Patient data discovery platforms as enablers of biomedical and translational research: a systematic review

Background: The global shift from paper health records to electronic ones has led to an impressive growth of biomedical digital data along the past two decades. Exploring and extracting knowledge from these data has the potential to enhance translational research and lead to positive outcomes for the population’s health and healthcare. Obective: The aim of this study was to conduct a systematic review to identify software platforms that enable discovery, secondary use and interoperability of biomedical data. Additionally, we aim evaluating the identified solutions in terms of clinical interest and main healthcare-related outcomes. Methods: A systematic search of the scientific literature published and indexed in Pubmed between January 2014 and September 2018 was performed. Inclusion criteria were as follows: relevance for the topic of bio- medical data discovery, English language, and free full text. To increase the recall, we developed a semi-auto- matic and incremental methodology to retrieve articles that cite one or more of the previous set. Results: A total number of 500 candidate papers were retrieved through this methodology. Of these, 85 were eligible for abstract assessment. Finally, 37 studies qualified for a full-text review, and 20 provided enough information for the study objectives. Conclusions: This study revealed that biomedical discovery platforms are both a current necessity and a sig- nificantly innovative agent in the area of healthcare. The outcomes that were identified, in terms of scientific publications, clinical studies and research collaborations stand as evidence.publishe

A formal architecture-centric and model driven approach for the engineering of science gateways

From n-Tier client/server applications, to more complex academic Grids, or even the most recent and promising industrial Clouds, the last decade has witnessed significant developments in distributed computing. In spite of this conceptual heterogeneity, Service-Oriented Architecture (SOA) seems to have emerged as the common and underlying abstraction paradigm, even though different standards and technologies are applied across application domains. Suitable access to data and algorithms resident in SOAs via so-called ‘Science Gateways’ has thus become a pressing need in order to realize the benefits of distributed computing infrastructures.In an attempt to inform service-oriented systems design and developments in Grid-based biomedical research infrastructures, the applicant has consolidated work from three complementary experiences in European projects, which have developed and deployed large-scale production quality infrastructures and more recently Science Gateways to support research in breast cancer, pediatric diseases and neurodegenerative pathologies respectively. In analyzing the requirements from these biomedical applications the applicant was able to elaborate on commonly faced issues in Grid development and deployment, while proposing an adapted and extensible engineering framework. Grids implement a number of protocols, applications, standards and attempt to virtualize and harmonize accesses to them. Most Grid implementations therefore are instantiated as superposed software layers, often resulting in a low quality of services and quality of applications, thus making design and development increasingly complex, and rendering classical software engineering approaches unsuitable for Grid developments.The applicant proposes the application of a formal Model-Driven Engineering (MDE) approach to service-oriented developments, making it possible to define Grid-based architectures and Science Gateways that satisfy quality of service requirements, execution platform and distribution criteria at design time. An novel investigation is thus presented on the applicability of the resulting grid MDE (gMDE) to specific examples and conclusions are drawn on the benefits of this approach and its possible application to other areas, in particular that of Distributed Computing Infrastructures (DCI) interoperability, Science Gateways and Cloud architectures developments

Pursuit of precision medicine: Systems biology approaches in Alzheimer\u27s disease mouse models.

Alzheimer\u27s disease (AD) is a complex disease that is mediated by numerous factors and manifests in various forms. A systems biology approach to studying AD involves analyses of various body systems, biological scales, environmental elements, and clinical outcomes to understand the genotype to phenotype relationship that potentially drives AD development. Currently, there are many research investigations probing how modifiable and nonmodifiable factors impact AD symptom presentation. This review specifically focuses on how imaging modalities can be integrated into systems biology approaches using model mouse populations to link brain level functional and structural changes to disease onset and progression. Combining imaging and omics data promotes the classification of AD into subtypes and paves the way for precision medicine solutions to prevent and treat AD

The BIM process for the architectural heritage: New communication tools based on AR/VR Case study: Palazzo di Città

The present study aims at presenting the application of the Building Information Modeling methodology to the case study of Palazzo di Città, the Turin City Hall, investigating the possibilities of integration of new technologies in Cultural Heritage preservation and valorization. From the survey phase to the communication of the CH to end-users, BIM methodology, combined with the latest digital innovations (AR, VR, 3d Laser Scanner and much more), allows a fast and highly communicative representation of buildings to both professionals and common visitors who interact with the building life-cycle. An important objective of this work is moreover to demonstrate the advantages of adopting and integrating this technologies in Real Estate Management at a national scale, fully testing the adaptability of parametric software and Virtual Reality modeling to complex and highly decorated buildings, confirming the potentiality of BIM software upon an uncommon field: the historic buildings. The case study is in fact Palazzo di Città, the baroque, seventieth century City Hall of Turin. The research fully meets the latest directives of European Union and other International Organizations in the field of digitization of archives and Public Property management, participating to the international community effort to overcome the contemporary deep Construction Field crisis. In particular, the methodology has been focused and adapted to the protection and management of our huge Heritage, founding its objectives on the quest of cost-saving processes and instruments, applied to the management of a CH. Through BIM it is in fact possible to increase the communication and cooperation among all the actors involved in the building life-cycle behaving as a common working platform. Draws, 3D model and database are shared by all the actors and integrated in the same digital structure, where control tools and cooperation can prevent the designers from errors, saving time and money in the construction phase. The particularity of the case study, Palazzo di Città, being contemporarily a CH, a public asset and a working space, allows a deep study of the possibilities of BIM applied to a complex building, touching very important aspects of a historic building management: digitization of the historic information, publication of modeling techniques of complex architectonical elements, transformations reconstruction, energy consumption control, Facility Management, dissemination, virtual reconstructions of the lost appearance and accessibility for people with sensory and motor impairments. Moreover, the last chapters of the study focus on the fruition of this paramount Turin CH, making available for all kind of people interesting and not well known aspects of the history of the building and of the city itself. This part of the research suggests a methodology to translate static 2d images and written descriptions of a CH into living and immersive VR environment, presenting in an interactive way the transformation of the Marble Hall, once called Aula Maior: the room where the Mayor meets his citizens. Besides the aspects related to the valorization and preservation of the CH, the study reserves considerable space to the deepening of technical aspects involving advanced parametric modeling techniques, use of BIM software and all the vital procedures necessary to the generation of an efficient management informative platform. The whole work is intended as a guide for future works, structuring a replicable protocol to achieve an efficient digitization of papery resources into a 3d virtual model

Pristup integraciji tehničkih prostora zasnovan na preslikavanjima iinženjerstvu vođenom modelima

In order to automate development of integration adapters in industrial settings, a model-driven approach to adapter specification is devised. In this approach, a domain-specific modeling language is created to allow specification of mappings between integrated technical spaces. Also proposed is the mapping automation engine that comprises reuse and alignment algorithms. Based on mapping specifications, executable adapters are automatically generated and executed. Results of approach evaluations indicate that it is possible to use a model-driven approach to successfully integrate technical spaces and increase the automation by reusing domainspecific mappings from previously created adapters.За потребе повећања степена аутоматизације развоја адаптера за интеграцију у индустријском окружењу, осмишљен је моделом вођен приступ развоју адаптера. У оквиру овог приступа развијен је наменски језик за спецификацију пресликавања између техничких простора који су предмет интеграције. Приступ обухвата и алгоритме за поравнање и поновно искориштење претходно креираних пресликавања са циљем аутоматизације процеса спецификације. На основу креираних пресликавања, могуће je аутоматски генерисати извршиви код адаптера. У испитивањима приступа, показано је да је могуће успешно применити моделом вођен приступ у интеграцији техничких простора као и да је могуће успешно повећати степен аутоматизације поновним искоришћењем претходно креираних пресликавања.Za potrebe povećanja stepena automatizacije razvoja adaptera za integraciju u industrijskom okruženju, osmišljen je modelom vođen pristup razvoju adaptera. U okviru ovog pristupa razvijen je namenski jezik za specifikaciju preslikavanja između tehničkih prostora koji su predmet integracije. Pristup obuhvata i algoritme za poravnanje i ponovno iskorištenje prethodno kreiranih preslikavanja sa ciljem automatizacije procesa specifikacije. Na osnovu kreiranih preslikavanja, moguće je automatski generisati izvršivi kod adaptera. U ispitivanjima pristupa, pokazano je da je moguće uspešno primeniti modelom vođen pristup u integraciji tehničkih prostora kao i da je moguće uspešno povećati stepen automatizacije ponovnim iskorišćenjem prethodno kreiranih preslikavanja

Synthesis and Assessment Product

This Synthesis and Assessment Product focuses on the connection between the scientific ability to predict climate on seasonal scales and the opportunity to incorporate such understanding into water resource management decisions. It directly addresses decision support experiments and evaluations that have used seasonal-to-interannual forecasts and observational data, and is expected to inform (1) decision makers about the relative success of experiences of others who have experimented with these forecasts and data in resource management; (2) climatologists, hydrologists, and social scientists on how to advance the delivery of decision-support resources that use the most recent forecast products, methodologies, and tools; and (3) science and resource managers as they plan for future investments in research related to forecasts and their role in decision support. It is important to note, however, that while the focus of this Product is on the water resources management sector, the findings within this Synthesis and Assessment Product may be directly transferred to other sectors

