cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.21430/m381lm05um
title: Roles of antiviral sensing and type I interferon signaling in the restriction of SARS-CoV-2 replication

description: Severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) is the causative agent of coronavirus disease 2019. Few studies have compared replication dynamics and host responses to SARS-CoV-2 in cell lines from different tissues and species. Therefore, we investigated the role of tissue type and antiviral genes during SARS-CoV-2 infection in nonhuman primate (kidney) and human (liver, respiratory epithelial, gastric) cell lines. We report different viral growth kinetics and release among the cell lines despite comparable ACE2 expression. Transcriptomics revealed that absence of STAT1 in nonhuman primate cells appeared to enhance inflammatory responses without effecting infectious viral titer. Deletion of RL-6 in respiratory epithelial cells increased viral replication. Impaired infectious virus release was detected in Huh7 but not Huh7.5 cells, suggesting a role for RIG1. Gastric cells MKN45 exhibited robust antiviral gene expression and supported viral replication. Data here provide insight into molecular pathogenesis of and alternative cell lines for studying SARS-CoV-2 infection.
DOI: 10.21430/m383dylcoe
title: Safety and immunogenicity in age de-escalation of PfSPZ Vaccine in Tanzania

description: The present trial will evaluate safety and tolerability as well as the vaccine-induced humoral and cellular immune responses in healthy Tanzanian adults, adolescents, children, and infants who receive doses of 1.8x10^6, 9.0x10^5, 4.5x10^5 or 2.7x10^5 PfSPZ of PfSPZ Vaccine by direct venous inoculation (DVI),compared with control groups receiving normal saline (NS) placebo by DVI. In addition, as an exploratory objective, controlled human malaria infection (CHMI) will be used to assess efficacy in adults three weeks following immunization.
DOI: 10.21430/m383vci57n
title: Impaired neutralizing antibody response to COVID-19 mRNA vaccines in cancer patients

description: In this study, we determined the neutralizing antibody response in 160 cancer patients diagnosed with chronic lymphocytic leukemia (CLL), lung cancer, breast cancer, and various non-Hodgkin's lymphomas (NHL), after they received two doses of mRNA vaccines. Serum from 46 mRNA vaccinated health care workers (HCWs) served as healthy controls. We discovered that (1) cancer patients exhibited reduced neutralizing antibody titer (NT50) compared to HCWs; (2) CLL and NHL patients exhibited the lowest NT50 levels, with 50-60% of them below the detection limit; (3) mean NT50 levels in patients with CLL and NHL was ~2.6 fold lower than those with solid tumors; and (4) cancer patients who received anti-B cell therapy exhibited significantly reduced NT50 levels. Our results demonstrate an urgent need for novel immunization strategies for cancer patients against SARS-CoV-2, particularly those with hematological cancers and those on anti-B cell therapies.
DOI: 10.21430/m385j155zw
title: Durable Humoral and Cellular Immune Responses 8 Months after Ad26.COV2.S Vaccination

description: To evaluate the 8-month durability of humoral and cellular immune responses after Ad26.COV2.S Vaccination
DOI: 10.21430/m38fw5zqhe
title: Inhibition of elastase enhances the adjuvanticity of alum and promotes anti-SARS-CoV-2 systemic and mucosal immunity

description: We investigated whether neutrophil elastase regulates the adjuvanticity of alum, and whether a strategy targeting neutrophil elastase could improve responses to injected vaccines. Mice coadministered a pharmacological inhibitor of elastase, or lacking elastase, developed high-affinity serum IgG and IgA antibodies after immunization with alum-adsorbed protein vaccines, including the spike protein of severe acute respiratory syndrome coronavirus 2 (SARS-Cov-2). These mice also developed broader antigen-specific CD4+ T cell responses, including high Th1 and T follicular helper (Tfh) responses. Interestingly, in the absence of elastase activity, mucosal SIgA responses were induced after systemic immunization with alum as adjuvant. Importantly, lack or suppression of elastase activity enhanced the magnitude of anti-SARS-CoV-2 spike subunit 1 (S1) antibodies, and these antibodies reacted with the same epitopes of spike 1 protein as sera from COVID-19 patients. Therefore, suppression of neutrophil elastase could represent an attractive strategy for improving the efficacy of alum-based injected vaccines for the induction of broad immunity, including mucosal immunity.
DOI: 10.21430/m38ootqncc
title: Early-pregnancy prediction of risk for pre-eclampsia using maternal blood leptin/ceramide ratio

