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http://roslincells.com/

Organization that supplies undifferentiated, clinical grade, human pluripotent stem cell lines to the life science community, and works with academic, clinical and commercial colleagues to enable and facilitate the use of these high grade cells in the development of new reagents, drugs and cellular therapeutics. They also seek to drive the economic development of the stem cell sector in Scotland. Their products can act as a valuable tool in supporting clients' drug discovery, development and clinical research programmes.

Proper citation: Roslin Cells (RRID:SCR_003857) Copy   

•   Source: SciCrunch Registry

http://www.avidrp.com/

Subsidiary of Eli Lilly and Company who develops new molecular imaging agents capable of changing the medical management of significant, chronic human diseases by identifying the first stages of pathological change, potentially assisting in earlier diagnosis, and better management and development of new therapies. The company has developed a radioactive tracer called florbetapir (18F). Florbetapir can be used to detect beta amyloid plaques in patients with memory problems using positron emission tomography (PET) scans, making the company the first to bring to market an FDA-approved method that can directly detect this hallmark pathology of Alzheimer's disease.

Proper citation: Avid Radiopharmaceuticals (RRID:SCR_003786) Copy   

•   Source: SciCrunch Registry

http://www.althia.es/

A biomedical company in Spain focused on the development of new tools for diagnosis and personalized treatment of oncological diseases and precancerous. It has three areas of activity in permanent innovation: Assistance in Diagnosis / Prognosis in solid and hematological tumors, Translational Research covering the gap between basic and clinical research and advanced radiotherapy treatments based image-guided single dose (SD-IGRT). Their objectives are: * Provide an integrated tissue and tumor molecular phenotype analysis using the most advanced technologies in diagnosis, to guide the most appropriate treatment for each patient. * Discover and validate molecular patterns by molecular systems and platforms including pathology, to generate predictive algorithms through computational biology, evolution and determining the response of patients with a particular tumor profile. Althia has laboratories equipped with the most advanced equipment and technologies in Barcelona and Granada Genyo Center, with offices in Madrid.

Proper citation: Althia (RRID:SCR_003918) Copy   

•   Source: SciCrunch Registry

http://www.nxstage.com/

A medical device company that develops, manufactures and markets innovative dialysis systems for the treatment of end-stage renal disease, or ESRD, and acute kidney failure.

Proper citation: NxStage Medical (RRID:SCR_004000) Copy   

•   Source: SciCrunch Registry

http://www.almirall.com/

A pharmaceutical company committed to provide valuable medicines through their own R&D efforts, licenses and collaborations. Through seeking innovative medicines they aim to become a relevant player in respiratory and dermatology diseases with also a strong interest in gastroenterology and pain. The company is headquartered in Barcelona, Spain, and has 14 affiliates in Europe and North America and trading capacity in 22 countries.

Proper citation: Almirall (RRID:SCR_003947) Copy   

•   Source: SciCrunch Registry

http://www.epo-berlin.com/

A small and medium-sized enterprise (SME) that has expertise in preclinical pharmacology, pharmacokinetics, and toxicology for the characterization of novel anticancer therapeutics and predictive biomarkers like: cytostatics, biologicals (peptides, antibodies), (anti)-hormones, immunomodulators (cytokines), and gene therapeutics. EPO has modern laboratories licensed for animal experiments and gene technology (S2) and a broad panel of murine and human tumor models growing in immunocompetent (SPF-quality, syngeneic strains) or immunodeficient mice (nude, SCID, NOD/SCID). EPO has established imaging technologies to monitor in vivo tumor growth.

Proper citation: Experimental Pharmacology and Oncology Berlin-Buch (RRID:SCR_003954) Copy   

•   Source: SciCrunch Registry

http://sourceforge.net/projects/hlaseq/

An open-source software tool for accurate genotyping the human HLA genes from Illumina GA high-throughput sequencing data.

