Search results for: probabilistic ontology

Authors: Ghazal Faraj, András Micsik

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Shapes Constraint Language (SHACL), a World Wide Web Consortium (W3C) language, provides well-defined shapes and RDF graphs, named "shape graphs". These shape graphs validate other resource description framework (RDF) graphs which are called "data graphs". The structural features of SHACL permit generating a variety of conditions to evaluate string matching patterns, value type, and other constraints. Moreover, the framework of SHACL supports high-level validation by expressing more complex conditions in languages such as SPARQL protocol and RDF Query Language (SPARQL). SHACL includes two parts: SHACL Core and SHACL-SPARQL. SHACL Core includes all shapes that cover the most frequent constraint components. While SHACL-SPARQL is an extension that allows SHACL to express more complex customized constraints. Validating the efficacy of dataset mapping is an essential component of reconciled data mechanisms, as the enhancement of different datasets linking is a sustainable process. The conventional validation methods are the semantic reasoner and SPARQL queries. The former checks formalization errors and data type inconsistency, while the latter validates the data contradiction. After executing SPARQL queries, the retrieved information needs to be checked manually by an expert. However, this methodology is time-consuming and inaccurate as it does not test the mapping model comprehensively. Therefore, there is a serious need to expose a new methodology that covers the entire validation aspects for linking and mapping diverse datasets. Our goal is to conduct a new approach to achieve optimal validation outcomes. The first step towards this goal is implementing SHACL to validate the mapping between the International Committee for Documentation (CIDOC) conceptual reference model (CRM) and one of its ontologies. To initiate this project successfully, a thorough understanding of both source and target ontologies was required. Subsequently, the proper environment to run SHACL and its shape graphs were determined. As a case study, we performed SHACL over a CIDOC-CRM dataset after running a Pellet reasoner via the Protégé program. The applied validation falls under multiple categories: a) data type validation which constrains whether the source data is mapped to the correct data type. For instance, checking whether a birthdate is assigned to xsd:datetime and linked to Person entity via crm:P82a_begin_of_the_begin property. b) Data integrity validation which detects inconsistent data. For instance, inspecting whether a person's birthdate occurred before any of the linked event creation dates. The expected results of our work are: 1) highlighting validation techniques and categories, 2) selecting the most suitable techniques for those various categories of validation tasks. The next plan is to establish a comprehensive validation model and generate SHACL shapes automatically.

Keywords: SHACL, CIDOC-CRM, SPARQL, validation of ontology mapping

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Authors: S. Chowdhury, A. Corlett

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Large tsunamis strike the British Columbia coast every few hundred years. The Cascadia Subduction Zone, which extends along the Pacific coast from Vancouver Island to Northern California is one of the most seismically active regions in Canada. Significant earthquakes have occurred in this region, including the 1700 Cascade Earthquake with an estimated magnitude of 9.2. Based on geological records, experts have predicted a 'great earthquake' of a similar magnitude within this region may happen any time. This earthquake is expected to generate a large tsunami that could impact the coastal communities on Vancouver Island. Since many of these communities are in remote locations, they are more likely to be vulnerable, as the post-earthquake relief efforts would be impacted by the damage to critical road infrastructures. To assess the coastal vulnerability within these communities, a hydrodynamic model has been developed using MIKE-21 software. We have considered a 500 year probabilistic earthquake design criteria including the subsidence in this model. The bathymetry information was collected from Canadian Hydrographic Services (CHS), and National Oceanic Atmospheric and Administration (NOAA). The arial survey was conducted using a Cessna-172 aircraft for the communities, and then the information was converted to generate a topographic digital elevation map. Both survey information was incorporated into the model, and the domain size of the model was about 1000km x 1300km. This model was calibrated with the tsunami occurred off the west coast of Moresby Island on October 28, 2012. The water levels from the model were compared with two tide gauge stations close to the Vancouver Island and the output from the model indicates the satisfactory result. For this study, the design water level was considered as High Water Level plus the Sea Level Rise for 2100 year. The hourly wind speeds from eight directions were collected from different wind stations and used a 200-year return period wind speed in the model for storm events. The regional model was set for 12 hrs simulation period, which takes more than 16 hrs to complete one simulation using double Xeon-E7 CPU computer plus a K-80 GPU. The boundary information for the local model was generated from the regional model. The local model was developed using a high resolution mesh to estimate the coastal flooding for the communities. It was observed from this study that many communities will be effected by the Cascadia tsunami and the inundation maps were developed for the communities. The infrastructures inside the coastal inundation area were identified. Coastal vulnerability planning and resilient design solutions will be implemented to significantly reduce the risk.

Keywords: tsunami, coastal flooding, coastal vulnerable, earthquake, Vancouver, wave propagation

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Authors: Ankan Roy, Niharika, Samir Kumar Patra

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Anomalous nexus of complex topological assemblies and spatiotemporal epigenetic choreography at chromosomal territory may forms the most sophisticated regulatory layer of gene expression in cancer. Colon cancer is one of the leading malignant neoplasms of the lower gastrointestinal tract worldwide. There is still a paucity of information about the complex molecular mechanisms of colonic cancerogenesis. Bioinformatics prediction and analysis helps to identify essential genes and significant pathways for monitoring and conquering this deadly disease. The present study investigates and explores potential hub genes as biomarkers and effective therapeutic targets for colon cancer treatment. Colon cancer patient sample containing gene expression profile datasets, such as GSE44076, GSE20916, and GSE37364 were downloaded from Gene Expression Omnibus (GEO) database and thoroughly screened using the GEO2R tool and Funrich software to find out common 2 differentially expressed genes (DEGs). Other approaches, including Gene Ontology (GO) and KEGG pathway analysis, Protein-Protein Interaction (PPI) network construction and hub gene investigation, Overall Survival (OS) analysis, gene correlation analysis, methylation pattern analysis, and hub gene-Transcription factors regulatory network construction, were performed and validated using various bioinformatics tool. Initially, we identified 166 DEGs, including 68 up-regulated and 98 down-regulated genes. Up-regulated genes are mainly associated with the Cytokine-cytokine receptor interaction, IL17 signaling pathway, ECM-receptor interaction, Focal adhesion and PI3K-Akt pathway. Downregulated genes are enriched in metabolic pathways, retinol metabolism, Steroid hormone biosynthesis, and bile secretion. From the protein-protein interaction network, thirty hub genes with high connectivity are selected using the MCODE and cytoHubba plugin. Survival analysis, expression validation, correlation analysis, and methylation pattern analysis were further verified using TCGA data. Finally, we predicted COL1A1, COL1A2, COL4A1, SPP1, SPARC, and THBS2 as potential master regulators in colonic cancerogenesis. Moreover, our experimental data highlights that disruption of lipid raft and RAS/MAPK signaling cascade affects this gene hub at mRNA level. We identified COL1A1, COL1A2, COL4A1, SPP1, SPARC, and THBS2 as determinant hub genes in colon cancer progression. They can be considered as biomarkers for diagnosis and promising therapeutic targets in colon cancer treatment. Additionally, our experimental data advertise that signaling pathway act as connecting link between membrane hub and gene hub.

