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http://www.nimh.nih.gov/about/director/index.shtml

Blog by the NIMH Director, Thomas R. Insel, M.D. Users may sort posts by topic and/or subsribe to the RSS Feed, http://www.nimh.nih.gov/site-info/feed-directors-blog.atom

Proper citation: NIMH Director's Blog (RRID:SCR_008841) Copy   

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https://www.med.upenn.edu/scxc/

Offers in vivo services specializing in immunodeficient and xenograft models (PDX, humanized immune system). Facility has dedicated BSL2 barrier space equipped with optical imaging, for applications ranging from immunotherapy, cancer biology, infectious diseases and regenerative medicine. Offers services centered around repository of live and fully annotated cells from adult patients with hematologic malignancies (AML, ALL, MPN, MDS), and hematopoietic stem/progenitor cells from healthy donors (BM, CB, and FL).

Proper citation: Pennsylvania University Perelman School of Medicine Stem Cell and Xenograft Core Facility (RRID:SCR_010035) Copy   

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http://neurobureau.projects.nitrc.org/ADHD200/Introduction.html

Preprocessed versions of the ADHD-200 Global Competition data including both preprocessed versions of structural and functional datasets previously made available by the ADHD-200 consortium, as well as initial standard subject-level analyses. The ADHD-200 Sample is pleased to announce the unrestricted public release of 776 resting-state fMRI and anatomical datasets aggregated across 8 independent imaging sites, 491 of which were obtained from typically developing individuals and 285 in children and adolescents with ADHD (ages: 7-21 years old). Accompanying phenotypic information includes: diagnostic status, dimensional ADHD symptom measures, age, sex, intelligence quotient (IQ) and lifetime medication status. Preliminary quality control assessments (usable vs. questionable) based upon visual timeseries inspection are included for all resting state fMRI scans. In accordance with HIPAA guidelines and 1000 Functional Connectomes Project protocols, all datasets are anonymous, with no protected health information included. They hope this release will open collaborative possibilities and contributions from researchers not traditionally addressing brain data so for those whose specialties lay outside of MRI and fMRI data processing, the competition is now one step easier to join. The preprocessed data is being made freely available through efforts of The Neuro Bureau as well as the ADHD-200 consortium. They ask that you acknowledge both of these organizations in any publications (conference, journal, etc.) that make use of this data. None of the preprocessing would be possible without the freely available imaging analysis packages, so please also acknowledge the relevant packages and resources as well as any other specific release related acknowledgements. You must be logged into NITRC to download the ADHD-200 datasets, http://www.nitrc.org/projects/neurobureau

Proper citation: ADHD-200 Preprocessed Data (RRID:SCR_000576) Copy   

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http://www.brighamandwomens.org/Departments_and_Services/radiology/Research/BRIC/default.aspx

Imaging Core facility that provides a comprehensive research imaging service to meet the needs of investigators and research subjects using imaging facilities at Brigham and Women's Hospital (BWH). A unique feature of BRIC is the complete anonymity of research subjects. Research image scheduling, image acquisition and image storage are all kept completely separate from BWH clinical Radiology systems. The BRIC provides the administrative infrastructure, customer service architecture and institutional support to promote investigative applications of imaging technologies.

Proper citation: BWH Research Imaging Core (RRID:SCR_002708) Copy   

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http://www.hcp.med.harvard.edu/ncs/

