2,586 research outputs found

    Undergraduate Catalog of Studies, 2023-2024

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    Natural and Technological Hazards in Urban Areas

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    Natural hazard events and technological accidents are separate causes of environmental impacts. Natural hazards are physical phenomena active in geological times, whereas technological hazards result from actions or facilities created by humans. In our time, combined natural and man-made hazards have been induced. Overpopulation and urban development in areas prone to natural hazards increase the impact of natural disasters worldwide. Additionally, urban areas are frequently characterized by intense industrial activity and rapid, poorly planned growth that threatens the environment and degrades the quality of life. Therefore, proper urban planning is crucial to minimize fatalities and reduce the environmental and economic impacts that accompany both natural and technological hazardous events

    A First Course in Causal Inference

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    I developed the lecture notes based on my ``Causal Inference'' course at the University of California Berkeley over the past seven years. Since half of the students were undergraduates, my lecture notes only require basic knowledge of probability theory, statistical inference, and linear and logistic regressions

    Undergraduate Catalog of Studies, 2022-2023

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    Integrated Approaches to Digital-enabled Design for Manufacture and Assembly: A Modularity Perspective and Case Study of Huoshenshan Hospital in Wuhan, China

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    Countries are trying to expand their healthcare capacity through advanced construction, modular innovation, digital technologies and integrated design approaches such as Design for Manufacture and Assembly (DfMA). Within the context of China, there is a need for stronger implementation of digital technologies and DfMA, as well as a knowledge gap regarding how digital-enabled DfMA is implemented. More critically, an integrated approach is needed in addition to DfMA guidelines and digital-enabled approaches. For this research, a mixed method was used. Questionnaires defined the context of Huoshenshan Hospital, namely the healthcare construction in China. Then, Huoshenshan Hospital provided a case study of the first emergency hospital which addressed the uncertainty of COVID-19. This extreme project, a 1,000-bed hospital built in 10 days, implemented DfMA in healthcare construction and provides an opportunity to examine the use of modularity. A workshop with a design institution provided basic facts and insight into past practice and was followed by interviews with 18 designers, from various design disciplines, who were involved in the project. Finally, multiple archival materials were used as secondary data sources. It was found that complexity hinders building systems integration, while reinforcement relationships between multiple dimensions of modularity (across organisation-process-product-supply chain dimensions) are the underlying mechanism that allows for the reduction of complexity and the integration of building systems. Promoting integrated approaches to DfMA relies on adjusting and coupling multi-dimensional modular reinforcement relationships (namely, relationships of modular alignment, modular complement, and modular incentive). Thus, the building systems integrator can use these three approaches to increase the success of digital-enabled DfMA

    Advances and Applications of DSmT for Information Fusion. Collected Works, Volume 5

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    This fifth volume on Advances and Applications of DSmT for Information Fusion collects theoretical and applied contributions of researchers working in different fields of applications and in mathematics, and is available in open-access. The collected contributions of this volume have either been published or presented after disseminating the fourth volume in 2015 in international conferences, seminars, workshops and journals, or they are new. The contributions of each part of this volume are chronologically ordered. First Part of this book presents some theoretical advances on DSmT, dealing mainly with modified Proportional Conflict Redistribution Rules (PCR) of combination with degree of intersection, coarsening techniques, interval calculus for PCR thanks to set inversion via interval analysis (SIVIA), rough set classifiers, canonical decomposition of dichotomous belief functions, fast PCR fusion, fast inter-criteria analysis with PCR, and improved PCR5 and PCR6 rules preserving the (quasi-)neutrality of (quasi-)vacuous belief assignment in the fusion of sources of evidence with their Matlab codes. Because more applications of DSmT have emerged in the past years since the apparition of the fourth book of DSmT in 2015, the second part of this volume is about selected applications of DSmT mainly in building change detection, object recognition, quality of data association in tracking, perception in robotics, risk assessment for torrent protection and multi-criteria decision-making, multi-modal image fusion, coarsening techniques, recommender system, levee characterization and assessment, human heading perception, trust assessment, robotics, biometrics, failure detection, GPS systems, inter-criteria analysis, group decision, human activity recognition, storm prediction, data association for autonomous vehicles, identification of maritime vessels, fusion of support vector machines (SVM), Silx-Furtif RUST code library for information fusion including PCR rules, and network for ship classification. Finally, the third part presents interesting contributions related to belief functions in general published or presented along the years since 2015. These contributions are related with decision-making under uncertainty, belief approximations, probability transformations, new distances between belief functions, non-classical multi-criteria decision-making problems with belief functions, generalization of Bayes theorem, image processing, data association, entropy and cross-entropy measures, fuzzy evidence numbers, negator of belief mass, human activity recognition, information fusion for breast cancer therapy, imbalanced data classification, and hybrid techniques mixing deep learning with belief functions as well