Keywords: hub genes, colon cancer, DNA methylation, epigenetic engineering, bioinformatic predictions

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Authors: Mohammed El Raey, Moustafa Osman Mohammed

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The spatial-ecological modeling is relating sustainable dispersions with social development. Sustainability with spatial-ecological model gives attention to urban environments in the design review management to comply with Earth’s System. Naturally exchange patterns of ecosystems have consistent and periodic cycles to preserve energy flows and materials in Earth’s System. The probabilistic risk assessment (PRA) technique is utilized to assess the safety of industrial complex. The other analytical approach is the Failure-Safe Mode and Effect Analysis (FMEA) for critical components. The plant safety parameters are identified for engineering topology as employed in assessment safety of industrial ecology. In particular, the most severe accidental release of hazardous gaseous is postulated, analyzed and assessment in industrial region. The IAEA- safety assessment procedure is used to account the duration and rate of discharge of liquid chlorine. The ecological model of plume dispersion width and concentration of chlorine gas in the downwind direction is determined using Gaussian Plume Model in urban and ruler areas and presented with SURFER®. The prediction of accident consequences is traced in risk contour concentration lines. The local greenhouse effect is predicted with relevant conclusions. The spatial-ecological model is also predicted the distribution schemes from the perspective of pollutants that considered multiple factors of multi-criteria analysis. The data extends input–output analysis to evaluate the spillover effect, and conducted Monte Carlo simulations and sensitivity analysis. Their unique structure is balanced within “equilibrium patterns”, such as the biosphere and collective a composite index of many distributed feedback flows. These dynamic structures are related to have their physical and chemical properties and enable a gradual and prolonged incremental pattern. While this spatial model structure argues from ecology, resource savings, static load design, financial and other pragmatic reasons, the outcomes are not decisive in artistic/ architectural perspective. The hypothesis is an attempt to unify analytic and analogical spatial structure for development urban environments using optimization software and applied as an example of integrated industrial structure where the process is based on engineering topology as optimization approach of systems ecology.

Keywords: spatial-ecological modeling, spatial structure orientation impact, composite structure, industrial ecology

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Authors: Nejoud Alostad, Anup Bora, Prashant Dhote

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Kuwait Oil Company (KOC) has been producing from its major reservoirs that are well defined and highly productive and of superior reservoir quality. These reservoirs are maturing and priority is shifting towards difficult reservoir to meet future production requirements. This paper discusses the results of the detailed integrated study for one of the satellite complex field discovered in the early 1960s. Following acquisition of new 3D seismic data in 1998 and re-processing work in the year 2006, an integrated G&G study was undertaken to review Lower Cretaceous prospectivity of this reservoir. Nine wells have been drilled in the area, till date with only three wells showing hydrocarbons in two formations. The average oil density is around 300API (American Petroleum Institute), and average porosity and water saturation of the reservoir is about 23% and 26%, respectively. The area is dissected by a number of NW-SE trending faults. Structurally, the area consists of horsts and grabens bounded by these faults and hence compartmentalized. The Wara/Burgan formation consists of discrete, dirty sands with clean channel sand complexes. There is a dramatic change in Upper Wara distributary channel facies, and reservoir quality of Wara and Burgan section varies with change of facies over the area. So predicting reservoir facies and its quality out of sparse well data is a major challenge for delineating the prospective area. To characterize the reservoir of Wara/Burgan formation, an integrated workflow involving seismic, well, petro-physical, reservoir and production engineering data has been used. Porosity and water saturation models are prepared and analyzed to predict reservoir quality of Wara and Burgan 3rd sand upper reservoirs. Subsequently, boundary conditions are defined for reservoir and non-reservoir facies by integrating facies, porosity and water saturation. Based on the detailed analyses of volumetric parameters, potential volumes of stock-tank oil initially in place (STOIIP) and gas initially in place (GIIP) were documented after running several probablistic sensitivity analysis using Montecalro simulation method. Sensitivity analysis on probabilistic models of reservoir horizons, petro-physical properties, and oil-water contacts and their effect on reserve clearly shows some alteration in the reservoir geometry. All these parameters have significant effect on the oil in place. This study has helped to identify uncertainty and risks of this prospect particularly and company is planning to develop this area with drilling of new wells.

Keywords: original oil-in-place, sensitivity, uncertainty, sandstone, reservoir modeling, Monte-Carlo simulation

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Authors: Farid Khosravikia, Patricia Clayton

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The main objective of this work is to evaluate the advantages and disadvantages of various machine learning techniques in two key steps of seismic hazard and risk assessment of different types of structures. The first step is the development of ground-motion models, which are used for forecasting ground-motion intensity measures (IM) given source characteristics, source-to-site distance, and local site condition for future events. IMs such as peak ground acceleration and velocity (PGA and PGV, respectively) as well as 5% damped elastic pseudospectral accelerations at different periods (PSA), are indicators of the strength of shaking at the ground surface. Typically, linear regression-based models, with pre-defined equations and coefficients, are used in ground motion prediction. However, due to the restrictions of the linear regression methods, such models may not capture more complex nonlinear behaviors that exist in the data. Thus, this study comparatively investigates potential benefits from employing other machine learning techniques as statistical method in ground motion prediction such as Artificial Neural Network, Random Forest, and Support Vector Machine. The results indicate the algorithms satisfy some physically sound characteristics such as magnitude scaling distance dependency without requiring pre-defined equations or coefficients. Moreover, it is shown that, when sufficient data is available, all the alternative algorithms tend to provide more accurate estimates compared to the conventional linear regression-based method, and particularly, Random Forest outperforms the other algorithms. However, the conventional method is a better tool when limited data is available. Second, it is investigated how machine learning techniques could be beneficial for developing probabilistic seismic demand models (PSDMs), which provide the relationship between the structural demand responses (e.g., component deformations, accelerations, internal forces, etc.) and the ground motion IMs. In the risk framework, such models are used to develop fragility curves estimating exceeding probability of damage for pre-defined limit states, and therefore, control the reliability of the predictions in the risk assessment. In this study, machine learning algorithms like artificial neural network, random forest, and support vector machine are adopted and trained on the demand parameters to derive PSDMs for them. It is observed that such models can provide more accurate estimates of prediction in relatively shorter about of time compared to conventional methods. Moreover, they can be used for sensitivity analysis of fragility curves with respect to many modeling parameters without necessarily requiring more intense numerical response-history analysis.

Keywords: artificial neural network, machine learning, random forest, seismic risk analysis, seismic hazard analysis, support vector machine

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Authors: Hanan Begali, Shahi Dost, Annett Ziegler, Markus Cornberg, Maria-Esther Vidal, Anke R. M. Kraft

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Chronic hepatitis B virus (HBV) infection can be treated with nucleot(s)ide analog (NA), for example, which inhibits HBV replication. However, they have hardly any influence on the functional cure of HBV, which is defined by hepatitis B surface antigen (HBsAg) loss. NA needs to be taken life-long, which is not available for all patients worldwide. Additionally, NA-treated patients are still at risk of developing cirrhosis, liver failure, or hepatocellular carcinoma (HCC). Although each patient has the same components of the immune system, immune responses vary between patients. Therefore, a deeper understanding of the immune response against HBV in different patients is necessary to understand the parameters leading to HBV cure and to use this knowledge to optimize HBV therapies. This requires seamless integration of an enormous amount of diverse and fine-grained data from viral markers, e.g., hepatitis B core-related antigen (HBcrAg) and hepatitis B surface antigen (HBsAg). The data integration system relies on the assumption that profiling human immune systems requires the analysis of various variables (e.g., demographic data, treatments, pre-existing conditions, immune cell response, or HLA-typing) rather than only one. However, the values of these variables are collected independently. They are presented in a myriad of formats, e.g., excel files, textual descriptions, lab book notes, and images of flow cytometry dot plots. Additionally, patients can be identified differently in these analyses. This heterogeneity complicates the integration of variables, as data management techniques are needed to create a unified view in which individual formats and identifiers are transparent when profiling the human immune systems. The proposed study (HBsRE) aims at integrating heterogeneous data sets of 87 chronically HBV-infected patients, e.g., clinical data, immune cell response, and HLA-typing, with knowledge encoded in biomedical ontologies and open-source databases into a knowledge-driven framework. This new technique enables us to harmonize and standardize heterogeneous datasets in the defined modeling of the data integration system, which will be evaluated in the knowledge graph (KG). KGs are data structures that represent the knowledge and data as factual statements using a graph data model. Finally, the analytic data model will be applied on top of KG in order to develop a deeper understanding of the immune profiles among various patients and to evaluate factors playing a role in a holistic profile of patients with HBsAg level loss. Additionally, our objective is to utilize this unified approach to stratify patients for new effective treatments. This study is developed in the context of the project “Transforming big data into knowledge: for deep immune profiling in vaccination, infectious diseases, and transplantation (ImProVIT)”, which is a multidisciplinary team composed of computer scientists, infection biologists, and immunologists.

