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Novel geometric representations and optimized frameworks for deep learning models of interatomic potentials
No full textAquesta tesi explora avenços en potencials de xarxes neuronals per a simulacions atomístiques, abordant el doble repte de la precisió i l'eficiència. Mitjançant noves representacions geomètriques i marcs optimitzats, té com a objectiu enllaçar la química computacional tradicional amb enfocaments moderns basats en IA. Les contribucions principals inclouen el desenvolupament de TensorNet, un model equivariant que explota representacions de tensors cartesians per a predir amb precisió energies i forces moleculars. A més, aquest treball estén TensorNet per a incorporar els estats de càrrega i espín, ampliant així la seva aplicabilitat. Les millores en el marc TorchMD-Net, incloent el suport per a CUDA graphs i les optimitzacions de PyTorch 2.0, augmenten significativament el rendiment computacional i la usabilitat per a la dinàmica molecular. Combinant arquitectures de models innovadores amb una infraestructura de programari eficient, aquesta investigació avança el camp dels potencials interatòmics d'aprenentatge automàtic.This thesis explores advancements in neural network potentials for atomistic simulations, addressing the dual challenges of accuracy and efficiency. Through novel geometric representations and optimized frameworks, it aims to bridge traditional computational chemistry and modern AI-based approaches. Key contributions include the development of TensorNet, an equivariant model exploiting Cartesian tensor representations to predict molecular energies and forces accurately. Additionally, this work extends TensorNet to incorporate charge and spin states, broadening its applicability. Enhancements to the TorchMD-Net framework, including support for CUDA graphs and PyTorch 2.0 optimizations significantly improve computational performance and usability for molecular dynamics. By combining innovative model architectures with efficient software infrastructure, this research advances the field of machine learning interatomic potentialsPrograma de Doctorat en Tecnologies de la Informació i les Comunicacion
Environmental exposures and long COVID in a prospective population-based study in Catalonia (COVICAT study)
No full textThis study makes use of data generated by the GCAT-Genomes for Life and Cohort study of the Genomes of Catalonia, Fundacio IGTP. IGTP is part of the CERCA Program/Generalitat de Catalunya. GCAT was funded by Acción de Dinamización del ISCIII-MINECO and the Ministry of Health of the Generalitat of Catalunya (ADE 10/00026), with additional support by the Agència de Gestió d'Ajuts Universitaris i de Recerca (AGAUR) (SGR 01537), Spanish National Grant PI18/01512, TED2021-130626B-I00, La MaratoTV3 167/C/2021, VEIS project (001-P-001647) [co-funded by European Regional Development Fund (ERDF), "A way to build Europe"], and the European Union under grant agreement number 101046314 (END-VOC). Additional data included in this study was obtained in part by the COVICAT Study Group (Cohort Covid de Catalunya) supported by ISGlobal and IGTP, EIT COVID-19 Rapid Response activity 20873A and SR20-01024 La Caixa Foundation. We acknowledge support from the Spanish Ministry of Science and Innovation and State Research Agency through the "Centro de Excelencia Severo Ochoa 2019-2023" Program (CEX2018-000806-S) and from the Generalitat de Catalunya through the CERCA Program. A.S. received funding from the Swiss National Science Foundation (grant number P500PM_210781). B.H. received funding from the Instituto de Salud Carlos III (ISCIII) and the European Union NextGenerationEU/PRTR (grant IHMC22/00017)
The development of crop production in the northern Horn of Africa: a review of the archaeobotanical evidence
No full textThis article presents a synthesis of the hypotheses and evidence for plant domestication and the origins of agriculture in the northern Horn of Africa. To date, available archaeological data point to an introduction of agricultural practices to Ethiopia during the late Holocene, c. 1600 BC, influenced by adjacent areas including eastern Sudan, Egypt and southern Arabia. The archaeobotanical record shows that farming in the northern highlands was based on the cultivation of barley, linseed and lentils, combined with the exploitation of local wild grasses from the Panicoideae and Chloridoideae sub-families. This indicates that local populations also played a role in the development of productive activities in the region, a process that might have been in place before the arrival of the southwest Asian