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ABSTRACT:
SUBMITTER: Meißner A
PROVIDER: S-EPMC8039800 | biostudies-literature |
REPOSITORIES: biostudies-literature
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Project description:The Bioinformatics group at the National Cancer Research Institute (IST) of Genoa has been involved since many years in the development and maintenance of biomedical information systems. Among them, the Common Access to Biological Resources and Information network services offer access to more than 130,000 biological resources, like strains of micro-organisms and human and animal cell lines, included in 29 collections from some of the most known European Biological Resource Centers. An Sequence Retrieval System (SRS) implementation of the TP53 Mutation Database of the International Agency for Research on Cancer (Lyon) was made available in order to improve interoperability of this data with other molecular biology databases. 'SRS by WS (SWS)', a system for retrieving information on public SRS sites and for directly querying them, was also implemented. In order to make this information available through application programming interfaces, we implemented a suite of free web services (WS), called the 'IST Bioinformatics Web Services (IBWS)'. A support web site, including a description of the system, a list of available WS together with help pages, links to corresponding WSDLs and forms for testing services, is available at http://bioinformatics.istge.it/ibws/. WSDL definitions can also be retrieved directly at http://bioinformatics.istge.it:8080/axis/services.
| S-EPMC2896171 | biostudies-literature
Project description:Die Covid-19-Krise verschärft die bereits lebhaft geführte Diskussion um regionale Disparitäten in der Daseinsvorsorge. Insbesondere im dünnbesiedelten, ländlichen Raum hatten viele Kommunen schon vor der aktuellen Ausnahmesituation Schwierigkeiten, attraktive medizinische Versorgung, Bildungsinfrastruktur, öffentlichen Personennahverkehr oder Breitbandinternet bereitzustellen. Während einerseits die weitere Stärkung urbaner Zentren zur Diskussion steht, wird den Menschen im ländlichen Raum andererseits ein Gefühl des Verlassenwerdens attestiert, das auf einen kulturellen Stadt-Land-Konflikt hinzudeuten scheint. Der vorliegende Beitrag bietet den Auftakt für die kleinräumige empirisch fundierte Debatte um Daseinsvorsorge und die Entfremdung von etablierten Parteien in Deutschland. Die Analyse beruht auf einem zu diesem Zweck aufgebauten Datensatz, der neben einem Index der Daseinsvorsorge auch eine Auswertung der Distanz zum nächstgelegenen Bahnhof und der Erreichbarkeit des nächstgelegenen Krankenhauses auf Gemeindeebene für die Bundestagswahl 2017 sowie die Europawahl 2019 erlaubt. Wie aus anderen westlichen Demokratien zu erwarten, geht auch in Deutschland ein besseres AfD-Ergebnis mit einer schwächeren Daseinsvorsorge einher. Ein Teil dieses Effektes ist jedoch schlicht auf die Divergenz zwischen ländlichem Raum und urbaner Agglomeration zurückzuführen und zeigt sich entgegen der Erwartungen weniger deutlich oder gar nicht zwischen kleineren ländlichen Gemeinden. Zudem steigt die Zustimmung zum Rechtspopulismus weder mit zunehmender Distanz zum nächstgelegenen Bahnhof noch mit einer höheren Kommunalverschuldung. Trotzdem deutet auch in den kleineren Gemeinden einiges auf Erfolge der AfD in Räumen politischer Entfremdung und wirtschaftlicher Schwierigkeiten hin. Robust schneidet die rechtspopulistische Partei umso besser ab desto geringer die vorherrschende Wahlbeteiligung desto stärker die Gemeinde von Abwanderung betroffen sowie desto angespannter der Arbeitsmarkt ist. Eine innovative Wirtschaft vor Ort hat hingegen das Potenzial, die Zustimmung zu den Rechtspopulisten abzumildern. Zusatzmaterial online Zusätzliche Informationen sind in der Online-Version dieses Artikels (10.1007/s41358-020-00239-y) enthalten.
| S-EPMC7607891 | biostudies-literature
Project description:Atopic dermatitis (AD) is a chronic pruritic inflammatory skin disease. We recently described an animal model in which repeated epicutaneous applications of a house dust mite extract and Staphylococcal enterotoxin B induced eczematous skin lesions. In this study we showed that global gene expression patterns are very similar between human AD skin and allergen/staphylococcal enterotoxin B–induced mouse skin lesions, particularly in the expression of genes related to epidermal growth/differentiation, skin barrier, lipid/energy metabolism, immune response, or extracellular matrix. In this model, mast cells and T cells, but not B cells or eosinophils, were shown to be required for the full expression of dermatitis, as revealed by reduced skin inflammation and reduced serum IgE levels in mice lacking mast cells or T cells (TCRb-/- or Rag1-/-). The clinical severity of dermatitis correlated with the numbers of mast cells, but not eosinophils. Consistent with the idea that T helper type 2 (Th2) cells play a predominant role in allergic diseases, the receptor for the Th2-promoting cytokine thymic stromal lymphopoietin and the high-affinity IgE receptor, FceRI, were required to attain maximal clinical scores. Therefore, this clinically relevant model provides mechanistic insights into the pathogenic mechanism of human AD.
