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Understanding the human genome is a big research challenge. The huge complexity and amount of genome data require extremely effective and efficient data management policies. A first crucial point is to obtain a shared understanding of the domain, which becomes a very hard task considering the number of different genome data sources. To make things more complicated, those data sources deal with different parts of genome-based information: we not only need to understand them well, but also to integrate and intercommunicate all the relevant information. The protein perspective is a good example: rich, well-known repositories such as UniProt provide a lot of valuable information that it is not easy to interpret and manage when we want to generate useful results. Proteomes and basic information, protein-protein interaction, protein structure, protein processing events, protein function, etc. provide a lot of information is that needs to be conceptually characterized and delimited. To facilitate the essential common understanding of the domain, this paper uses the case of proteins to analyze the data provided by Uniprot in order to make a sound conceptualization work for identifying the relevant domain concepts. A conceptual model of proteins is the result of this conceptualization process, explained in detail in this work. This holistic conceptual model of proteins presented in this paper is the result of achieving a precise ontological commitment. It establishes concepts and their relationships that are significant in order to have a solid basis to efficiently manage relevant genome data related to proteins.

Precision medicine has emerged as a disrupting medical model to transform a historically reactive medicine into a proactive one that focuses on delivering individualized treatment. A relevant challenge of precision medicine is to integrate the large amount of omics data that exists. This data has a high degree of heterogeneity, dispersion, and isolation. In addition, there is a lack of a solid ontological commitment regarding domain concepts and definitions, and a unified guideline of how to transform data into knowledge is missing. In this work, we report our experience applying conceptual modeling to deal with these challenges in a specific genomics dimension, i.e., Precision Medicine. To do so, we have applied conceptual modeling techniques. The use of these techniques allows us to create representations of the world (i.e., conceptual schemes) that can be used for the purposes of understanding, communicating, and problem-solving. They also help to establish a common ontological framework to facilitate both communication and knowledge evolution in complex domains. We identify a set of limitations that emerged after working in a precision medicine context, and we describe how we have solved them using conceptual modeling. Thus, the main contribution of this work is to present the subsequent Conceptual Schema that allowed us to overcome these limitations, which provides a better representation of proteomics data and eases its integration.

While Product-Service Systems (PSS) have a potential sustainability impact by increasing a product's life and reducing resource consumption, the lack of ownership might lead to less responsible user behavior. Smart PSS can overcome this obstacle and guarantee correct and safe PSS use. In this context, intelligent connected vehicles (ICVs) with PSS can effectively reduce traffic accidents and ensure the safety of vehicles and pedestrians by guaranteeing optimal and safe vehicle operation. A core subsystem to support that is the collision-warning system (CWS). Existing CWSs are, however, limited to in-car warning; users have less access to the warning information, so the result of CWS for collision avoidance is insufficient. Therefore, CWS needs to be extended to include more elements and stakeholders in the collision scenario. This paper aims to provide a novel understanding of extended CWS (ECWS), outline the conceptual framework of ECWS, and contribute a conceptual modeling approach of ECWS from the smart PSS perspective at the functional level. It defines an integrated solution of intelligent products and warning services. The function is modeled based on the Theory of Inventive Problem Solving (TRIZ). Functions of an ECWS from the perspective of smart PSS can be comprehensively expressed to form an overall solution of integrated intelligent products, electronic services, and stakeholders. Based on the case illustration, the proposed method can effectively help function modeling and development of the ECWS at a conceptual level. This can effectively avoid delays due to traffic accidents and ensure the safety of vehicles and pedestrians. [ABSTRACT FROM AUTHOR]

