Towards an Environment for doing Data Science that runs in Browsers

International audience—This article proposes a path for doing Data Science using browsers as computing and data nodes. This novel idea is motivated by the cross-fertilized fields of desktop grid computing, data management in grids and clouds, Web technologies such as Nosql tools, models of interactions and programming models in grids, cloud and Web technologies. We propose a methodology for the modeling, analyzing, implemention and simulation of a prototype able to run a MapReduce job in browsers. This work allows to better understand how to envision the big picture of Data Science in the context of the Javascript language for programming the middleware, the interactions between components and browsers as the operating system. We explain what types of applications may be impacted by this novel approach and, from a general point of view how a formal modeling of the interactions serves as a general guidelines for the implementation. Formal modeling in our methodology is a necessary condition but it is not sufficient. We also make round-trips between the modeling and the Javascript or used tools to enrich the interaction model that is the key point, or to put more details into the implementation. It is the first time to the best of our knowledge that Data Science is operating in the context of browsers that exchange codes and data for solving computational and data intensive programs. Computational and data intensive terms should be understand according to the context of applications that we think to be suitable for our system

Probiotic Potential and Safety Evaluation of Enterococcus faecalis OB14 and OB15, Isolated From Traditional Tunisian Testouri Cheese and Rigouta, Using Physiological and Genomic Analysis

Lactic acid bacteria (LAB) strains OB14 and OB15 were isolated from traditional Tunisian fermented dairy products, Testouri cheese and Rigouta, respectively. They were identified as Enterococcus faecalis by the MALDI TOF-MS (matrix assisted laser desorption-ionization time of flight mass spectrometry) biotyper system and molecular assays (species-specific PCR). These new isolates were evaluated for probiotic properties, compared to E. faecalis Symbioflor 1 clone DSM 16431, as reference. The bacteria were found to be tolerant to the harsh conditions of the gastrointestinal tract (acidity and bile salt). They were low to moderate biofilm producers, can adhere to Caco-2/TC7 intestinal cells and strengthen the intestinal barrier through the increase of the transepithelial electrical resistance (TER). Susceptibility to ampicillin, vancomycin, gentamicin and erythromycin has been tested using the broth microdilutions method. The results demonstrated that E. faecalis OB14 and OB15 were sensitive to the clinically important ampicillin (MIC = 1 μg/mL) and vancomycin (MIC = 2 μg/mL) antibiotics. However, Whole Genome Sequencing (WGS) showed the presence of tetracycline resistance and cytolysin genes in E. faecalis OB14, and this led to high mortality of Galleria Mellonella larvae in the virulence test. Hierarchical cluster analysis by MALDI TOF-MS biotyper showed that E. faecalis OB15 was closely related to the E. faecalis Symbioflor 1 probiotic strain than to OB14, and this has been confirmed by WGS using the average nucleotide identity (ANI) and Genome-to-Genome Hybridization similarity methods. According to these results, E. faecalis OB15 seems to be reliable for future development as probiotic, in food or feed industry

The global burden of cancer attributable to risk factors, 2010-19 : a systematic analysis for the Global Burden of Disease Study 2019

