cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.21430/m3etol8tgs
title: Expression of genes associated with immunoproteasome processing of major histocompatibility complex peptides is indicative of protection with adjuvanted RTS,S malaria vaccine.

description: The goals of the present study were to determine whether there is a gene expression profile that is predictive of an individual's response to the adjuvanted RTS,S malaria vaccine and to identify the time at which that profile can be discerned before challenge.
DOI: 10.21430/m3exemmv8m
title: Modeling Viral Immunity and Antagonism in Dendritic Cells

description: A suite of ex vivo perturbations are applied to explore DC response
DOI: 10.21430/m3f210a2ma
title: Longitudinal study to common vaccines

description: Goal: To understand the longevity of humoral immune protection and the role played by memory B cells after common vaccinations. To quantify the heterogeneity in antibody responses to different vaccines and viruses. To quantify the time to loss of protective immunity to each vaccine or virus at the population level. Methods: Performed longitudinal data analysis on antibody titers for viral antigens (vaccinia, measles, mumps, rubella, varicella-zoster virus, and Epstein-Barr virus) and nonreplicating antigens (tetanus and diphtheria) in 45 subjects for a period of up to 26 years. Used a mixed-effects modeling framework to characterize the heterogeneity in antibody responses and to determine how variation in the magnitude and decay rate affect how protective immunity is lost at the population level to different virus and vaccine antigens. Results: Antiviral antibody responses were remarkably stable, with half-lives ranging from an estimated 50 years for varicella-zoster virus to more than 200 years for other viruses such as measles and mumps. Antibody responses against tetanus and diphtheria antigens waned more quickly, with estimated half-lives of 11 years and 19 years, respectively. B-cell memory was long-lived, but there was no significant correlation between peripheral memory B-cell numbers and antibody levels for five of the eight antigens tested. The statistical analysis and models helped to stratify the heterogenity factors and quantified each in a single plot to view interplays of factors, such as the fast-decay of anti-nonreplicating-antigens is compensated for by the higher magnitude of responses (relative to the level for protection) which explains a higher fraction of vaccinated individuals have protective immunity to tetanus and diphtheria than to measles, rubella, and vaccinia in the first 4 decades, suggesting the need for reevaluation of their boosting schedules.
DOI: 10.21430/m3f266silj
title: Dog Sarcoma Therapy

description: The drug eBAT is a bispecific angiotoxin targeted to both tumor and tumor neovasculature for sarcomas. It has been shown effectively kills canine hemangiosarcoma and human sarcoma cells in vitro. The paper studied the drug in an in vivo ontarget companion dog trial. Splenectomized dogs with minimal residual disease were given one cycle of eBAT followed by adjuvant doxorubicin in an adaptive dose-finding, phase I II study of 23 dogs with spontaneous, stage I II, splenic hemangiosarcoma. eBAT improved 6-month survival from &lt;40% in a comparison population to approximately 70% in dogs treated at a biologically active dose (50 ï¿½g/kg). Six dogs were long-term survivors, living &gt;450 days. The expected targeted markers, uPAR and EGFR, are validated in both human and canine sarcoma samples. The results support further translation of eBAT for human patients with sarcomas and perhaps other EGFR-expressing malignancies.
DOI: 10.21430/m3f47ksllp
title: Correlation between human innate and adaptive immune responses to T-cell independent or dependent meningococcal vaccines.

description: Thirty healthy adults (18-45 years of age) with no history of prior meningococcal vaccination and no contraindications to immunization will be vaccinated using either the meningococcal conjugate vaccine (MCV) or the meningococcal non-conjugate polysaccharide vaccine (MPSV). The study will be conducted as a randomized double blinded trial. Vaccine administration will be performed by an unblinded vaccine administrator, who will not be involved in subsequent assessments. Blood samples will be collected on Days D0 (at enrollment) and D3, D7, D14, D30 and D180 post vaccination to study innate and adaptive immunity markers. Even though meningococcal vaccination is considered safe, volunteers are asked to report any local or systemic AEs for 30 days post vaccination and any SAEs for 180 days post vaccination.
DOI: 10.21430/m3f5qe35ro
title: LEA29Y (Belatacept) Emory Edmonton Protocol (LEEP) (CIT-04) and Extended Follow Up after Islet Transplantation in Type 1 Diabetes (CIT-08)