The baseline NCS, fielded from the fall of 1990 to the spring of 1992, was the first nationally representative mental health survey in the U.S. to use a fully structured research diagnostic interview to assess the prevalences and correlates of DSM-III-R disorders. The baseline NCS respondents were re-interviewed in 2001-02 (NCS-2) to study patterns and predictors of the course of mental and substance use disorders and to evaluate the effects of primary mental disorders in predicting the onset and course of secondary substance disorders. In conjunction with this, an NCS Replication survey (NCS-R) was carried out in a new national sample of 10,000 respondents. The goals of the NCS-R are to study trends in a wide range of variables assessed in the baseline NCS and to obtain more information about a number of topics either not covered in the baseline NCS or covered in less depth than we currently desire. A survey of 10,000 adolescents (NCS-A) was carried out in parallel with the NCS-R and NCS-2 surveys. The goal of NCS-A is to produce nationally representative data on the prevalences and correlates of mental disorders among youth. The NCS-R and NCS-A, finally, are being replicated in a number of countries around the world. Centralized cross-national analysis of these surveys is being carried out by the NCS data analysis team under the auspices of the World Health Organization (WHO) World Mental Health Survey Initiative. In order to provide an easily accessible database which can be updated and checked on a regular basis, we have created a public use file system containing all the documents from the NCS and NCS-R programs. These file systems can be accessed through the Internet and either downloaded onto a disk or printed. We will update the system on a regular basis to add newly completed paper abstracts and other documents. In addition, the NCS and NCS-R data can be accessed through ICPSR (Inter-university Consortium for Political and Social Research). Any updates to the data to correct coding or classification errors will be made available along with written documentation of the changes in ICPSR''s quarterly newsletter.

Proper citation: National Comorbidity Survey (RRID:SCR_004588) Copy   

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http://eyebrowse.cit.nih.gov/

EyeBrowse displays expressed sequence tag (EST) cDNA clones from eye tissues (derived from NEIBank and other sources) aligned with current versions of the human, rhesus, mouse, rat, dog, cow, chicken, or zebrafish genomes, including reference sequences for known genes. This gives a simplified view of gene expression activity from different parts of the eye across the genome. The data can be interrogated in several ways. Specific gene names can be entered into the search window. Alternatively, regions of the genome can be displayed. For example, entering two STS markers separated by a semicolon (e.g. RH18061;RH80175) allows the display of the entire chromosomal region associated with the mapping of a specific disease locus. ESTs for each tissue can then be displayed to help in the selection of candidate genes. In addition, sequences can be entered into a BLAT search and rapidly aligned on the genome, again showing eye derived ESTs for the same region. EyeBrowse includes a custom track display SAGE data for human eye tissues derived from the EyeSAGE project. The track shows the normalized sum of SAGE tag counts from all published eye-related SAGE datasets centered on the position of each identifiable Unigene cluster. This indicates relative activity of each gene locus in eye. Clicking on the vertical count bar for a particular location will bring up a display listing gene details and linking to specific SAGE counts for each eye SAGE library and comparisons with normalized sums for neural and non-neural tissues. To view or alter settings for the EyeSAGE track on EyeBrowse, click on the vertical gray bar at the left of the display. Other custom tracks display known eye disease genes and mapped intervals for candidate loci for retinal disease, cataract, myopia and cornea disease. These link back to further information at NEIBank. For mouse, there is custom track data for ChIP-on-Chip of RNA-Polymerase-II during photoreceptor maturation.

Proper citation: EyeBrowse (RRID:SCR_008000) Copy   

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http://www.hgvs.org/dblist/dblist.html

A list of various databases freely available to the public, including several mutation and variation resources, such as education resources for teachers students provided by the Human Genome Variation Society. Databases listed include: * Locus Specific Mutation Databases * Disease Centered Central Mutation Databases * Central Mutation and SNP Databases * National and Ethnic Mutation Databases * Mitochondrial Mutation Databases * Chromosomal Variation Databases * Other Mutation Databases ( i.e. your round holes don''''t fit our square pegs) * Clinical and Patient Aspects Databases * Non Human Mutation Databases * Artificial Mutations Only * Other Related Databases * Education Resources for Teachers and Students

Proper citation: Human Genome Variation Society: Databases and Other Tools (RRID:SCR_006876) Copy   

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http://www.uniprot.org/program/Chordata

