PhenoExam: gene set analyses through integration of different phenotype databases.

BACKGROUND: Gene set enrichment analysis (detecting phenotypic terms that emerge as significant in a set of genes) plays an important role in bioinformatics focused on diseases of genetic basis. To facilitate phenotype-oriented gene set analysis, we developed PhenoExam, a freely available R package for tool developers and a web interface for users, which performs: (1) phenotype and disease enrichment analysis on a gene set; (2) measures statistically significant phenotype similarities between gene sets and (3) detects significant differential phenotypes or disease terms across different databases. RESULTS: PhenoExam generates sensitive and accurate phenotype enrichment analyses. It is also effective in segregating gene sets or Mendelian diseases with very similar phenotypes. We tested the tool with two similar diseases (Parkinson and dystonia), to show phenotype-level similarities but also potentially interesting differences. Moreover, we used PhenoExam to validate computationally predicted new genes potentially associated with epilepsy. CONCLUSIONS: We developed PhenoExam, a freely available R package and Web application, which performs phenotype enrichment and disease enrichment analysis on gene set G, measures statistically significant phenotype similarities between pairs of gene sets G and G' and detects statistically significant exclusive phenotypes or disease terms, across different databases. We proved with simulations and real cases that it is useful to distinguish between gene sets or diseases with very similar phenotypes. Github R package URL is https://github.com/alexcis95/PhenoExam . Shiny App URL is https://alejandrocisterna.shinyapps.io/phenoexamweb/ .

CIoTVID: Towards an Open IoT-Platform for Infective Pandemic Diseases such as COVID-19.

The factors affecting the penetration of certain diseases such as COVID-19 in society are still unknown. Internet of Things (IoT) technologies can play a crucial role during the time of crisis and they can provide a more holistic view of the reasons that govern the outbreak of a contagious disease. The understanding of COVID-19 will be enriched by the analysis of data related to the phenomena, and this data can be collected using IoT sensors. In this paper, we show an integrated solution based on IoT technologies that can serve as opportunistic health data acquisition agents for combating the pandemic of COVID-19, named CIoTVID. The platform is composed of four layers-data acquisition, data aggregation, machine intelligence and services, within the solution. To demonstrate its validity, the solution has been tested with a use case based on creating a classifier of medical conditions using real data of voice, performing successfully. The layer of data aggregation is particularly relevant in this kind of solution as the data coming from medical devices has a very different nature to that coming from electronic sensors. Due to the adaptability of the platform to heterogeneous data and volumes of data; individuals, policymakers, and clinics could benefit from it to fight the propagation of the pandemic.

IoTCrawler: Challenges and Solutions for Searching the Internet of Things.

Due to the rapid development of the Internet of Things (IoT) and consequently, the availability of more and more IoT data sources, mechanisms for searching and integrating IoT data sources become essential to leverage all relevant data for improving processes and services. This paper presents the IoT search framework IoTCrawler. The IoTCrawler framework is not only another IoT framework, it is a system of systems which connects existing solutions to offer interoperability and to overcome data fragmentation. In addition to its domain-independent design, IoTCrawler features a layered approach, offering solutions for crawling, indexing and searching IoT data sources, while ensuring privacy and security, adaptivity and reliability. The concept is proven by addressing a list of requirements defined for searching the IoT and an extensive evaluation. In addition, real world use cases showcase the applicability of the framework and provide examples of how it can be instantiated for new scenarios.

Commissioning of the Controlled and Automatized Testing Facility for Human Behavior and Control (CASITA).

Human behavior is one of the most challenging aspects in the understanding of building physics. The need to evaluate it requires controlled environments and facilities in which researchers can test their methods. In this paper, we present the commissioning of the Controlled and Automatized Testing Facility for Human Behavior (CASITA). This is a controlled space emulation of an office or flat, with more than 20 environmental sensors, 5 electrical meters, and 10 actuators. Our contribution shown in this paper is the development of an infrastructure-Artificial Intelligence (AI) model pair that is perfectly integrated for the study of a variety of human energy use aspects. This facility will help to perform studies about human behavior in a controlled space. To verify this, we have tested this emulation for 60 days, in which equipment was turned on and off, the settings of the conditioning system were modified remotely, and lighting operation was similar to that in real behaviors. This period of commissioning generated 74.4 GB of raw data including high-frequency measurements. This work has shown that CASITA performs beyond expectations and that sensors and actuators could enable research on a variety of disciplines related to building physics and human behavior. Also, we have tested the PROPHET software, which was previously used in other disciplines and found that it could be an excellent complement to CASITA for experiments that require the prediction of several pertinent variables in a given study. Our contribution has also been to proof that this package is an ideal "soft" addition to the infrastructure. A case study forecasting energy consumption has been performed, concluding that the facility and the software PROPHET have a great potential for research and an outstanding accuracy.

