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http://www.cdc.gov/nccdphp/ace/

A clinical study linking childhood maltreatment and later-life health and well-being. As a collaboration between the Centers for Disease Control and Prevention and Kaiser Permanente''s Health Appraisal Clinic in San Diego, Health Maintenance Organization (HMO) members undergoing a comprehensive physical examination provided detailed information about their childhood experience of abuse, neglect, and family dysfunction. Over 17,000 members chose to participate. To date, over 50 scientific articles have been published and over 100 conference and workshop presentations have been made. Future Directions: The ACE study is now in its 10th year and the prospective phase is currently underway. In this ongoing stage of the study, data are being gathered from various sources including outpatient medical records, pharmacy utilization records, and hospital discharge records to track the subsequent health outcomes and health care use of ACE Study participants. In addition, an examination of National Death Index records will be conducted to establish the relationship between ACE and mortality among the ACE Study population. The ACE Study findings suggest that these experiences are major risk factors for the leading causes of illness and death as well as poor quality of life in the United States. Progress in preventing and recovering from the nation''s worst health and social problems is likely to benefit from the understanding that many of these problems arise as a consequence of adverse childhood experiences. :Sponsors: This resource is supported by the Centers for Disease Control and Prevention and the Kaiser Permanente''s Health Appraisal Clinic in San Diego.

Proper citation: Adverse Childhood Experiences Study (RRID:SCR_008382) Copy   

•   Source: SciCrunch Registry

http://diademchallenge.org/data_sets.html

A software development competition, the DIADEM Challenge,to benefit the scientific community by encouraging the development of better software for automating three-dimensional reconstructions of neuronal arbors. The intent of the Sponsors is to ensure that the best software submitted for the competition is made available to the scientific community within a reasonable time and on reasonable terms. No purchase is necessary to enter or win. The competition will have two rounds. As of April 10, 2009, individuals and teams may register to participate in the competition and may download sets of image stacks (Data Sets) of non-human animal brains along with three-dimensional reconstructions for some of these Data Sets for training purposes. Submissions of software, including executable programs, supporting documentation, and reconstruction files for the Data Sets, must be uploaded to the competition website no later than April 9, 2010. In order to be eligible to win the competition, the individuals and at least one member of any teams whose submissions are selected for the Final Round (Finalists) must participate in the Final Round and scientific conference. Personal participation in the Final Round and scientific conference is important for two main reasons: first, because the Finalists software will be tested at the Final Round against additional Data Sets so that the judges can select a winner or winners, and second, because the larger scientific conference, of which the Final Round will be a part, is intended to foster extensive scientific interaction among neuroscientists and computational scientists, including plenary and poster sessions to discuss challenges, solutions, and future directions. There are 5 datasets, all of which have to be reconstructed for the qualifier phase. Once you have registered your group, dataset download information will be sent to you via E-mail. The 5 datasets are: - Cerebellar Climbing Fibers - Hippocampal CA3 Interneuron - Neocortical Layer 6 Axons - Neuromuscular Projection Fibers - Olfactory Projection Fibers Sponsors: The sponsors of this competition are: Allen Institute for Brain Science, Seattle, Washington; Howard Hughes Medical Institute (HHMI), Chevy Chase, Maryland; and Krasnow Institute for Advanced Study, George Mason University, Fairfax, Virginia.

Proper citation: DIADEM Challenge: DIgital reconstruction of Axonal and DEndritic Morphology (DIADEM) Software Development Competition (RRID:SCR_008262) Copy   

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http://flj.hinv.jp/

A human full-length cDNA sequence analysis database focused on mRNA varieties caused by variations of transcription start site (TSS) and splicing. Also available is ATGpr, a program for identifying the translational initiation codons in cDNA sequences. Data are derived from several full-length cDNA studies in Japan. Human gene number was estimated to be 20-25 thousand. However, the number of human mRNA varieties was predicted to be about 100 thousand. The varieties are thought to be caused by variations of TSS and splicing. In their previous human cDNA project, about 30 thousand of FLJ human full-length sequenced cDNAs were deposited to DDBJ/GenBank/EMBL, and they obtained about 1.4 million of 5''-end sequences (5''-EST) of FLJ full-length cDNAs from about 100 kinds of cDNA libraries consist of human tissues and cells constructed by oligo-capping method. The majority of the insert cDNA sizes were over 2 kb and the full-length rate of 5''-end was 90. And our FLJ cDNAs were covered about 80 of human genes. About 22 thousand of finished grades of full-length sequenced cDNAs were obtained in this project. The sequence analysis databases is focused on mRNA variations using human genome and cDNA sequences, FLJ full-length sequenced cDNAs, 5-ESTs of FLJ full-length cDNAs and other cDNA sequences described below. After those sequences were mapped onto the human genome sequences, clustering of the cDNA sequences were done based on the mapping results.

