PROTOTYPICAL CASES FOR RETRIEVAL, REUSE, AND KNOWLEDGE MAINTENANCE IN BIOMEDICAL CASE-BASED REASONING

Representing biomedical knowledge is an essential task in biomedical informatics intelligent systems. Case-based reasoning (CBR) holds the promise to represent contextual knowledge in a way that was not possible before with traditional knowledge-based methods. One main issue in biomedical CBR is dealing with the rate of generation of new knowledge in biomedical fields, which often makes the content of a case base partially obsolete. This article proposes to make use of the concept of prototypical case to ensure that a CBR system would keep update with current research advances in the biomedical field. Prototypical cases have served various purposes in biomedical CBR systems, among which to organize and structure the memory, to guide the retrieval as well as the reuse of cases, and to serve as bootstrapping a CBR system memory when real cases are not available in sufficient quantity and/or quality. This paper emphasizes the different roles prototypical cases can play in CBR systems, and presents knowledge maintenance as a very important novel role for these prototypical cases.     

Principal motion components for one-shot gesture recognition

This paper introduces principal motion components (PMC), a new method for one-shot gesture recognition. In the considered scenario a single training video is available for each gesture to be recognized, which limits the application of traditional techniques (e.g., HMMs). In PMC, a 2D map of motion energy is obtained per each pair of consecutive frames in a video. Motion maps associated to a video are processed to obtain a PCA model, which is used for recognition under a reconstruction-error approach. The main benefits of the proposed approach are its simplicity, easiness of implementation, competitive performance and efficiency. We report experimental results in one-shot gesture recognition using the ChaLearn Gesture Dataset; a benchmark comprising more than 50,000 gestures, recorded as both RGB and depth video with a Kinect?camera. Results obtained with PMC are competitive with alternative methods proposed for the same data set.     

Stabilization of the inverted pendulum around its homoclinic orbit

The inverted pendulum has been used as a benchmark for motivating the study of nonlinear control techniques. We propose a simple controller for balancing the inverted pendulum and raise it to its upper equilibrium position while the cart displacement is brought to zero. The control strategy is based on an energy approach of the cart and pendulum system.     

An MDA approach to knowledge engineering

This paper proposes an MDA approach to knowledge engineering, centered on the CommonKADS knowledge model. The latter corresponds to the CIM level of MDA whereas PRR, which represents production rules and rulesets, corresponds to the PIM level. The paper explores the mapping between CommonKADS knowledge models and production rules and rulesets based on PRR. Mapping CommonKADS knowledge models into PRR is very useful, due to the fact that the CIM level remains relatively unexplored, despite its key role in MDA. This motivates our choice to focus on the CIM and PIM levels. Furthermore, the mapping between PIM and PSM (i.e. the implementation of production rules in specific rule-based systems) constitutes less of an issue. To map CommonKADS knowledge models into PRR production rules and rulesets, we propose and illustrate a set of transformations. To ease these transformations, we start by grouping elements of the CommonKADS knowledge models into so-called “inference groups”. We propose and illustrate an algorithm that defines these inference groups automatically. The definition of transformations between models (CIM to PIM levels) requires a specific metamodel for CommonKADS as well as a dedicated metamodel for PRR. Unlike PRR, there is no published CommonKADS metamodel. This paper proposes a comprehensive CommonKADS knowledge metamodel. We describe and discuss an example, applying the whole approach.     

Genetic Elements Orchestrating Lactobacillus crispatus Glycogen Metabolism in the Vagina

Glycogen in the female lower reproductive tract is a major carbon source for colonization and acidification by common vaginal Lactobacillus species, such as Lactobacillus crispatus. Previously, we identified the amylopullulanase encoding gene pulA of Lactobacillus crispatus to correlate with the ability to autonomously utilize glycogen for growth. Here, we further characterize genetic variation and differential regulation of pulA affecting the presence of its gene product on the outer surface layer. We show that alpha-glucan degrading activity dissipates when Lactobacillus crispatus is grown on glucose, maltose and maltotriose, in agreement with carbon catabolite repression elements flanking the pulA gene. Proteome analysis of the S-layer confirmed that the amylopullulanase protein is highly abundant in an S-layer enriched fraction, but not in a strain with a defective amylopullulanase variant or in an amylopullulanase-sufficient strain grown on glucose. In addition, we provide evidence that Lactobacillus crispatus pulA mutants are relevant in vivo, as they are commonly observed in metagenome datasets of human vaginal microbial communities. Analysis of the largest publicly available dataset of 1507 human vaginal metagenomes indicates that among the 270 samples that contain a Lactobacillus crispatus pulA gene, 62 samples (23%) had a defective variant of this gene. Taken together, these results demonstrate that both environmental, as well as genetic factors explain the variation of Lactobacillus crispatus alpha-glucosidases in the vaginal environment.     