description: CIT-04: This trial is a prospective, two-center, open-label, pilot study of islet transplantation assessing the safety and efficacy of a steroid-free, calcineurin inhibitor-free based immunosuppressive regimen with belatacept in subjects with long-standing type 1 diabetes (T1D) that is refractory 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/m3fp7gyree
title: Whole tumor RNA-sequencing and deconvolution of glioma transcriptional signature

description: Using whole tumor RNA-sequencing and mathematical deconvolution strategies to characterize low-grade glioma exosystem of several preclinical mouse models of neurofibromatosis type 1 (NF1) optic glioma, a low-grade astrocytoma whose formation and maintenance requires productive interactions between non-neoplastic and neoplastic cells. The result demonstrate that optic gliomas generated by altering the germline Nf1 gene mutation, the glioma cell of origin, or the presence of co-existing genetic alterations represent molecularly-distinct tumors. However, these optic glioma tumors share a 25-gene core signature, not found in normal optic nerve, that is normalized by microglia inhibition (minocycline), but not conventional (carboplatin) or molecularly-targeted (rapamycin) chemotherapy. In addition, a genetic signature conferred by Pten reduction and corrected by PI3K inhibition was identified, which predicts progression-free survival in patients with either low-grade or high-grade glioma. Collectively, these findings support the concept that gliomas are composite ecological systems whose biology and response to therapy may be best defined by examining the tumor as a whole.
DOI: 10.21430/m3fvo9sm7y
title: Malaria Vaccine in Healthy Adults

description: This study will evaluate whether administration of two investigational malaria vaccines (257049 and Ad35.CS.01 vaccines) combined in one immunization schedule increases protection against malaria infection as compared to protection induced by the 257049 vaccine alone. The study will also evaluate the safety and the immune response to the new combination of the two experimental malaria vaccines.
DOI: 10.21430/m3g5nit3nl
title: Immune Development in Pediatric Transplantation (CTOTC-02)

description: This is a multi-center, prospective, observational cohort study in pediatric renal transplant recipients. Target accrual in this study is 75 subjects over 2 years. Enrolled subjects will be categorized based on pre-enrollment CMV and EBV serology testing and be placed in the viral positive group, viral negative group, or split serology group. Subjects in the split serology group will not count towards study accrual target but will be included in analyses. CMV and EBV serology tests obtained for transplant evaluation will be collected retrospectively and used to categorize subjects. Subjects with previously negative serologies but later have positive serology results as indicated by testing on day of transplantation will be placed into the viral positive group. Subjects will have 6 study visits over 12 months as participants in this study.
DOI: 10.21430/m3g6v89cie
title: EZH2 as an Therapy Target in Lung Cancer

description: As a master regulator of chromatin function, the lysine methyltransferase EZH2 orchestrates transcriptional silencing of developmental gene networks. Overexpression of EZH2 is commonly observed in human epithelial cancers. Overexpression of EZH2 is commonly observed in human epithelial cancers. The paper demonstrated the causal role of EZH2 overexpression in NSCLC with humEZH2 in mouse models of lung adenocarcinoma, which featured distinct transcription program from KRAS- and EGFR models. To target EZH2-dependent cancers, the lab designed an open-source EZH2 inhibitor JQEZ5 and shown antitumor efficacy in preclinical studies in EZH2-driven models.
DOI: 10.21430/m3geiupy7r
title: Responses to Inactivated Influenza Vaccine (IIV) in adults with or without antibiotics

description: Single center, open mechanistic study in which subjects will be randomized to receive IIV per label at day 4 of a 5 day course of a specific antibiotic regimen (Group A) or IIV alone (Group B)
DOI: 10.21430/m3h1u3kjmz
title: Early pregnancy vaginal microbiome trends and preterm birth (see companion study SDY1341)

description: This study seeks to identify vaginal microbial community characteristics over time in a large predominantly African-American cohort of pregnant women and test whether particular community characteristics are associated with the risk for subsequent preterm birth.
DOI: 10.21430/m3hfae4es9
title: RG-HRV16 Inoculum Dose Determination

description: The study will have a single-blind, 5+5 design for dose finding with dose de-escalation with a maximum of 4 groups of up to 10 healthy, HRV16 seronegative adult subjects inoculated with either placebo or a dose of 100, 500, 1000 or 10,000 TCD50 of RG-HRV16. Household or close contacts of research subjects will be invited to join in a surveillance portion of the protocol in order to obtain safety information on the transmission and severity of RG-HRV16 colds.
DOI: 10.21430/m3hxqpvm9e
title: B-cell Immunity to Influenza (SLVP017) 2011

