bluuebunny/crossref_metadata_2025_split huggingface dataset:
CD64 and CD169 could help differentiate bacterial from viral infections in Emergency Department
Authors: Bourgoin Pénélope , Soliveres Thomas , Barbaresi Alexandra , Loundou Anderson , Arnoux Isabelle , Bernot Denis , Morange Pierre-Emmanuel , Michelet Pierre , Malergue Fabrice , Markarian Thibaut 
Published: November 2020

ABSTRACTBackgroundThe identification of a bacterial, viral or even non-infectious cause is essential in the management of febrile syndrome in the emergency department (ED) setting, especially in epidemic contexts such as flu or CoVID-19.ObjectivesThe aim of this study was to assess discriminative performances of two biomarkers, CD64 on neutrophils (nCD64) and CD169 on monocytes (mCD169), using a new flow cytometry procedure, in patients presenting with fever to the ED. Human leucocyte antigen-DR on monocytes (mHLA-DR), HLA-ABC ratio (rHLA-ABC), and CD64 on monocytes (mCD64) were also assessed.Methods85 adult patients presenting with potential infection were included during the 2019 flu season in the ED of La Timone Hospital. They were divided into four diagnostic outcomes according to their clinical records: no-infection, bacterial infection, viral infection and co-infection.ResultsmCD169 was elevated in patients suffering from Flu A virus or Respiratory Syncytial Virus, while nCD64 was mainly found elevated in subjects with Streptococcus pneumoniae. In total, 38 (45%) patients were diagnosed with bacterial infections, 11 (13%) with viral infections and 29 (34%) with co-infections. nCD64 and mCD169 showed 90% and 80% sensitivity, and 78% and 91% specificity, respectively, for identifying patients with bacterial or viral infections. Other biomarkers had lower discriminative performances.ConclusionsnCD64 and mCD169 have potential for accurately distinguishing bacterial and acute viral infections. Combined in an easy and rapid flow cytometry procedure, they constitute a potential improvement for infection management in the ED setting, and could even help for the triage of patients during emerging epidemics.
They’re Dying in the Suburbs: COVID-19 Cases and Deaths by Geography in Louisiana (USA)
Authors: Schnake-Mahl Alina , Bilal Usama 
Published: November 2020

AbstractThe national COVID-19 conversation in the US has mostly focused on urban areas, without sufficient examination of another geography with large vulnerable populations: the suburbs. While suburbs are often thought of as areas of uniform affluence and racial homogeneity, over the past 20 years, poverty and diversity have increased substantially in the suburbs. In this study, we compare geographic and temporal trends in COVID-19 cases and deaths in Louisiana, one of the few states with high rates of COVID-19 during both the spring and summer. We find that incidence and mortality rates were initially highest in New Orleans. By the second peak, trends reversed: suburban areas experienced higher rates than New Orleans and similar rates to other urban and rural areas. We also find that increased social vulnerability was associated with increased positivity and incidence during the first peak. During the second peak, these associations reversed in New Orleans while persisting in other urban, suburban, and rural areas. The work draws attention to the high rates of COVID-19 cases and deaths in suburban areas and the importance of metropolitan-wide actions to address COVID-19.RegistrationN/AFunding sourceNIH (DP5OD26429) and RWJF (77644)Code and data availabilityCode for replication along with data is available here: https://github.com/alinasmahl1/COVID_Louisiana_Suburban/.
U-shaped-aggressiveness of SARS-CoV-2: Period between initial symptoms and clinical progression to COVID-19 suspicion. A population-based cohort study
Authors: Morgenstern-Kaplan Dan , Buitano-Tang Bruno , Martínez-Gil Mercedes , Zaldívar-Pérez Pavón Andrea , Talavera Juan O. 
Published: November 2020

