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http://www.utsa.edu/claibornelab/

The long-term goals of my research are to understand the relationship between neuronal structure and function, and to elucidate the factors that affect neuronal morphology and function over the lifespan of the mammal. Currently we are examining 1) the effects of synaptic activity on neuronal development; 2) the effects of estrogen on neuronal morphology and on learning and memory; and, 3) the effects of aging on neuronal structure and function. We have focused our efforts on single neurons in the hippocampal formation, a region that is critical for certain forms of learning and memory in rodents and humans. From the portal, you may click on a cell in your region of interest to see the complete database of cells from that region. You may also explore the Neuron Database: * Comparative Electrotonic Analysis of Three Classes of Rat Hippocampal Neurons. (Raw data available) * Quantitative, three-dimensional analysis of granule cell dendrites in the rat dentate gyrus. * Dendritic Growth and Regression in Rat Dentate Granule Cells During Late Postnatal Development.(Raw data available) * A light and electron microscopic analysis of the mossy fibers of the rat dentate gyrus.

Proper citation: University of Texas at San Antonio Laboratory of Professor Brenda Claiborne (RRID:SCR_008064) Copy   

•   Source: SciCrunch Registry

http://www.snprc.org/

Center that supports studies of nonhuman primate models of human diseases, including common chronic diseases and infectious diseases and the effects that genetics and the environment have on physiological processes and disease susceptibility. SNPRC encourages the use of its resources by investigators from the national and international biomedical research communities.

Proper citation: Southwest National Primate Research Center (RRID:SCR_008292) Copy   

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http://cprc.rcm.upr.edu/

Center for the study of non-human primates. Its mission is the study and use of non-human primates as models for studies of social and biological interactions and for the discovery of methods of prevention, diagnosis and treatment of diseases that afflict humans. Through the stewardship of three unique facilities—Cayo Santiago Field Station, Sabana Seca Field Station, and the Laboratory of Primate Morphology supports a diverse range of research programs that enhance understanding of primate biology and behavior, with direct applications in biomedical and translational research.

Proper citation: Caribbean Primate Research Center (RRID:SCR_008345) Copy   

•   Source: SciCrunch Registry

http://www.brainvoyager.de/BV2000OnlineHelp/BrainVoyagerWebHelp/Talairach_brain_atlas.htm

The Talairach brain atlas visualized via BrainVoyager (Commercial software) can be used to visualize Brodmann areas as they were defined for the Talairach brain (Talairach & Tournaux, 1988) and to compare regions of subjects with respect to the Brodmann areas. The demarcated areas are based on the Talairach demon, which is a digitized version of the Talairach atlas and which has been transferred into BrainVoyager VOI files by Matthias Ruf, Mannheim. Using the Brodman.voi file you may ask questions like the following: What is the signal time course of subject N in experiment A within Brodmann area X ?. Note, however, that the defined areal boundaries should be used only as a rough guideline for determining the location of activated regions: There is substantial variation of histologically defined areas between subjects. Since cytoarchitectonically defined Brodmann areas are not available in vivo, we advise to use the provided information with care. The TalairachBrain.vmr file is located in the same folder as your BrainVoyager executable file. It can be loaded as any VMR project by using the Open... item in the File menu (or the Open icon). The TalairachBrain.vmr file is also loaded automatically when using the glass brain visualization tool.

Proper citation: BrainVoyager: Talairach Brain Atlas (RRID:SCR_008800) Copy   

•   Source: SciCrunch Registry

http://www.pathonet.org

PathoNet is a virtual meeting place for pathologists from all over the world. They can use it as a virtual pathology laboratory in which they can exchange their views on their cases. Join us and share your experience. Special or rare cases maybe very useful in the diagnostic practice. Everybody who would like to use digital microscopy in human, veterinary or forensic pathology; in laboratory medicine, in human anatomy; in experimental research, and when teaching can benefit from this resource. Additionally, practicing physicians, students, tutors, experts and researchers can all contribute and benefit from PathoNet. Sponsors: This resource is supported by 3DHISTECH Ltd.

