bluuebunny/crossref_metadata_2025_split huggingface dataset:
Aetiology of Lobar Pneumonia Determined by Multiplex Molecular Analyses of Lung and Pleural Aspirate Specimens in The Gambia
Authors: Mackenzie Grant A , McLellan Jessica , Machuka Eunice , Ndiaye Malick , Pathirana Jayani , Fombah Augustin , Abatan Baderinwa , Hossain Ilias , Manjang Ahmed , Greenwood Brian , Hill Philip C 
Published: July 2021

AbstractBackgroundPneumonia aetiology generally relies on insensitive blood cultures or an assumption that organisms in the pharynx are causal. We determined the causes of lobar pneumonia in rural Gambia using lung aspiration.MethodsPneumonia surveillance was undertaken among all ages. Blood culture and chest radiographs were performed routinely while lung or pleural aspirates were collected from selected patients. 7-valent pneumococcal conjugate vaccine (PCV7) was introduced in August 2009 and replaced by PCV13 from May 2011. We used conventional microbiology, and from April 8, 2011 to July 17, 2012, utilized a multiplex PCR assay on lung aspirates. We calculated proportions with pathogens, associations between co-infecting pathogens, and PCV effectiveness.Results2,550 patients were admitted with clinical pneumonia; 741 with lobar pneumonia or pleural effusion. We performed multiplex PCR on 156 lung and 4 pleural aspirates. Pathogens were detected in 116 specimens, Streptococcus pneumoniae (n=68), Staphylococcus aureus (n=26), and Haemophilus influenzae type b (n=11). Bacteria (n=97) were more common than viruses (n=49). Common viruses were bocavirus (n=11) and influenza (n=11). Co-infections were frequent (n=55). M. catarrhalis was detected in eight patients and in every case there was co-infection with S. pneumoniae. The odds ratio of vaccine-type pneumococcal pneumonia in patients with two or three compared to zero doses of PCV was 0.17 (95% CI 0.06, 0.51).ConclusionsLobar pneumonia in rural Gambia was caused primarily by bacteria, particularly S. pneumoniae and S. aureus. Co-infection was common and M. catarrhalis always co-infected with S. pneumoniae. PCV was highly efficacious against vaccine-type pneumococcal pneumonia.Key MessagesWhat is the key question?Using specimens directly from the infected lung, what is the aetiology of lobar pneumonia in rural West Africa?What is the bottom line?Using specimens directly from the infected lung, Streptococcus pneumoniae and Staphylococcus aureus were the predominant causes of lobar pneumonia in rural West Africa and pneumococcal conjugate vaccine effectively prevented pneumococcal pneumonia.Why read on?Learn about the certain aetiology of lobar pneumonia in 160 Gambian patients with specimens directly from the lung.
Neurological, neuropsychiatric and psychiatric symptoms during COVID-19 infection and after recovery: a systematic review of observational studies
Authors: Stavrou Maria , Solomou Solomis , Kythreotou Anthousa , Ioannou Antreas , Lioutas Eva , Lioutas Joanna , Karayiannis Peter 
Published: July 2021

ABSTRACTBackgroundThe SARS-CoV-2 virus causes a wide spectrum of disease severity. Initial manifestations include fever, dry cough, and constitutional symptoms, which may progress to respiratory disease. There may also be neurological and psychiatric manifestations, involving both the central and peripheral nervous system.MethodsWe performed a literature search of the databases PubMed, EMBASE, The Cochrane Library and Web of Science for observational studies reporting neurological, psychiatric, and neuropsychiatric effects of COVID-19. This was followed by a narrative synthesis to summarise the data and discuss neuropsychiatric associations, symptom severity, management, and recovery.FindingsThe most frequently reported neurological symptoms were ageusia, hyposmia/anosmia, dizziness, headache, and loss of consciousness. Statistically significant relationships were noted between Asian ethnicity and peripheral neuropathy (p=0.0001) and neuro-syndromic symptoms (p=0.001). ITU admission was found to have a statistically significant relationship with male sex (p=0.024). Depression and anxiety were also identified both during and after infection. The most frequent treatments used were intravenous immunoglobulins, followed by antibiotics, antivirals, and hydroxychloroquine; with mean treatment duration of 6 days.InterpretationVarious neuropsychiatric symptoms have been associated with COVID-19 infection. More studies are required to further our knowledge in the management of neurological and psychiatric symptoms during and after COVID-19 infection
Genetic variants in the SHISA6 gene are associated with delayed cognitive impairment in two family datasets
Authors: Ramos Jairo , Caywood Laura J. , Prough Michael B. , Clouse Jason E. , Herington Sharlene D. , Slifer Susan H. , Fuzzell M. Denise , Fuzzell Sarada L. , Hochstetler Sherri D. , Miskimen Kristy L. , Main Leighanne R. , Osterman Michael D. , Laframboise Owen , Zaman Andrew F. , Whitehead Patrice L. , Adams Larry D. , Laux Renee A. , Song Yeunjoo E. , Foroud Tatiana M. , Mayeux Richard P. , George-Hyslop Peter St. , Ogrocki Paula K. , Lerner Alan J. , Vance Jeffery M. , Cuccaro Michael L. , Haines Jonathan L. , Pericak-Vance Margaret A. , Scott William K. 
Published: July 2021

