cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.21430/m30o36dljz
title: Adaptive and innate immunity in sPTB

description: This study is a meta-analysis evaluating differential gene expression signals in spontaneous preterm birth (sPTB). Three studies related to sPTB with maternal whole blood samples were selected in publicly available datasets, resulting in data from 339 samples. A meta-analysis of the aggregated and normalized transcriptomic datasets led to identification of 210 genes differentially expressed in sPTB relative to term birth. These genes were enriched in immune related pathways, showing upregulation of innate immunity and downregulation of adaptive immunity in women who delivered preterm. Additional analyses identified potential clinically relevant biomarkers.
DOI: 10.21430/m31dfmakjw
title: Whole exome sequencing reveals HSPA1L as a genetic risk factor for spontaneous preterm birth

description: Preterm birth is the leading cause of infant mortality, and prematurity is further associated with serious morbidities in later life. Genetic and environmental risk factors play a role in the susceptibility to preterm birth. Despite numerous studies, the genetic basis for preterm birth remains poorly defined. We investigated the presence of rare, possibly risk associated nucleotide variants in mothers with spontaneous preterm births (SPTB). The first set of mothers with family history of recurrent preterm births was of northern Finnish origin. An additional set of mothers (sister pairs, both giving birth preterm) of European origin was also studied. Whole exome sequencing identified multiple rare, likely damaging HSPA1L variants in several families affected by SPTB, and this gene was associated with the glucocorticoid receptor signaling pathway. Potential involvement of one of the HSPA1L variants in SPTB was further supported by large GWAS dataset. In addition, this variant alters protein post-translational modification potential, and thus may affect protein stability and its function as a chaperone.
DOI: 10.21430/m31k9qn0om
title: Vaginal Virome and Preterm Birth (See companion study SDY1206)

description: Higher vaginal eukaryotic DNA viral diversity during pregnancy is associated with
DOI: 10.21430/m31moiu91d
title: Genomic profiles of glioma progression

description: Gliomas are diverse neoplasms with multiple molecular subtypes. How tumor-initiating mutations relate to molecular subtypes as these tumors evolve during malignant progression remains unclear. We used genetically-engineered mouse models, histopathology, genetic lineage tracing, expression profiling, and copy number analyses to examine how genomic tumor diversity evolves during the course of malignant progression from low-to high-grade disease.
DOI: 10.21430/m3208rb6vb
title: Platelets attach to lung ILC2 expressing PSGL-1 and influence ILC2 function

description: Electron microscopy demonstrates that mouse lung ILC2 expressing PSGL-1 have platelets attached to their surface and that platelet depletion reduces lung ILC2 proliferation and Th2 cytokines suggesting ILC2 function is influenced by attachment to platelets
DOI: 10.21430/m32422nuzu
title: Preeclampsia Study

description: Preeclampsia is one of the most severe pregnancy complications and a leading cause of maternal death. However, early diagnosis of preeclampsia remains a clinical challenge, only limited information of select immune cell subsets is available. The goal is to detect characteristic immune dysfunctions in the maternal blood prior to the clinical onset of preeclampsia. The study used a high-dimensional mass cytometry immunoassay to characterize the dynamic changes of over 370 immune cell features in maternal blood during healthy and preeclamptic pregnancies. Results: A set of eight cell-specific immune features that accurately predict the preeclampsia well before the clinical diagnosis is identified. Several features recapitulated previously known immune dysfunctions in preeclampsia, such as elevated pro-inflammatory innate immune responses early in pregnancy and impaired regulatory T (Treg) cell signaling. The analysis revealed additional novel immune responses that were strongly associated with, and preceded the onset of preeclampsia, notably abnormal STAT5ab signaling dynamics in CD4+T cell subsets (AUC 0.92, p = 8.0E-5). These results provide a global readout of the dynamics of the maternal immune system early in pregnancy and lay the groundwork for identifying clinically-relevant immune dysfunctions for the prediction and prevention of preeclampsia
DOI: 10.21430/m32aarfe8u
title: Transcriptional responses induced by controlled human malaria infection (CHMI)

