scholarly journals How to deal with Haplotype data: An Extension to the Conceptual Schema of the Human Genome

2016 ◽  
Author(s):  
José Fabián Reyes Román ◽  
Oscar Pastor ◽  
Francisco Valverde ◽  
David Roldán
Keyword(s):  
Human Genome ◽  
Conceptual Modeling ◽  
Relevant Information ◽  
Management Approach ◽  
Conceptual Schema ◽  
Database Structure ◽  
New Findings ◽  
Definition Of ◽  
Novel Concept ◽  
High Level

The goal of this work is to describe the advantages of the application of Conceptual Modeling (CM) in complex domains, such as genomics. Nowadays, the study and comprehension of the human genome is a major challenge due to its high level of complexity. The constant evolution in the genomic domain contributes to the generation of ever larger amounts of new data, which means that if we do not manage it correctly data quality could be compromised (i.e., problems related with heterogeneity and inconsistent data). In this paper, we propose the use of a Conceptual Schema of the Human Genome (CSHG), designed to understand and improve our ontological commitment to the domain and also extend (enrich) this schema with the integration of a novel concept: Haplotypes. Our focus is on improving the understanding of the relationship between genotype and phenotype, since new findings show that this question is more complex than was originally thought. Here we present the first steps in our data management approach with haplotypes (variations, frequencies and populations) and discuss the database evolution to support this data. Each new version in our conceptual schema (CS) introduces changes to the underlying database structure that has essential and practical implications for better understanding and managing the relevant information. A solution based on conceptual models gives a clear definition of the domain with direct implications in the medical field (Precision Medicine), in which Genomic Information Systems (GeIS) play a very important role.

scholarly journals On how to generalize species-specific conceptual schemes to generate a species-independent Conceptual Schema of the Genome

2021 ◽  
Vol 22 (S13) ◽  
Author(s):  
Alberto García S. ◽  
Juan Carlos Casamayor
Keyword(s):  
Human Genome ◽  
Conceptual Modeling ◽  
Genetic Diagnosis ◽  
Use Cases ◽  
Use Case ◽  
Conceptual Schema ◽  
Conceptual Schemes ◽  
Modeling Techniques ◽  
Species Specific ◽  
Specific Species

Abstract Background Understanding the genome, with all of its components and intrinsic relationships, is a great challenge. Conceptual modeling techniques have been used as a means to face this challenge. The heterogeneity and idiosyncrasy of genomic use cases mean that conceptual modeling techniques are used to generate conceptual schemes that focus on too specific scenarios (i.e., they are species-specific conceptual schemes). Our research group developed two different conceptual schemes. The first one is the Conceptual Schema of the Human Genome, which is intended to improve Precision Medicine and genetic diagnosis. The second one is the Conceptual Schema of the Citrus Genome, which is intended to identify the genetic cause of relevant phenotypes in the agri-food field. Methods Our two conceptual schemes have been ontologically compared to identify their similarities and differences. Based on this comparison, several changes have been performed in the Conceptual Schema of the Human Genome in order to obtain the first version of a species-independent Conceptual Schema of the Genome. Identifying the different genome information items used in each genomic case study has been essential in achieving our goal. The changes needed to provide an expanded, more generic version of the Conceptual Schema of the Human Genome are analyzed and discussed. Results This work presents a new CS called the Conceptual Schema of the Genome that is ready to be adapted to any specific working genome-based context (i.e., species-independent). Conclusion The generated Conceptual Schema of the Genome works as a global, generic element from which conceptual views can be created in order to work with any specific species. This first working version can be used in the human use case, in the citrus use case, and, potentially, in more use cases of other species.

