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A REST-based web application designed for visualizing deep sequencing data and other genome annotation data.
Proper citation: Anno-J (RRID:SCR_008192) Copy
The Fungal Genetics Stock Center is a resource available to the Fungal Genetics research community and to educational and research organizations in general. While some fungi can cause disease in humans, most people have innate immunity against fungi. Some people with diseases of the immune system are at increased risk of infection by fungi. Drugs have been developed in the last 5 years that help with this. Fungal Genetics is the study of genes and genetic traits in fungi. In the past this has been important in the elucidation of what a gene is, what the genetic material is, how genes relate to enzymes, how enzymes relate to traits and how important traits change or evolve. In the present, Fungal Genetics is important to understanding how fungi are pathogens of plants and animals, how fungi can be used in industry for the production of enzymes, chemicals, food, and drugs. Fungi are also essential to processing bio-mass in the attempt to use ethanol as a fuel source. The FGSC is funded largely by a grant from the National Science Foundation (Award Number 0235887) of the United States of America. Sponsors: Supported by a grant from the National Science Foundation.
Proper citation: Fungal Genetics Stock Center (RRID:SCR_008143) Copy
http://www.projects.roslin.ac.uk/cdiv/
THIS RESOURCE IS NO LONGER IN SERVICE, documented on July 16, 2013. The objective of the project is the standardization of micro-satellite markers used within participating laboratories, use of DNA markers to define genetic diversity and to enable monitoring of breeds to promote conservation programs where required, and the determination of diversity present in rare and local breeds across Europe. The blood typing laboratories are now beginning to use micro-satellite markers as an alternative to serology for parentage verification, and are selecting a common set to be used from the several hundred micro-satellite markers available that cover the bovine genome, produced as part of the Bovine genome mapping project (See BovMaP). Work with micro-satellite markers has shown that they are valuable tools for examining genetic diversity and phylogeny in many species. However, for work carried out in different laboratories to be comparable, it is essential that the same markers are used. To maintain the compatibility of data generated by the various typing labs, it is essential that all laboratories adopt the same markers and typing protocols. It is therefore of paramount importance that the blood typing laboratories and research labs that are examining the genetic structure of the cattle populations adopt a common panel of the best micro-satellite markers available. Some pilot comparative work has been undertaken through the International Society for Animal Genetics, but so far this has only involved the blood typing laboratories. One objective of this project is to facilitate the comparison of the micro-satellite markers currently in use in the different types of laboratory and determine the efficiency of the markers available in revealing genetic differences within and among breeds. It will also be important to compare the use of markers in different laboratories to determine how robust they are and how easily results can be compared. From comparison of the markers, those that are most suitable will be selected to form a panel which will be recommended for pedigree validation and genetic surveys. Cattle are an important source of food in Europe, and intense selection has resulted in the development of specialized breeds. Selection for high-producing dairy cattle has been successful, but one associated drawback is that the cattle population, both in Europe and North America, has been skewed dramatically towards one breed, the Holstein/Friesian. So there has been a decline in the number of individuals of other breeds, and hence a general erosion of the genetic base of the cattle population. The progressive move towards the North American-type Holstein animals has also resulted in the requirement for high input/high output farming and intensive management schemes. The impact of this on the environment has been significant, e.g. pollution problems arising from the need for high nitrogen fertilizers to produce sufficient high quality fodder, and disposal problems associated with slurry waste. Poorer areas of the community have been unable to compete with such farming systems, and are more suited to low input/low output farming using traditional stock. It is however the future perspective that is of greatest concern. It is impossible to predict requirements for cattle production - quality, production type, management systems, etc. The ability to switch rapidly to alternative production will be dependent on the genetic base of the population available to selection programs. It is therefore essential to maintain the greatest genetic diversity possible in the cattle population. Whilst current farming practices are perceived to be both efficient and acceptable, the breeds less favored by commercial farmers will dwindle. It is therefore important that on an European scale efficient management of these breeds maintains the widest genetic base possible. This project aims to carry out a survey of the current genetic base of the European cattle population and to provide the tools to assist breeding programs to maintain a broad base. The blood typing laboratories are now beginning to use micro-satellite markers as an alternative to serology for parentage verification, and are selecting a common set to be used from the several hundred micro-satellite markers available that cover the bovine genome, produced as part of the Bovine genome mapping project. Early work to measure genetic diversity used blood groups to show differences between breeds and the diversity present. Unfortunately, the number of loci available are limited, with only the B system being sufficiently polymorphic to be really useful. However, since there is a wealth of information available from such typing, this information can be used to estimate changes in the genetic structure of cattle populations across Europe over the past twenty years. More recently mini-satellite probes have been used to generate ''genetic fingerprints'' which have been used to show differences between individuals. Such fingerprints have been used to estimate genetic diversity - the greater the number of bands revealed by the fingerprint being equated with greater diversity. This is valid within limits. The main disadvantage of the fingerprint approach is that the chromosomal location and number of loci being sampled, and so the proportion of the genome examined, is unknown. The allelic bands on the gel cannot be easily identified, so allele inheritance cannot be addressed making it impossible to trace ancestry. Through the EC funded BovMaP project, large numbers of highly polymorphic micro-satellite markers have become available, which are being mapped on the bovine genome. These markers are particularly suited to measuring genetic diversity, and markers can be selected to cover the entire genome.
Proper citation: CaDBase: Genetic diversity in cattle (RRID:SCR_008146) Copy
http://locus.jouy.inra.fr/cgi-bin/bovmap/intro.pl
THIS RESOURCE IS NO LONGER IN SERVICE, documented August 22, 2016. Database containing information on the cattle genome comprising loci list, phenes list, homology query, cattle maps, gene list, and chromosome homology. The objective of BovMap is to develop a set of anchored loci for the cattle genome map. In total, 58 clones were hybridized with chromosomes and identified loci on 22 of the 31 different bovine chromosomes. Three clones contained satellite DNA. Two or more markers were placed on 12 chromosomes. Sequencing of the microsatellites and flanking regions was performed directly from 43 cosmids, as previously reported. Primers were developed for 39 markers and used to describe the polymorphism associated with the corresponding loci. Users are also allowed to summit their own data for Bovmap. An integrated cytogenetic and meiotic map of the bovine genome has also been developed around the Bovmap database. One objective that Bovmap uses as the mapping strategy for the bovine genome uses large insert clones as a tool for physical mapping and as a source of highly polymorphic microsatellites for genetic typing.
Proper citation: BovMap Database (RRID:SCR_008145) Copy
The E. coli Genome Project has the goal of completely sequencing the E. coli and human genomes. They began isolation of an overlapping lambda clonebank of E. coli K-12 strain MG1655. Those clones served as the starting material in our initial efforts to sequence the whole genome. Improvements in sequencing technology have since reached the point where whole-genome sequencing of microbial genomes is routine, and the human genome has in fact been completed. They initiated additional sequencing efforts, concentrating on pathogenic members of the family Enterobacteriaceae -- to which E. coli belongs. They also began a systematic functional characterization of E. coli K-12 genes and their regulation, using the whole genome sequence to address how the over 4000 genes of this organism act together to enable its survival in a wide range of environments.
Proper citation: E. coli Genome project (RRID:SCR_008139) Copy
THIS RESOURCE IS NO LONGER IN SERVICE, documented August 18, 2016. Provides opportunities for information sharing and research collaboration among NIDAs networks across the country. It gives researchers and clinicians access to networks locations, people, expertise, and resources to help synergize efforts, improve efficiency, and accelerate scientific discovery. It currently consists of 14 networks and more than 230 sites involved in research and data collection sponsored by NIDA around the nation. The NNP was developed to provide the opportunity for these organizations to learn about each other and potentially work together on research collaboration and data collection in the future. In December 2008, NIDA added the first in a series of Research Interest Groups to the NNP to encourage more interdisciplinary collaboration among network and non-network grantees.
Proper citation: NIDA Networking Project: Facilitating information exchange and research collaboration (RRID:SCR_008138) Copy
http://www.glycoforum.gr.jp/science/word/wordE.html#indexW
Glycoword presents up-to-the-minute glycoscience-related keywords, selected by researchers in various fields of the science and interpreted intelligibly by specialists with expertise on each of the fields in the hope of bringing about a better understanding of the rapidly growing modern glycoscience. The website contains information on the following: -lectin -proteoglycan -glycoprotein -glycolipid -saccharide -glycotechnology -glycopathology -glycogene -structural glycobiology -immunity & sugar chain -nervous system & sugar chain -comparative glycomics and life evolution -glycobiology in plant defense -infection & sugar chain -quality control, trafficking and sorting of glycoproteins -fertilization / development & sugar chain
Proper citation: Glycoword (RRID:SCR_008135) Copy
http://www.dhmc.org/goto/parkinson
A Parkinson's disease portal that provides information, materials, and programs to help Parkinson's patients and their care partners manage their everyday lives. The Center aims to enhance the quality of life for people with Parkinson's and their care partners and increase public awareness and education on Parkinson's disease. It provides resources for regional support group meetings, referrals to regional physicians, allied health professionals, home care agencies, and other resources, and information on current therapies and research programa. It also provides materials such as informational pamphlets and booklets, videos, DVDs, newsletters, and educational materials.
Proper citation: Parkinsons Center at Dartmouth-Hitchcock Medical Center (RRID:SCR_008096) Copy
http://www.cureparkinsons.org.uk
A patient led charity that funds research which will have an impact on the lives of people with Parkinson's, with the hope of an eventual cure for the condition. The Cure Parkinson's Trust has the clear goal of finding a cure for Parkinson's disease by investing in under resourced and underfunded projects that offer a possible cure in the future. This trust's primary role is identifying, funding and evaluating research projects, as well as hosting scientific forums to bring together relevant scientists within the field to discuss key areas of research and technology. Cure Parkinson's provides researchers with information on current research, research events, and the ability to apply for grants through the Cure Parkinson's Trust.
Proper citation: Cure Parkinson's Trust (RRID:SCR_008095) Copy
http://www.antibodies-online.com
Resells antibodies incorporating quality control metrics for antibody reagents. Antibodies-online is based in Germany and provides valuable content in terms of information about antibodies, recent research news and specific news about current antibodies. All these informations are generated by antibodies-online staff or external databases like Pubmed, EMBL Harvester or from Google Scholar.
Proper citation: Antibodies Online GmbH (RRID:SCR_008092) Copy
A portal to the Mouse Atlas of Gene Expression Project and Dissecting Gene Expression Networks in Mammalian Organogenesis Project. This Atlas will define the normal state for many tissues by determining, in a comprehensive and quantitative fashion, the number and identity of genes expressed throughout development. The resource will be comprehensive, quantitative, and publicly accessible, containing data on essentially all genes expressed throughout select stages of mouse development. Serial Analysis of Gene Expression (SAGE) is the gene expression methodology of choice for this work. Unlike expressed sequence tags (ESTs) and gene chip data, SAGE data are independent of prior gene discovery and are quantitative. Furthermore, SAGE data are digital, easily exchanged between laboratories for comparison and can be added to by scientists for years to come. Thus, this Atlas will include a data structure and data curation strategy that will facilitate the ongoing collection of gene expression data, even after the completion of this project. The Mouse Atlas project compromises 202 SAGE Libraries from 198 tissues. The list of libraries is available in a number of different groupings, including groups of libraries taken from specific tissue locations and libraries taken from specific developmental stages. Furthermore, this atlas will assemble gene expression profiles for a few focused experiments that will test hypotheses related to the techniques employed, tumor models and models of abnormal development. This will test the resource and provide quality control, validation and demonstrate applicability. Additionally, The Mammalian Organogenesis - Regulation by Gene Expression Networks (MORGEN) project will provide a complete, permanent, and accurate picture of mouse gene expression in the heart (atrioventricular canal and outflow tract), pancreas, and liver; new techniques to understand the interplay of proteins governing the expression of genes key to the development of these organ systems; and the identification of the master regulatory switches that control development of the tissues.
Proper citation: Mouse Gene Expression at the BC Cancer Agency (RRID:SCR_008091) Copy
http://bioinformatics.ekmd.huji.ac.il/milano/
THIS RESOURCE IS NO LONGER IN SERVICE, documented August 23, 2016. MILANO provides a useful tool for the automatic custom annotation of microarray results which is based on all the available literature. It has two major advances over similar tools: the ability to expand gene names to include all their informative synonyms while removing synonyms that are not informative and access to the GeneRIF database which provides short summaries of curated articles relevant to known genes. MILANO allows annotation of lists of genes derived from microarray results by user defined terms. The annotation strategy is based on counting the number of literature co-occurrences of each gene on the list with a user defined term. This strategy allows the customization of the annotation procedure and thus overcomes one of the major limitations of the functional annotations usually provided with microarray results. MILANO expands the gene names to include all their informative synonyms while filtering out gene symbols that are likely to be less informative as literature searching terms. It supports searching two literature databases: GeneRIF and Medline (through PubMed), allowing retrieval of both quick and comprehensive results. MILANO''s ability can improve microarray analysis by analyzing a list of 150 genes that were affected by p53 overproduction. This analysis reveals that it enables immediate identification of known p53 target genes on this list and assists in sorting the list into genes known to be involved in p53 related pathways, apoptosis and cell cycle arrest. This program performs automatic searches in PubMed or the GeneRIF collection for articles containing co-occurrences of search terms with a list of genes (e.g. from a microarray experiment). The program is used by pasting the list of Gene ID''s or symbols in the Primary Search Term field, and the list of cross-reference search terms in the Secondary Search Term field. The output is a table containing the number of hits for each pair of search terms. Sample input is provided in the fields, so you can just click submit and see what happens. If you want to run data of your own, delete the sample input first.
Proper citation: Microarray Literature-based Annotation (RRID:SCR_008206) Copy
MitoRes, is a comprehensive and reliable resource for massive extraction of sequences and sub-sequences of nuclear genes and encoded products targeting mitochondria in metazoa. It has been developed for supporting high-throughput in-silico analyses aimed to studies of functional genomics related to mitochondrial biogenesis, metabolism and to their pathological dysfunctions. It integrates information from the most accredited world-wide databases to bring together gene, transcript and encoded protein sequences associated to annotations on species name and taxonomic classification, gene name, functional product, organelle localization, protein tissue specificity, Enzyme Classification (EC), Gene Ontology (GO) classification and links to other related public databases. The section Cluster, has been dedicated to the collection of data on protein clustering of the entire catalogue of MitoRes protein sequences based on all versus all global pair-wise alignments for assessing putative intra- and inter-species functional relationships. The current version of MitoRes is based on the UniProt release 4 and contains 64 different metazoan species. The incredible explosion of knowledge production in Biology in the past two decades has created a critical need for bioinformatic instruments able to manage data and facilitate their retrieval and analysis. Hundreds of biological databases have been produced and the integration of biological data from these different resources is very important when we want to focus our efforts towards the study of a particular layer of biological knowledge. MitoRes is a completely rebuilt edition of MitoNuc database, which has been extensively modified to deal successfully with the challenges of the post genomic era. Its goal is to represent a comprehensive and reliable resource supporting high-quality in-silico analyses aimed to the functional characterization of gene, transcript and amino acid sequences, encoded by the nuclear genome and involved in mitochondrial biogenesis, metabolism and pathological dysfunctions in metazoa. The central features of MitoRes are: # an integrated catalogue of protein, transcript and gene sequences and sub-sequences # a Web-based application composed of a wide spectrum of search/retrieval facilities # a sequence export manager allowing massive extraction of bio-sequences (genes, introns, exons, gene flanking regions, transcripts, UTRs, CDS, proteins and signal peptides) in FASTA, EMBL and GenBank formats. It is an interconnected knowledge management system based on a MySQL relational database, which ensures data consistency and integrity, and on a Web Graphical User Interface (GUI), built in Seagull PHP Framework, offering a wide range of search and sequence extraction facilities. The database is compiled extracting and integrating information from public resources and data generated by the MitoRes team. The MitoRes database consists of comprehensive sequence entries whose core data are protein, transcript and gene sequences and taxonomic information describing the biological source of the protein. Additional information include: bio-sequences structure and location, biological function of protein product and dynamic links to both, external public databases used as data resources and public databases reporting complementary information. The core entity of the MitoRes database is represented by the protein so that each MitoRes entry is generated for each protein reported in the UniProt database as a nuclear encoded protein involved in mitochondrial biogenesis and function. Sponsors: MitoRes has been supported by Ministero Universit e Ricerca Scientifica, Italy (PRIN, Programma Biotecnologie legge 95/95-MURST 5, Proiect MURST Cluster C03/2000, CEGBA). Currently it is supported by operating grants from the Ministero dellIstruzione, dellUniversit e della Ricerca (MIUR), Italy (PNR 2001-2003 (FIRB art.8) D.M. 199, Strategic Program: Post-genome, grant 31-063933 and Project n.2, Cluster C03 L. 488/929).
Proper citation: MitoRes (RRID:SCR_008208) Copy
Merger of the Max Planck Institute of Neurobiology and the Max Planck Institute of Ornithology and has been renamed to Circuits - Computation – Models. Department devoted to the study of how the brain computes to understand neural information processing at the level of individual neurons and small neural circuits.
Proper citation: Max Planck Institute for Biological Intelligence Circuits - Computation – Models (RRID:SCR_008048) Copy
THIS RESOURCE IS NO LONGER IN SERVICE, documented August 29, 2016. An algorithm that finds articles most relevant to a genetic sequence. In the genomic era, researchers often want to know more information about a biological sequence by retrieving its related articles. However, there is no available tool yet to achieve conveniently this goal. Here, a new literature-mining tool MedBlast is developed, which uses natural language processing techniques, to retrieve the related articles of a given sequence. An online server of this program is also provided. The genome sequencing projects generate such a large amount of data every day that many molecular biologists often encounter some sequences that they know nothing about. Literature is usually the principal resource of such information. It is relatively easy to mine the articles cited by the sequence annotation; however, it is a difficult task to retrieve those relevant articles without direct citation relationship. The related articles are those described in the given sequence (gene/protein), or its redundant sequences, or the close homologs in various species. They can be divided into two classes: direct references, which include those either cited by the sequence annotation or citing the sequence in its text; indirect references, those which contain gene symbols of the given sequence. A few additional issues make the task even more complicated: (1) symbols may have aliases; and (2) one sequence may have a couple of relatives that we want to take into account too, which include redundant (e.g. protein and gene sequences) and close homologs. Here the issues are addressed by the development of the software MedBlast, which can retrieve the related articles of the given sequence automatically. MedBlast uses BLAST to extend homology relationships, precompiled species-specific thesauruses, a useful semantics technique in natural language processing (NLP), to extend alias relationship, and EUtilities toolset to search and retrieve corresponding articles of each sequence from PubMed. MedBlast take a sequence in FASTA format as input. The program first uses BLAST to search the GenBank nucleic acid and protein non-redundant (nr) databases, to extend to those homologous and corresponding nucleic acid and protein sequences. Users can input the BLAST results directly, but it is recommended to input the result of both protein and nucleic acid nr databases. The hits with low e-values are chosen as the relatives because the low similarity hits often do not contain specific information. Very long sequences, e.g. 100k, which are usually genomic sequences, are discarded too, for they do not contain specific direct references. User can adjust these parameters to meet their own needs.
Proper citation: MedBlast (RRID:SCR_008202) Copy
https://sites.google.com/site/dadadenoiser/
Infers both the sample genotypes and error parameters that produced a metagenome data set.
Proper citation: DADA (RRID:SCR_008205) Copy
http://neuroinformatics.usc.edu/
The USC Brain Project is engaged in the effort to develop new tools and methodologies for neuroinformatics in modeling neural mechanisms of visuomotor coordination and exploring the evolution of the human language-ready brain, as well as conducting work in both neural modeling and database construction in relation to rehabilitation after stroke. Sponsors: USCBP is funded by the University of Southern California.
Proper citation: University of Southern California Brain Project (RRID:SCR_008044) Copy
http://www.imagwiki.nibib.nih.gov/
Special interest group that brings together program officers who have a shared interest in applying modeling and analysis methods to biomedical systems. The meetings are formatted to facilitate an open discussion of what is currently being supported, and for planning future directions in these areas. At each meeting, time is allotted to hear focused presentations from one or two participants to discuss issues relating to modeling and analysis across the government agencies. Discussions also occur online, and participants are informed of talks, conferences and other activities of interest to the group. IMAG recognized that the modeling community is on the forefront of thinking across the biological continuum, rather than just focusing at one scale or level of resolution. In addition IMAG identified a strong desire among modelers to form multi-disciplinary partnerships across varied research communities. Overall Intent of IMAG through the MSM Consortium is: * To develop new methodologies that span across biological scales * To develop multiscale methodologies applicable to biomedical, biological and behavioral research * To develop methodologies within the local multidisciplinary team and within the larger Framework environment * To further promote multiscale modeling through model sharing This wiki contains information relevant to the IMAG (Interagency Modeling and Analysis Group) and the MSM (Multi-scale Modeling Consortium).