Dinamičko formiranje distribuiranog mikro okruženja u računarstvu u oblaku

This thesis presents research in the field of distributed systems. We present the dynamic organization of geodistributed edge nodes into micro data-centers forming micro clouds to cover any arbitrary area and expand capacity, availability, and reliability. A cloud organization is used as an influence with adaptations for a different environment with a clear separation of concerns, and native applications model that can leverage the newly formed system. With the separation of concerns setup, edge-native applications model, and a unified node organization, we are moving towards the idea of edge computing as a service, like any other utility in cloud computing. We also give formal models for all protocols used for the creation of such a system.U sklopu disertacije izvršeno je istraživanje u oblasti distribuiranih sistema. Predstavili smo dinamičku organizaciju geo-distribuiranih čvorova u mikro centre za obradu podataka koji formiraju mikro okruženja računarstva u oblaku kako bi pokrili bilo koje proizvoljno područje i proširili kapacitet, dostupnost i pouzdanost. Koristili smo organizaciju računarstva u oblaku kao inspiraciju, sa adaptacijama za drugačije okruženje sa jasnom podelom nadležnosti, i modelom aplikacija koji može da iskoristi novoformirani sistem. Jasna podela nadležnosti, model aplikacija i dinamička organizacijom čvorova, čine da se predstavljeni model ponude kao i bilo koji drugi uslužni servis. Takođe dajemo formalne modele za sve protokole koji se koriste za stvaranje takvog sistema

Precision health approaches: ethical considerations for health data processing

This thesis provides insights and recommendations on some of the most crucial elements necessary for an effective, legally and ethically sound implementation of precision health approaches in the Swiss context (and beyond), specifically for precision medicine and precision public health. In this regard, this thesis recognizes the centrality of data in these two abovementioned domains, and the ethical and scientific imperative of ensuring the widespread and responsible sharing of high quality health data between the numerous stakeholders involved in healthcare, public health and associated research domains. It also recognizes the need to protect not only the interests of data subjects but also those of data processors. Indeed, it is only through a comprehensive assessment of the needs and expectations of each and every one regarding data sharing activities that sustainable solutions to known ethical and scientific conundrums can be devised and implemented. In addition, the included chapters in this thesis emphasize recommending solutions that could be convincingly applied to real world problems, with the ultimate objective of having a concrete impact on clinical and public health practice and policies, including research activities. Indeed, the strengths of this thesis reside in a careful and in-depth interdisciplinary assessment of the different issues at stake in precision health approaches, with the elaboration of the least disruptive solutions (as far as possible) and recommendations for an easy evaluation and subsequent adoption by relevant stakeholders active in these two domains. This thesis has three main objectives, namely (i) to investigate and identify factors influencing the processing of health data in the Swiss context and suggest some potential solutions and recommendations. A better understanding of these factors is paramount for an effective implementation of precision health approaches given their strong dependence on high quality and easily accessible health datasets; (ii) to identify and explore the ethical, legal and social issues (ELSI) of innovative participatory disease surveillance systems – also falling under precision health approaches – and how research ethics are coping within this field. In addition, this thesis aims to strengthen the ethical approaches currently used to cater for these ELSIs by providing a robust ethical framework; and lastly, (iii) to investigate how precision health approaches might not be able to achieve their social justice and health equity goals, if the impact of structural racism on these initiatives is not given due consideration. After a careful assessment, this thesis provides recommendations and potential actions that could help these precision health approaches adhere to their social justice and health equity goals. This thesis has investigated these three main objectives using both empirical and theoretical research methods. The empirical branch consists of systematic and scoping reviews, both adhering to the PRISMA guidelines, and two interview-based studies carried out with Swiss expert stakeholders. The theoretical branch consists of three chapters, each addressing important aspects concerning precision health approaches

Workflow-Management für Produktentwicklungsprozesse

Workflow-Management-Systeme unterstützen die elektronische Abwicklung von Arbeitsprozessen, sogenannten Workflows. Heutige Systeme erzwingen meist die starre Ausführung vormodellierter Workflows, was ihre praktische Tauglichkeit auf Anwendungsgebiete mit starren Prozessen beschränkt. In vielen Anwendungsbereichen sind Arbeitsprozesse jedoch meist nur semi-strukturiert. Dieses Merkmal ist aufgrund kreativer Teilaufgaben auch typisch für alle Produktentwicklungsprozesse, für die in dieser Arbeit adäquate Modellierungs- und Ausführungskonzepte vorgestellt werden. Diese Konzepte wurden im WEP-Workflow-Management-Systems (WEP = Workflow Management for Engineering Processes) zur Demonstration der Machbarkeit und des praktischen Nutzens prototypisch implementiert