Grant List
Represents Grant table in the DB
GET /v1/grants?page%5Bnumber%5D=1392&sort=-start_date
{ "links": { "first": "https://cic-apps.datascience.columbia.edu/v1/grants?page%5Bnumber%5D=1&sort=-start_date", "last": "https://cic-apps.datascience.columbia.edu/v1/grants?page%5Bnumber%5D=1392&sort=-start_date", "next": null, "prev": "https://cic-apps.datascience.columbia.edu/v1/grants?page%5Bnumber%5D=1391&sort=-start_date" }, "data": [ { "type": "Grant", "id": "7796", "attributes": { "award_id": "1ZIAAI001327-01", "title": "Immunity to SARS-CoV-2 After Natural Infection or Vaccination", "funder": { "id": 4, "ror": "https://ror.org/01cwqze88", "name": "National Institutes of Health", "approved": true }, "funder_divisions": [ "National Institute of Allergy and Infectious Diseases (NIAID)" ], "program_reference_codes": [], "program_officials": [], "start_date": null, "end_date": null, "award_amount": 109107, "principal_investigator": { "id": 23609, "first_name": "Mark", "last_name": "Connors", "orcid": null, "emails": "", "private_emails": "", "keywords": null, "approved": true, "websites": null, "desired_collaboration": null, "comments": null, "affiliations": [ { "id": 1540, "ror": "https://ror.org/043z4tv69", "name": "National Institute of Allergy and Infectious Diseases", "address": "", "city": "", "state": "MD", "zip": "", "country": "United States", "approved": true } ] }, "other_investigators": [], "awardee_organization": { "id": 1540, "ror": "https://ror.org/043z4tv69", "name": "National Institute of Allergy and Infectious Diseases", "address": "", "city": "", "state": "MD", "zip": "", "country": "United States", "approved": true }, "abstract": "Our laboratory is engaged in the study of the immune response to SARS-CoV-2 in two major areas. The first of these is the study of the immune response to natural infection. The second is the response to virus-like particles or replicating recombinant adenovirus type 4 vaccines. We are collaborators on a large natural history study of up to 300 survivors of SARS-CoV-2 and their household contacts, led by Dr. Michael Sneller. In this study, serum and peripheral blood mononuclear cells are sampled during acute infection and over 3 years. Our laboratory will be primarily responsible for measuring the cellular immune response to SARS-CoV-2 gene products. A large panel of functions of T cells specific for SARS-CoV-2, including frequency, cytokine secretion, and cytolytic capacity, will be measured over time to examine the dynamics of frequency and functions, and the potential correlations with disease severity. In a separate effort, two vaccine platforms that are being developed for HIV, have been repurposed to induce immunity against SARS-CoV-2. Over the past several years our section has developed several vaccine platforms for use as vaccines to present viral surface glycoproteins. Both replicating vectors and virus-like particles (VLPs) have proven to be highly immunogenic platforms in rabbit and human studies. After vaccination with Ad4 expressing influenza H5 Vietnam (Ad4-H5-Vtn), participants developed levels of neutralizing antibodies that were much higher and more durable than those induced by the licensed Sanofi vaccine (Matsuda et al., Science Immunology, 2019). In addition, H5-specific B cell expansions, and neutralizing antibody hypermutation and potency, continued for 6-12 months after a single intranasal vaccination. Vaccinee responses could be increased to even higher levels by boosting with the licensed H5 vaccine. More recently, we have developed VLP platforms to present viral surface glycoproteins. For RSV, this platform has been shown to induce levels of neutralizing antibodies above those induced by RSV infection in small animals. In our work, we have been able to use VLPs to induce H5-specific neutralizing antibodies titers in rabbits of approximately 1:1000 after two immunizations. The reason for the HSIS to pursue the COVID-19 spike protein in these formats is two-fold. First, it will provide us with experience with another viral surface glycoprotein beyond HIV, RSV, and influenza. Second and more important, most of the approaches being considered as vaccines against COVID-19 are not complex, high valency particles, or replicating vaccines. Of the currently licensed anti-viral vaccines, only two forms provide a sufficiently potent B cell stimulus that they confer lifelong immunity. These are live-attenuated viruses and virus-like particles. Over the past several years there has been great progress in understanding the immunology that underlies the success of these approaches. Both have the potential to present the nave B cell with viral surface glycoproteins in the appropriate conformation that approximates the disease causing virus against which they protect. They can induce pro-inflammatory cytokines and contain TLR agonists that drive B cell responses. Perhaps most importantly, they are particulate in nature. There is very good experimental evidence that particulate immunogens are considerably more potent than other forms. The COVID-19 spike protein is immunogenic, relatively conserved, and with regard to immunogenicity, should behave similarly to stabilized RSV F or influenza H5. For these reasons, we feel that the more immunogenic replicating or VLP approaches will provide an important complement to other approaches being pursued.", "keywords": [ "2019-nCoV", "Agonist", "Animals", "Antibody titer measurement", "Antigens", "Antiviral Agents", "Area", "Attenuated", "B-Lymphocytes", "COVID-19", "Complement", "Disease", "Frequencies", "Goals", "HIV", "Household", "Human", "Immune response", "Immunity", "Immunization", "Immunology", "Infection", "Inflammatory", "Influenza", "Laboratories", "Measurement", "Measures", "Membrane Glycoproteins", "Molecular Conformation", "Natural