Ensemble-based genetic algorithm explainer with automized image segmentation: A case study on melanoma detection dataset

Explainable Artificial Intelligence (XAI) makes AI understandable to the human user particularly when the model is complex and opaque. Local Interpretable Model-agnostic Explanations (LIME) has an image explainer package that is used to explain deep learning models. The image explainer of LIME needs some parameters to be manually tuned by the expert in advance, including the number of top features to be seen and the number of superpixels in the segmented input image. This parameter tuning is a time-consuming task. Hence, with the aim of developing an image explainer that automizes image segmentation, this paper proposes Ensemblebased Genetic Algorithm Explainer (EGAE) for melanoma cancer detection that automatically detects and presents the informative sections of the image to the user. EGAE has three phases. First, the sparsity of chromosomes in GAs is determined heuristically. Then, multiple GAs are executed consecutively. However, the difference between these GAs are in different number of superpixels in the input image that result in different chromosome lengths. Finally, the results of GAs are ensembled using consensus and majority votings. This paper also introduces how Euclidean distance can be used to calculate the distance between the actual explanation (delineated by experts) and the calculated explanation (computed by the explainer) for accuracy measurement. Experimental results on a melanoma dataset show that EGAE automatically detects informative lesions, and it also improves the accuracy of explanation in comparison with LIME efficiently. The python codes for EGAE, the ground truths delineated by clinicians, and the melanoma detection dataset are available at https://github.com/KhaosResearch/EGAEThis work has been partially funded by grant PID2020-112540RBC41 (funded by MCIN/AEI/10.13039/501100011033/, Spain), AETHERUMA, Spain (A smart data holistic approach for context-aware data analytics: semantics and context exploitation). Funding for open access charge: Universidad de Málaga/CBUA. Additionally, we thank Dr. Miguel Ángel Berciano Guerrero from Unidad de Oncología Intercentros, Hospitales Univesitarios Regional Virgen de la Victoria de Málaga, and Instituto de Investigaciones Biomédicas (IBIMA), Málaga, Spain, for his support in images selection and general medical orientation in the particular case of Melanoma

GENECI: A novel evolutionary machine learning consensus-based approach for the inference of gene regulatory networks

Gene regulatory networks define the interactions between DNA products and other substances in cells. Increasing knowledge of these networks improves the level of detail with which the processes that trigger different diseases are described and fosters the development of new therapeutic targets. These networks are usually represented by graphs, and the primary sources for their correct construction are usually time series from differential expression data. The inference of networks from this data type has been approached differently in the literature. Mostly, computational learning techniques have been implemented, which have finally shown some specialization in specific datasets. For this reason, the need arises to create new and more robust strategies for reaching a consensus based on previous results to gain a particular capacity for generalization. This paper presents GENECI (GEne NEtwork Consensus Inference), an evolutionary machine learning approach that acts as an organizer for constructing ensembles to process the results of the main inference techniques reported in the literature and to optimize the consensus network derived from them, according to their confidence levels and topological characteristics. After its design, the proposal was confronted with datasets collected from academic benchmarks (DREAM challenges and IRMA network) to quantify its accuracy. Subsequently, it was applied to a real-world biological network of melanoma patients whose results could be contrasted with medical research collected in the literature. Finally, it has been proved that its ability to optimize the consensus of several networks leads to outstanding robustness and accuracy, gaining a certain generalization capacity after facing the inference of multiple datasetsThis work has been partially funded by grant (funded by MCIN/AEI/10.13039/501100011033/) PID2020-112540RB-C41, AETHER-UMA, Spain (A smart data holistic approach for context-aware data analytics: semantics and context exploitation) and Andalusian PAIDI program, Spain with grant P18-RT-2799. Funding for open access charge: Universidad de Málaga, Spain/CBUA. Adrián SeguraOrtiz is supported by Grant FPU21/03837 (Spanish Ministry of Science, Innovation and Universities, Spain

Digital literacy and the use of augmented reality in teaching science in Secondary Education

