bluuebunny/crossref_metadata_2025_split huggingface dataset:
Rare variants in IFFO1, DTNB and NLRC3 associate with Alzheimer’s disease CSF profile of neuronal injury and inflammation
Authors: Neumann Alexander , Küçükali Fahri , Bos Isabelle , Vos Stephanie J.B. , Engelborghs Sebastiaan , De Pooter Tim , Joris Geert , De Rijk Peter , De Roeck Ellen , Tsolaki Magda , Verhey Frans , Martinez-Lage Pablo , Tainta Mikel , Frisoni Giovanni , Blin Oliver , Richardson Jill , Bordet Régis , Scheltens Philip , Popp Julius , Peyratout Gwendoline , Johannsen Peter , Frölich Lutz , Vandenberghe Rik , Freund-Levi Yvonne , Streffer Johannes , Lovestone Simon , Legido-Quigley Cristina , Kate Mara ten , Barkhof Frederik , Strazisar Mojca , Zetterberg Henrik , Bertram Lars , Visser Pieter Jelle , van Broeckhoven Christine , Sleegers Kristel ,   EMIF-AD study group,   Alzheimer’s Disease Neuroimaging Initiative
Published: July 2021

AbstractAlzheimer’s disease (AD) biomarkers represent several neurodegenerative processes, such as synaptic dysfunction, neuronal inflammation and injury, as well as amyloid pathology. We performed an exome-wide rare variant analysis of six AD biomarkers (β-amyloid, total/phosphorylated tau, Nfl, YKL-40, and Neurogranin) to discover genes associated with these markers. Genetic and biomarker information was available for 480 participants from two studies: EMIF-AD and ADNI. We applied a principal component (PC) analysis to derive biomarkers combinations, which represent statistically independent biological processes. We then tested whether rare variants in 9,576 protein-coding genes associate with these PCs using a Meta-SKAT test. We also tested whether the PCs are intermediary to gene effects on AD symptoms with a SMUT test. One PC loaded on Nfl and YKL-40, indicators of neuronal injury and inflammation. Three genes were associated with this PC: IFFO1, DTNB and NLRC3. Mediation tests suggest, that these genes also affect dementia symptoms via inflammation/injury. We also observed an association between a PC loading on Neurogranin, a marker for synaptic functioning, with GABBR2 and CASZ1, but no mediation effects. The results suggest that rare variants in IFFO1, DTNB and NLRC3 heighten susceptibility to neuronal injury and inflammation, potentially by altering cytoskeleton structure and immune activity disinhibition, resulting in an elevated dementia risk. GABBR2 and CASZ1 were associated with synaptic functioning, but mediation analyses suggest that the effect of these two genes on synaptic functioning is not consequential for AD development.
Performance evaluation of a multinational data platform for critical care in Asia
Authors: Pisani Luigi , Rashan Thalha , Shamal Maryam , Ghose Aniruddha , Vijayaraghavan Bharath Kumar Tirupakuzhi , Tripathy Swagata , Aryal Diptesh , Hashmi Madiha , Nor Basri , Minh Yen Lam , Dondorp Arjen M. , Haniffa Rashan , Beane Abi 
Published: July 2021

ABSTRACTObjectiveWe aimed to evaluate the quality of a multinational intensive care unit (ICU) network of registries of critically ill patients established in seven Asian low and middle income countries (LMICs).MethodsThe Critical Care Asia federated registry platform enables ICUs to collect clinical, outcome and process data for aggregate and unit-level analysis. The evaluation used the standardised criteria of the Directory of Clinical Databases (DoCDat) and a framework for data quality assurance in medical registries. Six reviewers assessed structure, coverage, reliability and validity of the ICU registry data. Case mix and process measures on patient episodes from June to December 2020 were analysed.ResultsData on 20,507 consecutive patient episodes from 97 ICUs in Afghanistan, Bangladesh, India, Malaysia, Nepal, Pakistan and Vietnam were included. The quality level achieved according to the ten prespecified DoCDat criteria was high (average score 3.4 out of 4) as was the structural and organizational performance -- comparable to ICU registries in high-income countries. Identified strengths were types of variables included, reliability of coding, data completeness and validation. Potential improvements include extension of national coverage.ConclusionThe Critical Care Asia platform evaluates well using standardised frameworks for data quality and equally to registries in resource-rich settings.FundingThis work was undertaken as part of the existing Wellcome Innovations Flagship award, Collaboration for Research, Improvement and Training in Critical CARE in ASIA (ref. 215522/Z/19/Z). The funder had no role in the decision to publish or in the preparation of this manuscript.
Investigation research on the demand of pre-job training for nursing students in higher vocational colleges
Authors: Liu Li , Qiu Xiaojing , Li Yahui , Yang Junzheng 
Published: July 2021