Proper citation: FLJ Human cDNA Database (RRID:SCR_008253) Copy   

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http://herpnet.org/

HerpNET is a collaborative effort by natural history museums to establish a global network of herpetological collections data. Sixty-four institutions are participating in the HerpNET community, with an open ended invitation to institutions who would like to join. Currently 56 institutions are available on the specimen searching portal, with data from over 5.5 million specimens available for searching. VertNet: The Future HerpNET, ORNIS, MaNIS and FishNet2 are taxon-based web portals that now serve georeferenced data on vertebrates from over 90 global institutions. Together these comprise VertNET, a cooperative project working to maintain and expand these distributed database projects. Future plans include biodiversity informatics workshops, enhancement of the portal design, better searching capabilities, and a dynamic cache to expand performance and analytic features. Sponsors: This resource is supported by the National Science Foundation (NSF No. 0132303) and by a GBIF DIGIT .

Proper citation: HerpNET (RRID:SCR_008374) Copy   

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http://www.bioinf.uni-freiburg.de/Software

This resource takes you to the Server and Web-Applications of the University of Freiburg Bioinformatics Group. Sponsors: This resource is supported by University of Freiburg. Keywords: Server, Web application, Bioinformatics, Software,

Proper citation: University of Freiburg Bioinformatics Group: Servers and Web-Applications (RRID:SCR_008256) Copy   

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http://www.oege.org/software/hwe-mr-calc.shtml

This portal leads to the Chi-sq Hardy-Weinberg equilibrium test calculator for biallelic markers (SNPs, indels etc), including analysis for ascertainment bias for dominant/recessive models (due to biological or technical causes.) The purpose of this web program is for estimating possible missingness and an approach to evaluating missingness under different genetic models. Mendelian randomization (MR) permits causal inference between exposures and a disease. It can be compared with randomized controlled trials. Whereas in a randomized controlled trial the randomization occurs at entry into the trial, in MR the randomization occurs during gamete formation and conception. Several factors, including time since conception and sampling variation, are relevant to the interpretation of an MR test. Particularly important is consideration of the missingness of genotypes that can be originated by chance, genotyping errors, or clinical ascertainment. Testing for Hardy-Weinberg equilibrium (HWE) is a genetic approach that permits evaluation of missingness. Through this tool, the authors demonstrate evidence of nonconformity with HWE in real data. They also perform simulations to characterize the sensitivity of HWE tests to missingness. Unresolved missingness could lead to a false rejection of causality in an MR investigation of trait-disease association. These results indicate that large-scale studies, very high quality genotyping data, and detailed knowledge of the life-course genetics of the alleles/genotypes studied will largely mitigate this risk. Sponsors: This resource is supported by an Intermediate Fellowship (grant FS/05/065/19497) from the British Heart Foundation.