Proper citation: HLASeq (RRID:SCR_004185) Copy   

•   Source: SciCrunch Registry

http://www.celgene.com

An American global biotechnology company that manufactures drug therapies for cancer and inflammatory disorders. The company's major products are Thalomid (thalidomide), which is approved for the acute treatment of the cutaneous manifestations of moderate to severe erythema nodosum leprosum (ENL), as well as in combination with dexamethasone for patients with newly diagnosed multiple myeloma, and Revlimid (lenalidomide), for which the company has received FDA and EMA approval in combination with dexamethasone for the treatment of multiple myeloma patients who have received at least one prior therapy. Revlimid is also approved in the United States for the treatment of patients with transfusion-dependent anemia due to Low- or Intermediate-1-risk Myelodysplastic syndromes (MDS) associated with a deletion 5q cytogenetic abnormality with or without additional cytogenetic abnormalities. Both Thalomid and Revlimid are sold through proprietary risk-management distribution programs to ensure safe and appropriate use of these pharmaceuticals. Vidaza is approved for the treatment of patients with MDS. Celgene also receives royalties from Novartis Pharma AG on sales of the entire Ritalin family of drugs, which are widely used to treat Attention Deficit Hyperactivity Disorder (ADHD). (Adapted from Wikipedia) There are numerous clinical trials at major medical centers using compounds from Celgene. Investigational compounds are being studied for patients with incurable hematological and solid tumor cancers, including multiple myeloma, myelodysplastic syndromes, chronic lymphocyte leukemia (CLL), non-Hodgkin's lymphoma (NHL), glioblastoma, and ovarian, pancreatic and prostate cancer.

Proper citation: Celgene (RRID:SCR_002955) Copy   

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http://snpper.chip.org/

Retrieve known single-nucleotide polymorphisms (SNPs) by position or by association with a gene; save, filter, analyze, display or export SNP sets; explore known genes using names or chromosome positions.