agricultural package. After the first millennium BC, amidst an increase in sedentary settlements in the region, new domesticated crops appeared in the archaeological record. These include exogenous crops such as emmer wheat, but also indigenous plants such as t¿ef and noog, which were locally domesticated likely throughout the Pre-Aksumite period. With the rise of the Aksumite Kingdom, c. 50 BC¿AD 700, the agricultural package again expanded to include of a wide range of pulses, geophytes and other economic crops. Macrobotanical remains of sorghum and finger millet also appear for the first time during this period, although this contrasts with the microbotanical record of the region, which points to an earlier presence. In the southern highlands and southwest Ethiopia, evidence of Plectranthus edulis (Vatke) Agnew (Ethiopian potato or Oromo potato) has been identified by the late first millennium BC, pointing towards an earlier domestication than previously considered. Similarly, enset and coffee remains have been documented during the early first millennium AD. Altogether, new studies are needed to confirm some of these hypotheses, as archaeobotanical studies in the northern Horn are still limited. The combination of macrobotanical and microbotanical data, along with ethnoarchaeological and experimental research programs and linguistic studies, will be of critical importance for refining our current understanding of the processes associated with plant domestication and the introduction of crop production in the region
Adaptar les escoles al canvi climàtic amb mesures verdes, blaves i grises a Barcelona: una avaluació amb mètodes mixtos
No full textEn el marc del programa Urban Innovative Actions de la Comissió Europea, l’any 2020, es van transformar onze escoles de primària de la ciutat de Barcelona en refugis climàtics, amb l’objectiu de millorar el confort tèrmic i promoure el benestar a les escoles. L’adaptació d’aquestes escoles al canvi climàtic es va dur a terme mitjançant la incorporació de vegetació (verd), punts d’aigua (blau), estructures d’ombra i elements per seure al patis, així com a través de la implementació de mesures de refrigeració passiva als edificis (gris). Els patis transformats es van obrir a la comunitat local durant els períodes no escolars. Aquesta tesi té com a objectiu avaluar l’impacte de les intervencions implementades en la salut i el seus determinants, tant a l’àmbit escolar com comunitari. Per aconseguir-ho, es van dur a terme dos estudis de mètodes mixtos amb disseny quasiexperimental pre-post. Es van realitzar un qüestionari i sessions de fotoveu amb l’alumnat i es va entrevistar al professorat per avaluar l’efecte de les intervencions sobre aspectes com la percepció de l’entorn, el joc i el comportament social, i la salut i el benestar al pati escolar (Estudi I), així com en relació amb la percepció de confort i benestar dins l’aula (Estudi II). Un tercer estudi avalua l’ús i les percepcions de les intervencions a l’àmbit comunitari a través d’un disseny qualitatiu amb un enfocament etnogràfic espontani (Estudi III). Els resultats mostren un impacte positiu de les intervencions en la percepció de l’entorn, el confort tèrmic i el benestar físic i mental de l’alumnat, tant a l’interior com al pati de l’escola. La creació de noves àrees naturalitzades, amb ombra i amb elements per seure al pati ha disminuït el joc esportiu, ha incrementat les oportunitats de joc percebudes i ha promogut relacions més igualitàries entre nenes i nens. A l’àmbit comunitari, els patis transformats són valorats positivament com a refugis climàtics. Fora d’horari escolar, els patis són utilitzats com espais d’oci a l’aire lliure i socialització, especialment entre les famílies i grups de nois adolescents. Els resultats obtinguts mostren els beneficis d’adaptar les escoles al canvi climàtic mitjançant aquestes intervencions verdes, blaves i grises, suggerint la necessitat d’ampliar-ho a altres escoles i comunitats amb contextos similars.En el marco del programa Urban Innovative Actions de la Comisión Europea, en 2020, se transformaron once escuelas de primaria de la ciudad de Barcelona en refugios climáticos, con el objetivo de mejorar el confort térmico y promover el bienestar en las escuelas. La adaptación de estas escuelas al cambio climático se llevó a cabo mediante la incorporación de vegetación (verde), puntos de agua (azul), elementos de sombra y para sentarse en los patios, así como a través de la implementación de medidas de refrigeración pasiva en los edificios (gris). Los patios transformados se abrieron a la comunidad local durante los períodos no escolares. Esta