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/m3hxymfm42
title: Novel correlates of protection against influenza A(H1N1)pdm virus infection

description: To assess potential alternative correlates of protection, blood samples from participants in a Nicaraguan household transmission study with confirmed exposure to A(H1N1)pdm virus were tested using the classical HI assay as well as in enzyme-linked immunosorbent assays (ELISAs) that measured antibodies against the full-length HA, the HA stalk domain or the neuraminidase (NA).
DOI: 10.21430/m3i9qjdmau
title: AFR in drug resistance of cisplatin in bladder cancer

description: Mechanistic study of why elevated tumor suppressor ARF expression in aggressive subtypes of Muscle-invasive bladder cancer (MIBC) is associated with poor outcome and attenuated response to chemotherapy (cisplatin). The study was investigated In both GEMM and murine xenograft models of human MIBC. Resistance was mediated in part by the integrin-binding protein ITGB3BP (CENPR) and reflected ARF-dependent impairment of protein translation, which was exaggerated by drug treatment.
DOI: 10.21430/m3ibgbx9jo
title: Prior dengue virus infection and risk of Zika: a pediatric cohort in Nicaragua

description: To study the potential impact of previous exposure to dengue virus on Zika virus (ZIKV) infection outcome, we analyzed the 2016 Zika epidemic in Managua, Nicaragua, in a pediatric cohort with well-characterized dengue virus (DENV) immune histories.
DOI: 10.21430/m3id8zc1at
title: Transcriptional profiling of HBV-naive subjects before vaccination against Hepatitis A/B viruses, Diphtheria/Tetanus toxoids and Cholera.

description: One hundred and seventy four (174) generally healthy, Hepatitis B virus (HBV) naive, adult residents of Quebec were vaccinated with two doses of Twinrix (HBsAg and Hepatitis A virus - Glaxo Smith-Kline), generic Tetanus-diphtheria booster (tetanus and diphtheria - Sanofi-Pasteur), and Dukoral (recombinant cholera toxin B subunit and whole killed Vibrios - Sanofi Pasteur) according to the respective product labels. Blood samples were taken immediately prior to vaccination. Pre-vaccination high dimensional analyses of blood using transcriptional profiling and flow cytometry revealed that subjects having increased memory B cell frequencies and higher expression of genes downstream of B cell receptor signaling responded more strongly to the HBV vaccine whereas subjects having higher expression of inflammatory related genes and greater numbers of activated innate immune cells showed a weaker response to this vaccine.
DOI: 10.21430/m3ifol9mkv
title: Single-cell RNA-Seq analysis of MTB and DENV immune responses

description: Single-cell RNA-Seq analysis of MTB and DENV transcriptional profile was performed
DOI: 10.21430/m3ijd4lqr5
title: UT_SSc

description: HLA Genotyping
DOI: 10.21430/m3ir2j7xww
title: Comparative analysis of neonatal and adult immune responses after in vitro rhinovirus stimulation

description: Rhinovirus infections during infancy account for the majority of respiratory illness health care utilization and are an associated risk factor for subsequent development of allergic asthma. Neonatal type I interferon production is diminished compared to adults after stimulation with TLR agonists. However, broad profiling of immune cell responses to infectious rhinovirus has not been undertaken and we hypothesized that additional immune differences can be identified in neonates. Rhinovirus infections during infancy account for the majority of respiratory illness health care utilization and are an associated risk factor for subsequent development of allergic asthma. Neonatal type I interferon production is diminished compared to adults after stimulation with TLR agonists. However, broad profiling of immune cell responses to infectious rhinovirus has not been undertaken and we hypothesized that additional immune differences can be identified in neonates.
DOI: 10.21430/m3ixmi1pco
title: Small Sample- Big Data: The Gambia

