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Latest publications: ELDERMET research has recently been published in the Proceedings of the National Academy of Sciences (USA). This work focuses on the composition and stability of the intestinal bacteria in older Irish adults. Read the paper here. Would you like to be part of ELDERMET? We are currently looking for people, aged 65 years or older, living in the community. All we ask is that you live in the Cork area, or are willing to travel to Cork, and have recently (within the last two/three weeks) taken any kind of antibiotic. It doesnt matter if you are still taking the antibiotic, as long as the finishing date isnt more than four weeks before your first visit to ELDERMET. ELDERMET Objectives To assess the composition of the faecal microbiota of elderly volunteers in the Irish population, using state-of-the-art molecular techniques. To correlate diversity, composition, and metabolic potential of the faecal microbial metagenome with health, diet and lifestyle indices that are a) likely to be influenced by the microbiota or b) to influence the microbiota. To develop recommendations for specific dietary ingredients, foodstuffs, functional foods and/or dietary supplements, that will improve the health of elderly consumers. To provide evidence-based recommendations for prospective studies to determine the molecular mechanisms for health improvements promoted by specific food ingredients that modulate components of the microbiota. ELDERMET Rationale The human intestinal microbiota is made up of approximately 1000 genetically unique organisms (phylotypes ) [1]. The bacteria present in the intestine make an important contribution to: metabolism executed in the gut [2] health, in diverse activites from pain perception [3] to cognitive function [4]. There is an increasing body of evidence linking alterations in the human gut microbiota with Inflammatory Bowel Disease [5, 6] and Irritable Bowel Syndrome [7]. The changing pattern of the gut microbiota in elderly subjects [8, 9] may be linked to host changes such as immunosenescence, increased susceptibility to disease and potentially systemic effects. The composition of the intestinal microbiota may be modulated by dietary components including prebiotics [10]. ELDERMET will determine the baseline composition of the gut microbiota of several hundred elderly Irish subjects using a combination of traditional culutre and molecular (culture-independent) methodologies. ELDERMET will explore potential correlations between microbiota composition and a range of health indices; cross-referencing data to dietary intake. Data will be analyzed in the context of the related FHRI projects in Nutrigenomics, Food Consumption, Food Safety, and Diet-Health. ELDERMET will provide recommendations to all stakeholders (including health practitioners and the health service, the food industry and the general public) on how to improve health based on defined modifications to dietary intake. Sponsor. This work is supported by the Goverment of Ireland Department of Agriculture Fisheries and Food/Health Research Board Food for Health Research Initiative award to the ELDERMET project as well as by a Science Foundation Ireland award to the Alimentary Pharmabiotic Centre. M.J.C. is now funded by a fellowship from the Health Research Board of Ireland.

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• SciCrunch
• 17 years ago - by Anonymous

THIS RESOURCE IS NO LONGER IN SERVICE, documented on March 11, 2013. Web-based tool to explore the relationship between population frequency and extended linkage disequilibrium measured as haplotype homozygosity of observed haplotypes within a specified candidate region. Haplotype homozygosity (HH) is an effective measure of linkage disequilibrium (LD) for more than 2 markers. If we want to see, how LD breaks down with increasing distance to a specified core region, we can calculate HH in a stepwise manner as extended HH (EHH, Sabeti et al. 2002). EHH is calculated between a distance x and the specified core region for a chromosome population carrying a single core haplotype. Distance x increases stepwise to the most outlying marker. The procedure is repeated for each core haplotype. HH is evaluated as HH = sum(pi2) - 1/n / 1 - 1/n with pi being the relative haplotype frequency and n the sample size. It corrects for sampling effects (Sabatti & Risch 2002). The variance of HH is estimated according to Nei (1975). EHH estimates the level of haplotype splitting due to recombination and mutation at extended regions on both sides of a specified core region. It may be used to explore haplotype-specific LD patterns, e.g. for disease associated haplotypes. In combination with the core haplotype frequency it may also serve as an indicator of recent positive selection. Frequent core haplotypes with an unusually high long-range LD are supposed to be positively selected. The various core haplotypes can serve as internal controls. Input file: A text file consisting of a haplotype (chromosome) population

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• SciCrunch
• 17 years ago - by Anonymous

A software tool, text mining based, for annotating text with gene ontology terms. The tool combines knowledge-driven methods on top of a standard vector- space retrieval approach to identify pointers to ontology terms. Passage selection methods were tested based on vocabulary density estimation using several terminologies of the domain. The tool improves on standard retrieval approaches based on vector-space similarities by using a Boolean completion principle.