AbstractBackgroundEarly identification of different COVID-19 clinical presentations may depict distinct pathophysiological mechanisms and guide management strategies.ObjectiveTo determine the aggressiveness of SARS-CoV-2 using symptom progression in COVID-19 patients.DesignHistoric cohort study of Mexican patients. Data from January-April 2020 were provided by the Health Ministry.SettingPopulation-based. Patients registered in the Epidemiologic Surveillance System in Mexico.ParticipantsSubjects who sought medical attention for clinical suspicion of COVID-19. All patients were subjected to RT-PCR testing for SARS-CoV-2.MeasurementsWe measured the Period between initial symptoms and clinical progression to COVID-19 suspicion (PISYCS) and compared it to the primary outcomes (mortality and pneumonia).Results65,500 patients were included. Reported fatalities and pneumonia were 2176 (3.32%), and 11568 (17.66%), respectively. According to the PISYCS, patients were distributed as follows: 14.89% in <24 hours, 43.25% between 1-3 days, 31.87% between 4-7 days and 9.97% >7 days. The distribution for mortality and pneumonia was 5.2% and 22.5% in <24 hours, 2.5% and 14% between 1-3 days, 3.6% and 19.5% between 4-7 days, 4.1% and 20.6% >7 days, respectively (p<0.001). Adjusted-risk of mortality was (OR [95% CI], p-value): <24 hours= 1.75 [1.55-1.98], p<0.001; 1-3 days= 1 (reference value); 4-7 days= 1.53 [1.37-1.70], p<0.001; >7 days= 1.67 [1.44-1.94], p<0.001. For pneumonia: <24 hours= 1.49 [1.39-1.58], p<0.001; 1-3 days= 1; 4-7 days= 1.48 [1.41-1.56], p<0.001; >7 days= 1.57 [1.46-1.69], p<0.001.LimitationsUsing a database fed by large numbers of people carries the risk of data inaccuracy. However, this imprecision is expected to be random and data are consistent with previous studies.ConclusionThe PISYCS shows a U-shaped SARS-CoV-2 aggressiveness pattern. Further studies are needed to corroborate the time-related pathophysiology behind these findings.
Use of a systems engineering framework to assess perceptions and practices about antimicrobial resistance of workers on large dairy farms in Wisconsin
Authors: Kates Ashley E. , Knobloch Mary Jo , Konkel Ali , Young Amanda , Steinberger Andrew , Shutske John , Ruegg Pamela L. , Sethi Ajay K. , Goldberg Tony , de Campos Juliana Leite , Suen Garret , Safdar Nasia 
Published: November 2020

AbstractWe studied farmworker practices potentially contributing to transmission of bacteria and antimicrobial resistant genes (ARGs) among animals and farm workers to identify human behavioral interventions to reduce exposure risk. Ten focus groups were conducted on eight farms to explore potentially high-risk practices and farmworker knowledge and experiences with antimicrobial use and resistance using the Systems Engineering in Patient Safety (SEIPS) framework. Farmworkers were asked to describe common tasks and the policies guiding these practices. We found workers demonstrated knowledge of the role of antibiotic stewardship in preventing the spread of ARGs. Knowledge of various forms of personal protective equipment was higher for workers who commonly reported glove-use. Knowledge regarding the importance of reducing ARG transmission varied but was greater than previously reported. Programs to reduce ARG spread on dairy farms should focus on proper hand hygiene and personal protective equipment use but at the level of knowledge, beliefs, and practices.
The association between socioeconomic status and mobility reductions in the early stage of England’s COVID-19 epidemic
Authors: Lee Won Do , Qian Matthias , Schwanen Tim 
Published: November 2020

AbstractThis study uses mobile phone data to examine how socioeconomic status was associated with the extent of mobility reduction during the spring 2020 lockdown in England in a manner that considers both potentially confounding effects and spatial dependency and heterogeneity. It shows that socioeconomic status as approximated through income and occupation was strongly correlated with the extent of mobility reduction. It also demonstrates that the specific nature of the association of socioeconomic status with mobility reduction varied markedly across England. Finally, the analysis suggests that the ability to restrict everyday mobility in response to a national lockdown is distributed in a spatially uneven manner, and may need to be considered a luxury or, failing that, a tactic of survival for specific social groups.
Simulating Pandemic Disease Spread and the Impact of Interventions in Complex Societal Networks
Authors: Mytelka Daniel S. 
Published: November 2020

AbstractIntroductionProjecting disease spread is challenging because of the heterogeneous nature of human interactions, including both natural societal interactions and how they change in response to pandemics. Simulations can provide important guidance regarding the likely impact of interventions on an assumed base case.MethodsThis paper uses assumptions based on the COVID-19 pandemic to construct a Susceptible-Infectious-Recovered model representative of US society, focusing on the interrelationships of groups with differing contact networks (essential/non-essential workers and urban/non-urban populations). The model is used to explore the impact of interventions (reduced interactions, vaccinations and selective isolation) on overall and group-specific disease spread.ResultsIn the absence of herd immunity, temporary interventions will only reduce the overall number of disease cases moderately and spread them over a greater period of time unless they virtually eliminate disease and no new infections occur from exogenous sources. Vaccinations can provide stronger benefit, but can be limited by efficacy and utilization rates.ConclusionsWhile a highly effective and broadly utilized vaccine might halt disease spread, some combination of increased long-term surveillance and selective isolation of the most vulnerable populations might be necessary to minimize morbidity and mortality if only moderately effective vaccines are available.
The power and limitations of genomics to track COVID-19 outbreaks: a case study from New Zealand
Authors: Geoghegan Jemma L , Douglas Jordan , Ren Xiaoyun , Storey Matthew , Hadfield James , Silander Olin K , Freed Nikki E , Jelley Lauren , Jefferies Sarah , Sherwood Jillian , Paine Shevaun , Huang Sue , Sporle Andrew , Baker Michael G , Murdoch David R , Drummond Alexei J , Welch David , Simpson Colin R , French Nigel , Holmes Edward C , de Ligt Joep 
Published: November 2020

