Curator Dashboard

Blog is first and foremost dedicated to circuitry, all the way from a small cluster of connections in a small brain area to wide-spread circuitry between several brain areas (local, regional and functional connectivity). My Philosophy (on neuroscience): I do not think that functions of the brain (and/or mind) can be localized to certain areas (modular zones). This is a distributed, interactive function in a neural network. Second, there is usually an underlying tone that relates to the hippocampus, and/or the post has a systems-level approach to it. Postings will most likely be in a review-esque fashion. This is really meant to be an information resource. I hope to get more opinion pieces in there sometime. Posts are usually what I am currently researching, interested in, or what I have previously done research on at one time. I also want to build a community of professionals and others interested in neuroscience and/or psychology (philosophy of mind, too!). The blog, in general, helps everything (the information) stay fresh in my mind.

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• SciCrunch
• 15 years ago - by Anonymous

Clinical trial investigating whether a specific class of antihypertensive drugs (beta-adrenergic blockers, calcium channel blockers, or angiotensin converting enzyme inhibitors) and/or the level of blood pressure would influence progression of hypertensive kidney disease in African Americans. The initiative consisting of 21 clinical centers and a data-coordinating center is followed by a Continuation of AASK Cohort Study to investigate the environmental, socio-economic, genetic, physiologic, and other co-morbid factors that influence progression of kidney disease in a well-characterized cohort of African Americans with hypertensive kidney disease. Only patients who were previously in the randomized trial are eligible for the cohort study. A significant discovery was made in the treatment strategy for slowing kidney disease caused by hypertension. Angiotensin-converting enzyme (ACE) inhibitors, compared with calcium channel blockers, were found to slow kidney disease progression by 36 percent, and they drastically reduced the risk of kidney failure by 48 percent in patients who had at least one gram of protein in the urine, a sign of kidney failure. ACE inhibitors have been the preferred treatment for hypertension caused by diabetes since 1994; however, calcium channel blockers have been particularly effective in controlling blood pressure in African Americans. The AASK study now recommends ACE inhibitors to protect the kidneys from the damaging effects of hypertension. The Continuation of AASK Cohort Study will be followed at the clinical centers. The patients will be provided with the usual clinical care given to all such patients at the respective centers. Baseline demographic information, selected laboratory tests, and other studies are being obtained at the initiation of the Continuation Study. The patients will be seen quarterly at the centers, and some selected studies done at these visits. Samples will be obtained and stored for additional studies and analyses at a later date.

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• dkNET
• 14 years ago - by Anonymous

Genomic data set on Type 2 Diabetes in African-Americans derived via admixture mapping, a method for genome-wide association analysis based on admixture-generated linkage disequilibrium. This collaborative group has identified 1,478 African Americans with Type 2 Diabetes (T2D) from the Jackson Heart Study and Multiethnic Cohort Study, as well as 498 controls from the Jackson Heart Study who are normoglycemic despite high body mass index and older age. All samples were genotyped (using the Illumina BeadLab platform) for 1,291 polymorphic markers chosen to be extremely different in frequency between west Africans and European Americans. Evidence for association to diabetes at each marker as reported by the ANCESTRYMAP software are reported in the downloadable table. They calculate that this study has statistical power to detect loci where African or European ancestry on average confers multiplicative increased risk of 1.35-fold or more. The fact that they did not detect a statistically significant signal of association in the scan suggests that any genetic risk factors for T2D do not confer different risks due to ancestry that differ by this factor. The genome scan results are publicly available (Excel file) prior to publication so that researchers interested in the genetics of T2D can use the results of the scan to prioritize follow-up of any regions of interest.

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• SciCrunch
• 17 years ago - by Anonymous

Data analysis service and software program that perform Operantional Taxonomic Units (OTUs) finding. It uses a three-step clustering for identifying OTUs. The first-step clustering is raw read filtering and trimming. The second step is error-free reads picking.. At the last step, OTU clustering is done at different distanct cutoffs (0.01, 0.02, 0.03... 0.12).

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• SciCrunch
• 13 years ago - by Anonymous

Initiative which defines standards for the description and exchange of aggregations of Web resources. The intent of the effort is to develop standards that generalize across all web-based information including the increasing popular social networks of web 2.0. The goal of these standards is to expose the rich content in these aggregations (sometimes called compound digital objects, they may combine distributed resources with multiple media types including text, images, data, and video) to applications that support authoring, deposit, exchange, visualization, reuse, and preservation. The specific aim of the ORE effort is to promote (through creation or endorsement) effective and consistent mechanisms which: facilitate discovery of compound digital objects; reference (or link to) these objects (as well as parts thereof); obtain a variety of disseminations of these objects; aggregate and disaggregate objects; and enable processing of objects by automated agents.

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• SciCrunch
• 17 years ago - by Anonymous

A Matlab package for working with graphs that uses the Boost Graph Library to efficiently implement the graph algorithms. MatlabBGL is designed to work with large sparse graphs with hundreds of thousands of nodes.