The Discrete Event System Specification (DEVS) is a modular and hierarchical Modeling and Simulation (M&S) formalism based on systems theory that provides a general methodology for the construction of reusable models. Well-defined M&S structures have a positive impact when building simulation models because they can be applied systematically. However, even when DEVS can be used to model routing situations, the structures that emerge from this kind of problem are significant due to the handling of the flow of events. Often, the modeler ends with a lot of simulation models that refer to variants of the same component. The goal of this paper is to analyze the routing process domain from a conceptual modeling perspective through the use of a new DEVS extension called Routed DEVS (RDEVS). The RDEVS formalism is conceptually defined as a subclass of DEVS that manages a set of identified events inside a model network where each node combines a behavioral description with a routing policy. In particular, we study the modeling effort required to solve the M&S of routing problems scenarios employing a comparison between RDEVS modeling solutions and DEVS modeling strategies. Such a comparison is based on measures that promote the capture of the behavioral complexity of the final models. The results obtained highlight the modeling benefits of the RDEVS formalism as a constructor of routing processes. The proposed solution reduces the modeling effort involved in DEVS by specifying the event routing process directly in the RDEVS models using design patterns. The novel contribution is an advance in the understanding of how DEVS as a system modeling formalism supports best practices of software engineering in general and conceptual modeling in particular. The reusability and flexibility of the final simulation models, along with designs with low coupling and high cohesion, are the main benefits of the proposal that improve the M&S task applying a conceptual modeling perspective. [ABSTRACT FROM AUTHOR]

Background: This 4-year research project focuses on 6 social community enterprises (SCEs) that operate in 5 neighborhoods in a Dutch city. Residents of these neighborhoods face problems such as poor average levels of physical and mental health, high unemployment rates, and weak social cohesion. SCEs offer residents social, cultural, and work-related activities and are therefore believed to help these persons develop themselves and strengthen the social ties in the community. Because of a lack of empirical evidence; however, it is unclear whether and how SCEs benefit the health and well-being of participants. Objective: This paper outlines a protocol for an evaluation study on the impact of SCEs, aiming to determine (1) to what extent SCEs affect health and well-being of participating residents, (2) what underlying processes and mechanisms can explain such impact, and (3) what assets are available to SCEs and how they can successfully mobilize these assets. Methods: A mixed methods multiple-case study design including repeated measurements will be conducted. Six SCEs form the cases. An integrated model of SCE health intervention will be used as the theoretical basis. First, the impact of SCEs is measured on the individual and community level, using questionnaires and in-depth interviews conducted with participants. Second, the research focuses on the underlying processes and mechanisms and the organizational and sociopolitical factors that influence the success or failure of these enterprises in affecting the health and well-being of residents. At this organizational level, in-depth interviews are completed with SCE initiators and stakeholders, such as municipal district managers. Finally, structurally documented observations are made on the organizational and sociopolitical context of the SCEs. Results: This research project received funding from the Netherlands Organization for Health Research and Development in 2018. Data collection takes place from 2018 until 2022. Data analysis starts after the last round of data collection in 2022 and finalizes in 2024. Expected results will be published in 2023 and 2024. Conclusions: Despite the societal relevance of SCEs, little empirical research has been performed on their functioning and impact. This research applies a variety of methods and includes the perspectives of multiple stakeholders aiming to generate new empirical evidence. The results will enable us to describe how SCE activities influence intermediate and long-term health outcomes and how the organizational and sociopolitical context of SCEs may shape opportunities or barriers for health promotion. As the number of these initiatives in the Netherlands is increasing rapidly, this research can benefit many SCEs attempting to become more effective and increase their impact. The findings of this research will be shared directly with relevant stakeholders through local and national meetings and annual reports and disseminated among other researchers through scientific publications. [ABSTRACT FROM AUTHOR]