The Endothelium and COVID-19: An Increasingly Clear Link Brief Title: Endotheliopathy in COVID-19

The endothelium has a fundamental role in the cardiovascular complications of coronavirus disease 2019 (COVID-19). Infection with severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) particularly affects endothelial cells. The virus binds to the angiotensin-converting enzyme 2 (ACE-2) receptor (present on type 2 alveolar cells, bronchial epithelial cells, and endothelial cells), and induces a cytokine storm. The cytokines tumor necrosis factor alpha, interleukin-1 beta, and interleukin-6 have particular effects on endothelial cells—leading to endothelial dysfunction, endothelial cell death, changes in tight junctions, and vascular hyperpermeability. Under normal conditions, apoptotic endothelial cells are removed into the bloodstream. During COVID-19, however, endothelial cells are detached more rapidly, and do not regenerate as effectively as usual. The loss of the endothelium on the luminal surface abolishes all of the vascular responses mediated by the endothelium and nitric oxide production in particular, which results in greater contractility. Moreover, circulating endothelial cells infected with SARS-CoV-2 act as vectors for viral dissemination by forming clusters that migrate into the circulation and reach distant organs. The cell clusters and the endothelial dysfunction might contribute to the various thromboembolic pathologies observed in COVID-19 by inducing the formation of intravascular microthrombi, as well as by triggering disseminated intravascular coagulation. Here, we review the contributions of endotheliopathy and endothelial-cell-derived extracellular vesicles to the pathogenesis of COVID-19, and discuss therapeutic strategies that target the endothelium in patients with COVID-19.     

On the applicability of the Heliosat-2 method to assess surface solar irradiance in the Intertropical Convergence Zone,French Guiana

Measurements of daily means of surface solar irradiance made at four ground stations in French Guiana are compared to estimates from the HelioClim-3 database produced by the Heliosat-2 method applied to Meteosat satellite images. The bias ranges from 12 W m^?2 (6% of the mean of measurements) to 23 W m^?2 (12%), depending on the stations. The root mean square difference ranges between 23 W m^?2 (11%) and 35 W m^?2 (18%). The correlation coefficient (r) is close to 0.9. Better results are observed during the rainy season than during the dry season. Uncertainties are mainly due to the presence of clouds, large viewing angles of the Meteosat satellite, and limitations of the atmospheric transmittance model under the tropical atmospheric conditions. It is concluded that the Heliosat-2 method provides new knowledge about solar radiation in French Guiana.     

Relevance of the skewness index in DTI exploration of multiple sclerosis

Object  To this day, no parameter can really monitor the progression of multiple sclerosis (MS). In this study, an index the skewness (S) derived from parameters calculated in diffusion tensor imaging (DTI) has been tested on MS patients for its ability to monitor the disease course. Materials and methods  Eighteen patients underwent two examinations within 3 months consisting of a clinical evaluation (EDSS) and DTI acquisitions on a 1.5 T imager. Tensor was calculated thanks to“home-made” software. Mean diffusivity (MD) and fractional anisotropy (FA) histograms were described for normal-appearing white matter (NAWM) and gray matter (GM) of patients with S and also with usually indices peak position (pp) and peak height (ph) for the whole group of patients and for two separate groups according to their clinical status (EDSS  ≤  3 and EDSS  > 3 at month 0). Results  Although no significant clinical evolution is observed over 3 months, S in GM showed a significant shift for both MD/FA histograms towards abnormal values for the whole group of patients (p = 0.02/p = 0.04) and for the group with EDSS  ≤  3 (p = 0.04/p = 0.007), while ph and pp do not. Conclusion  S in GM could be an alternative marker to monitor the disease course before the repercussion on the clinical score.     

A New Strategy to Preserve and Assess Oxygen Consumption in Murine Tissues

Mitochondrial dysfunctions are implicated in several pathologies, such as metabolic, cardiovascular, respiratory, and neurological diseases, as well as in cancer and aging. These metabolic alterations are usually assessed in human or murine samples by mitochondrial respiratory chain enzymatic assays, by measuring the oxygen consumption of intact mitochondria isolated from tissues, or from cells obtained after physical or enzymatic disruption of the tissues. However, these methodologies do not maintain tissue multicellular organization and cell-cell interactions, known to influence mitochondrial metabolism. Here, we develop an optimal model to measure mitochondrial oxygen consumption in heart and lung tissue samples using the XF24 Extracellular Flux Analyzer (Seahorse) and discuss the advantages and limitations of this technological approach. Our results demonstrate that tissue organization, as well as mitochondrial ultrastructure and respiratory function, are preserved in heart and lung tissues freshly processed or after overnight conservation at 4 °C. Using this method, we confirmed the repeatedly reported obesity-associated mitochondrial dysfunction in the heart and extended it to the lungs. We set up and validated a new strategy to optimally assess mitochondrial function in murine tissues. As such, this method is of great potential interest for monitoring mitochondrial function in cohort samples.