Keywords: chronic hepatitis B infection, immune response, knowledge graphs, ontology

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Authors: Esteban Maioli

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Generational studies have an important research tradition in social and human sciences. On the one hand, the speed of social change in the context of globalization imposes the need to research the transformations are identified both the subjectivity of the agents involved and its inclusion in the institutional matrix, specifically employment. Generation Z, (generally considered as the population group whose birth occurs after 1995) have unique psycho-social characteristics. Gen Z is characterized by a different set of values, beliefs, attitudes and ambitions that impact in their concrete action in organizational structures. On the other hand, managers often have to deal with generational differences in the workplace. Organizations have members who belong to different generations; they had never before faced the challenge of having such a diverse group of members. The members of each historical generation are characterized by a different set of values, beliefs, attitudes and ambitions that are manifest in their concrete action in organizational structures. Gen Z it’s the only one who can fully be considered "global," while its members were born in the consolidated context of globalization. Some salient features of the Generation Z can be summarized as follows. They’re the first fully born into a digital world. Social networks and technology are integrated into their lives. They are concerned about the challenges of the modern world (poverty, inequality, climate change, among others). They are self-expressive, more liberal and open to change. They often bore easily, with short attention spans. They do not like routine tasks. They want to achieve a good life-work balance, and they are interested in a flexible work environment, as opposed to traditional work schedule. They are critical thinkers, who come with innovative and creative ideas to help. Research design considered methodological triangulation. Data was collected with two techniques: a self-administered survey with multiple choice questions and attitudinal scales applied over a non-probabilistic sample by reasoned decision. According to the multi-method strategy, also it was conducted in-depth interviews. Organizations constantly face new challenges. One of the biggest ones is to learn to manage a multi-generational scope of work. While Gen Z has not yet been fully incorporated (expected to do so in five years or so), many organizations have already begun to implement a series of changes in its recruitment and development. The main obstacle to retaining young talent is the gap between the expectations of iGen applicants and what companies offer. Members of the iGen expect not only a good salary and job stability but also a clear career plan. Generation Z needs to have immediate feedback on their tasks. However, many organizations have yet to improve both motivation and monitoring practices. It is essential for companies to take a review of organizational practices anchored in the culture of the organization.

Keywords: employment, expectations, generation Z, organizational culture, organizations, psycho-social characteristics

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Authors: Anthony F. Peressini

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The concept of race has recently come prominently back into discussion in the context of medicine and medical science, along with renewed effort to biologize racial concepts. This paper argues that this renewed effort to biologize race by way of medicine and population genetics fail on their own terms, and more importantly, that the philosophical project of biologizing race ought to be recognized for what it is—a retrograde racial project—and abandoned. There is clear agreement that standard racial categories and concepts cannot be grounded in the old way of racial naturalism, which understand race as a real, interest-independent biological/metaphysical category in which its members share “physical, moral, intellectual, and cultural characteristics.” But equally clear is the very real and pervasive presence of racial concepts in individual and collective consciousness and behavior, and so it remains a pressing area in which to seek deeper understanding. Recent philosophical work has endeavored to reconcile these two observations by developing a “thin” conception of race, grounded in scientific concepts but without the moral and metaphysical content. Such “thin,” science-based analyses take the “commonsense” or “folk” sense of race as it functions in contemporary society as the starting point for their philosophic-scientific projects to biologize racial concepts. A “philosophic-scientific analysis” is a special case of the cornerstone of analytic philosophy: a conceptual analysis. That is, a rendering of a concept into the more perspicuous concepts that constitute it. Thus a philosophic-scientific account of a concept is an attempt to work out an analysis of a concept that makes use of empirical science's insights to ground, legitimate and explicate the target concept in terms of clearer concepts informed by empirical results. The focus in this paper is on three recent philosophic-scientific cases for retaining “race” that all share this general analytic schema, but that make use of “medical necessity,” population genetics, and human genetic clustering, respectively. After arguing that each of these three approaches suffers from internal difficulties, the paper considers the general analytic schema employed by such biologizations of race. While such endeavors are inevitably prefaced with the disclaimer that the theory to follow is non-essentialist and non-racialist, the case will be made that such efforts are not neutral scientific or philosophical projects but rather are what sociologists call a racial project, that is, one of many competing efforts that conjoin a representation of what race means to specific efforts to determine social and institutional arrangements of power, resources, authority, etc. Accordingly, philosophic-scientific biologizations of race, since they begin from and condition their analyses on “folk” conceptions, cannot pretend to be “prior to” other disciplinary insights, nor to transcend the social-political dynamics involved in formulating theories of race. As a result, such traditional philosophical efforts can be seen to be disciplinarily parochial and to address only a caricature of a large and important human problem—and thereby further contributing to the unfortunate isolation of philosophical thinking about race from other disciplines.

Keywords: population genetics, ontology of race, race-based medicine, racial formation theory, racial projects, racism, social construction

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Authors: Nuno Biga

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Artificial Intelligence (AI) allows machines to interpret information and learn from context analysis, giving them the ability to make predictions adjusted to each specific situation. In addition to learning by performing deterministic and probabilistic calculations, the 'artificial brain' also learns through information and data provided by those who train it, namely its users. The "Assisted-BIGAMES" version of the Accident & Emergency (A&E) simulator introduces the concept of a "Virtual Assistant" (VA) that provides users with useful suggestions, namely to pursue the following operations: a) to relocate workstations in order to shorten travelled distances and minimize the stress of those involved; b) to identify in real time the bottleneck(s) in the operations system so that it is possible to quickly act upon them; c) to identify resources that should be polyvalent so that the system can be more efficient; d) to identify in which specific processes it may be advantageous to establish partnership with other teams; and e) to assess possible solutions based on the suggested KPIs allowing action monitoring to guide the (re)definition of future strategies. This paper is built on the BIGAMES© simulator and presents the conceptual AI model developed in a pilot project. Each Virtual Assisted BIGAME is a management simulator developed by the author that guides operational and strategic decision making, providing users with useful information in the form of management recommendations that make it possible to predict the actual outcome of different alternative management strategic actions. The pilot project developed incorporates results from 12 editions of the BIGAME A&E that took place between 2017 and 2022 at AESE Business School, based on the compilation of data that allows establishing causal relationships between decisions taken and results obtained. The systemic analysis and interpretation of this information is materialised in the Assisted-BIGAMES through a computer application called "BIGAMES Virtual Assistant" that players can use during the Game. Each participant in the Virtual Assisted-BIGAMES permanently asks himself about the decisions he should make during the game in order to win the competition. To this end, the role of the VA of each team consists in guiding the players to be more effective in their decision making through presenting recommendations based on AI methods. It is important to note that the VA's suggestions for action can be accepted or rejected by the managers of each team, and as the participants gain a better understanding of the game, they will more easily dispense with the VA's recommendations and rely more on their own experience, capability, and knowledge to support their own decisions. Preliminary results show that the introduction of the VA provides a faster learning of the decision-making process. The facilitator (Serious Game Controller) is responsible for supporting the players with further analysis and the recommended action may be (or not) aligned with the previous recommendations of the VA. All the information should be jointly analysed and assessed by each player, who are expected to add “Emotional Intelligence”, a component absent from the machine learning process.

