Search results for: S. Roche

Authors: Siobhan O’Shea, Sangeetha Vijaysri Nair, Hee Cheol Kim, Charles Thomas Nugent, Cheuk Yan William Tong, Sam Douthwaite, Andrew Worlock

Abstract:

The Aptima® HIV-1 Quant Dx Assay is a fully automated assay on the Panther system. It is based on Transcription- Mediated Amplification and real time detection technologies. This assay is intended for monitoring HIV-1 viral load in plasma specimens and for the detection of HIV-1 in plasma and serum specimens. Nine-hundred and seventy nine specimens selected at random from routine testing at St Thomas’ Hospital, London were anonymised and used to compare the performance of the Aptima HIV-1 Quant Dx assay and Roche COBAS® AmpliPrep/COBAS® TaqMan® HIV-1 Test, v2.0. Two-hundred and thirty four specimens gave quantitative HIV-1 viral load results in both assays. The quantitative results reported by the Aptima Assay were comparable to those reported by the Roche COBAS AmpliPrep/COBAS TaqMan HIV-1 Test, v2.0 with a linear regression slope of 1.04 and an intercept on -0.097. The Aptima assay detected HIV-1 in more samples than the COBAS assay. This was not due to lack of specificity of the Aptima assay because this assay gave 99.83% specificity on testing plasma specimens from 600 HIV-1 negative individuals. To understand the reason for this higher detection rate a side-by-side comparison of low level panels made from the HIV-1 3rd international standard (NIBSC10/152) and clinical samples of various subtypes were tested in both assays. The Aptima assay was more sensitive than the COBAS assay. The good sensitivity, specificity and agreement with other commercial assays make the HIV-1 Quant Dx Assay appropriate for both viral load monitoring and detection of HIV-1 infections.

Keywords: HIV viral load, Aptima, Roche, Panther system.

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Authors: Wided Batita, Stéphane Roche, Claude Caron

Abstract:

Geodesign is an emergent term related to a new and complex process. Hence, it needs to rethink tools, technologies and platforms in order to efficiently achieve its goals. A few tools have emerged since 2010 such as CommunityViz, GeoPlanner, etc. In the era of Web 2.0 and collaboration, WikiGIS has been proposed as a new category of tools. In this paper, we present WikiGIS functionalities dealing mainly with the iteration and traceability management to support the collaboration of the Geodesign process. Actually, WikiGIS is built on GeoWeb 2.0 technologies —and primarily on wiki— and aims at managing the tracking of participants’ editing. This paper focuses on a simplified simulation to illustrate the strength of WikiGIS in the management of traceability and in the access to history in a Geodesign process. Indeed, a cartographic user interface has been implemented, and then a hypothetical use case has been imagined as proof of concept.

Keywords: Geodesign, history, traceability, tracking of participants’ editing, WikiGIS.

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Authors: J. Grira, Y. Bédard, S. Roche

Abstract:

The aim of this research is to design a collaborative framework that integrates risk analysis activities into the geospatial database design (GDD) process. Risk analysis is rarely undertaken iteratively as part of the present GDD methods in conformance to requirement engineering (RE) guidelines and risk standards. Accordingly, when risk analysis is performed during the GDD, some foreseeable risks may be overlooked and not reach the output specifications especially when user intentions are not systematically collected. This may lead to ill-defined requirements and ultimately in higher risks of geospatial data misuse. The adopted approach consists of 1) reviewing risk analysis process within the scope of RE and GDD, 2) analyzing the challenges of risk analysis within the context of GDD, and 3) presenting the components of a risk-based collaborative framework that improves the collection of the intended/forbidden usages of the data and helps geo-IT experts to discover implicit requirements and risks.

Keywords: Collaborative risk analysis, intention of use, Geospatial database design, Geospatial data misuse.

