35436 research outputs found
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Advancing edge-based clustering and graph embedding for biological network analysis: a case study in RASopathies
Full text linkUnderstanding and predicting biological processes from protein–protein interaction (PPI) networks requires accurate and efficient representations of their structure. However, many existing methods fail to capture the complex, overlapping modular structure of biological systems. To address this, we propose a network embedding strategy that improves both biological interpretability and predictive power. By transforming networks into a low-dimensional space while preserving key topological properties, embedding enables the discovery of novel functional relationships. Pre-clustering a network before embedding enhances representation quality, i.e. the ability to preserve meaningful structural and functional properties in the embedding space. However, traditional non-overlapping clustering methods can introduce bias by ignoring the overlapping nature of biological communities. We overcome this limitation by integrating the Hierarchical Link Clustering (HLC) algorithm into an embedding workflow tailored for large, weighted, undirected networks. First, we introduce two optimized HLC implementations for Python and R, both outperforming existing methods in clustering accuracy and scalability. Then, by restricting random walks to HLC-defined communities, we improve the representation of biological pathways, as shown using Reactome on the human PPI network. We also apply our full cluster embedding workflow to analyze RASopathies, a group of interrelated disorders with a diverse range of phenotypes, caused by mutations in genes from the RAS/MAPK pathway. This approach was used not only to represent known pathways, but also to identify potential novel gene candidates associated with RASopathies, including Noonan and Costello syndrome. HLC implementations are available in the CDLIB library (https://github.com/GiulioRossetti/cdlib), and at https://github.com/jimrperkins/linkcomm for Python and R, respectively.Funding for open access charge: Universidad de Málaga / CBU
Towards the quantum-safe web: benchmarking post-quantum TLS
Full text linkThe transition to a quantum-resistant Internet is a
complex process that depends on the integration of post-quantum
cryptographic primitives into existing security protocols. This
paper analyzes the impact that the primitives selected by NIST
in their post-quantum cryptography competition has on a critical
Internet security protocol, the TLS protocol. The analysis is
facilitated by a framework that enables the implementation
of an evaluation scenario in which different post-quantum
primitives can be tested under identical conditions, ensuring
a fair comparison. Our results indicate that the computational
overhead introduced by current post-quantum standards in TLS
is comparable to that of traditional algorithms, and even more
efficient at high security levels. However, their significant impact
on data transmission constrains the transition to a full-fledged
quantum-safe web.Funding for open access charge: Universidad de Málaga/CBUA
Integrative Signal Processing and Explainable Artificial Intelligence for Functional Connectivity Modeling in Language Disorders.
Full text linkThis thesis sets the stage for early diagnosis and individualized interventions for language disorders,
with implications that extend to other neurological conditions.This thesis explores the integration of advanced signal processing techniques and Explainable Artificial Intelligence (XAI) methodologies to enhance the understanding and modeling of functional connectivity of EEG signals in the context of language disorders, particularly Developmental Dyslexia (DD). Developmental dyslexia is a neurobiological condition affecting reading skills linked to neural synchronization deficits, making it a prime candidate for innovative diagnostic approaches.
The approach uses non-invasive brain recording techniques, mainly Electroencephalogram (EEG), to assess connectivity through Cross Frequency Coupling (CFC) metrics. A methodological framework is established, combining classical signal processing with the design of Deep Learning (DL) architectures, including Convolutional Neural Network (CNN) and Recurrent Neural Network (RNN). These models are designed to capture complex patterns in EEG data while maintaining interpretability through XAI techniques like SHapley Additive exPlanations (SHAP) or attention layers in the network architecture. These methods are also used to evaluate the lateralization effect in language processing. Key contributions include the development of novel deep learning architectures tailored for Phase-To-Amplitude Coupling (PAC) estimation, classification methods for differential diagnosis, and explainable tools to aid clinicians in understanding EEG based connectivity metrics. The proposed models demonstrate improved accuracy in identifying dyslexic neural patterns, highlighting the role of neural synchronization deficits in language processing anomalies. Moreover, different entrainment profiles to auditory stimuli were found when studying local and long-range neural coupling by
means of CFC. The findings advance the field of neurodiagnostics by offering robust, interpretable AI-driven methods to study functional connectivity
Evaluation of a virtual objective structured clinical examination in the metaverse (Second Life) to assess the clinical skills in emergency radiology of medical students in Spain: a cross-sectional study
Full text linkPurpose: The objective structured clinical examination (OSCE) is an effective but resource-intensive tool for assessing clinical competence. This study hypothesized that imple-menting a virtual OSCE in the Second Life (SL) platform in the metaverse as a cost-effective alternative will effectively assess and enhance clinical skills in emergency radiology while being feasible and well-received. The aim was to evaluate a virtual radiology OSCE in SL as a formative assessment, focusing on feasibility, educational impact, and students’ perceptions.