Keywords: artificial intelligence (AI), gamification, key performance indicators (KPI), machine learning, management simulators, serious games, virtual assistant

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Authors: A. P. Mikhailovich, V. V. Fomin, E. M. Agapitov, V. E. Rogachev, E. A. Kostousova, E. S. Perekhodova

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Woody vegetation among the upper limit of its habitat is a sensitive indicator of biota reaction to regional climate changes. Quantitative assessment of temporal and spatial changes in the distribution of trees and plant biocenoses calls for the development of new modeling approaches based upon selected data from measurements on the ground level and ultra-resolution aerial photography. Statistical models were developed for the study area located in the Polar Urals. These models allow obtaining probabilistic estimates for placing Siberian Larch trees into one of the three age intervals, namely 1-10, 11-40 and over 40 years, based on the Weilbull distribution of the maximum horizontal crown projection. Authors developed the distribution map for larch trees with crown diameters exceeding twenty centimeters by deciphering aerial photographs made by a UAV from an altitude equal to fifty meters. The total number of larches was equal to 88608, forming the following distribution row across the abovementioned intervals: 16980, 51740, and 19889 trees. The results demonstrate that two processes can be observed in the course of recent decades: first is the intensive forestation of previously barren or lightly wooded fragments of the study area located within the patches of wood, woodlands, and sparse stand, and second, expansion into mountain tundra. The current expansion of the Siberian Larch in the region replaced the depopulation process that occurred in the course of the Little Ice Age from the late 13ᵗʰ to the end of the 20ᵗʰ century. Using data from field measurements of Siberian larch specimen biometric parameters (including height, diameter at root collar and at 1.3 meters, and maximum projection of the crown in two orthogonal directions) and data on tree ages obtained at nine circular test sites, authors developed a model for artificial neural network including two layers with three and two neurons, respectively. The model allows quantitative assessment of a specimen's age based on height and maximum crone projection values. Tree height and crown diameters can be quantitatively assessed using data from aerial photographs and lidar scans. The resulting model can be used to assess the age of all Siberian larch trees. The proposed approach, after validation, can be applied to assessing the age of other tree species growing near the upper tree boundaries in other mountainous regions. This research was collaboratively funded by the Russian Ministry for Science and Education (project No. FEUG-2023-0002) and Russian Science Foundation (project No. 24-24-00235) in the field of data modeling on the basis of artificial neural network.

Keywords: treeline, dynamic, climate, modeling

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Authors: A. Falenski, A. Kaesbohrer, M. Filter

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Introduction: Risk assessments can be performed in various ways and in different degrees of complexity. In order to assess risks associated with imported foods additional information needs to be taken into account compared to a risk assessment on regional products. The present review is an overview on currently available best practise approaches and data sources used for food import risk assessments (IRAs). Methods: A literature review has been performed. PubMed was searched for articles about food IRAs published in the years 2004 to 2014 (English and German texts only, search string “(English [la] OR German [la]) (2004:2014 [dp]) import [ti] risk”). Titles and abstracts were screened for import risks in the context of IRAs. The finally selected publications were analysed according to a predefined questionnaire extracting the following information: risk assessment guidelines followed, modelling methods used, data and software applied, existence of an analysis of uncertainty and variability. IRAs cited in these publications were also included in the analysis. Results: The PubMed search resulted in 49 publications, 17 of which contained information about import risks and risk assessments. Within these 19 cross references were identified to be of interest for the present study. These included original articles, reviews and guidelines. At least one of the guidelines of the World Organisation for Animal Health (OIE) and the Codex Alimentarius Commission were referenced in any of the IRAs, either for import of animals or for imports concerning foods, respectively. Interestingly, also a combination of both was used to assess the risk associated with the import of live animals serving as the source of food. Methods ranged from full quantitative IRAs using probabilistic models and dose-response models to qualitative IRA in which decision trees or severity tables were set up using parameter estimations based on expert opinions. Calculations were done using @Risk, R or Excel. Most heterogeneous was the type of data used, ranging from general information on imported goods (food, live animals) to pathogen prevalence in the country of origin. These data were either publicly available in databases or lists (e.g., OIE WAHID and Handystatus II, FAOSTAT, Eurostat, TRACES), accessible on a national level (e.g., herd information) or only open to a small group of people (flight passenger import data at national airport customs office). In the IRAs, an uncertainty analysis has been mentioned in some cases, but calculations have been performed only in a few cases. Conclusion: The current state-of-the-art in the assessment of risks of imported foods is characterized by a great heterogeneity in relation to general methodology and data used. Often information is gathered on a case-by-case basis and reformatted by hand in order to perform the IRA. This analysis therefore illustrates the need for a flexible, modular framework supporting the connection of existing data sources with data analysis and modelling tools. Such an infrastructure could pave the way to IRA workflows applicable ad-hoc, e.g. in case of a crisis situation.

Keywords: import risk assessment, review, tools, food import

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Authors: Luminiţa Duţică, Gheorghe Duţică

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One of the most powerful language innovation in the twentieth century music was the heterophony–hypostasis of the vertical syntax entered into the sphere of interest of many composers, such as George Enescu, Pierre Boulez, Mauricio Kagel, György Ligeti and others. The heterophonic syntax has a history of its growth, which means a succession of different concepts and writing techniques. The trajectory of settling this phenomenon does not necessarily take into account the chronology: there are highly complex primary stages and advanced stages of returning to the simple forms of writing. In folklore, the plurimelodic simultaneities are free or random and originate from the (unintentional) differences/‘deviations’ from the state of unison, through a variety of ornaments, melismas, imitations, elongations and abbreviations, all in a flexible rhythmic and non-periodic/immeasurable framework, proper to the parlando-rubato rhythmics. Within the general framework of the multivocal organization, the heterophonic syntax in elaborate (academic) version has imposed itself relatively late compared with polyphony and homophony. Of course, the explanation is simple, if we consider the causal relationship between the sound vocabulary elements – in this case, the modalism – and the typologies of vertical organization appropriate for it. Therefore, adding up the ‘classic’ pathway of the writing typologies (monody – polyphony – homophony), heterophony - applied equally to the structures of modal, serial or synthesis vocabulary – reclaims necessarily an own macrotemporal form, in the sense of the analogies enshrined by the evolution of the musical styles and languages: polyphony→fugue, homophony→sonata. Concerned about the prospect of edifying a new musical ontology, the composer Ştefan Niculescu experienced – along with the mathematical organization of heterophony according to his own original methods – the possibility of extrapolation of this phenomenon in macrostructural plan, reaching this way to the unique form of ‘synchrony’. Founded on coincidentia oppositorum principle (involving the ‘one-multiple’ binom), the sound architecture imagined by Ştefan Niculescu consists in one (temporal) model / algorithm of articulation of two sound states: 1. monovocality state (principle of identity) and 2. multivocality state (principle of difference). In this context, the heterophony becomes an (auto)generative mechanism, with macrotemporal amplitude, strategy that will be grown by the composer, practically throughout his creation (see the works: Ison I, Ison II, Unisonos I, Unisonos II, Duplum, Triplum, Psalmus, Héterophonies pour Montreux (Homages to Enescu and Bartók etc.). For the present demonstration, we selected one of the most edifying works of Ştefan Niculescu – Simphony II, Opus dacicum – where the form of (heterophony-)synchrony acquires monumental-symphonic features, representing an emblematic case for the complexity level achieved by this type of vertical syntax in the twentieth century music.