    20th SC@RUG 2023 proceedings 2022-2023

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    Automated and foundational verification of low-level programs

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    Formal verification is a promising technique to ensure the reliability of low-level programs like operating systems and hypervisors, since it can show the absence of whole classes of bugs and prevent critical vulnerabilities. However, to realize the full potential of formal verification for real-world low-level programs one has to overcome several challenges, including: (1) dealing with the complexities of realistic models of real-world programming languages; (2) ensuring the trustworthiness of the verification, ideally by providing foundational proofs (i.e., proofs that can be checked by a general-purpose proof assistant); and (3) minimizing the manual effort required for verification by providing a high degree of automation. This dissertation presents multiple projects that advance formal verification along these three axes: RefinedC provides the first approach for verifying C code that combines foundational proofs with a high degree of automation via a novel refinement and ownership type system. Islaris shows how to scale verification of assembly code to realistic models of modern instruction set architectures-in particular, Armv8-A and RISC-V. DimSum develops a decentralized approach for reasoning about programs that consist of components written in multiple different languages (e.g., assembly and C), as is common for low-level programs. RefinedC and Islaris rest on Lithium, a novel proof engine for separation logic that combines automation with foundational proofs.Formale Verifikation ist eine vielversprechende Technik, um die Verlässlichkeit von grundlegenden Programmen wie Betriebssystemen sicherzustellen. Um das volle Potenzial formaler Verifikation zu realisieren, müssen jedoch mehrere Herausforderungen gemeistert werden: Erstens muss die Komplexität von realistischen Modellen von Programmiersprachen wie C oder Assembler gehandhabt werden. Zweitens muss die Vertrauenswürdigkeit der Verifikation sichergestellt werden, idealerweise durch maschinenüberprüfbare Beweise. Drittens muss die Verifikation automatisiert werden, um den manuellen Aufwand zu minimieren. Diese Dissertation präsentiert mehrere Projekte, die formale Verifikation entlang dieser Achsen weiterentwickeln: RefinedC ist der erste Ansatz für die Verifikation von C Code, der maschinenüberprüfbare Beweise mit einem hohen Grad an Automatisierung vereint. Islaris zeigt, wie die Verifikation von Assembler zu realistischen Modellen von modernen Befehlssatzarchitekturen wie Armv8-A oder RISC-V skaliert werden kann. DimSum entwickelt einen neuen Ansatz für die Verifizierung von Programmen, die aus Komponenten in mehreren Programmiersprachen bestehen (z.B., C und Assembler), wie es oft bei grundlegenden Programmen wie Betriebssystemen der Fall ist. RefinedC und Islaris basieren auf Lithium, eine neue Automatisierungstechnik für Separationslogik, die maschinenüberprüfbare Beweise und Automatisierung verbindet.This research was supported in part by a Google PhD Fellowship, in part by awards from Android Security's ASPIRE program and from Google Research, and in part by a European Research Council (ERC) Consolidator Grant for the project "RustBelt", funded under the European Union’s Horizon 2020 Framework Programme (grant agreement no. 683289)