SummaryBackgroundReal-time genomic sequencing has played a major role in tracking the global spread and local transmission of SARS-CoV-2, contributing greatly to disease mitigation strategies. After effectively eliminating the virus, New Zealand experienced a second outbreak of SARS-CoV-2 in August 2020. During this August outbreak, New Zealand utilised genomic sequencing in a primary role to support its track and trace efforts for the first time, leading to a second successful elimination of the virus.MethodsWe generated the genomes of 80% of the laboratory-confirmed samples of SARS-CoV-2 from New Zealand’s August 2020 outbreak and compared these genomes to the available global genomic data.FindingsGenomic sequencing was able to rapidly identify that the new COVID-19 cases in New Zealand belonged to a single cluster and hence resulted from a single introduction. However, successful identification of the origin of this outbreak was impeded by substantial biases and gaps in global sequencing data.InterpretationAccess to a broader and more heterogenous sample of global genomic data would strengthen efforts to locate the source of any new outbreaks.FundingThis work was funded by the Ministry of Health of New Zealand, New Zealand Ministry of Business, Innovation and Employment COVID-19 Innovation Acceleration Fund (CIAF-0470), ESR Strategic Innovation Fund and the New Zealand Health Research Council (20/1018 and 20/1041).
Surveillance study of acute neurological manifestations among 439 Egyptian patients with COVID-19 in Assiut and Aswan university hospitals
Authors: Khedr Eman M , Abo-Elfetoh Noha , Daef Enas , Hassan Hebatallah M. , Amin Mariam T , Soliman Radwa K , Attia Alaa A , Zarzour Amro A , Zain Mohamed , Mohamed-Hussein Aliae , Hashem Maiada K , Hassany Sahar M , Aly Ahmed , Shoap Ahmed , Saber Mostafa 
Published: November 2020

AbstractBackgroundCOVID-19 can be accompanied by acute neurological complications of both central and peripheral nervous systems (CNS and PNS). In this study we estimate the frequency of such complications among hospital in-patients with COVID-19 in Assiut and Aswan University Hospitals.Material and MethodsWe screened all patients with suspected COVID-19 admitted from 1 June to 10 August 2020 to the university hospitals of Assiut and Aswan in Upper Egypt. Clinical and laboratory data, CT/MRI of chest and brain, and neurophysiology were performed for each patient if indicated.Results439 patients had confirmed/probable COVID-19; neurological manifestations occurred in 222. Of these 117 had acute neurological disease; the remainder had non-specific neuropsychiatric symptoms such as headache, vertigo, and depression. The CNS was affected in 75 patients: 55 had stroke; the others had convulsions (5), encephalitis (6), hypoxic encephalopathy (4), cord myelopathy (2), relapse of RR-MS (2), and meningoencephalitis (1). The PNS was affected in 42 patients: the majority had anosmia and ageusia (31); the others had GBS (4), peripheral neuropathy (3), myasthenia gravis (2), or myositis (2). Fever, respiratory symptoms and headache, were the most common general symptoms. Hypertensions, Diabetes Mellitus, ischemic heart disease were the most common comorbidities in patients with CNS affection.ConclusionIn COVID⍰19, both the CNS and PNS are affected. Stroke was the most common complication for CNS and anosmia and/or ageusia were common for PNS diseases. However there were 6 cases encephalitis, 2 cases of spinal cord myelopathy, 2 cases of MG and 2 cases of myositis.
Neurite orientation dispersion and density imaging in cocaine use disorder
Authors: Rasgado-Toledo Jalil , Shah Apurva , Ingalhalikar Madhura , Garza-Villarreal Eduardo A. 
Published: November 2020