Providing Personalized Energy Management and Awareness Services for Energy Efficiency in Smart Buildings.

Considering that the largest part of end-use energy consumption worldwide is associated with the buildings sector, there is an inherent need for the conceptualization, specification, implementation, and instantiation of novel solutions in smart buildings, able to achieve significant reductions in energy consumption through the adoption of energy efficient techniques and the active engagement of the occupants. Towards the design of such solutions, the identification of the main energy consuming factors, trends, and patterns, along with the appropriate modeling and understanding of the occupants' behavior and the potential for the adoption of environmentally-friendly lifestyle changes have to be realized. In the current article, an innovative energy-aware information technology (IT) ecosystem is presented, aiming to support the design and development of novel personalized energy management and awareness services that can lead to occupants' behavioral change towards actions that can have a positive impact on energy efficiency. Novel information and communication technologies (ICT) are exploited towards this direction, related mainly to the evolution of the Internet of Things (IoT), data modeling, management and fusion, big data analytics, and personalized recommendation mechanisms. The combination of such technologies has resulted in an open and extensible architectural approach able to exploit in a homogeneous, efficient and scalable way the vast amount of energy, environmental, and behavioral data collected in energy efficiency campaigns and lead to the design of energy management and awareness services targeted to the occupants' lifestyles. The overall layered architectural approach is detailed, including design and instantiation aspects based on the selection of set of available technologies and tools. Initial results from the usage of the proposed energy aware IT ecosystem in a pilot site at the University of Murcia are presented along with a set of identified open issues for future research.

PLEIAData: consumption, HVAC, temperature, weather and motion sensor data for smart buildings applications.

The current cost that energy represents is crucial in a field like climate control which has high energy demands, therefore its reduction must be prioritized. The expansion of ICT and IoT come with an extensive deployment of sensors and computation infrastructure creating an opportunity to analyze and optimize energy management. Data on building internal and external conditions is essential for developing efficient control strategies in order to minimize energy consumption while maintaining users' comfort inside. We here present a dataset that provides key features that could be useful for a wide range of applications in the context of modeling temperature and consumption via Artificial Intelligence algorithms. The data gathering has taken place for almost 1 year in the Pleiades building of the University of Murcia, which is a pilot building of the European project PHOENIX aiming to improve building energy efficiency.

The correlation between point-of-care ultrasound and digital tomosynthesis when used with suspected COVID-19 pneumonia patients in primary care.

BACKGROUND: The use of lung ultrasound (LU) with COVID-19 pneumonia patients should be validated in the field of primary care (PC). Our study aims to evaluate the correlation between LU and radiographic imaging in PC patients with suspected COVID-19 pneumonia. METHODS: This observational, prospective and multicentre study was carried out with patients from a PC health area whose tests for COVID-19 and suspected pneumonia had been positive and who then underwent LU and a digital tomosynthesis (DT). Four PC physicians obtained data regarding the patients' symptoms, examination, medical history and ultrasound data for 12 lung fields: the total amount of B lines (zero to four per field), the irregularity of the pleural line, subpleural consolidation, lung consolidation and pleural effusion. These data were subsequently correlated with the presence of pneumonia by means of DT, the need for hospital admission and a consultation in the hospital emergency department in the following 15 days. RESULTS: The study was carried out between November 2020 and January 2021 with 70 patients (40 of whom had pneumonia, confirmed by means of DT). Those with pneumonia were older, had a higher proportion of arterial hypertension and lower oxygen saturation (sO2). The number of B lines was higher in patients with pneumonia (16.53 vs. 4.3, p < 0.001). The area under the curve for LU was 0.87 (95% CI 0.78-0.96, p < 0.001), and when establishing a cut-off point of six B lines or more, the sensitivity was 0.875 (95% CI 0.77-0.98, p < 0.05), the specificity was 0.833 (95% CI 0.692-0.975, p < 0.05), the positive-likelihood ratio was 5.25 (95% CI 2.34-11.79, p < 0.05) and the negative-likelihood ratio was 0.15 (95% CI 0.07-0.34, p < 0.05). An age of ≥ 55 and a higher number of B lines were associated with admission. Patients who required admission (n = 7) met at least one of the following criteria: ≥ 55 years of age, sO2 ≤ 95%, presence of at least one subpleural consolidation or ≥ 21 B lines. CONCLUSIONS: LU has great sensitivity and specificity for the diagnosis of COVID-19 pneumonia in PC. Clinical ultrasound findings, along with age and saturation, could, therefore, improve decision-making in this field.