Keywords: heterophony, modalism, serialism, synchrony, syntax

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Authors: Yi-Hao Wong, Li-Li Chan, Chee-Onn Leong, Stephen Ambu, Joon-Wah Mak, Priyasashi Sahu

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Background: Acanthamoeba is a genus of amoebae which lives as a free-living in nature or as a human pathogen that causes severe brain and eye infections. Virulence potential of Acanthamoeba is not constant and can change with growth conditions. DNA methylation, an epigenetic process which adds methyl groups to DNA, is used by eukaryotic cells, including several human parasites to control their gene expression. We used qPCR, siRNA gene silencing, and RNA sequencing (RNA-Seq) to study DNA-methyltransferase gene family (DNMT) in order to indicate the possibility of its involvement in programming Acanthamoeba virulence potential. Methods: A virulence-attenuated Acanthamoeba isolate (designation: ATCC; original isolate: ATCC 50492) was subjected to mouse passages to restore its pathogenicity; a virulence-reactivated isolate (designation: AC/5) was generated. Several established factors associated with Acanthamoeba virulence phenotype were examined to confirm the succession of reactivation process. Differential gene expression of DNMT between ATCC and AC/5 isolates was performed by qPCR. Silencing on DNMT gene expression in AC/5 isolate was achieved by siRNA duplex. Total RNAs extracted from ATCC, AC/5, and siRNA-treated (designation: si-146) were subjected to RNA-Seq for comparative transcriptomic analysis in order to identify the genome-wide effect of DNMT in regulating Acanthamoeba gene expression. qPCR was performed to validate the RNA-Seq results. Results: Physiological and cytophatic assays demonstrated an increased in virulence potential of AC/5 isolate after mouse passages. DNMT gene expression was significantly higher in AC/5 compared to ATCC isolate (p ≤ 0.01) by qPCR. si-146 duplex reduced DNMT gene expression in AC/5 isolate by 30%. Comparative transcriptome analysis identified the differentially expressed genes, with 3768 genes in AC/5 vs ATCC isolate; 2102 genes in si-146 vs AC/5 isolate and 3422 genes in si-146 vs ATCC isolate, respectively (fold-change of ≥ 2 or ≤ 0.5, p-value adjusted (padj) < 0.05). Of these, 840 and 1262 genes were upregulated and downregulated, respectively, in si-146 vs AC/5 isolate. Eukaryotic orthologous group (KOG) assignments revealed a higher percentage of downregulated gene expression in si-146 compared to AC/5 isolate, were related to posttranslational modification, signal transduction and energy production. Gene Ontology (GO) terms for those downregulated genes shown were associated with transport activity, oxidation-reduction process, and metabolic process. Among these downregulated genes were putative genes encoded for heat shock proteins, transporters, ubiquitin-related proteins, proteins for vesicular trafficking (small GTPases), and oxidoreductases. Functional analysis of similar predicted proteins had been described in other parasitic protozoa for their survival and pathogenicity. Decreased expression of these genes in si146-treated isolate may account in part for Acanthamoeba reduced pathogenicity. qPCR on 6 selected genes upregulated in AC/5 compared to ATCC isolate corroborated the RNA sequencing findings, indicating a good concordance between these two analyses. Conclusion: To the best of our knowledge, this study represents the first genome-wide analysis of DNA methylation and its effects on gene expression in Acanthamoeba spp. The present data indicate that DNA methylation has substantial effect on global gene expression, allowing further dissection of the genome-wide effects of DNA-methyltransferase gene in regulating Acanthamoeba pathogenicity.

Keywords: Acanthamoeba, DNA methylation, RNA sequencing, virulence

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Authors: Carolina Busco, Daniela Osses

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The development of digital literacy has become a fundamental element that allows for citizen inclusion, access to quality jobs, and a labor market capable of responding to the digital economy. There are no methodological instruments available in Chile to measure the workforce’s digital literacy and improve national policies on this matter. Thus, the objective of this research is to develop a survey to measure digital literacy in a sample of 200 Chilean workers. Dimensions considered in the instrument are sociodemographics, access to infrastructure, digital education, digital skills, and the ability to use e-government services. To achieve the research objective of developing a digital literacy model of indicators and a research instrument for this purpose, along with an exploratory analysis of data using factor analysis, we used an empirical, quantitative-qualitative, exploratory, non-probabilistic, and cross-sectional research design. The research instrument is a survey created to measure variables that make up the conceptual map prepared from the bibliographic review. Before applying the survey, a pilot test was implemented, resulting in several adjustments to the phrasing of some items. A validation test was also applied using six experts, including their observations on the final instrument. The survey contained 49 items that were further divided into three sets of questions: sociodemographic data; a Likert scale of four values ranked according to the level of agreement; iii) multiple choice questions complementing the dimensions. Data collection occurred between January and March 2022. For the factor analysis, we used the answers to 12 items with the Likert scale. KMO showed a value of 0.626, indicating a medium level of correlation, whereas Bartlett’s test yielded a significance value of less than 0.05 and a Cronbach’s Alpha of 0.618. Taking all factor selection criteria into account, we decided to include and analyze four factors that together explain 53.48% of the accumulated variance. We identified the following factors: i) access to infrastructure and opportunities to develop digital skills at the workplace or educational establishment (15.57%), ii) ability to solve everyday problems using digital tools (14.89%), iii) online tools used to stay connected with others (11.94%), and iv) residential Internet access and speed (11%). Quantitative results were discussed within six focus groups using heterogenic selection criteria related to the most relevant variables identified in the statistical analysis: upper-class school students; middle-class university students; Ph.D. professors; low-income working women, elderly individuals, and a group of rural workers. The digital divide and its social and economic correlations are evident in the results of this research. In Chile, the items that explain the acquisition of digital tools focus on access to infrastructure, which ultimately puts the first filter on the development of digital skills. Therefore, as expressed in the literature review, the advance of these skills is radically different when sociodemographic variables are considered. This increases socioeconomic distances and exclusion criteria, putting those who do not have these skills at a disadvantage and forcing them to seek the assistance of others.

Keywords: digital literacy, digital society, workforce digitalization, digital skills

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Authors: Mathuravech Thanaphon, Thephasit Nat

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The Electricity Generating Authority of Thailand (EGAT) is focusing on expanding its pumped storage hydropower (PSH) capacity to increase the reliability of the system during peak demand and allow for greater integration of renewables. To achieve this requirement, Thailand will have to double its current renewable electricity production. To address the challenges of balancing supply and demand in the grid with increasing levels of RE penetration, as well as rising peak demand, EGAT has already been studying the potential for additional PSH capacity for several years to enable an increased share of RE and replace existing fossil fuel-fired generation. In addition, the role that pumped-storage hydropower would play in fulfilling multiple grid functions and renewable integration. The proposed sites for new PSH would help increase the reliability of power generation in Thailand. However, most of the electricity generation will come from RE, chiefly wind and photovoltaic, and significant additional Energy Storage capacity will be needed. In this paper, the impact of integrating the PSH system on the adequacy of renewable rich power generating systems to reduce the thermal power generating units is investigated. The variations of system adequacy indices are analyzed for different PSH-renewables capacities and storage levels. Power Development Plan 2018 rev.1 (PDP2018 rev.1), which is modified by integrating a six-new PSH system and RE planning and development aftermath in 2030, is the very challenge. The system adequacy indices through power generation are obtained using Multi-Objective Genetic Algorithm (MOGA) Optimization. MOGA is a probabilistic heuristic and stochastic algorithm that is able to find the global minima, which have the advantage that the fitness function does not necessarily require the gradient. In this sense, the method is more flexible in solving reliability optimization problems for a composite power system. The optimization with hourly time step takes years of planning horizon much larger than the weekly horizon that usually sets the scheduling studies. The objective function is to be optimized to maximize RE energy generation, minimize energy imbalances, and minimize thermal power generation using MATLAB. The PDP2018 rev.1 was set to be simulated based on its planned capacity stepping into 2030 and 2050. Therefore, the four main scenario analyses are conducted as the target of renewables share: 1) Business-As-Usual (BAU), 2) National Targets (30% RE in 2030), 3) Carbon Neutrality Targets (50% RE in 2050), and 5) 100% RE or full-decarbonization. According to the results, the generating system adequacy is significantly affected by both PSH-RE and Thermal units. When a PSH is integrated, it can provide hourly capacity to the power system as well as better allocate renewable energy generation to reduce thermal generations and improve system reliability. These results show that a significant level of reliability improvement can be obtained by PSH, especially in renewable-rich power systems.

