluuebunny/crossref_metadata_2025_split huggingface dataset:
Persistently lower bone mass and bone turnover among South African children living with well controlled HIV
Authors: Shen Yanhan , Shiau Stephanie , Strehlau Renate , Burke Megan , Patel Faeezah , Johnson Cara T. , Rizkalla Bridgette , Dympna Gallagher , Kuhn Louise , Coovadia Ashraf , Yin Michael T. , Arpadi Stephen M. 
Published: June 2021

Objective:
We evaluated longitudinal trends and associations between bone mass, bone turnover and inflammatory markers among South African children living with HIV (CLHIV) and controls.

Design:
We previously reported decreased bone mass among CLHIV independent of marked inflammation and increased bone turnover. The goal of this study was to evaluate longitudinal changes in bone mass, bone turnover and inflammation over 2 years.

Methods:
Longitudinal analyses were conducted among 220 CLHIV and 220 controls. Anthropometric measurements, physical activity, antiretroviral regimen, virologic and immunologic status, whole body (WB) and lumbar spine (LS) bone mineral content (BMC) and bone mineral density (BMD) were collected (enrollment, 12 and 24 months). Bone turnover markers including C-telopeptide of type I collagen (CTx) and procollagen type I N-terminal propeptide (P1NP) and inflammatory markers including interleukin-6 (IL-6), tumor necrosis factor-alpha (TNF-alpha), soluble CD14 and high-sensitivity C-reactive protein (hsCRP) were collected at enrollment and 24 months.

Results:
Compared with controls, CLHIV had significantly lower mean WB-BMC, WB-BMD, WB-BMC z scores, LS-BMC and LS-BMD as well as lower bone formation (P1NP) and resorption (CTx), and higher hsCRP and soluble CD14 over 24 months. CLHIV on efavirenz (EFV) had consistently lower TNF-alpha and IL-6 compared with those on ritonavir-boosted lopinavir (LPV/r) at all time points.

Conclusion:
Over 2 years of follow-up, South African CLHIV had persistently lower bone mass, bone turnover, and macrophage activation. Lower bone mass and higher pro-inflammatory cytokine profiles were consistently observed among those on LPV/r-based compared with EFV-based regimens.
The symptomatology of cerebrospinal fluid HIV RNA escape: a large case-series
Authors: Chan Terrence Y.-H. , De Zan Valentina , Gregg Alistair , Alagaratnam Jasmini , Gerevini Simonetta , Antinori Andrea , D’Arminio Monforte Antonella , Saracino Annalisa , Trunfio Mattia , Everitt Alex , Rackstraw Simon , Marta Monica , Calcagno Andrea , Cinque Paola , Winston Alan 
Published: June 2021

Objective:
To characterize the clinical, laboratory and radiological characteristics of persons with HIV (PWH) presenting with cerebrospinal fluid (CSF) HIV RNA escape.

Design:
Retrospective case review of PWH presenting with symptomatic CSF HIV RNA escape at seven tertiary HIV clinical sites in the United Kingdom and Italy.

Method:
PWH with symptomatic CSF HIV RNA escape episodes were identified and data obtained from medical records. CSF HIV RNA escape was defined as quantifiable CSF HIV RNA in unquantifiable plasma HIV RNA or CSF HIV RNA greater than plasma HIV RNA in cases where plasma HIV RNA was quantifiable. The onset of clinical symptoms was classified as acute (<2 weeks–6 months), or chronic (>6 months) and differences in presentation in those with CSF HIV RNA below and above 1000 copies/ml determined.

Results:
We identified 106 PWH with CSF HIV RNA escape (65 male); 68 (64%) PWH had acute presentations and 38 (36%) had chronic presentations. Cognitive decline (n = 54; 50.9%), confusion (n = 20; 18.9%) and headache (n = 28; 26.4%) were the most common presentations, with cognitive decline being more common in PWH who presented chronically compared with PWH who presented acutely (73.7% vs. 35.3%, P = 0.0002). Sixty PWH had CSF HIV RNA at least 1000 copies/ml and presented more frequently with confusion (n = 15/60; 25.0%) compared with PWH with CSF HIV RNA less than 1000 copies/ml at presentation (n = 5/46; 10.9%; P = 0.03).