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• SciCrunch
• 17 years ago - by Anonymous

Drew Scientific manufactures and sells Analytical Instruments and Reagents world-wide : Cell Counters for Clinical Hematology Cell Counters for Veterinary Hematology and Research Hemoglobin Analyzers for Diabetes (HbA1c) Reagents and Controls You can place an order on us in a variety of ways : by post, by fax, or by email. See the Contact Us page for addresses and telephone numbers. This section is to enable you to send an order by email. We need the following information : Your Order Number Your Company or Organisation Your contact name (and phone number if we don''t already know it). Your full email address. This is essential so that we can reply to you. The Delivery details (As Normal is acceptable if you are a frequent customer.) Your requested delivery date. A list of the items you require, with Part Number and Quantity. We will acknowledge your order by email, confirming the availability of the items, the delivery date, the price and the delivery details. In many parts of the world our customers are supported by our local distributors. If appropriate, we will pass your order to the relevant distributor and put them in touch with you. You can fill in the email order form directly with the above information, or you may use the Frequent Items tab to add those items that are most frequently ordered. Please use the Spares or Consumables lists to find the Part Numbers of any other items you require. But please do this before you start to fill in the Order Form, because if you leave this Ordering section before submitting your order, you will lose any data you have entered, and will have to enter it again.

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• SciCrunch
• 17 years ago - by Anonymous

The ImageJ installations below correspond to the WCIF ImageJ manual. The manual is written for this particular installation of ImageJ. This ImageJ installation has, among other plugins, one that links to an online version of the manual. The online manual is more up-to-date than the PDF version. Windows users Download WCIF ImageJ bundle (~23Mb) v1.34i, 3rd March 2005 with J2SE 5.0 (formerly J2SE 1.5). For Windows: download and run program. Mac and Linux users Download your OS specific version of ImageJ from the ImageJ website then extract the following file to the plugins folder. Download WCIF ImageJ bundle plugins only (~2Mb) This contains only the plugins, IJ preferences, LUTs and plugin source code. Image Processing and Analysis Software ImageJ LSM Browser (*.lsm) Axiovision viewer (*.zvi) Manufacturers of our microscopes and related equipment Zeiss - Microscopes and imaging systems. P.A.L.M. Microlaser Technologies - Manufacturer of our laser capture system. Sutter Instruments - Micromanipulators. Uniblitz - Shutters. Ludl - Manufacturers of our motorised x-, y-stage Hamamatsu - Digital cameras. Molecular Probes - Dyes and reagents. Scanalytics - Image acquisition and processing software. MicroBrightField - Developers of the Neurolucida and Stereo Investigator software. DVC - Digital cameras. Bitplane - Developers of the Imaris suite of software. AutoQuant - Developers of the AutoDeblur deconvolution software

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• SciCrunch
• 17 years ago - by Anonymous