Construction simulation has been an active area of research in the last six decades. Nevertheless, there has been a gap between academia and industry in realizing the capabilities of simulation to support decision-making in construction. One of the well-recognized reasons is the difficulty of undertaking comprehensive simulation studies by construction practitioners, who usually lack sufficient knowledge and skills to adequately build simulation models. Efforts to bridge this gap have been focused on simplifying the computer coding and model implementation stages of construction simulation studies with limited research on the early stage of defining the model and abstracting the system, i.e., conceptual modeling. The conceptual modeling stage is known to be one of the most difficult tasks in a simulation study. Thus, several frameworks to support building conceptual models have been proposed in simulation literature. This study contributes to the research efforts to promote simulation in the construction industry through the adoption of a conceptual modeling framework. It demonstrates the application of the proposed conceptual modeling framework in a case study of piling operations. The findings of this paper reinforced the significance of conceptual modeling by confirming the role of the conceptual model as a communication link between stakeholders. Moreover, the conceptual model was used as a specification document for developing a flexible model that can be replicated in other settings. The use of a documented conceptual model assisted in managing the overall simulation study efficiently, which, in turn, lead to reductions in time and effort for different modeling activities. [ABSTRACT FROM AUTHOR]

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Conceptual modeling of domain object hierarchies, such as product hierarchies or organization hierarchies, is difficult due to the intricate nature of nonphysical domain objects organized in such hierarchies. Modeling domain object hierarchies as part-whole hierarchies covers their hierarchical structure, yet to capture their meaning, part-whole hierarchies have to be combined with specialization and multi-level instantiation. To this end we introduce the deep domain object (DDO) multi-level modeling pattern and approach. With the DDO approach, subclasses and metaclasses are induced by and integrated with the part-whole hierarchy. The approach is aligned with the multi-level theory (MLT) and formalized by a metamodel and a set of deductive rules implemented in F-Logic. The proof-of-concept prototype is used for automated application of the pattern and for querying induced multi-level models. [ABSTRACT FROM AUTHOR]

Abstract Permafrost is a large reservoir of soil organic carbon, accounting for about half of all the terrestrial storage, almost equivalent to twice the atmospheric carbon storage. Hence, permafrost degradation under global warming may induce a release of a substantial amount of additional greenhouse gases, leading to further warming. In addition to gradual degradation through heat conduction, the importance of abrupt thawing or erosion of ice-rich permafrost has recently been recognized. Such ice-rich permafrost has evolved over a long timescale (i.e., tens to hundreds of thousands of years). Although important, knowledge on the distribution of vulnerability to degradation, i.e., location and stored amount of ground ice and soil carbon in ice-rich permafrost, is still limited largely due to the scarcity of accessible in situ data. Improving the future projections for the Arctic using the Earth System Models will lead to a better understanding of the current vulnerability distribution, which is a prerequisite for conducting climatic and biogeochemical assessment that currently constitutes a large source of uncertainty. In this study, present-day circum-Arctic distributions (north of 50° N) in ground ice and organic soil carbon content are produced by a new approach to combine a newly developed conceptual carbon-ice balance model, and a downscaling technique with the topographical and hydrological information derived from a high-resolution digital elevation model (ETOPO1). The model simulated the evolution of ground ice and carbon for the recent 125 thousand years (from the Last Interglacial to the present) at 1° resolution. The 0.2° high-resolution circum-Arctic maps of the present-day ground ice and soil organic carbon, downscaled from the 1° simulations, were reasonable compared to the observation-based previous maps. These data, together with a map of vulnerability of ice-rich permafrost to degradation served as initial and boundary condition data for model improvement and the future projection of additional greenhouse gas release potentially caused by permafrost degradation.

The complex societal challenges of the twenty-first Century require scientific researchers and academically educated professionals capable of conducting scientific research in complex problem contexts. Our central claim is that educational approaches inspired by a traditional empiricist epistemology insufficiently foster the required deep conceptual understanding and higher-order thinking skills necessary for epistemic tasks in scientific research. Conversely, we argue that constructivist epistemologies (developed in the philosophy of science in practice) provide better guidance to educational approaches to promote research skills. We also argue that teachers adopting a constructivist learning theory do not necessarily embrace a constructivist epistemology. On the contrary, in educational practice, novel educational approaches that adopt constructivist learning theories (e.g., project-based learning, PjBL) often maintain traditional empiricist epistemologies. Philosophers of science can help develop educational designs focused on learning to conduct scientific research, combining constructivist learning theory with constructivist epistemology. We illustrate this by an example from a bachelor’s program in Biomedical Engineering, where we introduce conceptual models and modeling as an alternative to the traditional focus on hypothesis testing in conducting scientific research. This educational approach includes the so-called B&K method for (re-)constructing scientific models to scaffold teaching and learning conceptual modeling. [ABSTRACT FROM AUTHOR]

This work is interested in observation, in scientific knowledge acquired from what is perceived (Link making Sense) from a complex systemic world. The approach leads to proposing the concept of imprint within the interdisciplinary framework "System -Reality - World as perceived - Model " and testing it against data, then to proposing systemic ontology as an approach. This makes it possible to deploy the Link making Shape from the systemic domain to the world as perceived, to analyze and describe the relevant part in the data and to show how the whole of this mostly symbolic work can contribute, with respect to semantic, technological and digital aspects, to better control data collection and analysis and Earth observation as a whole. Illustrations mainly focus on oasis. This work discusses its contribution to constructing an observation science. [ABSTRACT FROM AUTHOR]

Land administration (LA) is concerned with processes. Simply put, LA cannot be understood, built, or improved unless the processes associated with it are understood. When it comes to the processes involved in LA, two general processes can be identified, namely registration and dissemination. Nowadays, processes are implemented electronically; however, paper-based thinking is still present, and the performance of processes is impeded by siloed data management. These issues could be addressed through the employment of standards such as the Land Administration Domain Model. Processes are not yet part of the standard, but their inclusion in future extensions is planned. Moreover, a literature analysis indicated that there is no standardized methodology or model available for describing LA processes. Consequently, we modeled one part of land administration processes, namely data dissemination, by developing a methodology and model to describe it. The methodology was developed with the goal of providing guidelines for other researchers when modeling use cases of data dissemination processes by enabling comparisons of models, searching for best practices, and developing standardized process models. Additionally, the methodology was tested on a conceptual use case to prove its viability. Furthermore, a model based on conceptual modeling and an activity-centric process modeling approach was developed and linked to existing classes of the Land Administration Domain Model. The organizational and technological challenges which might arise when improving data dissemination processes are discussed, and possible outcomes of the developed methodology and model are provided.

In multilingual semantic representation, the interaction between humans and computers faces the challenge of understanding meaning or semantics, which causes ambiguity and inconsistency in heterogeneous information. This paper proposes a Machine Natural Language Parser (MParser) to address the semantic interoperability problem between users and computers. By leveraging a semantic input method for sharing common atomic concepts, MParser represents any simple English sentence as a bag of unique and universal concepts via case grammar of an explainable machine natural language. In addition, it provides a human and computer-readable and -understandable interaction concept to resolve the semantic shift problems and guarantees consistent information understanding among heterogeneous sentence-level contexts. To evaluate the annotator agreement of MParser outputs that generates a list of English sentences under a common multilingual word sense, three expert participants manually and semantically annotated 75 sentences (505 words in total) in English. In addition, 154 non-expert participants evaluated the sentences' semantic expressiveness. The evaluation results demonstrate that the proposed MParser shows higher compatibility with human intuitions. [ABSTRACT FROM AUTHOR]

In Europe and indeed worldwide, the General Data Protection Regulation (GDPR) provides protection to individuals regarding their personal data in the face of new technological developments. GDPR is widely viewed as the benchmark for data protection and privacy regulations that harmonizes data privacy laws across Europe. Although the GDPR is highly beneficial to individuals, it presents significant challenges for organizations monitoring or storing personal information. Since there is currently no automated solution with broad industrial applicability, organizations have no choice but to carry out expensive manual audits to ensure GDPR compliance. In this paper, we present a complete GDPR UML model as a first step toward designing automated methods for checking GDPR compliance. Given that the practical application of the GDPR is influenced by national laws of the EU Member States, we suggest a two-tiered description of the GDPR, generic and specialized. In this paper, we provide (1) the GDPR conceptual model we developed with complete traceability from its classes to the GDPR, (2) a glossary to help understand the model, (3) the plain-English description of 35 compliance rules derived from GDPR along with their encoding in OCL and (4) the set of 20 variations points derived from GDPR to specialize the generic model. We further present the challenges we faced in our modeling endeavor, the lessons we learned from it and future directions for research. [ABSTRACT FROM AUTHOR]

