78 research outputs found

    Data Recipes: Toward Creating How-To Knowledge Base for Earth Science Data

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    Both the diversity and volume of Earth science data from satellites and numerical models are growing dramatically, due to an increasing population of measured physical parameters, and also an increasing variety of spatial and temporal resolutions for many data products. To further complicate matters, Earth science data delivered to data archive centers are commonly found in different formats and structures. NASA data centers, managed by the Earth Observing System Data and Information System (EOSDIS), have developed a rich and diverse set of data services and tools with features intended to simplify finding, downloading, and working with these data. Although most data services and tools have user guides, many users still experience difficulties with accessing or reading data due to varying levels of familiarity with data services, tools, and or formats. The data recipe project at Goddard Earth Science Data and Information Services Center (GES DISC) was initiated in late 2012 for enhancing user support. A data recipe is a How-To online explanatory document, with step-by-step instructions and examples of accessing and working with real data (http:disc.sci.gsfc.nasa.govrecipes). The current suite of recipes has been found to be very helpful, especially to first-time-users of particular data services, tools, or data products. Online traffic to the data recipe pages is significant, even though the data recipe topics are still limited. An Earth Science Data System Working Group (ESDSWG) for data recipes was established in the spring of 2014, aimed to initiate an EOSDIS-wide campaign for leveraging the distributed knowledge within EOSDIS and its user communities regarding their respective services and tools. The ESDSWG data recipe group is working on an inventory and analysis of existing data recipes and tutorials, and will provide guidelines and recommendation for writing and grouping data recipes, and for cross linking recipes to data products. This presentation gives an overview of the data recipe activites at GES DISC and ESDSWG. We are seeking requirements and input from a broader data user community to establish a strong knowledge base for Earth science data research and application implementations

    Comparison of methods for in-house screening of HLA*B57:01 to prevent abacavir hypersensitivity in HIV-1 care

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    Abacavir is a nucleoside reverse transcriptase inhibitor used as part of combination antiretroviral therapy in HIV-1-infected patients. Because this drug can cause a hypersensitivity reaction that is correlated with the presence of the HLA-B*57:01 allotype, screening for the presence of HLA-B*57:01 is recommended before abacavir initiation. Different genetic assays have been developed for HLA-B*57:01 screening, each with specific sensitivity, turnaround time and assay costs. Here, a new real-time PCR (qPCR) based analysis is described and compared to sequence specific primer PCR with capillary electrophoresis (SSP PCR CE) on 149 patient-derived samples, using sequence specific oligonucleotide hybridization combined with high resolution SSP PCR as gold standard. In addition to these PCR based methods, a complementary approach was developed using flow cytometry with an HLA-B17 specific monoclonal antibody as a pre-screening assay to diminish the number of samples for genetic testing. All three assays had a maximum sensitivity of >99. However, differences in specificity were recorded, i.e. 84.3%, 97.2% and >99% for flow cytometry, qPCR and SSP PCR CE respectively. Our data indicate that the most specific and sensitive of the compared methods is the SSP PCR CE. Flow cytometry pre-screening can substantially decrease the number of genetic tests for HLA-B*57:01 typing in a clinical setting

