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https://spin.niddk.nih.gov/bax/software/TALOS-N/

Software package for prediction of protein backbone and sidechain torsion angles from NMR chemical shifts.

Proper citation: TALOS-N (RRID:SCR_022800) Copy   

•   Source: SciCrunch Registry

https://bioconductor.org/packages/release/bioc/html/Maaslin2.html

SoftwareR package that identifies microbial taxa correlated with factors of interest using generalized linear models and mixed models.Used for efficiently determining multivariable association between clinical metadata and microbial meta'omic features.

Proper citation: MaAsLin2 (RRID:SCR_023241) Copy   

•   Source: SciCrunch Registry

https://github.com/ParkerLab/ataqv

Software package for QC and visualization of ATAC-seq results. Used to examine aligned reads and report basic metrics, including reads mapped in proper pairs, optical or PCR duplicates, reads mapping to autosomal or mitochondrial references, ratio of short to mononucleosomal fragment counts, mapping quality, various kinds of problematic alignments.

Proper citation: ataqv (RRID:SCR_023112) Copy   

•   Source: SciCrunch Registry

https://github.com/qianli10000/mtradeR

Software R package implements Joint model with Matching and Regularization and simulation pipeline. Used to test association between taxa and disease risk, and adjusted for correlated taxa screened by pre-selection procedure in abundance and prevalence, individually.

Proper citation: mtradeR (RRID:SCR_022977) Copy   

•   Source: SciCrunch Registry

http://ubbmc.buffalo.edu/research/ibsos.php

Multi-center placebo-controlled randomized clinical trial to assess the short-term and long-term efficacy of cognitive behavior therapy (CBT) for irritable bowel syndrome (IBS) using two treatment delivery systems: self administered CBT and therapist administered CBT. Long term project goals are to develop an effective self-administered behavioral treatment program that can enhance the quality of patient care, improve clinical outcomes, and decrease the economic and personal costs of one of the most prevalent and intractable gastrointestinal disorders.

Proper citation: Irritable Bowel Syndrome Outcome Study (RRID:SCR_001504) Copy   

•   Source: SciCrunch Registry

https://www.clinicaltrials.gov/study/NCT00064753

Multi-center, randomized, double blind controlled clinical trial to determine whether treatment with a standard multivitamin augmented with high doses of folic acid, vitamin B6 and vitamin B12 reduces the rate of cardiovascular disease outcomes in renal transplant recipients relative to participants receiving a similar multivitamin that contains no folic acid. This study hopes to show that by reducing the level of homocysteine in the body, the risk of heart disease is also reduced among kidney transplant patients.

Proper citation: Folic Acid for Vascular Outcome Reduction in Transplantation (RRID:SCR_001505) Copy   

•   Source: SciCrunch Registry

https://clinicaltrials.gov/study/NCT00342927?term=AREA%5BBasicSearch%5D(NIDDK%20endocrine%20and%20diabetes)%20AND%20AREA%5BSponsorSearch%5D(NIDDK)%20AND%20AREA%5BOverallStatus%5D(NOT_YET_RECRUITING%20OR%20RECRUITING%20OR%20ACTIVE_NOT_RECRUITING)&rank=1

Multicenter observational study designed to identify genetic determinants of diabetic nephropathy. It is conducted in eleven U.S. clinical centers and a coordinating center, and with four ethnic groups (European Americans, African Americans, Mexican Americans, and American Indians). Two strategies are used to localize susceptibility genes: a family-based linkage study and a case-control study using mapping by admixture linkage disequilibrium (MALD). In the family-based study, probands with diabetic nephropathy are recruited with their parents and selected siblings. Linkage analyses will be conducted to identify chromosomal regions containing genes that influence the development of diabetic nephropathy or related quantitative traits such as serum creatinine concentration, urinary albumin excretion, and plasma glucose concentrations. Regions showing evidence of linkage will be examined further with both genetic linkage and association studies to identify genes that influence diabetic nephropathy or related traits. Two types of MALD studies are being done. One is a case-control study of unrelated individuals of Mexican American heritage in which both cases and controls have diabetes, but only the case has nephropathy. The other is a case-control study of African American patients with nephropathy (cases) and their spouses (controls) unaffected by diabetes and nephropathy; offspring are genotyped when available to provide haplotype data. The specific goals of this program: * Delineate genomic regions associated with the development and progression of renal disease(s) * Evaluate whether there is a genetic link between diabetic nephropathy and diabetic retinopathy * Improve outcomes * Provide protection for people at risk and slow the progression of renal disease * Help establish a resource for genetic studies of kidney disease and diabetic complications by creating a repository of genetic samples and a database * Encourage studies of the genetics of progressive renal disease

