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http://www.uchicagoddrcc.org/research-cores/integrated-translational-research-core

Core that serves as both a central repository for all the samples and data shared by the other cores and a catalyst for interdisciplinary research.

Proper citation: University of Chicago Digestive Diseases Research Core Center Integrated Translational Research Core (RRID:SCR_015606) Copy   

•   Source: SciCrunch Registry

https://github.com/compbiolabucf/APA-Scan

Software Python tool for detection and visualization of annotated and potential alternative polyadenylation events in downstream 3'-UTR of gene among two different biological conditions. Used for detection and visualization of 3'-UTR alternative polyadenylation with RNA-seq and 3'-end-seq data.

Proper citation: APA-Scan (RRID:SCR_022974) Copy   

•   Source: SciCrunch Registry

https://generanger.maayanlab.cloud/gene/A2M?database=ARCHS4

Web server application that provides access to processed data about expression of human genes and proteins across human cell types, tissues, and cell lines from several atlases. Used to explore single gene expression across tissues and cell types.

Proper citation: GeneRanger (RRID:SCR_023622) Copy   

•   Source: SciCrunch Registry

https://targetranger.maayanlab.cloud/

Web server application that identifies targets from user inputted RNA-seq samples collected from cells we wish to target. By comparing inputted samples with processed RNA-seq and proteomics data from several atlases, TargetRanger identifies genes that are highly expressed in target cells while lowly expressed across normal human cell types, tissues, and cell lines.

Proper citation: TargetRanger (RRID:SCR_023621) Copy   

•   Source: SciCrunch Registry

https://repository.niddk.nih.gov/study/36

Data set and biosepecimens of a multi-center clinical trial to determine if treatment with beta-cell antigens can delay the onset of Type 1 Diabetes Mellitus (Type 1 DM) in non-diabetic relatives of persons with Type 1 DM. Insulin is a well characterized antigen specifically produced by beta-cells, and it was used for this purpose in the initial DPT-1 studies. The protocol for high risk subjects uses daily subcutaneous insulin injections and an annual course of intravenous insulin treatment, while the protocol for intermediate risk subjects uses daily doses of insulin administered orally. Neither injected nor oral insulin at the doses used were observed to delay or prevent diabetes, although further studies are needed to test whether oral insulin can delay diabetes in people in the intermediate risk group with high titers of insulin autoantibodies.