Methods: Two virtual 6-station OSCE rooms dedicated to emergency radiology were developed in SL. Sixth-year medical students completed the OSCE during a 1-hour session in 2022–2023, followed by feedback including a correction checklist, individual scores, and group comparisons. Students completed a questionnaire with Likert-scale questions, a 10-point rating, and open-ended comments. Quantitative data were analyzed using the Student t-test and the Mann-Whitney U test, and qualitative data through thematic analysis. Results: In total, 163 students participated, achieving mean scores of 5.1±1.4 and 4.9±1.3 (out of 10) in the 2 virtual OSCE rooms, respectively (P=0.287). One hundred seventeen students evaluated the OSCE, praising the teaching staff (9.3±1.0), project organization (8.8±1.2), OSCE environment (8.7±1.5), training usefulness (8.6±1.5), and formative self-assessment (8.5±1.4). Likert-scale questions and students’ open-ended comments highlighted the virtual environment’s attractiveness, case selection, self-evaluation usefulness, project excellence, and training impact. Technical difficulties were reported by 13 students (8%).
Conclusion: This study demonstrated the feasibility of incorporating formative OSCEs in SL as a useful teaching tool for undergraduate radiology education, which was cost-effec-tive and highly valued by students.Educational Innovation Project of the University of Malaga PIE22-045
Los Asensio de la Cerda, una “revelación” en la escultura andaluza del XVIII. Reflexiones y nuevas atribuciones post scriptvm
No full textLa editorial sólo da permiso para acceder a los metadatos.La publicación en 2023 de nuestra monografía dedicada a los Asensio
de la Cerda marcó un punto de inflexion en la historiografía sobre la escultura andaluza
del XVIII. Un artículo de 2006 fue la primera avanzadilla sobre una familia
de escultores que ocupó un lugar relevante en el panorama artistico de su tiempo.
El presente trabajo propone una reflexión sobre la trama investigadora que permitió resolver, entre ambas fechas, numerosas incógnitas sobre la saga y sus circunstancias. En momentos sucesivos han venido prodigándose aportaciones de varios investigadores que han permitido generar entre todos un trabajo colaborativo para construir una vision total e integradora sobre el particular. Asimismo, presentamos aquí nuevas propuestas atributivas
Multi-scale Temporal Pose analysis for Gait Recognition
No full texthttps://www.springernature.com/gp/open-science/policies/book-policiesThe problem of gait recognition has primarily focused on using silhouette or visual modalities to describe the gait cycle. While these methods offer rich representations, they are heavily influenced by visual covariates like body contours or carrying objects. Pose-based methods provide greater robustness against these covariates, but current approaches have yet to effectively extract rich features from pose sequences, leading to suboptimal performance. In this work, we introduce MuSTGaitPose, a model architecture that implements multi-scale temporal analysis of pose sequences to extract richer gait features. Our model features the Multi-scale Temporal Block (MuST Block), which scans pose sequences at multiple time scales to identify key temporal patterns at each scale. We also developed Multi-scale Temporal Attention Fusion (MuSTAF) to optimally aggregate the multi-scale features based on their relative importance at each spatial and temporal location. Thus, our approach produces a combined feature that emphasizes the most relevant gait patterns across all gridded time scales. Additionally, we leverage pose heatmaps for a richer descriptor. Extensive experiments show that our approach outperforms previous pose-based methods, achieving mean Rank-1 accuracies of 90.9% on the CASIA-B and 86.2% on the SUSTech1K datasets, as well as a true acceptance rate of 95.8% at a false acceptance rate of 1% on the FVG-B dataset
Resting-state functional connectivity alterations in post-stroke cognitive impairment: a systematic review