This is the website of the Structural Brain Mapping Group at the Department of Psychiatry, University of Jena. Our principal research focuses on the development of methods for structural brain imaging and their application. Specific areas of interest include the investigation of structural brain plasticity and schizophrenia research. Regional structural brain changes are among the most robust biological findings in schizophrenia, yet the underlying pathophysiological changes remain poorly understood. Recent evidence suggests that abnormal neuronal/dendritic plasticity is related to alterations in membrane lipids. We examined whether serum activity of membrane lipid remodeling/repairing cytosolic phospholipase A2 (PLA2) were related to regional brain structure in magnetic resonance images (MRI). The study involved 24 schizophrenia patients, who were either drug-nave or off antipsychotic medication, and 25 healthy controls. Using voxel-based morphometry (VBM) analysis of T1-high-resolution MRI-images, we correlated both gray matter and white matter changes with serum PLA2-activity. PLA2 activity was increased in patients, consistent with previous findings. VBM group comparison of patients vs. controls showed abnormalities of frontal and medial temporal cortices/hippocampus, and left middle/superior temporal gyrus in first-episode patients. Group comparison of VBM/ PLA2-correlations revealed a distinct pattern of disease-related interactions between gray/white matter changes in patients and PLA2-activity: in first-episode patients (n = 13), PLA2-activity was associated with structural alterations in the left prefrontal cortex and the bilateral thalamus. Recurrent-episode patients (n = 11) showed a wide-spread pattern of associations between PLA2-activity and structural changes in the left (less right) prefrontal and inferior parietal cortex, the left (less right) thalamus and caudate nucleus, the left medial temporal and orbitofrontal cortex and anterior cingulum, and the cerebellum. Our findings demonstrate a potential association between membrane lipid biochemistry and focal brain structural abnormalities in schizophrenia. Differential patterns in first-episode vs. chronic patients might be related to PLA2-increase at disease-onset reflecting localized regenerative activity, whereas correlations in recurrent- episode patients might point to less specific neurodegenerative aspects of disease progression.

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• SciCrunch
• 17 years ago - by Anonymous

The genome of the domesticated dog, a close evolutionary relation to human, is a powerful new tool for understanding the human genome. Comparison of the dog with human and other mammals reveals key information about the structure and evolution of genes and genomes. The unique breeding history of dogs, with their extraordinary behavioral and physical diversity, offers the opportunity to find important genes underlying diseases shared between dogs and humans, such as cancer, diabetes, and epilepsy. The Canine Genome Sequencing Project produced a high-quality draft sequence of a female boxer named Tasha. By comparing Tasha with many other breeds, the project also compiled a comprehensive set of SNPs (single nucleotide polymorphisms) useful in all dog breeds. These closely spaced genomic landmarks are critical for disease mapping. By comparing the dog, rodent, and human lineages, researchers at the Broad Institute uncovered exciting new information about human genes, their evolution, and the regulatory mechanisms governing their expression. Using SNPs, researchers describe the strikingly different haplotype structure in dog breeds compared with the entire dog population. In addition, they show that by understanding the patterns of variation in dog breeds, scientists can design powerful gene mapping experiments for complex diseases that are difficult to map in human populations. Contribute Although the astounding generosity of Eli and Edythe L. Broad and several other venture philanthropists empowers our scientists to tackle many of the most important problems at the cutting edge of genomic medicine, there are many other critical challenges that they cannot yet pursue because of limited resources. We need additional visionary partners to join the Broads and the Broad Institute in transforming medicine with the power of genomics.

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• SciCrunch
• 17 years ago - by Anonymous

Sustainability plan EpiData Software has since 2000 grown from securing the principles of Epi Info V6 to an independent and documentation based system with several translations and numerous downloads. To secure continued viability organisations and governments work is being done to secure for the future, see also the license principles - the ambition is to convert the programs to open-source within few years. Contributions are used for costs of development after version 1.5 (e.g. refining of programming, enhancing speed, maintenance of website, to pay for absence from paid work to do EpiData or other developmental and promotional efforts for EpiData). About the EpiData Association EpiData Software is from EpiData Entry version 2.0 and above released by the non-profit organisation The EpiData Association Odense, Denmark (In Danish: EpiData foreningen). The association receives NO baseline budget from anyone. The association has no employees Postal adress is: The EpiData Association, att. Jens Lauritsen, Enghavevej 34, DK5230 Odense M, Denmark, Europe The body of users of EpiData form the most important part of the basis of the EpiData Association. Those who choose to register as users will be asked when desicions are to made regarding additions to the program. Needs for documentation etc. Registration is done by adding your e-mail to the Information list. Supporting members or institutions adds to the foundation and development of EpiData by securing funding to pay for the associated costs. List of donors. The board of the association is made up of the core persons developing EpiData, currently Jens M.Lauritsen and Michael Bruus in collaboration with experienced users and the Friends Of EpiData group (FoED), comprising a group of international persons wishing to support the development of EpiData Sponsor. Without support from a number of NGO''s, Universities, Regional Health Authorities and other funding bodies EpiData development would have stopped