The purpose of the article is to summarize the methodological experience of work on the value-semantic component of modeling the media image of territory in the process of creating a media text of different genres and designs, to characterize the pedagogical technologies of teaching text construction using conceptual representations of society, its cultural memory. The article presents the characteristics of methodological materials on the formation of the competence of the media text author working with the territory's media image used in the ours of training "Journalism", "Advertising and Public Relations" – the bachelor's degree, the master's degree. Cognitive means of a media text addressed to the sociocode of culture have been highlighted. Using them, the textured material is percepted and processed in modeling the media image of a country or a region. Active and interactive teaching methods focused on reflection and conscious use of these tools in the media text author's creative activity have been structured. The authors propose several tasks for active, problem-based learning and articulate the culturological model of education in forming professional competencies in modeling a media image, which replenishes the educational environment with sociocultural meanings characteristic of a person's territory. [ABSTRACT FROM AUTHOR]

Massive quantities of the pelagic brown macroalgae Sargassum spp. (sargassum) have been invading the Caribbean and West African shores since 2011, causing devastating effects on the coastal ecosystem and local economy. Little is known about sargassum beaching dynamics and the capacity of the coastal system to naturally remove beached sargassum. Here, we characterize the temporal variation in arriving and beached sargassum in a reef lagoon using a 5.2‐year data set of hourly optical imagery, and identify the governing hydrometeorological conditions. Image classification reveals interannual variability in the start, duration, and intensity of the sargassum arrival season. Arrivals are associated with relatively low energy onshore directed winds and waves, and offshore abundance of sargassum. Furthermore, nearshore sargassum mat size is found to decrease with decreasing wave/wind energy. Once sargassum beaches, a berm of wrack is formed. Natural wrack removal was observed under elevated water levels and increased wave action. Three types of wrack removal were distinguished, depending on the water level η with respect to the berm crest height zc and berm crest toe zt: gradual berm destruction with gaps developing in the seaward berm edge that grow larger with time (Type I; zt<ηzc) or in the dunes (Type III; η≫zc). Higher energy waves activate the reef circulation, which is suspected to flush part of the wrack out of the reef lagoon. We propose a conceptual model of nearshore sargassum dynamics in a reef lagoon system. Plain Language Summary: Unusually large masses of seaweed (Sargassum spp.) have been washing ashore along the Caribbean and West African coasts since 2011. The seaweed floods threaten coral reefs, seagrass beds, fish and turtles, and harm local economy as it discourages beach tourism. The seaweed, originating from the Atlantic Ocean, drifts in mats on the water surface with the ocean currents. It is unclear how seaweed arrives in nearshore waters and washes up the beach, and how long it resides once beached. We used hourly images of a reef lagoon (Puerto Morelos, Mexico) to study the beaching and natural removal of seaweed since 2015. The largest masses of seaweed beached in spring and summer of 2018 and 2019, whereas 2016 was hardly affected. Seaweed arrived under onshore directed weak winds and low waves, with the seaweed mat size increasing with weaker winds and lower waves. Higher waves and elevated water levels removed seaweed from the beach and brought it back in the water column. Seaweed was rapidly removed when the waves overtopped the seaweed deposit, and was removed gradually when waves reached only part of the deposit. Under high waves, the reef promotes currents that can flush seaweed out of the reef lagoon. Key Points: Video monitoring allows the characterization of pelagic sargassum beaching and wrack dynamicsSargassum deposits are removed from the beach and resuspended under elevated water levels and increased wave actionNearshore sargassum mat size decreases with increasing wave and wind energy [ABSTRACT FROM AUTHOR]