History", "Nature", "Oryctolagus cuniculus", "Participant", "Particulate", "Peripheral Blood Mononuclear Cell", "Proteins", "Respiratory Syncytial Virus Infections", "Sampling", "Science", "Severity of illness", "Stimulus", "Study of serum", "Survivors", "T-Lymphocyte", "Time", "Vaccination", "Vaccines", "Vietnam", "Viral", "Viral Vaccines", "Viral Vector", "Virus", "Virus-like particle", "Work", "acute infection", "cytokine", "experience", "gene product", "immunogenic", "immunogenicity", "neutralizing antibody", "particle", "recombinant adenovirus", "response", "success", "vector" ], "approved": true } }, { "type": "Grant", "id": "7798", "attributes": { "award_id": "1ZIAES102025-15", "title": "Allergic sensitization through the airway", "funder": { "id": 4, "ror": "https://ror.org/01cwqze88", "name": "National Institutes of Health", "approved": true }, "funder_divisions": [ "National Institute of Environmental Health Sciences (NIEHS)" ], "program_reference_codes": [], "program_officials": [], "start_date": null, "end_date": null, "award_amount": 1668512, "principal_investigator": { "id": 23611, "first_name": "DONALD N", "last_name": "COOK", "orcid": null, "emails": "", "private_emails": "", "keywords": null, "approved": true, "websites": null, "desired_collaboration": null, "comments": null, "affiliations": [ { "id": 1605, "ror": "https://ror.org/00j4k1h63", "name": "National Institute of Environmental Health Sciences", "address": "", "city": "", "state": "NC", "zip": "", "country": "United States", "approved": true } ] }, "other_investigators": [], "awardee_organization": { "id": 1605, "ror": "https://ror.org/00j4k1h63", "name": "National Institute of Environmental Health Sciences", "address": "", "city": "", "state": "NC", "zip": "", "country": "United States", "approved": true }, "abstract": "Allergic asthma stems from inappropriate immune responses to inhaled antigens. Thus, to prevent or treat allergic asthma, it is important to identify the cellular and molecular mechanisms that initially give rise to allergic sensitization, as well as the pathways that regulate allergic inflammation once it has begun. Accordingly, our laboratory uses mouse models of asthma in which the animals are senstized to a variety of inhaled allergens. For example, ovalbumin (OVA) is delivered to the airway together with various adjuvants. Such adjuvants include ligands of various toll-like receptors (TLRs), including lipopolysaccharide (LPS) and bacterial flagellin, as well as molecules that have protease activity. Pulmonary dendritic cells lining the airway epithelium take up OVA and migrate to draining thoracic lymph nodes to present allergen-derived peptides to naive T cells. These cells differentiate into T helper (Th)2 or Th17 cells that upon challenge with OVA produce IL-13 and IL-17, respectively. This in turn leads to airway eosinophilia and neutrophilia and gives rise to airway hyperresponsiveness (AHR). Th17 responses to inhaled allergens might be one means to distinguish severe asthma from less serious Th2-mediated diseases of the airway. IWe also study the differential impact of various environmental agents on pulmonary dendritic cell activation, and how these agents can act as adjuvants in the lung to promote allergic sensitization through the airway. We have found that many types of molecules can act as adjuvants, but can trigger distinct molecular pathways that give rise to different forms of asthma. For example, bacterial products, such as LPS and flagellin, promote allergic sensitization by activating the TNF pathway, whereas protease adjuvants act through the cytokine, IL-33. There are two major populations of resident lung dendritic cells. One population displays the cell surface molecule, CD103, whereas the other subset displays a different marker, CD11b. The latter can be divided into multiple distinct subsets by mass cytometry, single cell RNA-sequencing and flow cytometery. We are comparing the functions of these dendritic cell subsets following their culture with antigen-specific, naive T cells. Finally, we are also studying how allergens interact with the airway epithelium and whether signals derived from the epithelium can modulate dendritic cell function. We hypothesize that this epithelial - dendritic cell cross talk is critical for orchestrating immune responses to inhaled allergens. Together, these approaches should allow us to identify and characterize cellular and molecular mechanisms that lead to allergic sensitization to inhaled allergens. This project involves research on human coronavirus, novel coronavirus, COVID-19, Severe Acute Respiratory Syndrome coronavirus disease, SARS coronavirus, SARS-coronavirus-2, SARS-cov-2, SARS-cov2, SARS-related coronavirus 2, Severe acute respiratory syndrome coronavirus 2, SARS-Associated Coronavirus, SARS-cov, or SARS-Related Coronavirus.", "keywords": [ "2019-nCoV", "Adjuvant", "Affect", "Airway Disease", "Allergens", "Allergic", "Allergic inflammation", "Animals", "Antigens", "Asthma", "COVID-19", "Cell Differentiation process", "Cell physiology", "Cell surface", "Cells", "Cytometry", "Dendritic Cells", "Dendritic cell activation", "Environment", "Eosinophilia", "Epithelial", "Epithelial Cells", "Epithelium", "Extrinsic asthma", "Flagellin", "Genes", "Goals", "ITGAM gene", "Immune response", "Individual", "Inhalation", "Interleukin-13", "Interleukin-17", "Laboratories", "Lead", "Ligands", "Lipopolysaccharides", "Lung", "Lung diseases", "Mediating", "Molecular", "Mus", "Mutation", "Neutrophilia", "Ovalbumin", "Pathway interactions", "Peptide Hydrolases", "Peptides", "Population", "Quality of life", "Regulation", "Research", "Role", "SARS coronavirus", "Severe Acute Respiratory Syndrome", "Signal Transduction", "T-Lymphocyte", "TNF gene", "Testing", "Thoracic Lymph Node", "Toll-like receptors", "airway