Keywords: pumped storage hydropower, renewable energy integration, system adequacy, power development planning, RE100, multi-objective genetic algorithm

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Authors: Charalabos Antonatos, Mariza Panoutsopoulou, Georgios K. Georgakilas, Evangelos Evangelou, Yiannis Vasilopoulos

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The extended tissue damage and severe clinical outcomes of autoimmune diseases, accompanied by the high annual costs to the overall health care system, highlight the need for an efficient therapy. Increasing knowledge over the pathophysiology of specific chronic inflammatory diseases, namely Psoriasis (PsO), Inflammatory Bowel Diseases (IBD) consisting of Crohn’s disease (CD) and Ulcerative colitis (UC), and Rheumatoid Arthritis (RA), has provided insights into the underlying mechanisms that lead to the maintenance of the inflammation, such as Tumor Necrosis Factor alpha (TNF-α). Hence, the anti-TNFα biological agents pose as an ideal therapeutic approach. Despite the efficacy of anti-TNFα agents, several clinical trials have shown that 20-40% of patients do not respond to treatment. Nowadays, high-throughput technologies have been recruited in order to elucidate the complex interactions in multifactorial phenotypes, with the most ubiquitous ones referring to transcriptome quantification analyses. In this context, a random effects meta-analysis of available gene expression cDNA microarray datasets was performed between responders and non-responders to anti-TNFα therapy in patients with IBD, PsO, and RA. Publicly available datasets were systematically searched from inception to 10th of November 2020 and selected for further analysis if they assessed the response to anti-TNFα therapy with clinical score indexes from inflamed biopsies. Specifically, 4 IBD (79 responders/72 non-responders), 3 PsO (40 responders/11 non-responders) and 2 RA (16 responders/6 non-responders) datasetswere selected. After the separate pre-processing of each dataset, 4 separate meta-analyses were conducted; three disease-specific and a single combined meta-analysis on the disease-specific results. The MetaVolcano R package (v.1.8.0) was utilized for a random-effects meta-analysis through theRestricted Maximum Likelihood (RELM) method. The top 1% of the most consistently perturbed genes in the included datasets was highlighted through the TopConfects approach while maintaining a 5% False Discovery Rate (FDR). Genes were considered as Differentialy Expressed (DEGs) as those with P ≤ 0.05, |log2(FC)| ≥ log2(1.25) and perturbed in at least 75% of the included datasets. Over-representation analysis was performed using Gene Ontology and Reactome Pathways for both up- and down-regulated genes in all 4 performed meta-analyses. Protein-Protein interaction networks were also incorporated in the subsequentanalyses with STRING v11.5 and Cytoscape v3.9. Disease-specific meta-analyses detected multiple distinct pro-inflammatory and immune-related down-regulated genes for each disease, such asNFKBIA, IL36, and IRAK1, respectively. Pathway analyses revealed unique and shared pathways between each disease, such as Neutrophil Degranulation and Signaling by Interleukins. The combined meta-analysis unveiled 436 DEGs, 86 out of which were up- and 350 down-regulated, confirming the aforementioned shared pathways and genes, as well as uncovering genes that participate in anti-inflammatory pathways, namely IL-10 signaling. The identification of key biological pathways and regulatory elements is imperative for the accurate prediction of the patient’s response to biological drugs. Meta-analysis of such gene expression data could aid the challenging approach to unravel the complex interactions implicated in the response to anti-TNFα therapy in patients with PsO, IBD, and RA, as well as distinguish gene clusters and pathways that are altered through this heterogeneous phenotype.

Keywords: anti-TNFα, autoimmune, meta-analysis, microarrays

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Authors: Nicole Merkle, Stefan Zander

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Ambient Assisted Living (AAL) describes a technological and methodological stack of (e.g. formal model-theoretic semantics, rule-based reasoning and machine learning), different aspects regarding the behavior, activities and characteristics of humans. Hence, a semantic representation of the user environment and its relevant elements are required in order to allow assistive agents to recognize situations and deduce appropriate actions. Furthermore, the user and his/her characteristics (e.g. physical, cognitive, preferences) need to be represented with a high degree of expressiveness in order to allow software agents a precise evaluation of the users’ context models. The correct interpretation of these context models highly depends on temporal, spatial circumstances as well as individual user preferences. In most AAL approaches, model representations of real world situations represent the current state of a universe of discourse at a given point in time by neglecting transitions between a set of states. However, the AAL domain currently lacks sufficient approaches that contemplate on the dynamic adaptions of context-related representations. Semantic representations of relevant real-world excerpts (e.g. user activities) help cognitive, rule-based agents to reason and make decisions in order to help users in appropriate tasks and situations. Furthermore, rules and reasoning on semantic models are not sufficient for handling uncertainty and fuzzy situations. A certain situation can require different (re-)actions in order to achieve the best results with respect to the user and his/her needs. But what is the best result? To answer this question, we need to consider that every smart agent requires to achieve an objective, but this objective is mostly defined by domain experts who can also fail in their estimation of what is desired by the user and what not. Hence, a smart agent has to be able to learn from context history data and estimate or predict what is most likely in certain contexts. Furthermore, different agents with contrary objectives can cause collisions as their actions influence the user’s context and constituting conditions in unintended or uncontrolled ways. We present an approach for dynamically updating a semantic model with respect to the current user context that allows flexibility of the software agents and enhances their conformance in order to improve the user experience. The presented approach adapts rules by learning sensor evidence and user actions using probabilistic reasoning approaches, based on given expert knowledge. The semantic domain model consists basically of device-, service- and user profile representations. In this paper, we present how this semantic domain model can be used in order to compute the probability of matching rules and actions. We apply this probability estimation to compare the current domain model representation with the computed one in order to adapt the formal semantic representation. Our approach aims at minimizing the likelihood of unintended interferences in order to eliminate conflicts and unpredictable side-effects by updating pre-defined expert knowledge according to the most probable context representation. This enables agents to adapt to dynamic changes in the environment which enhances the provision of adequate assistance and affects positively the user satisfaction.

