scholarly journals Curated compendium of human transcriptional biomarker data

2017 ◽  
Author(s):  
Nathan P. Golightly ◽  
Anna I. Bischoff ◽  
Avery Bell ◽  
Parker D. Hollingsworth ◽  
Stephen R. Piccolo
Keyword(s):  
Machine Learning Algorithms ◽  
Data Reuse ◽  
Clinical Settings ◽  
The Public ◽  
The Past ◽  
Genome Wide ◽  
Gene Level ◽  
Public Repositories ◽  
Reproducible Manner

AbstractGenome-wide transcriptional profiles provide broad insights into cellular activity. One important use of such data isto identify relationships between transcription levels and patient outcomes. These translational insights can guide the development of biomarkers for predicting outcomes in clinical settings. Over the past decades, data from many translational-biomarker studies have been deposited in public repositories, enabling other scientists to reuse the data in follow-up studies. However, data-reuse efforts require considerable time and expertise because transcriptional data are generated using heterogeneous profiling technologies, preprocessed using diverse normalization procedures, and annotated in non-standard ways. To address this problem, we curated a compendium of 45 translational-biomarker datasets from the public domain. To increase the data’s utility, we reprocessed the raw expression data using a standard computational pipeline and standardized the clinical annotations in a fully reproducible manner (see osf.io/ssk3t). We believe these data will be particularly useful to researchers seeking to validate gene-level findings or to perform benchmarking studies—for example, to compare and optimize machine-learning algorithms’ ability to predict biomedical outcomes.

scholarly journals Navigating Public Microarray Databases

2004 ◽  
Vol 5 (6-7) ◽  
pp. 471-479 ◽  
Author(s):  
Christopher J. Penkett ◽  
Jürg Bähler
Keyword(s):  
Data Sources ◽  
European Bioinformatics Institute ◽  
Published Data ◽  
Expression Data ◽  
The Public ◽  
Genome Wide ◽  
Public Repositories ◽  
Set Up ◽  
Downstream Analysis ◽  
Microarray Studies

With the ever-escalating amount of data being produced by genome-wide microarray studies, it is of increasing importance that these data are captured in public databases so that researchers can use this information to complement and enhance their own studies. Many groups have set up databases of expression data, ranging from large repositories, which are designed to comprehensively capture all published data, through to more specialized databases. The public repositories, such as ArrayExpress at the European Bioinformatics Institute contain complete datasets in raw format in addition to processed data, whilst the specialist databases tend to provide downstream analysis of normalized data from more focused studies and data sources. Here we provide a guide to the use of these public microarray resources.

scholarly journals Reanalysis of MERS, SARS and COVID-19 Infection Datasets using VirOmics Playground Reveals Common Patterns in Gene and Protein Expression

2020 ◽  
Author(s):  
Axel Martinelli ◽  
Murodzhon Akhmedov ◽  
Ivo Kwee
Keyword(s):  
Protein Expression ◽  
Bioinformatic Analysis ◽  
Data Sets ◽  
The Public ◽  
The Past ◽  
Genome Wide ◽  
Gene And Protein Expression ◽  
Heterogeneous Nature ◽  
User Friendly

AbstractThree lethal lower respiratory tract coronavirus epidemics have occurred over the past 20 years. This coincided with major developments in genome-wide gene and protein expression analysis, resulting in a wealth of datasets in the public domain. Seven such in vitro studies were selected for comparative bioinformatic analysis through the VirOmics Playground, a user-friendly visualisation and exploration platform we recently developed. Despite the heterogeneous nature of the data sets, several commonalities could be observed across studies and species. Differences, on the other hand, reflected not only variations between species, but also other experimental variables, such as cell lines used for the experiments, infection protocols and potential discrepancies between transcriptome and proteome data. The results presented here are available online and can be replicated through the VirOmics Playground.

