Ontology Population via NLP Techniques in Risk Management

In this paper we propose an NLP-based method for Ontology Population from texts and apply it to semi automatic instantiate a Generic Knowledge Base (Generic Domain Ontology) in the risk management domain. The approach is semi-automatic and uses a domain expert intervention for validation. The proposed approach relies on a set of Instances Recognition Rules based on syntactic structures, and on the predicative power of verbs in the instantiation process. It is not domain dependent since it heavily relies on linguistic knowledge. A description of an experiment performed on a part of the ontology of the PRIMA project (supported by the European community) is given. A first validation of the method is done by populating this ontology with Chemical Fact Sheets from Environmental Protection Agency . The results of this experiment complete the paper and support the hypothesis that relying on the predicative power of verbs in the instantiation process improves the performance.Information Extraction, Instance Recognition Rules, Ontology Population, Risk Management, Semantic Analysis

Study the Effect of Cyp19 Gene Polymorphism in Some Genital Hormones and Some Milk Traits in Local Ewes

أجريت هذه الدراسة لغرض دراسة تعدد الاشكال الوراثية polymorphism  لجين CYP19 ومعرفة تاثيرها على تراكيز هرموني الاستروجين والبروجيستيرون في النعاج العواسية المحلية ٬ جمعت عينات الدم من النعاج العواسية في حقول العتبة الحسينية الواقعة على طريق نجف /كربلاء وهذا فيما يخص الجانب الحقلي، تم قياس تراكيز هرمون الاستروجين وهرمون البروجستيرون ٬حيث سجل اعلى تركيز في هرمون الاستروجين (pg/ml16.3349) واقل تركيز(9.3885pg/ml) وكان اعلى تركيز في هرمون البروجيستيرون(0.5893ng/ml ) واقل تركيز (ng/ml0.1302) تم عزل الحزمة الجينية للاكسون الثالث التابعة للجينCYP19 البالغ حجمها140 bp وتحديد التراكيب الوراثية Genotype)) لها تبعا لاختلاف تسلسل النيوكليوتيدات وعلاقتها بتراكيز الاستروجين و البروجيستيرون في عينات الدراسة كانت نسب توزيع التراكيب الوراثية لجين CYP19في عينة النعاج العواسية المحلية %6.25 و%31.25و%62.50 لكل من التراكيب الوراثية TT  و TCوCC على التتابع، واظهرت نتائج قياس تركيز الاستروجين تفوقاً معنوياً على مستوى احتمالية (P≤0.05 ) في الطراز الوراثي TT و TC (15,5745,15,4617) على التوالي مقارنة بالطراز الوراثيCC ( 14.2362)في حين لم يكن هنالك فرق معنوي بين   الطرازين الوراثيين TTوTC.أوضحت نتائج قياس تركيز البروجيستيرون تفوقاً معنوياً على مستوى احتمالية P≤0.05 في الطراز الوراثي TC (.47770)على الطرازين الوراثيين TT و CC (0.3288,0.2469)بينما انخفض تركيز البروجيستيرون للطراز الوراثي TT انخفاظا معنويا مقارنة بالطراز الوراثي TC و CC. توصلت الدراسة الحالية الى شيوع التركيب الوراثي TCلجينCYP19 على التركيبين الوراثيين TTوCCوان لتعدد الاشكال الوراثي Polymorphism لجين CYP19 في Exon3 تاثيراً معنوياً  على تراكيز الاستروجيين والبروجيستيرون  إذ تفوقت الافراد الحاملة للتركيب الوراثي TC لجين CYP19 على التراكيب الوراثية TT وCCفي تراكيز هرموني الاستروجين والبروجيستيرون.This study was carried out for the studying CYP19 gene polymorphism and its effect in concentrations of estrogen and progesterone in local ectopic ewes. Blood samples were collected from ewes in the fields of Husseiniya on the Najaf / Karbala road. In terms of the field side, estrogen concentrations The highest concentration of progesterone (0.5893 ng / ml) and the lowest concentration (ng / ml0.1302) was the isolation of the genetic bundle For the third CYP19 genome of 140 bp and the determination of the structures Genotype). The genotype of the CYP19 gene in the sample of local ewes was 6.25%, 31.25%, and 62.50% for the TT, TC and CC sequences in the sequence. Concentration measurement results Estrogen had a significant effect on the level of P (0.05) in the genotype TT and TC (15,5745,15,4617) respectively, compared with the CC model (14.2362), while there was no significant difference between the TT and TC models. Progesterone significantly exceeded the P00.05 probability level in the Ur model (0.47770) on the genotype TT and CC (0.3288,0.2469). The progesterone concentration of the TT genotype decreased significantly compared with TC and CC. The study found that the genetic makeup of the gene CYP19 on the genetic structures of TT and CCW and the polymorphism of CYP19 gene in Exon3 had a significant effect on estrogens and progesterone concentrations. Individuals carrying the genetic makeup of the gene CYP19 were superior to the TT and CC structures in estrogen and progesterone concentrations