Keywords: ambient intelligence, machine learning, semantic web, software agents

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Authors: Andrea N. Alarcon, Julian D. Castro, Gloria C. Rojas, Paola A. Vaca, Santiago Ortiz, Gustavo Martinez, Pablo D. Lemoine

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Recently, electoral results across many countries have shown to be inconsistent with rational decision theory, which states that individuals make decisions based on maximizing benefits and reducing risks. An alternative explanation has emerged: Fear and rage-driven vote have been proved to be highly effective for political persuasion and mobilization. This phenomenon has been evident in the 2016 elections in the United States, 2006 elections in Mexico, 1998 elections in Venezuela, and 2004 elections in Bolivia. In Colombia, it has occurred recently in the 2016 plebiscite for peace and 2018 presidential elections. The aim of this study is to explain this phenomenon using cultural cognition theory, referring to the psychological predisposition individuals have to believe that its own and its peer´s behavior is correct and, therefore, beneficial to the entire society. Cultural cognition refers to the tendency of individuals to fit perceived risks, and factual beliefs into group shared values; the Cultural Cognition Worldview Scales (CCWS) measures cultural perceptions through two different dimensions: Individualism-communitarianism and hierarchy-egalitarianism. The former refers to attitudes towards social dominance based on conspicuous and static characteristics (sex, ethnicity or social class), while the latter refers to attitudes towards a social ordering in which it is expected from individuals to guarantee their own wellbeing without society´s or government´s intervention. A probabilistic national sample was obtained from different polls from the consulting and public opinion company Centro Nacional de Consultoría. Sociodemographic data was obtained along with CCWS scores, a subjective measure of left-right ideological placement and vote intention for 2019 Mayor´s elections were also included in the questionnaires. Finally, the question “In your opinion, what is the greatest risk Colombia is facing right now?” was included to identify perceived risk in the population. Preliminary results show that Colombians are highly distributed among hierarchical communitarians and egalitarian individualists (30.9% and 31.7%, respectively), and to a less extent among hierarchical individualists and egalitarian communitarians (19% and 18.4%, respectively). Males tended to be more hierarchical (p < .000) and communitarian (p=.009) than females. ANOVA´s revealed statistically significant differences between groups (quadrants) for the level of schooling, left-right ideological orientation, and stratum (p < .000 for all), and proportion differences revealed statistically significant differences for groups of age (p < .001). Differences and distributions for vote intention and perceived risks are still being processed and results are yet to be analyzed. Results show that Colombians are differentially distributed among quadrants in regard to sociodemographic data and left-right ideological orientation. These preliminary results indicate that this study may shed some light on why Colombians vote the way they do, and future qualitative data will show the fears emerging from the identified values in the CCWS and the relation this has with vote intention.

Keywords: communitarianism, cultural cognition, egalitarianism, hierarchy, individualism, perceived risks

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Authors: Vijaya Dixit Aasheesh Dixit

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Shipbuilding industry operates in Engineer Procure Construct (EPC) context. Product mix of a shipyard comprises of various types of ships like bulk carriers, tankers, barges, coast guard vessels, sub-marines etc. Each order is unique based on the type of ship and customized requirements, which are engineered into the product right from design stage. Thus, to execute every new project, a shipyard needs to upgrade its production expertise. As a result, over the long run, holistic learning occurs across different types of projects which contributes to the knowledge base of the shipyard. Simultaneously, in the short term, during execution of a project comprising of multiple sister ships, repetition of similar tasks leads to learning at activity level. This research aims to capture above learnings of a shipyard and incorporate learning curve effect in project scheduling and materials procurement to improve project performance. Extant literature provides support for the existence of such learnings in an organization. In shipbuilding, there are sequences of similar activities which are expected to exhibit learning curve behavior. For example, the nearly identical structural sub-blocks which are successively fabricated, erected, and outfitted with piping and electrical systems. Learning curve representation can model not only a decrease in mean completion time of an activity, but also a decrease in uncertainty of activity duration. Sister ships have similar material requirements. The same supplier base supplies materials for all the sister ships within a project. On one hand, this provides an opportunity to reduce transportation cost by batching the order quantities of multiple ships. On the other hand, it increases the inventory holding cost at shipyard and the risk of obsolescence. Further, due to learning curve effect the production scheduled of each consequent ship gets compressed. Thus, the material requirement schedule of every next ship differs from its previous ship. As more and more ships get constructed, compressed production schedules increase the possibility of batching the orders of sister ships. This work aims at integrating materials management with project scheduling of long duration projects for manufacturing of multiple sister ships. It incorporates the learning curve effect on progressively compressing material requirement schedules and addresses the above trade-off of transportation cost and inventory holding and shortage costs while satisfying budget constraints of various stages of the project. The activity durations and lead time of items are not crisp and are available in the form of probabilistic distribution. A Stochastic Mixed Integer Programming (SMIP) model is formulated which is solved using evolutionary algorithm. Its output provides ordering dates of items and degree of order batching for all types of items. Sensitivity analysis determines the threshold number of sister ships required in a project to leverage the advantage of learning curve effect in materials management decisions. This analysis will help materials managers to gain insights about the scenarios: when and to what degree is it beneficial to treat a multiple ship project as an integrated one by batching the order quantities and when and to what degree to practice distinctive procurement for individual ship.

Keywords: learning curve, materials management, shipbuilding, sister ships

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Authors: Pomozova Kseniia, Gorlachev Gennadiy, Chernyaev Aleksandr, Golanov Andrey

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In clinical practice, and especially in stereotactic radiosurgery planning, the significance of diffusion-weighted imaging (DWI) is growing. This makes the existence of software capable of quickly processing and reliably visualizing diffusion data, as well as equipped with tools for their analysis in terms of different tasks. We are developing the «MRDiffusionImaging» software on the standard C++ language. The subject part has been moved to separate class libraries and can be used on various platforms. The user interface is Windows WPF (Windows Presentation Foundation), which is a technology for managing Windows applications with access to all components of the .NET 5 or .NET Framework platform ecosystem. One of the important features is the use of a declarative markup language, XAML (eXtensible Application Markup Language), with which you can conveniently create, initialize and set properties of objects with hierarchical relationships. Graphics are generated using the DirectX environment. The MRDiffusionImaging software package has been implemented for processing diffusion magnetic resonance imaging (dMRI), which allows loading and viewing images sorted by series. An algorithm for "masking" dMRI series based on T2-weighted images was developed using a deformable surface model to exclude tissues that are not related to the area of interest from the analysis. An algorithm of distortion correction using deformable image registration based on autocorrelation of local structure has been developed. Maximum voxel dimension was 1,03 ± 0,12 mm. In an elementary brain's volume, the diffusion tensor is geometrically interpreted using an ellipsoid, which is an isosurface of the probability density of a molecule's diffusion. For the first time, non-parametric intensity distributions, neighborhood correlations, and inhomogeneities are combined in one segmentation of white matter (WM), grey matter (GM), and cerebrospinal fluid (CSF) algorithm. A tool for calculating the coefficient of average diffusion and fractional anisotropy has been created, on the basis of which it is possible to build quantitative maps for solving various clinical problems. Functionality has been created that allows clustering and segmenting images to individualize the clinical volume of radiation treatment and further assess the response (Median Dice Score = 0.963 ± 0,137). White matter tracts of the brain were visualized using two algorithms: deterministic (fiber assignment by continuous tracking) and probabilistic using the Hough transform. The proposed algorithms test candidate curves in the voxel, assigning to each one a score computed from the diffusion data, and then selects the curves with the highest scores as the potential anatomical connections. White matter fibers were visualized using a Hough transform tractography algorithm. In the context of functional radiosurgery, it is possible to reduce the irradiation volume of the internal capsule receiving 12 Gy from 0,402 cc to 0,254 cc. The «MRDiffusionImaging» will improve the efficiency and accuracy of diagnostics and stereotactic radiotherapy of intracranial pathology. We develop software with integrated, intuitive support for processing, analysis, and inclusion in the process of radiotherapy planning and evaluating its results.