A - 31 Competitiveness Drives Young University Students off the Couch

2021 ◽  
Vol 36 (4) ◽  
pp. 671-671
Author(s):  
Wong RE ◽  
Webber AM ◽  
Bergauer A ◽  
Dougall N ◽  
Garcia-Barrera MA
Keyword(s):  
Physical Activity ◽  
Individual Differences ◽  
Strategic Planning ◽  
University Students ◽  
Sedentary Behaviour ◽  
Public Health Recommendation ◽  
The Public ◽  
The Past ◽  
Canadian City

Abstract Objective Purpose. Daily physical activity (PA) is effective in supporting cognitive and physical health. However, many Canadians do not meet the public health recommendation of at least 150 mins/week of moderate-to-vigorous PA. The current study examined individual differences in traits such as motivation (intrinsic-IM, extrinsic-EM), and competitiveness, as well as executive abilities (strategic planning; SP) in predicting physical activity and sedentary behaviour. Methods Method. 102 university students ages 18 to 30 (M = 20.78 years; 74% female) were recruited from a mid-sized Canadian city. Using a formula that differentially weighted moderate and vigorous activity (measured with the International PA Questionnaire), we fit a linear model predicting PA within the past week by SP (Executive Function Index), IM and EM (Global Motivation Scale), and competitiveness (Revised Competitiveness Scale). Results Results. Only competitiveness predicted PA within the past week (β = 0.309, p = 0.001). Follow-up regressions indicated enjoyment of the activity being the most predictive component (β =0.231, p = 0.017). Both EM (β = 0.202, p = 0.015) and IM (β = −0.223, p = 0.012) predicted sedentary behaviour when accounting for competitiveness and demographics (age, gender). Conclusions Conclusions. Strategic planning and motivation did not predict exercise within the past week and therefore did not appear to serve as precursors to PA engagement in this university sample. Competitiveness, and in particular the enjoyment of the activity, significantly predicted exercise engagement; however, IM was negatively associated with sedentary behaviour, whereas EM was positively associated, suggesting motivational differences in sedentary behaviour but not physical exercise. Further research is required to account for individual differences in physical activity engagement.

E-cigarette users commonly stealth vape in places where e-cigarette use is prohibited

2018 ◽  
Vol 28 (5) ◽  
pp. 493-497 ◽  
Author(s):  
Jessica M Yingst ◽  
Courtney Lester ◽  
Susan Veldheer ◽  
Sophia I Allen ◽  
Ping Du ◽  
...  
Keyword(s):  
Logistic Regression Model ◽  
Health And Safety ◽  
Health Impact ◽  
Cigarette Use ◽  
Public Place ◽  
Potential Health ◽  
The Public ◽  
The Past ◽  
Common Behaviour

Introduction‘Stealth vaping’ is the practice of vaping discreetly in places where electronic cigarette (e-cigarette) use is prohibited. While anecdotal evidence suggests that stealth vaping is common, there have been no formal studies of the behaviour. The purpose of this study is to examine stealth vaping behaviour among experienced e-cigarette users.MethodsData were collected from the follow-up survey of a large longitudinal cohort study of adult experienced e-cigarette users conducted in January 2017. To measure stealth vaping behaviour, participants were asked ‘Have you ever ‘stealth vaped’, that is to say, used an e-cig in a public place where it was not approved and attempted to conceal your e-cig use? (yes/no)’. Participants indicating yes completed additional questions about the frequency of stealth vaping and were asked to select all the locations where they commonly stealth vape. Frequencies were used to examine the overall prevalence, frequency and common locations for stealth vaping. A logistic regression model was run to predict stealth vaping.ResultsApproximately two-thirds (64.3%, n=297/462) of the sample reported ever stealth vaping, of which 52.5% (n=156/297) reported stealth vaping in the past week. Among stealth vapers (n=297), 31% reported owning a smaller device solely for stealth vaping. The most common places to stealth vape included at work (46.8%), followed by bars/nightclubs (42.1%), restaurants (37.7%), at the movies (35.4%) and in airports/on airplanes (11.7%). Predictors of stealth vaping were greater dependence and owning a smaller device solely for stealth vaping.ConclusionsStealth vaping is a common behaviour for many experienced e-cigarette users. More research is needed to understand the reasons for stealth vaping and its potential health and safety implications. This information could help researchers and regulators to design interventions to minimise the public health impact of stealth vaping.

scholarly journals Genetic Variation in NFATC2 Is Associated with a Higher Risk of Asparaginase Allergy