AbstractObjectivesTo investigate the pre-job training demand of nursing students in higher vocational colleges, lay a foundation for the development of scientific and standardized pre-job training program and help nursing students smoothly transition to clinical practice state from student status.MethodsA self-designed questionnaire was used to investigate 822 nursing students of grade 2018 in our school from four aspects: the necessity of pre-job training, the demand content of pre-job training, the demand of skill enhancement program, and the stress source of pre-internship.ResultsDemand rate of the pre-job training of nursing students in the college was 99.5%, and main demand of the training content were nursing skill training (96.8%), nursing safety and occupational protection (95.1%), nursing theory training (92.9%); the main demand of nursing skills enhancement program were closed intravenous infusion (90.3%), (intradermal, subcutaneous, intramuscular) injection (87.8%), cardiopulmonary resuscitation (81.8%), and indwelling catheterization (77.5%); the main stress sources of pre-internship was lack of confidence in theory and skills, accounts for 61.1% in total 760 students.ConclusionThe pre-job training courses in higher vocational colleges should be close to the clinical needs of students, it is necessary to carry out pre-job training courses according to main demand of the training content, the main demand of nursing skills enhancement program and the main stress sources of pre-internship in the college; this article may provide reference for our school and other vocational colleges to develop pre-job training program.
Does trust in government improve Covid-19’s crisis management?
Authors: Apeti Ablam Estel 
Published: July 2021

AbstractCountries have adopted several measures to control the spread of Covid-19. However, substantial differences remain in terms of performance in controlling the virus, potentially due to heterogeneity in citizen engagement with government measures. Drawing on this observation, this paper seeks to analyze the effect of pre-crisis ties, particularly trust in government, on crisis management, proxied by the number of Covid-19 cases and deaths per million population. We examine this question based on a sample of 41 countries for which data are available. Results reveal that a high level of trust in government predicts better crisis management in terms of relatively low levels of cases and deaths. These results, which successfully pass a series of robustness tests, may vary according to level of contamination and increase with time.JEL ClassificationE71, H12, I12, I18, I38, Z18
A systematic review and meta-analysis of inpatient mortality associated with nosocomial and community COVID-19 exposes the vulnerability of immunosuppressed adults
Authors: Ponsford Mark J. , Ward Tom JC , Stoneham Simon , Dallimore Clare M. , Sham Davina , Osman Khalid , Barry Simon , Jolles Stephen , Humphreys Ian R. , Farewell Daniel 
Published: July 2021

AbstractBackgroundLittle is known about the mortality of hospital-acquired (nosocomial) COVID-19 infection globally. We investigated the risk of mortality and critical care admission in hospitalised adults with nosocomial COVID-19, relative to adults requiring hospitalisation due to community-acquired infection.MethodsWe systematically reviewed the peer-reviewed and pre-print literature from 1/1/2020 to 9/2/2021 without language restriction for studies reporting outcomes of nosocomial and community-acquired COVID-19. We performed a random effects meta-analysis (MA) to estimate the 1) relative risk of death and 2) critical care admission, stratifying studies by patient cohort characteristics and nosocomial case definition.Results21 studies were included in the primary MA, describing 8,246 admissions across 8 countries during the first wave, comprising 1517 probable or definite nosocomial COVID-19, and 6729 community-acquired cases. Across all studies, the risk of mortality was 1.31 times greater in patients with nosocomial infection, compared to community-acquired (95% CI: 1.01 to 1.70). Rates of critical care admission were similar between groups (Relative Risk, RR=0.74, 95% CI: 0.50 to 1.08). Immunosuppressed patients diagnosed with nosocomial COVID-19 were twice as likely to die in hospital as those admitted with community-acquired infection (RR=2.14, 95% CI: 1.76 to 2.61).ConclusionsAdults who acquire SARS-CoV-2 whilst already hospitalised are at greater risk of mortality compared to patients admitted following community-acquired infection; this finding is largely driven by a substantially increased risk of death in individuals with malignancy or who had undergone transplantation. These findings inform public health and infection control policy, and argue for individualised clinical interventions to combat the threat of nosocomial COVID-19, particularly for immunosuppressed groups.Systematic review registration: PROSPERO CRD42021249023
SARS-CoV-2 seroprevalence in asymptomatic or mild symptomatic people and symptomatic patients with negative PCR results: The hidden perspective in epidemiological reports
Authors: Hajiahmadi Nazila , Mojtahedzadeh Faezeh , Yari Atefeh , Tat Mahdi , Soleimanjahi Hoorieh , Jamehdar Saeid Amel , Jafari Mitra , Asli Samira , Dorostkar Rohollah , Nazemipour Maryam , Mansournia Mohammad Ali , Bamdad Taravat 
Published: July 2021