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• SciCrunch
• 17 years ago - by Anonymous

This web site is your introduction to the world of Florida Aquaculture. It represents a compilation of information about a division in the Florida Department of Agriculture and Consumer Services-the Division of Aquaculture. The Division plays a key role in the regulation of aquaculture facilities and shellfish processing plants, is responsible for opening/closing of shellfish harvesting waters to protect human health, ensures the continued productivity of oyster reefs through a restoration program and issues leases of submerged state lands for aquaculture. The creation of this division is unprecedented for a state agriculture department. Florida''s Division of Aquaculture is one-of-a-kind and serves a unique industry like no other in the United States. Please browse this site and learn more about Florida Aquaculture. I welcome your comments on the topics contained in this web site.

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• SciCrunch
• 17 years ago - by Anonymous

his table shows the metadata and links to sources of the data and citations associated with the publicly available metagenome sequences used in the Dinsdale, Edwards, et al., analysis of 87 different metagenomes. The links will take you to the annotated sequences in the metagenomics SEED, CAMERA, and the NCBI Short Read Archve. Please note that all metagenomes are currently available to download via the ftp links, some are available in the meta-RAST, and other links will be added as soon as they become available. Citations for individual metagenomes will also be added as and when they become available. DNA sequences for all metagenomes are avaialble via anonymous FTP. Sponsor. This project was supported by the Gordon and Betty Moore Foundation Marine Microbial Initiative, National Science Foundation grants (F.R. and D.L.V.), a Department of Commerce ATP grant (F.R.), a National Research Initiative Competitive Grant from the USDA Cooperative State Research, Education and Extension Service (B.W.), the National Institute of Allergy and Infectious Diseases, the National Institutes of Health and the Department of Health and Human Services (R.S.).

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• SciCrunch
• 17 years ago - by Anonymous

Dialog provides critical information from the world''s most authoritative publishers, combined with the tools to search every bit of it with speed and precision. With direct operations in 27 countries, Dialog products and services are a combination of highly accurate online research tools offering access to unique and relevant databases designed to meet the specific needs of a wide range of users. Information professionals and end-users at business, professional, scientific, academic and government organizations in more than 100 countries prize Dialog services to meet their searching needs. As part of the Deep Web, which is estimated to be 500 times larger than the content accessible via Web search engines, Dialog products offer unparalleled depth and breadth of content coupled with the ability to search with precision and speed. Our collection of over 900 databases handles more than 700,000 searches and delivers over 17 million document page views per month. Searchable content on Dialog services includes articles and reports from thousands of real-time news feeds, newspapers, broadcast transcripts and trade publications, plus market research reports and analyst notes providing support for financial decision-making, as well as in-depth repositories of scientific and technical data, patents, trademarks and other intellectual property data. Additional content areas include government regulations, social sciences, food and agriculture, reference, energy and environment, chemicals, pharmaceuticals and medicine.

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• SciCrunch
• 17 years ago - by Anonymous

It was founded in 1985 by Professor Rury Holman, specialises in performing diabetes-related national and multinational mega trials in partnership with the NHS, NIH, MRC, BHF, DUK, academic institutions and industry. The DTU also undertakes major modelling and statistical programmes to utilise fully the data available from its many studies, with a particular emphasis on modelling diabetes and cardiovascular disease processes. Current studies include 4-T, ACE, TECOS and UKPDS~Post Study Monitoring. Sponsor. Funded by the UK National Institute for Health Research

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• SciCrunch
• 14 years ago - by Anonymous

R package to identify differentially expressed genes from RNA-Seq data.

