Integration of a graph-based model indexer in commercial modelling tools

Softeam has over 20 years of experience providing UML-based modelling solutions, such as its Modelio modelling tool, and its Constellation enterprise model management and collaboration environment. Due to the increasing number and size of the models used by Softeam’s clients, Softeam joined the MONDO FP7 EU research project, which worked on solutions for these scalability challenges and produced the Hawk model indexer among other results. This paper presents the technical details and several case studies on the integration of Hawk into Softeam’s toolset. The first case study measured the performance of Hawk’s Modelio support using varying amounts of memory for the Neo4j backend. In another case study, Hawk was integrated into Constellation to provide scalable global querying of model repositories. Finally, the combination of Hawk and the Epsilon Generation Language was compared against Modelio for document generation: for the largest model, Hawk was two orders of magnitude faster.

Acumen : an open-source testbed for cyber-physical systems research

Developing Cyber-Physical Systems requires methods and tools to support simulation and verification of hybrid (both continuous and discrete) models. The Acumen modeling and simulation language is an open source testbed for exploring the design space of what rigorousbut- practical next-generation tools can deliver to developers of Cyber- Physical Systems. Like verification tools, a design goal for Acumen is to provide rigorous results. Like simulation tools, it aims to be intuitive, practical, and scalable. However, it is far from evident whether these two goals can be achieved simultaneously. This paper explains the primary design goals for Acumen, the core challenges that must be addressed in order to achieve these goals, the “agile research method” taken by the project, the steps taken to realize these goals, the key lessons learned, and the emerging language design.

Design and implementation of an enterprise application integration solution for science and research outcomes information management using guaraná technology

This document presents an Enterprise Application Integration based proposal for research outcomes and technological information management. The proposal addresses national and international science and research outcomes information management, and corresponding information systems. Information systems interoperability problems, approaches, technologies and integration tools are presented and applied to the research outcomes information management case. A business and technological perspective is provided, including the conceptual analysis and modelling, an integration solution based in a Domain-Specific Language (DSL) and the integration platform to execute the proposed solution. For illustrative purposes, the role and information system needs of a research unit is assumed as the representative case.

"Going outside": discussing the connection between pedagogical practices with digital tools and outdoor learning in early childhood and primary education

Technology has an important role in children's lives and education. Based on several projects developed with ICT, both in Early Childhood Education (3-6 years old) and Primary Education (6-10 years old), since 1997, the authors argue that research and educational practices need to "go outside", addressing ways to connect technology with outdoor education. The experience with the projects and initiatives developed supported a conceptual framework, developed and discussed with several partners throughout the years and theoretically informed. Three main principles or axis have emerged: strengthening Children's Participation, promoting Critical Citizenship and establishing strong Connections to Pedagogy and Curriculum. In this paper, those axis will be presented and discussed in relation to the challenge posed by Outdoor Education to the way ICT in Early Childhood and Primary Education is understood, promoted and researched. The paper is exploratory, attempting to connect theoretical and conceptual contributions from Early Childhood Pedagogy with contributions from ICT in Education. The research-based knowledge available is still scarce, mostly based on studies developed with other purposes. The paper, therefore, focus the connections and interpellations between concepts established through the theoretical framework and draws on the almost 20 years of experience with large and small scale action-research projects of ICT in schools. The more recent one is already testing the conceptual framework by supporting children in non-formal contexts to explore vineyards and the cycle of wine production with several ICT tools. Approaching Outdoor Education as an arena where pedagogical and cultural dimensions influence decisions and practices, the paper tries to argue that the three axis are relevant in supporting a stronger connection between technology and the outdoor.

Data, Software, and Advanced Computational Usage of University of Washington Research Leaders

Scientific research is increasingly data-intensive, relying more and more upon advanced computational resources to be able to answer the questions most pressing to our society at large. This report presents findings from a brief descriptive survey sent to a sample of 342 leading researchers at the University of Washington (UW), Seattle, Washington in 2010 and 2011 as the first stage of the larger National Science Foundation project “Interacting with Cyberinfrastructure in the Face of Changing Science.” This survey assesses these researcher’s use of advanced computational resources, data, and software in their research. We present high-level findings that describe UW researchers’: demographics, interdisciplinarity, research groups, data use, software and computational use—including software development and use, data storage and transfer activities, and collaboration tools, and computing resources. These findings offer insights into the state of computational resources in use during this time period as well as offering a look at the data intensiveness of UW researchers.

Epistemic, Ontic, Axiologic, and Praxic Constructs in Knowledge Organization Research

The work of knowledge organization requires a particular set of tools. For instance we need standards of content description like Anglo-American Cataloging Rules Edition 2, Resource Description and Access (RDA), Cataloging Cultural Objects, and Describing Archives: A Content Standard. When we intellectualize the process of knowledge organization – that is when we do basic theoretical research in knowledge organization we need another set of tools. For this latter exercise we need constructs. Constructs are ideas with many conceptual elements, largely considered subjective. They allow us to be inventive as well as allow us to see a particular point of view in knowledge organization. For example, Patrick Wilson’s ideas of exploitative control and descriptive control, or S. R. Ranganathan’s fundamental categories are constructs. They allow us to identify functional requirements or operationalizations of functional requirements, or at least come close to them for our systems and schemes. They also allow us to carry out meaningful evaluation.What is even more interesting, from a research point of view, is that constructs once offered to the community can be contested and reinterpreted and this has an affect on how we view knowledge organization systems and processes. Fundamental categories are again a good example in that some members of the Classification Research Group (CRG) argued against Ranganathan’s point of view. The CRG posited more fundamental categories than Ranganathan’s five, Personality, Matter, Energy, Space, and Time (Ranganathan, 1967). The CRG needed significantly more fundamental categories for their work.1 And these are just two voices in this space we can also consider the fundamental categories of Johannes Kaiser (1911), Shera and Egan, Barbara Kyle (Vickery, 1960), and Eric de Grolier (1962). We can also reference contemporary work that continues comparison and analysis of fundamental categories (e.g., Dousa, 2011).In all these cases we are discussing a construct. The fundamental category is not discovered; it is constructed by a classificationist. This is done because it is useful in engaging in the act of classification. And while we are accustomed to using constructs or debating their merit in one knowledge organization activity or another, we have not analyzed their structure, nor have we created a typology. In an effort to probe the epistemological dimension of knowledge organization, we think it would be a fruitful exercise to do this. This is because we might benefit from clarity around not only our terminology, but the manner in which we talk about our terminology. We are all creative workers examining what is available to us, but doing so through particular lenses (constructs) identifying particular constructs. And by knowing these and being able to refer to these we would consider a core competency for knowledge organization researchers.

Linked Data in the Digital Humanities: Examples, Projects, and Tools

Harnessing the potential of semantic web technologies to support and diversify scholarship is gaining popularity in the digital humanities. This talk describes a number of projects utilising Linked Data ranging from musicology and library metadata, to the representation of the narrative structure, philological, bibliographical, and museological data of ancient Mesopotamian literary compositions.

Trichoderma in Brazil: history, research, commercialization and perspectives.

2008

Competencies Required in Education Research and Teaching Systematization according to Students from the Preschool, Primary and Secondary Education Programs of the University of Costa Rica

The purpose of this paper is to present the results of two online forums carried out with the participation of 42 students of the Licenciaturas  in Preschool Education, Primary Education and Secondary Education of the University of Costa Rica. The main purpose of the forums was to determine the insights of the participant students about the competencies they have achieved in the field of education research, and which have been the essential tools for them to systematize their own teaching practices. The discussion forums were part of the course FD5091 Métodos de Investigación Educativa [Education Research Methods] of the School of Teacher Education, delivered from March-April 2010.  Of the sample, 60 percent were students of the Preschool teaching program, 35 percent were from the Primary Education teaching program and 5 percent were from the Secondary Education teaching program in the fields of Science, Mathematics and Social Studies. According to the insights and beliefs showed by the participants –both, the future teachers and the profession practitioners–, there are no opportunities for research or systematization of their own teaching mediation, in the current work situation.(1) Translator’s Note: In Costa Rica, the “Licenciatura” is a one-year post-Bachelor study program, usually including thesis. “Primary Education” refers to students from the 1st to 6th grades, and “Secondary Education” refers to students from the 7th to 11th grades.

Print versus digital texts: understanding the experimental research and challenging the dichotomies

This article presents the results of a systematic critical review of interdisciplinary literature concerned with digital text (or e-text) uses in education and proposes recommendations for how e-texts can be implemented for impactful learning. A variety of e-texts can be found in the repertoire of educational resources accessible to students, and in the constantly changing terrain of educational technologies, they are rapidly evolving, presenting new opportunities and affordances for student learning. We highlight some of the ways in which academic studies have examined e-texts as part of teaching and learning practices, placing a particular emphasis on aspects of learning such as recall, comprehension, retention of information and feedback. We also review diverse practices associated with uses of e-text tools such as note-taking, annotation, bookmarking, hypertexts and highlighting. We argue that evidence-based studies into e-texts are overwhelmingly structured around reinforcing the existing dichotomy pitting print-based (‘traditional’) texts against e-texts. In this article, we query this approach and instead propose to focus on factors such as students’ level of awareness of their options in accessing learning materials and whether they are instructed and trained in how to take full advantage of the capabilities of e-texts, both of which have been found to affect learning performance.

Machine learning tools for protein annotation: the cases of transmembrane β-barrel and myristoylated proteins

Biology is now a “Big Data Science” thanks to technological advancements allowing the characterization of the whole macromolecular content of a cell or a collection of cells. This opens interesting perspectives, but only a small portion of this data may be experimentally characterized. From this derives the demand of accurate and efficient computational tools for automatic annotation of biological molecules. This is even more true when dealing with membrane proteins, on which my research project is focused leading to the development of two machine learning-based methods: BetAware-Deep and SVMyr. BetAware-Deep is a tool for the detection and topology prediction of transmembrane beta-barrel proteins found in Gram-negative bacteria. These proteins are involved in many biological processes and primary candidates as drug targets. BetAware-Deep exploits the combination of a deep learning framework (bidirectional long short-term memory) and a probabilistic graphical model (grammatical-restrained hidden conditional random field). Moreover, it introduced a modified formulation of the hydrophobic moment, designed to include the evolutionary information. BetAware-Deep outperformed all the available methods in topology prediction and reported high scores in the detection task. Glycine myristoylation in Eukaryotes is the binding of a myristic acid on an N-terminal glycine. SVMyr is a fast method based on support vector machines designed to predict this modification in dataset of proteomic scale. It uses as input octapeptides and exploits computational scores derived from experimental examples and mean physicochemical features. SVMyr outperformed all the available methods for co-translational myristoylation prediction. In addition, it allows (as a unique feature) the prediction of post-translational myristoylation. Both the tools here described are designed having in mind best practices for the development of machine learning-based tools outlined by the bioinformatics community. Moreover, they are made available via user-friendly web servers. All this make them valuable tools for filling the gap between sequential and annotated data.

Applications of network-based approaches in drug research

Recent research trends in computer-aided drug design have shown an increasing interest towards the implementation of advanced approaches able to deal with large amount of data. This demand arose from the awareness of the complexity of biological systems and from the availability of data provided by high-throughput technologies. As a consequence, drug research has embraced this paradigm shift exploiting approaches such as that based on networks. Indeed, the process of drug discovery can benefit from the implementation of network-based methods at different steps from target identification to drug repurposing. From this broad range of opportunities, this thesis is focused on three main topics: (i) chemical space networks (CSNs), which are designed to represent and characterize bioactive compound data sets; (ii) drug-target interactions (DTIs) prediction through a network-based algorithm that predicts missing links; (iii) COVID-19 drug research which was explored implementing COVIDrugNet, a network-based tool for COVID-19 related drugs. The main highlight emerged from this thesis is that network-based approaches can be considered useful methodologies to tackle different issues in drug research. In detail, CSNs are valuable coordinate-free, graphically accessible representations of structure-activity relationships of bioactive compounds data sets especially for medium-large libraries of molecules. DTIs prediction through the random walk with restart algorithm on heterogeneous networks can be a helpful method for target identification. COVIDrugNet is an example of the usefulness of network-based approaches for studying drugs related to a specific condition, i.e., COVID-19, and the same ‘systems-based’ approaches can be used for other diseases. To conclude, network-based tools are proving to be suitable in many applications in drug research and provide the opportunity to model and analyze diverse drug-related data sets, even large ones, also integrating different multi-domain information.

Methods and tools to foster territorial approaches for the assessment of food supply chains

The challenges of the current global food systems are often framed around feeding the world's growing population while meeting sustainable development for future generations. Globalization has brought to a fragmentation of food spaces, leading to a flexible and mutable supply chain. This poses a major challenge to food and nutrition security, affecting also rural-urban dynamics in territories. Furthermore, the recent crises have highlighted the vulnerability to shocks and disruptions of the food systems and the eco-system due to the intensive management of natural, human and economic capital. Hence, a sustainable and resilient transition of the food systems is required through a multi-faceted approach that tackles the causes of unsustainability and promotes sustainable practices at all levels of the food system. In this respect, a territorial approach becomes a relevant entry point of analysis for the food system’s multifunctionality and can support the evaluation of sustainability by quantifying impacts associated with quantitative methods and understanding the territorial responsibility of different actors with qualitative ones. Against this background the present research aims to i) investigate the environmental, costing and social indicators suitable for a scoring system able to measure the integrated sustainability performance of food initiatives within the City/Region territorial context; ii) develop a territorial assessment framework to measure sustainability impacts of agricultural systems; and iii) define an integrated methodology to match production and consumption at a territorial level to foster a long-term vision of short food supply chains. From a methodological perspective, the research proposes a mixed quantitative and qualitative research method. The outcomes provide an in-depth view into the environmental and socio-economic impacts of food systems at the territorial level, investigating possible indicators, frameworks, and business strategies to foster their future sustainable development.

Plasma-activated liquids as promising tools for non-invasive selective treatment of epithelial ovarian cancer

Plasma medicine is a branch of plasma-promising biomedical applications that uses cold atmospheric plasma (CAP) as a therapeutic agent in treating a wide range of medical conditions including cancer. Epithelial ovarian cancer (EOC) is a highly malignant and aggressive form of ovarian cancer, and most patients are diagnosed at advanced stages which significantly reduces the chances of successful treatment. Treatment resistance is also common, highlighting the need for novel therapies to be developed to treat EOC. Research in Plasma Medicine has revealed that plasma has unique properties suitable for biomedical applications and medical therapies, including responses to hormetic stimuli. However, the exact mechanisms by which CAP works at the molecular level are not yet fully understood. In this regard, the main goal of this thesis is to identify a possible adjuvant therapy for cancer, which could exert a cytotoxic effect, without damaging the surrounding healthy cells. An examination of different plasma-activated liquids (PALs) revealed their potential as effective tools for significantly inhibiting the growth of EOC. The dose-response profile between PALs and their targeted cytotoxic effects on EOC cells without affecting healthy cells was established. Additionally, it was validated that PALs exert distinct effects on different subtypes of EOC, possibly linked to the cells' metabolism. This suggests the potential for developing new, personalized anticancer strategies. Furthermore, it was observed that CAP treatment can alter the chemistry of a biomolecule present in PAL, impacting its cytotoxic activity. The effectiveness of the treatment was also preliminarily evaluated in 3D cultures, opening the door for further investigation of a possible correlation between the tumor microenvironment and PALs' resistance. These findings shed light on the intricate interplay between CAP and the liquid substrate and cell behaviour, providing valuable insights for the development of a novel and promising CAP-based cancer treatment for clinical application.

Red flesh fruit in european pear (Pyrus communis): genetic sources, QTLs, candidate genes and tools for breeding

Red flesh fruit is a character which interest is increasing in several commercial species. Following a review of the research on the biosynthesis and accumulation of anthocyanin in pears (Chapter 1) the general aim of the project is reported in Chapter 2. Chapter 3 reports the results of a molecular analysis of 33 red-fleshed pear accessions, genotyped with 18 SSR markers with the aim of improving germplasm conservation strategies to support ongoing breeding programs. The molecular profiles revealed both cases of synonymy and homonymy and 6 unique genotypes were identified. The S-allele were established to highlight the genetic relationships among these landraces. Four of the unique genotypes have been clustered based on pomological data. In the Chapter 4, the work was directed to identify the putative genomic regions involved in the appearance of this character in pear fruit. A crossing population (‘Carmen’ x ‘Cocomerina Precoce’) segregating for the trait was phenotyped for 2 consecutive years and used for QTL analysis. A strong QTL was identified in a small genomic region related to the red flesh fruit trait at 27 Mb from the start of LG5. Two candidate genes were detected in this genomic region: ‘PcMYB114’ and ‘PcABCC2’. SSR marker SSR114 was found able to detect the red flesh phenotype segregation in all the red-fleshed pear accessions and segregating progenies tested. Chapter 5 focuses on examining the trend of anthocyanin synthesis and accumulation during the fruit development, from fruit set to ripening time. Three different trials were planned: qPCR and HPLC methods were performed to correlate the genes expression with the anthocyanin accumulation in ‘Cocomerina Precoce’ and six progenies. Total transcriptome sequencing was used to compare the differential genes expression between red and white-fleshed fruit. Chapter 6 reviews and analyses all the earlier study findings while providing new potential future perspectives.