description: Systems Biology Characterization in Early Life
DOI: 10.21430/m3j2fjivpw
title: MaHPIC: Host M. mulatta infected with P. coatneyi

description: MaHPIC: Experiment 03 - Macaca mulatta infected with Plasmodium coatneyi Hackeri strain to produce and integrate clinical, hematological, parasitological, and omics measures of acute, recrudescent, and chronic infections
DOI: 10.21430/m3j92gn8i3
title: Time series of global gene expression after trivalent influenza vaccination in humans

description: The relationship between gene expression patterns and humoral immune response to vaccination was analyzed in order to understand the interindividual variability among immune reponse to vaccination
DOI: 10.21430/m3k4g9ji49
title: Chikungunya virus infection immunoprofiling in pediatric cohort

description: Immunoprofiling of acute and convalescent blood samples from CHIKV infected children
DOI: 10.21430/m3kpgt3byf
title: Profiling of NK cell ligands on moocytes infected with Influenza A virus

description: Identify NK cell ligands regulated by influenza A virus infection using a monocyte-NK co-culture system and a Helios Mass cytometer. Two major ligands we found that contributed to the variance between the two strains were CD54 and CD112.
DOI: 10.21430/m3lbda3iam
title: Prematurity, Respiratory outcomes, Immune System, and Microbiome Study (PRISM)

description: This Clinical Research Study will investigate the relationships between sequential respiratory viral infections, patterns of intestinal and respiratory bacterial colonization, and adaptive cellular immune phenotypes which are associated with increased susceptibility to respiratory infections and long term respiratory morbidity in preterm and full term infants.
DOI: 10.21430/m3ljtcb0m1
title: Adjuvanted influenza-H1N1 vaccination reveals lymphoid signatures of age-dependent early responses and of clinical adverse events.

description: We show that within 24 h of receiving adjuvanted swine flu vaccine, healthy individuals made expansive, complex molecular and cellular responses that included overt lymphoid as well as myeloid contributions. Unexpectedly, this early response was subtly but significantly different in people older than _35 years.
DOI: 10.21430/m3lt8wvhvh
title: A Systems Vaccinology Approach Reveals Temporal Transcriptomic Changes of Immune Responses to the Yellow Fever 17D Vaccine.

description: In this study, we used a systems vaccinology approach to identify temporal changes in immune response signatures to the yellow fever (YF)-17D vaccine, with the aim of comprehensively characterizing immune responses associated with protective immunity.
DOI: 10.21430/m3m9y78qlf
title: Sequence-based HLA-A, B, C, DP, DQ, and DR typing

description: DNA sequence-based typing at the HLA-A, -B, -C, -DPB1, -DQA1, -DQB1, and -DRB1 loci
DOI: 10.21430/m3nbgea98c
title: Lymph node reservoirs for long-lived memory T cells

description: This study characterizes human memory T cells across multiple lymphoid and mucosal tissues from individual organ donors by transcriptional profling, high dimensional protein analysis on the single cell level by CyTOF, and T cell receptor repertoire profiling.
DOI: 10.21430/m3nel3qh3q
title: Antibody-dependent enhancement of severe dengue disease in humans

description: Using multiple statistical approaches to study a long-term pediatric cohort in Nicaragua, we show that risk of severe dengue disease is highest within a narrow range of pre-existing anti-DENV antibody titers. By contrast, we observe protection from all symptomatic dengue disease at high antibody titers. Data are available upon request (eharris@berkeley.edu), as is required by the IRB-approved protocol for the Pediatric Dengue Cohort Study. The materials and data used in this study are covered by standard material transfer agreements.
DOI: 10.21430/m3njtlgrt4
title: Determining the Immune Response to MVA85A (tuberculosis vaccine candidate)

description: Characterization of early gene expression changes after MVA85A vaccination and connection to immune response mechanism and magnitude.
DOI: 10.21430/m3nxe11ze6
title: Malaria Vaccine in Healthy Adults

description: This study will evaluate whether administration of two investigational malaria vaccines (257049 and Ad35.CS.01 vaccines) combined in one immunization schedule increases protection against malaria infection as compared to protection induced by the 257049 vaccine alone. The study will also evaluate the safety and the immune response to the new combination of the two experimental malaria vaccines.
DOI: 10.21430/m3p1tk6ixe
title: Systems Biology of Varicella Zoster Vaccination

