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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   

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http://www.prostatitis.org/symptomindex.html

Questionnaire developed by physicians in NIDDK's Chronic Prostatitis Collaborative Research Network that can help physicians to accurately measure the severity of prostatitis symptoms and their impact on a patient's lifestyle. The CPSI questionnaire assesses pain, urination, and the effect of chronic prostatitis on daily activities. With this information, researchers and physicians can reliably evaluate whether potential treatments are working. The questionnaire was originally published in the Journal of Urology in August 1999 (Vol. 162, pages 369-375). It is available as a PDF document in English, Spanish, German and Korean.

Proper citation: NIH Chronic Prostatitis Symptom Index (RRID:SCR_001482) Copy   

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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   

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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   

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https://www.medibeacon.com/science/preclinical/

Transdermal Glomerular Filtration Rate monitor used to assess renal function in mouse and rat models of acute kidney injury and chronic kidney disease.

Proper citation: MediBeacon: Transdermal GFR Monitor (RRID:SCR_024533) Copy   

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https://masst.gnps2.org/microbemasst/

Web taxonomically informed mass spectrometry search tool, tackles limited microbial metabolite annotation in untargeted metabolomics experiments. Leveraging database of over 60,000 microbial monocultures, users can search known and unknown MS/MS spectra and link them to their respective microbial producers via MS/MS fragmentation patterns.

Proper citation: microbeMASST (RRID:SCR_024713) Copy   

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http://metscape.ncibi.org

A software program that allows users to visualize and interpret human metabolim and expression profiling data by providing users with a bioinformatics framework. Its features include bulding and analyzing networks of genes and compounds, identifying enriched pathways from expression profiling data, and visualizing changes in metabolite data.

Proper citation: Metscape (RRID:SCR_014687) Copy   

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https://www.sanger.ac.uk/collaboration/sequencing-idd-regions-nod-mouse-genome/

Genetic variations associated with type 1 diabetes identified by sequencing regions of the non-obese diabetic (NOD) mouse genome and comparing them with the same areas of a diabetes-resistant C57BL/6J reference mouse allowing identification of single nucleotide polymorphisms (SNPs) or other genomic variations putatively associated with diabetes in mice. Finished clones from the targeted insulin-dependent diabetes (Idd) candidate regions are displayed in the NOD clone sequence section of the website, where they can be downloaded either as individual clone sequences or larger contigs that make up the accession golden path (AGP). All sequences are publicly available via the International Nucleotide Sequence Database Collaboration. Two NOD mouse BAC libraries were constructed and the BAC ends sequenced. Clones from the DIL NOD BAC library constructed by RIKEN Genomic Sciences Centre (Japan) in conjunction with the Diabetes and Inflammation Laboratory (DIL) (University of Cambridge) from the NOD/MrkTac mouse strain are designated DIL. Clones from the CHORI-29 NOD BAC library constructed by Pieter de Jong (Children's Hospital, Oakland, California, USA) from the NOD/ShiLtJ mouse strain are designated CHORI-29. All NOD mouse BAC end-sequences have been submitted to the International Nucleotide Sequence Database Consortium (INSDC), deposited in the NCBI trace archive. They have generated a clone map from these two libraries by mapping the BAC end-sequences to the latest assembly of the C57BL/6J mouse reference genome sequence. These BAC end-sequence alignments can then be visualized in the Ensembl mouse genome browser where the alignments of both NOD BAC libraries can be accessed through the Distributed Annotation System (DAS). The Mouse Genomes Project has used the Illumina platform to sequence the entire NOD/ShiLtJ genome and this should help to position unaligned BAC end-sequences to novel non-reference regions of the NOD genome. Further information about the BAC end-sequences, such as their alignment, variation data and Ensembl gene coverage, can be obtained from the NOD mouse ftp site.

Proper citation: Sequencing of Idd regions in the NOD mouse genome (RRID:SCR_001483) Copy   

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http://amp.pharm.mssm.edu/X2K/

Software tool to produce inferred networks of transcription factors, proteins, and kinases predicted to regulate the expression of the inputted gene list by combining transcription factor enrichment analysis, protein-protein interaction network expansion, with kinase enrichment analysis. It provides the results as tables and interactive vector graphic figures.

Proper citation: eXpression2Kinases (RRID:SCR_016307) Copy   

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https://psbweb05.psb.ugent.be/conet/microbialnetworks/spieceasi.php

Software R package estimates inverse covariance matrix from sequencing data.Statistical method for inference of microbial ecological networks from amplicon sequencing datasets.