Proper citation: SNPper (RRID:SCR_001963) Copy   

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https://www.wtccc.org.uk/

Consortium of 50 research groups across the UK to harness the power of newly-available genotyping technologies to improve our understanding of the aetiological basis of several major causes of global disease. The consortium has gathered genotype data for up to 500,000 sites of genome sequence variation (single nucleotide polymorphisms or SNPs) in samples ascertained for the disease phenotypes. Analysis of the genome-wide association data generated has lead to the identification of many SNPs and genes showing evidence of association with disease susceptibility, some of which will be followed up in future studies. In addition, the Consortium has gained important insights into the technical, analytical, methodological and biological aspects of genome-wide association analysis. The core of the study comprised an analysis of 2,000 samples from each of seven diseases (type 1 diabetes, type 2 diabetes, coronary heart disease, hypertension, bipolar disorder, rheumatoid arthritis and Crohn's disease). For each disease, the case samples have been ascertained from sites widely distributed across Great Britain, allowing us to obtain considerable efficiencies by comparing each of these case populations to a common set of 3,000 nationally-ascertained controls also from England, Scotland and Wales. These controls come from two sources: 1,500 are representative samples from the 1958 British Birth Cohort and 1,500 are blood donors recruited by the three national UK Blood Services. One of the questions that the WTCCC study has addressed relates to the relative merits of these alternative strategies for the generation of representative population cohorts. Genotyping for this main Case Control study was conducted by Affymetrix using the (commercial) Affymetrix 500K chip. As part of this study a total of 17,000 samples were typed for 500,000 SNPs. There are two additional components to the study. First, the WTCCC award is part-funding a study of host resistance to infectious diseases in African populations. The same approach has been used to type 2,000 cases of tuberculosis (TB) and 2,000 cases of malaria, as well as 2,000 shared controls. As well as addressing diseases of major global significance, and extending WTCCC coverage into the area of infectious disease, the inclusion of samples of African origin has obvious benefits with respect to methodological aspects of genome-wide association analysis. Second, the WTCCC has, for four additional diseases (autoimmune thyroid disease, breast cancer, ankylosing spondylitis, multiple sclerosis), completed an analysis of 15,000 SNPs designed to represent a large proportion of the known non-synonymous coding SNPs across the genome. This analysis has been performed at the WTSI using a custom Infinium chip (Illumina). Data release The genotypic data of the control samples (1958 British Birth Cohort and UK Blood Service) and from seven diseases analyzed in the main study are now available to qualified researchers. Summary genotype statistics for these collections are available directly from the website. Access to the individual-level genotype data and summary genotype statistics is by application to the Consortium Data Access Committee (CDAC) and approval subject to a Data Access Agreement. WTCCC2: A further round of GWA studies were funded in April 2008. These include 15 WTCCC-collaborative studies and 12 independent studies be supported totaling approximately 120,000 samples. Many of the studies represent major international collaborative networks that have together assembled large sample collections. WTCCC2 will perform genome-wide association studies in 13 disease conditions: Ankylosing spondylitis, Barrett's oesophagus and oesophageal adenocarcinoma, glaucoma, ischaemic stroke, multiple sclerosis, pre-eclampsia, Parkinson's disease, psychosis endophenotypes, psoriasis, schizophrenia, ulcerative colitis and visceral leishmaniasis. WTCCC2 will also investigate the genetics of reading and mathematics abilities in children and the pharmacogenomics of statin response. Over 60,000 samples will be analyzed using either the Affymetrix v6.0 chip or the Illumina 660K chip. The WTCCC2 will also genotype 3,000 controls each from the 1958 British Birth cohort and the UK Blood Service control group, and the 6,000 controls will be genotyped on both the Affymetrix v6.0 and Illumina 1.2M chips. WTCCC3: The Wellcome Trust has provided support for a further round of GWA studies in January 2009. These include 5 WTCCC-collaborative studies to be carried out in WTCCC3 and 5 independent studies, across a range of diseases. Many of the studies represent major international collaborative networks that have together assembled large sample collections. WTCCC3 will perform genome-wide association studies in the following 4 disease conditions: primary biliary cirrhosis, anorexia nervosa, pre-eclampsia in UK subjects, and the interactions between donor and recipient DNA related to early and late renal transplant dysfunction. The WTCCC3 will also carry out a pilot in a study of the genetics of host control of HIV-1 infection. Over 40,000 samples will be analyzed using the Illumina 660K chip. The WTCCC3 will utilize the 6,000 control genotypes generated by the WTCCC2.

Proper citation: Wellcome Trust Case Control Consortium (RRID:SCR_001973) Copy   

•   Source: SciCrunch Registry

http://www.cjdats.org

A cooperative research program to explore the issues related to the complex system of offender treatment services. Nine research centers and a Coordinating Center were created in partnership with researchers, criminal justice professionals, and drug abuse treatment practitioners to form a national research infrastructure. The establishment of CJ-DATS is an outstanding example of cooperation among Federal agencies with the research community... We need to understand how to provide better drug treatment services for criminal justice offenders to alter their drug use and criminal behavior. - Dr. Nora Volkow, Director of NIDA. CJ-DATS PHASE I In 2002, NIDA launched the National Criminal Justice����������Drug Abuse Treatment Studies (CJ-DATS). CJ-DATS is a multisite research program aimed at improving the treatment of offenders with drug use disorders and integrating criminal justice and public health responses to drug involved offenders. From 2002 through 2008, CJ-DATS researchers from 9 research centers, a coordinating center, and NIDA worked together with federal, state, and local criminal justice partners to develop and test integrated approaches to the treatment of offenders with drug use disorders. The areas that were studied included: * Assessing Offender Problems * Measuring Progress in Treatment and Recovery * Linking Criminal Justice and Drug Abuse Treatment * Adolescent Interventions * HIV and Hepatitis Risk Reduction * Understanding Systems CJ-DATS PHASE II In 2008, CJ-DATS began to focus on the problems of implementing research-based practices drug treatment practices. This research concerns the organizational and systems processes involved in implementing valid, evidence-based practices to reduce drug use and drug-related recidivism for individuals in the criminal justice system. 12 CJ-DATS Research Centers are conducting implementation research in three primary domains: * Research to improve the implementation of evidence-based assessment processes for offenders with drug problems * Implementing effective treatment for drug-involved offenders * Implementing evidence-based interventions to improve an HIV continuum-of-care for offenders