Background Understanding the magnitude of cancer burden attributable to potentially modifiable risk factors is crucial for development of effective prevention and mitigation strategies. We analysed results from the Global Burden of Diseases, Injuries, and Risk Factors Study (GBD) 2019 to inform cancer control planning efforts globally. Methods The GBD 2019 comparative risk assessment framework was used to estimate cancer burden attributable to behavioural, environmental and occupational, and metabolic risk factors. A total of 82 risk-outcome pairs were included on the basis of the World Cancer Research Fund criteria. Estimated cancer deaths and disability-adjusted life-years (DALYs) in 2019 and change in these measures between 2010 and 2019 are presented. Findings Globally, in 2019, the risk factors included in this analysis accounted for 4.45 million (95% uncertainty interval 4.01-4.94) deaths and 105 million (95.0-116) DALYs for both sexes combined, representing 44.4% (41.3-48.4) of all cancer deaths and 42.0% (39.1-45.6) of all DALYs. There were 2.88 million (2.60-3.18) risk-attributable cancer deaths in males (50.6% [47.8-54.1] of all male cancer deaths) and 1.58 million (1.36-1.84) risk-attributable cancer deaths in females (36.3% [32.5-41.3] of all female cancer deaths). The leading risk factors at the most detailed level globally for risk-attributable cancer deaths and DALYs in 2019 for both sexes combined were smoking, followed by alcohol use and high BMI. Risk-attributable cancer burden varied by world region and Socio-demographic Index (SDI), with smoking, unsafe sex, and alcohol use being the three leading risk factors for risk-attributable cancer DALYs in low SDI locations in 2019, whereas DALYs in high SDI locations mirrored the top three global risk factor rankings. From 2010 to 2019, global risk-attributable cancer deaths increased by 20.4% (12.6-28.4) and DALYs by 16.8% (8.8-25.0), with the greatest percentage increase in metabolic risks (34.7% [27.9-42.8] and 33.3% [25.8-42.0]). Interpretation The leading risk factors contributing to global cancer burden in 2019 were behavioural, whereas metabolic risk factors saw the largest increases between 2010 and 2019. Reducing exposure to these modifiable risk factors would decrease cancer mortality and DALY rates worldwide, and policies should be tailored appropriately to local cancer risk factor burden. Copyright (C) 2022 The Author(s). Published by Elsevier Ltd. This is an Open Access article under the CC BY 4.0 license.Peer reviewe

The global burden of adolescent and young adult cancer in 2019 : a systematic analysis for the Global Burden of Disease Study 2019

Background In estimating the global burden of cancer, adolescents and young adults with cancer are often overlooked, despite being a distinct subgroup with unique epidemiology, clinical care needs, and societal impact. Comprehensive estimates of the global cancer burden in adolescents and young adults (aged 15-39 years) are lacking. To address this gap, we analysed results from the Global Burden of Diseases, Injuries, and Risk Factors Study (GBD) 2019, with a focus on the outcome of disability-adjusted life-years (DALYs), to inform global cancer control measures in adolescents and young adults. Methods Using the GBD 2019 methodology, international mortality data were collected from vital registration systems, verbal autopsies, and population-based cancer registry inputs modelled with mortality-to-incidence ratios (MIRs). Incidence was computed with mortality estimates and corresponding MIRs. Prevalence estimates were calculated using modelled survival and multiplied by disability weights to obtain years lived with disability (YLDs). Years of life lost (YLLs) were calculated as age-specific cancer deaths multiplied by the standard life expectancy at the age of death. The main outcome was DALYs (the sum of YLLs and YLDs). Estimates were presented globally and by Socio-demographic Index (SDI) quintiles (countries ranked and divided into five equal SDI groups), and all estimates were presented with corresponding 95% uncertainty intervals (UIs). For this analysis, we used the age range of 15-39 years to define adolescents and young adults. Findings There were 1.19 million (95% UI 1.11-1.28) incident cancer cases and 396 000 (370 000-425 000) deaths due to cancer among people aged 15-39 years worldwide in 2019. The highest age-standardised incidence rates occurred in high SDI (59.6 [54.5-65.7] per 100 000 person-years) and high-middle SDI countries (53.2 [48.8-57.9] per 100 000 person-years), while the highest age-standardised mortality rates were in low-middle SDI (14.2 [12.9-15.6] per 100 000 person-years) and middle SDI (13.6 [12.6-14.8] per 100 000 person-years) countries. In 2019, adolescent and young adult cancers contributed 23.5 million (21.9-25.2) DALYs to the global burden of disease, of which 2.7% (1.9-3.6) came from YLDs and 97.3% (96.4-98.1) from YLLs. Cancer was the fourth leading cause of death and tenth leading cause of DALYs in adolescents and young adults globally. Interpretation Adolescent and young adult cancers contributed substantially to the overall adolescent and young adult disease burden globally in 2019. These results provide new insights into the distribution and magnitude of the adolescent and young adult cancer burden around the world. With notable differences observed across SDI settings, these estimates can inform global and country-level cancer control efforts. Copyright (C) 2021 The Author(s). Published by Elsevier Ltd.Peer reviewe

Cancer Incidence, Mortality, Years of Life Lost, Years Lived With Disability, and Disability-Adjusted Life Years for 29 Cancer Groups From 2010 to 2019: A Systematic Analysis for the Global Burden of Disease Study 2019.