ENVIRONMENTAL ASSESSMENT OF AL-HILLAH RIVER POLLUTION AT BABIL GOVERNORATE (IRAQ)

In this study, the environmental characteristics of Al-Hillah River were studied using geoinformatics applications, which is one of the geospatial techniques (GST). Applying this methodology, a geographic information system was developed, and it was supplied with laboratory data for the physical and chemical properties of 16 parameters for 2021. These data were linked to their spatial locations, using radar imagery of the Digital Elevation Model (Shuttle Radar Topography Mission), and Landsat ETM+7 satellite image. The results indicated that Al-Hillah River was affected by the liquid discharges of factories, cities, and farms spread on its sides, especially in the cities of Sadat Al-Hindiya, Al-Hillah, and Al-Hashimiyah. The seasonal changes in the climate affected some characteristics, including water temperature, pH, turbidity, total dissolved solids, and total hardness. The study showed that the concentration of sulfate (SO4) has risen above the permissible limits for the waters of Iraqi rivers. There are relatively high hardness and alkalinity values, but they were within the permissible limits. The study also showed that most of the results of environmental parameters that were used in the laboratory, were within the permissible limits of Iraqi water, except for sulfates. The justification for conducting this study is to help government agencies and decision-makers to adopt a correct vision for development projects that serve Babil Governorate. Also, it is the first time that the environmental characteristics of Al-Hillah River are studied using geoinformatics applications

Measuring routine childhood vaccination coverage in 204 countries and territories, 1980-2019 : a systematic analysis for the Global Burden of Disease Study 2020, Release 1

Background Measuring routine childhood vaccination is crucial to inform global vaccine policies and programme implementation, and to track progress towards targets set by the Global Vaccine Action Plan (GVAP) and Immunization Agenda 2030. Robust estimates of routine vaccine coverage are needed to identify past successes and persistent vulnerabilities. Drawing from the Global Burden of Diseases, Injuries, and Risk Factors Study (GBD) 2020, Release 1, we did a systematic analysis of global, regional, and national vaccine coverage trends using a statistical framework, by vaccine and over time. Methods For this analysis we collated 55 326 country-specific, cohort-specific, year-specific, vaccine-specific, and dosespecific observations of routine childhood vaccination coverage between 1980 and 2019. Using spatiotemporal Gaussian process regression, we produced location-specific and year-specific estimates of 11 routine childhood vaccine coverage indicators for 204 countries and territories from 1980 to 2019, adjusting for biases in countryreported data and reflecting reported stockouts and supply disruptions. We analysed global and regional trends in coverage and numbers of zero-dose children (defined as those who never received a diphtheria-tetanus-pertussis [DTP] vaccine dose), progress towards GVAP targets, and the relationship between vaccine coverage and sociodemographic development. Findings By 2019, global coverage of third-dose DTP (DTP3; 81.6% [95% uncertainty interval 80.4-82 .7]) more than doubled from levels estimated in 1980 (39.9% [37.5-42.1]), as did global coverage of the first-dose measles-containing vaccine (MCV1; from 38.5% [35.4-41.3] in 1980 to 83.6% [82.3-84.8] in 2019). Third- dose polio vaccine (Pol3) coverage also increased, from 42.6% (41.4-44.1) in 1980 to 79.8% (78.4-81.1) in 2019, and global coverage of newer vaccines increased rapidly between 2000 and 2019. The global number of zero-dose children fell by nearly 75% between 1980 and 2019, from 56.8 million (52.6-60. 9) to 14.5 million (13.4-15.9). However, over the past decade, global vaccine coverage broadly plateaued; 94 countries and territories recorded decreasing DTP3 coverage since 2010. Only 11 countries and territories were estimated to have reached the national GVAP target of at least 90% coverage for all assessed vaccines in 2019. Interpretation After achieving large gains in childhood vaccine coverage worldwide, in much of the world this progress was stalled or reversed from 2010 to 2019. These findings underscore the importance of revisiting routine immunisation strategies and programmatic approaches, recentring service delivery around equity and underserved populations. Strengthening vaccine data and monitoring systems is crucial to these pursuits, now and through to 2030, to ensure that all children have access to, and can benefit from, lifesaving vaccines. Copyright (C) 2021 The Author(s). Published by Elsevier Ltd.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