epithelium", "airway hyperresponsiveness", "asthma model", "cell type", "cytokine", "design", "draining lymph node", "environmental agent", "experimental study", "gene product", "human coronavirus", "improved", "interest", "mouse model", "novel", "novel coronavirus", "prevent", "response", "single-cell RNA sequencing", "stem" ], "approved": true } }, { "type": "Grant", "id": "7799", "attributes": { "award_id": "1ZICHD008958-05", "title": "Molecular Genomics Sequencing Core Facility", "funder": { "id": 4, "ror": "https://ror.org/01cwqze88", "name": "National Institutes of Health", "approved": true }, "funder_divisions": [ "Eunice Kennedy Shriver National Institute of Child Health and Human Development (NICHD)" ], "program_reference_codes": [], "program_officials": [], "start_date": null, "end_date": null, "award_amount": 2705152, "principal_investigator": { "id": 23612, "first_name": "Steven", "last_name": "Coon", "orcid": null, "emails": "", "private_emails": "", "keywords": null, "approved": true, "websites": null, "desired_collaboration": null, "comments": null, "affiliations": [ { "id": 1624, "ror": "", "name": "EUNICE KENNEDY SHRIVER NATIONAL INSTITUTE OF CHILD HEALTH & HUMAN DEVELOPMENT", "address": "", "city": "", "state": "", "zip": "", "country": "United States", "approved": true } ] }, "other_investigators": [], "awardee_organization": { "id": 1624, "ror": "", "name": "EUNICE KENNEDY SHRIVER NATIONAL INSTITUTE OF CHILD HEALTH & HUMAN DEVELOPMENT", "address": "", "city": "", "state": "", "zip": "", "country": "United States", "approved": true }, "abstract": "The primary mission of the Molecular Genomic Core (MGC) is to provide next-generation sequencing services to the NICHD community. During FY20, MGC sequenced 2509 samples submitted as 153 projects for 38 different NICHD principle investigators. This represents a modest 10% decrease compared the number of samples sequenced in the same period last year even though the COVID-19 pandemic closed the NIH for at least 3 months. These efforts generated 6,205 Giga-bases (6.2 Tera-bases) of sequenced DNA and RNA samples. In nearly all cases, MGC constructs the sequencing libraries, but MGC also provides sequencing for libraries generated by investigators. The types of samples sequenced include the following: RNA-Seq, microRNA-Seq, whole genome sequencing, whole exome sequencing, custom targeted exome sequencing, whole genome bisulfate sequencing, ribosomal profiling, HiC-Seq, ChIP-Seq, ATAC-Seq, single-cell-RNA-Seq and microbiome sequencing. In most cases, MGC provides primary bioinformatic analysis for samples we sequence. This includes quality checking, demultiplexing and alignment, then a first level of data analysis; for example, differential expression for RNA-Seq data, or variant calling for whole exome data. In addition, during FY20, the MGC has also collaborated bioinformatically with 24 investigators (60 projects with some bioinformatic contribution); in some cases, this involved analysis for projects sequenced outside of the MGC (3 of the 60 mentioned above). As part of MGC's ongoing educational commitment, MGC has sponsored the MGC Sequencing Seminar Series. MGC has co-hosted, along with the NHLBI Sequencing Core, an annual Sequencing Symposium, this year on Long-Read Sequencing.", "keywords": [ "ATAC-seq", "Base Sequence", "Bioinformatics", "Biological Sciences", "COVID-19 pandemic", "Cells", "ChIP-seq", "Chromium", "Communities", "Core Facility", "Counseling", "Custom", "DNA", "DNA Sequence", "DNA Sequencing Facility", "DNA sequencing", "Data", "Data Analyses", "Diagnosis", "Genes", "Genetic Research", "Genomics", "Hereditary Disease", "Ions", "Libraries", "MicroRNAs", "Mission", "Molecular", "National Heart Lung and Blood Institute", "National Institute of Child Health and Human Development", "Production", "RNA", "Research", "Research Personnel", "Sampling", "Series", "Services", "United States National Institutes of Health", "Variant", "base", "bioinformatics tool", "bisulfite sequencing", "computerized data processing", "design", "differential expression", "exome", "exome sequencing", "experimental study", "genome sequencing", "innovation", "methylome", "miRNA expression profiling", "microbiome sequencing", "next generation sequencing", "ribosome profiling", "single molecule", "single-cell RNA sequencing", "symposium", "targeted exome sequencing", "transcriptome sequencing", "whole genome" ], "approved": true } }, { "type": "Grant", "id": "7801", "attributes": { "award_id": "1ZICES043010-35", "title": "Computational Chemistry and Macromolecular Modeling", "funder": { "id": 4, "ror": "https://ror.org/01cwqze88", "name": "National Institutes of Health", "approved": true }, "funder_divisions": [ "National Institute of Environmental Health Sciences (NIEHS)" ], "program_reference_codes": [], "program_officials": [], "start_date": null, "end_date": null, "award_amount": 472295, "principal_investigator": { "id": 23613, "first_name": "William", "last_name": "Copeland", "orcid": null, "emails": "", "private_emails": "", "keywords": null, "approved": true, "websites": null, "desired_collaboration": null, "comments": null, "affiliations": [ { "id": 1605, "ror": "https://ror.org/00j4k1h63", "name": "National Institute of Environmental Health Sciences", "address": "", "city": "", "state": "NC", "zip": "", "country": "United States", "approved": true } ] }, "other_investigators": [], "awardee_organization": { "id": 1605, "ror": "https://ror.org/00j4k1h63", "name": "National Institute of Environmental Health Sciences", "address": "", "city": "", "state": "NC", "zip": "", "country": "United States", "approved": true }, "abstract": "During this fiscal year we continued to devote major effort to work aimed at applications of molecular dynamics and quantum mechanics/molecular mechanics