The Global Burden of Diseases, Injuries, and Risk Factors Study 2019 (GBD 2019) provided systematic estimates of incidence, morbidity, and mortality to inform local and international efforts toward reducing cancer burden. To estimate cancer burden and trends globally for 204 countries and territories and by Sociodemographic Index (SDI) quintiles from 2010 to 2019. The GBD 2019 estimation methods were used to describe cancer incidence, mortality, years lived with disability, years of life lost, and disability-adjusted life years (DALYs) in 2019 and over the past decade. Estimates are also provided by quintiles of the SDI, a composite measure of educational attainment, income per capita, and total fertility rate for those younger than 25 years. Estimates include 95% uncertainty intervals (UIs). In 2019, there were an estimated 23.6 million (95% UI, 22.2-24.9 million) new cancer cases (17.2 million when excluding nonmelanoma skin cancer) and 10.0 million (95% UI, 9.36-10.6 million) cancer deaths globally, with an estimated 250 million (235-264 million) DALYs due to cancer. Since 2010, these represented a 26.3% (95% UI, 20.3%-32.3%) increase in new cases, a 20.9% (95% UI, 14.2%-27.6%) increase in deaths, and a 16.0% (95% UI, 9.3%-22.8%) increase in DALYs. Among 22 groups of diseases and injuries in the GBD 2019 study, cancer was second only to cardiovascular diseases for the number of deaths, years of life lost, and DALYs globally in 2019. Cancer burden differed across SDI quintiles. The proportion of years lived with disability that contributed to DALYs increased with SDI, ranging from 1.4% (1.1%-1.8%) in the low SDI quintile to 5.7% (4.2%-7.1%) in the high SDI quintile. While the high SDI quintile had the highest number of new cases in 2019, the middle SDI quintile had the highest number of cancer deaths and DALYs. From 2010 to 2019, the largest percentage increase in the numbers of cases and deaths occurred in the low and low-middle SDI quintiles. The results of this systematic analysis suggest that the global burden of cancer is substantial and growing, with burden differing by SDI. These results provide comprehensive and comparable estimates that can potentially inform efforts toward equitable cancer control around the world.Funding/Support: The Institute for Health Metrics and Evaluation received funding from the Bill & Melinda Gates Foundation and the American Lebanese Syrian Associated Charities. Dr Aljunid acknowledges the Department of Health Policy and Management of Kuwait University and the International Centre for Casemix and Clinical Coding, National University of Malaysia for the approval and support to participate in this research project. Dr Bhaskar acknowledges institutional support from the NSW Ministry of Health and NSW Health Pathology. Dr Bärnighausen was supported by the Alexander von Humboldt Foundation through the Alexander von Humboldt Professor award, which is funded by the German Federal Ministry of Education and Research. Dr Braithwaite acknowledges funding from the National Institutes of Health/ National Cancer Institute. Dr Conde acknowledges financial support from the European Research Council ERC Starting Grant agreement No 848325. Dr Costa acknowledges her grant (SFRH/BHD/110001/2015), received by Portuguese national funds through