Data set of manually annotated chordata-specific proteins as well as those that are widely conserved. The program keeps existing human entries up-to-date and broadens the manual annotation to other vertebrate species, especially model organisms, including great apes, cow, mouse, rat, chicken, zebrafish, as well as Xenopus laevis and Xenopus tropicalis. A draft of the complete human proteome is available in UniProtKB/Swiss-Prot and one of the current priorities of the Chordata protein annotation program is to improve the quality of human sequences provided. To this aim, they are updating sequences which show discrepancies with those predicted from the genome sequence. Dubious isoforms, sequences based on experimental artifacts and protein products derived from erroneous gene model predictions are also revisited. This work is in part done in collaboration with the Hinxton Sequence Forum (HSF), which allows active exchange between UniProt, HAVANA, Ensembl and HGNC groups, as well as with RefSeq database. UniProt is a member of the Consensus CDS project and thye are in the process of reviewing their records to support convergence towards a standard set of protein annotation. They also continuously update human entries with functional annotation, including novel structural, post-translational modification, interaction and enzymatic activity data. In order to identify candidates for re-annotation, they use, among others, information extraction tools such as the STRING database. In addition, they regularly add new sequence variants and maintain disease information. Indeed, this annotation program includes the Variation Annotation Program, the goal of which is to annotate all known human genetic diseases and disease-linked protein variants, as well as neutral polymorphisms.

Proper citation: UniProt Chordata protein annotation program (RRID:SCR_007071) Copy   

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http://www.scienceexchange.com/facilities/magnetic-resonance-research-facility-mrrf-uiowa

The University of Iowa MR Research Facility was established in August of 2004 with the acquisition of a Siemens Trio 3T scanner, shared between research and clinical usage. While the Center is within the Department of Radiology, it is run as a Core University facility. The facility is managed on a daily basis by Vincent Magnotta, PhD, Alan Stolpen, MD, PhD, and Dan Thedens, PhD. Oversight is provided by a Research Advisory committee that reviews new project proposals and equipment acquisitions. Since its inception, the equipment managed by the Research Center has expanded. In 2006, a research dedicated Siemens Avanto 1.5T scanner was loaned to the University by Siemens Medical Solutions to support research studies. Then, in 2007 an NIH/NCRR High End Instrumentation grant supported the acquisition of a research dedicated Siemens TIM Trio 3T scanner. Standard operating hours for the research-dedicated 3T TIM Trio scanner are from 8:00 a.m. to 6:00 p.m., Monday through Friday. During this time, a technologist is provided to run the scanner. The shared research 3T TIM Trio scanner is available all day Tuesdays (8:00 a.m. - 4:30 p.m.), and Thursday afternoons (12:00 p.m. - 4:30 p.m.) for research studies. The shared Avanto 1.5T scanner is available Mondays, Wednesdays and Fridays from 2:00 p.m. to 4:00 p.m. The scanners are also available after-hours if technologist coverage is available, or if the user is certified to conduct MR studies on their own. The current rate for scanner usage is $600 per hour and can be scheduled in half hour increments.

Proper citation: University of Iowa Magnetic Resonance Research Facility (RRID:SCR_011014) Copy   

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http://www.scienceexchange.com/facilities/microarray-resource-core-bu

THIS RESOURCE IS NO LONGER IN SERVICE. Documented on May 22,2024. Microarray Resource Core offers the full line of microarray products available from Affymetrix. This includes expression profiling, miRNA, exon, genotyping, resequencing, and tiling arrays. As part of our standard service, the resource provides assistance with experimental design and data analysis. Arrays for other organisms are available; please contact us for with specific requests.

Proper citation: Boston University Microarray Resource Core (RRID:SCR_012491) Copy   

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http://rdocdb.nimh.nih.gov

A database that houses human subjects data related to mental health research. Data from 691 subjects are shared in RDoCdb and data from 100,500 subjects are shared in the NIMH Data Archive. Users can plan for data submission, share data, query data, or share their results related to a publication or finding.