Proper citation: Diabetes Prevention Type 1 (RRID:SCR_001467) Copy   

•   Source: SciCrunch Registry

https://www.clinicaltrials.gov/study/NCT00360646

Prospective and retrospective registry of well-characterized cases of drug-induced liver disease. The goals of Network include the development of standardized procedures to identify and fully characterize bona fide cases of drug- and complementary and alternative medicines (CAM)-induced liver injury, and to conduct controlled, clinical studies that will include extensive collection of data, serum, DNA, and tissue specimens. Cases of liver injury due to herbal medications are also included. The network will also develop terminology and standardized definitions for DILI, and to develop causality assessment instruments that are sensitive, specific, and reproducible. DILIN is funded by a cooperative agreement and includes five clinical centers and a central data coordinating center. The research goals of DILIN are to: * Create a registry of carefully documented DILI cases * Identify clinical, immunological, and environmental risk factors for drug- and CAM-mediated hepatotoxicity * Create a bank of biological specimens consisting of DNA, plasma, and immortalized lymphocytes to facilitate detailed genetic analyses * Characterize the natural history of drug- and CAM-induced DILI for at least six months following enrollment * Develop the capability to recontact these individuals over an extended period of time so that additional studies exploring DILI mechanisms can be performed Two studies are being initiated by the network. In the Retrospective Study, the implicated drugs are restricted to isoniazid, phenytoin, combination clavulanic acid/amoxicillin, and valproic acid (Depakote), Nitrofurantoin, Trimethoprim-sulfamethoxazole, Minocycline, and Quinolone antibiotics. These drugs were chosen because they are frequently administered to patients not receiving other hepatotoxic drugs, making it easier to establish causality. Patients must be alive, and the date of onset of the DILI episode must be on or after January 1, 1994. In the Prospective Study, all incident cases of drug- and CAM-induced liver injury are being considered. Initial presentation to a healthcare professional must be within the previous six months. A detailed medication history of the implicated DILI drug together with all prescription, OTC, and herbal medications is being recorded. Liver and serological tests are being performed to characterize the injury and to exclude competing causes of liver injury. A blood sample is also being drawn for plasma storage and DNA isolation. These cases will be followed longitudinally to characterize the long-term effects of the DILI episode. For both studies, documented, clinically significant DILI must be recorded in the patient's medical charts so that a causal determination can be made. Patients will be excluded if they are unwilling or unable to provide a blood sample or participate in the genetics component. Children under two years of age at the time of enrollment are excluded due to blood-volume requirements. If you have patients who are eligible to participate in either study, please contact one the DILIN clinical sites. As a general policy, the National Institute of Diabetes and Digestive and Kidney Diseases (NIDDK) invites investigator-initiated research project applications for ancillary studies to ongoing, large-scale clinical trials, epidemiological studies, and disease databases supported by the Institute. These studies are focused on a wide range of diseases and conditions including diabetes, obesity, acute and chronic liver disease, chronic kidney disease, and benign prostatic hyperplasia, among others.

Proper citation: Drug-Induced Liver Injury Network (RRID:SCR_001524) Copy   

•   Source: SciCrunch Registry

http://www.med.umich.edu/mgpc/cores/vivo.htm

Core facility that consists of the following 4 distinct programs: In Vivo Small Animal Studies Program, Organoid/Enteroid Modeling Program, Biospecimens Banking Service, and Clinical Design and Statistics.

Proper citation: University of Michigan Center for Gastrointestinal Research In Vivo Animal and Human Studies Core (RRID:SCR_015608) Copy   

•   Source: SciCrunch Registry

http://www.uchicagoddrcc.org/research-cores/tissue-and-cell-analysis-core

Core whose services include anatomic pathology review of human and experimental animal tissues as well as consultation in the best approaches for such analyses, cost-effective and high quality processing and staining of formalin-fixed paraffin-embedded tissues, and making collections of human tissue and imaging technologies available to researchers.

Proper citation: University of Chicago Digestive Diseases Research Core Center Tissue and Cell Imaging Core (RRID:SCR_015607) Copy   

•   Source: SciCrunch Registry

https://cran.rstudio.com/web/packages/accucor/index.html

Software as isotope natural abundance correction algorithm that is needed especially for high resolution mass spectrometers. Natural abundance correction of mass spectrometer data.

Proper citation: AccuCor (RRID:SCR_023046) Copy   

•   Source: SciCrunch Registry

http://secrepedia.org

Encyclopedia of white and brown adipocyte secretome in mouse models and humans as key prerequisite to elucidating role of these mediators in normal physiology and disease.

Proper citation: Secrepedia (RRID:SCR_022590) Copy   

•   Source: SciCrunch Registry

https://github.com/FunctionalUrology/SpheroScan

Software tool for analyzing images of spheroids. Designed to streamline process of spheroid segmentation, area calculation, and downstream analysis of spheroid image data, and can help to standardize and accelerate analysis of spheroid assay results.

Proper citation: SpheroScan (RRID:SCR_023886) Copy   

•   Source: SciCrunch Registry

https://github.com/kwanjeeraw/metabox

Software R toolbox for thorough metabolomic data analysis, integration and interpretation. Metabox 2.0 is updated version of R package Metabox and includes several methods for data processing, statistical analysis, biomarker analysis, integrative analysis and data interpretation.

