cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.21430/m3sm4yltlh
title: Scleroderma: Cyclophosphamide or Transplantation (SCOT)

description: This prospective, randomized, open-label, multi-center, 2-arm, Phase II clinical trial will randomize approximately 114 subjects with severe SSc in the United States and Canada. Subjects will be randomly assigned in a 1:1 ratio to a treatment of high-dose immunosuppressive therapy with autologous stem cell rescue (HDIT transplantation) or to treatment of monthly pulse IV cyclophosphamide. Subjects will be stratified by treatment center. The initial treatment period will be approximately 3 months for the HDIT transplantation arm (from the time of initiation of mobilization until the day of transplant) and 12 months for the cyclophosphamide arm. Subjects will be followed for up to 72 months after randomization. The study will continue for 54 months after the last subject is randomized.
DOI: 10.21430/m3t5g6gg5x
title: Immune Profiling Assay Development for Pertussis vaccines

description: The specific aims of this study are to develop cell-mediated and serological assays for the evaluation of the type and quality of immune cell and antibody responses to Pertussis vaccination.
DOI: 10.21430/m3t9r8js6g
title: Dendritic Cell Maturation Dynamics

description: This study characterizes and maps human dendritic cell subset distribution, migration and function across multiple lymphoid and mucosal tissues from individual organ donors aged &lt;1-93 years of age. .
DOI: 10.21430/m3tejv0f4i
title: Small Sample- Big Data- Papua New Guinea Newborn Pilot Study

description: Systems Biology Characterization in Early Life
DOI: 10.21430/m3testtest
title: Expanded PD-1hi CXCR5- T peripheral helper cells promote B cells responses in lupus via IL-21

description: Evaluate the T cell populations altered in the circulation of patients with SLE by highdimensionalmass cytometry. We identify a highly expanded population of PD-1hi CXCR5- Tcells in SLE patients, including in early SLE patients studied prior to initiation of strongimmunosuppressive therapies. By phenotype, transcriptome, and function, these cells are Tphcells, a peripherally homing B cell helper population
DOI: 10.21430/m3thzoc0fs
title: Development of a Comprehensive Antibody Staining Database using a Standardized Analytics Pipeline

description: This project aims to establish a comprehensive reference database of protein expression patterns across peripheral blood immune cell subsets
DOI: 10.21430/m3tryb4whx
title: Meta-Analysis of Vaginal Microbiome Data Provides New Insights On Preterm Birth

description: The study aims to identify differences in vaginal microbiota of pre-term and term deliveries and also non-pregnant women.
DOI: 10.21430/m3tsyo4t3l
title: MaHPIC: Host M. mulatta infected with homologous and heterologous strains of P. cynomolgi

description: MaHPIC Experiments E23, E24, E25: M. mulatta infected with P. cynomolgi B strain and P. cynomolgi strain ceylonensis in homologous and heterologous challenges to produce and integrate clinical, hematological, parasitological, and omics measures of acute primary malaria infection and relapses in non-human primates
DOI: 10.21430/m3ufzvm91i
title: Baked Egg or Egg Oral Immunotherapy for Children With Egg Allergy (CoFAR7)

description: The purpose of this study is to compare Baked Egg vs. Egg Oral Immunotherapy for inducing sustained unresponsiveness to egg exposure in children.
DOI: 10.21430/m3uh9qgiy2
title: Peanut Sublingual Immunotherapy (CoFAR4)

description: This is a multi-center, 1:1 randomized, double-blind, placebo-controlled, through the 5 gm Oral Food Challenge (OFC) at week 44, trial to investigate the safety and immunologic effects of daily peanut SLIT immunotherapy for peanut allergy. Following the blinded phase, subjects who are using the active peanut SLIT treatment will receive 120 weeks of open label peanut SLIT doses. After completing the blinded segment, subjects receiving placebo will be offered desensitization with a buildup and a maintenance period of 44 weeks at which time a 5 gm OFC will be performed. The target maintenance dose will be higher in this cohort than the initial cohort. This is followed by 120 weeks of continued maintenance peanut SLIT therapy at the higher dose.
DOI: 10.21430/m3v2g6pbys
title: Identification of Three Rheumatoid Arthritis Disease Subtypes By Machine Learning Integration of Synovial Histologic Features and RNA Sequencing Data