Proper citation: RDoCdb (RRID:SCR_013796) Copy   

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http://aging.brain-map.org/

The Aging, Dementia and Traumatic Brain Injury Study is a detailed neuropathologic, molecular and transcriptomic characterization of brains of control and TBI exposure cases from a unique aged population-based cohort from the Adult Changes in Thought (ACT) study. The study contains six data sets: histology and immunohistochemistry, in situ hybridization, rna-seq, protein quantification by luminex, isoprostane quantification, and specimen metadata.

Proper citation: Aging Dementia and Traumatic Brain Injury Study (RRID:SCR_014554) Copy   

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http://www.catstests.com/Product08.htm

THIS RESOURCE IS NO LONGER IN SERVICE, documented on July 17, 2013. This free neuropsychological evaluation software, Repeat, examines performance on a serial reaction time task thought to depend upon implicit memory. Participant's acquisition of a repeating stimulus sequence is assessed in this task. Repeat is a modification of procedures reported by Nissen and Bullemer (1987) and by Lewick, Hill and Bizot (1988). The computer screen is divided into quadrants. A single X, appears in one of the quadrants. The participant's task is either, depending on response modality, to strike as quickly as possible the key (4, 5, 1, 2 on the numeric keypad) corresponding to the quadrant in which the X appears or to position the mouse pointer over the quadrant and click it. The X then appears according to a repeating pre-programmed sequence in a different quadrant and the participant is required to respond as quickly as possible to that X. A trial is made up of a series of the repeating sequence. Sequence order and length and the number of iterations of the sequence are predetermined by the experimenter. CATs Repeat also allows for the interleaving of a randomly positioned X between each sequenced X. Alternatively a series of random presentations can be programmed to allow for assessment of the baseline speed of responding, that is a condition under which the participant can acquire no anticipatory information to enhance speed of responding. Repeat also contains a dual-task or split attention component modeled after a task reported by Nissen and Bullemer (1987). This task is identical to the one described above except that either a low or high tone is presented with each X presentation and the participant is asked to count the number of low tones they heard during a trial. The relative frequency of low tones is experimenter definable. Finally Repeat allows for the assessment of the explicit knowledge the participant may have acquired of the sequence. This component of the task is modeled after the generate procedure reported by Nissen and Bullemer (1987). At any point in the experiment the participant can be asked to begin predicting where the X will appear next. At this time no normative data is available for this test.

Proper citation: Colorado Assessment Tests - Repeat (RRID:SCR_001565) Copy   

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http://www.nbrc.nite.go.jp/e/index.html

Collection of microbial resources and perform taxonomic characterization of individual microorganisms such as bacteria including actinomycetes and archaea, yeasts, fungi, algaes, bacteriophages and DNA resources for academic research and industrial applications. NBRC is a member of WFCC, OECD Global BRC Network, ACM and JSCC. They are certified by quality management system ISO 9001. To provide attractive biological resources with useful information attached, they actively collect potentially useful biological resources (microorganisms and cloned genes) and distributes them to promote basic research as well as industrial applications. At the Biological Resource Center, they explore, isolate and identify microorganisms from various natural environments and at the same time accept scientifically and industrially useful microorganisms from researchers in academic and industrial sectors. The microbial DNA library constructed at the Biotechnology Development Center is also part of their collection. To improve and expand the collection, new methodologies for the isolation, identification and preservation of microorganisms and DNA will be investigated and developed so as to provide biological resources of higher quality. Their resources serve, for example, as the standard for determining antimicrobial activity, in aseptic tests as well as for the production of pharmaceutical substances and will be constantly reinforced for wider distribution to researchers in academia and industries. Please refer to the catalog shown at the NBRC website for details.