Proper citation: PATHONET (RRID:SCR_008674) Copy   

•   Source: SciCrunch Registry

http://www.muschealth.com/multimedia/Podcasts/index.aspx?type=main

The MUSChealth.com Podcast Library, featuring podcasts on a variety of topics related to your health and our services here at MUSC. These medical podcasts are hosted by MUSC faculty, physicians and special guests and are produced and directed by Linda Austin, M.D. Current topics include: * Academics and Education * Aging, Geriatrics and Caregiving * Alcohol and Drug Dependency * Allergies and Asthma * Ashley River Tower * Bones, Joints, Muscles and Spine * Cancer * Children''s Health * Cosmetic Surgery * Dental * Dermatology/Skin Problems * Diabetes, Endocrinology and Metabolism * Digestive Health * ENT: Ear, Nose and Throat * Executive Health * Eye Health * General Health and Wellness * Heart and Vascular Health * Hospice * Kohl''s Take a Minute for Kids * Lungs and Breathing * Men''s Health * Mental Health * MUSC News and Events * Neurological Health * Organ Transplant * Osteoporosis * Pregnancy - Week by Week * Pregnancy and Childbirth * Radiology * Research and Clinical Trials * SC Health, Leadership and Policy * Sports Medicine * Stroke * Urology * Weight Loss Surgery Follow-up * Weight Management * Women''s Health

Proper citation: MUSC Health Podcast Library (RRID:SCR_008827) Copy   

•   Source: SciCrunch Registry

http://bcb.cs.tufts.edu/dflat/

We are an interdisciplinary team dedicated to annotating gene function related to human fetal development. We are contributing new functional annotation to the Gene Ontology, curating and mining gene sets suitable for the interpretation of developmental genomic data, and creating the computational tools needed to apply genomics for better understanding the molecular mechanisms of human development. Our GO annotation is in the process of being incorporated into the GOA public release. The GONE (Gene Ontology Non-Eligible) database is where we store annotations relevant to our research but that don''t quite meet GOA''s standards. Usually an annotation falls into this category because either the gene/protein described is a family of genes/proteins rather than a specific one, there is no UniProt ID to identify the gene/protein in the system, a GO term does not yet exist to describe the particular function, process, or location of the gene/protein, the species is not clearly identifiable in the paper, or the evidence is not as reliable (GO evidence codes TAS and NAS). As individual annotations these are more suspect than current GO annotation. However, for functional analysis of expression data, these gene sets can be valuable even with a certain amount of noise. We also include here a link to the supplementary data from our forthcoming PSB 2011 paper on gene set mining.

Proper citation: DFLAT (RRID:SCR_010738) Copy   

•   Source: SciCrunch Registry

http://brainandsociety.org/the-brain-observatory

Formerly a topical portal studying the brain which collected and imaged 1000 human brains, the Brain Observatory has partnered with the Institute for Brain and Society to build virtual laboratories that will feed directly into the database of images and knowledge created in the context of the Human Brain Library. The Brain Observatory will also host exhibits, conferences, and events aimed at promoting a heightened awareness of brain research and how its results can benefit personal brain fitness and mental health.

Proper citation: Brain Observatory (RRID:SCR_010641) Copy   

•   Source: SciCrunch Registry

http://bio-bwa.sourceforge.net/

Software for aligning sequencing reads against large reference genome. Consists of three algorithms: BWA-backtrack, BWA-SW and BWA-MEM. First for sequence reads up to 100bp, and other two for longer sequences ranged from 70bp to 1Mbp.

Proper citation: BWA (RRID:SCR_010910) Copy   

•   Source: SciCrunch Registry

http://www.viprbrc.org/brc/home.do?decorator=vipr

Provides searchable public repository of genomic, proteomic and other research data for different strains of pathogenic viruses along with suite of tools for analyzing data. Data can be shared, aggregated, analyzed using ViPR tools, and downloaded for local analysis. ViPR is an NIAID-funded resource that support the research of viral pathogens in the NIAID Category A-C Priority Pathogen lists and those causing (re)emerging infectious diseases. It provides a dedicated gateway to SARS-CoV-2 data that integrates data from external sources (GenBank, UniProt, Immune Epitope Database, Protein Data Bank), direct submissions, analysis pipelines and expert curation, and provides a suite of bioinformatics analysis and visualization tools for virology research.

