Toward Tool-Independent Summaries for Symbolic Execution (Artifact)

The artifact contains the extended versions of the tools angr and AVD with support for the symbolic reflection API proposed in the paper. Additionally, the artifact contains the source code of SumBoundVerify, our novel tool for the bounded-verification of symbolic summaries for the C programming language. The artifact contains all the scripts and datasets required to obtain the results presented in the paper, including: a library of 67 symbolic summaries implemented using the proposed symbolic reflection API; two symbolic test suites designed to test two open source C libraries; and the source code of the third-party summaries that were validated checked with SumBoundVerify

Toward Tool-Independent Summaries for Symbolic Execution

We introduce a new symbolic reflection API for implementing tool-independent summaries for the symbolic execution of C programs. We formalise the proposed API as a symbolic semantics and extend two state-of-the-art symbolic execution tools with support for it. Using the proposed API, we implement 67 tool-independent symbolic summaries for a total of 26 libc functions. Furthermore, we present SumBoundVerify, a fully automatic summary validation tool for checking the bounded correctness of the symbolic summaries written using our symbolic reflection API. We use SumBoundVerify to validate 37 symbolic summaries taken from 3 state-of-the-art symbolic execution tools, angr, Binsec and Manticore, detecting a total of 24 buggy summaries

Impact of data structure layout on performance

One key issue to design parallel applications that scale on multicore systems is how to overcome the memory bottleneck. This paper presents a study of the impact of data structure layouts in locality of memory references, providing insights on strategies to ameliorate the memory bottleneck. The paper compares the performance of Java and C++ STL collections and presents the impact of locality of reference optimisations in a molecular dynamics simulation case study. The case study shows that the selected data structure layout has impact on single core performance, becoming a critical factor in the application scalability on multicore systems. Moreover, data collections provided in the Java language compromise performance due to pointer chasing and lack of spatial locality of memory references.This work is funded by ERDF - European Regional Development Fund through the COMPETE Programme (operational programme for competitiveness) and by National Funds through the FCT - Fundac a o para a Ciencia e a Tecnologia (Portuguese Foundation for Science and Technology) within projects FCOMP-01-0124- FEDER-010152 and FCOMP-01-0124-FEDER-011413

Projeto Action Girls: Desenvolver o potencial das raparigas e mulheres no desporto

1st International Meeting on Sport, Education and Communities: Beyond the Field organizado pelo Observatório de Desporto, Educação, Comunidades (ODEC), 1-2 junho, 202

Candida auris in Intensive Care Setting: The First Case Reported in Portugal

(This article belongs to the Special Issue Genomic Epidemiology of Fungal Diseases 2023)Candida auris is an opportunistic human pathogen that has rapidly spread to multiple countries and continents and has been associated with a high number of nosocomial outbreaks. Herein, we report the first case of C. auris in Portugal, which was associated with a patient transferred from Angola to an ICU in Portugal for liver transplantation after a SARS-CoV-2 infection. C. auris was isolated during the course of bronchoalveolar lavage, and it was subjected to antifungal susceptibility testing and whole-genome sequence analysis. This isolate presents low susceptibility to azoles and belongs to the genetic clade III with a phylogenetic placement close to African isolates. Although clade III has already been reported in Europe, taking into account the patient’s clinical history, we cannot discard the possibility that the patient’s colonization/infection occurred in Angola, prior to admission in the Portuguese hospital. Considering that C. auris is a fungal pathogen referenced by WHO as a critical priority, this case reinforces the need for continuous surveillance in a hospital settingThis work was supported by funding from the European Union EU4Health Programme under grant agreement no. 101113460 (GENEO) and by national funds through the Foundation for Science and Technology (FCT), I.P., under Individual CEEC 2022.00851.CEECIND/CP1748/CT0001.info:eu-repo/semantics/publishedVersio