description: Comparison of VZV vaccination in individuals of different ages to decipher the molecular mechanisms underlying variable vaccine responses.
DOI: 10.21430/m3p7q1zrxj
title: Islet Transplantation in Type 1 Diabetes (CIT-07) and Extended Follow Up after Islet Transplantation in Type 1 Diabetes (CIT-08)

description: CIT-07: The purpose of this study is to determine the safety and effectiveness of islet transplantation, combined with immunosuppressive medications, for treating type 1 diabetes in individuals experiencing hypoglycemia unawareness and severe hypoglycemic episodes. 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/m3q1c6388o
title: Mechanisms Underlying Asthma Exacerbations Prevented and Persistent With Immune-Based Therapy (ICAC-29)

description: MUPPITS-1 is a prospective, longitudinal, nested case-control study designed to identify changes in gene transcription predictive of and associated with asthma exacerbations in children with difficult-to-control, exacerbation-prone asthma.
DOI: 10.21430/m3q1zbwog2
title: B-cell responses to meningococcal vaccine.

description: Comparison of plain-polysaccharide and protein-polysaccharide conjugate vaccines.
DOI: 10.21430/m3qhf445nf
title: Smallpox vaccination with LC16m8 vaccinia virus provides a gene expression profile similar to DryVax vaccination

description: Transcriptional analysis of global gene expression changes in naive subjects in response to smallpox vaccination with either DryVax or the replication-competent, attenuated LC16m8 vaccinia virus.
DOI: 10.21430/m3qw34u2sg
title: KIR and HLA in MS

description: Our goal is to carry out case/control association analyses for Multiple Sclerosis using our high resolution NGS HLA and MALDI-TOF KIR genotyping methods.
DOI: 10.21430/m3r9n6os6c
title: CRISPR-Cas9 Engineering in Primary Cell Protocol

description: Ex vivo genome editing of primary human T cells can be used to identify viral host factors
DOI: 10.21430/m3rkbkoyks
title: Extensive homeostatic T cell phenotypic variation within the Collaborative Cross

description: The Collaborative Cross (CC) is a panel of reproducible recombinant inbred mouse strains with high levels of standing genetic variation, thereby affording unprecedented opportunity to perform experiments in a small animal model containing controlled genetic diversity while allowing for genetic replicates. Here, we advance the utility of this unique mouse resource for immunology research, as it allows for both examination and genetic dissection of mechanisms behind adaptive immune states in mice with distinct and defined genetic makeups. This approach is founded on quantitative trait locus mapping: identifying genetically variant genome regions associated with phenotypic variance in traits-of-interest. Furthermore, the CC can be utilized for mouse model development; distinct strains have unique immunophenotypes and immune properties, making them suitable for research on particular diseases and infections. Here, we describe variation in cellular immune phenotypes across F1 crosses of CC strains, and reveal novel quantitative trait loci responsible for several immune phenotypes.
DOI: 10.21430/m3rp599g2m
title: Toward more predictable birthdays

description: Low-cost methods for monitoring fetal development could improve prenatal care, especially in low-resource settings. By measuring the levels of certain placental RNA transcripts in maternal blood, Ngo et al. developed two noninvasive blood tests that provide a window into the progression of individual pregnancies. In a small proof-of-concept study, the first blood test predicted fetal age and delivery date with an accuracy comparable to that of ultrasound. The second blood test, also examined in a small pilot study, discriminated women at risk of preterm delivery from those who delivered at full term. The next step will be to assess the reliability of the tests in large, blinded clinical trials.
DOI: 10.21430/m3rt6lajh3
title: Baminercept in Sjogren's Syndrome (ASJ02)

description: The purpose of the study is to find out if the experimental study agent, baminercept, is effective in treating patients with Sjogren's syndrome. The study will also determine if the study agent can be safely given to patients with Sjogren's syndrome; examine how it affects symptoms of the disease; and attempt to understand how baminercept affects the underlying mechanisms of Sjogren's syndrome and the immune system.
DOI: 10.21430/m3sa04cc03
title: Flow Cytometry of T cells for TB Resistance Study

description: FCS and workspaces files from T cell ICS Flow Cytometry