description: Whole blood RNA-Seq was applied to investigate gene expression kinetics in Tanzanian males who underwent controlled malaria infection by intradermal injection with aseptic, purified, cryopreserved Plasmodium falciparum sporozoites.
DOI: 10.21430/m32k1q3iap
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/m32ln9gibl
title: MaHPIC: Host Aotus nancymaae infected with P. vivax Brazil VII

description: MaHPIC: Experiment 15: Aotus nancymaae infected with P. vivax Brazil VII to produce clinical and omics measures of primary infections and relapses.
DOI: 10.21430/m33887d0yt
title: Prevention of Cardiac Allograft Vasculopathy Using Rituximab (Rituxan) Therapy in Cardiac Transplantation (CTOT-11)

description: This is a phase 2, prospective, multi-center, randomized, placebo-controlled clinical trial in which 300 primary heart transplant recipients with a negative PRA will be randomized (1:1) to placebo (IV day 0 and 12 post-transplant) plus conventional immunosuppression (tacrolimus or equivalent, MMF or equivalent, and rapid steroid taper) versus induction therapy with anti-CD20 mAb (1gm IV on day 0 and day 12 post-transplant) plus conventional immunosuppression.
DOI: 10.21430/m33b64bque
title: Monozygotic and Dizygotic Twin Pair T-Cell Responses to Influenza Vaccination SLVP018 2013

description: Evaluate the variation in immune response between individuals and assess whether it changes as a function of age and similarity in genetic and environmental background (by comparing differences between monozygotic and dizygotic twin pairs of different ages).
DOI: 10.21430/m33f47fe9u
title: Next Generation Sequencing RNA Seq data from UKE Phase I rVSV ZEBOV vaccine clinical trial, from full blood samples on Days 0,1,3,7

description: 10 adult participants of dose group 3x10^6 pfu, and 10 participants of dose group 20x10^6 pfu. Reads were aligned to the human reference assembly (GRCh38.p7) using STAR software (v2.4.2a; option '--quantMode GeneCounts'). Gene annotation was obtained from Ensembl (release 79, ensemble.org). VOOM+Limma analysis (R software, version 3.2.2) was used to assess differential gene expression at each post-vaccination day (d1, d3 and d7) against baseline (d0). Next, we intergreted gene expression data and antibody response using an sPLS algorithm, in order to down-select genes correlating with multivariate antibody responses at days 28, 54, 84,180.
DOI: 10.21430/m33gz8ur05
title: Efficacy of Islet After Kidney Transplantation (CIT-06) and Extended Follow Up after Islet Transplantation in Type 1 Diabetes (CIT-08)

description: CIT-06: The purpose of this study is to assess the benefit of islet transplantation in type 1 diabetic kidney transplant recipients. 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/m33psz2fhv
title: Human microbiome characterization through massive shotgun sequencing of circulating cell-free DNA.

description: Sequence data from cell free DNA found in 1351 blood samples collected from 188 patient was analyzed and assembled. 3761 of the 7190 larger contiguous regions generated were novel, with little or no homology to existing sequencing data. Presence of coding sequences in the contigs was confirmed in independent experiments and by direct PCR. The organisms identified represent entirely novel taxa, showing a substantially broader diversity in the human microbiome than previously appreciated.
DOI: 10.21430/m340dhry4y
title: Human Immune Signature of Zika virus infection

description: T cell human Immune Signature of Zika infection was studied
DOI: 10.21430/m34dagm5w4
title: Interferon Responses in Eczema Herpeticum (ADRN-01)

description: Atopic dermatitis (AD) is a chronic skin disorder characterized by recurrent viral skin infections. A small subset of patients with AD suffer from disseminated viral infections, e.g., eczema herpeticum (ADEH+), after herpes simplex infection (HSV) or eczema vaccinatum (EV) after smallpox vaccination. Interferon (IFN)-g plays a critical role in the innate and acquired immune responses by activating macrophages, enhancing natural killer cell activation, and promoting T cell differentiation, as well as regulating B cell isotype switching to immunoglobulin (Ig) G2a. Recent studies have demonstrated that IFN-g generation was significantly decreased after stimulation with HSV ex vivo. The purpose of this study is to determine if deficient IFN-g induction leads to susceptibility to HSV infection in ADEH+ patients.
DOI: 10.21430/m34f1r11om
title: Humoral responses to Influenza vaccination in aged populations - Year 2 2012 (See companion studies SDY272 2011, SDY648 2013, SDY739 2014, SDY819 2015)