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• SciCrunch
• 13 years ago - by Anonymous

It is a publicly available web-based database that aims to provide further understanding of protein-ligand interactions. It''s a resource containing biomolecular data, including binding energies, Tanimoto ligand similarity scores and protein sequence similarities of protein-ligand complexes. The PLD contains biomolecular data including calculated binding energies, Tanimoto ligand similarity scores and protein percentage sequence similarities. The database has potential for application as a tool in molecular design.

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• SciCrunch
• 17 years ago - by Anonymous

Database of records from patients with Parkinson's disease (n = 15), Huntington's disease (n = 20), or amyotrophic lateral sclerosis (n = 13). Records from 16 healthy control subjects are also included here. The raw data were obtained using force-sensitive resistors, with the output roughly proportional to the force under the foot. Stride-to-stride measures of footfall contact times were derived from these signals.

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• SciCrunch
• 16 years ago - by Anonymous

Database for storing, retrieving, and displaying the information derived from piggyBac (PB) insertions (Insert) and their characterizations in the mouse genome with piggyBac transposon system. Quick Search and Advanced Search tools have been provided to find information in the PBmice database, the result is centered on Inserts and provides information related to the Inserts. A mapping database is linked to PBmice too. This mapping database allows row experiment data to be inputted in. All the mature data can be allowed publish to PBmice. PBmice Source Code is available with a License Agreement.

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• SciCrunch
• 16 years ago - by Anonymous

BitterDB is a free and searchable database of bitter compounds. It currently holds over 550 bitter compounds obtained from the literature and from Merck index and their associated 25 human bitter taste receptors (hT2Rs). BitterDB provides several ways to investigate the bitter world: search for bitter compounds by different criteria, search for bitter molecules with structure similar to a query compound, blast bitter receptors and more. New! 2D plots of bitter receptors are available in the receptors pages. The alignment contains the sequences of the 25 human bitter taste receptors. The alignment shows the secondary structure for each receptor as predicted by TOPCONS. In each trans-membrane helix X, the most conserved residue (X.50 in Ballesteros-Weinstein numbering) is indicated. The alignment was generated using ClustalW2.

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• SciCrunch
• 15 years ago - by Anonymous

Sleep EEG dataset from 8 subjects in European Data Format (EDF) including original recordings and their hypnograms as described in B Kemp, AH Zwinderman, B Tuk, HAC Kamphuisen, JJL Obery��. Analysis of a sleep-dependent neuronal feedback loop: the slow-wave microcontinuity of the EEG. IEEE-BME 47(9):1185-1194 (2000). The recordings were obtained from Caucasian males and females (21 - 35 years old) without any medication; they contain horizontal EOG, FpzCz and PzOz EEG, each sampled at 100 Hz. The sc* recordings also contain the submental-EMG envelope, oro-nasal airflow, rectal body temperature and an event marker, all sampled at 1 Hz. The st* recordings contain submental EMG sampled at 100 Hz and an event marker sampled at 1 Hz. The 4 sc* recordings were obtained in 1989 from ambulatory healthy volunteers during 24 hours in their normal daily life, using a modified cassette tape recorder. The 4 st* recordings were obtained in 1994 from subjects who had mild difficulty falling asleep but were otherwise healthy, during a night in the hospital, using a miniature telemetry system with very good signal quality.

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• SciCrunch
• 14 years ago - by Anonymous

This software package implements an algorithm for accurate and consistent segmentation / labeling on a group of images. The images should be in Analyze format with paired header and image files. All images should be preprocessed so that they have been affinely aligned together.

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• SciCrunch
• 13 years ago - by Anonymous

Resource out of service. Documented on May, 5th, 2021.The Dali Database is based on all-against-all 3D structure comparison of protein structures in the Protein Data Bank (PDB). The structural neighborhoods and alignments are automatically maintained and regularly updated using the Dali search engine. The Dali Database contains structural alignments of PDB90 versus the full PDB using DaliLite. The data can be viewed interactively here, or downloaded in its entirety Users may search by PDB identifier or keyword.

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• SciCrunch
• 17 years ago - by Anonymous

A GUI desktop tool for calculating and displaying metrics to assess the success of Next Generation Sequencing mapping tools. BAMstats is written in Java and based around the Picard API.

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• SciCrunch
• 13 years ago - by Anonymous

Database of human histone variants, sites of their post-translational modifications and various histone modifying enzymes. The database covers 5 types of histones, 8 types of their post-translational modifications and 13 classes of modifying enzymes. Many data fields are hyperlinked to other databases (e.g. UnprotKB/Swiss-Prot, HGNC, OMIM, Unigene etc.). Additionally, this database also provides sequences of promoter regions (-700 TSS +300) for all gene entries. These sequences were extracted from the UCSC genome browser. Sites of post-translational modifications of histones were manually searched from PubMed listed literature. Current version contains information for about ~50 histone proteins and ~150 histone modifying enzymes. HIstome is a combined effort of researchers from two institutions, Advanced Center for Treatment, Research and Education in Cancer (ACTREC), Navi Mumbai and Center of Excellence in Epigenetics (CoEE), Indian Institute of Science Education and Research (IISER), Pune.