Fundação para a Ciência e Tecnologia, IP under the Norma Transitória grant DL57/2016/CP1334/CT0006. Dr Ghith acknowledges support from a grant from Novo Nordisk Foundation (NNF16OC0021856). Dr Glasbey is supported by a National Institute of Health Research Doctoral Research Fellowship. Dr Vivek Kumar Gupta acknowledges funding support from National Health and Medical Research Council Australia. Dr Haque thanks Jazan University, Saudi Arabia for providing access to the Saudi Digital Library for this research study. Drs Herteliu, Pana, and Ausloos are partially supported by a grant of the Romanian National Authority for Scientific Research and Innovation, CNDS-UEFISCDI, project number PN-III-P4-ID-PCCF-2016-0084. Dr Hugo received support from the Higher Education Improvement Coordination of the Brazilian Ministry of Education for a sabbatical period at the Institute for Health Metrics and Evaluation, between September 2019 and August 2020. Dr Sheikh Mohammed Shariful Islam acknowledges funding by a National Heart Foundation of Australia Fellowship and National Health and Medical Research Council Emerging Leadership Fellowship. Dr Jakovljevic acknowledges support through grant OI 175014 of the Ministry of Education Science and Technological Development of the Republic of Serbia. Dr Katikireddi acknowledges funding from a NHS Research Scotland Senior Clinical Fellowship (SCAF/15/02), the Medical Research Council (MC_UU_00022/2), and the Scottish Government Chief Scientist Office (SPHSU17). Dr Md Nuruzzaman Khan acknowledges the support of Jatiya Kabi Kazi Nazrul Islam University, Bangladesh. Dr Yun Jin Kim was supported by the Research Management Centre, Xiamen University Malaysia (XMUMRF/2020-C6/ITCM/0004). Dr Koulmane Laxminarayana acknowledges institutional support from Manipal Academy of Higher Education. Dr Landires is a member of the Sistema Nacional de Investigación, which is supported by Panama’s Secretaría Nacional de Ciencia, Tecnología e Innovación. Dr Loureiro was supported by national funds through Fundação para a Ciência e Tecnologia under the Scientific Employment Stimulus–Institutional Call (CEECINST/00049/2018). Dr Molokhia is supported by the National Institute for Health Research Biomedical Research Center at Guy’s and St Thomas’ National Health Service Foundation Trust and King’s College London. Dr Moosavi appreciates NIGEB's support. Dr Pati acknowledges support from the SIAN Institute, Association for Biodiversity Conservation & Research. Dr Rakovac acknowledges a grant from the government of the Russian Federation in the context of World Health Organization Noncommunicable Diseases Office. Dr Samy was supported by a fellowship from the Egyptian Fulbright Mission Program. Dr Sheikh acknowledges support from Health Data Research UK. Drs Adithi Shetty and Unnikrishnan acknowledge support given by Kasturba Medical College, Mangalore, Manipal Academy of Higher Education. Dr Pavanchand H. Shetty acknowledges Manipal Academy of Higher Education for their research support. Dr Diego Augusto Santos Silva was financed in part by the Coordenação de Aperfeiçoamento de Pessoal de Nível Superior - Brasil Finance Code 001 and is supported in part by CNPq (302028/2018-8). Dr Zhu acknowledges the Cancer Prevention and Research Institute of Texas grant RP210042