description: Gene expression analysis of RA and OA synovial tissue revealed 3 distinct synovial subtypes. These labels were used to generate a histologic scoring algorithm in which the histologic scores were found to be associated with parameters of systemic inflammation, including the erythrocyte sedimentation rate, CRP levels, and autoantibody levels. Comparison of gene expression patterns to clinical features revealed a potentially clinically important distinction: mechanisms of pain may differ in patients with different synovial subtypes.
DOI: 10.21430/m3vcnpmd4b
title: Mitochondrial and Nuclear Ancestry Association to PTB

description: Genome-wide genotyping studies of cohorts of preterm and term individuals were evaluated. Mitochondrial haplogroup and nuclear ancestry for individuals were determined and used to develop a scoring for the degree to which mitochondrial ancestry is divergent from nuclear ancestry. Infants with higher degrees of divergent mitochondrial ancestry were at increased risk for preterm birth (0.124 for preterm vs 0.105 for term infants; P &lt; .05). This finding was validated in 1 of 2 replication cohorts. Greater degrees of divergent ancestry correlating with earlier delivery within the primary study population was observed, but this finding was not replicated in secondary cohorts born preterm. Individuals with divergent patterns of mitochondrial and nuclear ancestry are at increased risk for preterm birth. These findings may in part explain the higher rates of preterm birth in African Americans and in individuals with a matrilineal family history of preterm birth.
DOI: 10.21430/m3vf5f8ane
title: CD4 Nicaragua Epitope ID

description: We performed DENV-specific epitope screening studies in the general population of Managua. Peptides with the capacity to bind HLA DR molecules most common in the Nicaraguan population have been predicted and screened in an HLA matched fashion in blood donors from the Nicaraguan Red Cross previously exposed to dengue virus.
DOI: 10.21430/m3vra7inn8
title: Activation of the PD-1 Pathway Contributes to Immune Escape in EGFR-Driven Lung Tumors

description: We show that autochthonous EGFR-driven lung tumors inhibit anti-tumor immunity by activating the PD-1/PD-L1 pathway to suppress T cell function and increase levels of pro-inflammatory cytokines. These findings indicate that EGFR functions as an oncogene through non-cell autonomous mechanisms and raise the possibility that other oncogenes may drive immune escape.
DOI: 10.21430/m3vrz0zs5p
title: Perceived Barriers to Patient Adherence after Pediatric Solid Organ Transplantation (CTOTC-05)

description: This is a two part prospective, observational, multi-center cohort study of SOT recipients. The first part is a cross sectional comparison of perceived barriers to adherence to post-transplant immunosuppressant regimens in parents of children (0-11 years) versus adolescents (12-21 years). The second is a longitudinal study to evaluate whether perceived barriers to adherence increase with time during the first year following transplantation.
DOI: 10.21430/m3vtdibf4t
title: Memory B Cells with cross-reactive Abs to fluA(H1-H3)

description: To understand how the humoral immune system generates and matures protective responses to influenza virus infections and vaccinations. The group isolated B membory single cell clones from three unrelated, adult donors post TIV-vaccination, characterized the cross-reacting Abs to fluA (H1-H3) antigens, and generated the VDJ lineage tree of Bmem clones from one donor. The lineage and crystal structure analysis showed that members of a lineage had a BCR structure similar to that of a previously described Ab, encoded by different gene segments. Comparison showed that both Abs contacted the HA receptor-binding site through long heavy-chain third complementarity determining regions (HCDR3). Affinities of the clonal-lineage BCRs for historical influenza-virus HAs from both group 1 (H1) and group 2 (H3) viruses suggested that serial responses to seasonal influenza exposures had elicited the lineage and driven affinity maturation.
DOI: 10.21430/m3vydm1mim
title: Transcriptomic Analysis of CD4+ T Cells Reveals Novel Immune Signatures of Latent Tuberculosis. (See SDY820 for corresponding PBMC results.)