AbstractCocaine use disorder (CUD) is characterized by compulsive searching for cocaine that produces cognitive deficits, including lack of inhibition and decision-making. Several studies have shown that cocaine users exhibit brain volume and diffusion-based white-matter alterations in a wide variety of brain regions. However, the non-specificity of standard volumetric and diffusion-tensor methods to detect structural micropathology may lead to wrong conclusions. To better understand microstructural pathology in CUD, we analyzed 60 CUD participants (3 female) and 43 non-CUD controls (HC; 2 female) retrospectively from our cross-sectional Mexican SUD neuroimaging dataset (SUDMEX-CONN), using multi-shell diffusion-weighted imaging and the neurite orientation dispersion and density imaging (NODDI) analysis whose aims to more accurately model micro-structural pathology. We used Viso values of NODDI that employ a three-compartment model in white (WM) and gray-matter (GM). These values were correlated with clinical measures, including psychiatric severity status, impulsive behavior and pattern of cocaine and tobacco use in the CUD group. As hypothesized, we found higher whole-brain microstructural pathology in WM and GM in CUD patients than controls. ROI analysis revealed higher Viso-NODDI values in superior longitudinal fasciculus, cingulum, hippocampus cingulum, forceps minor and Uncinate fasciculus, as well as in frontal and parieto-temporal GM structures. Correlations between significant ROIs showed a dependency of impulsivity and years of cocaine consumption over Viso-NODDI. However, we did not find correlations with psychopathology measures. Overall, microstructural pathology seems to be present in CUD both in gray and white-matter, however their clinical relevance remains questionable.
Cerebrospinal fluid total tau levels indicate aberrant neuronal plasticity in Alzheimer’s disease
Authors: Visser Pieter Jelle , Reus Lianne M. , Gobom Johan , Jansen Iris , Dicks Ellen , Tsolaki Magda , Verhey Frans R.J. , Popp Julius , Martinez-Lage Pablo , Vandenberghe Rik , Lleó Alberto , Molinuevo José Luís , Engelborghs Sebastiaan , Freund-Levi Yvonne , Froelich Lutz , Sleegers Kristel , Dobricic Valerija , Hong Shengjun , Lovestone Simon , Streffer Johannes , Vos Stephanie J.B. , Bos Isabelle ,   ADNI, Smit August B. , Blennow Kaj , Scheltens Philip , Teunissen Charlotte E. , Bertram Lars , Zetterberg Henrik , Tijms Betty M. 
Published: November 2020

AbstractAlzheimer’s disease (AD) is characterised by abnormal amyloid beta and tau processing. Previous studies reported that cerebrospinal fluid (CSF) total tau (t-tau) levels vary between patients. Here we show that CSF t-tau variability is associated with distinct impairments in neuronal plasticity mediated by gene repression factors SUZ12 and REST. AD individuals with abnormal t-tau levels have increased CSF concentrations of plasticity proteins regulated by SUZ12 and REST. AD individuals with normal t-tau, on the contrary, have decreased concentrations of these plasticity proteins and increased concentrations in proteins associated with blood-brain and blood CSF-barrier dysfunction. Genomic analyses suggested that t-tau levels in part depend on genes involved in gene expression. The distinct plasticity abnormalities in AD as signaled by t-tau urge the need for personalised treatment.
‘Necessity is the mother of invention’: Specialist palliative care service innovation and practice change in response to COVID-19. Results from a multi-national survey (CovPall)
Authors: Dunleavy Lesley , Preston Nancy , Bajwah Sabrina , Bradshaw Andy , Cripps Rachel , Fraser Lorna K , Maddocks Matthew , Hocaoglu Mevhibe , Murtagh Fliss EM , Oluyase Adejoke , Sleeman Katherine E , Higginson Irene , Walshe Catherine 
Published: November 2020