Proper citation: Criminal Justice Drug Abuse Treatment Studies (RRID:SCR_006996) Copy   

•   Source: SciCrunch Registry

http://www.cdc.gov/labstandards/diabetes_dasp.html

Program that develops materials and methods to improve measurements of autoantibodies that are predictive of type 1 diabetes. These are the most sensitive and meaningful measures for predicting this disease. Historically, autoantibody measures have been variable among laboratories; therefore, this program, in collaboration with the Immunology of Diabetes Society, was established. The goals of DASP are to improve laboratory methods, evaluate laboratory performance, support the development of sensitive and specific measurement technologies, and develop reference methods. Currently, 48 key laboratories from 19 countries participate in DASP.

Proper citation: Diabetes Autoantibody Standardization Program (RRID:SCR_006929) Copy   

•   Source: SciCrunch Registry

http://www.ivyfoundation.org/

Funds patient-focused research on gliomas to develop better diagnostics and treatments that lead to long-term survival and a high quality of life for patients with brain tumors. The goal is to decrease the suffering of patients with brain tumors. With an ultimate goal to cure brain cancer, their immediate goal is to improve diagnostics and treatment. They are dedicated to improving the lives of all patients with brain cancer by funding research that they hope will lead to the doubling of life expectancy of patients with brain cancer. Their goal is to do this within the next seven years. Since 2005 they''ve committed more than $50 million to research into brain tumors, with the expectation that this will lead to better diagnostics and therapies. They are dedicated to this search because funding leads to answers, and answers lead to hope.

Proper citation: Ben and Catherine Ivy Foundation (RRID:SCR_006333) Copy   

•   Source: SciCrunch Registry

http://snps.ccbr.utoronto.ca:8080/SNPdryad/

Service to predict deleterious non-synonymous human Single Nucleotide Polymorphisms (SNPs) using only orthologous protein sequences.

Proper citation: SNPdryad (RRID:SCR_006414) Copy   

•   Source: SciCrunch Registry

http://www.nactem.ac.uk/GREC/

A semantically annotated corpus of 240 MEDLINE abstracts (167 on the subject of E. coli species and 73 on the subject of the Human species) intended for training information extraction (IE) systems and/or resources which are used to extract events from biomedical literature. The corpus has been manually annotated with events relating to gene regulation by biologists. Each event is centered on either a verb (e.g. transcribe) or nominalized verb (e.g. transcription) and annotation consists of identifying, as exhaustively as possible, the structurally-related arguments of the verb or nominalized verb within the same sentence. Each event argument is then assigned the following information: * A semantic role from a fixed set of 13 roles which are tailored to the biomedical domain. * A biomedical concept type (where appropriate). The corpus in available for download in 2 formats: * A standoff format, based on the BioNLP'09 Shared Task format * An XML format, based on the GENIA event annotation format

Proper citation: GREC Corpus (RRID:SCR_006719) Copy   

•   Source: SciCrunch Registry

http://www.chuq.qc.ca/fr/

Network of three teaching hospitals affiliated with the medical school of Université Laval and several specialized institutions in Quebec City.

Proper citation: University of Quebec Hospital Centre; Quebec; Canada (RRID:SCR_006740) Copy   

•   Source: SciCrunch Registry

https://www.bioconductor.org/packages//2.12/bioc/html/dexus.html

Software package that identifies differentially expressed genes in RNA-Seq data under all possible study designs such as studies without replicates, without sample groups, and with unknown conditions. It works also for known conditions, for example for RNA-Seq data with two or multiple conditions. RNA-Seq read count data can be provided both by the S4 class Count Data Set and by read count matrices. Differentially expressed transcripts can be visualized by heatmaps, in which unknown conditions, replicates, and samples groups are also indicated. This software is fast since the core algorithm is written in C. For very large data sets, a parallel version of DEXUS is provided in this package. DEXUS is a statistical model that is selected in a Bayesian framework by an EM algorithm. It does not need replicates to detect differentially expressed transcripts, since the replicates (or conditions) are estimated by the EM method for each transcript. The method provides an informative/non-informative value to extract differentially expressed transcripts at a desired significance level or power.