Keywords: diffusion-weighted imaging, medical imaging, stereotactic radiosurgery, tractography

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Authors: William Michael Short

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Semantic Web’ technologies such as the Unified Medical Language System Metathesaurus, SNOMED-CT, and MeSH have been touted as transformational for the way users access online medical and health information, enabling both the automated analysis of natural-language data and the integration of heterogeneous healthrelated resources distributed across the Internet through the use of standardized terminologies that capture concepts and relationships between concepts that are expressed differently across datasets. However, the approaches that have so far characterized ‘semantic bioinformatics’ have not yet fulfilled the promise of the Semantic Web for medical and health information retrieval applications. This paper argues within the perspective of cognitive linguistics and cognitive anthropology that four features of human meaning-making must be taken into account before the potential of semantic technologies can be realized for this domain. First, many semantic technologies operate exclusively at the level of the word. However, texts convey meanings in ways beyond lexical semantics. For example, transitivity patterns (distributions of active or passive voice) and modality patterns (configurations of modal constituents like may, might, could, would, should) convey experiential and epistemic meanings that are not captured by single words. Language users also naturally associate stretches of text with discrete meanings, so that whole sentences can be ascribed senses similar to the senses of words (so-called ‘discourse topics’). Second, natural language processing systems tend to operate according to the principle of ‘one token, one tag’. For instance, occurrences of the word sound must be disambiguated for part of speech: in context, is sound a noun or a verb or an adjective? In syntactic analysis, deterministic annotation methods may be acceptable. But because natural language utterances are typically characterized by polyvalency and ambiguities of all kinds (including intentional ambiguities), such methods leave the meanings of texts highly impoverished. Third, ontologies tend to be disconnected from everyday language use and so struggle in cases where single concepts are captured through complex lexicalizations that involve profile shifts or other embodied representations. More problematically, concept graphs tend to capture ‘expert’ technical models rather than ‘folk’ models of knowledge and so may not match users’ common-sense intuitions about the organization of concepts in prototypical structures rather than Aristotelian categories. Fourth, and finally, most ontologies do not recognize the pervasively figurative character of human language. However, since the time of Galen the widespread use of metaphor in the linguistic usage of both medical professionals and lay persons has been recognized. In particular, metaphor is a well-documented linguistic tool for communicating experiences of pain. Because semantic medical knowledge-bases are designed to help capture variations within technical vocabularies – rather than the kinds of conventionalized figurative semantics that practitioners as well as patients actually utilize in clinical description and diagnosis – they fail to capture this dimension of linguistic usage. The failure of semantic technologies in these respects degrades the efficiency and efficacy not only of medical research, where information retrieval inefficiencies can lead to direct financial costs to organizations, but also of care provision, especially in contexts of patients’ self-management of complex medical conditions.

Keywords: ambiguity, bioinformatics, language, meaning, metaphor, ontology, semantic web, semantics

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Authors: Margaret Boone Rappaport, Christopher J. Corbally

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The ancient ape ancestral population from which living great ape and human species evolved had demographic features affecting their evolution. The population was large, had great genetic variability, and natural selection was effective at honing adaptations. The emerging populations of chimpanzees and humans were affected more by founder effects and genetic drift because they were smaller. Natural selection did not disappear, but it was not as strong. Consequences of the 'population crash' and the human effective population size are introduced briefly. The history of the ancient apes is written in the genomes of living humans and great apes. The expansion of the brain began before the human line emerged. Coalescence times for some genes are very old – up to several million years, long before Homo sapiens. The mismatch between gene trees and species trees highlights the anthropoid speciation processes, and gives the human genome history a fuzzy, probabilistic quality. However, it suggests traits that might form a foundation for capacities emerging later. A theoretical model is presented in which the genomes of early ape populations provide the substructure for the emergence of religious capacity later on the human line. The model does not search for religion, but its foundations. It suggests a course by which an evolutionary line that began with prosimians eventually produced a human species with biologically based religious capacity. The model of the sequential emergence of religious capacity relies on cognitive science, neuroscience, paleoneurology, primate field studies, cognitive archaeology, genomics, and population genetics. And, it emphasizes five trait types: (1) Documented, positive selection of sensory capabilities on the human line may have favored survival, but also eventually enriched human religious experience. (2) The bonobo model suggests a possible down-regulation of aggression and increase in tolerance while feeding, as well as paedomorphism – but, in a human species that remains cognitively sharp (unlike the bonobo). The two species emerged from the same ancient ape population, so it is logical to search for shared traits. (3) An up-regulation of emotional sensitivity and compassion seems to have occurred on the human line. This finds support in modern genetic studies. (4) The authors’ published model of morality's emergence in Homo erectus encompasses a cognitively based, decision-making capacity that was hypothetically overtaken, in part, by religious capacity. Together, they produced a strong, variable, biocultural capability to support human sociability. (5) The full flowering of human religious capacity came with the parietal expansion and smaller face (klinorhynchy) found only in Homo sapiens. Details from paleoneurology suggest the stage was set for human theologies. Larger parietal lobes allowed humans to imagine inner spaces, processes, and beings, and, with the frontal lobe, led to the first theologies composed of structured and integrated theories of the relationships between humans and the supernatural. The model leads to the evolution of a small population of African hominins that was ready to emerge with religious capacity when the species Homo sapiens evolved two hundred thousand years ago. By 50-60,000 years ago, when human ancestors left Africa, they were fully enabled.

Keywords: genetic drift, genomics, parietal expansion, religious capacity

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Authors: Andreas Rudisch, Ralf Lampert, Andreas Kolbitsch

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It is a well-known fact among the engineering community that earthquakes with comparatively low magnitudes can cause serious damage to nonstructural components (NSCs) of buildings, even when the supporting structure performs relatively well. Past research works focused mainly on NSCs of nuclear power plants and industrial plants. Particular attention should also be given to architectural façade elements of old masonry buildings (e.g. ornamental figures, balustrades, vases), which are very vulnerable under seismic excitation. Large numbers of these historical nonstructural components (HiNSCs) can be found in highly frequented historical city centers and in the event of failure, they pose a significant danger to persons. In order to estimate the vulnerability of acceleration sensitive HiNSCs, the peak horizontal floor acceleration (PHFA) is used. The PHFA depends on the dynamic characteristics of the building, the ground excitation, and induced nonlinearities. Consequently, the PHFA can not be generalized as a simple function of height. In the present research work, an extensive case study was conducted to investigate the influence of induced nonlinearity on the PHFA for old masonry buildings. Probabilistic nonlinear FE time-history analyses considering three different hazard levels were performed. A set of eighteen synthetically generated ground motions was used as input to the structure models. An elastoplastic macro-model (multiPlas) for nonlinear homogenized continuum FE-calculation was calibrated to multiple scales and applied, taking specific failure mechanisms of masonry into account. The macro-model was calibrated according to the results of specific laboratory and cyclic in situ shear tests. The nonlinear macro-model is based on the concept of multi-surface rate-independent plasticity. Material damage or crack formation are detected by reducing the initial strength after failure due to shear or tensile stress. As a result, shear forces can only be transmitted to a limited extent by friction when the cracking begins. The tensile strength is reduced to zero. The first goal of the calibration was the consistency of the load-displacement curves between experiment and simulation. The calibrated macro-model matches well with regard to the initial stiffness and the maximum horizontal load. Another goal was the correct reproduction of the observed crack image and the plastic strain activities. Again the macro-model proved to work well in this case and shows very good correlation. The results of the case study show that there is significant scatter in the absolute distribution of the PHFA between the applied ground excitations. An absolute distribution along the normalized building height was determined in the framework of probability theory. It can be observed that the extent of nonlinear behavior varies for the three hazard levels. Due to the detailed scope of the present research work, a robust comparison with code-recommendations and simplified PHFA distributions are possible. The chosen methodology offers a chance to determine the distribution of PHFA along the building height of old masonry structures. This permits a proper hazard assessment of HiNSCs under seismic loads.

Keywords: nonlinear macro-model, nonstructural components, time-history analysis, unreinforced masonry

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