description: T cell immune signature associated with latent TB infection as well as BCG vaccination was studied
DOI: 10.21430/m3w0nbncxa
title: Optimization of Belatacept Usage As A Means of Avoiding CNI and steroids in Renal Transplantation (CTOT-10)

description: The purpose of this study was to assess whether a new drug, Nulojix (belatacept), would minimize serious long term side effects associated with anti-rejection medications while still protecting the new kidney from damage. The researchers also wanted to learn more about the safety of this treatment and long term health of the transplanted kidney.
DOI: 10.21430/m3xnru4k3v
title: Subcutaneous Immunotherapy for Mouse in Adults (SCITMO/ICAC-26)

description: The primary objective of the study is to assess if treatment with mouse subcutaneous immunotherapy (SCIT), using the per protocol allergenic extract doses, is safe. This will be done by determining the rate of related adverse events and serious adverse events in the course of treatment.
DOI: 10.21430/m3xnt9fcyt
title: Transcriptomes From Human Tissue Biopsies During Pregnancy

description: The aim of this study was to understand changes that take place in the uterine myometrium and cervix during preterm birth at a cellular level. This study presents the workflow for generating single cell transcriptomes derived from primary human uterine and cervical tissue obtained during planned cesarean hysterectomies. Using a catalogue of 310 single cell transcriptomes from cervical and uterine biopsies, cell types present in these biopsies were inferred and specific genes defining each of the cellular types present in the tissue were identified.
DOI: 10.21430/m3xrjhrpbc
title: AMP Rheumatoid Arthritis Synovial Phase 1

description: The primary goal for RA synovial P1 studies are: To establish feasibility of obtaining ultrasound-guided synovial biopsies in the United States (U.S.) by comparing to frozen synovial biopsies obtained in the United Kingdom (U.K.)
DOI: 10.21430/m3xtbr8f18
title: Systems biology approach predicts immunogenicity of the yellow fever vaccine in humans

description: A major challenge in vaccinology is to prospectively determine vaccine efficacy. Here we have used a systems biology approach to identify early gene signatures that predicted immune responses in humans vaccinated with yellow fever vaccine YF-17D. Vaccination induced genes that regulate virus innate sensing and type I interferon production. Computational analyses identified a gene signature, including complement protein C1qB and eukaryotic translation initiation factor 2 alpha kinase 4, an orchestrator of the integrated stress response that correlated with and predicted YF-17D CD8+ T cell responses with up to 90% accuracy in an independent, blinded trial. A distinct signature, including B cell growth factor TNFRS17, predicted the neutralizing antibody response with up to 100% accuracy. These data highlight the utility of systems biology approaches in predicting vaccine efficacy.
DOI: 10.21430/m3yzy4pxcs
title: Safety and Effectiveness of Low Molecular Weight Sulfated Dextran in Islet Transplantation (CIT-01)

description: The purpose of this study is to assess the safety and effectiveness of low molecular weight sulfated dextran (LMW-SD) on post-transplant islet function in people with type 1 diabetes who have responded to intensive insulin therapy.
DOI: 10.21430/m3z0lcnugg
title: Viral Triggers in Pediatric Lung Transplantation (CTOTC-03)

description: This is a non-randomized observational study to determine whether respiratory viral infections increase the risk of bronchiolitis obliterans syndrome, obliterative bronchiolitis, death or retransplantation in pediatric lung transplant recipients.
DOI: 10.21430/m3z4slis4q
title: PROGENI-KI (CTOT-08)

description: To validate specific proteogenomic biomarker panels for AR and CAN/IFTA in a prospective, serial blood and urine monitoring study of kidney transplant recipients with protocol biopsies.
DOI: 10.21430/m3z6i3umvl
title: Peritransplant Deoxyspergualin in Islet Transplantation in Type 1 Diabetes (CIT-03) and Extended Follow Up after Islet Transplantation in Type 1 Diabetes (CIT-08)

description: CIT-03: Type 1 diabetes is an autoimmune disease in which the insulin-producing pancreatic beta cells are destroyed, resulting in poor blood sugar control. The purpose of this study is to assess the safety and efficacy of deoxyspergualin (DSG), an immunosuppressant drug, on post-transplant islet function in people with type 1 diabetes who have not responded to intensive insulin therapy. CIT-08: The purpose of this protocol is to collect long-term follow-up information on the safety and efficacy of islet transplantation in CIT subjects after their completion in their CIT parent study.
DOI: 10.21430/m3zu72to6v
title: Systems Biology of 2011 trivalent Influenza vaccine (TIV) in young and elderly individuals, healthy or with T2D (see companion study SDY61 2007, SDY270 2009, SDY56 2010)

description: Blood samples will be collected at days 0 (pre-vaccination) and 3,7,30,180 after vaccination, and used to Identify signatures of innate immunity, plasmablasts, lymphocytes and monocytes which correlate with antibody responses to the vaccine.
DOI: 10.21430/m3zwnrqpcg
title: Suspect screening for chemicals in pregnant women