Blood ◽  
2014 ◽  
Vol 124 (21) ◽  
pp. 63-63
Author(s):  
Christian A. Fernandez ◽  
Colton Smith ◽  
Wenjian Yang ◽  
Charles G. Mullighan ◽  
Chunxu Qu ◽  
...  
Keyword(s):  
Risk Factors ◽  
Immune Responses ◽  
Clinical Diagnostics ◽  
Institutional Policy ◽  
E Coli ◽  
The Past ◽  
Genome Wide ◽  
Patent Rights ◽  
Gene Level ◽  
Level Analysis

Abstract Asparaginase is an important drug for the treatment of acute lymphoblastic leukemia (ALL); however, hypersensitivity reactions to asparaginase can lead to suboptimal asparaginase exposure and to a higher risk of disease recurrence. Factors influencing the frequency of asparaginase hypersensitivity include asparaginase formulation, the schedule of asparaginase administration, and concurrent chemotherapy. In addition, using a candidate gene approach, our group previously identified a genetic association between HLA-DRB1*07:01 and asparaginase hypersensitivity in patients of European ancestry.[PMID 24970932] The objective of our current study was to use a genome-wide approach to identify additional genetic loci associated with hypersensitivity and to assess the relative importance of HLA-DRB1 as a genetic risk factor. Asparaginase hypersensitivity was assessed in children with ALL enrolled on SJCRH protocols Total XIIIA (n = 154), Total XV (n = 498) and Total XVI (n = 271) or Children’s Oncology Group (COG) protocols POG 9906 (n = 222) and AALL0232 (n = 2,163). Patients enrolled on protocols Total XIIIA, Total XV and POG 9906 received native E. coli asparaginase during treatment, whereas patients on Total XVI and AALL0232 received PEGylated E. coli asparaginase. Hypersensitivities were graded according to the NCI common toxicity criteria, and reactions of grade 2 and above were considered cases. Germline DNA was genotyped using the Affymetrix 500K, Affymetrix 6.0, or the Illumina Exome Beadchip array. Univariate analysis of risk factors associated with asparaginase hypersensitivity using the combined cohort of patients (n = 3,308) identified a significant positive association with treatment arm (P < 2.2x10-16; highest risk in patients enrolled on Total XV), native E coli asparaginase formulation (P < 2.2x10-16), age < 10 years (P = 3.3x10-4), male gender (P = 0.06), and racial ancestry (P = 2.1x10-4; highest risk among African ancestry). In multivariate analysis, treatment arm (P < 2.2x10-16), gender (P = 0.04), racial ancestry (P = 0.07), and ALL lineage (P = 0.003) remained significant risk factors. A multivariate logistic regression model adjusted for treatment arm, racial ancestry, gender, age, and ALL lineage was used to identify genomic variants associated with asparaginase hypersensitivity in the combined patient cohort. The minor allele of an intronic polymorphism in NFATC2 (rs6021191) was associated with hypersensitivity at the genome-wide significance threshold (P = 2.6x10-8, OR = 3.17). The minor allele frequency (MAF) for the NFATC2 high-risk variant was highest in non-European ancestries (MAF European = 0.001, MAF African = 0.142, MAF Hispanic = 0.043, MAF Asian = 0.151, MAF Other = 0.034). Using RNA-seq data available from the ALL tumor samples of 65 SJCRH patients, we found that patients carrying the variant had higher expression of NFATC2 compared to non-carriers (P = 1.0x10-3). NFATC2 is known to play a critical role in inducing T-cell gene transcription during immune responses. The strongest association detected using SNPs from the Illumina Exome array was found in HLA-DRB1 (rs17885382, P = 4.0x10-6, OR = 1.65), and the SNP is in near complete linkage disequilibrium with the HLA-DRB1*07:01 allele, which we previously found associated with asparaginase hypersensitivity. A gene-level analysis was performed using SNP-set Kernel Association Test (SKAT), and the gene with the strongest association with hypersensitivity was PPT2, located in the HLA class III region on chromosome 6 (P = 3.70x10-6). To determine potential biological pathways differentially represented by the genes identified by our analysis, we used Ingenuity Pathway Analysis on the top 1% of genes associated with hypersensitivity as identified by our single SNP (68 genes) and gene level analysis (18 genes). We found an enrichment of genes (8 out of 21 genes, P = 2.6x10-5) within the top network involved in humoral immunity, suggesting that other genes regulating immune responses may also contribute to the risk of developing asparaginase hypersensitivity. In conclusion, the top inherited genetic loci (NFATC2, HLA-DRB1*0701, PPT2) associated with asparaginase hypersensitivity are directly involved in human immune response, and pathway analysis suggests that inherited variations in other genes involved in humoral immunity likely play a role in the development of asparaginase hypersensitivity. Disclosures Evans: St. Jude: In accordance with institutional policy (St. Jude), I and/or my spouse have in the past received a portion of the income St. Jude receives from licensing patent rights related to TPMT polymorphisms as clinical diagnostics. Patents & Royalties. Relling:St. Jude: In accordance with institutional policy (St. Jude), I and/or my spouse have in the past received a portion of the income St. Jude receives from licensing patent rights related to TPMT polymorphisms as clinical diagnostics. Patents & Royalties.