Revisiter les grilles de PCs avec des technologies du Web et le Cloud computing

The context of this work is at the intersection of grid computing, the new Web technologies and the Clouds and services on demand contexts. Desktop Grid have been proposed as an alternative to supercomputers by the federation of thousands of desktops. The details of the implementation of such an architecture, in terms of resource sharing mechanisms, remain very hard. Meanwhile, the Web has completely changed the way we access information. The equipment, in turn, have evolved from desktops or laptops to tablets, smartphones or NetPCs. Our approach is to rethink Desktop Grids from a reflexion and a formal framework to develop them rigorously and better control future technological developments. We have reconsidered the interactions between the traditional components of a Desktop Grid based on the Web technology, and given birth to RedisDG, a new Desktop Grid middelware capable to operate on small devices, ie smartphones, tablets like the more traditional devicves (PCs). Our system is entirely based on the publish-subscribe paradigm. RedisDG is developped with Python and uses Redis as advanced key-value cache and store.Le contexte de cette thèse est à l’intersection des contextes des grilles de calculs, des nouvelles technologies du Web ainsi que des Clouds et des services à la demande. Depuis leur avènement au cours des années 90, les plates-formes distribuées, plus précisément les systèmes de grilles de calcul (Grid Computing), n’ont pas cessé d’évoluer permettant ainsi de susciter multiple efforts de recherche. Les grilles de PCs ont été proposées comme une alternative aux super-calculateurs par la fédération des milliers d’ordinateurs de bureau. Les détails de la mise en oeuvre d’une telle architecture de grille, en termes de mécanismes de mutualisation des ressources, restent très difficile à cerner. Parallèlement, le Web a complètement modifié notre façon d’accéder à l’information. Le Web est maintenant une composante essentielle de notre quotidien. Les équipements ont, à leur tour, évolué d’ordinateurs de bureau ou ordinateurs portables aux tablettes, lecteurs multimédias, consoles de jeux, smartphones, ou NetPCs. Cette évolution exige d’adapter et de repenser les applications/intergiciels de grille de PCs qui ont été développés ces dernières années. Notre contribution se résume dans la réalisation d’un intergiciel de grille de PCs que nous avons appelé RedisDG. Dans son fonctionnement, RedisDG reste similaire à la plupart des intergiciels de grilles de calcul, c’est-à-dire qu’il est capable d’exécuter des applications sous forme de «sacs de tâches» dans un environnement distribué, assurer le monitoring des noeuds, valider et certifier les résultats. L’innovation de RedisDG, réside dans l’intégration de la modélisation et la vérification formelles dans sa phase de conception, ce qui est non conventionnel mais très pertinent dans notre domaine. Notre approche consiste à repenser les grilles de PCs à partir d’une réflexion et d’un cadre formel permettant de les développer, de manière rigoureuse et de mieux maîtriser les évolutions technologiques à venir

Re-examaning the Desktop Grids with Web Technologies and Cloud Computing

Le contexte de cette thèse est à l’intersection des contextes des grilles de calculs, des nouvelles technologies du Web ainsi que des Clouds et des services à la demande. Depuis leur avènement au cours des années 90, les plates-formes distribuées, plus précisément les systèmes de grilles de calcul (Grid Computing), n’ont pas cessé d’évoluer permettant ainsi de susciter multiple efforts de recherche. Les grilles de PCs ont été proposées comme une alternative aux super-calculateurs par la fédération des milliers d’ordinateurs de bureau. Les détails de la mise en oeuvre d’une telle architecture de grille, en termes de mécanismes de mutualisation des ressources, restent très difficile à cerner. Parallèlement, le Web a complètement modifié notre façon d’accéder à l’information. Le Web est maintenant une composante essentielle de notre quotidien. Les équipements ont, à leur tour, évolué d’ordinateurs de bureau ou ordinateurs portables aux tablettes, lecteurs multimédias, consoles de jeux, smartphones, ou NetPCs. Cette évolution exige d’adapter et de repenser les applications/intergiciels de grille de PCs qui ont été développés ces dernières années. Notre contribution se résume dans la réalisation d’un intergiciel de grille de PCs que nous avons appelé RedisDG. Dans son fonctionnement, RedisDG reste similaire à la plupart des intergiciels de grilles de calcul, c’est-à-dire qu’il est capable d’exécuter des applications sous forme de «sacs de tâches» dans un environnement distribué, assurer le monitoring des noeuds, valider et certifier les résultats. L’innovation de RedisDG, réside dans l’intégration de la modélisation et la vérification formelles dans sa phase de conception, ce qui est non conventionnel mais très pertinent dans notre domaine. Notre approche consiste à repenser les grilles de PCs à partir d’une réflexion et d’un cadre formel permettant de les développer, de manière rigoureuse et de mieux maîtriser les évolutions technologiques à venir.The context of this work is at the intersection of grid computing, the new Web technologies and the Clouds and services on demand contexts. Desktop Grid have been proposed as an alternative to supercomputers by the federation of thousands of desktops. The details of the implementation of such an architecture, in terms of resource sharing mechanisms, remain very hard. Meanwhile, the Web has completely changed the way we access information. The equipment, in turn, have evolved from desktops or laptops to tablets, smartphones or NetPCs. Our approach is to rethink Desktop Grids from a reflexion and a formal framework to develop them rigorously and better control future technological developments. We have reconsidered the interactions between the traditional components of a Desktop Grid based on the Web technology, and given birth to RedisDG, a new Desktop Grid middelware capable to operate on small devices, ie smartphones, tablets like the more traditional devicves (PCs). Our system is entirely based on the publish-subscribe paradigm. RedisDG is developped with Python and uses Redis as advanced key-value cache and store