A voyage to Ancient Greek Harbours on board Limenoscope

2007 ◽  
Vol 7 (1) ◽  
pp. 253-260 ◽  
Author(s):  
T. Theodoulou ◽  
C. Memos
Keyword(s):  
Black Sea ◽  
General Public ◽  
Aegean Sea ◽  
Relevant Information ◽  
The Black Sea ◽  
Ancient Greek ◽  
Web Based ◽  
Database Structure ◽  
Historical Role ◽  
Concise Information

Limenoscope is a web based database aiming at promoting the cultural heritage regarding ancient Greek harbours and disseminate the relevant information equally to the general public and to researchers with an interest in that particular cognitive field. The scope of the project is the realization of a database, where one can search for concise information relevant to the historical role, the topography, the morphology, as well as the technical works and installations of ancient harbours in the Mediterranean and the Black Sea. The Database started off with the registration of harbours located in the Aegean Sea and Cyprus, dating from Archaic to Byzantine times. Special emphasis is laid on the bibliographical update of the data forms of the harbour sites, as well as on the related references in ancient literature. The database enables the locating of these sites on a general map, where photographs, plans etc. are also archived. The principles of the database structure are briefly presented along with an example, that of the harbour of Phalasarna, among the harbours registered therein.

Europe

2020 ◽  
pp. 649-666
Author(s):  
Andrea Renda
Keyword(s):  
Artificial Intelligence ◽  
Digital Technology ◽  
Policy Framework ◽  
Expert Group ◽  
Ethical Guidelines ◽  
Ethical Implications ◽  
Strong Focus ◽  
Ethics Guidelines ◽  
Definition Of ◽  
High Level

This chapter assesses Europe’s efforts in developing a full-fledged strategy on the human and ethical implications of artificial intelligence (AI). The strong focus on ethics in the European Union’s AI strategy should be seen in the context of an overall strategy that aims at protecting citizens and civil society from abuses of digital technology but also as part of a competitiveness-oriented strategy aimed at raising the standards for access to Europe’s wealthy Single Market. In this context, one of the most peculiar steps in the European Union’s strategy was the creation of an independent High-Level Expert Group on AI (AI HLEG), accompanied by the launch of an AI Alliance, which quickly attracted several hundred participants. The AI HLEG, a multistakeholder group including fifty-two experts, was tasked with the definition of Ethics Guidelines as well as with the formulation of “Policy and Investment Recommendations.” With the advice of the AI HLEG, the European Commission put forward ethical guidelines for Trustworthy AI—which are now paving the way for a comprehensive, risk-based policy framework.

Applying Conceptual Modeling to Better Understand the Human Genome

2016 ◽  
pp. 404-412 ◽  
Author(s):  
José F. Reyes Román ◽  
Óscar Pastor ◽  
Juan Carlos Casamayor ◽  
Francisco Valverde
Keyword(s):  
Human Genome ◽  
Conceptual Modeling

scholarly journals The Evolving Landscape of the Molecular Epidemiology of Malignant Pleural Mesothelioma

2021 ◽  
Vol 10 (5) ◽  
pp. 1034
Author(s):  
Sara Lettieri ◽  
Chandra Bortolotto ◽  
Francesco Agustoni ◽  
Filippo Lococo ◽  
Andrea Lancia ◽  
...  
Keyword(s):  
Molecular Epidemiology ◽  
Malignant Pleural Mesothelioma ◽  
Strong Association ◽  
Pleural Mesothelioma ◽  
The European Union ◽  
Long Latency ◽  
Substantial Risk ◽  
Novel Biomarkers ◽  
Definition Of ◽  
Novel Concept

Malignant pleural mesothelioma (MPM) is a rare and aggressive malignancy that most commonly affects the pleural lining of the lungs. It has a strong association with exposure to biopersistent fibers, mainly asbestos (80% of cases) and—in specific geographic regions—erionite, zeolites, ophiolites, and fluoro-edenite. Individuals with a chronic exposure to asbestos generally have a long latency with no or few symptoms. Then, when patients do become symptomatic, they present with advanced disease and a worse overall survival (about 13/15 months). The fibers from industrial production not only pose a substantial risk to workers, but also to their relatives and to the surrounding community. Modern targeted therapies that have shown benefit in other human tumors have thus far failed in MPM. Overall, MPM has been listed as orphan disease by the European Union. However, molecular high-throughput profiling is currently unveiling novel biomarkers and actionable targets. We here discuss the natural evolution, mainly focusing on the novel concept of molecular epidemiology. The application of innovative endpoints, quantification of genetic damages, and definition of genetic susceptibility are reviewed, with the ultimate goal to point out new tools for screening of exposed subject and for designing more efficient diagnostic and therapeutic strategies.

scholarly journals Shape Sensing of a Complex Aeronautical Structure with Inverse Finite Element Method