scholarly journals Evolution of vestibular schwannoma surgery: the long journey to current success

2005 ◽  
Vol 18 (4) ◽  
pp. 1-6 ◽  
Author(s):  
Andrei Koerbel ◽  
Alireza Gharabaghi ◽  
Sam Safavi-Abbasi ◽  
Marcos Tatagiba ◽  
Madjid Samii
Keyword(s):  
Vestibular Schwannoma ◽  
Clinical Settings ◽  
Recurrence Rates ◽  
The Past ◽  
Long Term Follow Up ◽  
Microsurgical Techniques ◽  
Functional Preservation ◽  
Neurosurgical Techniques

The extraordinary improvement of patient outcome after surgical treatment for vestibular schwannomas is relatively recent and has occurred mainly over the last 30 years. The introduction of microsurgical techniques has resulted in increasing degrees of precise anatomical and functional preservation of the facial and cochlear nerves. An expanded microsurgical technique accompanied by continuous electrophysiological monitoring has resulted in marked changes in the primary goals for this surgery. Whereas in the past the primary goal of vestibular schwannoma management was to preserve the patient's life, the objective in vestibular schwannoma treatment today is to preserve neurological function. Long-term follow-up examinations show negligible recurrence rates, indicating that the aim of preservation of nerve function does not limit the completeness of tumor removal with modern neurosurgical techniques. Despite these advances in preserving the anatomical integrity of, for example, the cochlear nerve, losses of function and even deafness may occur postoperatively in some cases. Current biological and technical research in experimental and clinical settings addresses these problems. In this article, the authors report in detail the developments achieved in vestibular schwannoma surgery and the great clinicians to whom these results can be credited.

scholarly journals Determining the Most Popular Streaming Service using Machine Learning

2019 ◽  
Vol 9 (2) ◽  
pp. 316-318
Keyword(s):  
Machine Learning ◽  
Learning Algorithms ◽  
Machine Learning Algorithms ◽  
The Public ◽  
The Past ◽  
Popular Medium ◽  
Supervised Classifiers ◽  
Streaming Services ◽  
Streaming Service ◽  
Compare And Contrast

Over the past years, twitter has become a popular medium for sharing views and ideas about personalities, brands, products or services. Analyzing sentiment of people to figure out the popularity of different streaming service by the twitter profiles is helpful for determining positive or negative views. This is a comparative analysis to predict or show which of the chosen streaming services is most familiar or liked by the public. To do this, different machine learning algorithms are used to computationally identify and categorize public opinions to draw a final result. The machine learning algorithms used here are Linear SVC, Naïve Bayes and Decision Tree. These help in receiving the data and predict the output within an acceptable range. The data in this case has been extracted from Twitter using Twitter API. Twitter API takes the parameters that can access many features of Twitter and also post and find tweets containing desired words. This includes data cleaning which refers to exclude the incorrect and unnecessary forms of data. This makes the way of data processing easier, faster and more compatible. On analyzing, the frequently used words are assessed. The classifying words are trained using the above mentioned algorithms. These algorithms are the supervised classifiers which are effective and efficient when the quantity of the data is huge. Using one or more algorithms helps to decide, compare and contrast the results. Once the classifiers are trained, testing is done. Testing gives the proper assessment of the data that is required for the desired results. The performance of the test set can be checked to draw a final result. Hence, comparing the results obtained for different streaming services helps to decide the most popular streaming service.