description: To develop a blood test for the prediction of pre-eclampsia (PE) early in gestation, the study identified Leptin (Lep) and ceramide (Cer) as novel biomarkers through meta-analysis of 6 GEO placenta studies and pubmed literature mining on “Leptin;Lipid Metabolism”. The proposed biomarkers were further tested in 15 participants enrolled at ProMDxed, and validated in 40 sera from women who participated in a longitudinal study at Stanford University. The study demonstrated the longitudinal measurement of maternal Lep/Cer (d18:1/25:0) ratio allows the non-invasive assessment of PE to identify pregnancy at high risk in early gestation, outperforming the established sFlt-1/PlGF ratio test.
DOI: 10.21430/m392gkbpxd
title: Ethmoidal sinus scRNA from CRSwNP and CRSsNP

description: scRNA-Seq data from ethmoidal sinus samples from subjects with chronic rhinosinusitis with nasal polyposis and chronic rhinosinusitis without nasal polyposis
DOI: 10.21430/m39yvooysv
title: Efficacy of clinical evaluations for COVID-19 on the front line

description: We conducted a retrospective review of patients assessed for possible COVID-19 illness at our urban medical center in Los Angeles, California. We carefully reviewed all clinical records to ascertain the provider's level of clinical suspicion for COVID-19 illness and compared these assessments with available results of SARS-CoV-2 testing, in addition to longitudinal data on clinical outcomes.
DOI: 10.21430/m3a57h738q
title: Severely ill COVID-19 patients display impaired exhaustion features in SARS-CoV-2-reactive CD8+ T cells

description: Here, we report on the single-cell transcriptomes of >80,000 virus-reactive CD8+ T cells, obtained using a modified Antigen-Reactive T cell Enrichment (ARTE) assay, from 39 COVID-19 patients and 10 healthy subjects. COVID-19 patients segregated into two groups based on whether the dominant CD8+ T cell response to SARS-CoV-2 was 'exhausted' or not. CD8+ T cells reactive to influenza and respiratory syncytial virus from healthy subjects displayed polyfunctional features and enhanced glycolysis. Cells with such features were largely absent in SARS-CoV-2-reactive cells from both COVID-19 patients and healthy controls non-exposed to SARS-CoV-2. Overall, our single-cell analysis revealed substantial diversity in the nature of CD8+ T cells responding to SARS-CoV-2.
DOI: 10.21430/m3a944ebox
title: Reduced COVID-19 Vaccine Response in Patients Treated with Biologic Therapies for Asthma

description: Despite animal studies showing decreased vaccine-induced humoral immunity there is a paucity of literature available in asthma patient population following SARS-CoV-2 vaccination.
DOI: 10.21430/m3a9w2xky2
title: Nitrate in Drinking Water during Pregnancy and sPTM

description: To investigate the association between elevated nitrate in drinking water and spontaneous preterm birth, A within-mother retrospective cohort study of births in California ( screened 6 million birth certificate records from 2000-2011 and constructed an investigation set with ~ 1.4M consecutive sibling births ) was conducted. The public water system monitoring records to estimate nitrate concentrations in drinking water for each woman's residence during gestation were used for the association study. Two conditional logistic regression models were estimated for the odds of preterm birth at 20-31 and 32-36 wk, respectively.
DOI: 10.21430/m3abfz7ty8
title: Regimen verification phase: Sequential optimization of dose and schedule of PfSPZ Vaccine, verified by randomized, controlled, double-blind immunization and controlled human malaria infection in malaria-naive, healthy adult volunteers in Germany