ABSTRACTBackgroundStudies of cognitive impairment (CI) in Amish communities have identified sibships containing multiple CI and cognitively unimpaired (CU; unaffected after age 75) individuals. We hypothesize that these CU individuals may carry protective alleles delaying age at onset (AAO) of CI, preserving cognition in older age despite increased genetic risk. As well, the genetic and cultural isolation in the Amish since the early 1800s may have reduced the complexity of the genetic architecture of CI, increasing the power to detect protective alleles in this population. With this in mind we conducted a genome-wide study (GWAS) to identify loci associated with AAO of CI in a sample of Amish adults over age 75.Methods1,522 individuals aged 43-99 (mean age 73.1, 42% men) screened at least once for CI using the Modified Mini-Mental State exam (3MS) were genotyped using Illumina chipsets. Genotypes were imputed for 7,815,951 single nucleotide variants (SNV) with minor allele frequency (MAF) > 1%. The outcome studied was age, defined as 1) age at the first 3MS result indicating impairment (AAO; 3MS <87; 362 CI individuals) or 2) age at last normal exam (3MS >=87, 1,160 CU individuals). Cox mixed-effects models examined association between age and each SNV, adjusting for sex and familial relationships. To replicate genome-wide significant findings, SNVs in a 1 Megabase region centered on the peak SNV were examined for association with age using these same methods in the NIA-LOAD family study dataset (1,785 AD cases, 1,565 unaffected controls, mean age 73.5.ResultsThree SNV were significantly associated (p<5 x 10-8) with AAO in the Amish, on chromosomes 6 (rs14538074; HR=3.35), 9 (rs534551495; HR=2.82), and 17 (rs146729640; Hazard Ratio (HR)=6.38). Each region found the common allele associated with later AAO. Replication analysis detected association at rs146729640, with nominal statistical significance (HR=1.49, p=0.02).ConclusionsThe replicated genome-wide significant association with AAO on chromosome 17 suggest this may be novel locus associated with delayed onset of AD. The associated SNP is located in the SHISA6 gene, which is involved in post-synaptic transmission in the hippocampus and is a biologically plausible candidate gene for AD.
The protocol for a scoping review analyzing the association between physical activity interventions after a genitourinary cancer diagnosis and incidences of depression and anxiety
Authors: Grob Sydney , Mucci Lorelei , McGrath Colleen 
Published: July 2021

AbstractThe following is a protocol for a planned scoping review of the effect of physical activity interventions on incidences of depression and anxiety incidences in men diagnosed with a genitourinary cancer. If exercise interventions are found to correlate with lower incidences of depression and anxiety, physical activity interventions offer a potentially modifiable, low-cost, accessible, and natural intervention to improve quality of life outcomes in men with genitourinary cancers. We plan to screen literature from publicly available databases, PubMed and Embase, for intervention studies in this area by implementing abstract/title and full-text screening by two independent reviewers followed by data extraction performed by two independent reviewers. Results will be synthesized in narrative format accompanied by relevant tabulated findings. We anticipate no ethical risks while completing this scoping review. Upon completion of this scoping review, results will be disseminated via publication.Article Summary (Strengths and Limitations)This scoping review will address a critical area of potentially-modifiable interventions to improve quality-of-life indicators in genitourinary cancer survivorship research.This scoping review could inform the use of readily available, low-cost, and low-barrier, treatment options to men suffering from depression and anxiety.This review is limited to information from interventional studies only as a preliminary review of available research.This review is limited to interventional studies in male cancer patients of specific genitourinary cancers (prostate, bladder, kidney, testicular).
High resolution linear epitope mapping of the receptor binding domain of SARS-CoV-2 spike protein in COVID-19 mRNA vaccine recipients
Authors: Nitahara Yuko , Nakagama Yu , Kaku Natsuko , Candray Katherine , Michimuko Yu , Tshibangu-Kabamba Evariste , Kaneko Akira , Yamamoto Hiromasa , Mizobata Yasumitsu , Kakeya Hiroshi , Yasugi Mayo , Kido Yasutoshi 
Published: July 2021