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• SciCrunch
• 13 years ago - by Anonymous

The Diabetes Genetics Initiative is a collaboration of the Broad Institute of MIT and Harvard, Lund University, and Novartis Institutes for BioMedical Research The Diabetes Genetics Initiative combines the resources and expertise of the Novartis Institutes for BioMedical Research, the Broad Institute of MIT and Harvard, and Lund University to identify the genetic determinants of type 2 diabetes. This unique collaboration aims to collect and analyze samples from type 2 diabetic patients from nations across the globe, performing whole genome scans to provide a comprehensive view of the DNA sequence variants associated with the disease. This partnership has been forged with the explicit goal of making this vast amount of crucial data available to researchers globally and free of cost, which should lead to a greater understanding of disease biology and speed the development of more effective therapies. Contribute Although the astounding generosity of Eli and Edythe L. Broad and several other venture philanthropists empowers our scientists to tackle many of the most important problems at the cutting edge of genomic medicine, there are many other critical challenges that they cannot yet pursue because of limited resources. We need additional visionary partners to join the Broads and the Broad Institute in transforming medicine with the power of genomics.

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• SciCrunch
• 17 years ago - by Anonymous

This demonstration application illustrates how Hierarchical Temporal Memory (HTM) can be applied to video recognition. The HTM network in this demo has been trained to locate people in surveillance video footage. You can see how the HTM operates by experimenting with the sample videos that are bundled with this application. For each video, the application will process it in real time on your machine and track the locations of people and other moving objects, while correctly discriminating between the two. This demonstration application, called Vision4, gives a sense of how Hierarchical Temporal Memory (HTM) performs in recognizing objects in static images. Sponsor. Numenta has fewer than twenty employees and has been privately funded by its founders, board members, and close associates.

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• SciCrunch
• 17 years ago - by Anonymous

Core facility that provides the following services: Magnetic resonance spectrometer training service, Magnetic Resonance Instrument Access. Welcome to the Magnetic Resonance Facility of the Department of Chemistry and Chemical Biology, Harvard University, in the Laukien-Purcell Instrumentation Center.

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• SciCrunch
• 13 years ago - by Anonymous

His research interests cover many different questions in population genetics and molecular evolution. He considers himself an evolutionary geneticist, with strengths in computational biology and stochastic models. He has worked on frequency-dependent selection models, spatial genetic models, indel evolution models, sequence alignment, and phylogenetic models. His current research involves estimating indel rates and length distributions, applying population genetic models to phylogeny reconstruction, and finding de novo mutations and SNPs from next-gen sequencing of human genomes. In addition to running De Rerum Natura, Reed also manages the largest group blog on evolution, The Pandas Thumb. In addition he develops plugins and hacks for the Movable Type blogging software. He is an expert on dispatching MT under FastCGI and Lighttpd, as well as integrating it with jQuery. He was editor and designer of The Open Laboratory: The Best Science Writing on Blogs 2007. He is co-creator of Prof. Steve Steve. Partners. Movable Type Site Meter Melody Lulu

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• SciCrunch
• 17 years ago - by Anonymous

Daylight provides enterprise-level cheminformatics software technologies to life science companies. Our superior chemistry, high performance, and open architecture have earned Daylight a reputation for delivering the state-of-the-art in chemical information processing since 1987. Daylight Chemical Information Systems, Inc. is a privately held company with corporate offices in Aliso Viejo, CA and research offices in Santa Fe, NM and Cambridge, England. Support At Daylight, support means a wide array of services that are designed to empower users to make the most of Daylight software. We offer detailed administration documentation and guides through this website. Our User Group Meetings allow in-depth exploration of our technology. And, of course, our support staff is available to assist you whenever the need occurs. Download - Downloading current releases as well as contributed code, system requirements, installation directions, and release information Reference Guides - List of available documentation such as programming guides and user manuals. Cheminformatics - List of additional general resources including introductory materials, theory manual, tutorials and user meeting archives. Sponsor. Daylight