description: The study is to take place at Institut fur Tropenmedizin, Eberhard Karls Universitat Tubingen, Tubingen Germany. The study has two phases: 1) dose optimization, and 2) regimen verification. In the first phase groups A, B1, B2, C1, C2 and C3 will be vaccinated sequentially in a pre-specified order, followed by homologous CHMI with 3,200 PfSPZ Challenge (NF54) three weeks after last vaccine injection. Dose optimization phase A: 9x10^5 PfSPZ on Days 0, 7 and 28 (n = 6) B1: 1.35x10^6 PfSPZ on Days 0 and 7 (n = 6) B2: 1.35x10^6 PfSPZ on Days 0, 7, and 28 (n = 6) C1: 2.7x10^6 PfSPZ on Day 0 (n = 6) C2: 2.7x10^6 PfSPZ on Day 0 and 7 (n = 6) C3: 2.7x10^6 PfSPZ on Days 0, 7 and 28 (n = 6) In parallel to CHMI with PfSPZ Challenge (NF54) during the optimization phase, a total of nine volunteers will receive either 800, 1,600 or 3,200 PfSPZ Challenge (7G8) (PfSPZ Challenge (7G8) dose finding) to assess safety, tolerability and infectivity of PfSPZ Challenge (7G8) in malaria-naive healthy adult volunteers. PfSPZ Challenge (7G8) dose finding/infection D1: 800 PfSPZ (n = 3) D2: 1,600 PfSPZ (n = 3) D3: 3,200 PfSPZ (n = 3) Subsequently, the shortest efficacious regimen (V1) and a three-dose regimen (Day 0, 7 and 28) of the highest safe dose (V2) will be selected and verified against placebo (normal saline (NS)). Groups V1 and V2 will be vaccinated at approximately the same time and undergo repeat CHMI three and eight weeks after the last immunization. Volunteers will either receive PfSPZ Vaccine or NS as placebo. Allocation will be random and double blind. Repeat CHMI will be done with PfSPZ Challenge (NF54) and PfSPZ Challenge (7G8), given in a randomized sequence. All immunizations are given by direct venous inoculation (DVI). Regimen verification phase V1: Shortest efficacious regimen (n = 12) against placebo (n = 6) V2: Maximum regimen (n = 12) against placebo (n = 6) P1: Placebo for V1 group (n=6) P2 Placebo for V2 group (n=6).
DOI: 10.21430/m3aji51ql1
title: SARS-CoV-2 antibodies protect against reinfection for at least 6 months in a multicentre seroepidemiological workplace cohort

description: To identify the potential for SARS-CoV-2 reinfection
DOI: 10.21430/m3b4ht6szu
title: Longitudinal COVID-19-vaccination-induced antibody responses and Omicron neutralization in patients with lung cancer

description: There are major knowledge gaps for managing patients with lung cancer in the COVID-19 era which need to be filled. To address these key issues, we prospectively studied the magnitude and kinetics of the humoral response to COVID-19 mRNA vaccination in a well annotated lung cancer population.
DOI: 10.21430/m3b6163wg1
title: Serological analysis reveals an imbalanced IgG subclass composition associated with COVID-19 disease severity

description: A serological analysis of 536 convalescent healthcare workers reveals that SARS-CoV-2-specific and virus-neutralizing antibody levels are elevated in individuals that experience severe disease. The severity-associated increase in SARS-CoV-2-specific antibody is dominated by immunoglobulin G (IgG), with an IgG subclass ratio skewed toward elevated receptor binding domain (RBD)- and S1-specific IgG3. In addition, individuals that experience severe disease show elevated SARS-CoV-2-specific antibody binding to the inflammatory receptor FcɣRIIIa. Based on these correlational studies, we propose that spike-specific IgG subclass utilization may contribute to COVID-19 disease severity through potent Fc-mediated effector functions. These results may have significant implications for SARS-CoV-2 vaccine design and convalescent plasma therapy.
DOI: 10.21430/m3b9czcvux
title: CMV Plasma Proteomics in Kidney Transplant