Proper citation: Virus Pathogen Resource (ViPR) (RRID:SCR_012983) Copy   

•   Source: SciCrunch Registry

https://www.nia.nih.gov/alzheimers

Portal for Alzheimer's disease that compiles, archives and disseminates information about current treatments, diagnostic tools and ongoing research for health professions, people with AD, their families and the public. The Center provides informational services and referrals for AD symptoms, diagnosis and treatment for patients; clinical trial information and literature searches for researchers; training materials and guidelines for caregivers; and Spanish language resources.

Proper citation: Alzheimer's Disease Education and Referral Center (RRID:SCR_012787) Copy   

•   Source: SciCrunch Registry

http://www.kegg.jp/

Integrated database resource consisting of 16 main databases, broadly categorized into systems information, genomic information, and chemical information. In particular, gene catalogs in completely sequenced genomes are linked to higher-level systemic functions of cell, organism, and ecosystem. Analysis tools are also available. KEGG may be used as reference knowledge base for biological interpretation of large-scale datasets generated by sequencing and other high-throughput experimental technologies.

Proper citation: KEGG (RRID:SCR_012773) Copy   

•   Source: SciCrunch Registry

http://www.tmslab.org/tmscore.php

At the Berenson-Allen Center for Noninvasive Brain Stimulation (CNBS) at Beth Israel Deaconess Medical Center and Harvard Medical School we have three distinct missions: Research, Education and Patient Care. Our research explores brain-behavior relations, brain plasticity and its modulation, employing different noninvasive brain stimulation techniques combined with careful task design, electroencephalography, and functional brain imaging. Educational efforts feature several Continuing Medical Education Courses including a week long intensive course in noninvasive brain stimulation offered 3 times per year. Our clinical program offers noninvasive brain stimulation for treatment of neuropsychiatric disorders such as depression and schizophrenia, epilepsy, and chronic pain. Clinical work also includes studies of central motor conduction time, cortical excitability, and noninvasive cortical mapping.

Proper citation: BIDMC Transcranial Magnetic Stimulation Core (RRID:SCR_011022) Copy   

•   Source: SciCrunch Registry

https://gillisweb.cshl.edu/Primate_MTG_coexp/

We aligned single-nucleus atlases of middle temporal gyrus (MTG) of 5 primates (human, chimp, gorilla, macaque and marmoset) and identified 57 consensus cell types common to all species. We provide this resource for users to: 1) explore conservation of gene expression across primates at single cell resolution; 2) compare with conservation of gene coexpression across metazoa, and 3) identify genes with changes in expression or connectivity that drive rapid evolution of human brain.

Proper citation: Gene functional conservation across cell types and species (RRID:SCR_023292) Copy   

•   Source: SciCrunch Registry

https://chordate.bpni.bio.keio.ac.jp/chordate/faba/1.4/top.html

Image resource including ascidian's three-dimensional (3D) and cross-sectional images through the developmental time course. These images were reconstructed from more than 3,000 high-resolution real images collected by confocal laser scanning microscopy (CLSM) at newly defined 26 distinct developmental stages (stages 1-26) from fertilized egg to hatching larva, which were grouped into six periods named the zygote, cleavage, gastrula, neurula, tailbud, and larva periods. The data set will be helpful in standardizing developmental stages for morphology comparison as well as for providing guidelines for several functional studies of a body plan in chordate.

Proper citation: Four-dimensional Ascidian Body Atlas (RRID:SCR_001691) Copy   

•   Source: SciCrunch Registry

http://www.tbi-impact.org/?p=impact%2Fcalc&btn_calc=GO+TO+CALCULATOR

A calculator that calculates the prediction models for 6 month outcome after Traumatic Brain Injury. Based on extensive prognostic analysis the IMPACT investigators have developed prognostic models for predicting 6 month outcome in adult patients with moderate to severe head injury (Glasgow Coma Scale <=12) on admission. By entering the characteristics into the calculator, the models will provide an estimate of the expected outcome at 6 months. We present three models of increasing complexity (Core, Core + CT, Core + CT + Lab). These models were developed and validated in collaboration with the CRASH trial collaborators on large numbers of individual patient data (the IMPACT database). The models discriminate well, and are particularly suited for purposes of classification and characterization of large cohorts of patients. Extreme caution is required when applying the estimated prognosis to individual patients. The sequential prediction models may be used as an aid to estimate 6 month outcome in patients with severe or moderate traumatic brain injury (TBI). However, the prediction rule can only complement, never replace, clinical judgment and can therefore be used only as a decision-support system.