Full text linkPost-stroke cognitive impairment is a common and highly disabling multi-domain cognitive decline with unclear pathophysiological mechanisms. Its extent may be predicted by functional neuroimaging techniques, which could enhance our understanding of its underlying pathophysiology. Synthesize the state-of-the-art knowledge on resting-state functional magnetic resonance imaging findings in post-stroke cognitive impairment, their correlation with cognitive performance and the secondary compensatory connectivity changes. We performed a qualitative systematic literature review of reported data of resting-state functional magnetic resonance imaging abnormalities in post-stroke cognitive impairment, consulting the electronic databases Medline, Scopus, Web of Science, Cochrane, and BASE until June 2024. We selected 23 studies. They reported several key brain areas and network abnormalities associated with post-stroke cognitive impairment compared to controls and non-demented patients. The main areas with decreased functional connectivity were the medial prefrontal cortex, the inferior frontal gyrus, the posterior and anterior cingulate cortex, the precuneus and the hippocampus. The principal network altered was the default mode network, which includes the majority of the brain structures previously mentioned. Additionally, increased functional connectivity in other contralesionally areas may represent maladaptive or compensatory changes post-stroke. Resting-state functional magnetic resonance imaging is a promising tool for studying functional changes associated with post-stroke cognitive impairment. It may enhance our understanding of its pathophysiology and improve selection of suitable period or candidates for cognitive rehabilitation.Funding for open access charge: Universidad de Málaga / CBU
Análisis de los factores predictores de recidiva de hepatocarcinoma tras trasplante hepático: 20 años de experiencia de un equipo de trasplante.
Full text linkAntecedentes. El carcinoma hepatocelular (CHC) es un tumor con alta mortalidad a nivel global. La mayoría de los CHC se desarrollan sobre hepatopatías crónicas en estadios avanzados. El alto riesgo de CHC en este grupo de pacientes justifica la aplicación de cribados. El trasplante hepático (TH) es una opción de tratamiento curativo en casos seleccionados de CHC sobre hígado cirrótico. La recidiva de CHC es un factor importante que afecta a la supervivencia de los pacientes trasplantados. En los últimos años, se han desarrollado múltiples modelos para identificar a los pacientes con mayor riesgo de recidiva de CHC tras el TH.
Material y métodos. Estudio de cohortes retrospectivo y unicéntrico en el que se analizaron los pacientes trasplantados por CHC durante los 20 años de experiencia del programa de trasplante en nuestro centro. Se evaluó la supervivencia de los pacientes trasplantados por CHC, la recurrencia del CHC postrasplante y la influencia de los distintos factores descritos en la literatura como relacionados con la recurrencia. Como novedad, se compararon los resultados obtenidos entre los dos periodos del programa de trasplante (1995-2010 y 2010-2020).
Resultados. Se incluyeron 265 pacientes en el estudio. La supervivencia global fue del 68% a los 5 años, 58% a los 10 años, 45% a los 15 años y 34% a los 20 años. La tasa de recurrencia global del carcinoma hepatocelular (CHC) fue del 14,5%. El 54% de las recidivas ocurrieron de forma temprana, en los dos primeros años después del trasplante. Las variables asociadas con la recurrencia del CHC fueron el nivel de alfafetoproteína antes del trasplante (ng/ml), la presencia de más de un nódulo tumoral pretrasplante, el tamaño del nódulo mayor (mm) y la presencia de factores de mal pronóstico en el análisis anatomopatológico del explante.Se realizó un análisis de regresión logística que generó un modelo con una sensibilidad del 85,7% y una especificidad del 35,7% para predecir las recidivas en nuestra muestra. Se realizó un análisis univariable que identificó los 17,31 ng/ml de AFP como el punto de corte óptimo para predecir la recidiva en la muestra analizada. Se compararon los dos periodos, sin encontrar diferencias en la supervivencia de los pacientes trasplantados, la recurrencia del CHC ni en la influencia de las distintas variables sobre la recurrencia. Conclusiones: El trasplante hepático es una opción terapéutica válida y vigente que permite mejorar la supervivencia de los pacientes con CHC. La supervivencia de los pacientes trasplantados por CHC es similar a la de otras series publicadas, incluyendo el registro europeo de trasplante hepático. La supervivencia y las recidivas fueron similares en ambos periodos. Las variables relacionadas con la recurrencia fueron: el número de nódulos > 1, la histología de mal pronóstico, el tamaño del nódulo mayor (mm) y los niveles de AFP pretrasplante (ng/ml). Los pacientes trasplantados siguiendo los criterios “up to seven” no presentaron una mayor recidiva en comparación con los trasplantados siguiendo criterios de Milán. La mayoría de las recurrencias se detectan durante los dos primeros años postrasplante, por lo que se justifica realizar un seguimiento más estrecho durante este periodo, especialmente en aquellos pacientes en los que el modelo predice un alto riesgo de recurrencia
The role of the Bacillus subtilis extracellular matrix in mediating interspecies interactions.