tesis tiene como objetivo evaluar el impacto de las intervenciones implementadas en la salud y sus determinantes, tanto a nivel escolar como comunitario. Para ello, se llevaron a cabo dos estudios de métodos mixtos con diseño cuasiexperimentales pre-post. Se llevaron a cabo un cuestionario y sesiones de fotovoz con el alumnado y se entrevistó al profesorado para evaluar el efecto de las intervenciones sobre aspectos como la percepción del entorno, el juego y el comportamiento social, y la salud y el bienestar en el patio escolar (Estudio I), así como en relación con la percepción del confort y bienestar en el aula (Estudio II). Un tercer estudio evalúa el uso y percepciones de las intervenciones a nivel comunitario a través de un diseño cualitativo con un enfoque etnográfico espontáneo (Estudio III). Los resultados muestran un impacto positivo de las intervenciones en la percepción del entorno, el confort térmico y el bienestar físico y mental del alumnado, tanto en el interior como en el patio de la escuela. La creación de nuevas áreas naturalizadas, con sombra y elementos para sentarse ha disminuido el juego deportivo, ha incrementado las oportunidades de juego y ha promovido relaciones más igualitarias entre niñas y niños. A nivel comunitario, los patios transformados son valorados positivamente como refugios climáticos. Fuera del horario escolar, los patios son utilizados como espacios de ocio al aire libre y socialización, especialmente entre familias y grupos de chicos adolescentes. Los resultados obtenidos muestran los beneficios de adaptar las escuelas al cambio climático mediante intervenciones verdes, azules y grises, sugiriendo la necesidad de ampliarlo a otras escuelas y comunidades con contextos similares.Within the framework of the Urban Innovative Actions programme of the European Commission, in 2020, eleven primary schools in the city of Barcelona were transformed into climate shelters to improve thermal comfort and promoting well-being at schools. The adaptation of the schools to climate change was carried out by incorporating vegetation (green), water points (blue), shading and seating elements in the schoolyards, as well as through the implementation of passive cooling measures in the buildings (grey). The transformed schoolyards were opened to the local community during non-school periods. This thesis aims to evaluate the impact of the implemented interventions on health and its determinants, both at school and community levels. To this end, two mixed-method studies with a pre-post quasi-experimental design were conducted. A questionnaire and photovoice sessions were conducted with students and, also, teachers were interviewed to evaluate the effect of the interventions on aspects such as the perception of the environment, play and social behaviour, and health and well-being in the schoolyard (Study I), as well as in relation to comfort and well-being in the classroom (Study II). A third study evaluates the use and perceptions of the interventions at community level through a qualitative design with a spontaneous ethnographic approach (Study III). The results showed a positive impact of the interventions on the perception of the school environment, thermal comfort, and physical and mental well-being of the students, both inside and in the schoolyard. The creation of new naturalized areas, with shade and seating elements, in the schoolyard decreased sport games, increased perceived play opportunities and promoted more egalitarian relations between girls and boys. At the community level, the transformed schoolyards were positively valued as climate shelters. Outside school hours, the schoolyards were used as outdoor leisure and socialization spaces, especially among families and groups of adolescent boys. The results show the benefits of adapting schools to climate change through green, blue, and gray interventions, suggesting the need to expand it to other schools and communities with similar contexts.Universitat Pompeu Fabra. Doctorat en Biomedicin
Drosophila ovarian stem cell niche ageing involves coordinated changes in transcription and alternative splicing