Proper citation: Family Investigation of Nephropathy of Diabetes (RRID:SCR_001525) Copy   

•   Source: SciCrunch Registry

https://clinicaltrials.gov/study/NCT01885559

Consortium established to design and implement clinical trials of treatments that might slow the progressive loss of renal function in Polycystic Kidney Disease (PKD). Two multicenter randomized, double-blind, placebo controlled clinical trials are running concurrently to study the efficacy of renin-angiotensin-aldosterone system blockade on the progression of cystic disease (kidney volume) and on the decline in renal function in autosomal dominant polycystic kidney disease (ADPKD). Study A is to study whether intensive ACE-I/ARB blockade decrease the progression of cystic disease compared to ACE-I monotherapy patients with early disease, relatively preserved renal function, and high-normal BP or hypertension. Study B is to study whether intensive ACE-I/ARB blockade as compared to ACE-I monotherapy slow the decline in kidney function, end-stage of renal disease, or death in the setting of standard blood pressure control in hypertensive patients with moderately advanced disease.

Proper citation: HALT PKD (RRID:SCR_001529) Copy   

•   Source: SciCrunch Registry

http://www.isletstudy.org/

Network of centers to conduct studies of islet transplantation in patients with type 1 diabetes to improve the safety and long-term success of methods for transplanting islets. It is the aim of this trial to improve methods of isolating islets, to improve techniques for the administering those transplanted islets; and to develop approaches to minimize the toxic effects of immunosuppressive drugs required for transplantation.

Proper citation: Clinical Islet Transplantation Study (RRID:SCR_001515) Copy   

•   Source: SciCrunch Registry

https://sites.cscc.unc.edu/cscc/projects/RIVUR%20

Multicenter, randomized, double-blind, placebo-controlled trial is designed to determine whether daily antimicrobial prophylaxis is superior to placebo in preventing recurrence of urinary tract infection (UTI) in children with vesicoureteral reflux (VUR). The basic eligibility criteria are: (1) age at randomization of at least 2 months, but less than 6 years, (2) a diagnosed first febrile or symptomatic UTI within 42 days prior to randomization that was appropriately treated, and (3) presence of Grade I-IV VUR based on voiding cystourethrogram (VCUG). Patients will be randomly assigned to treatment for 2 years with daily antimicrobial prophylaxis (trimethoprim-sulfamethoxazole) or placebo. The study is designed to recruit 600 children (approximately 300 in each treatment group) over an 18-24 month period. The primary endpoint is recurrence of UTI. In addition, patients will be evaluated for secondary endpoints related to renal scarring and antimicrobial resistance. Scarring will be determined based on renal scintigraphy by 99mTc dimercaptosuccinic (DMSA) scan. Quality of life, compliance, safety parameters, utilization of health resources, and change in VUR will be assessed periodically throughout the study.

Proper citation: RiVuR (RRID:SCR_001539) Copy   

•   Source: SciCrunch Registry

http://cihd.cores.utah.edu/mgd/

Core facility which provides custom TALEN and Crispr-Cas9 DNA nucleases to induce targeted mutations in a genomic region of interest. It also provides hardware, reagents, and expertise for optimizing and performing HRMA for genes of interest.

Proper citation: Center for Iron and Heme Disorders at the University of Utah Mutation Generation and Detection Core (RRID:SCR_015339) Copy   

•   Source: SciCrunch Registry

http://animalcare.umich.edu/business-services/germ-free-mouse-facility

Core that provides services to the University of Michigan community and can also ship germ-free mice to locations worldwide. Its projects include studies investigating inflammatory bowel disease and cancer, host microbiome interactions, infectious disease pathogenesis, and mammalian and bacterial metabolism.