description: Background. Cytomegalovirus (CMV) infection, either de novo or a reactivation infection, is recognized to result in detrimental alloimmune effects, inclusive of higher susceptibility to graft rejection and opportunistic infections and a substantive impact on chronic graft injury and reduced transplant survival. We studied perturbations in the circulating host proteome serially, before and after transplantation, and during and after CMV DNA replication (DNAemia), as measured by quantitative polymerase chain reaction (QPCR), to obtain further insights into the evolution and pathogenesis of CMV infection in an immunocompromised host. Method. LC-MS-based proteomics was conducted on 168 serially banked plasma samples, at protocol times of 3- and 12-months post-transplant, before and 1 week and 1 month after detection of CMV DNAemia. Sixty-two propensity score-matched kidney transplant recipients were enrolled, stratified by CMV replication status into 31 with CMV DNAemia and 31 without CMV DNAemia. Plasma proteins were analyzed using an LCMS 8060 triple quadrupole mass spectrometer. Differential expression analysis was conducted using R and Limma. An integrative analysis with transcriptome data on matching PBMCs was also carried out. Result. Samples were segregated based on their proteomic profiles with respect to their CMV Dnaemia status. A subset of 17 plasma proteins was observed to predict the onset of CMV at 3 months post-transplant enriching platelet degranulation (FDR, 4.83E-06), acute inflammatory response (FDR, 0.0018), blood coagulation (FDR, 0.0018) pathways. Analysis of plasma proteome comparing patients with and without DNAemia revealed an increase in the immune complex proteins and immune-related protein as a response to CMV infection. Compared to pre-DNAemia plasma proteome, post-DNAemia timepoint plasma proteome revealed increased protein levels of proteins such as anti-inflammatory adipokine vaspin (SERPINA12), copper binding protein ceruloplasmin (CP), complement activating protein CFH enriching immune processes such as complement activation (FDR=0.03), Humoral immune response (FDR=0.01), innate immune response (FDR=0.01). Conclusion. High throughput plasma proteomics revealed proteomic perturbation impacting immune system-associated pathways during CMV infection and provided insights into biomarkers for CMV disease prediction and resolution. Further studies to understand the clinical impact of these pathways in formulating different types and duration of anti-viral therapies in the immunocompromised host.
DOI: 10.21430/m3bam4cn94
title: Neutralizing antibody against SARS-CoV-2 spike in COVID-19 patients, health care workers, and convalescent plasma donors

description: This study designs and describes usefulness of a SARS-CoV-2 S bearing lentivirus inGluc neutralization assay. The study highlights a wide phenotypic variation in human antibody responses against SARS-CoV-2 and demonstrates the efficacy of the newly designed lentivirus pseudotype assay for high-throughput serological surveys of neutralizing antibody titers in large cohorts.
DOI: 10.21430/m3bcc13tun
title: Association of maternal prenatal selenium concentration and PTB

description: To determine the association of maternal Selenium (Se) concentrations during pregnancy with PTB risk and gestational duration in a large number of samples (9946 singleton live births ) obtained from 17 geographically diverse study cohorts. Se concentrations were determined by (ICP-MS) measurements. The associations were analyzed using logistic and linear regressions. The results were then combined using fixed-effect and random-effect meta-analysis. The study observed statistically significant associations between maternal Se concentration and PTB at some sites, this did not generalize across the entire cohort. The largest effect sizes were observed in UK (Liverpool) cohort, and most significant associations were observed in samples from Malawi.
DOI: 10.21430/m3bg02p6re
title: Antibodies elicited by SARS-CoV-2 infection or mRNA vaccines have reduced neutralizing activity against Beta and Omicron pseudoviruses