2013-12-10 | GSE53132 | GEO
Project description:Seit dem ersten Auftreten der Coronavirus-Krankheit 2019 (COVID-19) in China sind nur wenige Wochen vergangen. In dieser Zeit hat sich die Infektion weltweit ausgebreitet. Doch auch das Wissen über das neuartige Coronavirus (SARS-CoV-2) ist gewachsen. Dieser Artikel fasst die wichtigsten Erkenntnisse zusammen und gibt einen Überblick, wie die limitierte Datenlage hinsichtlich Schwangerschaft und Geburt einzuschätzen ist. (Stand: 21.03.2020)
| S-EPMC7417749 | biostudies-literature
Project description:PurposeMeasurement of IgE specific to purified house dust mite (HDM) allergens may improve allergy diagnosis. This study aimed to investigate the sensitization profiles of Korean HDM allergic subjects suffering from respiratory allergy and atopic dermatitis (AD) to Der f 1, Der f 2, Der f 6, Der f 8, Der f 10, and Der f 20.MethodsRecombinant HDM allergens were produced in Pichia pastoris (Der f 1) or Escherichia coli (5 allergens). IgE reactivity to the individual recombinant allergens and total extract of mite was assessed by ELISA.ResultsDer f 1 was recognized by 79.1%, Der f 2 by 79.1%, Der f 6 by 9.3%, Der f 8 by 6.2%, Der f 10 by 6.2%, and Der f 20 by 6.6% of the patients' sera tested, while the prevalence of IgE reactivity to total mite extract was 94.7%. Combination of Der f 1 and Der f 2 had a sensitivity of 87.6%. Specific IgE to Der f 2 alone was detected from 89.4% of HDM-sensitized respiratory allergy subjects and 92.3% to the combination of the 2 major allergens Der f 1 and Der f 2. However, sera from fewer patients with AD, namely 72.4% and 71.0%, recognized Der f 1 and Der f 2, respectively. The combination of 2 major allergens allowed diagnosis of 84.5% of the AD patients. No correlation between sensitization to specific allergens and HDM allergy entity was found.ConclusionsDer f 2 was the most frequently sensitized allergen among the HDM-sensitized respiratory and AD patients in Korea, and the combination of the group 1 and 2 major allergens increased the diagnostic sensitivity. Minor allergens did not significantly improve diagnostic sensitivity. However, further studies are needed to analyze the relationship between sensitization to other HDM allergens and the disease entity of the HDM allergy.
| S-EPMC4509661 | biostudies-literature
Project description:Manual curation of biomedical literature has become extremely tedious process due to its exponential growth in recent years. To extract meaningful information from such large and unstructured text, newer and more efficient mining tool is required. Here, we introduce PALM-IST, a computational platform that not only allows users to explore biomedical abstracts using keyword based text mining but also extracts biological entity (e.g., gene/protein, drug, disease, biological processes, cellular component, etc.) information from the extracted text and subsequently mines various databases to provide their comprehensive inter-relation (e.g., interaction, expression, etc.). PALM-IST constructs protein interaction network and pathway information data relevant to the text search using multiple data mining tools and assembles them to create a meta-interaction network. It also analyzes scientific collaboration by extraction and creation of "co-authorship network," for a given search context. Hence, this useful combination of literature and data mining provided in PALM-IST can be used to extract novel protein-protein interaction (PPI), to generate meta-pathways and further to identify key crosstalk and bottleneck proteins. PALM-IST is available at www.hpppi.iicb.res.in/ctm.
| S-EPMC4437304 | biostudies-literature
Project description:Atopic dermatitis (AD) is a chronic pruritic inflammatory skin disease. We recently described an animal model in which repeated epicutaneous applications of a house dust mite extract and Staphylococcal enterotoxin B induced eczematous skin lesions. In this study we showed that global gene expression patterns are very similar between human AD skin and allergen/staphylococcal enterotoxin B–induced mouse skin lesions, particularly in the expression of genes related to epidermal growth/differentiation, skin barrier, lipid/energy metabolism, immune response, or extracellular matrix. In this model, mast cells and T cells, but not B cells or eosinophils, were shown to be required for the full expression of dermatitis, as revealed by reduced skin inflammation and reduced serum IgE levels in mice lacking mast cells or T cells (TCRb-/- or Rag1-/-). The clinical severity of dermatitis correlated with the numbers of mast cells, but not eosinophils. Consistent with the idea that T helper type 2 (Th2) cells play a predominant role in allergic diseases, the receptor for the Th2-promoting cytokine thymic stromal lymphopoietin and the high-affinity IgE receptor, FceRI, were required to attain maximal clinical scores. Therefore, this clinically relevant model provides mechanistic insights into the pathogenic mechanism of human AD. A total of six samples were analyzed. Back skin samples from healthy or AD-induced C57BL/6, PLC-beta 3 KO (C57BL/6 background), and NC/Nga mice were collected for total RNA extraction. Pooled RNA from 2-4 mice per condition were used for analysis.