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Authors: Jérôme Azé, Mathieu Roche, Yves Kodratoff, Michèle Sebag

Abstract:

Term Extraction, a key data preparation step in Text Mining, extracts the terms, i.e. relevant collocation of words, attached to specific concepts (e.g. genetic-algorithms and decisiontrees are terms associated to the concept “Machine Learning" ). In this paper, the task of extracting interesting collocations is achieved through a supervised learning algorithm, exploiting a few collocations manually labelled as interesting/not interesting. From these examples, the ROGER algorithm learns a numerical function, inducing some ranking on the collocations. This ranking is optimized using genetic algorithms, maximizing the trade-off between the false positive and true positive rates (Area Under the ROC curve). This approach uses a particular representation for the word collocations, namely the vector of values corresponding to the standard statistical interestingness measures attached to this collocation. As this representation is general (over corpora and natural languages), generality tests were performed by experimenting the ranking function learned from an English corpus in Biology, onto a French corpus of Curriculum Vitae, and vice versa, showing a good robustness of the approaches compared to the state-of-the-art Support Vector Machine (SVM).

Keywords: Text-mining, Terminology Extraction, Evolutionary algorithm, ROC Curve.

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Authors: Vladyslav Povoroznyuk, Anna Musiienko, Nataliia Dzerovych, Roksolana Povoroznyuk, Oksana Ivanyk

Abstract:

Deficiency and insufficiency of Vitamin D is a pandemic of the 21^st century. Obesity patients have a lower level of vitamin D, but the literature data are contradictory. The purpose of this study is to investigate deficiency and insufficiency vitamin D in postmenopausal women with obesity. We examined 1007 women aged 50-89 years. Mean age was 65.74±8.61 years; mean height was 1.61±0.07 m; mean weight was 70.65±13.50 kg; mean body mass index was 27.27±4.86 kg/m², and mean 25(OH) D levels in serum was 26.00±12.00 nmol/l. The women were divided into the following six groups depending on body mass index: I group – 338 women with normal body weight, II group – 16 women with insufficient body weight, III group – 382 women with excessive body weight, IV group – 199 women with obesity of class I, V group – 60 women with obesity of class II, and VI group – 12 women with obesity of class III. Level of 25(OH)D in serum was measured by means of an electrochemiluminescent method - Elecsys 2010 analyzer (Roche Diagnostics, Germany) and cobas test-systems. 34.4% of the examined women have deficiency of vitamin D and 31.4% insufficiency. Women with obesity of class I (23.60±10.24 ng/ml) and obese of class II (22.38±10.34 ng/ml) had significantly lower levels of 25 (OH) D compared to women with normal body weight (28.24±12.99 ng/ml), p=0.00003. In women with obesity, BMI significantly influences vitamin D level, and this influence does not depend on the season.

Keywords: Obesity, body mass index, vitamin D deficiency/insufficiency, postmenopausal women, age.

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Authors: J. Bernasovska, I. Boronova, J. Poracova, M. Mydlarova Blascakova, V. Szabadosova, P. Ruzbarsky, E. Petrejcikova, I. Bernasovsky

Abstract:

The paper presents the results of the molecular genetics analysis in sports research, with special emphasis to use genetic information in diagnosing of motoric predispositions in Roma boys from East Slovakia. The ability and move are the basic characteristics of all living organisms. The phenotypes are influenced by a combination of genetic and environmental factors. Genetic tests differ in principle from the traditional motoric tests, because the DNA of an individual does not change during life. The aim of the presented study was to examine motion abilities and to determine the frequency of ACTN3 (R577X) gene in Roma children. Genotype data were obtained from 138 Roma and 155 Slovak boys from 7 to 15 years old. Children were investigated on physical performance level in association with their genotype. Biological material for genetic analyses comprised samples of buccal swabs. Genotypes were determined using Real Time High resolution melting PCR method (Rotor-Gene 6000 Corbett and Light Cycler 480 Roche). The software allows creating reports of any analysis, where information of the specific analysis, normalized and differential graphs and many information of the samples are shown. Roma children of analyzed group legged to non-Romany children at the same age in all the compared tests. The % distribution of R and X alleles in Roma children was different from controls. The frequency of XX genotype was 9.26%, RX 46.33% and RR was 44.41%. The frequency of XX genotype was 9.26% which is comparable to a frequency of an Indian population. Data were analyzed with the ANOVA test.

Keywords: ACTN3 gene, R577X polymorphism, Roma children, Slovakia, sports performance.

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