No full textLa interacción entre microorganismos y plantas es fundamental para la salud vegetal y la producción de alimentos. Bacterias como Pseudomonas y Bacillus desempeñan un papel clave al promover el crecimiento vegetal y combatir patógenos mediante la producción de metabolitos secundarios. Bacillus subtilis destaca por su capacidad para formar biofilms y su matriz extracelular (MEC), compuesta por proteínas como TasA y lipopéptidos como fengicina, que son esenciales en sus interacciones con plantas y hongos patógenos como Botrytis cinerea.
Esta tesis doctoral explora los mecanismos moleculares detrás de las interacciones de B. subtilis con Pseudomonas chlororaphis y B. cinerea. Se demuestra que B. subtilis responde al ataque del sistema de secreción tipo VI (T6SS) de Pseudomonas mediante la esporulación, un mecanismo de supervivencia regulado por el factor σW y las histidina quinasas KinA y KinB. Además, se investiga el papel de la MEC en el antagonismo con B. cinerea, mostrando que TasA y fengicina actúan de manera sinérgica: TasA se adhiere a las hifas fúngicas, desorganizando su pared celular, mientras que fengicina induce estrés oxidativo y la formación de clamidosporas, estructuras de resistencia del hongo.
La interacción entre B. subtilis y B. cinerea es bidireccional y dinámica. El hongo contrarresta la agresión bacteriana mediante la degradación de fengicina y la producción de oxilipinas, moléculas con actividad antibacteriana. Por su parte, B. subtilis degrada el quitosano de la pared celular fúngica para obtener nutrientes y aumentar su población. Estos hallazgos resaltan la complejidad de las interacciones microbianas, donde la competencia y la coexistencia dependen de estrategias metabólicas y ecológicas flexibles. En conjunto, esta investigación aporta nuevos conocimientos sobre los mecanismos de defensa y adaptación de B. subtilis en entornos competitivos, con implicaciones significativas para el control biológico de patógenos en la agricultura sostenible
La ciudad como refugio y motor de la biodiversidad.
Full text linkConferencia inaugural en el 51º CONGRESO NACIONAL DE LA ASOCIACIÓN DE PARQUES Y JARDINESIt is more than evident that we are at the beginning of a change of era. A change very similar to the transition from the Gothic to the Renaissance. Then it was brought about by the printing press, naval advances and the connection with other continents, and today it is brought about by Artificial Intelligence, aeronautics and the race towards the outside world. Its consequences are to be expected, as then, to be a rebirth, a profound transformation in the way human beings conceive the world, knowledge, art and life in general.
The turning point towards this era of change was anticipated by Crutzen and Stoermer (2000) as the Anthropocene, defined by technological progress, the multiplication of production and consumption, and explosive population growth thanks to improvements in food and health. For some authors, this global population growth acquires, in a misanthropic but realistic vision, a behaviour similar to that of a ‘plague’ (Rodriguez Anido et al. 2024).
James Lovelock (2021) in his latest major essay, Novacene: The Coming Age of Hyperintelligence, goes even further, and as he already advanced in Gaia (1985), he draws a conceptually different world, which we are approaching at breakneck speed. According to his analysis, the new era that is now beginning will no longer have only life forms based on RNA and DNA codes, but on other codes based on digital electronics, what he calls cyborgs (free thinkers without the encumbrance of human rules), which will cause us to lose our status as the most intelligent and dominant creatures on Earth, and the only ones in the Universe.
In both the Anthropocene and the Novacene, the question centres some of its extremes on the fact that, while the demographic growth of our species is unconscionable, at the same time the concentration of individuals in collective habitats is unique, in an evolution similar to that of other eusocial species (Harrison et al. 2018)