AbstractThe prompt rollout of the coronavirus disease (COVID-19) messenger RNA (mRNA) vaccine is facilitating population immunity, which shall become more dominant than natural infection-induced immunity. At the beginning of the vaccine era, understanding the epitope profiles of vaccine-elicited antibodies will be the first step in assessing functionality of vaccine-induced immunity. In this study, the high-resolution linear epitope profiles of Pfizer-BioNTech COVID-19 mRNA vaccine recipients and COVID-19 patients were delineated by using microarrays mapped with overlapping peptides of the receptor binding domain (RBD) of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) spike protein. The vaccine-induced antibodies targeting RBD had broader distribution across the RBD than that induced by the natural infection. Thus, relatively lower neutralizability was observed when a half-maximal neutralization titer measured in vitro by live virus neutralization assays was normalized to a total anti-RBD IgG titer. However, mutation panel assays targeting the SARS-CoV-2 variants of concern have shown that the vaccine-induced epitope variety, rich in breadth, may grant resistance against future viral evolutionary escapes, serving as an advantage of vaccine-induced immunity.ImportanceEstablishing vaccine-based population immunity has been the key factor in attaining herd protection. Thanks to expedited worldwide research efforts, the potency of messenger RNA vaccines against the coronavirus disease 2019 (COVID-19) is now incontestable. The next debate is regarding the coverage of SARS-CoV-2 variants. At the beginning of this vaccine era, it is of importance to describe the similarities and differences between the immune responses of COVID-19 vaccine recipients and naturally infected individuals. In this study, we demonstrated that the antibody profiles of vaccine recipients are richer in variety, targeting a key protein of the invading virus, than those of naturally infected individuals. Yet vaccine-elicited antibodies included more non-neutralizing antibodies than infection-elicited, their breadth in antibody variations suggested possible resilience against future SARS-CoV-2 variants. The antibody profile achieved by vaccinations in naive individuals pose important insight into the first step towards vaccine-based population immunity.
Modelling, Simulations and Analysis of the First and Second COVID-19 Epidemics in Beijing
Authors: Min Lequan 
Published: July 2021

AbstractBackgroundIn December 2019, a novel coronavirus-induced pneumonia (COVID-19) broke out in Wuhan, China. On 19 January and on 8 June 2020, there were two wave COVID-19 epidemics happened in Beijing. Modelling, simulations and analysis for the two wave epidemics are important issues.MethodsThis study introduces a symptomatic-asymptomatic-recoverer-death differential equation model (SARDDE). It presents the conditions of the asymptotical stability on the disease-free equilibrium of the SARDDE. It proposes the necessary conditions of disease spreading for the SARDDE. Based on the reported data of the first and the second COVID-19 epidemics in Beijing and numerical simulations, it determines the parameters of the SARDDE, respectively.ResultsNumerical simulations of the SARDDE describe well the outcomes of the current symptomatic and asymptomatic individuals, the recovered symptomatic and asymptomatic individuals, and the died infected individuals, respectively. The numerical simulations obtain the following results.The transmission rate of the symptomatic infections caused by the symptomatic individuals in the second Beijing epidemic is about two times higher than the one in the first Beijing epidemic.Both the symptomatic and the asymptomatic individuals cause lesser asymptomatic spread than symptomatic spread.The blocking rates of 89.32% and 97.48% (reaching the infection turning points) to the symptomatic infections cannot prevent the spreads of the first and the second COVID-19 epidemics in Beijing, respectively.That on the day 28, the symptomatic infection blocking rates reached to 100% has made the second Beijing epidemics epidemic end on day 56.That on the day 98, the symptomatic infection blocking rates reached to 100% has made the the first Beijing epidemics epidemic end on day 140.Keeping the blocking rates, the recovery rates and the death rates reaching the infection turning points would make the numbers of current hospitalized infected individuals reach, on day 140, 208958 individuals and 25017 individuals for the two Beijing epidemics, respectively.ConclusionsVirtual simulations suggest that the strict prevention and control strategies implemented by Beijing government are effective and necessary; using the data from the beginning to the days after about two weeks after the turning points can estimate well and approximately the following outcomes of the two COVID-19 epidemics, respectively. To avoid multiple epidemic outbreaks, a recommendation is that the authorities need to have maintained the prevention and control measures implemented, at least, 7 days after reaching the turning point until new current infection cases disappear. It is expected that the research can provide better understanding, explaining, and dominating for epidemic spreads, prevention and control measures.
Durable Humoral and Cellular Immune Responses Following Ad26.COV2.S Vaccination for COVID-19
Authors: Barouch Dan H. , Stephenson Kathryn E. , Sadoff Jerald , Yu Jingyou , Chang Aiquan , Gebre Makda , McMahan Katherine , Liu Jinyan , Chandrashekar Abishek , Patel Shivani , Gars Mathieu Le , de Groot Anne Marit , Heerwegh Dirk , Struyf Frank , Douoguih Macaya , van Hoof Johan , Schuitemaker Hanneke 
Published: July 2021