Conclusion:
Cognitive decline, confusion and headache are the most frequent presenting symptoms of CSF HIV RNA escape and their relative frequency varied according to symptom onset and CSF HIV RNA concentration.
Infection prevention measures in acute care settings based on severe acute respiratory syndrome coronavirus 2 transmission patterns and risk: a review
Authors: Yen Christina F. , van den Berg Polly , Pepe Dana E. 
Published: June 2021

Purpose of review
During the coronavirus disease 2019 pandemic, when facing extraordinary infection prevention challenges, acute care settings have balanced routine patient safety needs while minimizing severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) transmission risk to patients and healthcare personnel (HCP). Mitigation strategies in acute care settings are based on a combination of basic science, environmental, and epidemiologic evidence. Here, we review the literature on SARS-CoV-2 transmission, how it has shaped infection prevention interventions in acute care settings, and the results of such measures to reduce transmission.

Recent findings
HCP adherence to transmission-based precautions in acute care settings, such as the use of personal protective equipment (PPE), is essential to mitigating SARS-CoV-2 spread. Although the SARS-CoV-2 virus has been isolated in nonrespiratory body sites, such exposure has not been shown to definitively cause transmission in humans. Epidemiologic evidence has demonstrated that implementation and adherence to infection prevention strategies reduces acute setting transmission.

Summary
Given SARS-CoV-2 infection occurs primarily through respiratory transmission, preventing HCP acquisition requires fidelity to consistent PPE usage. Infection prevention strategies and implementation of transmission-based precautions have reduced spread and outbreaks. Epidemiologic studies of acute care outbreaks often include reports of PPE nonadherence and community exposure contributing to SARS-CoV-2 transmission within this setting.
IMPACT OF COVID-19 PANDEMIC ON SICKNESS ABSENCE FOR MENTAL ILL HEALTH IN NATIONAL HEALTH SERVICE STAFF
Authors: van der Plaat Diana A , Edge Rhiannon , Coggon David , van Tongeren Martie , Muiry Rupert , Parsons Vaughan , Cullinan Paul , Madan Ira 
Published: June 2021

AbstractObjectiveTo explore the patterns of sickness absence in National Health Service (NHS) staff attributable to mental ill health during the first wave of the Covid-19 epidemic in March – July 2020DesignCase-referent analysis of a secondary data setSettingNHS Trusts in EnglandParticipantsPseudonymised data on 959,356 employees who were continuously employed by NHS trusts during 1 January 2019 to 31 July 2020Main Outcome MeasuresTrends in the burden of sickness absence due to mental ill health from 2019 to 2020 according to demographic, regional and occupational characteristics.ResultsOver the study period, 164,202 new sickness absence episodes for mental ill health were recorded in 12.5% (119,525) of the study sample. There was a spike of sickness absence for mental ill health in March-April 2020 (899,730 days lost) compared with 519,807 days in March-April 2019; the surge was driven by an increase in new episodes of long-term absence and had diminished by May/June 2020. The increase was greatest in those aged >60 years (227%) and among employees of Asian and Black ethnic origin (109%-136%). Among doctors and dentists the number of days absent declined by 12.7%. The biggest increase was in London (122%) and the smallest in the East Midlands (43.7%); the variation between regions reflected the rates of Covid-19 sickness absence during the same period.ConclusionAlthough the Covid-19 epidemic led to an increase in sickness absence attributed to mental ill health in NHS staff, this had substantially declined by May/June 2020, corresponding with the decrease in pressures at work as the first wave of the epidemic subsided.Article SummaryStrengths and limitations of this studyLarge study populationStudy population were not self-selectedJob exposure matrix allowed adjustment for occupational exposureData did not extend to the start of the second wave in September 2020
Reopening International Borders without Quarantine: Contact Tracing Integrated Policy against COVID-19
Authors: Yu Zidong , Zhu Xiaolin , Liu Xintao , Chen Xiang , Wei Tao , Yuan Hsiang-Yu , Xu Yang , Zhu Rui , He Huan , Wang Hui , Wong Man-sing , Jia Peng , Shi Wen-zhong , Chen Wu 
Published: June 2021