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• SciCrunch
• 17 years ago - by Anonymous

EH is a program to test and estimate linkage disequilibrium between different markers or between a disease locus and markers. This is an updated version in which the previous disease (case-control) option has been deleted (but see below how to work with case-control data). The program is written in Free Pascal, which is compatible with (but mch more flexible than) Turbo Pascal. Free Pascal is available for various platforms, e.g. Windows and Linux. The data are taken to consist of a number of individuals collected at random from a population. Based on these sample data, the EH program estimates allele frequencies for each marker. Haplotype frequencies are estimated with allelic association (H1) and without (H0). The EH program also provides log likelihood, chi-square and the number of degrees of freedom under hypotheses H0 and H1. For more information please refer to Terwilliger and Ott (1994). Notes: For sparse data (relatively few observations with large numbers of alleles), the chi-square approximation to the test statistics used by EH is unreliable. Then, more sophisticated programs are recommended. Another program for estimating haplotype frequencies is SNPHAP. It is very flexible although it is restricted to analyzing bi-allelic markers. Also, PHASE is very useful for estimating haplotype frequencies and for inferring haplotypes to individuals. See Marchini et al. (2006). Files in this package (Windows): EH.PAS: Source code of EH program. EH.EXE: Executable code of EH program, which is compiled with a maximum of 30 alleles per locus, 10 loci, 1000 haplotypes, and 3600 genotype patterns (product of numbers of genotypes at each locus). EH.DAT, EH.OUT, etc: Sample input and output files. Input file The EH program does not require additional programs although you need a Pascal compiler (Free Pascal) to recompile the program when you change program constants. There is one input file whose name the user can determine, for example, EH.DAT (this is the default name). It contains the numbers of alleles for each marker and the observations for each genotype. First line: Number of alleles at the first marker, number of alleles at the second marker, and so on. Assuming you have 2 markers, the first marker has 2 alleles and the second marker has 3, you write 2 3 in the first line. The order of markers in the remainder of the input file is determined by the order of markers you entered in the first line. Subsequent lines: Number of observations for given genotypes. These numbers must be arranged as follows: The number of columns is the number of the possible genotypes at the last locus. Let M be the number of alleles at the last locus, then the number of the possible genotypes equals M(M 1)/2. For example, if the last locus has two alleles, then there are 3 possible genotypes which are 1/1, 1/2 and 2/2. Therefore, in each row there are 3 columns corresponding to the genotypes 1/1, 1/2, 2/2. Similarly, if the last marker has three alleles, then there are 6 columns corresponding to 1/1, 1/2, 2/2, 1/3, 2/3, 3/3. The number of rows is the product of the number of the possible genotypes at the first (N - 1) markers, where N is the total number of markers. That is, no. of rows = L1(L1 1)/2 L2(L2 1)/2 ... Li(Li 1)/2 ..., where Li is the number of alleles at the i-th locus. For example, assume you have 3 loci and the first and the second locus each have 2 alleles, and the third locus has 3 alleles. Thus, there are 6 columns and 9 rows (see example 1 below). However, if the first locus has 3 alleles and the second and third have 2 alleles each, there are 18 rows and 3 columns. The output file from the EH program, EH.OUT by default, contains the estimated haplotype frequencies and their corresponding log likelihoods. Sponsor. supported by the Wellcome Trust, the National Institutes of Health (NIH), The SNP Consortium, the Wolfson Foundation, the Nuffield Trust, and the Engineering and Physical Sciences Research Council. M.S. is supported by NIH grant 1RO1HG/LM02585-01. N.P. is a recipient of a K-01 NIH career-transition award. G.R.A. is supported by NIH National Human Genome Research Institute grant HG02651. E.E. is supported by the California Institute for Telecommunications and Information Technology, Calit2. Computational resources for HAP were provided by Calit2 and National Biomedical Computational Resource grant P41 RR08605 (National Center for Research Resources, NIH).