Proper citation: Hardy-Weinberg Equilibrium Calculator (RRID:SCR_008371) Copy   

•   Source: SciCrunch Registry

http://www.hopkins-hivguide.org/

Launched in 2004, the HIV Guide is a single disease resource, with two main parts: the HIV database, which is accessed by searching on diagnosis, drug name, pathogen, or management or by accessing the resistance tool, and there are also browsable areas of the site, which include news, features, continuing medical education programs and other types of additional readings and information. Guides are authored by academic clinicians and subject to rigorous peer review. You may browse the guide by: Diagnosis Covering opportunistic infections, malignancies, and complications of therapy. Drugs Includes indications, dosing, drug interactions, and author recommendations. Pathogen - Describes microbiology, clinical syndromes, and therapy. Management Including antiretroviral therapy guidelines and strategies. Resistance Tool Provides up-to-date interpretation of genotypic resistance test results. Whether searching for a drug, a pathogen, a diagnosis, or a management issue, your search results will be delivered in a concise and standard form designed to give you the most clinically useful information first, with the option to go deeper if you choose. If you search by diagnosis, you will receive a page listing points covering establishment of a diagnosis, related pathogens, treatment recommendations, issues to consider on follow up, references and more. At each step, we provide you immediately with the information you need to treat the diagnosis and give you the option to read more or more deeply if you choose. On the diagnosis page, you are also provided with links to the information sheet for each drug that may be prescribed, and if you indicate which drug you intend to use, you will be provided with relevant drug selected comments. If you search by drug, you will receive a page listing FDA indications, usual adult dosing, adverse drug reactions, drug interactions, spectrum, and forms. You are also able to access full pharmacological information (mechanism, absorption, Cmax, volume of distribution, protein binding, metabolism/excretion, t _, dosing for glomerular filtration of 50-80, dosing for glomerular filtration of 10-50, dosing for glomerular filtration of <10 ml/min, dosing in hemodialysis, dosing in peritoneal dialysis, dosing in cavh, dosing for decreased hepatic function, pregnancy risk, and breast feeding compatibility). If you search by pathogen, you will receive a page covering the microbiology, clinical relevance, sites of infection, drug selected comments, other information and references. You are also provided with links to information for each drug that may be prescribed, and if you indicate which drug you intend to use, you will be provided with the drug selected comments for that choice. If you search by management, you will receive a page listing definition, indications, and clinical recommendations and additional details, including references. If you click on more wherever it appears on a page, you will find more detailed material about the topic. In addition, the HIV Guide homepage contains a Features section and Literature Review that contain synopses and articles about pertinent topics. The Publications section also provides .pdf versions of the Hopkins HIV Report. Prices represent the cost per unit specified, reflecting the Average Wholesale Price (AWP). AWP prices are taken from the Red Book, manufacturer information, and the McKesson database. These prices are updated every six months. We have listed up to 10 FDA-approved indications for uses of drugs. Though in some cases more may exist, for brevity and formatting issues authors and editors have chosen what they deem the most important. Also listed are disease states for which a drug may be likely prescribed regardless of FDA approval status (see Non-FDA approved uses). The HIV Guide is primarily focused on adult care but does cover issues of perinatal transmission. The material presented on this site represents the considered opinion of the Hopkins expert listed as the author of the module as of the date indicated. The reference section contains an annotated list of the articles that the author considers to be most relevant to the topic. Where authoritative guidelines exist, such as CDC, IDSA or Medical Letter guidelines, they are referenced and discussed along with the author''s recommendations presented.

Proper citation: HIV Guide (RRID:SCR_008252) Copy   

•   Source: SciCrunch Registry

https://www.nasw.org

Association whose goal is to foster the spread of accurate scientific information.

Proper citation: National Association of Science Writers (RRID:SCR_014929) Copy   

•   Source: SciCrunch Registry

https://www.nihstrokenet.org/#annotations:4TlyYopcEeaUdC-3RQ97KQ

NIH network designed to follow and help conduct clinical trials and research studies investigating acute stroke treatment, stroke prevention, and stroke recovery and rehabilitation. Clinical trials are listed once they are reviewed, approved, and ready for volunteer recruitment.

Proper citation: NIH StrokeNet (RRID:SCR_014648) Copy   

•   Source: SciCrunch Registry

https://www.broadinstitute.org/ccle/

A collaborative project between the Broad Institute and the Novartis Institutes for Biomedical Research and its Genomics Institute of the Novartis Research Foundation, with the goal of conducting a detailed genetic and pharmacologic characterization of a large panel of human cancer models. The CCLE also works to develop integrated computational analyses that link distinct pharmacologic vulnerabilities to genomic patterns and to translate cell line integrative genomics into cancer patient stratification. The CCLE provides public access to genomic data, analysis and visualization for about 1000 cell lines.

Proper citation: Cancer Cell Line Encyclopedia (RRID:SCR_013836) Copy   

•   Source: SciCrunch Registry

http://expertnet.org

A portal that connects users to reserch expertise and resources within Florida's universities. Users can search for experts (principal investigators), funded research projects, centers and institutes, technology licensing opportunities, speakers, and instructional programs.