No full textGene expression (GE) and alternative splicing (AS) contribute to the formation of new interaction networks with potentially significant cellular functions. Here, we investigate ageing in the Drosophila female germline stem cell (GSC) niche and describe functional changes in both GE and AS. The GSC niche comprises three types of support cells, whose ageing transcriptomes reveal differential GE and AS variations related to cell adhesion, cytoskeleton and neural signalling. Because each population show distinctive GE and AS changes, niche cell types possess unique ageing signatures. Depending on the cell population, groups of genes display changes in both GE and AS, revealing a coordinated regulation of transcription and splicing during niche ageing. One such gene is Fasciclin 2, a neural adhesion molecule that we find is essential for niche functioning. Furthermore, genes involved in AS undergo changes in GE and/or AS themselves, providing a mechanistic explanation for the coordination of these two processes during niche ageing. This is the case of the splicing factor Smu1, described here as a key element necessary for ovarian niche homeostasis.The following grants provided financial support: PID2020-115040GB-I00 (MI), PID2021-125480NB-I00 and CEX2020-001088-M (A.G-.R.), funded by MICIU/AEI/10.13039/501100011033; P20_00888 funded by the Junta de Andalucía (A.G-.R.); and by ERDF, EU. D.E-R. (FPU15/06664) and J.H-R. (FPU17/03230) were funded by FPU contracts from the MECD
Adaptative mechanisms of sleep for cognition and memory
No full textDurant el son, els estímuls sensorials externs es filtren mentre el cervell es
prepara per consolidar nous records. Aquest equilibri sorgeix d’alternar recursos
endògens entre la vigilància de l’entorn i la consolidació de memòries. Els fusos i
les oscil·lacions lentes mantenen la continuïtat del son filtrant estímuls sensorials
i afavorint la memòria. Hem investigat la resposta a estímuls auditius complexos
durant el son, utilitzant un paradigma naturalista per avaluar si fusos i
oscil·lacions lentes es modulaven segons expectatives musicals generades. Per
aprofundir en el paper de les oscil·lacions en l’estabilització de l’aprenentatge
diari, vam examinar una malaltia neurodesenvolupamental amb discapacitat
intel·lectual sense tasca prèvia al son. Vam trobar que les oscil·lacions del son
poden passar de filtrar estímuls auditius complexos a donar suport a processos
endògens de consolidació. Els dèficits d’aquestes oscil·lacions en consolidar
memòries van revelar un perfil matisat amb potencial per estratificar pacients i
guiar estratègies terapèutiques.During sleep, external sensory stimuli are filtered as the brain prepares to
consolidate new memories. This balance arises from alternating endogenous
resources between environmental monitoring and enabling systems consolidation
and synaptic regulation. Spindles and slow oscillations preserve sleep continuity
by filtering sensory input and aiding memory strengthening. We investigated how
complex auditory stimuli are processed during sleep, using a novel naturalistic
auditory paradigm to assess whether spindles and SOs were modulated by
musical expectations. To further explore sleep oscillations’ role in stabilizing daily
learning, we examined a neurodevelopmental disease with intellectual disability to
address trait-like memory consolidation mechanisms without a pre-sleep task. We
found that sleep oscillations may shift from gating complex auditory stimuli to
supporting endogenous consolidation processes. Sleep oscillation deficits in
memory consolidation revealed a nuanced profile potentially aiding patient
stratification and guiding novel therapeutic strategies.Programa de Doctorat en Biomedicin
A scrutiny of the Linz-Moreno question
No full textIn this research note we delve into the Linz-Moreno question-one of the most employed measures of national and regional identity in political science-by analzsing three different assumptions that the indicator relies upon: First, we test whether this instrument captures a negative linear trend between identities. Second, we examine whether the Linz-Moreno question also captures identity intensity. Third, we focus on the middle-identity category and examine whether it encapsulates people's dual sense of belonging where there are two different national identities. Using data from the Making Electoral Democracy Work Project for the Spanish/Catalan case, we show that the Linz-Moreno question meets the assumptions of linearity, intensity, and the meaning of the role of the central category when capturing Catalan identity feelings. However, it fails to capture Spanish identity intensity and preferences, which over-represents the dual-identity middle category. Our empirical findings have crucial consequences for researchers working in the field of national/regional identities
Un bon aprofitat : campanya contra el maltracte alimentari pel Banc dels Aliments
No full textTutor: Lluís Trillo