AbstractBackgroundSARS-CoV-2 has led to the current pandemic of respiratory disease. The reports of confirmed COVID-19 cases based on molecular tests do not completely cover the total number of infected people. These reports do not include the asymptomatic or mildly symptomatic patients and also the patients with false-negative RT-PCR results, while the infection is contagious in all of these conditions.ObjectiveIn this study, we tried to improve our conception of the hidden perspective of SARS-CoV-2 in epidemiological reports.MethodsFrom May 30 to June 17, 2020, blood samples were collected from two groups of people: asymptomatic or mild symptomatic volunteer participants and severe symptomatic hospitalized patients with negative PCR results. Detection of SARS-CoV-2 antibody was done with ELISA kit targeting N or S proteins.ResultsTotally 716 samples from volunteer participants and 81 samples from symptomatic hospitalized patients with negative PCR were evaluated. The test performance-adjusted seroprevalence (95% CI) of SARS-CoV-2 anti-N IgG was 17.3% (8.8%, 25.8%) for volunteers and 25.5% (12.8%, 39.7%) for anti-N and S IgM in hospitalized group. There was an association between high-risk occupations, high-risk behaviors, or symptomatic diseases with positive SARA-Cov-2 N antibody results. Among anti-N positive infected individuals, 49.2% (21.4%, 78.8%) were anti-S positive.ConclusionThe results showed that SARS-COV-2 infection occurs in asymptomatic or mildly symptomatic individuals, but in more than half of them, the produced antibody is not protective. Findings of hospitalized patients also showed that the combination of IgM assay with real-time PCR improves the detection of the disease by more than 25% in negative molecular cases.
Vaccine serologic responses among transplant patients associate with COVID-19 infection and T peripheral helper cells
Authors: Lemieux Jacob E. , Li Amy , Gentili Matteo , Perugino Cory A. , Weiss Zoe F. , Bowman Kathryn , Ankomah Pierre , Liu Hang , Lewis Gregory D. , Bitar Natasha , Lipiner Taryn , Hacohen Nir , Pillai Shiv S. , Goldberg Marcia B. 
Published: July 2021

AbstractBackgroundTherapeutically immunosuppressed transplant recipients exhibit attenuated responses to COVID-19 vaccines. To better understand the immune alterations that determined poor vaccine response, we correlated quantities of circulating T and B cell subsets at baseline with longitudinal serologic responses to SARS-CoV-2 mRNA vaccination in heart and lung transplant recipients.MethodsSamples at baseline and at approximately 8 and 30 days after each vaccine dose for 22 heart and lung transplant recipients with no history of COVID-19, four heart and lung transplant recipients with prior COVID-19 infection, and 12 healthy controls undergoing vaccination were analyzed. Anti-spike protein receptor binding domain (RBD) IgG and pseudovirus neutralization activity were measured. Proportions of B and T cell subsets at baseline were comprehensively quantitated.ResultsAt 8-30 days post vaccination, healthy controls displayed robust anti-RBD IgG responses, whereas heart and lung transplant recipients showed minimally increased responses. A parallel absence of activity was observed in pseudovirus neutralization. In contrast, three of four (75%) transplant recipients with prior COVID-19 infection displayed robust responses at levels comparable to controls. Baseline levels of activated PD-1+ HLA-DR+ CXCR5- CD4+ T cells (also known as T peripheral helper [TPH] cells) and CD4+ T cells strongly predicted the ability to mount a response.ConclusionsImmunosuppressed patients have defective vaccine responses but can be induced to generate neutralizing antibodies after SARS-CoV-2 infection. Strong correlations of vaccine responsiveness with baseline TPH and CD4+ T cell numbers highlights a role for T helper activity in B cell differentiation into antibody secreting cells during vaccine response.
The QuantuMDx Q-POC™ SARS-CoV-2 RT-PCR assay for rapid detection of COVID-19 at point-of-care: preliminary evaluation of a novel technology
Authors: Caffry Jessica , Selby Matthew , Barr Katie , Morgan George , McGurk David , Scully Philip , Park Catherine , Caridis Anna-Maria , Southworth Emily , Morrison Jack , Clark David J , Eckersely Nickolas , Groppelli Elisabetta , Kirwan Daniela E. , Monahan Irene , Augustin Yolanda , Toombs Colin , Planche Tim , Staines Henry M , Krishna Sanjeev 
Published: July 2021