Proper citation: Sparse Inverse Covariance Estimation for Ecological Association Inference (RRID:SCR_022646) Copy   

•   Source: SciCrunch Registry

https://github.com/compbiolabucf/TEDDY

Software package to impute gene expression for all participants, whether they have partially or completely missing gene expression.

Proper citation: Teddy study IA prediction (RRID:SCR_023303) Copy   

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http://www.t1diabetes.nih.gov/t1d-raid/index.shtml

NOTE: The T1D-RAID program is not currently accepting applications. Cooperative program that makes available, on a competitive basis, NCI resources for the pre-clinical development of drugs, natural products, and biologics to facilitate translation to the clinic of novel, scientifically meritorious therapeutic interventions for type 1 diabetes and its complications. A partial listing of those services includes: high-throughput screening, studies in animal models, formulation, pharmacology and toxicology studies, and bulk substances acquisition. Requests to T1D-RAID are brief (20 pages or less), and should clearly outline the resources required to ready the proposed therapeutic agent for clinical trials. T1D-RAID should enable entry into the clinic of promising molecules that are not otherwise likely to receive an adequate and timely clinical test. T1D-RAID is designed to accomplish the tasks that are rate-limiting in bringing discoveries from the laboratory to the clinic. Once a project has been approved, NIDDKstaff interact directly with the Principal Investigator (PI). NCI contractors perform the T1D-RAID-approved tasks under the direction of NIDDKand NCI staff. The required tasks will vary from project to project. In some cases T1D-RAID will support only one or two key missing steps necessary to bring a compound to the clinic; in other cases it may be necessary to supply the entire portfolio of development requirements needed to file an IND. Examples of tasks that can be supported by T1D-RAID include, but are not limited to: * Definition or optimization of dose and schedule for in vivo activity * Development of pharmacology assays * Conduct of pharmacology studies with a pre-determined assay * Acquisition of bulk substance (GMP and non-GMP) * Scale-up production from lab-scale to clinical-trials lot scale * Development of suitable formulations * Development of analytical methods for bulk substances * Production of dosage forms * Stability assurance of dosage forms * Range-finding initial toxicology * IND-directed toxicology, with correlative pharmacology and histopathology * Planning of clinical trials * Regulatory affairs, so that FDA requirements are likely to be satisfied by participating investigators seeking to test new molecular entities in the clinic * IND filing advice The output of T1D-RAID activities will be both products and information that will be made fully available to the originating investigator for support of an IND application and clinical trials. T1D-RAID does not sponsor clinical trials.

Proper citation: Type 1 Diabetes - Rapid Access to Intervention Development (RRID:SCR_000203) Copy   

•   Source: SciCrunch Registry

https://labnodes.vanderbilt.edu/community/profile/id/2228

THIS RESOURCE IS NO LONGER IN SERVICE. Documented on August 13,2025.Core facility that provides access to isolated pancreatic islets from normal and diabetic models and performs islet functional analysis. The IPA Core also provides solutions for high-resolution whole slide imaging and access to image analysis tools for quantitative assessment of pancreatic islet morphology.

Proper citation: Vanderbilt Diabetes Research and Training Center Islet Procurement and Analysis Core (RRID:SCR_000896) Copy   

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http://www.med.upenn.edu/idom/drc/cores/mouse.html

Core which provides researchers with resources for performing metabolic studies in mice. It also provides services, innovative techniques, and helpful consultation to both experienced and novice investigators with regards to metabolic questions.

Proper citation: Penn Diabetes Research Center Mouse Phenotyping Physiology and Metabolism Core (RRID:SCR_000888) Copy   

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http://archives.niddk.nih.gov/patient/crisp/rp-crisp.aspx