description: To evaluate the magnitude and breadth of the neutralizing antibody response over time in individuals after infection and in mRNA-vaccinated individuals
DOI: 10.21430/m3bgvpr3cn
title: Longitudinal SARS-CoV-2 mRNA Vaccine-Induced Humoral Immune Responses in Patients with Cancer

description: Long-term studies of immunogenicity of SARS-CoV-2 vaccines in patients with cancer are needed to inform evidence-based guidelines for booster vaccinations and to tailor sequence and timing of vaccinations to elicit improved humoral responses.
DOI: 10.21430/m3c1cz1mf2
title: Functional characterization of CD4+ T cell receptors crossreactive for SARS-CoV-2 and endemic coronaviruses

description: We used the viral functional expansion of specific T cells (ViraFEST) platform to identify T cell responses crossreactive for the spike (S) glycoproteins of SARS-CoV-2 and common cold coronaviruses (CCCs) at the T cell receptor (TCR) clonotype level in convalescent COVID-19 patients (CCPs) and SARS-CoV-2–unexposed donors. Memory CD4+ T cell clonotypes that crossrecognized the S proteins of SARS-CoV-2 and at least one other CCC were detected in 65% of CCPs and unexposed donors. Several of these TCRs were shared among multiple donors. Crossreactive T cells demonstrated significantly impaired SARS-CoV-2–specific proliferation in vitro relative to monospecific CD4+ T cells, which was consistent with lower functional avidity of their TCRs for SARS-CoV-2 relative to CCC.
DOI: 10.21430/m3cjtcgudp
title: Immunosuppression Withdrawal for Stable Pediatric Liver Transplant Recipients (iWITH)

description: Anti-rejection medicines, also known as immunosuppressive drugs, are prescribed to organ transplant recipients to prevent rejection of the new organ. Long-term use of these medicines places transplant recipients at higher risk of serious infections and certain types of cancer. This study seeks to: 1) Find out if it is safe to slowly reduce and then completely stop the immunosuppression taken by children who have received liver transplants. This process is called 'immunosuppression withdrawal'or ISW. 2) Find blood or liver biopsy tests that can help transplant doctors in the future to predict if it is safe to decrease or stop immunosuppression drugs in children who have had a liver transplant.
DOI: 10.21430/m3ck1f3hpk
title: Durability of Anti-Spike Antibodies in Infants After Maternal COVID-19 Vaccination or Natural Infection

description: To evaluate the persistence of vaccine-induced maternal anti-S IgG in infant blood and compared persistence of infant anti-S IgG after maternal vaccination vs natural infection.
DOI: 10.21430/m3couzopk1
title: Targeted Microbiome Transplant in Atopic Dermatitis (ADRN-08)

description: The purpose of this study is to examine the safety and effectiveness of a new therapy, commensal lotion containing infection fighting bacteria, on decreasing or eliminating the infection causing bacteria found on the skin of Atopic Dermatitis (AD) patients.
DOI: 10.21430/m3d4fznyfr
title: Multiscale PHATE identifies multimodal signatures of COVID-19

description: Multiscale PHATE is a machine learning novel tool for dimensionality reduction and data exploration that can be applied to biological data sets to learn and visualize
DOI: 10.21430/m3dm6e1y0r
title: Comparison of Subgenomic and Total RNA in SARS-CoV-2 Challenged Rhesus Macaques