Proper citation: Metabox (RRID:SCR_024443) Copy   

•   Source: SciCrunch Registry

http://www.childrennetwork.org/

Database of clinical information and serum and tissue samples from children across the United States and Canada with Biliary Atresia, Idiopathic Neonatal Hepatitis, Cystic Fibrosis Liver Disease, Alagille Syndrome, Alpha-1 Antitrypsin Deficiency, Bile Acid Synthesis Defects, Mitochondrial Hepatopathies, and Progressive Familial Intrahepatic Cholestasis in order to facilitate research and to perform clinical, epidemiological, and therapeutic trials in these important pediatric liver diseases. Three NIDDK-funded consortia, Biliary Atresia Research Consortium (BARC), Cholestatic Liver Disease Consortium (CLiC), and the Cystic Fibrosis Liver Disease (CFLD) Network were consolidated to form ChiLDREN. Most of the ChiLDREN studies are natural history studies aimed at acquiring information and data that will provide a better understanding of these rare conditions. Participants will be asked to allow study personnel to obtain information from medical records and an interview, and to collect blood, urine, and tissue samples when clinically indicated, in order to understand the causes of these diseases and to improve the diagnosis and treatment of children with these diseases. All of the information obtained in these studies is confidential and no names or identifying information are used in the study.

Proper citation: Childhood Liver Disease Research and Education Network (RRID:SCR_001497) Copy   

•   Source: SciCrunch Registry

http://dknet.org/

The NIDDK Information Network (dkNET) is a community-based network to serve needs of basic and clinical investigators that includes large pools of data and research resources relevant to mission of National Institute of Diabetes and Digestive and Kidney Disease.

Proper citation: NIDDK Information Network (dkNET) (RRID:SCR_001606) Copy   

•   Source: SciCrunch Registry

https://edic.bsc.gwu.edu

Publications from a multi-center, longitudinal, observational study examining the risk factors associated with the long-term complications of type 1 diabetes. The study began in 1994 and follows the 1441 participants previously enrolled in the Diabetes Control and Complications Trial (DCCT), http://diabetes.niddk.nih.gov/dm/pubs/control/index.aspx. The primary aim of EDIC is to examine the long-term effects of conventional vs. intensive diabetes treatment received during the DCCT on the subsequent development and progression of microvascular, neuropathic and cardiovascular complications. This involves studying the influence of genetic factors and other factors such as HbA1c, blood pressure, lipid levels, and treatment modalities on the development and progression of these complications. Annual or biennial measurements (using DCCT methods, standardized protocols and central laboratories) of vascular events, albumin excretion, GFR, ECG, ankle-brachial BP index, serum lipids and HbA1c allows the following analyses: 1) continuation of intention-to-treat analyses to determine long-term effects of prior separation of glycemic levels; 2) risk factors for macrovascular outcomes; 3) correlation of progression of micro- and macrovascular outcomes. The current updated version of the EDIC Protocol is available for download. EDIC is made up of 28 clinical centers, one data coordinating center and one clinical coordinating center.

Proper citation: Epidemiology of Diabetes Interventions and Complications (RRID:SCR_001468) Copy   

•   Source: SciCrunch Registry

https://clinicaltrials.gov/study/NCT01619475

Study consisting of nine liver transplant centers with expertise in adult living-donor liver transplantation (LDLT) and a central data coordinating center to provide valuable information on the outcomes of adult to adult living donor liver transplantation (AALDLT) to aid decisions made by physicians, patients, and potential donors. The study will establish and maintain the infrastructure required to accrue and follow sufficient numbers of patients being considered for and undergoing AALDLT to provide generalizable data from adequately powered studies. The major aims of A2ALL are as follows: * Quantify the impact of choosing LDLT on the candidate for transplantation * Characterize the difference between LDLT and deceased donor liver transplant (DDLT) in terms of post-transplant outcomes, including patient and graft survival, surgical morbidity, and resource utilization on the recipient of a transplant * Determine the short- and long-term health and quality of life (QOL) impact of donation, including (a) morbidity after liver donation and (b) long-term health-related QOL of donors. * Standardize and assess the role of informed consent in affecting the decision to donate and satisfaction after living liver donation * Other aims include comparison of the severity of recurrence of hepatocellular carcinoma for DDLT versus LDLT, the systematic characterization of liver regeneration and function in donors and recipients, the evaluation of the differences in the immune response to LDLT versus DDLT, and the establishment of a robust data and sample repository on liver transplantation that may be used to study clinical and biological questions as new technologies and resources become available. Patients enrolled in the study will be followed and managed in a standardized fashion.