AbstractBackgroundSpecialist palliative care services have a key role in a whole system response to COVID-19. There is a need to understand service response to share good practice and prepare for future care.AimTo map and understand specialist palliative care services innovations and practice changes in response to COVID-19 (CovPall).DesignOnline survey of specialist palliative care providers, disseminated via key stakeholders. Data collected on service characteristics, innovations and changes in response to COVID-19. Statistical analysis included frequencies, proportions and means, and free-text comments were analysed using a qualitative framework approach.Setting/participantsInpatient palliative care units, home nursing services, hospital and home palliative care teams from any country.Results458 respondents: 277 UK, 85 Europe (except UK), 95 World (except UK and Europe), 1 missing country. 54.8% provided care across 2+ settings; 47.4% hospital palliative care teams, 57% in-patient palliative care units, and 57% home palliative care teams. The crisis context meant services implemented rapid changes. Changes involved streamlining, extending and increasing outreach of services, using technology to facilitate communication, and implementing staff wellbeing innovations. Barriers included; fear and anxiety, duplication of effort, information overload, funding, and IT infrastructure issues. Enablers included; collaborative teamwork, pooling of staffing resources, staff flexibility, a pre-existing IT infrastructure and strong leadership.ConclusionsSpecialist palliative care services have been flexible, highly adaptive and have adopted a ‘frugal innovation’ model in response to COVID-19. In addition to financial support, greater collaboration is essential to minimise duplication of effort and optimise resource use.ISRCTN16561225https://doi.org/10.1186/ISRCTN16561225Key StatementsWhat is already known about the topic?Specialist palliative care is part of a whole healthcare system response to COVID-19.Services need to make practice changes in response to the global pandemic.What this paper addsSpecialist palliative care services responded rapidly to COVID-19 in both planning for change and then adapting to needs and requirements.Services often relied on ‘improvisation’, ‘quick fixes’ and ‘making do’ when responding to the COVID-19 crisis.Implications for practice, theory or policyIn addition to financial support, greater collaboration is essential to build organisational resilience and drive forward innovation, by minimising duplication of effort and optimising resource use.The effectiveness and sustainability of any changes made during the crisis needs further evaluation.
Fine mapping of the HLA locus in Parkinson’s disease in Europeans
Authors: Yu Eric , Ambati Aditya , Andersen Maren Stolp , Krohn Lynne , Estiar Mehrdad A. , Saini Prabhjyot , Senkevich Konstantin , Sosero Yuri L. , Kumar Sreelatha Ashwin Ashok , Ruskey Jennifer A. , Asayesh Farnaz , Spiegelman Dan , Toft Mathias , Viken Marte K. , Sharma Manu , Blauwendraat Cornelis , Pihlstrøm Lasse , Mignot Emmanuel , Gan-Or Ziv 
Published: November 2020

AbstractObjectiveTo fine map the association between human leukocyte antigen (HLA) genes and Parkinson’s disease (PD) that was discovered using genome-wide association studies (GWASs).MethodsWe performed a thorough analysis of the HLA locus in 13,770 PD patients, 20,214 proxy-cases and 490,861 controls of European origin. We used GWAS data to impute HLA types and performed multiple regression models to examine the association of specific HLA types, different haplotypes and specific amino acid changes. We further performed conditional analyzes to identify specific alleles or genetic variants that drive the association with PD.ResultsFour HLA types were associated with PD after correction for multiple comparisons, HLA-DQA1*03:01, HLA-DQB1*03:02, HLA-DRB1*04:01 and HLA-DRB1*04:04. Haplotype analyzes followed by amino-acid analysis and conditional analyzes suggested that the association is protective and primarily driven by three specific amino acid polymorphisms present in most HLA-DRB1*04 subtypes - 11V, 13H and 33H (OR=0.87 95%CI=0.83-0.90, p<8.23×10−9 for all three variants). No other effects were present after adjustment for these amino acids.ConclusionsOur results suggest that specific variants in the HLA-DRB1 gene are associated with reduced risk of PD, providing additional evidence for the role of the immune system in PD. Although effect size is small and has no diagnostic significance, understanding the mechanism underlying this association may lead to identification of new targets for therapeutics development.
Effect of specific non-pharmaceutical intervention policies on SARS-CoV-2 transmission in the counties of the United States
Authors: Yang Bingyi , Huang Angkana T. , Garcia-Carreras Bernardo , Hart William E. , Staid Andrea , Hitchings Matt D.T. , Lee Elizabeth C. , Howe Chanelle J. , Grantz Kyra H. , Wesolowksi Amy , Lemaitre Joseph Chadi , Rattigan Susan , Moreno Carlos , Borgert Brooke , Dale Celeste , Quigley Nicole , Cummings Andrew , McLorg Alizée , LoMonaco Kaelene , Schlossberg Sarah , Barron-Kraus Drew , Shrock Harrison ,   UFCOVID Interventions Team, Lessler Justin , Laird Carl D. , Cummings Derek A.T. 
Published: November 2020

AbstractNon-pharmaceutical interventions (NPIs) remain the only widely available tool for controlling the ongoing SARS-CoV-2 pandemic. We estimated weekly values of the effective basic reproductive number (Reff) using a mechanistic metapopulation model and associated these with county-level characteristics and NPIs in the United States (US). Interventions that included school and leisure activities closure and nursing home visiting bans were all associated with an Reff below 1 when combined with either stay at home orders (median Reff 0.97, 95% confidence interval (CI) 0.58-1.39)* or face masks (median Reff 0.97, 95% CI 0.58-1.39)*. While direct causal effects of interventions remain unclear, our results suggest that relaxation of some NPIs will need to be counterbalanced by continuation and/or implementation of others.