Sensors ◽  
2021 ◽  
Vol 21 (4) ◽  
pp. 1388
Author(s):  
Daniele Oboe ◽  
Luca Colombo ◽  
Claudio Sbarufatti ◽  
Marco Giglio
Keyword(s):  
Finite Element Method ◽  
Finite Element ◽  
Boundary Conditions ◽  
Strain Field ◽  
Element Analysis ◽  
Inverse Finite Element Method ◽  
Shape Sensing ◽  
Definition Of ◽  
High Level ◽  
Element Method

The inverse Finite Element Method (iFEM) is receiving more attention for shape sensing due to its independence from the material properties and the external load. However, a proper definition of the model geometry with its boundary conditions is required, together with the acquisition of the structure’s strain field with optimized sensor networks. The iFEM model definition is not trivial in the case of complex structures, in particular, if sensors are not applied on the whole structure allowing just a partial definition of the input strain field. To overcome this issue, this research proposes a simplified iFEM model in which the geometrical complexity is reduced and boundary conditions are tuned with the superimposition of the effects to behave as the real structure. The procedure is assessed for a complex aeronautical structure, where the reference displacement field is first computed in a numerical framework with input strains coming from a direct finite element analysis, confirming the effectiveness of the iFEM based on a simplified geometry. Finally, the model is fed with experimentally acquired strain measurements and the performance of the method is assessed in presence of a high level of uncertainty.

scholarly journals Sustainability and Stakeholder Awareness: A Case Study of a Scottish University

2021 ◽  
Vol 13 (8) ◽  
pp. 4186
Author(s):  
Abdulhakeem Raji ◽  
Abeer Hassan
Keyword(s):  
Signaling Theory ◽  
Relevant Information ◽  
Voluntary Exercise ◽  
Communication Tool ◽  
Individual Interviews ◽  
Study Approach ◽  
Research Findings ◽  
Definition Of ◽  
The University

This paper adopted a case study approach to investigate the sustainability practices of a Scottish university in order to understand if sustainability forms part of its central policy agenda. As such, the paper focuses on the levels of awareness and disclosure of their sustainable practices, measuring the impacts and effectiveness of those initiatives. This paper introduces signaling theory to explore the idea that appropriate communication via integrated thinking can close the gap between the organization and its stakeholders. We believe that the provision of this relevant information will lead to better communication between the organization and its stakeholders, supporting a signaling theory interpretation. Therefore, we are suggesting that integrated thinking is an internal process that organizations can follow to increase the level of disclosure as a communication tool with stakeholders. From the literature reviewed, four themes were identified (definition of university sustainability, sustainability awareness, disclosure framework within universities, and level of accountability). The research adopted a pragmatic view and conducted individual interviews with participants belonging to three stakeholder groups (members of the university’s senior management, the governing council, and the student union executive). Although this study focused on just one Scottish university, it should still provide some insight for the better understanding of the underpinning issues surrounding the sustainability accountability practices of Scottish universities in general. The research findings indicated that the university prioritized only two sustainability dimensions—economic and environmental—and that the university still perceived sustainability as a voluntary exercise. Additionally, it is evident that the university had no framework in place for measuring its sustainability delivery—and therefore had no established medium of communicating these activities to its stakeholders. Moreover, research findings showed that the social and educational context of sustainability was lacking at the university. The university has done little or nothing to educate its stakeholders on sustainability.

scholarly journals Quaternion Processing Techniques for Color Synthesized NDT Thermography

2021 ◽  
Vol 11 (2) ◽  
pp. 790
Author(s):  
Pablo Venegas ◽  
Rubén Usamentiaga ◽  
Juan Perán ◽  
Idurre Sáez de Ocáriz
Keyword(s):  
Signal To Noise Ratio ◽  
High Capacity ◽  
Synthetic Data ◽  
Relevant Information ◽  
Color Images ◽  
Destructive Testing ◽  
Application Procedure ◽  
Definition Of ◽  
Characterization Procedure ◽  
Processing Techniques