Proper citation: MMPC-University of Michigan Medical School Animal Care and Germ-Free Mouse Core (RRID:SCR_015344) Copy   

•   Source: SciCrunch Registry

http://medicine.iupui.edu/ICBM

Core facility which provides access to and training on optical microscopy instruments to Indiana University researchers.

Proper citation: Indiana University Cooperative Center of Excellence in Hematology Optical Microscopy Core (RRID:SCR_015347) Copy   

•   Source: SciCrunch Registry

http://www.cancer.iu.edu/research-trials/facilities/angiobiocore/index.shtml

Core facility which conducts validated and reproducible in vitro and in vivo angiogenesis, endothelial, hematopoietic and multi-parametric flow cytometry assays and their role in normal and patient-related hematologic and cardiovascular disorders.

Proper citation: Indiana University Cooperative Center of Excellence in Hematology Angiogenesis Core (RRID:SCR_015345) Copy   

•   Source: SciCrunch Registry

http://www.cancer.iu.edu/research-trials/facilities/flow-cytometry/index.shtml

Core facility which provides flow cytometry consultation, technical advice, flow cytometric analysis and cell sorting services as well as flow cytometric image analysis.

Proper citation: Indiana University School of Medicine Flow Cytometry Core Facility (RRID:SCR_015346) Copy   

•   Source: SciCrunch Registry

http://sharedresources.fredhutch.org/core-facilities/scientific-imaging

THIS RESOURCE IS NO LONGER IN SERVICE.Documented on July 27,2022. Scientific imaging service that serves as a centralized facility for imaging and visualization. The core facility provides access to time lapse and 3-D microscopy and quantitative autoradiography.

Proper citation: Fred Hutchinson Cancer Research Center Co-operative Center for Excellence in Hematology Scientific Imaging (RRID:SCR_015340) Copy   

•   Source: SciCrunch Registry

http://medicine.yale.edu/labmed/ycceh/cores/core_d/index.aspx

Core facility which provides expertise, technical assistance, and mice for human-into-mouse xenotransplantation studies. Mouse models include MITRG-SKI (KnockIn) mice that express human cytokines and huSIRPa from the endogenous murine loci in the Rag-/- IL-2Ry -/- background. It also offers training and technical assistance in the study of hematopoiesis and benign hematologic questions in mice.

Proper citation: Yale Cooperative Center of Excellence in Hematology Animal Modeling Core (RRID:SCR_015349) Copy   

•   Source: SciCrunch Registry

http://zfrhmaps.tch.harvard.edu/cemh/CoreB.htm

Zebrafish core facility which generates and maintains transgenic and mutant fish lines for hematology research. It also provides expertise and training in model production, study design, and fish production for research.

Proper citation: Boston Children's Hospital Center of Excellence in Molecular Hematology Zebrafish Core (RRID:SCR_015355) Copy   

•   Source: SciCrunch Registry

http://zfrhmaps.tch.harvard.edu/cemh/CoreC.htm

Core facility for basic and translational stem cell research. The core's areas of expertise include human pluripotent stem cell biology, cGMP cell manufacturing, reprogramming, genome editing, genotyping, laboratory automation, chemical screening, and imaging/image analysis.

Proper citation: Boston Children's Hospital Center of Excellence in Molecular Hematology Stem Cell Engineering and Analysis Core (RRID:SCR_015352) Copy   

•   Source: SciCrunch Registry

https://labnodes.vanderbilt.edu/resource/view/id/10800/community_id/1418

THIS RESOURCE IS NO LONGER IN SERVICE. Documented on July 6th,2023. Core whose objective is to provide investigators at Vanderbilt and outside institutions a means to accurately assess cardiovascular phenotypes in mouse models of diabetes and metabolic disease. The CPC uses validated approaches and state-of-the-art instrumentation that allow for sensitive screening of phenotypic variations.

Proper citation: MMPC-Vanderbilt University School of Medicine Cardiovascular Pathophysiology Core (RRID:SCR_015353) Copy   

•   Source: SciCrunch Registry