simulations required to help support the computational chemistry and molecular modeling needs of NIEHS scientists. Some projects involved creation of solution structures of peptides and proteins using state-of-the-art molecular dynamics simulations and the others involved a careful look at the reactive dynamics at or near the active site of the biological systems of interest. Several docking studies and energy characterization studies are highlights of our efforts. Most computational chemistry and molecular modeling tools that have been utilized in the present research efforts are either developed by us or modified by us. Almost all tools used in the analysis of molecular dynamics trajectories required to obtain predicted solution structures and in the energy decomposition schemes of quantum mechanics/molecular mechanics (QMMM) calculations are also written by us. The current list of projects includes (but not limited to) solution structure evaluations of Tristetraproline (a protein involved in RNA degradation) of various species that affects RNA binding; Topoisomerase-2 reaction dynamics, Phosphopeptide interactions of the Nbs1 N-terminal FHA-BRCT1/2 domains; modeling of DNA polymerase activity with the inclusion of some modified-ribonucleotides (and modified pyrophosphates in the case of the reverse reaction) at both classical and QMMM level; DNA dynamics in the presence of carcinogenic dye molecules; juvenile dermatomyositis and the muscle structural protein mutations; interactions of lipids with CYP2J2 proteins; binding of various small molecules such as BPA and its derivatives on estrogen receptor, its mutants and androgen receptor; quantum mechanical characterization of small drug-like molecules; reversal of drug resistance by small molecules ABCB1 and ABCG2 expressing multidrug resistant tumor cells; role of various metal ions in nucleotide insertion during DNA polymerase action; GATA3 mutant modeling; modeling dGTP Triphosphohydrolase; hydrophobic lipid interactions with allergen proteins such as Bla g1; modeling novel mutations in mitochondrial single-strand binding protein; Small molecule docking onto PUF family proteins; damaged DNA structure characterizations using molecular dynamics simulations. In addition, several proteins related to Covid-19 were modeled to be used in various research activities. These research activities include modeling Spike-protein trimer; interactions of hyluronic acid with the spike protein; interactions of spike protein with nicotinamide acetylcholine receptor; structure evaluation of SARS-CoV-2 Endoribonuclease Nsp15; Zinc binding to Covid-19 cyctein proteases and the RNA-dependent RNA-polymerase; small molecule interactions with Mpro. In addition, as a measure for efficient spending and also as a precautionary measure to carry out our functions under constraints of budgetary restrictions, we have been continuing to explore the idea of testing and setting up computer servers based on low cost, off-the-shelf components and GPUs to efficiently run MD simulations that require heavy utilization of multiple processors to sample systems with millions of atoms and to complete QMMM calculations that demand access to a large sum of memory at a given instance due to inherent complexity of the calculations.", "keywords": [ "2019-nCoV", "ABCB1 gene", "ABCG2 gene", "Acids", "Active Sites", "Affect", "Allergens", "Androgen Receptor", "Area", "Attention", "Binding", "Binding Proteins", "Biological", "COVID-19", "CYP2J2 gene", "Cholinergic Receptors", "Classical Mechanics", "Computers", "DNA", "DNA Damage", "DNA Structure", "DNA-Directed DNA Polymerase", "Dermatomyositis", "Diphosphates", "Docking", "Drug resistance", "Dyes", "Endoribonucleases", "Estrogen Receptors", "Evaluation", "GATA3 gene", "Goals", "Health", "Human", "Hydrophobicity", "Ions", "Lipids", "Measures", "Mechanics", "Memory", "Metals", "Methodology", "Methods", "Mitochondria", "Modeling", "Molecular Analysis", "Molecular Conformation", "Multi-Drug Resistance", "Mutation", "N-terminal", "National Institute of Environmental Health Sciences", "Niacinamide", "Nucleotides", "Peptide Hydrolases", "Pharmaceutical Preparations", "Phosphopeptides", "Procedures", "Process", "Protein Family", "Proteins", "Quantum Mechanics", "RNA Binding", "RNA Degradation", "RNA-Directed RNA Polymerase", "Reaction", "Research", "Research Activity", "Research Personnel", "Resort", "Ribonucleotides", "Role", "Running", "Sampling", "Scheme", "Scientist", "Structural Protein", "Structure", "Sum", "System", "Technology", "Testing", "Time", "Topoisomerase", "Translating", "Work", "Zinc", "base", "biological systems", "carcinogenicity", "computational chemistry", "computing resources", "cost", "dGTPase", "functional hypothalamic amenorrhea", "improved", "interest", "molecular dynamics", "molecular mechanics", "molecular modeling", "muscular structure", "mutant", "nanosecond", "neoplastic cell", "novel", "peptide structure", "quantum", "simulation", "small molecule", "tool" ], "approved": true } }, { "type": "Grant", "id": "7803", "attributes": { "award_id": "1ZIABC011934-01", "title": "Bacteriophage Lambda vaccine displaying coronavirus antigens", "funder": { "id": 4, "ror": "https://ror.org/01cwqze88", "name": "National Institutes of Health", "approved": true }, "funder_divisions": [ "National Cancer Institute (NCI)" ], "program_reference_codes": [], "program_officials": [], "start_date": null, "end_date": null, "award_amount": 161209, "principal_investigator": { "id": 23614, "first_name": "DONALD", "last_name": "COURT", "orcid": null, "emails": "", "private_emails": "", "keywords": null, "approved": true, "websites": null, "desired_collaboration": null, "comments": null, "affiliations": [ { "id": 1601, "ror": "", "name": "DIVISION OF BASIC SCIENCES - NCI", "address": "", "city": "", "state": "", "zip": "", "country": "United States", "approved": true } ] }, "other_investigators": [], "awardee_organization": { "id": 1601, "ror": "", "name": "DIVISION OF BASIC SCIENCES - NCI", "address": "", "city": "", "state": "", "zip": "", "country": "United States", "approved": true }, "abstract": "The lambda capsid (coat protein(s)) can be engineered to contain and display on its surface specific epitope(s) of disease-causing agents. Thus, the lambda vaccine does not rely on using attenuated or killed organisms as the vaccine. The lambda system also does not rely on the use of drug-resistant plasmid clones and expression of vaccine proteins from those clones. Additionally, because the lambda phage on which the vaccine is created is very specific for E. coli K12; it does not infect and spread in other organisms or even other E. coli subspecies. We have used recombineering to engineer phage lambda to display foreign proteins or segments of proteins on the lambda capsid surface. The lambda capsid D protein is present in 320 copies, and we have displayed on lambda foreign peptides fused to either the N or C terminus of the D protein. These modified phages can be produced in bulk, purified and used as vaccine delivery vehicles. We initiated this phage vector system to display cancer proteins on lambda particles pursue creation of cancer vaccines.", "keywords": [ "Antigens", "Attenuated", "Bacteriophage lambda", "Bacteriophages", "COVID-19", "Cancer Vaccines", "Capsid", "Capsid Proteins", "Coronavirus", "Disease", "Disease Outbreaks", "Drug resistance", "Drug usage", "Engineering", "Epitopes", "Escherichia coli", "Escherichia coli K12", "Human", "Malignant Neoplasms", "Organism", "Peptides", "Plasmids", "Proteins", "Surface", "System", "Time", "Vaccine Production", "Vaccines", "Virus", "delta protein", "particle", "vaccine delivery", "vector" ], "approved": true } }, { "type": "Grant", "id": "7806", "attributes": { "award_id": "1ZICMH002888-14", "title": "Scientific and Statistical Computing Core", "funder": { "id": 4, "ror": "https://ror.org/01cwqze88", "name": "National Institutes of Health", "approved": true }, "funder_divisions": [ "National Institute of Mental Health (NIMH)" ], "program_reference_codes": [], "program_officials": [], "start_date": null, "end_date": null, "award_amount": 1962771, "principal_investigator": { "id": 23617, "first_name": "Robert", "last_name": "Cox", "orcid": null, "emails": "", "private_emails": "", "keywords": null, "approved": true, "websites": null, "desired_collaboration": null, "comments": null, "affiliations": [ { "id": 1604, "ror": "https://ror.org/04xeg9z08", "name": "National Institute of Mental Health", "address": "", "city": "", "state": "MD", "zip": "", "country": "United States", "approved": true } ] }, "other_investigators": [], "awardee_organization": { "id": 1604, "ror": "https://ror.org/04xeg9z08", "name": "National Institute of Mental Health", "address": "", "city": "", "state": "MD", "zip": "", "country": "United States", "approved": true }, "abstract": "The principal mission of the Core is to help NIH researchers with analyses of their fMRI (brain activation mapping) and structural MRI (brain anatomy) data. Along the way, we also help non-NIH investigators, many in the USA but also some abroad. Several levels of help are provided, from short-term immediate aid to long-term development and planning. Consultations: The shortest-term help comprises in-person consultations with investigators about issues that arise in their research. The issues involved are quite varied, since there are many steps in carrying out fMRI and MRI data analyses and there are many different types of experiments. Common problems include: - How to set up experimental design so that data can be analyzed effectively? - Interpretation and correction of MRI imaging artifacts (for example: participant head motion during scanning; image warping due to magnetic field anomalies). - How to set up time series analysis to extract brain activation effects of interest, and to suppress non-activation artifacts (e.g., from breathing)? - Why don't AFNI results agree with SPM/FSL/other software? - How to analyze data to reveal connections between brain regions during specific mental tasks, or at rest? - How to recognize poor quality data? - How to carry out reliable inter-patient (group) statistical analysis, especially when non-MRI data (e.g., genetic information, age, disease rating) needs to be incorporated? - How to get good registration between the functional results and the anatomical reference images, and between the brain images from different participants? - What sequence of programs is \"best\" for analyzing a particular kind of data? - Reports of real or imagined bugs in the AFNI software, as well as feature requests (small, large, extravagant). - Analysis problems related to diffusion weighted MRI data, which are acquired to reveal anatomical connections in the brain. There are familiar themes in many of these consultations, but each meeting and each experiment raises unique questions, and requires digging into the goals and details of the research project in order to ensure that nothing critical is being overlooked. The first question asked by a user is often not the right question at all. Complex statistical or data processing issues are often raised. Often, software needs to be developed or modified to help researchers answer their specific questions. Helping with the Methods sections of papers, or with responses to reviewers, is often part of our duties. Educational Efforts: The Core developed (and updated) a 40-hour hands-on course on how to design and analyze fMRI data that was taught once at the NIH during FY 2020 to about 200 students. All material for this continually evolving course (software, sample data, scripts, PDF