Proper citation: NBRC (RRID:SCR_002660) Copy   

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https://neuropsychological-assessment-tests.com/sanzen-tower-london-test

CATs Tower of London test is a free, computer-based software test originally developed by Shallice (1982) to investigate problem solving in subjects with damage to the frontal lobes. The CATs Tower of London Test comes with one preprogrammed test along with extensive normative data for that test. You can also create a test using your design. Briefly, subjects are required to move colored beads from a window on the left (working area) until they achieve the arrangement in the window on the right (goal position). Subjects are instructed to try to achieve the goal arrangement in as few moves as possible. The software contains a Tower of London test. The test contains trials with 3 beads and 3 pegs, 4 beads and 4 pegs, and 5 beads and 5 pegs. You can use the Setup screen to create a test using your design. A test can contain 3, 4, and 5 bead problems with varying number of moves required for the optimal solution. In Shallice's initial investigation using the Tower of London, patients with damage to the left anterior frontal lobe demonstrated impaired planning (i.e., greater number of moves required for solution). Patients with damage to the right anterior, and left or right posterior areas of the frontal lobes were not impaired. Thus, results from this initial study provided support for the view that the left anterior frontal lobe area is involved in the planning required for solving the Tower of London test. Recent studies using neuroimaging techniques support this notion. Studies using regional cerebral blood flow (rCBF) imaging indicate an involvement of the left frontal lobes in the planning required for successfully completing the Tower of London puzzle. Studies of patients with damage to the frontal lobes indicate less cortical specificity, but are consistent with the view that the frontal lobes are involved in the planning required for solving this puzzle.

Proper citation: Colorado Assessment Tests - Tower of London (RRID:SCR_003507) Copy   

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http://www.mdvu.org/library/

THIS RESOURCE IS NO LONGER IN SERVICE, documented April 15, 2016. The Movement Disorder Virtual University (MDVU) Resource Library contains detailed movement disorder information and resources including rating scales, scoring sheets, patient fact sheets, teaching slide sets, research news, meeting reports, anatomical illustrations, movement disorder treatment and rehabilitation directory, a glossary, support organizations, drug package information, and a library of links.

Proper citation: Movement Disorder Virtual University (MDVU): Resource Library (RRID:SCR_002719) Copy   

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http://fantom.gsc.riken.jp/4/

The FANTOM consortium is an international collaborative research project initiated and organized by the RIKEN Omics Science Center. In earlier FANTOM efforts we cloned and annotated 103,000 full-length cDNAs from mouse and distributed them to researchers throughout the world. FANTOM1-3 focused on identifying the transcribed components of mammalian cells. This work improved estimates of the total number of genes and their alternative transcript isoforms in both human and mouse, expanded gene families, and revealed that a large fraction of the transcriptome is non-coding. In addition, with the development of Cap Analysis of Gene Expression (CAGE) FANTOM3 could map a large fraction of transcription start sites and revise our models of promoter structure. This updated web resource provides the previous FANTOM results mapped to current genome builds and presents the results of FANTOM4. In FANTOM4 the focus has changed to understanding how these components work together in the context of a biological network. Using deepCAGE (deep sequencing with CAGE) we monitored the dynamics of transcription start site (TSS) usage during a time course of monocytic differentiation in the acute myeloid leukemia cell line THP-1. This allowed us to identify active promoters, monitor their relative expression and define relevant regions for carrying out transcription factor binding site predictions. Computational methods were then used to build a network model of gene expression in this leukemia and the transcription factors key to its regulation. This work gives the first picture of the wiring between genes involved in acute myeloid leukemia and provides a strategy for identifying key factors that determine cell fates. In addition to the network, FANTOM4 data was used in two additional analyses. The first identified a novel class of short RNAs associated with transcription start sites and the second focused on the role of repetitive element expression in the transcriptome. TOOLS *Genome Browser: graphical display of genomic features, such as promoters, exon structures, H3K9 acetylation, transcription factors positioning on the genome, coupled with gene and promoter activities. *EdgeExpressDB: regulatory interactions, such as transcriptional regulation, post-transcriptional silencing with miRNA, and PPI, coupled with gene and promoter activities. *SwissRegulon: FANTOM4 TF regulation is predicted using Motif Activity Response Analysis (MARA) developed by Erik van Nimwegen at Biozentrum. Follow the link to carry out MARA on your own dataset. *Custom Tracks on the UCSC Genome Browser: FANTOM4 tracks on the UCSC Genome Browser Database. *The RIKEN integrated database of mammals: Integration of FANTOM4 data with other mammalian resources, in particular, produced by RIKEN.