Proper citation: Florida ExpertNet (RRID:SCR_013959) Copy   

•   Source: SciCrunch Registry

http://www.rarekidneystones.org

An organization of various participants and independent efforts representing four major diseases of hereditary nephrolithiasis. The Consortium facilitates cooperative exchange of information and resources among investigators, clinicians, patients, and researchers in order to improve care and outcomes for patients with rare stone diseases. The consortium promotes ready availability of diagnostic testing, pooling of clinical experiences, and availability of tissue banks in order to advance the science.

Proper citation: Rare Kidney Stone Consortium (RKSC) (RRID:SCR_014413) Copy   

•   Source: SciCrunch Registry

http://www.ucl.ac.uk/ploras#annotations:QXuC2C7REeaxtw-aEPo07Q

A research project investigating the difficulties of recovering language after stroke (aphasia). The overall aim of the study is to give future stroke survivors accurate predictions of their aphasia recovery by creating clinical tools and discerning why some patients recover from aphasia better than others.

Proper citation: Predicting Language Outcome and Recovery After Stroke (PLORAS) (RRID:SCR_014498) Copy   

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http://lincsportal.ccs.miami.edu/dcic-portal/

Portal which provides a unified interface for searching LINCS dataset packages and reagents. Users can use the portal to access datasets, small molecules, cells, genes, proteins and peptides, and antibodies.

Proper citation: LINCS Data Portal (RRID:SCR_014939) Copy   

•   Source: SciCrunch Registry

http://iclac.org

An independent committee established to improve visibility of cell lines and promote awareness and authentication testing to combat false or misidentified cell lines. It contains a databases of cross-contaminated or otherwise misidentified cell lines, as well as resources to familiarize users of cell lines and the problem of misidentification. Their Terms of Reference defines false or misidentified cell lines and other commonly used terms, as well as sets out the committee goals and ground rules.

Proper citation: International Cell Line Authentication Committee (RRID:SCR_014414) Copy   

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https://singlecell.broadinstitute.org/single_cell

Portal specializes in visualizing and disseminating single cell data. Allows you to use natural language and faceted search to discover other scientists’ research and share your own findings. Each study includes information on cell types, singular or multiple gene expression, and spatial transcriptomics. Interactive visualizations allow to explore cell clusters and search for related genes.

Proper citation: Single Cell Portal (RRID:SCR_014816) Copy   

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http://becs.aalto.fi/en/research/bayes/drifter/

Model based Bayesian method for eliminating physiological noise from fMRI data. This algorithm uses image voxel analysis to isolate the cardiac and respiratory noise from the relevant data.

Proper citation: DRIFTER (RRID:SCR_014937) Copy   

•   Source: SciCrunch Registry

https://grade.bsc.gwu.edu/web/grade/home

A comparative study that aims to determine which combination of two medications is best for glycemic control in Type 2 Diabetes, has the fewest side effects, and is the most beneficial for overall health. GRADE is a randomized clinical trial of participants diagnosed with type 2 diabetes within the past 10 years who are already on metformin. Participants will be randomly assigned to 1 of 4 commonly-used glucose-lowering drugs (glimepiride, sitagliptin, liraglutide, and basal insulin glargine), plus metformin, and will be followed for up to 7 years.

Proper citation: Glycemic Reduction Approaches in Diabetes: A Comparative Effectiveness Study (GRADE) (RRID:SCR_014384) Copy   

•   Source: SciCrunch Registry

https://www.janelia.org/confocal-imagery-management-and-analysis-tools

A discovery platform used to analyze and annotate imagery for individual projects, while assembling shared data resources. It was originally applied to Drosophila neuronal anatomy and neuroblast lineage analysis and is currently being extended to support mouse whole-brain projection tracing. The Workstation is both a pipeline management system that extracts entities from 3D imagery and a suite of tools that enable scientists to annotate large imagery datasets. A Entity-Attribute-Value (EAV) graph permits any element to be annotated by users with custom ontologies. By allowing any entity to have multiple parents, the graph can be re-arranged by each user without copying the underlying image data.

Proper citation: Janelia Workstation (RRID:SCR_014302) Copy   

•   Source: SciCrunch Registry

http://www.3dhistech.com/pannoramic_viewer

Software tool as a digital virtual microscope for viewing and moving scanned histological slides and for making annotations and measurements on them. Used in digital pathology. Helps to simplify the areas of the pathology workflow where imaging, slide digitization, storage, archivation, visualization and analysis are performed.

Proper citation: Pannoramic Viewer (RRID:SCR_014424) Copy   

•   Source: SciCrunch Registry