slides, captioned videos) are freely available on our Web site (https://afni.nimh.nih.gov). The course material includes sample datasets, used to illustrate the entire process, starting with images output by MRI scanners and continuing through to the collective statistical analysis of groups of participants. The Covid-19 pandemic canceled the Spring 2020 NIH course; instead, we accelerated our production of AFNI Academy videos. By invitation, and prior to Covid-19. we also taught versions of this course at 4 non-NIH sites (expenses for these trips were sponsored by the hosts). More than 1000 AFNI forum postings were made by Core members, mostly in answer to queries from users. Algorithm and Software Development: The longest-term support consists of developing (or adapting) new methods and software for MRI data analysis, both to solve current problems and in anticipation of new needs. All of our software is incorporated into the AFNI package, which is Unix/Linux/Macintosh-based open-source and is available for download by anyone in source code (GitHub) or binary formats (Core server). New programs are created, and old programs modified, in response to specific user requests and in response to the Core's vision of what will be needed in the future. The Core also assists NIH labs in setting up computer systems for use with AFNI and maintains an active Web site with a forum for questions (and answers) about (f)MRI data analysis. Notable developments during FY 2020 include: - A set of new detailed instructional videos for using AFNI was created: the AFNI Academy. This collection will continue to grow into 2021 (at least). - A technique for detecting left-right flipping of human brain images was developed when Core staff noticed that a few percent of downloadable open datasets were marked with the wrong spatial orientation. This tool is now included in the AFNI standard data processing stream. - The Bayesian region of interest (ROI) analysis tools mentioned in last year's reports have been significantly extended to analyze new types of fMRI datasets, including connectivity (brain networks) and inter-participant correlations (e.g., during movie watching). - A standard processing pipeline for diffusion weighted MRI datasets was created, in collaboration with the Pierpaoli group in NIBIB. - A 5-day hackathon was held at the NIH campus in November 2019, attended by 20 neuroscience computational experts, and a number of projects were started as part of the Cores outreach efforts to the Open Source community. - Core staff presented at the (virtual) Organization for Human Brain Mapping Annual Meeting in 2020. - New quality control (QC) tools were added to the AFNI standard computing pipelines, making it easy for users to view summaries of the image processing steps and results, to help with data and analysis quality judgments (e.g., how many data points were corrupted by head motion). - A 3D Brodmann area brain atlas (human), and two 3D animal brain atlases were incorporated into AFNI. Public Health Impact: From Oct 2019 to Aug 2020, the principal AFNI publication has been cited in 477 papers (cf Scopus). Most of our work supports basic research into brain function, but some of our work is more closely tied to or applicable to specific diseases: - We collaborate with Dr. Alex Martin (NIMH) to apply our resting state analysis methods to autism spectrum disorder. - We consult frequently with NIMH researchers (e.g., Drs. Pine, Ernst, Grillon, Leibenluft) working in mood and anxiety disorders. - We consult with Dr. Elliot Stein (NIDA) in his research applying fMRI methods to drug abuse and addiction, and with Dr. Reza Momenan (NIAAA) in his studies of alcoholism. - We collaborate with Dr Ernesta Meintjes (U Cape Town) on data analysis of the effects of prenatal alcohol exposure on the brains of infants and toddlers. - Our instant 3D correlation tool is being used for mapping intact brain tissue in stroke patients, and for mapping brain connectivity to aid in deep-brain stimulation surgical planning. - Our precise registration tools (for aligning fMRI scans to anatomical reference scans) are important for individual participant applications of brain mapping, such as pre-surgical fMRI planning. - Our real-time fMRI software (first in the world) is being used for studies on brain mapping feedback in neurological disorders, is used daily for quality control at the NIH fMRI scanners, and is used at a few extramural sites. - Components of AFNI are being used in analyses of drug effects in human brain data, including studies of depression, drug abuse, psychosis, and smoking (based on citations in FY 2020).", "keywords": [ "3-Dimensional", "Academy", "Age", "Alcoholism", "Anatomy", "Animals", "Anxiety Disorders", "Atlases", "Basic Science", "Brain", "Brain Mapping", "Brain imaging", "Brain region", "Breathing", "Brodmann&apos", "s area", "COVID-19", "COVID-19 pandemic", "Collaborations", "Collection", "Communities", "Complex", "Computer Systems", "Computer software", "Consult", "Consultations", "Core Facility", "Data", "Data Analyses", "Data Reporting", "Data Set", "Deep Brain Stimulation", "Development", "Development Plans", "Diffusion Magnetic Resonance Imaging", "Disease", "Drug Addiction", "Drug abuse", "Educational process of instructing", "Ensure", "Experimental Designs", "Extramural Activities", "Feedback", "Fetal Alcohol Exposure", "Fetal alcohol effects", "Functional Magnetic Resonance Imaging", "Future", "Goals", "Head", "Hour", "Human", "Human Activities", "Image", "Individual", "Infant", "Institution", "Instruction", "Judgment", "Left", "Libraries", "Linux", "Literature", "MRI Scans", "Magnetic Resonance Imaging", "Mental Depression", "Methodology", "Methods", "Mission", "Mood Disorders", "Morphologic artifacts", "Motion", "National Institute of Biomedical