2013-12-10 | E-GEOD-53132 | biostudies-arrayexpress
Project description:We outline what an integrated approach to language research that connects experimental, theoretical, and neurobiological domains of inquiry would look like, and ask to what extent unification is possible across domains. At the center of the program is the idea that computational/representational (CR) theories of language must be used to investigate its neurobiological (NB) foundations. We consider different ways in which CR and NB might be connected. These are (1) A Correlational way, in which NB computation is correlated with the CR theory; (2) An Integrated way, in which NB data provide crucial evidence for choosing among CR theories; and (3) an Explanatory way, in which properties of NB explain why a CR theory is the way it is. We examine various questions concerning the prospects for Explanatory connections in particular, including to what extent it makes sense to say that NB could be specialized for particular computations.
| S-EPMC4405236 | biostudies-literature
Project description:Background and Purpose- We aim to identify factors associated with imaging-confirmed lacunar strokes and improve their rapid clinical identification early after symptom onset using data from the IST-3 (Third International Stroke Trial). Methods- We selected patients likely to have lacunar infarcts as those presenting with: Oxfordshire Community Stroke Project lacunar syndrome; a random sample with National Institutes of Health Stroke Scale (NIHSS) score <7; and recent lacunar infarct identified on imaging by IST-3 central blinded expert panel. An independent reviewer rated brain scans of this sample and classified visible infarcts according to type, size, and location. We investigated factors associated with presence of lacunar infarct on a 24 to 48 hour follow-up scan using multivariable logistic regression and calculated sensitivity and specificity of Oxfordshire Community Stroke Project alone and in combination with NIHSS score <7. Results- We included 568 patients (330 lacunar syndrome; 147 with NIHSS score <7; 91 with lacunar infarct on baseline imaging, numbers exclude overlaps between groups), mean (±SD) age, 73.2 (±13.6) years, 316 (56%) males, and median NIHSS score 5 (IQR, 4-8). On 24 to 48 hour scan, 138 (24%) patients had lacunar infarcts, 176 (31%) other infarct subtypes, 254 (45%) no visible infarct. Higher baseline systolic blood pressure (odds ratio, 1.01 [95% CI, 1.01-1.02]) and preexisting lacunes (odds ratio, 2.29 [95% CI, 1.47-3.57) were associated with recent lacunar infarcts. Sensitivity and specificity of lacunar syndrome was modest (58% and 45%, respectively), but adding NIHSS score <7 increased specificity (99%), positive and negative predictive values (97% and 87%, respectively). Conclusions- In patients presenting within 6 hours of stroke onset, adding NIHSS score <7 to Oxfordshire Community Stroke Project lacunar syndrome classification may increase specificity for identifying lacunar stroke early after stroke onset. Our findings may help selection of patients for clinical trials of lacunar stroke and should be validated externally. Registration- URL: http://www.controlled-trials.com/; Unique identifier: ISRCTN25765518.
| S-EPMC7185055 | biostudies-literature
Project description:BackgroundIntravenous recombinant tissue plasminogen activator (rt-PA) is approved for use in selected patients with ischaemic stroke within 3 hours of symptom onset. IST-3 seeks to determine whether a wider range of patients may benefit.DesignInternational, multi-centre, prospective, randomized, open, blinded endpoint (PROBE) trial of intravenous rt-PA in acute ischaemic stroke. Suitable patients must be assessed and able to start treatment within 6 hours of developing symptoms, and brain imaging must have excluded intracerebral haemorrhage. With 1000 patients, the trial can detect a 7% absolute difference in the primary outcome. With 3500 patients, it can detect a 4.0% absolute benefit & with 6000, (mostly treated between 3 & 6 hours), it can detect a 3% benefit. TRIAL PROCEDURES: Patients are entered into the trial by telephoning a fast, secure computerised central randomisation system or via a secure web interface. Repeat brain imaging must be performed at 24-48 hours. The scans are reviewed 'blind' by expert readers. The primary measure of outcome is the proportion of patients alive and independent (Modified Rankin 0-2) at six months (assessed via a postal questionnaire mailed directly to the patient). Secondary outcomes include: events within 7 days (death, recurrent stroke, symptomatic intracranial haemorrhage), outcome at six months (death, functional status, EuroQol).Trial registrationISRCTN25765518.
| S-EPMC2442584 | biostudies-literature