Proper citation: FANTOM DB (RRID:SCR_002678) Copy   

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https://neuropsychological-assessment-tests.com/sanzen-reaction-time-test

Reaction Time is free neuropsychological evaluation software designed to assess subject's speed of processing on three relatively simple tasks. Tasks include a simple reaction time test, a choice test, and a conditional choice test. Participants are shown a series of visual stimuli on a computer screen and asked to respond by pulling an appropriate trigger on a standard game pad. Both reaction time and the trigger pulled are recorded for subsequent analysis. Tasks to be used in the test, the average inter-stimulus interval and the number of stimuli presented for each task can be set by the investigator. The analysis includes means and standard deviations for response latencies for a single session, as well as the capability of evaluating a participant's performance on a particular session against their performance on a series of sessions. This test requires the use of a game pad that supports at least four buttons and provides a right and left trigger button. We have tested several different brands of inexpensive game pads and have found them acceptable; however we have standardized on Microsoft's SideWinder and have used it in collecting the normative data for this test.

Proper citation: Colorado Assessment Tests - Reaction Time (RRID:SCR_003516) Copy   

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http://www.catstests.com/Product04.htm

THIS RESOURCE IS NO LONGER IN SERVICE, documented on July 16, 2013. Visual span tests have been frequently used to assess non-verbal short-term memory. The free computer-based CATs Visual Span provides you with a flexible package for designing tests of visual spatial memory. You can create your own unique tests or variations on previously reported versions of the visual span test. For example in the Corsis Block-Tapping Test the examiner places nine blocks on a board and taps them in a designated sequence. The participant is required to repeat the sequence. Over trials the length of the sequence is increased (see Milner, 1971). The Knox Cube Imitation Test uses four blocks and essentially follows the same logic. The Wechsler Memory Scale - Revised includes a two part visual memory span test. In this test the examiner points at boxes on an eight box card in a prearranged sequence and the subject is required to repeat back the sequence. The initial trial starts with a sequence of two blocks and increases over trials. The two parts of this test are a forward visual span test and a reverse visual span test. Tests similar to these and more can be setup with the CATs Visual Span.

Proper citation: Colorado Assessment Tests - Visual Span (RRID:SCR_003513) Copy   

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http://www.bcgsc.ca/project/pleiades-promoter-project

Project to generate human DNA promoters of less than 4 kb (MiniPromoters) to drive gene expression in defined brain regions of therapeutic interest for diseases such as Alzheimer, Parkinson, Huntington, Amyotrophic Lateral Sclerosis, Multiple Sclerosis, Spinocerebellar Ataxia, Depression, Autism, and Cancer. Project develops and shares tools like human MiniPromoters that drive region- and cell-specific gene expression in the mouse brain, expression constructs, mouse embryonic stem cell lines, and knock-in mice all of which carry brain-specific MiniPromoters. Project is daughter of Genome Canada Project, Atlas of Gene Expression in Mouse Development, within which mouse brain gene expression data have already been gathered. Project team has collaborated with International BioPharma Solutions Ltd., management and communications consulting company specializing in product development and commercialization advice. Project will explore challenging interface between science and journalism with focus on genomics and gene therapy.

Proper citation: Pleiades Promoter Project: Genomic Resources Advancing Therapies for Brain Disorders (RRID:SCR_003282) Copy   

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