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

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

The evolving SARS-CoV-2 epidemic in Africa: Insights from rapidly expanding genomic surveillance

INTRODUCTION Investment in Africa over the past year with regard to severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) sequencing has led to a massive increase in the number of sequences, which, to date, exceeds 100,000 sequences generated to track the pandemic on the continent. These sequences have profoundly affected how public health officials in Africa have navigated the COVID-19 pandemic. RATIONALE We demonstrate how the first 100,000 SARS-CoV-2 sequences from Africa have helped monitor the epidemic on the continent, how genomic surveillance expanded over the course of the pandemic, and how we adapted our sequencing methods to deal with an evolving virus. Finally, we also examine how viral lineages have spread across the continent in a phylogeographic framework to gain insights into the underlying temporal and spatial transmission dynamics for several variants of concern (VOCs). RESULTS Our results indicate that the number of countries in Africa that can sequence the virus within their own borders is growing and that this is coupled with a shorter turnaround time from the time of sampling to sequence submission. Ongoing evolution necessitated the continual updating of primer sets, and, as a result, eight primer sets were designed in tandem with viral evolution and used to ensure effective sequencing of the virus. The pandemic unfolded through multiple waves of infection that were each driven by distinct genetic lineages, with B.1-like ancestral strains associated with the first pandemic wave of infections in 2020. Successive waves on the continent were fueled by different VOCs, with Alpha and Beta cocirculating in distinct spatial patterns during the second wave and Delta and Omicron affecting the whole continent during the third and fourth waves, respectively. Phylogeographic reconstruction points toward distinct differences in viral importation and exportation patterns associated with the Alpha, Beta, Delta, and Omicron variants and subvariants, when considering both Africa versus the rest of the world and viral dissemination within the continent. Our epidemiological and phylogenetic inferences therefore underscore the heterogeneous nature of the pandemic on the continent and highlight key insights and challenges, for instance, recognizing the limitations of low testing proportions. We also highlight the early warning capacity that genomic surveillance in Africa has had for the rest of the world with the detection of new lineages and variants, the most recent being the characterization of various Omicron subvariants. CONCLUSION Sustained investment for diagnostics and genomic surveillance in Africa is needed as the virus continues to evolve. This is important not only to help combat SARS-CoV-2 on the continent but also because it can be used as a platform to help address the many emerging and reemerging infectious disease threats in Africa. In particular, capacity building for local sequencing within countries or within the continent should be prioritized because this is generally associated with shorter turnaround times, providing the most benefit to local public health authorities tasked with pandemic response and mitigation and allowing for the fastest reaction to localized outbreaks. These investments are crucial for pandemic preparedness and response and will serve the health of the continent well into the 21st century

Peuplement semi-automatique d'ontologies basé sur le TALN‎ : applications à une ontologie en management de risques

Ce travail s'inscrit dans le cadre d'Ingénierie Ontologique et aborde une problématique liée au peuplement d'ontologie qui consiste à apprendre des instances de concepts, ainsi que des relations en s'appuyant sur l'extraction d'information. Dans cette thèse, nous proposons une approche semi-automatique de peuplement d'ontologie à partir de textes en langage naturel. Cette approche permet de transformer les connaissances qui se trouvent dans les textes vers la base de connaissances associée à une ontologie sous la forme d'instances de concepts et de relations. L'approche est basée sur des techniques de TALN combinées (statistiques, morphosyntaxiques et sémantiques) avec intégration des pondérations automatiques pour l'évaluation des connaissances extraites et l'aide à la décision. La validation de nos propositions se base sur la réalisation d'un prototype nomme OntoPRiMa.This work falls under the Ontological Engineering framework and deals with the issues related to ontology population that consists of learning instances of concepts as well as relations by relying on the information extraction. In this thesis, we propose a semi-automatic ontology population approach from natural language texts. This approach allows to move the knowledge found in the texts into the knowledge based associated to an ontology as instances of concepts and relations. The approach is based on combined NLP techniques (statistic, morphosyntactic and semantic) with integration of automatic weighting for evaluating the extracted knowledge and providing decision support. The validation of our proposals is based on the realization of a prototype named OntoPRiMa