A five-year prospective cohort study following 240 patients who have autosomal-dominant polycystic kidney disease (PKD) to determine whether changes in anatomic characteristics of their kidneys as measured by magnetic resonance imaging will be useful in providing surrogate measures for disease progression. CRISP's overall goal is to develop methods that would facilitate shortening the observation period necessary to determine efficacy of treatment interventions in PKD patients. Specific goals of this study are to: * Quantify cyst growth and ascertain severity of renal parenchymal involvement by sequential measurement of total kidney volume and the ratio of intact parenchyma to renal parenchyma occupied by cysts over time * Establish useful clinical correlations of imaging data with other markers of disease progression * Identify and test other potential markers or indices of disease progression, for example, assessment of loss of heterozygosity of renal cells shed in the urine, or other markers, in cohorts of patients with PKD * Gain information about the cost-effectiveness, patient acceptability, and advantages and disadvantages of different imaging techniques used serially in patients with PKD. Some experience has been gained in establishing that repeat imaging of the same PKD patient, using these techniques, yields reproducible estimates of kidney size and the proportion of renal parenchyma occupied by cysts. MRI may also have the advantage of permitting simultaneous estimation of GFR. Ultrasound has the advantage of being more cost-effective and perhaps more acceptable to patients for repetitive studies, but the measurements may be less accurate and reproducible. Nonetheless, there is very limited experience in applying these techniques to follow progression of the renal disease. Development of improved, reproducible imaging methods that assess cyst growth and provide markers of disease progression could markedly improve the feasibility of clinical trials. Participating clinical centers are Emory University, the Mayo Clinic, University of Kansas, and the University of Alabama at Birmingham. The data coordinating and imaging analysis center is at Washington University. (PI has since moved to University of Pittsburgh) The study found that kidney enlargement resulting from the expansion of cysts is continuous, quantifiable, and associated with the decline of renal function. Cystic expansion occurs at a consistent rate per individual, although it is heterogeneous in the population, and that larger kidneys are associated with more rapid decrease in renal function. These anatomic characteristics of patient kidneys may provide useful surrogate measures for disease progression, and hence enhance the development of targeted therapies for autosomal dominant PKD. CRISP III is a five-year prospective cohort study to follow ~170 remaining autosomal dominant polycystic kidney disease (ADPKD) patients who were part of the original CRISP cohort study. CRISP III will verify and extend the preliminary observations of CRISP to determine the extent to which quantitative (kidney volume and blood flow, and hepatic and kidney cyst volume) or qualitative (cyst distribution and character) structural parameters predict renal insufficiency and develop and test new metrics to quantify and monitor disease progression. Urine metabolites and the genome will be correlated with the progression of disease to look for new, predictive disease biomarkers. This information from CRISP III will help determine if the kidney enlargement, blood flow, cyst distribution, or urine metabolites can function as an informative surrogate measure for disease progression.

Proper citation: Consortium for Radiologic Imaging Studies of Polycystic Kidney Disease (RRID:SCR_000690) Copy   

•   Source: SciCrunch Registry

https://www.clinicaltrials.gov/study/NCT00021814

Multi-center double-masked, placebo-controlled randomized clinical trial designed to evaluate the long-term efficacy of finasteride, or doxazosin, or the combination of both, in delaying or preventing the clinical progression of symptomatic benign prostatic hyperplasia (BPH). MTOPS was the largest and longest study to test whether drug therapy can prevent or delay the noncancerous growth of the prostate. A unique feature of MTOPS that has not been done in prior studies of pharmacotherapy of BPH is the biopsy substudy. A total of 1,082 volunteers from the 2,931 participants randomized during the full-scale phase are currently participating in this substudy. Biopsies of the prostate will be obtained on these volunteers at predetermined times during the course of the trial to evaluate the status of the prostate at key event times. The purpose of the substudy was to provide additional information regarding the histopathobiology of BPH and to test existing biomarkers for their prognostic ability regarding response to drug therapy.

Proper citation: Medical Therapy of Prostatic Symptoms (RRID:SCR_001556) Copy   

•   Source: SciCrunch Registry

http://www.ndep.nih.gov/

Federal government public education program that promotes diabetes prevention and control. They aim to reduce the morbidity and mortality associated with diabetes and its complications. The NDEP is jointly sponsored by the National Institutes of Health and the Centers for Disease Control and Prevention and over 200 partner organizations. Target audiences include people with diabetes and those at risk, including the racial and ethnic populations disproportionately affected by the disease, health care providers and payers and purchasers of health care.