Imaging and Bioengineering", "National Institute of Drug Abuse", "National Institute of Mental Health", "National Institute on Alcohol Abuse and Alcoholism", "Online Systems", "Operative Surgical Procedures", "Output", "Panic", "Paper", "Participant", "Patients", "Persons", "Pharmaceutical Preparations", "Process", "Production", "Psyche structure", "Psychotic Disorders", "Public Health", "Publications", "Quality Control", "Reporting", "Research", "Research Personnel", "Research Project Grants", "Rest", "Sampling", "Scanning", "Site", "Slide", "Smoking", "Software Tools", "Source Code", "Space Perception", "Statistical Computing", "Statistical Data Interpretation", "Stream", "Structure", "Students", "Techniques", "Technology", "Time", "Time Series Analysis", "Toddler", "United States National Institutes of Health", "Update", "Vision", "Work", "algorithm development", "animal data", "autism spectrum disorder", "base", "brain tissue", "computational neuroscience", "computerized data processing", "data quality", "data standards", "design", "experimental study", "flexibility", "genetic information", "gigabyte", "hackathon", "human data", "image processing", "image warping", "imaging modality", "imaging software", "interest", "learning" ], "approved": true } }, { "type": "Grant", "id": "7813", "attributes": { "award_id": "1ZIADA000632-01", "title": "Changes in Substance Use Following COVID-19: Harnessing Digital Phenotyping", "funder": { "id": 4, "ror": "https://ror.org/01cwqze88", "name": "National Institutes of Health", "approved": true }, "funder_divisions": [ "National Institute on Drug Abuse (NIDA)" ], "program_reference_codes": [], "program_officials": [], "start_date": null, "end_date": null, "award_amount": 274468, "principal_investigator": { "id": 23623, "first_name": "Brenda", "last_name": "Curtis", "orcid": null, "emails": "", "private_emails": "", "keywords": null, "approved": true, "websites": null, "desired_collaboration": null, "comments": null, "affiliations": [ { "id": 1626, "ror": "https://ror.org/00fq5cm18", "name": "National Institute on Drug Abuse", "address": "", "city": "", "state": "MD", "zip": "", "country": "United States", "approved": true } ] }, "other_investigators": [], "awardee_organization": { "id": 1626, "ror": "https://ror.org/00fq5cm18", "name": "National Institute on Drug Abuse", "address": "", "city": "", "state": "MD", "zip": "", "country": "United States", "approved": true }, "abstract": "The Covid-19 pandemic is a major global and national health emergencyand although it should be unnecessary to point that out, there are places where it is not yet believed, making the emergency all the more dire. Across the US, Covid-19 is disproportionately impacting communities of color, people with lower incomes, and people who lack stable housing. The Covid-19 pandemic is also colliding with a preexisting and ongoing pandemic: substance use disorders (SUDs). People with SUDs are particularly vulnerable to the health, social, and economic impacts of Covid-19and the number of people with SUDs is likely to increase with the economic and psychological stress of Covid-19. The aims of this project are to 1) investigate the effects of the Covid-19 pandemic on drug use, drug-related behaviors, and consequences of drug use, in people with and without SUDs at the start of the study; 2) investigate bidirectional effects between the Covid-19 pandemic and access/adherence to treatment, in people who have or develop SUDs; and 3) improve methodology for detection of daily-life behavioral markers of (a) movement patterns, (b) social interactions, support, and distancing, (c) substance use, (d) resilience and wellbeing, and (e) psychological problems (including pandemic-specific problems).", "keywords": [ "Adherence", "Alcohol consumption", "Alcohol or Other Drugs use", "Algorithms", "Behavior", "Behavioral", "COVID-19", "COVID-19 pandemic", "Color", "Communities", "Data", "Detection", "Drug usage", "Economics", "Emergency Situation", "Enrollment", "Environment", "Geographic Locations", "Health", "Housing", "Incidence", "Knowledge", "Life", "Low income", "Measures", "Mental Health", "Methodology", "Movement", "Overdose", "Participant", "Patients", "Pattern", "Personal Satisfaction", "Pharmaceutical Preparations", "Phenotype", "Policies", "Psychological Stress", "Recommendation", "Relapse", "Risk", "Safety", "Shelter facility", "Social Impacts", "Social Interaction", "Substance Use Disorder", "Symptoms", "Time", "Trauma", "United States", "Withdrawal", "alcohol use disorder", "coronavirus disease", "digital", "economic impact", "experience", "improved", "medication-assisted treatment", "opioid use disorder", "pandemic disease", "psychologic", "psychosocial", "resilience", "smartphone Application", "substance misuse", "temporal measurement", "tool", "treatment adherence" ], "approved": true } }, { "type": "Grant", "id": "7815", "attributes": { "award_id": "1ZIADK075112-06", "title": "The Molecular, Cellular, and Genetic characterization of Human Adipose Tissue and its Role in Metabolism", "funder": { "id": 4, "ror": "https://ror.org/01cwqze88", "name": "National Institutes of Health", "approved": true }, "funder_divisions": [ "National Institute of Diabetes and Digestive and Kidney Diseases (NIDDK)" ], "program_reference_codes": [], "program_officials": [], "start_date": null, "end_date": null, "award_amount": 252781, "principal_investigator": { "id": 23625, "first_name": "Aaron", "last_name": "Cypess", "orcid": null, "emails": "", "private_emails": "", "keywords": null, "approved": true, "websites": null, "desired_collaboration": null, "comments": null, "affiliations": [ { "id": 1600, "ror": "https://ror.org/00adh9b73", "name": "National Institute of Diabetes and Digestive and Kidney Diseases", "address": "", "city": "", "state": "MD", "zip": "", "country": "United