Infrared thermography is a widely used technology that has been successfully applied to many and varied applications. These applications include the use as a non-destructive testing tool to assess the integrity state of materials. The current level of development of this application is high and its effectiveness is widely verified. There are application protocols and methodologies that have demonstrated a high capacity to extract relevant information from the captured thermal signals and guarantee the detection of anomalies in the inspected materials. However, there is still room for improvement in certain aspects, such as the increase of the detection capacity and the definition of a detailed characterization procedure of indications, that must be investigated further to reduce uncertainties and optimize this technology. In this work, an innovative thermographic data analysis methodology is proposed that extracts a greater amount of information from the recorded sequences by applying advanced processing techniques to the results. The extracted information is synthesized into three channels that may be represented through real color images and processed by quaternion algebra techniques to improve the detection level and facilitate the classification of defects. To validate the proposed methodology, synthetic data and actual experimental sequences have been analyzed. Seven different definitions of signal-to-noise ratio (SNR) have been used to assess the increment in the detection capacity, and a generalized application procedure has been proposed to extend their use to color images. The results verify the capacity of this methodology, showing significant increments in the SNR compared to conventional processing techniques in thermographic NDT.

scholarly journals A fatal toxic shock-like syndrome post COVID-19 infection in a child

2021 ◽  
Vol 47 (1) ◽  
Author(s):  
Houda Ajmi ◽  
Wissem Besghaier ◽  
Wafa Kallala ◽  
Abdelhalim Trabelsi ◽  
Saoussan Abroug
Keyword(s):  
Ejection Fraction ◽  
Pediatric Intensive Care ◽  
Fresh Frozen Plasma ◽  
Multiple Organ ◽  
Clinical Feature ◽  
Fresh Frozen ◽  
Life Threatening ◽  
High Doses ◽  
Definition Of ◽  
High Level

Abstract Background Children affected by Coronavirus disease 2019 (COVID-19) showed various manifestations. Some of them were severe cases presenting with multi-system inflammatory syndrome (MIS-C) causing multiple organ dysfunction. Case presentation We report the case of a 12-year-old girl with recent COVID-19 infection who presented with persistent fever, abdominal pain and other symptoms that meet the definition of MIS-C. She had lymphopenia and a high level of inflammatory markers. She was admitted to pediatric intensive care unit since she rapidly developed refractory catecholamine-resistant shock with multiple organ failure. Echocardiography showed a small pericardial effusion with a normal ejection fraction (Ejection Fraction = 60%) and no valvular or coronary lesions. The child showed no signs of improvement even after receiving intravenous immunoglobulin, fresh frozen plasma, high doses of Vasopressors and corticosteroid. His outcome was fatal. Conclusion Pediatric patients affected by the new COVID-19 related syndrome may show severe life-threatening conditions similar to Kawasaki disease shock syndrome. Hypotension in these patients results from heart failure and the decreased cardiac output. We report a new severe clinical feature of SARS-CoV-2 infection in children in whom hypotension was the result of refractory vasoplegia.

scholarly journals Genomic Tackling of Human Satellite DNA: Breaking Barriers through Time

2021 ◽  
Vol 22 (9) ◽  
pp. 4707
Author(s):  
Mariana Lopes ◽  
Sandra Louzada ◽  
Margarida Gama-Carvalho ◽  
Raquel Chaves
Keyword(s):  
Human Genome ◽  
Satellite Dna ◽  
Repetitive Sequences ◽  
Nucleotide Composition ◽  
Genomic Component ◽  
Genomic Studies ◽  
Human Genomic ◽  
Definition Of ◽  
High Degree

(Peri)centromeric repetitive sequences and, more specifically, satellite DNA (satDNA) sequences, constitute a major human genomic component. SatDNA sequences can vary on a large number of features, including nucleotide composition, complexity, and abundance. Several satDNA families have been identified and characterized in the human genome through time, albeit at different speeds. Human satDNA families present a high degree of sub-variability, leading to the definition of various subfamilies with different organization and clustered localization. Evolution of satDNA analysis has enabled the progressive characterization of satDNA features. Despite recent advances in the sequencing of centromeric arrays, comprehensive genomic studies to assess their variability are still required to provide accurate and proportional representation of satDNA (peri)centromeric/acrocentric short arm sequences. Approaches combining multiple techniques have been successfully applied and seem to be the path to follow for generating integrated knowledge in the promising field of human satDNA biology.

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