Proper citation: National Diabetes Education Program (RRID:SCR_001477) Copy   

•   Source: SciCrunch Registry

http://www.bsc.gwu.edu/dpp/protocol.htmlvdoc

Observational clinical trial studying the long term effect of diet and exercise and the diabetes medication, metformin, on the delay of type 2 diabetes in participants of the Diabetes Prevention Program (DPP). The Diabetes Prevention Program (DPP) was a multi-center trial examining the ability of an intensive lifestyle or metformin to prevent or delay the development of diabetes in a high risk population due to the presence of impaired glucose tolerance (IGT). The DPP has ended early demonstrating that lifestyle reduced diabetes onset by 58% and metformin reduced diabetes onset by 31%. The DPPOS is designed to take advantage of the scientifically and clinically valuable DPP participants. This group of participants is nearly 50% minority and represents the largest IGT population ever studied. Clinically important research questions remain that focus on 1)durability of the prior DPP intervention, 2) determination of the clinical course of precisely known new onset diabetes, in particular regarding CVD, CVD risk factors and atherosclerosis and microvascular disease, 3)close examination of these topics in men vs women and in minority populations. More than 87% of the original surviving DPP cohort has joined DPPOS as of December, 2007 and, to date, after 5 years of DPPOS and 10 years of combined DPP/DPPOS, 93% of the DPPOS cohort continue to attend annual follow-up visits. Interim analyses performed after 5 years of DPPOS have demonstrated a durable effect of diabetes prevention associated with the lifestyle and metformin interventions with 34 and 19% reductions in diabetes incidence, respectively, compared with the placebo group. Interim analyses also reveal significant reductions from baseline in CVD risk factors in the lifestyle intervention group, but with decreased utilization of glucose-lowering and lipid-lowering medications. Analyses of the participants in the placebo group who have developed diabetes during DPP/DPPOS, compared with those who have remained non-diabetic, reveal an increased frequency of retinopathy and microalbuminuria. The current, updated protocol describes the DPPOS including the revisions incorporated to complete the second five-years of the study. DPPOS participants have blood samples stored at the time of each annual visit. Specimens are stored at the study CBL until after the primary study outcomes are reported. DNA samples were previously collected and are stored at the NIDDKsample repository for DPP participants.

Proper citation: Diabetes Prevention Program Outcomes Study (RRID:SCR_001502) Copy   

•   Source: SciCrunch Registry

https://www.lookaheadtrial.org

16-center, randomized clinical trial investigating the long-term health consequences of an intensive lifestyle intervention program designed to achieve and maintain weight loss by decreased caloric intake and increased physical activity in overweight volunteers with type 2 diabetes. The Look AHEAD cohort comprises approximately 5,000 overweight or obese participants with type 2 diabetes, aged 45-76. Participants were randomized to one of two interventions: an intensive lifestyle intervention designed to produce and sustain weight loss over the long term or a diabetes support and education arm. Participants will be followed for a total of 11 to 13.5 years from randomization. The primary hypothesis is that the incidence rate of the first post-randomization occurrence of a composite outcome, which includes * cardiovascular death (including fatal myocardial infarction and stroke), * non-fatal myocardial infarction, * hospitalized angina, and * non-fatal stroke, over a planned follow-up period of up to 13.5 years will be reduced among participants assigned to the Lifestyle Intervention compared to those assigned to the control condition, Diabetes Support and Education. Look AHEAD will also test for reductions in the incidence of three secondary composite outcomes and examine the effect of the intervention on cardiovascular disease risk factors, diabetes control and complications, general health, and quality of life, and psychological outcomes. The cost and cost-effectiveness of the Lifestyle Intervention relative to Diabetes Support and Education will be assessed. The Look AHEAD intensive lifestyle intervention ended September, 2012. Participants continue to be followed to determine the long-term effects of the intervention on health outcomes.

Proper citation: Look AHEAD (RRID:SCR_001490) Copy   

•   Source: SciCrunch Registry

https://repository.niddk.nih.gov/study/44

Randomized controlled clinical trial to understand how increasing hemodialysis to six times a week from the standard of three times a week may result in improved heart health. Subjects were recruited from dialysis units associated with designated Clinical Centers in the U.S. and Canada and followed for 1 year. Subjects will be randomized to either conventional hemodialyis Daily HD delivered for at least 2.5 hours (typically 3 to 4 hours), 3 days per week, or to more frequent hemodialysis delivered for 1.5 - 2.75 hours, 6 days per week. The study has two co-primary outcomes: 1) a composite of mortality with the change over 12 months in left ventricular mass by magnetic resonance imaging, and 2) a composite of mortality with the change over 12 months in the SF-36 RAND physical health composite (PHC) quality of life scale. In addition, main secondary outcomes have been designated for each of seven outcome domains: 1) cardiovascular structure and function (change in LV mass), 2) health-related quality of life/physical function (change in the PHC), 3) depression/burden of illness (change in Beck Depression Inventory), 4) nutrition (change in serum albumin), 5) cognitive function (change in the Trail Making Test B), 6) mineral metabolism (change in average predialysis serum phosphorus), and 7) clinical events (rate of non-access hospitalization or death). Hypertension and anemia are also main outcome domains, but without designation of single first priority outcomes.

Proper citation: Frequent Hemodialysis Network Daily Trial (RRID:SCR_001527) Copy   

•   Source: SciCrunch Registry