description: The purpose of this study was to measure the B cell responses to the Trivalent Inactivated influenza Vaccine(TIV) in young and aged subjects, and measure their different B cell subsets.
DOI: 10.21430/m34i2celsw
title: A Retrospective Multicenter Study to Determine 4-Year Clinical Outcomes in Subjects Previously Enrolled in the CTOT-05 Study (CTOT-18)

description: This study is a multicenter, non-randomized, retrospective study to collect long term (4 years post-transplant) clinical outcome data on subjects previously enrolled in the CTOT-05 study.
DOI: 10.21430/m34ppebza7
title: Clinical Islet Transplantation Consortium (CITC)

description: The CIT consortium conducted a total of 9 studies across North America (CIT02 through CIT08) and the Nordic region (CIT01). CIT08 was a long-term follow-up study for interested participants at the North American sites. The target population is individuals with type 1 diabetes, normal kidney function, and intractable hypoglycemia. All studies treated participants with up to 3 separate infusions of islets.
DOI: 10.21430/m34rfpukx4
title: Pregnancy induces an earlier chronotype in both mice and women

description: Wrist actigraphy was obtained for two weeks before conception and then throughout pregnancy. Chronotype was measured by determining the time of sleep onset from the actigraphy profile of each 24-hour period (12 PM to 12 PM the next day) during the first (gestational weeks 4 through 13), second (weeks 14 through 27) and third trimesters (week 28 until delivery).
DOI: 10.21430/m35flwnxh1
title: AMP Lupus Network Project: Molecular Characterization of Lupus Nephritis and Correlation with Response to Therapy

description: Phase I will be devoted to the study of at least 45 subjects with lupus nephritis and 25 controls with the intent of achieving the following goals: (i) to assess feasibility of obtaining a sufficient yield of high quality data based on current and refined AMP SOPs, (ii) to assess recruitment rates and the number of sites necessary to effectively recruit for Phase II, (iii) to ensure that the technologies developed in Phase 0 are working well, especially with regard to transport and scaling up to handle specimens from multiple sites; (iv) to demonstrate that the selected technologies can be used for the purpose of reliably differentiating lupus nephritis kidneys from kidney tissue without lupus nephritis, (v) where necessary, to further refine the technologies before embarking on a large-scale project; and most importantly (vi) to provide critical data upon which to make rational decisions about key elements of the Phase II study design (e.g., eligibility criteria, estimates of variation for power calculations, and site-specific capability regarding patient recruitment, specimen handling, etc.).
DOI: 10.21430/m36bwccnh7
title: Eosinophilic Esophagitis Databank (CoFAR5)

description: Eosinophilic esophagitis (EoE) is a newly recognized chronic disease that is increasingly being diagnosed in children and adults. Many patients with EoE also have food allergies. EoE is characterized by inflammation and accumulation of a specific type of immune cell, called an eosinophil, in the esophagus. While there have been several large studies of EoE, very few have focused on the roles the immune system, genetics/heredity, and the environment in EoE. The samples and information collected from participants will help to identify and understand the genetic mechanisms underlying eosinophilic esophagitis. The Cincinnati Children's Hospital Medical Center will serve as the Central Laboratory for genetic characterization studies.
DOI: 10.21430/m36n1byft5
title: Zoster vaccine in young and elderly

description: Double center, open label study in which adult healthy volunteers will be vaccinated with Zoster vaccine.
DOI: 10.21430/m36x4bh892
title: Transcriptional profiling of yellow fever vaccine-naive participants bafore and after vaccination against yellow fever.