Efektivitas Layanan Darurat Jakarta Siaga 112 dalam Penanganan Kebakaran oleh UPT. Pusat Data & Informasi Kebencanaan BPBD Provinsi DKI Jakarta

2020 ◽  
Vol 16 (1) ◽  
Author(s):  
Musa Musa
Keyword(s):  
Emergency Service ◽  
Fire Management ◽  
Emergency Services ◽  
The Public ◽  
Information Center ◽  
Disaster Data ◽  
In Fire ◽  
Document Review

This research was conducted to determine the Effectiveness of Jakarta Siaga 112 Emergency Services in Fire Management by UPT. Disaster Data & Information Center of BPBD DKI Jakarta Province by paying attention to aspects contained in the Effectiveness of the Jakarta Siaga Emergency Service Program 112. The research method was carried out with a case study method with data collection techniques using interview methods and document review. Interviews were conducted on 10 (ten) key informants, document review focused on documents related to the Jakarta Emergency Alert Service 112 Effectiveness research in Fire Management. The results showed that the Effectiveness of Jakarta Siaga 112 Emergency Services in Fire Management by UPT. The Center for Disaster Data & Information BPBD DKI Jakarta Province Its effectiveness is still low, due to the Implementation of Emergency Services Jakarta Standby 112 in Fire Management implemented by UPT. Disaster Data & Information Center of BPBD DKI Jakarta Province in terms of the Target Group Understanding of the Program, the Achievement of the Program Objectives aspects, and the Program Follow-up aspects. It is recommended to continue to disseminate this Emergency Service to the public, it is necessary to increase the firm commitment of the Head of 8 SKPD related to fire management so that all units play a role in accordance with the Standard Operating Procedures (SOPs) for Fire Management and the evaluation and follow-up of program services that are held periodically 3 once a month.Keywords: Effectiveness, Emergency Services, Fire Handling

The Suffering of the Perpetrators: The Ethics of Traumatic German Historicity in Karen Bass's Young Adult World War II Novels

2014 ◽  
Vol 7 (1) ◽  
pp. 64-77
Author(s):  
Doris Wolf
Keyword(s):  
World War Ii ◽  
Young Adult ◽  
Public Sphere ◽  
Childhood Studies ◽  
Historical Narratives ◽  
World War ◽  
The Public ◽  
The Past ◽  
Adult World ◽  
The Public Sphere

This paper examines two young adult novels, Run Like Jäger (2008) and Summer of Fire (2009), by Canadian writer Karen Bass, which centre on the experiences of so-called ordinary German teenagers in World War II. Although guilt and perpetration are themes addressed in these books, their focus is primarily on the ways in which Germans suffered at the hands of the Allied forces. These books thus participate in the increasingly widespread but still controversial subject of the suffering of the perpetrators. Bringing work in childhood studies to bear on contemporary representations of German wartime suffering in the public sphere, I explore how Bass's novels, through the liminal figure of the adolescent, participate in a culture of self-victimisation that downplays guilt rather than more ethically contextualises suffering within guilt. These historical narratives are framed by contemporary narratives which centre on troubled teen protagonists who need the stories of the past for their own individualisation in the present. In their evacuation of crucial historical contexts, both Run Like Jäger and Summer of Fire support optimistic and gendered narratives of individualism that ultimately refuse complicated understandings of adolescent agency in the past or present.

The End of History Museums: What's Plan B??

2008 ◽  
Vol 30 (4) ◽  
pp. 9-27 ◽  
Author(s):  
Cary Carson
Keyword(s):  
Historic Sites ◽  
The Public ◽  
End Of History ◽  
House Museums ◽  
The Past ◽  
History Museums ◽  
Plan B ◽  
The End Of History ◽  
The Way

Abstract Are historic sites and house museums destined to go the way of Oldsmobiles and floppy disks?? Visitation has trended downwards for thirty years. Theories abound, but no one really knows why. To launch a discussion of the problem in the pages of The Public Historian, Cary Carson cautions against the pessimistic view that the past is simply passéé. Instead he offers a ““Plan B”” that takes account of the new way that learners today organize information to make history meaningful.

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