ABSTRACTInterim immunogenicity and efficacy data for the Ad26.COV2.S vaccine for COVID-19 have recently been reported1-3. We describe here the 8-month durability of humoral and cellular immune responses in 20 individuals who received one or two doses of 5×1010 vp or 1011 vp Ad26.COV2.S and in 5 participants who received placebo2. We evaluated antibody and T cell responses on day 239, which was 8 months after the single-shot vaccine regimen (N=10) or 6 months after the two-shot vaccine regimen (N=10), although the present study was not powered to compare these regimens3. We also report neutralizing antibody responses against the parental SARS-CoV-2 WA1/2020 strain as well as against the SARS-CoV-2 variants D614G, B.1.1.7 (alpha), B.1.617.1 (kappa), B.1.617.2 (delta), P.1 (gamma), B.1.429 (epsilon), and B.1.351 (beta).
An Autoantigen Profile from Jurkat T-Lymphoblasts Provides a Molecular Guide for Investigating Autoimmune Sequelae of COVID-19
Authors: Wang Julia Y. , Zhang Wei , Roehrl Michael W. , Roehrl Victor B. , Roehrl Michael H. 
Published: July 2021

AbstractIn order to understand autoimmune phenomena contributing to the pathophysiology of COVID-19 and post-COVID syndrome, we have been profiling autoantigens (autoAgs) from various cell types. Although cells share numerous autoAgs, each cell type gives rise to unique COVID-altered autoAg candidates, which may explain the wide range of symptoms experienced by patients with autoimmune sequelae of SARS-CoV-2 infection. Based on the unifying property of affinity between autoantigens (autoAgs) and the glycosaminoglycan dermatan sulfate (DS), this paper reports 140 candidate autoAgs identified from proteome extracts of human Jurkat T-cells, of which at least 105 (75%) are known targets of autoantibodies. Comparison with currently available multi-omic COVID-19 data shows that 125 (89%) of DS-affinity proteins are altered at protein and/or RNA levels in SARS-CoV-2-infected cells or patients, with at least 94 being known autoAgs in a wide spectrum of autoimmune diseases and cancer. Protein alterations by ubiquitination and phosphorylation in the viral infection are major contributors of autoAgs. The autoAg protein network is significantly associated with cellular response to stress, apoptosis, RNA metabolism, mRNA processing and translation, protein folding and processing, chromosome organization, cell cycle, and muscle contraction. The autoAgs include clusters of histones, CCT/TriC chaperonin, DNA replication licensing factors, proteasome and ribosome proteins, heat shock proteins, serine/arginine-rich splicing factors, 14-3-3 proteins, and cytoskeletal proteins. AutoAgs such as LCP1 and NACA that are altered in the T cells of COVID patients may provide insight into T-cell responses in the viral infection and merit further study. The autoantigen-ome from this study contributes to a comprehensive molecular map for investigating acute, subacute, and chronic autoimmune disorders caused by SARS-CoV-2.
Does prior healthcare experience predict success on clinical courses and add value to admissions processes?
Authors: Darling-Pomranz Claire , Gray James , Spencer David 
Published: July 2021