description: In utero exposure to environmental chemicals can adversely impact pregnancy outcomes and childhood health but minimal biomonitoring data exist on the majority of chemicals used in commerce.
DOI: 10.21430/m304zdgvq2
title: PROGENI-LI (CTOT-14)

description: Prospective, non-randomized, observational study of LT recipients investigating proteogenomic signatures of AR, HCV-R and CKD.
DOI: 10.21430/m3060tkh6f
title: Distinct antibody responses to SARS-CoV-2 in children and adults

description: Clinical manifestations of COVID-19 caused by the new coronavirus SARS-CoV-2 are associated with age. Here, we show distinct antibody responses in children and adults after SARS-CoV-2 infection.
DOI: 10.21430/m30j52enn6
title: Treated HIV infection induces alterations in phenotype but not HIV-specific function of peripheral blood natural killer cells

description: Natural killer (NK) cells are the predominant antiviral cells of the innate immune system, and may play an important role in acquisition and disease progression of HIV. While untreated HIV infection is associated with distinct alterations in the peripheral blood NK cell repertoire, less is known about how NK phenotype is altered in the setting of long-term viral suppression with antiretroviral therapy (ART), as well as how NK memory can impact functional responses. As such, we sought to identify changes in NK cell phenotype and function using high-dimensional mass cytometry to simultaneously analyze both surface and functional marker expression of peripheral blood NK cells in a cohort of ART-suppressed, HIV+ patients and HIV- healthy controls.
DOI: 10.21430/m3129qbms5
title: Th17 reprograming of T cells in systemic juvenile idiopathic arthritis

description: Systemic juvenile idiopathic arthritis (sJIA) begins with fever, rash, and high-grade systemic inflammation but commonly progresses to a persistent afebrile arthritis. The basis for this transition is unknown. To evaluate a role for lymphocyte polarization, we characterized T cells from patients with acute and chronic sJIA.
DOI: 10.21430/m31t6shtyd
title: Crowdsourcing Assessment of Maternal Blood Multi-omics for Predicting Gestational Age and Preterm Birth

description: This study utilized longitudinal whole blood transcriptomic and plasma proteomic data, and leveraged the Dialogue for Reverse Engineering Assessments and Methods (DREAM) crowdsourcing framework to develop predictive models for gestational age and preterm birth.
DOI: 10.21430/m31zxg1mzw
title: Vaginal dysbiosis increases risk of PPROM, neonatal sepsis and is exacerbated by erythromycin

description: To understand the dynamics of vaginal microbiota compositions associated with PPROM and the impact by antibiotics, the study prospectively assessed vaginal microbiota prior to and following PPROM using MiSeq-based sequencing of 16S rRNA gene amplicons and examined the impact of erythromycin prophylaxis on bacterial load and community structures. RESULTS: vaginal dysbiosis characterised by Lactobacillus spp. depletion was present prior to the rupture of fetal membranes in approximately a third of cases and persisted following membrane rupture. Vaginal dysbiosis was exacerbated by erythromycin treatment particularly in women initially colonised by Lactobacillus spp. Lactobacillus depletion and increased relative abundance of Sneathia spp. were associated with subsequent funisitis and early onset neonatal sepsis. This highlights vaginal microbiota as a potentially modifiable antenatal risk factor for PPROM and suggests that routine use of erythromycin for PPROM be re-examined.
DOI: 10.21430/m324y3362v
title: Proteomic Signatures Predict Preeclampsia in Individual Cohorts but not Across Cohorts

description: The study aim was to discover bio-signatures predicting the risk of preeclampsia in two independent cohorts (Stanford and Detroit) of pregnant women using a highly-multiplexed and aptamer-based proteomic array (SomaLogic).
DOI: 10.21430/m32wawrye2
title: Multiomics Characterization of PTB in Low- and Middle-Income Countries

description: This study analyzed multiomics data of plasma and urine samples collected from May 2014 to June 2017 from pregnant women in 5 biorepository cohorts in low- and middle-income countries. The comparative analysis of Cell-free transcriptomics, urine metabolomics, and plasma proteomics between term and preterm birth concluded that major biological adaptations during term pregnancy follow a generalizable model and the predictive accuracy for PTB was augmented by combining various omics data sets
DOI: 10.21430/m33iiy5ard
title: Immune Response to IAV