Hoy día la tecnología ocupa un lugar destacado en la sociedad, por lo que es fundamental para desenvolverse en ella con éxito tener adquirida la competencia digital. Los docentes deben desarrollarla de forma adecuada para que su labor educativa sea eficaz y para poder transmitirla a su alumnado. Un ejemplo del uso de la tecnología en educación que se encuentra en auge es la utilización didáctica de la Realidad Aumentada, que ofrece al área de las ciencias una gran cantidad de posibilidades para facilitar el proceso de enseñanza-aprendizaje. El objetivo que se plantea en el presente estudio es conocer la incidencia de la competencia digital en el empleo de la realidad aumentada como recurso didáctico en la impartición de clases relacionadas con las ciencias. El método utilizado es de tipo cuantitativo no experimental, de corte descriptivo, correlacional y con carácter predictivo. La recogida de datos se ha llevado a cabo mediante un cuestionario ad hoc sobre competencia digital docente y realidad aumentada, con diferentes niveles de respuesta. Los resultados muestran que la realidad aumentada es un recurso que ha sido usado por parte de los docentes que imparten ciencias, presentando estos un nivel de competencia digital medio. Se concluye afirmando que los docentes que utilizan la realidad aumentada presentan más competencia digital que aquellos que no lo usan.Today, technology is a major issue in society, so it is essential to have acquired digital competence in order to be successful in it. An example of the growing use of technology in education is the didactic use of Augmented Reality, which offers the area of science a wealth of possibilities to facilitate the teaching-learning process. The aim of this study is to understand the impact of digital competence on the use of augmented reality as a teaching resource in science-related classes. The method used is quantitative, non-experimental, descriptive, correlational and predictive. The data collection has been carried out through an ad hoc questionnaire on digital teaching competence and augmented reality with different levels of response. The results show that augmented reality is a resource that has been used by teachers teaching science, presenting them with an average level of digital competence. We conclude by stating that teachers who use augmented reality are more digitally competent than those who do not.

Evaluating the cancer therapeutic potential of cardiac glycosides

Cardiac glycosides, also known as cardiotonic steroids, are a group of natural products that share a steroid-like structure with an unsaturated lactone ring and the ability to induce cardiotonic effects mediated by a selective inhibition of the Na(+)/K(+)-ATPase. Cardiac glycosides have been used for many years in the treatment of cardiac congestion and some types of cardiac arrhythmias. Recent data suggest that cardiac glycosides may also be useful in the treatment of cancer. These compounds typically inhibit cancer cell proliferation at nanomolar concentrations, and recent high-throughput screenings of drug libraries have therefore identified cardiac glycosides as potent inhibitors of cancer cell growth. Cardiac glycosides can also block tumor growth in rodent models, which further supports the idea that they have potential for cancer therapy. Evidence also suggests, however, that cardiac glycosides may not inhibit cancer cell proliferation selectively and the potent inhibition of tumor growth induced by cardiac glycosides in mice xenografted with human cancer cells is probably an experimental artifact caused by their ability to selectively kill human cells versus rodent cells. This paper reviews such evidence and discusses experimental approaches that could be used to reveal the cancer therapeutic potential of cardiac glycosides in preclinical studie

Feasibility Study of a Proton Irradiation Facility for Radiobiological Measurements at an 18 MeV Cyclotron

A feasibility study of an experimental setup for the irradiation of biological samples at the cyclotron facility installed at the National Centre of Accelerators (Seville, Spain) is presented. This cyclotron, which counts on an external beam line for interdisciplinary research purposes, produces an 18 MeV proton beam, which is suitable for the irradiation of mono-layer cultures for the measurement of proton cell damages and Relative Biological Effectiveness (RBE) at energies below the beam nominal value. Measurements of this kind are of interest for proton therapy, since the variation of proton RBE at the distal edge of the Bragg curve may have implications in clinical proton therapy treatments. In the following, the characteristics of the beam line and the solutions implemented for the irradiation of biological samples are described. When dealing with the irradiation of cell cultures, low beam intensities and broad homogeneous irradiation fields are required, in order to assure that all the cells receive the same dose with a suitable dose rate. At the cyclotron, these constraints have been achieved by completely defocusing the beam, intercepting the beam path with tungsten scattering foils and varying the exit-window-to-sample distance. The properties of the proton beam thus obtained have been analysed and compared with Monte Carlo simulations. The results of this comparison, as well as the experimental measurement of the lateral dose profiles expected at the position of samples are presented. Meaningful dose rates of about 2–3 Gy/min have been obtained. Homogeneous lateral dose profiles, with maximum deviations of 5%, have been measured at a distance of approximately 50 cm in air from the exit window, placing a tungsten scattering foil of 200 μm in the beam path