AbstractObjectivesThis work sought to assess whether prior clinical experience provided any guide to likely course achievement from three completed cohorts of Physician Associates at the University of Sheffield.MethodsSixty students who entered the PA course at TUoS since it began in 2016 were included in the study. Each students’ original course application was reviewed for healthcare experience and mapped against first sit examination scores. Statistical analysis was undertaken with a two-tailed t-test.ResultsNo correlation was found between previous healthcare experience and performance in examinations. Students with previous healthcare experience performed slightly worse than those without in the OSCE examination but not at a level of statistical significance.ConclusionsThe use of clinical experience as part of the criteria of entry does not predict success on a Physician Associate course. We support the position of the 2010 Ottawa conference that quality assured methodologies along with objective cut offs for previous academic attainment are the most appropriate way to select students for clinical courses.
Navigating uncertain illness trajectories for young children with serious infectious illness: a mixed-methods modified grounded theory study
Authors: Neill Sarah , Bray Lucy , Carter Bernie , Roland Damian , Carrol Enitan D , Bayes Natasha , Riches Lucie , Hughes Joanne , Pandey Poornima , O’Donnell Jennifer , Palmer-Hill Sue 
Published: July 2021

AbstractInfectious illness is the biggest cause of death in children due to a physical illness, particularly in children under five years. If mortality is to be reduced for this group of children, it is important to understand factors affecting their pathways to hospital.The aim of this study was to retrospectively identify organisational and environmental factors, and individual child, family, and professional factors affecting timing of admission to hospital for children under five years of age with a serious infectious illness (SII).MethodsAn explanatory modified grounded theory mixed methods design was used in collaboration with parents. Two stages of data collection were conducted: Stage 1, interviews with 22 parents whose child had recently been hospitalised with a SII and 14 health professionals (HPs) involved in their pre-admission trajectories; Stage 2, focus groups with 18 parents and 16 HPs with past experience of SII in young children. Constant comparative analysis generated the explanatory theory.FindingsThe core category was ‘navigating uncertain illness trajectories for young children with serious infectious illness’. Uncertainty was prevalent throughout the parents’ and HPs’ stories about their experiences of navigating social rules and overburdened health services for these children. The complexity of and lack of continuity within services, family lives, social expectations and hierarchies provided the context and conditions for children’s, often complex, illness trajectories. Parents reported powerlessness and perceived criticism leading to delayed help-seeking. Importantly, parents and professionals missed symptoms of serious illness. Risk averse services were found to refer more children to emergency departments.ConclusionsParents and professionals have difficulties recognising signs of SII in young children and can feel socially constrained from seeking help. The increased burden on services has made it more difficult for professionals to spot the seriously ill child.
Model-based Evaluation of Continued COVID-19 Risk at Long Term Care Facilities
Authors: Fosdick Bailey K. , Bayham Jude , Dilliott Jake , Ebel Gregory D. , Ehrhart Nicole 
Published: July 2021

AbstractThe COVID-19 pandemic severely impacted long-term care facilities resulting in the death of approximately 8% of residents nationwide. As COVID-19 case rates decline and state and county restrictions are lifted, facility managers, local and state health agencies are challenged with defining their own policies moving forward to appropriately mitigate disease transmission. The continued emergence of variants of concern has highlighted the need for a readily available tool that can be employed at the facility-level to determine best practices for mitigation and ensure resident and staff safety. To assist leadership in determining the impact of various infection surveillance and response strategies, we developed an agent-based model and an online dashboard interface that simulates COVID-19 infection within congregate care settings under various mitigation measures. In this paper, we demonstrate how this dashboard can be used to quantify the continued risk for COVID-19 infections within a facility given a designated testing schedule and vaccine requirements. Our results highlight the critical nature of testing cadence, test sensitivity and specificity, and the impact of removing asymptomatic infected individuals from the workplace. We also show that monthly surveillance testing at long-term care facilities is unlikely to successfully mitigate SARS-CoV-2 outbreaks in congregate care settings.DisclosuresThis work was supported by Colorado State University’s Center for Healthy Aging, the Center for Vector-Bourne Infectious Disease, the Office of the Vice President for Research, the College of Health and Human Sciences, the Collage of Natural Sciences, the College of Veterinary Medicine and Biomedical Sciences, and the Walter Scott Jr College of Engineering.