Treball de fi de grau en Publicitat i Relacions PúbliquesEl malbaratament alimentari és un dels grans desafi aments ambientals, econòmics i socials del nostre temps. Aquest Treball Final de Grau desenvolupa una proposta de comunicació creativa per combatre’l promovent el seu concepte oposat: l’aprofi tament. La campanya, ideada per al Banc dels Aliments, busca educar i conscienciar la població catalana sota el concepte “Un bon aprofi tat”, utilitzat com a eix creatiu amb humor i ironia. Mitjançant jocs de paraules i comparacions visuals, es vol captar l’atenció i provocar la refl exió de públics diversos a través d’una estratègia multicanal.El desperdicio alimentario es uno de los grandes retos ambientales, económicos y sociales de nuestro tiempo. Este Trabajo Final de Grado desarrolla una propuesta de comunicación creativa para combatirlo, promoviendo su concepto opuesto: el aprovechamiento. La campaña, pensada para el Banco de Alimentos, tiene como objetivo educar y sensibilizar a la población catalana mediante el concepto “Un buen aprovechado”, usado como eje creativo con humor e ironía. Con juegos de palabras y comparaciones visuales, se pretende captar la atención y provocar la refl exión a través de una estrategia multicanal.Food waste is one of today’s major environmental, economic, and social challenges. This Final Degree Project develops a creative communication proposal to fi ght food waste by promoting its opposite concept: food appreciation. The campaign, designed for the Food Bank, aims to educate and raise awareness among the Catalan population using the concept “A true food saver” as a humorous and ironic creative axis. Through wordplay and visual comparisons, the campaign seeks to engage a wide audience using a multichannel strategy
Probability of cartel detection: an application to the Peruvian case
No full textTreball fi de màster de: Master's Degree in Specialized Economic Analysis: Competition and Market Regulation. Curs 2024-2025Tutors: Fabian Gaessler, Rosa Ferrer, i Massimo MottaThis paper provides, to our knowledge, the first empirical estimate of the probability of cartel detection in Peru —a critical parameter used by the Peruvian competition authority (INDECOPI) to set cartel fines. Building on Bryant and Eckerd (1991), we calibrate a birth-and-death Markov model using the observed duration of cartels sanctioned by INDECOPI since its foundation. Our results indicate that the annual probability of detection lies between 18% and 31%, with a point estimate of 25%. This figure shall be interpreted as an upper bound, and places Peru at the higher end of international benchmarks.Este trabajo presenta, según nuestro entendimiento, la primera estimación empírica de la probabilidad de detección de carteles en el Perú —insumo clave usado por la agencia de competencia (INDECOPI) para estimar multas a carteles. Siguiendo a Bryant y Eckerd (1991), calibramos un modelo de “nacimiento y muerte” de Markov usando la duración de carteles sancionados por el INDECOPI desde su fundación. Nuestros resultados indican que la probabilidad anual de detección fluctúa entre 18% y 31%, con una estimación central de 25%. El resultado constituye un límite máximo del parámetro real, y se encuentra en el rango superior de estimaciones internacionales
FLCCR is a fluorescent reporter system that quantifies the duration of different cell cycle phases at the single-cell level in fission yeast
No full textFission yeast is an excellent model system that has been widely used to study the mechanism that control cell cycle progression. However, there is a lack of tools that allow to measure with high precision the duration of the different phases of the cell cycle in individual cells. To circumvent this problem, we have developed a fluorescent reporter that allows the quantification of the different phases of the cell cycle at the single-cell level in most genetic backgrounds. To prove the accuracy of this fluorescent reporter, we have tested the reporter in strains known to have a delay in the G1/S or G2/M transitions, confirming the strength and versatility of the system. An advantage of this reporter is that it eliminates the need for culture synchronization, avoiding stressing the cells. Using this reporter, we show that unperturbed cells lacking Sty1 have a standard cell cycle length and distribution and that the extended length of these cells is due to their increased cell growth rate but not to alterations in their cell cycle progression.This work was supported by grant PID2022-136449NB-I00 funded by MICIU/AEI/10.13039/501100011033 and ERDF/EU to J.A. and by Unidad de Excelencia Maria de Maeztu (CEX2018-000792-M) to J.A. and E.H. E.H. is a recipient of an ICREA Academia Award (Generalitat de Catalunya). The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript