Wie wir das Immunsystem gezielt starken konnen
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ABSTRACT:
SUBMITTER: Schmiedel V
PROVIDER: S-EPMC8423507 | biostudies-literature |
REPOSITORIES: biostudies-literature
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Project description:The GMO Panel has previously assessed genetically modified (GM) cotton DAS-24236-5 × DAS-21Ø23-5 and concluded that it is as safe as its conventional counterpart and other appropriate comparators with respect to potential effects on human and animal health and the environment in the context of its intended uses. On 17 November 2020, the European Commission requested EFSA to evaluate new DNA sequence information and updated bioinformatics data for cotton DAS-24236-5 × DAS-21Ø23-5 and to indicate whether the conclusions of the GMO Panel on the previously assessed cotton DAS-24236-5 × DAS-21Ø23-5 remain valid. The new sequence data of DAS-24236-5 showed the change of one nucleotide that results in one amino acid substitution, in the newly expressed Cry1F (synpro_L620Q) compared to the sequence originally reported. The GMO Panel concludes that this amino acid substitution in the protein is a mutation. Nonetheless with the exception of the bioinformatics analysis, the studies performed for the risk assessment of Cry1F in cotton DAS-24236-5 × DAS-21Ø23-5 remain valid. In addition, the new sequencing data showed a change in one nucleotide in the 5' flanking region of DAS-21Ø23-5 compared to the original sequence reported on the stack cotton DAS-24236-5 × DAS-21Ø23-5. The bioinformatic analyses of the newly sequenced DAS-21Ø23-5 event in the stack DAS-24236-5 × DAS-21Ø23-5 shows that the nucleotide difference is in the 5' flanking region outside the ORFs that span the 5' junction and is therefore not considered further in the safety assessment. Based on the information provided, the GMO Panel concludes that the corrected sequence does not give rise to any safety concerns, and therefore, the original risk assessment of cotton DAS-24236-5 × DAS-21Ø23-5 remains valid.
| S-EPMC9234918 | biostudies-literature
Project description:MotivationDasty3 is a highly interactive and extensible Web-based framework. It provides a rich Application Programming Interface upon which it is possible to develop specialized clients capable of retrieving information from DAS sources as well as from data providers not using the DAS protocol. Dasty3 provides significant improvements on previous Web-based frameworks and is implemented using the 1.6 DAS specification.AvailabilityDasty3 is an open-source tool freely available at http://www.ebi.ac.uk/dasty/ under the terms of the GNU General public license. Source and documentation can be found at http://code.google.com/p/dasty/.Contacthhe@ebi.ac.uk.
| S-EPMC3167052 | biostudies-literature
Project description:A large number of diverse, complex, and distributed data resources are currently available in the Bioinformatics domain. The pace of discovery and the diversity of information means that centralised reference databases like UniProt and Ensembl cannot integrate all potentially relevant information sources. From a user perspective however, centralised access to all relevant information concerning a specific query is essential. The Distributed Annotation System (DAS) defines a communication protocol to exchange annotations on genomic and protein sequences; this standardisation enables clients to retrieve data from a myriad of sources, thus offering centralised access to end-users.We introduce MyDas, a web server that facilitates the publishing of biological annotations according to the DAS specification. It deals with the common functionality requirements of making data available, while also providing an extension mechanism in order to implement the specifics of data store interaction. MyDas allows the user to define where the required information is located along with its structure, and is then responsible for the communication protocol details.
| S-EPMC3441562 | biostudies-literature
Project description:BackgroundRoughly 25 years ago, the United States National Institute on Drug Abuse (US NIDA) initiated the creation of public use datasets for its National Household Survey on Drug Abuse, since re-named the National Survey on Drug Use and Health (NSDUH). The Substance Abuse and Mental Health Services Administration (SAMHSA), which assumed responsibility for the survey in 1992, has continued and expanded this effort to make the survey data available to researchers. During 2012, SAMHSA created a "Restricted-Use Data Analysis System" (R-DAS) to provide researchers with the capability to create tabulations using restricted NSDUH variables not otherwise available on the public-use files.MethodsThis methods focused article is intended to help potential users of R-DAS-like online data analysis systems by (i) clarifying statistical issues involving approximation of confidence intervals (CI), (ii) providing a way to estimate CI when tabular output is suppressed with an 'error message' based on confidentiality restrictions, and (iii) showing how to make pairwise comparisons of estimates not otherwise allowed.ResultsFor illustration purposes, some empirical estimates are presented on a topic of continuing of public health concern in the US namely, extra-medical use of pain relievers (generally opioids), where the drugs are being used to get high and otherwise outside the boundaries intended by prescribing clinicians.ConclusionThe R-DAS makes it possible to derive state-level estimates of male-female and age-related differences in incidence of extra-medical prescription pain reliever (EMPPR) use, not previously reported in peer-reviewed articles, and not available without research approaches described here.
| S-EPMC6003776 | biostudies-literature
Project description:BACKGROUND: Centralised resources such as GenBank and UniProt are perfect examples of the major international efforts that have been made to integrate and share biological information. However, additional data that adds value to these resources needs a simple and rapid route to public access. The Distributed Annotation System (DAS) provides an adequate environment to integrate genomic and proteomic information from multiple sources, making this information accessible to the community. DAS offers a way to distribute and access information but it does not provide domain experts with the mechanisms to participate in the curation process of the available biological entities and their annotations. RESULTS: We designed and developed a Collaborative Annotation System for proteins called DAS Writeback. DAS writeback is a protocol extension of DAS to provide the functionalities of adding, editing and deleting annotations. We implemented this new specification as extensions of both a DAS server and a DAS client. The architecture was designed with the involvement of the DAS community and it was improved after performing usability experiments emulating a real annotation task. CONCLUSIONS: We demonstrate that DAS Writeback is effective, usable and will provide the appropriate environment for the creation and evolution of community protein annotation.
| S-EPMC3115852 | biostudies-other
Project description:BackgroundThe Distributed Annotation System (DAS) is a network protocol for exchanging biological data. It is frequently used to share annotations of genomes and protein sequence.ResultsHere we present several extensions to the current DAS 1.5 protocol. These provide new commands to share alignments, three dimensional molecular structure data, add the possibility for registration and discovery of DAS servers, and provide a convention how to provide different types of data plots. We present examples of web sites and applications that use the new extensions. We operate a public registry of DAS sources, which now includes entries for more than 250 distinct sources.ConclusionOur DAS extensions are essential for the management of the growing number of services and exchange of diverse biological data sets. In addition the extensions allow new types of applications to be developed and scientific questions to be addressed. The registry of DAS sources is available at http://www.dasregistry.org.
| S-EPMC2031907 | biostudies-literature
Project description:BACKGROUND: DAS is a widely adopted protocol for providing syntactic interoperability among biological databases. The popularity of DAS is due to a simplified and elegant mechanism for data exchange that consists of sources exposing their RESTful interfaces for data access. As a growing number of DAS services are available for molecular biology resources, there is an incentive to explore this protocol in order to advance data discovery and integration among these resources. RESULTS: We developed DASMiner, a Matlab toolkit for querying DAS data sources that enables creation of integrated biological models using the information available in DAS-compliant repositories. DASMiner is composed by a browser application and an API that work together to facilitate gathering of data from different DAS sources, which can be used for creating enriched datasets from multiple sources. The browser is used to formulate queries and navigate data contained in DAS sources. Users can execute queries against these sources in an intuitive fashion, without the need of knowing the specific DAS syntax for the particular source. Using the source's metadata provided by the DAS Registry, the browser's layout adapts to expose only the set of commands and coordinate systems supported by the specific source. For this reason, the browser can interrogate any DAS source, independently of the type of data being served. The API component of DASMiner may be used for programmatic access of DAS sources by programs in Matlab. Once the desired data is found during navigation, the query is exported in the format of an API call to be used within any Matlab application. We illustrate the use of DASMiner by creating integrative models of histone modification maps and protein-protein interaction networks. These enriched datasets were built by retrieving and integrating distributed genomic and proteomic DAS sources using the API. CONCLUSION: The support of the DAS protocol allows that hundreds of molecular biology databases to be treated as a federated, online collection of resources. DASMiner enables full exploration of these resources, and can be used to deploy applications and create integrated views of biological systems using the information deposited in DAS repositories.