New markers for human ovarian cancer that link platinum resistance to the cancer stem cell phenotype and define new therapeutic combinations and diagnostic tools

BACKGROUND: Ovarian cancer is the leading cause of gynecologic cancer-related death, due in part to a late diagnosis and a high rate of recurrence. Primary and acquired platinum resistance is related to a low response probability to subsequent lines of treatment and to a poor survival. Therefore, a comprehensive understanding of the mechanisms that drive platinum resistance is urgently needed. METHODS: We used bioinformatics analysis of public databases and RT-qPCR to quantitate the relative gene expression profiles of ovarian tumors. Many of the dysregulated genes were cancer stem cell (CSC) factors, and we analyzed its relation to therapeutic resistance in human primary tumors. We also performed clustering and in vitro analyses of therapy cytotoxicity in tumorspheres. RESULTS: Using bioinformatics analysis, we identified transcriptional targets that are common endpoints of genetic alterations linked to platinum resistance in ovarian tumors. Most of these genes are grouped into 4 main clusters related to the CSC phenotype, including the DNA damage, Notch and C-KIT/MAPK/MEK pathways. The relative expression of these genes, either alone or in combination, is related to prognosis and provide a connection between platinum resistance and the CSC phenotype. However, the expression of the CSC-related markers was heterogeneous in the resistant tumors, most likely because there were different CSC pools. Furthermore, our in vitro results showed that the inhibition of the CSC-related targets lying at the intersection of the DNA damage, Notch and C-KIT/MAPK/MEK pathways sensitize CSC-enriched tumorspheres to platinum therapies, suggesting a new option for the treatment of patients with platinum-resistant ovarian cancer. CONCLUSIONS: The current study presents a new approach to target the physiology of resistant ovarian tumor cells through the identification of core biomarkers. We hypothesize that the identified mutations confer platinum resistance by converging to activate a few pathways and to induce the expression of a few common, measurable and targetable essential genes. These pathways include the DNA damage, Notch and C-KIT/MAPK/MEK pathways. Finally, the combined inhibition of one of these pathways with platinum treatment increases the sensitivity of CSC-enriched tumorspheres to low doses of platinum, suggesting a new treatment for ovarian cancerSpanish Ministry of Education FPU12/01380Spanish Ministry of Economy and Competitivity, Plan Estatal de I + D + I 2013–2016Spanish Ministry of Science, Innovation and Universities (RTI2018–097455-B-I00)CIBER de Cáncer (CD16/12/00275)Spanish Consejería de Salud of the Junta de Andalucia (PI-0397-2017

Evaluación de recursos hídricos y balance hidrogeológico en acuíferos kársticos de montaña. Caso de la Sierra de Grazalema (Cádiz, España)

En este trabajo se presenta el procedimiento para evaluar los recursos hídricos y realizar el balance hidrogeológico de los acuíferos kársticos de la Sierra de Grazalema (provincia de Cádiz, España), durante el periodo 2012/13-2014/15. Por una parte se han cuantificado las salidas de los acuíferos a partir de la integración del hidrograma de los manantiales y por otra se han estimado las entradas, mediante diversas ecuaciones de balance hídrico del suelo: Thornthwaite, Blaney-Criddle y Hargreaves. Los valores medios anuales de recursos determinados con la ecuación de Hargreaves son los que más se asemejan a las salidas medidas en la mayoría de los acuíferos. Sin embargo, en uno de ellos se ha detectado un exceso medio anual de 31 hm3/año de las entradas con respecto a las salidas, que podría estar ligado a transferencias subterráneas a otros sistemas kársticos circundantesUniversidad de Málaga. Campus de Excelencia Internacional Andalucía Tec

Optical imaging spectroscopy for rapid, primary screening of SARS-CoV-2: a proof of concept