    Comparative genomics of recent adaptation in Candida pathogens

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    [eng] Fungal infections pose a serious health threat, affecting >1,000 million people and causing ~1.5 million deaths each year. The problem is growing due to insufficient diagnostic and therapeutic options, increased number of susceptible patients, expansion of pathogens partly linked to climate change and the rise of antifungal drug resistance. Among other fungal pathogens, Candida species are a major cause of severe hospital-acquired infections, with high mortality in immunocompromised patients. Various Candida pathogens constitute a public health issue, which require further efforts to develop new drugs, optimize currently available treatments and improve diagnostics. Given the high dynamism of Candida genomes, a promising strategy to improve current therapies and diagnostics is to understand the evolutionary mechanisms of adaptation to antifungal drugs and to the human host. Previous work using in vitro evolution, population genomics, selection inferences and Genome Wide Association Studies (GWAS) have partially clarified such recent adaptation, but various open questions remain. In the three research articles that conform this PhD thesis we addressed some of these gaps from the perspective of comparative genomics. First, we addressed methodological issues regarding the analysis of Candida genomes. Studying recent adaptation in these pathogens requires adequate bioinformatic tools for variant calling, filtering and functional annotation. Among other reasons, current methods are suboptimal due to limited accuracy to identify structural variants from short read sequencing data. In addition, there is a need for easy-to-use, reproducible variant calling pipelines. To address these gaps we developed the “personalized Structural Variation detection” pipeline (perSVade), a framework to call, filter and annotate several variant types, including structural variants, directly from reads. PerSVade enables accurate identification of structural variants in any species of interest, such as Candida pathogens. In addition, our tool automatically predicts the structural variant calling accuracy on simulated genomes, which informs about the reliability of the calling process. Furthermore, perSVade can be used to analyze single nucleotide polymorphisms and copy number-variants, so that it facilitates multi-variant, reproducible genomic studies. This tool will likely boost variant analyses in Candida pathogens and beyond. Second, we addressed open questions about recent adaptation in Candida, using perSVade for variant identification. On the one hand, we investigated the evolutionary mechanisms of drug resistance in Candida glabrata. For this, we used a large-scale in vitro evolution experiment to study adaptation to two commonly-used antifungals: fluconazole and anidulafungin. Our results show rapid adaptation to one or both drugs, with moderate fitness costs and through few mutations in a narrow set of genes. In addition, we characterize a novel role of ERG3 mutations in cross-resistance towards fluconazole in anidulafungin-adapted strains. These findings illuminate the mutational paths leading to drug resistance and cross-resistance in Candida pathogens. On the other hand, we reanalyzed ~2,000 public genomes and phenotypes to understand the signs of recent selection and drug resistance in six major Candida species: C. auris, C. glabrata, C. albicans, C. tropicalis, C. parapsilosis and C. orthopsilosis. We found hundreds of genes under recent selection, suggesting that clinical adaptation is diverse and complex. These involve species-specific but also convergently affected processes, such as cell adhesion, which could underlie conserved adaptive mechanisms. In addition, using GWAS we predicted known drivers of antifungal resistance alongside potentially novel players. Furthermore, our analyses reveal an important role of generally-overlooked structural variants, and suggest an unexpected involvement of (para)sexual recombination in the spread of resistance. Taken together, our findings provide novel insights on how Candida pathogens adapt to human-related environments and suggest candidate genes that deserve future attention. In summary, the results of this thesis improve our knowledge about the mechanisms of recent adaptation in Candida pathogens, which may enable improved therapeutic and diagnostic applications.