AbstractWith the COVID-19 vaccination widely implemented in most countries, propelled by the need to revive the tourism economy, there is a growing prospect for relieving the social distancing regulation and reopening borders in tourism-oriented countries and regions. The need incentivizes stakeholders to develop border control strategies that fully evaluate health risks if mandatory quarantines are lifted. In this study, we have employed a computational approach to investigate the contact tracing integrated policy in different border reopening scenarios in Hong Kong, China. Built on a modified SEIR epidemic model with a 30% vaccination coverage, the results suggest that scenarios with digital contact tracing and quick isolation intervention can reduce the infectious population by 92.11% compared to those without contact tracing. By further restricting the inbound population with a 10,000 daily quota and applying moderate-to-strong community non-pharmacological interventions (NPIs), the average daily confirmed cases in the forecast period of 60 days can be well controlled at around 9 per day (95% CI: 7–12). Two main policy recommendations are drawn from the study. First, digital contact tracing would be an effective countermeasure for reducing local virus spread, especially when it is applied along with a moderate level of vaccination coverage. Second, implementing a daily quota on inbound travelers and restrictive community NPIs would further keep the local infection under control. This study offers scientific evidence and prospective guidance for developing and instituting plans to lift mandatory border control policies in preparing for the global economic recovery.
The prevalence, incidence, prognosis and risk factors for depression and anxiety in a UK cohort during the COVID-19 pandemic
Authors: Jia Ru , Ayling Kieran , Chalder Trudie , Massey Adam , Gasteiger Norina , Broadbent Elizabeth , Coupland Carol , Vedhara Kavita 
Published: June 2021

AbstractBackgroundThe COVID-19 pandemic had profound immediate impacts on population mental health. However, in whom the effects may be prolonged is less clear.AimsTo investigate the prevalence, incidence, prognosis, and risk factors for depression and anxiety reported in a UK cohort over three distinct periods in the pandemic in 2020.MethodAn online survey was distributed to a UK community cohort (n=3097) at three points: April (baseline), July-September (T2) and November-December (T3). Participants completed validated measures of depression and anxiety on each occasion and we prospectively explored the role of socio-demographic factors and psychological factors (loneliness, positive mood, perceived risk of and worry about COVID-19) as risk factors.ResultsDepression (PHQ-9 means - baseline: 7.69, T2: 5.53, T3: 6.06) and anxiety scores (GAD-7 means -baseline: 6.59, T2: 4.60, T3: 4.98) were considerably greater than pre-pandemic population norms. Women reported greater depression and anxiety than men. Being younger, having prior mental health disorders, more negative life events due to COVID-19, as well as greater loneliness and lower positive mood at baseline were significant predictors of poorer mental health outcomes.ConclusionThe negative impact of the COVID-19 pandemic on mental health has persisted to some degree. Younger people and individuals with prior mental health disorders were at greatest risk. Easing of restrictions might bring the opportunity for a return to social interaction, which could mitigate the risk factors of loneliness and positive mood.
A pan-European study of SARS-CoV-2 variants in wastewater under the EU Sewage Sentinel System
Authors: Agrawal Shelesh , Orschler Laura , Schubert Selina , Zachmann Kira , Heijnen Leo , Tavazzi Simona , Gawlik Bernd Manfred , de Graaf Miranda , Medema Gertjan , Lackner Susanne 
Published: June 2021

AbstractWastewater based surveillance employing qPCR has already shown its utility for monitoring SARS-CoV-2 at community level, and consequently the European Commission has recommended the implementation of an EU Sewage Sentinel System. However, using sequencing for the determination of genomic variants in wastewater is not fully established yet. Therefore, we focused on the sequencing analysis of SARS-CoV-2 RNA in wastewater samples collected across 20 European countries including 54 municipalities. Our results provide unprecedented insight into the abundance and the profile of the mutations associated with the variants of concerns: B.1.1.7, P.1, B.1.351 and B.1.617.2, which were present in various wastewater samples. This study shows that integrating genomic and wastewater-based epidemiology (WBE) can support the identification of variants circulating in a city at community level.
Impact of long-term care facility size on preparedness and adherence to infection prevention and control guidance for the mitigation of COVID-19
Authors:   Adherence to COVID-19 guidance, Wachholz Patrick Alexander , de Melo Ruth Caldeira , Jacinto Alessandro Ferrari , Villas Boas Paulo Jose Fortes 
Published: June 2021