| S-EPMC2789070 | biostudies-literature
Project description:The efficacy and non-target arthropod effects of transgenic DAS-21023-5 × DAS-24236-5 × SYN-IR102-7 Bt cotton, expressing proteins Cry1Ac, Cry1F and Vip3Aa19, was examined through field trials in Brazil. Fifteen field efficacy experiments were conducted from 2014 through the 2020 growing season across six different states in Brazil to evaluate performance against key lepidopteran pests through artificial infestations of Chrysodeixis includens (Walker), Spodoptera frugiperda (J.E. Smith,1797), Spodoptera cosmioides (Walker, 1858) and Chloridea virescens (F., 1781), and natural infestations of Alabama argillacea (Hübner) and S. frugiperda. The impact of this Bt cotton technology on the non-target arthropod community in Brazilian cotton production systems was also assessed in a multi-site experiment. DAS-21023-5 × DAS-24236-5 × SYN-IR102-7 cotton significantly reduced the feeding damage caused by S. frugiperda, S. cosmioides, C. includens, C. virescens and A. argillacea, causing high levels of mortality (greater than 99%) to all target lepidopteran pests evaluated during vegetative and/or reproductive stages of crop development. Non-target arthropod community-level analyses confirmed no unintended effects on the arthropod groups monitored. These results demonstrate the value of transgenic Bt cotton containing event DAS-21023-5 × DAS-24236-5 × SYN-IR102-7 for consideration as part of an integrated approach for managing key lepidopteran pests in Brazilian cotton production systems.
| S-EPMC8096009 | biostudies-literature
Project description:Aim: To adapt, translate, and utilize the Dimensional Apathy Scale (DAS) in Amyotrophic Lateral Sclerosis (ALS) to the Spanish population. Method: We recruited 104 ALS patients (67 of their caregivers) and 49 controls. Participants completed the Spanish-translated DAS, Geriatric Depression Scale- Short form. Patients were also administered the ALS Functional Rating Scale-Revised (ALSFRS-R). Caregivers additionally completed the informant/caregiver-rated Spanish-translated DAS. The DAS was translated to Spanish using a back-translation method. Test-retest and internal consistency reliability were examined. Divergent validity was assessed by comparing the DAS with the depression scale (GDS-15). Principal Component Analysis (PCA) was applied to explore the substructure of the Spanish DAS. Results: The internal consistency reliability of self-rated Spanish DAS was 0.72 and of the informant/caregiver-rated Spanish DAS was 0.84. Correlations between self-rated DAS subscales and GDS-15 were not statistically significant, with a good test-retest reliability. PCA analysis showed a similar substructure to the original DAS. ALS patients had significantly higher Initiation apathy than controls. Additionally, ALS patient informant/caregiver-rated DAS Emotional apathy was significantly higher than the self-rated, with no significant differences observed in the Executive and Initiation subscales. No association was found between DAS and functional impairment using the ALS Functional Rating Scale (ALSFRS-R). Conclusion: The Spanish translation of the DAS is valid and reliable for use in assessing multidimensional apathy in the Spanish population. Availability of the Spanish DAS will allow for future research to explore different apathy subtypes and their impact in ALS and other conditions.
| S-EPMC7573163 | biostudies-literature
Project description:ObjectiveThis article extends work on a social-ecological model of caregiver adjustment and describes the: (a) development and (b) validation of the Parent-Preschoolers Diabetes Adjustment Scale (PP-DAS), a broad measure of caregiver adjustment.MethodsParticipants were caregivers (nstudy1 = 51; nstudy2 = 177) of very young children (<6 years old) with Type 1 diabetes (T1D). In study 1, researchers and stakeholders collaborated to develop 92 items using the 5 domains of a social-ecological model of caregiver adjustment to the challenges of raising a very young child with T1D, and parents and researchers provided feedback on these items. In study 2, confirmatory factor analysis (CFA) and exploratory factor analysis (EFA) were used to examine the factor structure of the PP-DAS. Reliability and validity were also examined.ResultsAfter review by parents and researchers, 52 items were removed resulting in the 40-item version used in study 2. The CFA demonstrated poor fit with the five proposed domains of the social-ecological model, so an EFA was conducted and supported a different five-factor solution. Twenty items were removed due to low factor loadings or communalities, resulting in a final 20-item measure. The PP-DAS demonstrated adequate internal consistency (α's = .73-.84), convergent validity with parent psychological functioning and self-efficacy in T1D management, and criterion validity with hemoglobin A1c and adherence.ConclusionsThe PP-DAS is a valid and reliable measure of adjustment in caregivers of very young children with T1D. The PP-DAS may help identify caregivers who are having adjustment difficulties and would benefit from additional support.
| S-EPMC7029691 | biostudies-literature