States", "approved": true } ] }, "other_investigators": [], "awardee_organization": { "id": 1600, "ror": "https://ror.org/00adh9b73", "name": "National Institute of Diabetes and Digestive and Kidney Diseases", "address": "", "city": "", "state": "MD", "zip": "", "country": "United States", "approved": true }, "abstract": "The initial reports about human BAT distribution and lack of plasma biomarkers indicated that it would be a particularly challenging organ to study. An acute need was the precise anatomical localization of the tissue and the availability of human-derived brown and white fat progenitor cell models to understand its distinct physiology. In collaboration with Yu-Hua Tseng at Harvard Medical School, my group first reported the anatomical localization of the tissue and showed that human neck BAT shared the same developmental lineage as rodent interscapular BAT, the principal model system used for more than half a century. In collaboration with C. Ronald Kahn, we identified cell surface markers of white, brown, and beige human adipocytes that could be used to isolate and study the different adipocyte lineages. In parallel, Dr. Tseng's group generated clonal cell lines from human neck fat and characterized their adipogenic differentiation and metabolic function in vitro and in vivo after transplantation into immune deficient nude mice. Using clonal analysis and gene expression profiling, we identified unique sets of gene signatures in human preadipocytes that could predict the thermogenic potential of these cells once matured in culture into adipocytes. These data highlight the cellular heterogeneity in human BAT and WAT and provide novel gene targets to prime preadipocytes for thermogenic differentiation. Additional discoveries included the demonstration that altered miRNA processing disrupts brown/white adipocyte determination and associates with lipodystrophy; HIV-infected subjects with metabolic complications demonstrate increases in FGF21 in relationship to BAT gene expression; and IRF4 is a transcriptional driver of a program of thermogenic gene expression and energy expenditure. In collaboration with Kong Chen, Acting Chief of the Energy Metabolism Section, and Peter Herscovitch, Chief of the Positron Emission Tomography Department in the CRC, we have completed the first version of an PET/CT-based atlas of human BAT known as the BATlas 1.0. Anatomical and functional information about each depot is being catalogued as part of the larger effort of understanding the function and structure of the human brown and white adipose tissue mass. We are now in the process of expanding this collaboration with Bradford Wood, Director of NIH Center for Interventional Oncology, to be able to collect ultrasound-guided biopsies of the BAT. Recent collaborations with Dr. Siegfried Ussar and Dr. Chad Hunter have been established to better define human BAT lineage and adipogenesis. In addition, the ability of BAT activation to improve insulin sensitivity will be considered in the context of Covid-19 since patients with dysglycemia are at increased risk for complications. We will also determine if BAT is susceptible to Covid-19 entry.", "keywords": [ "Acute", "Adipocytes", "Adipose tissue", "Adult", "Anatomy", "Atlases", "Biological Markers", "Biological Models", "Biopsy", "COVID-19", "Catalogs", "Cell model", "Cell surface", "Cells", "Chad", "Clone Cells", "Collaborations", "Data", "Development", "Energy Metabolism", "FGF21 gene", "Fatty acid glycerol esters", "Gene Expression", "Gene Expression Profiling", "Gene Targeting", "Genetic", "Genetic Transcription", "Growth", "HIV", "Heterogeneity", "Human", "Human Cell Line", "IRF4 gene", "Immune", "In Vitro", "Intervention", "Lead", "Lipodystrophy", "Maps", "Metabolic", "Metabolism", "MicroRNAs", "Molecular", "Neck", "Nude Mice", "Oncology", "Organ", "PET/CT scan", "Patients", "Physiological", "Physiology", "Plasma", "Positron-Emission Tomography", "Process", "Reporting", "Risk", "Rodent", "Role", "Structure", "Testing", "Tissues", "Transplantation", "Ultrasonography", "United States National Institutes of Health", "Wood material", "base", "genetic signature", "improved", "in vivo", "insulin sensitivity", "lipid biosynthesis", "medical schools", "novel", "programs", "stem cells" ], "approved": true } }, { "type": "Grant", "id": "9536", "attributes": { "award_id": "2030139", "title": "Compounding Crises: Facing Hurricane Season in the Era of COVID-19", "funder": null, "funder_divisions": [], "program_reference_codes": [ "CK090", "RND123" ], "program_officials": [], "start_date": null, "end_date": null, "award_amount": 199890, "principal_investigator": null, "other_investigators": [], "awardee_organization": null, "abstract": "Test", "keywords": [ "covid", "research" ], "approved": true } }, { "type": "Grant", "id": "11681", "attributes": { "award_id": "1U01DA057849-01", "title": "Supported employment to create a community culture of SARS-CoV-2 rapid testing among people who inject drugs: PeerConnect2Test", "funder": { "id": 4, "ror": "https://ror.org/01cwqze88", "name": "National Institutes of Health", "approved": true }, "funder_divisions": [], "program_reference_codes": [], "program_officials": [], "start_date": null, "end_date": null, "award_amount": null, "principal_investigator": { "id": 26966, "first_name": "Camille C", "last_name": "Cioffi", "orcid": "https://orcid.org/0000-0003-2424-7473", "emails": "[email protected]", "private_emails": null, "keywords": "[]", "approved": true, "websites": "['psi.uoregon.edu']", "desired_collaboration": "", "comments": "", "affiliations": [] }, "other_investigators": [], "awardee_organization": null, "abstract": "", "keywords": [], "approved": true } } ], "meta": { "pagination": { "page": 1392, "pages": 1392, "count": 13920 } } }