AbstractBackgroundAccurate, affordable, and rapid point-of-care (PoC) diagnostics are critical to the global control and management of the COVID-19 pandemic. The current standard for accurate diagnosis of SARS-CoV-2 is laboratory-based reverse transcription polymerase chain reaction (RT-PCR). Here, we report a preliminary prospective performance evaluation of the QuantuMDx Q-POC™ SARS CoV-2 RT-PCR assay.MethodsBetween November 2020 and March 2021, we obtained 49 longitudinal nose and throat swabs from 29 individuals hospitalised with RT-PCR confirmed COVID-19 at St George’s NHS Foundation Trust, London (UK). In addition, we obtained 101 mid nasal swabs from healthy volunteers in June 2021. We then used these samples to evaluate the Q-POC™ SARS-CoV-2 RT-PCR assay. The primary analysis was to compare the sensitivity and specificity of the Q-POC™ test against a reference laboratory-based RT-PCR assay.ResultsThe overall sensitivity of the Q-POC™ test compared with the reference test was 96.88% (83.78%-99.92% CI) for a cycle threshold (Ct) cut-off value for the reference test of 35 and 80.00% (64.35% to 90.95% CI) without altering the reference test’s Ct cut-off value of 40.ConclusionsThe Q-POC™ test is a sensitive, specific and rapid point-of-care test for SARS-CoV-2 at a reference Ct cut-off value of 35. The Q-POC™ test provides an accurate and affordable option for RT-PCR at point-of-care without the need for sample pre-processing and laboratory handling. The Q-POC™ test would enable rapid diagnosis and clinical triage in acute care and other settings.
Machine Learning Model for Predicting Number of COVID19 Cases in Countries with Low Number of Tests
Authors: Hashim Samy , Farooq Sally , Syriopoulos Eleni , Cremer Kai de la Lande , Vogt Alexander , de Jong Nol , Aguado Victor L. , Popescu Mihai , Mohamed Ashraf K. , Amin Muhamed 
Published: July 2021

AbstractThe COVID-19 pandemic has presented a series of new challenges to governments and health care systems. Testing is one important method for monitoring and therefore controlling the spread of COVID-19. Yet with a serious discrepancy in the resources available between rich and poor countries not every country is able to employ widespread testing. Here we developed machine learning models for predicting the number of COVID-19 cases in a country based on multilinear regression and neural networks models. The models are trained on data from US states and tested against the reported infections in the European countries. The model is based on four features: Number of tests Population Percentage Urban Population and Gini index. The population and number of tests have the strongest correlation with the number of infections. The model was then tested on data from European countries for which the correlation coefficient between the actual and predicted cases R2 was found to be 0.88 in the multi linear regression and 0.91 for the neural network model. The model predicts that the actual number of infections in countries where the number of tests is less than 10% of their populations is at least 26 times greater than the reported numbers.
A global dataset of seaweed net primary productivity
Authors: Pessarrodona Albert , Filbee-Dexter Karen , Krumhansl Kira A. , Moore Pippa J. , Wernberg Thomas 
Published: July 2021

AbstractNet primary productivity (NPP) plays a pivotal role in the global carbon balance, but estimating the NPP of underwater habitats remains a challenging task. Seaweeds (marine macroalgae) form the largest and most productive underwater vegetated habitat on Earth. Yet, little is known about the distribution of their NPP at large spatial scales, despite more than 70 years of local-scale studies being scattered throughout the literature. We present a global dataset containing NPP records for 242 seaweed species at 419 individual sites distributed on all continents from the intertidal to 55 m depth. All records are standardized to annual aerial carbon production (g C m-2yr-1) and are accompanied by detailed taxonomical and methodological information. The dataset presented here provides a basis for local, regional and global comparative studies of the NPP of underwater vegetation, and is pivotal for achieving a better understanding of the role seaweeds play in the global coastal carbon cycle.
Single-cell multi-omic analysis of thymocyte development reveals drivers of CD4/CD8 lineage commitment
Authors: Steier Zoë , Aylard Dominik A. , McIntyre Laura L. , Baldwin Isabel , Yoon Kim Esther Jeong , Lutes Lydia K. , Ergen Can , Huang Tse-Shun , Robey Ellen A. , Yosef Nir , Streets Aaron 
Published: July 2021