AbstractAimTo evaluate the preparedness and adherence of Brazilian long-term care facilities (LTCFs) to the World Health Organization (WHO) infection prevention and control (IPC) guidance and examine the association of LTCF size with adherence to recommendations.MethodsWe conducted a cross-sectional study of LTCF managers for 12 consecutive weeks from May 5, 2020. We developed and pre-tested a 46-item questionnaire based on WHO IPC guidance that included multiple-choice and dichotomous questions as well as an open-ended question on the main difficulties encountered by the facility in tackling the pandemic. Using a global adherence score based on the adoption of 20 recommendations, we classified preparedness as (1)excellentfor LTCFs following ≥14 recommendations, (2)goodfor those following 10-13 recommendations, and (3)poorfor those following <10 recommendations. LTCF size was established as small, medium, and large according to a 2-step cluster analysis of the number of residents as a continuous variable. We used descriptive statistics and chi-square tests at a 5% significance level.ResultsOf 362 facilities included in the study, 308 (85.1%) adhered to 14 or more recommendations; 3 were classified as poorly adherent. Regarding LTCF size, we found a lower adherence to screening visitors for COVID-19 signs and symptoms (p=0.037) and to isolating patients until they have 2 negative laboratory tests (p=0.032) in larger facilities than in medium and small facilities.ConclusionsPreparedness for mitigating COVID-19 in Brazilian LTCFs was considered excellent for most of the proposed recommendations, regardless of LTCF size. Difficulties and problems with infrastructure and/or resident care were much less commonly reported than those related to maintenance of a sufficient stock of materials, workforce management, and financial distress.
Interferon-stimulated and metallothionein-expressing macrophages are associated with acute and chronic allograft dysfunction after lung transplantation
Authors: Moshkelgosha Sajad , Duong Allen , Wilson Gavin , Andrews Tallulah , Berra Gregory , Renaud-Picard Benjamin , Liu Mingyao , Keshavjee Shaf , MacParland Sonya , Yeung Jonathan , Martinu Tereza , Juvet Stephen 
Published: June 2021

AbstractLung transplant (LT) recipients experience episodes of immune-mediated acute lung allograft dysfunction (ALAD). ALAD episodes are a risk factor for chronic lung allograft dysfunction (CLAD), the major cause of death after LT. We have applied single-cell RNA sequencing (scRNAseq) to bronchoalveolar lavage (BAL) cells from stable and ALAD patients and to cells from explanted CLAD lung tissue to determine key cellular elements in dysfunctional lung allografts, with a focus on macrophages. We identified two alveolar macrophage (AM) subsets uniquely represented in ALAD. Using pathway analysis and differentially expressed genes, we annotated these as pro-inflammatory interferon-stimulated gene (ISG) and metallothionein-mediated inflammatory (MT) AMs. Functional analysis of an independent set of AMsin vitrorevealed that ALAD AMs exhibited a higher expression of CXCL10, a marker of ISG AMs, and increased secretion of pro-inflammatory cytokines compared to AMs from stable patients. Using publicly available BAL scRNAseq datasets, we found that ISG and MT AMs are associated with more severe inflammation in COVID-19 patients. Analysis of cells from four explanted CLAD lungs revealed similar macrophage populations. Using a single nucleotide variation calling algorithm, we also demonstrated contributions of donor and recipient cells to all AM subsets early post-transplant, with loss of donor-derived cells over time. Our data reveals extensive heterogeneity among lung macrophages after LT and indicates that specific sub-populations may be associated with allograft dysfunction, raising the possibility that these cells may represent important therapeutic targets.
Viral transduction and the dynamics of bacterial adaptation
Authors: Cherabier Philippe , Méléard Sylvie , Ferrière Régis 
Published: June 2021

AbstractTransduction - horizontal gene transfer (HGT) by viruses - is an important macroevolutionary force in prokaryotes, contributing to functional innovation and lineage diversification. In contrast, the role that transduction plays in bacterial microevolutionary adaptation is poorly known. By facilitating the transfer of beneficial alleles between host cells, transduction may accelerate adaptation. But transduction also carries the risk of transferring deleterious alleles, which, in addition to the demographic cost of viral infection, may hinder adaptation. Here we resolve the conflicting effects of transduction on bacterial adaptation in a simple eco-evolutionary model for large populations characterized by a quantitative (resource-use) trait with a single evolutionary optimum. Our model focuses on generalized transduction by virulent phages. Away from the optimum, the effect of transferring beneficial alleles dominates and transduction tends to accelerate adaptation. Close to the optimum, transduction generates a large amount of stochasticity in the population adaptive trajectory, thus hindering adaptation. Under disruptive selection, transduction may either limit (as sexual recombination would) or promote phenotypic diversification, or drive ‘transient optimization’ whereby phenotypic subpopulations recurrently visit the optimum. Our modeling framework paves the way to study complex adaptive feedbacks between bacterial hosts and phages generated by the combination of deterministic and stochastic effects of transduction.
Identification of enamel knot gene signature within the developing mouse molar
Authors: Winchester Emma Wentworth , Cotney Justin 
Published: June 2021