Effective testing is essential to control the coronavirus disease 2019 (COVID-19) transmission. Here we report a-proof-of-concept study on hyperspectral image analysis in the visible and near-infrared range for primary screening at the point-of-care of SARS-CoV-2. We apply spectral feature descriptors, partial least square-discriminant analysis, and artificial intelligence to extract information from optical diffuse reflectance measurements from 5 µL fluid samples at pixel, droplet, and patient levels. We discern preparations of engineered lentiviral particles pseudotyped with the spike protein of the SARS-CoV-2 from those with the G protein of the vesicular stomatitis virus in saline solution and artificial saliva. We report a quantitative analysis of 72 samples of nasopharyngeal exudate in a range of SARS-CoV-2 viral loads, and a descriptive study of another 32 fresh human saliva samples. Sensitivity for classification of exudates was 100% with peak specificity of 87.5% for discernment from PCR-negative but symptomatic cases. Proposed technology is reagent-free, fast, and scalable, and could substantially reduce the number of molecular tests currently required for COVID-19 mass screening strategies even in resource-limited settings.Ministerio de Ciencia e Innovación, 2020 Emergency Call for Research Projects about the SARS-CoV-2 virus and the COVID-19 disease Instituto de Salud Carlos III by Grant Number EQC2019-006240-PComisión Europea, Joint Research Center (JRC) HUMAINT project

Plasmon-enhanced magneto-optical activity in ferromagnetic membranes

Experimental and theoretical evidence of plasmon-enhanced Kerr rotation in purely ferromagnetic membranes with sufficiently small dimensions to be out of extraordinary optical transmission conditions (45 nm pore diameter, 90nm lattice constant), is reported in this work. It is shown that the spectral location of the enhanced Kerr rotation region varies as the refractive index of the material inside the pore is modified. A similar behavior is obtained if the pore radius changes while keeping the pore concentration unchanged. Those are clear signatures indicating that localized surface plasmon resonances propagating along the pores govern the magneto-optical response of the membraneWe acknowledge Spanish MICINN (Grant Nos. MAT2008-06765-C02-01/NAN, CSD2008-00023, and MAT2007-65420-C02-01), CSIC (Grant No. PIF 200560F0121 BIOPTOMAG), CM(Grant No. S-0505/MAT/0194 NANOMAGNET), and European Commission (Grant No. NMP3-SL-2008-214107-Nanomagma) for financial support.Peer reviewe

Coordinated downregulation of Spinophilin and the catalytic subunits of PP1, PPP1CA/B/C, contributes to a worse prognosis in lung cancer

The scaffold protein Spinophilin (Spinophilin, PPP1R9B) is one of the regulatory subunits of phosphatase-1 (PP1), directing it to distinct subcellular locations and targets. The loss of Spinophilin reduces PP1 targeting to pRb, thereby maintaining higher levels of phosphorylated pRb. Spinophilin is absent or reduced in approximately 40% of human lung tumors, correlating with the malignant grade. However, little is known about the relevance of the coordinated activity or presence of Spinophilin and its reported catalytic partners in the prognosis of lung cancer. In the present work, we show that the downregulation of Spinophilin, either by protein or mRNA, is related to a worse prognosis in lung tumors. This effect is more relevant in squamous cell carcinoma, SCC, than in adenocarcinoma. Downregulation of Spinophilin is related to a decrease in the levels of its partners PPP1CA/B/C, the catalytic subunits of PP1. A decrease in these subunits is also related to prognosis in SCC and, in combination with a decrease in Spinophilin, are markers of a poor prognosis in these tumors. The analysis of the genes that correlate to Spinophilin in lung tumors showed clear enrichment in ATP biosynthesis and protein degradation GO pathways. The analysis of the response to several common and pathway-related drugs indicates a direct correlation between the Spinophilin/PPP1Cs ratio and the response to oxaliplatin and bortezomib. This finding indicates that this ratio may be a good predictive biomarker for the activity of the drugs in these tumors with a poor prognosis.España, Mineco Plan Estatal de I+D+I 2013-2016España, ISCIII Fis: PI15/00045CIBER de Cáncer CB16/12/00275, CB16/12/00443, CB16/12/00442España, Junta de Andalucía, Consejeria de Ciencia e Innovacion CTS-1848España, Junta de Andalucía, Consejeria de Salud PI-0096-201