Images of the Qur’an in Western scholarship: a socio-narrative approach

AbstractDespite the huge body of research that has developed around the Qur’an in the West, there is still a dearth of research on how this scholarship represents the Qur’an and could contribute to feeding dominant narratives about Islam and Muslims in the West. To fill this gap, and drawing on socio-narrative theory, the present article analyzes the textual choices made in two works published in the well-established journal Arabica: Journal of Arabic and Islamic Studies, namely Christiansen’s ‘The Dark Koran: A Semantic Analysis of the Koranic Darknesses (ẓulumāt) and their Metaphorical Usage’, and Boisliveau’s ‘Polemics in the Koran: The Koran’s Negative Argumentation over its Own Origin’. Analysis reveals that the different discursive choices made by the authors draw on the anti-Islamic polemical tradition and activate a century-old narrative with much currency in the West. The article concludes that while Western scholarship on the Quran has provided valuable insight into this text, its historical context, and relationship to other religious texts, it produces contingent and situated knowledge that can still bear the traces of orientalist representations and misconceptions

Data Management for the RedisDG Scientific Workflow Engine

International audience—In this paper we investigate the general problem of controlling a scientific workflow service in terms of data management. We focus on the data management problem for the RedisDG scientific workflow engine. RedisDG is based on the Publish/Subscribe paradigm for the interaction between the different components of the system, hence new issues appear for scheduling. Indeed, the Publish/Subscribe paradigm utilization introduces different challenging problems, among them the design of effective solutions for managing data, on the fly, when tasks are published. Our contributions are twofold. First we add new functionalities to the RedisDG workflow engine with scheduling decisions related to the allocation of data intensive jobs to compute units and according to an efficient management of data and second we introduce a large set of experiments to validate our approaches. We analyze our results and we also sketch perspectives and insights. Experiments are conducted on the Grid'5000 testbed and the paper is a step forward to implement a 'Workflow engine as a Service' (WaaS)

Relationship of SNP rs2645429 in Farnesyl-Diphosphate Farnesyltransferase 1 Gene Promoter with Susceptibility to Lung Cancer

Background and Purpose. The mevalonate pathway is one of the major metabolic pathways that use acetyl-CoA to produce sterols and isoprenoids. These compounds can be effective in the growth and development of tumors. One of the enzymes involved in the mevalonate pathway is FDFT1. Different variants of this gene are involved in the risk of suffering various diseases. The present study examined the relationship between FDFT1 rs2645429 polymorphism and the risk of nonsmall cell lung cancer (NSCLC) in a population from southern Iran. Method. The genotypes of rs2645429 polymorphism of FDFT1 gene were examined in 95 samples: 34 patients with NSCLC and 61 healthy individuals by RFLP method. Results. The results of this study indicated that C allele of this polymorphism was effectively associated with the risk of NSCLC in the Iranian population (p value = 0.023; OR = 2.71; 95% CI = 1.12–6.59) and CC genotype has significant relation with susceptibility to NSCLC (p value = 0.029; OR = 3.02; 95% CI = 1.09–8.39). This polymorphism is located in the promoter region FDFT1 gene, and CC genotype may increase the activity of this promoter. This study also found a significant relationship between C allele and metastatic status. C allele was more common in NSCLC patients. (p=0.04). Conclusion. C allele of FDFT1 rs2645429 polymorphism gene can be a risk factor for NSCLC, whereas T allele probably has a low protective role