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• SciCrunch
• 15 years ago - by Anonymous

A set of tools to perform diffusion-weighted MRI white matter tractography in the presence of crossing fibres, using Constrained Spherical Deconvolution (Tournier et al.. 2004; Tournier et al. 2007), and a probabilisitic streamlines algorithm (e.g. Behrens et al., 2003; Parker et al., 2003). These applications have been written from scratch in C++, using the functionality provided by the GNU Scientific Library, and gtkmm. The software is currently capable of handling DICOM, NIfTI and AnalyseAVW image formats, amongst others. Installation * Unix/Linux * Microsoft Windows * Mac Os X, THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025.

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• SciCrunch
• 14 years ago - by Anonymous

Database of morphological phenotypes caused by mutation of essential genes in Saccharomyces cerevisiae, it allows storing, retrieving, visualizing and data mining the quantitative single-cell measurements extracted from micrographs of the temperature-sensitive (ts) mutant cells. PhenoM allows users to rapidly search and retrieve raw images and their quantified morphological data for genes of interest. The database also provides several data-mining tools, including a PhenoBlast module for phenotypic comparison between mutant strains and a Gene Ontology module for functional enrichment analysis of gene sets showing similar morphological alterations. About one-fifth of the genes in the budding yeast are essential for haploid viability and cannot be functionally assessed using standard genetic approaches such as gene deletion. To facilitate genetic analysis of essential genes, we and others have assembled collections of yeast strains expressing temperature-sensitive (ts) alleles of essential genes. To explore the phenotypes caused by essential gene mutation we used a panel of genetically engineered fluorescent markers to explore the morphology of cells in the ts strain collection using high-throughput microscopy. The database contains quantitative measurements of 1,909,914 cells and 78,194 morphological images for 775 temperature-sensitive mutants spanning 491 different essential genes in permissive temperature (26* C) and restrictive temperature (32* C). The morphological images were generated by high-content screening (HCS) technology.

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• SciCrunch
• 15 years ago - by Anonymous

Comprehensive set of protein domain families automatically generated from UniProt Knowledge Database. Automated clustering of homologous domains generated from global comparison of all available protein sequences., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025.

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• SciCrunch
• 17 years ago - by Anonymous

Functional Analysis of Transcriptional Networks (FunNet) is designed as an integrative tool for analyzing gene co-expression networks built from microarray expression data. The analytical model implemented in this tool involves two abstraction layers: transcriptional (i.e. gene expression profiles) and functional (i.e. biological themes indicating the roles of the analyzed transcripts). A functional analysis technique, which relies on Gene Ontology and KEGG annotations, is applied to extract a list of relevant biological themes from microarray gene expression data. Afterwards multiple-instance representations are built to relate relevant biological themes to their annotated transcripts. An original non-linear dynamical model is used to quantify the contextual proximity of relevant genomic themes based on their patterns of propagation in the gene co-expression network (i.e. capturing the similarity of the expression profiles of the transcriptional instances of annotating themes). In the end an unsupervised multiple-instance spectral clustering procedure is used to explore the modular architecture of the co-expression network by grouping together biological themes demonstrating a significant relationship in the co-expression network. Functional and transcriptional representations of the co-expression network are provided, together with detailed information on the contextual centrality of related transcripts and genomic themes. FunNet is provided both as a web-based tool and as a standalone R package. The standalone R implementation can be run on any operating system for which an R environment implementation is available (Windows, Mac OS, various flavors of Linux and Unix) and can be downloaded from the FunNet website, or from the worldwide mirrors of CRAN. Both implementations of the FunNet tool are provided freely under the GNU General Public License 2.0. Platform: Online tool, Windows compatible, Mac OS X compatible, Linux compatible, Unix compatible

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• SciCrunch
• 15 years ago - by Anonymous

Re-annotated gene expression / proteomics data from GEO by relating all probe IDs to Entrez Gene IDs once every three months, enabling you to find data from GEO, and compare them from different platforms and species. Platform Annotations adds the latest annotations to any uploaded probe / gene ID list file. Platform Comparison compares any two platforms to find corresponding probes mapping to the same gene. Cross-species mapping maps platform annotations to other species. Gene Search finds deposited platforms and samples in GEO that contain a list of genes. GPL ID Search finds the GPL ID (GEO platform ID) for your array. You can also download the latest annotations files for all arrays and their comprehensive universal gene identifier table, which relates all types of gene / protein / clone identifiers to Entrez Gene IDs for all species. Note: The database was last updated on 4/30/2011. They have successfully mapped 54932732 individual probes from 385099 GEO samples measuring 3519 GEO platforms across 217 species.

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• SciCrunch
• 17 years ago - by Anonymous