    Comprehensive characterization of LEDGF/p75 in a HIV-1-infected patient cohort

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    BACKGROUND: Lens epithelium derived growth factor/transcriptional co-activator p75 (LEDGF/p75) is an important cellular co-factor for the HIV enzyme integrase. In the present study, we evaluated if genetic variation in the LEDGF/p75 gene and mRNA expression levels might explain differences in HIV disease progression. METHODS: Samples were derived from a therapy-naïve patient cohort from the Ghent University Hospital and from the long-term-non-progressor patient Spanish RIS cohort. A comprehensive genomic scan of the coding region and 3’UTR of LEDGF/p75 was performed using high resolution melting curve analysis and Sanger sequencing to identify single nucleotide polymorphisms (SNPS). In addition, LEDGF/p75 mRNA expression levels were determined from patient PBMCs using RT-qPCR with validated reference genes for normalization. RESULTS: In total 325 patient samples were investigated, of which 291 (90%) of Caucasian and 34 (10%) of African origin, and among which a large group of Elite controllers (n=49) and Viremic controllers (n=62). In these samples, 24 SNPs were analyzed, including 5 in the coding region (2 synonymous and 3 non-synonymous), 17 in the flanking non-coding regions and in the 3’UTR, and two additional tagSNPs as described by Madlala et al. (Aids, 2011) in two South African cohorts. One SNP in the 3’UTR region (rs2737835, n=46) had a higher representation in Caucasian Elite controllers and was correlated with lower LEDGF/p75 mRNA levels (P=0.047) and with a slower CD4 decline (P= 0.042). rs2737828 (n=13) was under-represented in Caucasian HIV patients and linked to lower LEDGF/p75 expression (P=0.013). The presence of intron SNP (rs16933270, n=6) was associated with a slower CD4 decline in African patients (P=0.017), and this CD4 decline was comparable with that of African slow disease progressors. Interestingly, the presence of one tagSNP (rs12339417, n=95) was significantly correlated with a decreased viral load, but in contrast to the results of Madlala et al. (Aids, 2011), this SNP was not correlated with the CD4 slope and neither with LEDGF/p75 mRNA levels. CONCLUSIONS: Although the data of the present investigation was not entirely comparable with the results of Madlala et al. (Aids, 2011), our data supports their hypothesis that host factors influence HIV disease progression. The observed differences between the European and South African cohorts may be of ethnical origin, or due to different infection phases. In the investigated cohorts, two SNPs were associated with lower LEDGF/p75 mRNA expression in Caucasians, and one SNP was associated with slower disease progression in Africans. The significant correlation with the tagSNP (rs12339417) and the decreased viral load is surprising as this was not correlated with a delayed CD4 decline, nor with LEDGF/p75 expression. This might indicate that either conformational changes or factors upstream of mRNA transcription might influence the action of LEDGF/p75 in these HIV patients

    Exile Vol. XXVIII No. 1

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    Group Poems From Sake Circle / Monologue. Polylogue. Mollylogue. (or: A musing of young writer as a poor man. Hee hee hee.) by Chris Brougham Untitled Prose by Chris Paul In A Room by Robert F. Youngblood The Escape by Anne Gilson Untitled Poem by Becky Hinshaw A Cruel Hand by Chad Hussey Shaking Heads in Copley Square by Gregory MacDonald The Coming Age by Lynn Greene Seduction by Jacqueline Ondy Pointless Polarities by Ruth Wick The Ladies From The Fairmont Unitarian Church Poverty Relief Fund by Sharon S. McCartney Confessions of a Book Burner by Andy Acker The Congress of the Gods by Tage Danielsson (translated by Ari Kokko) Marble Bags by Mike Augusta Monsters by Sharon S. McCartney Unction by Bruce Leonard Dust of Allah by Andy Acker Buffalo Mountain by Sharon S. McCartney One Marriage by Becky Hinshaw Experience by Barry Pailet The Wings by Leonora Cravotta The Tale of Frankenstein\u27s Average by Tage Danielsson (translated by Ari Kokko) Want by Roger Butler / Cornpoem by Mike Augusta Cover Drawing By Peter Brook

    Characterization of LEDGF/p75 genetic variants and association with HIV-1 disease progression