description: For SARS-CoV-2, specific monitoring of actively replicating virus is critical for investigating the protective and therapeutic efficacy of vaccines, monoclonal antibodies, and antiviral drugs. We adapted a SARS-CoV-2 subgenomic RNA (sgRNA) RT-PCR assay to differentiate productive infection from inactivated or neutralized virus. Subgenomic RNAs are generated after cell entry and are poorly incorporated into mature virions, and thus may provide a marker for actively replicating virus. We show envelope (E) sgRNA was degraded by RNase in infected cell lysates, while genomic RNA (gRNA) was protected, presumably due to packaging into virions. To investigate the capacity of the sgRNA assay to distinguish input challenge virus from actively replicating virus in vivo, we compared the E sgRNA assay to a standard nucleoprotein (N) or E total (both gRNA and sgRNA) RNA in convalescent rhesus macaques and in antibody-treated rhesus macaques after experimental SARS-CoV-2 challenge. In both studies, the E sgRNA assay was negative, suggesting protective efficacy, whereas the N and E total RNA assays remained positive. These data suggest the potential utility of sgRNA to monitor actively replicating virus in prophylactic and therapeutic SARS-CoV-2 studies.
DOI: 10.21430/m3dn79zrcp
title: Regimen Optimization Trial of PfSPZ Vaccine in Equatorial Guinea (EGSPZV3)

description: This is a phase 1, randomized regimen optimization study of PfSPZ Vaccine in healthy Equatoguinean volunteers to determine if a condensed, rapid immunization regimen is safe and efficacious. Four different regimens 4 weeks or less in duration will be evaluated for safety, tolerability, immunogenicity, and protective efficacy in comparison to a gold standard 16-week regimen.
DOI: 10.21430/m3emgzh7g6
title: Immunological imprinting of the antibody response in COVID-19 patients

description: Here we longitudinally profile the early humoral immune response against SARS-CoV-2 in hospitalized coronavirus disease 2019 (COVID-19) patients and quantify levels of pre-existing immunity to OC43, HKU1 and 229E seasonal coronaviruses, and find a strong back-boosting effect to conserved but not variable regions of OC43 and HKU1 betacoronaviruses spike protein. However, such antibody memory boost to human coronaviruses negatively correlates with the induction of IgG and IgM against SARS-CoV-2 spike and nucleocapsid protein. Our findings thus provide evidence of immunological imprinting by previous seasonal coronavirus infections that can potentially modulate the antibody profile to SARS-CoV-2 infection.
DOI: 10.21430/m3ewp60hpz
title: Population impact of SARS-CoV-2 variants with enhanced transmissibility and/or partial immune escape

description: Variants with enhanced transmissibility frequently increase epidemic severity, whereas those with partial immune escape either fail to spread widely or primarily cause reinfections and breakthrough infections
DOI: 10.21430/m3f1f8ojdn
title: Comprehensive analysis of T cell immunodominance and immunoprevalence of SARS-CoV-2 epitopes in COVID-19 cases

description: T cells are involved in control of SARS-CoV-2 infection. To establish the patterns of immunodominance of different SARS-CoV-2 antigens and precisely measure virus-specific CD4+ and CD8+ T cells, we study epitope-specific T cell responses of 99 convalescent coronavirus disease 2019 (COVID-19) cases. Distinct patterns of immunodominance are observed, which differ for CD4+ T cells, CD8+ T cells, and antibodies. The class I and class II epitopes are combined into epitope megapools to facilitate identification and quantification of SARS-CoV-2-specific CD4+ and CD8+ T cells.
DOI: 10.21430/m3fbsm5oea
title: Immunological memory to SARS-CoV-2 assessed for up to 8 months after infection

description: SARS-CoV-2-specific IgG to the Spike protein was relatively stable over 6+ months, Spike-specific memory B cells were more abundant at 6 months than at 1 month post symptom onset. SARS-CoV-2-specific CD4+ T cells and CD8+ T cells declined with a half-life of 3-5 months.
DOI: 10.21430/m3fcc2j1rf
title: Immunophenotyping Assessment in a COVID-19 Cohort (IMPACC) A Prospective Cohort Study to Assess Longitudinal Immune Responses in Hospitalized Patients with COVID-19

description: This is a prospective observational cohort of adult participants hospitalized with known or presumptive COVID-19.