Proper citation: DEXUS (RRID:SCR_001309) Copy   

•   Source: SciCrunch Registry

http://octresearch.org/

Biomedical technology research center that pioneers and provides access to microscopic imaging instruments for biologic and clinical research. Optical coherence tomography (OCT) has evolved over the last two decades to become a standard of care for diagnostic ophthalmic imaging and is poised to make significant impact in the fields of cardiology and gastrointestinal endoscopy. Access to state-of-the-art instrumentation, however, has been limited to a relatively few research laboratories and the optimization of instruments for new biomedical applications has hindered the investigation of new opportunities. A major focus of CBORT will be to cultivate strategic research collaborations and respond to a pressing need for application-specific OCT instrumentation and hardware.

Proper citation: Center for Biomedical OCT Research (RRID:SCR_001418) Copy   

•   Source: SciCrunch Registry

http://www.bari2d.org/

A multicenter randomized clinical trial that aims to determine the best therapies for people with type 2 diabetes and moderately severe cardiovascular disease. 2368 participants were randomized at 49 sites in 6 countries. All subjects were given intensive medical therapy to control cholesterol and blood pressure and given counseling, if needed, to quit smoking and to lose weight. Beyond that, they compared whether prompt revascularization, either bypass surgery or angioplasty, e.g. stents, was more effective than medical therapy alone. At the same time, they also looked at which of two diabetes treatment strategies resulted in better outcomes����??insulin-providing versus insulin-sensitizing - that is, increasing the amount of insulin or making the insulin work better. Only patients with known type 2 diabetes and heart disease that could be treated appropriately with a revascularization OR medical therapy alone were eligible for the trial. Patients entered the study between January 2001 ����?? March 2005 and were followed for an average of five years. When a patient entered the study, physicians first decided whether that patient should receive stenting or bypass surgery. The patient then received their randomization assignment. All patients were treated in BARI 2D for both their diabetes and heart disease, as well as other risk factors that might effect those diseases, regardless of which group they were in. Diabetes-specific complications including retinopathy, nephropathy, neuropathy, and peripheral vascular disease were monitored regularly. Tests, blood samples, urine samples, and treatment cost data were obtained periodically through the trial and examined by experts at 7 central laboratories and other research partners. Experts on risk factors routinely oversaw treatments of all patients at 4 central management centers. A panel of independent experts reviewed data every six months to make sure that all patients were receiving safe care.

Proper citation: BARI 2D (RRID:SCR_001496) Copy   

•   Source: SciCrunch Registry

https://www.ara.com/mppd/

Computational model that can be used for estimating human and rat airway particle dosimetry. The model is applicable to risk assessment, research, and education. The MPPD model calculates the deposition and clearance of monodisperse and polydisperse aerosols in the respiratory tracts of rats and human adults and children (deposition only) for particles ranging in size from ultrafine (0.01 micrometers) to coarse (20 micrometers). The models are based on single-path and multiple-path methods for tracking air flow and calculating aerosol deposition in the lung. The single-path method calculates deposition in a typical path per airway generation, while the multiple-path method calculates particle deposition in all airways of the lung and provides lobar-specific and airway-specific information. Within each airway, deposition is calculated using theoretically derived efficiencies for deposition by diffusion, sedimentation, and impaction within the airway or airway bifurcation. Filtration of aerosols by the nose and mouth is determined using empirical efficiency functions. The MPPD model includes calculations of particle clearance in the lung following deposition.

Proper citation: Multiple-Path Particle Dosimetry Model (RRID:SCR_001486) Copy   

•   Source: SciCrunch Registry