description: Using the Collaborative Cross, a population of recombinant inbred mouse strains with high levels of genetic variation, we measured antibody response and weight change after infection with influenza-A virus.
DOI: 10.21430/m348t28t35
title: Superior mouse eosinophil depletion in vivo targeting transgenic Siglec-8 instead of endogenous Siglec-F: mechanisms and pitfalls

description: We uncovered shortcomings when using certain antibodies that target Siglec-F to deplete mouse eosinophils, while administration of anti-Siglec-8 antibody to Siglec-8 transgenic mice works well.
DOI: 10.21430/m351zmqt4j
title: Paired Heavy and Light Chain Immunoglobulin Reconstruction in Single-Cell RNA-Seq Data

description: We generated scRNA-Seq data for 20 human plasmablasts induced by seasonal flu vaccination.To reconstruct the paired heavy and light chain antibody genes, we developed several different in silico filtering strategies to enrich immunoglobulin transcripts, and then applied de novo assembly. This method successfully reconstructed productive IgH and IgL chains in 100% of cells analyzed. The accuracy of clonotype-assignment of individual cells was 94.5-98%, as validated by comparing BCR sequences reconstructed from NGS to those obtained by conventional single-B cell cloning methodology. This makes it possible to link the transcriptional programming of individual B cell clones at critical developmental stages with the eventual fate of the clonal lineage in vivo.
DOI: 10.21430/m35eomb2wh
title: Single-site, five-year experience with human eosinophil isolation by density gradient centrifugation and CD16 immunomagnetic negative separation

description: Little has been reported regarding the reliability of methods for the purification of human blood eosinophils. We retrospectively reviewed our experience with 350 consecutive eosinophil isolations.
DOI: 10.21430/m35h10g9td
title: The Underlying Mechanisms For S. Aureus Infection And Colonization Of Skin in People With Atopic Dermatitis With And Without Eczema Herpeticum (MRSA) (ADVN-10)

description: Staphylococcus aureus (S.aureus) is a bacterium that causes many painful skin and soft tissue conditions, such as scalded-skin syndrome, boils, or impetigo. Serious cases may result in deadly complications but S.aureus can usually be treated successfully with antibiotics. There are, however, certain strains which cannot be treated with standard antibiotics. Methicillin-resistant staphylococcus aureus (MRSA) is one such strain. MRSA is increasingly being seen in both hospital and community settings, making it a serious public health issue. People with Atopic Dermatitis (AD), particularly those with a history of Eczema Herpeticum (EH), may be at greater risk for infection by MRSA. The reason for this higher risk is unknown but may be linked to extended treatment with staphylococcus antibiotics in addition to the absence of certain proteins on their skin, which have immune function. The purpose of this study is to determine the reasons for MRSA infection in AD participants with and without a history of EH.
DOI: 10.21430/m368ximing
title: TIGIT is upregulated by HIV-1 infection and marks a highly functional adaptive and mature subset of natural killer cells

description: Performed a mass cytometry-based screen of NK cell receptor expression patterns in healthy controls and HIV+ individuals and then focused mechanistic studies on the expression and function of T cell immunoreceptor with Ig and ITIM domains (TIGIT)
DOI: 10.21430/m36ve0umf1
title: Sublingual Cockroach Safety Study (SCSS) (ICAC-10)

description: Immunotherapy may help reduce symptoms of allergy and asthma. Problems concerning compliance and adverse events with subcutaneous allergen immunotherapy have generated interest in delivering immunotherapy sublingually (under the tongue). The purpose of this study is to evaluate the safety of a cockroach extract given sublingually to people with perennial (year-round) allergic rhinitis, with or without asthma.
DOI: 10.21430/m379zlati0
title: Allele-specific expression changes dynamically during T cell activation in HLA and other autoimmune loci

description: Here we characterized the dynamics of genetic regulatory effects at eight time points during memory CD4+ T cell activation with high depth RNA-seq in healthy individuals. We discovered widespread dynamic allele-specific expression across the genome, where the balance of alleles changes over time, in 356 SNPs spanning 186 genes. These genes were four fold enriched in autoimmune loci. We found pervasive dynamic regulatory effects within six HLA genes, particularly for a major autoimmune risk gene, HLA-DQB1.