AbstractThe development of CD4 and CD8 T cells in the thymus is critical to adaptive immunity and is widely studied as a model of lineage commitment. Recognition of self-MHCI/II by the T cell antigen receptor (TCR) determines the lineage choice, but how distinct TCR signals drive transcriptional programs of lineage commitment remains largely unknown. We applied CITE-seq to measure RNA and surface proteins in thymocytes from wild-type and lineage-restricted mice to generate a comprehensive timeline of cell state for each lineage. These analyses revealed a sequential process whereby all thymocytes initiate CD4 lineage differentiation during an initial wave of TCR signaling, followed by a second TCR signaling wave that coincides with CD8 lineage specification. CITE-seq and pharmaceutical inhibition experiments implicate a TCR/calcineurin/NFAT/GATA3 axis in driving the CD4 fate. Overall, our data suggest that multiple redundant mechanisms contribute to the accuracy and efficiency of the lineage choice.
A phage parasite deploys a nicking nuclease effector to inhibit replication of its viral host
Authors: LeGault Kristen N. , Barth Zachary K. , DePaola Peter , Seed Kimberley D. 
Published: July 2021

ABSTRACTPLEs are phage parasites integrated into the chromosome of epidemicVibrio cholerae. In response to infection by its viral host ICP1, PLE excises, replicates and hijacks ICP1 structural components for transduction. Through an unknown mechanism PLE prevents ICP1 from transitioning to rolling circle replication (RCR), a prerequisite for efficient packaging of the viral genome. Here, we characterize a PLE-encoded nuclease, NixI, that blocks phage development likely by nicking ICP1’s genome as it transitions to RCR. NixI-dependent cleavage sites appear in ICP1’s genome during infection of PLE(+)V. cholerae. Purified NixI demonstratesin vitrospecificity for sites in ICP1’s genome and NixI activity is enhanced by a putative specificity determinant co-expressed with NixI during phage infection. Importantly, NixI is sufficient to limit ICP1 genome replication and eliminate progeny production. We identify distant NixI homologs in an expanded family of putative phage satellites in Vibrios that lack nucleotide homology to PLEs but nonetheless share genomic synteny with PLEs. More generally, our results reveal a previously unknown mechanism deployed by phage parasites to limit packaging of their viral hosts’ genome and highlight the prominent role of nuclease effectors as weapons in the arms race between antagonizing genomes.
2’,3’-cAMP treatment mimics stress molecular response inArabidopsis thaliana
Authors: Chodasiewicz Monika , Kerber Olga , Gorka Michal , Moreno Juan C. , Maruri-Lopez Israel , Minen Romina I. , Sampathkumar Arun , Nelson Andrew D. L. , Skirycz Aleksandra 
Published: July 2021

AbstractThe role of the RNA degradation product 2’,3’-cyclic adenosine monophosphate (2’,3’-cAMP) is poorly understood. Recent studies have identified 2’,3’-cAMP in plant material and determined its role in stress signaling. The level of 2’,3’-cAMP increases upon wounding, dark, and heat, and 2’,3’-cAMP by binding to an RNA-binding protein, Rbp47b, promotes stress granule (SG) assembly. To gain further mechanistic insight into 2’,3’-cAMP function, we used a multi-omics approach combining transcriptomics, metabolomics, and proteomics to dissectArabidopsisresponse to 2’,3’-cAMP treatment. We demonstrated that 2’,3’-cAMP is metabolized into adenosine, suggesting that the well-known cyclic nucleotide–adenosine pathway from human cells might also exist in plants. Transcriptomic analysis revealed only minor overlap between 2’,3’-cAMP-and adenosine-treated plants, suggesting that these molecules act through independent mechanisms. Treatment with 2’,3’-cAMP changed the levels of hundreds of transcripts, proteins, and metabolites, many previously associated with plant stress responses including protein and RNA degradation products, glucosinolates, chaperones and SG components. Finally, we demonstrated that 2’,3’-cAMP treatment influences the movement of processing bodies, supporting the role of 2’,3’-cAMP in the formation and motility of membraneless organelles.