AbstractIn most mammals, the primary teeth developin uteroand the cells capable of contributing to hard surface regeneration are lost before tooth eruption. These cells differentiate through a series of reciprocal induction steps between the epithelium and mesenchyme, initially orchestrated by an epithelial signaling center called the enamel knot. While the factors secreted by this structure are of interest to the dental regeneration and development communities, its small size makes it difficult to isolate for analysis. Here we describe our work to identify the enamel knot from whole E14 molars using publicly available scRNA-seq data. We identified 335 genes differentially expressed in the enamel knot compared to the surrounding tissues, including known enamel knot marker genes. We validated expression of the most highly enriched enamel knot marker genes and identified 42 novel marker genes of the enamel knot which provide excellent targets for future dental regeneration investigations.
I, We, andThey: A Linguistic and Narrative Exploration of the Authorship Process
Authors: Konopasky Abigail , O’Brien Bridget C. , Artino Anthony R. , Driessen Erik W. , Watling Christopher J. , Maggio Lauren A. 
Published: June 2021

AbstractIntroductionWhile authorship plays a powerful role in the academy, research indicates many authors engage in questionable practices like honorary authorship. This suggests that authorship may be acontested spacewhere individuals must exerciseagency--a dynamic and emergent process, embedded in context--to negotiate potentially conflicting norms among published criteria, disciplines, and informal practices. This study explores how authors narrate their own and others’ agency in making authorship decisions.MethodWe conducted a mixed-methods analysis of 24 first authors’ accounts of authorship decisions on a recent multi-author paper. Authors included 14 females and 10 males in health professions education (HPE) from U.S. and Canadian institutions (10 assistant, 6 associate, and 8 full professors). Analysis took place in three phases: (1) linguistic analysis of grammatical structures shown to be associated with agency (coding for main clause subjects and verb types); (2) narrative analysis to create a “moral” and “title” for each account; and (3) integration of (1) and (2).ResultsParticipants narrated other authors most frequently as main clause subjects (n= 191), then themselves (I;n= 151), inanimate nouns (it, the paper;n= 146), and author team (we;n= 105). Three broad types of agency were narrated:distributed(n= 15 participants), focusing on how resources and work were spread across team members;individual(n= 6), focusing on the first author’s action; andcollaborative(n= 3), focusing on group actions. These three types of agency contained four sub-types, e.g., supported, contested, task-based, negotiated.DiscussionThis study highlights the complex and emergent nature of agency narrated by authors when making authorship decisions. Published criteria offer us starting point--thestated rulesof the authorship game; this paper offers us a next step--theenactedandnarrated approachto the game.
Single-synapse analyses of Alzheimer’s disease implicate pathologic tau, DJ1, CD47, and ApoE
Authors: Phongpreecha Thanaphong , Gajera Chandresh R. , Liu Candace C. , Vijayaragavan Kausalia , Chang Alan L. , Becker Martin , Fallahzadeh Ramin , Fernandez Rosemary , Postupna Nadia , Sherfield Emily , Tebaykin Dmitry , Latimer Caitlin , Shively Carol A. , Register Thomas C. , Craft Suzanne , Montine Kathleen S. , Fox Edward J. , Poston Kathleen L. , Dirk Keene C. , Angelo Michael , Bendall Sean C. , Aghaeepour Nima , Montine Thomas J. 
Published: June 2021

AbstractSynaptic molecular characterization is limited for Alzheimer’s disease (AD). We used mass cytometry to quantify 38 probes in approximately 17 million single synaptic events from human brains without pathologic change or with pure AD or Lewy body disease (LBD), non-human primates (NHP), and PS/APP mice. Synaptic molecular integrity in humans and NHP was similar. Although not detected in human synapses, Aβ was in PS/APP mice synaptic events. Clustering and pattern identification of human synapses showed expected disease-specific differences, like increased hippocampal pathologic tau in AD and reduced caudate dopamine transporter in LBD, and revealed novel findings including increased hippocampal CD47 and lowered DJ1 in AD and higher ApoE in AD dementia. Our results were independently supported by multiplex ion beam imaging of intact tissue.