Proper citation: Adult to Adult Living Donor Liver Transplantation Cohort Study (RRID:SCR_001494) Copy   

•   Source: SciCrunch Registry

https://repository.niddk.nih.gov/study/119

Multi-center randomized clinical trial to determine if the addition of behavioral treatment to drug therapy for the treatment of urge incontinence will make it possible to discontinue the drug and still maintain a reduced number of accidents. The most popular treatments for urge incontinence are drug therapy and behavior therapy, each with its own limitations. In this clinical study, the Urinary Incontinence Treatment Network (UITN) aims to determine differences with the addition of behavioral treatment to drug therapy alone.

Proper citation: Behavior Enhances Drug Reduction of Incontinence (RRID:SCR_001495) Copy   

•   Source: SciCrunch Registry

http://pathology-anatomy.missouri.edu/research/diabetes.html

Standardization of c-peptide by calibrating C-peptide measurement to a reference method can increase comparability between laboratories. The C-peptide standardization program is supported to establish reliability in results and facilitate the conduct of international clinical trials. For c-peptide, purified or processed material shows significant matrix effects and cannot be used for calibration. The C-peptide program has evaluated the use of single donor and pooled specimens for use by manufacturers in the calibration of these assays and determined that this strategy will reduce C-peptide variability among different assay methods. The standardization process through manufacturer re-calibration is ongoing.

Proper citation: Standardization of C-peptide measurements (RRID:SCR_001499) Copy   

•   Source: SciCrunch Registry

http://www.healthystudy.org/

Primary prevention trial conducted in 42 middle schools at 7 locations across the US to impact risk factors for type 2 diabetes in adolescents. Students were recruited at the start of 6th grade (fall 2006) and followed to the end of 8th grade (spring 2009). Half of the schools were randomized to receive an intervention that integrated four components: the school nutrition environment, physical education class activities, behavior change initiatives, and educational and promotional communications activities.

Proper citation: HEALTHY study (RRID:SCR_001530) Copy   

•   Source: SciCrunch Registry

http://todaystudy.org/

Randomized, double blind, nationwide clinical trial to compare the efficacy and safety of three interventions to treat adolescents and youth with type 2 diabetes (T2D): (1) metformin alone, (2) metformin plus rosiglitazone, and (3) metformin plus an intensive lifestyle intervention called the TODAY Lifestyle Program (TLP). The secondary aims are to: compare and evaluate the safety of the three treatment arms; compare the effects of the three treatments on the pathophysiology of type 2 diabetes (T2D) with regards to beta cell function and insulin resistance, body composition, nutrition, physical activity and aerobic fitness, cardiovascular risk factors, microvascular complications, quality of life, and psychological outcomes; evaluate the influence of individual and family behaviors on treatment response; and compare the relative cost effectiveness of the three treatment arms. The study recruits patients over a three-year period and follows patients for a minimum of two years. Patients are randomized within two years of the diagnosis of T2D. Materials that were used for the study are made publicly available: * The TODAY Standard Diabetes Education (TSDE) program, developed especially for youth with type 2 diabetes. (All participants received the TSDE program) * The TODAY Lifestyle Program (TLP) that was among the treatments tested.

Proper citation: Treatment Options for type 2 Diabetes in Adolescents and Youth (RRID:SCR_001547) Copy   

•   Source: SciCrunch Registry