description: Mechanisms of poor responses to vaccines remain unknown. Yellow fever-naive adults were vaccinated with a yellow fever vaccine (YF-17D, Stamaril). Transcriptomic profiling of blood collected pre-vaccination and post-vaccination (day 3, 7, 14 and 84) was performed in order to identify candidate biomarkers of antibody response to the vaccine.
DOI: 10.21430/m37co9e6fq
title: YFV integrated mulitlineage and polyfunctional responses

description: Immunization with YF17D leades to an integrated immune response.
DOI: 10.21430/m37egahb65
title: B cell sequencing data from individuals with kidney transplantation (SNS01)

description: This data comes from peripheral blood from individuals that had a kidney transplantation. The study is a longitudinal study with data collected at time 0 (considered pre-transplant), 6 and 24 months after the transplant. They are classified in three clinical outcomes defined by pathology reads of serial allograft biopsies scored by Banff criteria and the chronic allograft damage index (CADI) score: Non progressors (NP; n=10) had low non incremental CADI score without acute rejection, progressors with no rejection (PNR; n=10) had incremental CADI score over 2 years without rejection, and progressors with rejection (PR; n=7) had incremental high CADI scores over 2 years with rejection episodes. This data reveal that the immune repertoire diversity of individuals that reject the organ is higher in comparison with those that did not reject the organ. Additionally, after 2 years of follow-up, patients who developed rejection show an overall reduction of B-celll diversity with persistence in and expansion of specific clones.
DOI: 10.21430/m37g7pmj7e
title: CD33 recruitment inhibits IgE-mediated anaphylaxis and desensitizes mast cells to allergen

description: Liposomal nanoparticles bearing an allergen and a high-affinity glycan ligand of the inhibitory receptor CD33 profoundly suppressed IgE-mediated activation of mast cells, prevented anaphylaxis in Tg mice with mast cells expressing human CD33, and desensitized mice to subsequent allergen challenge for several days
DOI: 10.21430/m37n6pjeqt
title: PTB-associated ancestry variants identification through genome-wide analysis

description: This study is a genome-wide association study analysis on 1,349 cases of preterm birth (PTB) and 12,595 ancestry-matched controls. Over 2 million single nucleotide polymorphisms (SNPs) were tested for associations with PTB across five subpopulations: Africa (AFR), the Americas (AMR), Europe (EUR), South Asia (SAS), and East Asia (EAS). Two intergenic loci were associated with PTB at a genome-wide level of significance: rs17591250 (P=4.55E-09) on chromosome 1 in the AFR population and rs1979081 (P=3.72E-08) on chromosome 8 in the AMR group. Several existing replication cohorts were queried and no support of these associations were found.
DOI: 10.21430/m384z5zxpi
title: ADRN Barrier/Immunoprofiling Exploratory Pilot Study (ADRN-04)

description: Atopic dermatitis, also called eczema, is a disease in which the skin is dry and scaly with severe itching. People with atopic dermatitis have defects in the skin barrier as well as defects in the immune system which fights off skin infections. People who have atopic dermatitis often have complications from viral and bacterial skin infections, such as recurring Staphylococcus aureus (S. aureus), or Staph infections. The purpose of this study is to look at how defects in the skin barrier and immune response affect risk for skin infections. The study will compare the skin barrier and immune response of people with and without atopic dermatitis in relation to whether Staph bacteria is growing on their skin.
DOI: 10.21430/m397zurmsi
title: Peanut Epicutaneous Immunotherapy (CoFAR6)

description: This study will evaluate whether peanut epicutaneous immunotherapy can protect individuals who are allergic to peanuts from having severe allergic reactions, when accidentally exposed to peanuts. The study also looks at the safety of the treatment and the effects it has on the immune system.
DOI: 10.21430/m39y58ssch
title: Humoral responses to Influenza vaccination in aged populations - Year 5 2015 (See companion studies SDY272 2011, SDY622 2012, SDY648 2013, SDY739 2014)

description: The purpose of this study was to measure the B cell and T cell responses to the Trivalent Inactivated influenza Vaccine(TIV) in young and aged subjects, and measure their different B cell subsets.
DOI: 10.21430/m3adhqnpy9
title: Immune Monitoring and CNI Withdrawal in Low Risk Recipients of Kidney Transplantation (CTOT-09)

description: The study will compare how well transplanted kidneys work and the response of people's immune systems as tacrolimus, a calcineurin inhibitor (CNI), is withdrawn. In addition, this research study will evaluate whether reducing immunosuppression can decrease some of these side effects while still preventing rejection of the kidney.
DOI: 10.21430/m3aukdixfi
title: T cell responses to H1N1v and a longitudinal study of seasonal influenza vaccination SLVP015 2014