[cat] Les infeccions fúngiques representen una greu amenaça per a la salut, afectant a més de 1.000 milions de persones i causant aproximadament 1,5 milions de morts cada any. El problema està augmentant a causa d’unes opcions terapèutiques i diagnòstiques insuficients, l'increment del nombre de pacients susceptibles, l'expansió dels patògens parcialment vinculada al canvi climàtic i l'augment de la resistència als fàrmacs antifúngics. D’entre diversos fongs patògens, els llevats del gènere Candida són una causa important d'infeccions nosocomials, amb una alta mortalitat en pacients immunodeprimits. Diverses espècies de Candida constitueixen un problema de salut pública, cosa que requereix més esforços per a desenvolupar nous medicaments, optimitzar els tractaments disponibles i millorar els diagnòstics. Tenint en compte el dinamisme genòmic d’aquests patògens, una estratègia prometedora per millorar les teràpies i diagnòstics actuals és comprendre els mecanismes evolutius d'adaptació als fàrmacs antifúngics i a l’hoste humà. Treballs anteriors utilitzant l'evolució in vitro, la genòmica de poblacions, les inferències de selecció i els estudis d'associació de genoma complet (GWAS, per les sigles en anglès) han aclarit parcialment aquesta adaptació recent, però encara hi ha diverses preguntes obertes. En els tres articles que conformen aquesta tesi doctoral, hem abordat algunes d'aquestes preguntes des de la perspectiva de la genòmica comparativa. En primer lloc, hem abordat qüestions metodològiques relatives a l'anàlisi dels genomes de les espècies Candida. L'estudi de l'adaptació recent en aquests patògens requereix eines bioinformàtiques adequades per a la detecció, filtratge i anotació funcional de variants genètiques. Entre altres raons, els mètodes actuals són subòptims a causa de la limitada precisió per identificar variants estructurals a partir de dades de seqüenciació amb lectures curtes. A més, hi ha una necessitat d’eines computacionals per a la detecció de variants que siguin senzilles d'utilitzar i reproduibles. Per abordar aquestes mancances, hem desenvolupat el mètode bioinformàtic "personalized Structural Variation detection" (perSVade), una eina que permet la detecció, filtratge i anotació de diversos tipus de variants, incloent-hi les variants estructurals, directament des de les lectures. PerSVade permet la identificació precisa de les variants estructurals en qualsevol espècie d'interès, com ara els patògens Candida. A més, la nostra eina prediu automàticament la precisió de la detecció d’aquestes variants en genomes simulats, la qual cosa informa sobre la fiabilitat del procés. Finalment, perSVade es pot utilitzar per analitzar altres tipus de variants, com els polimorfismes de nucleòtid únic o els canvis en el nombre de còpies, facilitant així estudis genòmics integrals i reproduibles. Aquesta eina probablement impulsarà les anàlisis genòmiques en els patògens Candida i també en altres espècies. En segon lloc, hem abordat algunes de les preguntes obertes sobre l'adaptació recent en els llevats Candida, utilitzant perSVade per a la identificació de variants. D'una banda, hem investigat els mecanismes evolutius de resistència als fàrmacs antifúngics en Candida glabrata. Per a això, hem utilitzat un experiment d'evolució in vitro a gran escala per estudiar l'adaptació a dos antifúngics comuns: el fluconazol i l’anidulafungina. Els nostres resultats mostren una adaptació ràpida a un o ambdós fàrmacs, amb un cost per al creixement moderat i a través de poques mutacions en un nombre reduït de gens. A més, hem caracteritzat un paper nou de les mutacions en ERG3 en la resistència creuada al fluconazol en soques adaptades a anidulafungina. Aquests descobriments aclareixen els processos mutacionals que condueixen a la resistència als fàrmacs i a la resistència creuada en els patògens Candida. D'altra banda, hem re-analitzat aproximadament 2.000 genomes i fenotips disponibles en repositoris públics per a comprendre els senyals genòmics de selecció recent i de resistència a fàrmacs antifúngics, en sis espècies rellevants de Candida: C. auris, C. glabrata, C. albicans, C. tropicalis, C. parapsilosis i C. orthopsilosis. Hem trobat centenars de gens sota selecció recent, suggerint que l'adaptació clínica és diversa i complexa. Aquests gens estan relacionats amb funcions específiques de cada espècie, però també trobem processos alterats de manera similar en diferents patògens, com per exemple l’adhesió cel·lular, cosa que indica fenòmens d’adaptació conservats. A part, utilitzant GWAS hem predit mecanismes esperats de resistència a antifúngics i també possibles nous factors. A més, les nostres anàlisis revelen un paper important de les variants estructurals, generalment poc estudiades, i suggereixen una implicació inesperada de la recombinació (para)sexual en la propagació de la resistència. En conjunt, els nostres descobriments proporcionen noves perspectives sobre com els patògens Candida s'adapten als entorns humans, i suggereixen gens candidats que mereixen investigacions futures. En resum, els resultats d’aquesta tesi milloren el nostre coneixement sobre els mecanismes d'adaptació recent en els patògens Candida, cosa que pot permetre el disseny de noves teràpies i diagnòstics
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