Proper citation: Interagency Modeling and Analysis Group and Multi-scale Modeling Consortium Wiki (RRID:SCR_008046) Copy
http://www.koki.hu/main.php?folderID=903
The aim of this laboratory is to understand how information is encoded in specific spatiotemporal activity patterns and structural configurations at the circuit, cellular, and molecular levels in the hippocampus, thereby enabling the process of memory. A major task is to find the neuronal codes of internal representations of memory items and the mapping rules between the levels of gene expression/proteins synthesis and the level of cognitive processing. Novel combinations of approaches, including multiple single-cell recording technology, patch-clamp electrophysiology, neuroanatomy/neurochemistry at the cellular and subcellular levels, and computational models are employed to test specific hypotheses about that mapping process (such as local circuit anatomy and activity-dependent short-term and long-term synaptic plasticity). Collaborations within the Institute allows the group to also incorporate gene targeting methods and behavioral learning/memory tests in their methodological repertoire. The laboratory has been focusing on the normal and pathological (epileptic, ischemic) activity of cortical networks, with particular attention to the generation of behaviour-dependent population discharge patterns (theta and gamma oscillations, hippocampal sharp waves). Anatomical, in vitro and in vivo electrophysiological, pharmacological and molecular techniques and modeling are combined to elucidate the functional roles of inhibitory cell types in the control of population synchrony and synaptic plasticity in the hippocampus, their local and subcortical modulation via selective afferent pathways (GABAergic and cholinergic septal, as well as serotonergic raphe input) and pre- or postsynaptic receptors. An expanding new direction of research is related to the role of endocannabinoid signaling in the activity-dependent modulation of GABAergic and glutamatergic transmission, and its involvement in anxiety-like behavior.
Proper citation: Institute of Experimental Medicine of the Hungarian Academy of Sciences: Laboratory of Cerebral Cortext Reserach (RRID:SCR_008041) Copy
http://www.scripps.edu/np/inia/index.html
Consortium set out to identify the molecular, cellular, and behavioral neuroadaptations that occur in the brain reward circuits associated with the extended amygdala and its connections. It is hypothesized that genetic differences and/or neuroadaptations in this circuitry are responsible for the individual differences in vulnerability to the excessive consumption of alcohol. Chronic exposure to alcohol results in neuroadaptive phenomena, including tolerance, sensitization, dependence, withdrawal, loss of control of drinking, and relapse that contribute to the development of excessive alcohol consumption. The INIA has the following goals: 1) To establish animal models to study specific neurobiological targets for vulnerability that lead to excessive consumption of alcohol at the molecular, cellular and neural circuit level of analysis, 2) To identify specific clusters of genes whose expression is regulated by alcohol and which are responsible for any given model of excessive alcohol consumption using gene expression arrays, differential display, mutagenesis directed at specific brain areas, and the development of new informatics tools to analyze and interpret gene expression, cellular circuitry and brain circuitry data with the use of transgenic and knockout approaches, and 3) To attract new and innovative investigators to the field of alcohol research by recruiting individuals for development of U01 grants and pilot projects and by developing online interactive capacity among INIA scientists and others, and by making the neuroinformatics integrated data sets accessible, searchable and interactive with other databases for all scientists interested in alcoholism research. The structure of INIA is envisioned as two domains, Dependence-induced drinking and Binge drinking, comprised of multiple U01 research grants. The flow of information within each domain moves from molecular, to cellular, to neurocircuitry levels of analysis. These U01s share information with the core facilities, which act as data depositories. The Administrative Core coordinates the flow of information among the Domains and Cores and disseminates the information back to the U01s. A Pilot Project program will identify exciting new areas for research and the continual recruitment of new investigators to the alcohol field. The INIA program is directed by an Administrative Core in close cooperation with the Animal Models, Gene Array and Neurocircuitry Cores via a Steering Committee and with the continual advice of the Scientific Advisory Committee.
Proper citation: Integrative Neuroscience Initiative on Alcoholism (RRID:SCR_008042) Copy
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