description: Systems biology approach to examine effects of seasonal flu vaccination in adults of different ages on gene expression, cytokine stimulation and serum cytokines with parameters such as immune senescence to uncover new markers and mechanisms behind failure of immune function in many older people.
DOI: 10.21430/m3av8vfycb
title: UC MAIT study

description: Establish whether MAIT cells participate in pathophysiology of UC
DOI: 10.21430/m3azydhb5z
title: Anthropoid primate specific retroviral element THE1B controls expression of CRH in placenta and alters gestation length

description: The proper timing of delivery is critical during pregnancy; if too early or too late, the baby will be at risk of serious health problems and even death. Corticotropin-releasing hormone (CRH) is a protein that can be detected in maternal blood, and its concentration correlates with the timing of birth. In humans and other anthropoid primates, CRH is made by the placenta, whereas in other mammals, it is produced in a specialized region of the brain. To understand the regulation and evolution of this key protein, we inserted the human CRH gene and nearby regions into the mouse genome, which resulted in human CRH expression in the mouse placenta. Mouse litters that make CRH in their placentas are born later than control mice, showing that CRH can directly affect birth timing. Using our mouse model, we then selectively deleted a remnant of an ancient retrovirus that is normally found in the DNA of anthropoid primates and demonstrated that this specific region controls expression of CRH in the placenta. Deletion of this region also restored normal birth timing in the mice by eliminating CRH production from the placenta. We propose that retroviral regulation of CRH in the placenta may be a mechanism of controlling birth timing in humans and other anthropoid primates.
DOI: 10.21430/m3bcukeu3x
title: Lack of detection of a human placenta microbiome in samples from preterm and term deliveries

description: Historically the human womb has been thought to be sterile in healthy pregnancies, but this idea has been challenged by recent studies using DNA sequence-based methods, which have suggested that the womb is colonized with bacteria. For example, analysis of DNA from placenta samples yielded small proportions of microbial sequences, which were proposed to represent normal bacterial colonization. However, an analysis by our group showed no distinction between background negative controls and placenta samples
DOI: 10.21430/m3bnbgk39s
title: B-cell Immunity to Influenza SLVP017 2009

description: Systems biology approach to examine effects of seasonal flu vaccination in adults of different ages on gene expression, cytokine stimulation and serum cytokines with parameters such as immune senescence to uncover new markers and mechanisms behind failure of immune function in many older people.
DOI: 10.21430/m3by9lgsbh
title: Merck Ad5/HIV induces broad innate immune activation that predicts CD8_ T-cell responses but is attenuated by preexisting Ad5 immunity.

description: To better understand how innate immune responses to vaccination can lead to lasting protective immunity, we used a systems approach to define immune signatures in humans over 1 wk following MRKAd5/HIV vaccination that predicted subsequent HIV-specific T-cell responses.
DOI: 10.21430/m3c4l4wd2z
title: Human Immune Signature of Dengue virus infection- Gene Expression of CD4 subsets

description: T cell human Immune Signature of Dengue infection was studied
DOI: 10.21430/m3c9848da7
title: A proteomic clock of human pregnancy

description: Advances in multiplexed platform technologies facilitated exploration of human plasma proteins in term pregnancies indicating the existence of a proteomic clock
DOI: 10.21430/m3ccg5xnff
title: An Observational Study of Childhood Food Allergy (CoFAR2)

description: Multi-center, prospective cohort study investigating the immunologic, genetic, clinical, and environmental factors associated with the development of peanut allergy in a cohort of children at risk.
DOI: 10.21430/m3cffno2v3
title: Systems Immunology of Malaria

description: Systems biology study to determine the molecular hallmarks of naturally acquired clinical immunity to Plasmodium falciparum (Pf) malaria using multi-omic datasets (including RNA-seq transcriptomics, Pf antigen microarray, multi-parameter flow cytometry, multiplex cytokine analysis) in a cohort of Malian children who underwent active bi-weekly surveillance during an intense 6-month malaria transmission season.
DOI: 10.21430/m3er3du6nw
title: Comparing aerosol and intradermal boost regimes of candidate TB vaccine MVA85A.

description: There is an urgent need for an effective tuberculosis (TB) vaccine. Heterologous prime-boost regimens with recombinant viral vectors are effective at inducing induce high levels of potent cellular immunity. MVA85A is a candidate TB vaccine designed to boost BCG-induced immunity.