Proper citation: IMPACT Prognostic Calculator (RRID:SCR_004730) Copy   

•   Source: SciCrunch Registry

http://blog.ketyov.com/

Bradley Voytek''''s blog is where he tries out new ideas. He will often be wrong, but that''''s the point. He is a Neuroscientist studying human cognition, neuroplasticity, and brain computer interfacing. Into really geeky stuff. World zombie neuroscience expert. Also runs brainSCANr.com with his wife, Jessica.

Proper citation: Oscillatory Thoughts (RRID:SCR_005481) Copy   

•   Source: SciCrunch Registry

http://bioapps.rit.albany.edu/MITOPRED/

THIS RESOURCE IS NO LONGER IN SERVICE, documented on July 16, 2013. It predicts nuclear-encoded mitochondrial proteins from all eukaryotic species including plants. Prediction is based on the occurrence patterns of Pfam domains (version 16.0) in different cellular locations, amino acid composition and pI value differences between mitochondrial and non-mitochondrial locations. Additionally, you may download MITOPRED predictions for complete proteomes. Re-calculated predictions are instantly accessible for proteomes of Saccharomyces cerevisiae, Caenorhabditis elegans, Drosophila, Homo sapiens, Mus musculus and Arabidopsis species as well as all the eukaryotic sequences in the Swiss-Prot and TrEMBL databases. Queries, at different confidence levels, can be made through four distinct options: (i) entering Swiss-Prot/TrEMBL accession numbers; (ii) uploading a local file with such accession numbers; (iii) entering protein sequences; (iv) uploading a local file containing protein sequences in FASTA format. The Mitopred algorithm works based on the differences in the Pfam domain occurrence patters and amino acid composition differences in different cellular compartments. Location specific Pfam domains have been determined from the entire eukaryotic set of Swissprot database. Similarly, differences in the amino acid composition between mitochondrial and non-mitochondrial sequences were pre-calculated. This information is used to calculate location-specific amino acid weights that are used to calculate amino acid score. Similarly, pI average values of the N-terminal 25 residues in different cellular location were also determined. This knowledge-base is accessed by the program during execution.

Proper citation: mitopred (RRID:SCR_006135) Copy   

•   Source: SciCrunch Registry

https://bioinformatics.oxfordjournals.org/content/21/4/557.full.pdf

THIS RESOURCE IS NO LONGER IN SERVICE, documented August 18, 2016. MAP-O-MAT is a web-based server for automated linkage mapping of human polymorphic DNA markers. The server uses publicly available genotype data for over 15,000 markers. It facilitates the verification of order and map distances for custom mapping sets using genotype data from the CEPH database, and from the Marshfield, SNP Consortium and Rutgers linkage maps. The CRI-MAP program is used for likelihood calculations and some mapping algorithms, and physical map positions are provided from the human genome assembly.

Proper citation: MAP-O-MAT (RRID:SCR_008197) Copy   

•   Source: SciCrunch Registry

http://igs-server.cnrs-mrs.fr/mgdb/Rickettsia/

THIS RESOURCE IS NO LONGER IN SERVICE, documented August 18, 2016. Rickettsia are obligate intracellular bacteria living in arthropods. They occasionally cause diseases in humans. To understand their pathogenicity, physiologies and evolutionary mechanisms, RicBase is sequencing different species of Rickettsia. Up to now we have determined the genome sequences of R. conorii, R. felis, R. bellii, R. africae, and R. massiliae. The RicBase aims to organize the genomic data to assist followup studies of Rickettsia. This website contains information on R. conorii and R. prowazekii. A R. conorii and R. prowazekii comparative genome map is also available. Images of genome maps, dendrogram, and sequence alignment allow users to gain a visualization of the diagrams.

Proper citation: Rickettsia Genome Database (RRID:SCR_007102) Copy   

•   Source: SciCrunch Registry