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    BACKGROUND: As Lens epithelium-derived growth factor (LEDGF/p75) is an important co-factor involved in HIV-1 integration, the LEDGF/p75-IN interaction is a promising target for the new class of allosteric HIV integrase inhibitors (LEDGINs). Few data are available on the genetic variability of LEDGF/p75 and the influence on HIV disease in vivo. This study evaluated the relation between LEDGF/p75 genetic variation, mRNA expression and HIV-1 disease progression in order to guide future clinical use of LEDGINs. METHODS: Samples were derived from a therapy-naĂŻve cohort at Ghent University Hospital and a Spanish long-term-non-progressor cohort. High-resolution melting curve analysis and Sanger sequencing were used to identify all single nucleotide polymorphisms (SNPs) in the coding region, flanking intronic regions and full 3'UTR of LEDGF/p75. In addition, two intronic tagSNPs were screened based on previous indication of influencing HIV disease. LEDGF/p75 mRNA was quantified in patient peripheral blood mononuclear cells (PBMC) using RT-qPCR. RESULTS: 325 samples were investigated from patients of Caucasian (n = 291) and African (n = 34) origin, including Elite (n = 49) and Viremic controllers (n = 62). 21 SNPs were identified, comprising five in the coding region and 16 in the non-coding regions and 3'UTR. The variants in the coding region were infrequent and had no major impact on protein structure according to SIFT and PolyPhen score. One intronic SNP (rs2737828) was significantly under-represented in Caucasian patients (P<0.0001) compared to healthy controls (HapMap). Two SNPs showed a non-significant trend towards association with slower disease progression but not with LEDGF/p75 expression. The observed variation in LEDGF/p75 expression was not correlated with disease progression. CONCLUSIONS: LEDGF/p75 is a highly conserved protein. Two non-coding polymorphisms were identified indicating a correlation with disease outcome, but further research is needed to clarify phenotypic impact. The conserved coding region and the observed variation in LEDGF/p75 expression are important characteristics for clinical use of LEDGINs.This work was partly supported by the Flemish Agency for Innovation by Science and Technology (CellCoVir - IWT file nr 60813). Linos Vandekerckhove is supported by the National Fund for Scientific Research – Belgium as Principal Investigator. The Spanish RIS cohort and HIV BioBank are integrated in the Spanish AIDS Research Network supported by Instituto de Salud Carlos III (Grant RD06/0006/0035) and FundaciĂłn para la InvestigaciĂłn y PrevenciĂłn del SIDA en España (FIPSE). The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.S

    Quality of life and salivary output in patients with head-and-neck cancer five years after radiotherapy

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    BACKGROUND: To describe long-term changes in time of quality of life (QOL) and the relation with parotid salivary output in patients with head-and-neck cancer treated with radiotherapy. METHODS: Forty-four patients completed the EORTC-QLQ-C30(+3) and the EORTC-QLQ-H&N35 questionnaires before treatment, 6 weeks, 6 months, 12 months, and at least 3.5 years after treatment. At the same time points, stimulated bilateral parotid flow rates were measured. RESULTS: There was a deterioration of most QOL items after radiotherapy compared with baseline, with gradual improvement during 5 years follow-up. The specific xerostomia-related items showed improvement in time, but did not return to baseline. Global QOL did not alter significantly in time, although 41% of patients complained of moderate or severe xerostomia at 5 years follow-up. Five years after radiotherapy the mean cumulated parotid flow ratio returned to baseline but 20% of patients had a flow ratio <25%. The change in time of xerostomia was significantly related with the change in flow ratio (p = 0.01). CONCLUSION: Most of the xerostomia-related QOL scores improved in time after radiotherapy without altering the global QOL, which remained high. The recovery of the dry mouth feeling was significantly correlated with the recovery in parotid flow ratio

    COVID-19 symptoms at hospital admission vary with age and sex: results from the ISARIC prospective multinational observational study

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    Background: The ISARIC prospective multinational observational study is the largest cohort of hospitalized patients with COVID-19. We present relationships of age, sex, and nationality to presenting symptoms. Methods: International, prospective observational study of 60 109 hospitalized symptomatic patients with laboratory-confirmed COVID-19 recruited from 43 countries between 30 January and 3 August 2020. Logistic regression was performed to evaluate relationships of age and sex to published COVID-19 case definitions and the most commonly reported symptoms. Results: ‘Typical’ symptoms of fever (69%), cough (68%) and shortness of breath (66%) were the most commonly reported. 92% of patients experienced at least one of these. Prevalence of typical symptoms was greatest in 30- to 60-year-olds (respectively 80, 79, 69%; at least one 95%). They were reported less frequently in children (≀ 18 years: 69, 48, 23; 85%), older adults (≄ 70 years: 61, 62, 65; 90%), and women (66, 66, 64; 90%; vs. men 71, 70, 67; 93%, each P &lt; 0.001). The most common atypical presentations under 60 years of age were nausea and vomiting and abdominal pain, and over 60 years was confusion. Regression models showed significant differences in symptoms with sex, age and country. Interpretation: This international collaboration has allowed us to report reliable symptom data from the largest cohort of patients admitted to hospital with COVID-19. Adults over 60 and children admitted to hospital with COVID-19 are less likely to present with typical symptoms. Nausea and vomiting are common atypical presentations under 30 years. Confusion is a frequent atypical presentation of COVID-19 in adults over 60 years. Women are less likely to experience typical symptoms than men
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