Epigenetic reprogramming by TET enzymes impacts co-transcriptional R-loops

PTDC/BIA-MOL/30438/2017 PTDC/MED-OUT/4301/2020 RiboMed 857119 PD/BD/128292/2017 LCF/PR/HP21/52310016 PTDC/BIA-MOL/6624/2020 PTDC/MED-ONC/7864/2020DNA oxidation by ten-eleven translocation (TET) family enzymes is essential for epigenetic reprogramming. The conversion of 5-methylcytosine (5mC) into 5-hydroxymethylcytosine (5hmC) initiates developmental and cell-type-specific transcriptional programs through mechanisms that include changes in the chromatin structure. Here, we show that the presence of 5hmC in the transcribed gene promotes the annealing of the nascent RNA to the template DNA strand, leading to the formation of an R-loop. Depletion of TET enzymes reduced global R-loops in the absence of gene expression changes, whereas CRISPR-mediated tethering of TET to an active gene promoted the formation of R-loops. The genome-wide distribution of 5hmC and R-loops shows a positive correlation in mouse and human stem cells and overlap in half of all active genes. Moreover, R-loop resolution leads to differential expression of a subset of genes that are involved in crucial events during stem cell proliferation. Altogether, our data reveal that epigenetic reprogramming via TET activity promotes co-transcriptional R-loop formation, disclosing new mechanisms of gene expression regulation.publishersversionpublishe

Adaptação transcultural do Empowering Disempowering Motivational Climate Questionnaire para a língua portuguesa e análise da invariância em atletas masculinos brasileiros e portugueses

The aim of the present study was to carry out the cross-cultural adaptation of the Portuguese version of "Empowering and Disempowering Motivational Climate" (EDMCQ-C), which evaluates the athletes' perception the motivational climate provided by the coach and to examinethe factorial invariance between Brazilians and Portuguese. The sample was composed by 963 male athletes from different sports (handball, basketball, soccer, futsal and volleyball), aged between 11 and 24 (M = 15.04 ± 1.88), of whom 553 were Brazilian (M = 15.81 ± 1.91) and 410 Portuguese athletes (M = 13.94 ± 1.30). The results of the confirmatory factorial analysis found satisfactory adjustment indices of the model for both portuguese (χ2/df = 1.67; CFI = 0.92; TLI = 0.91; SRMR = 0.06; RMSEA = 0.04) and brazilian (χ2/df = 1.92; CFI = 0.90; TLI = 0.89; SRMR = 0.05; RMSEA = 0.04). The results also showed that the model of measurement was invariant between Brazilian and Portuguese athletes (ΔCFI <0.01). In conclusion, the instrument used can be a useful to analyze the perception of Brazilian and Portuguese athletes for the motivational climate provided by the coach. O objetivo do presente estudo foi o de proceder à tradução e adaptação transcultural do “Empowering and Disempowering Motivational Climate Questionnaire-Coach” (EDMCQ-C) para a língua portuguesa e analisar a invariância da sua estrutura fatorial, quando aplicado a atletas brasileiros e portugueses. A amostra foi constituída por 963 atletas do sexo masculino, praticantes de diferentes desportos (andebol, basquetebol, futebol, futsal e voleibol), com idades compreendidas entre os 11 e os 24 anos (M = 15.04 ± 1.88), sendo 553 brasileiros (M = 15.81 ± 1.91) e 410 portugueses (M = 13.94 ± 1.30). Através do recurso à Análise Fatorial Confirmatória, foi possível verificar a existência de bons índices de ajustamento ao modelo teórico examinado, com uma solução reduzida constituída por 15 itens, distribuídos pelos cinco fatores do instrumento original (χ2/df = 2.38; CFI = 0.97; TLI = 0.96; SRMR = 0.03; RMSEA = 0.04). Complementarmente, a invariância do modelo de medida, quando aplicado a atletas brasileiros e portugueses, foi avaliada através da comparação do modelo com pesos fatoriais fixos e o modelo com coeficientes estruturais livres, tendo o resultado sido de ΔCFI = 0.01. Em conformidade, os resultados encontrados suportam a sugestão de que a versão adaptada para a língua portuguesa do EDMCQ-C evidencia boas propriedades psicométricas, podendo, portanto, constituir-se como uma ferramenta útil para avaliar as perceções de atletas brasileiros e portugueses sobre o clima motivacional que lhes é proporcionado pelos seus treinadores

Mobile real-time surveillance of Zika virus in Brazil

Submitted by Ana Maria Fiscina Sampaio ([email protected]) on 2016-11-29T17:59:25Z No. of bitstreams: 1 Faria N R Mobil real....pdf: 357343 bytes, checksum: 5e7279515aa41c01d0c75ed09a95c5b2 (MD5)Approved for entry into archive by Ana Maria Fiscina Sampaio ([email protected]) on 2016-11-29T18:43:34Z (GMT) No. of bitstreams: 1 Faria N R Mobil real....pdf: 357343 bytes, checksum: 5e7279515aa41c01d0c75ed09a95c5b2 (MD5)Made available in DSpace on 2016-11-29T18:43:34Z (GMT). No. of bitstreams: 1 Faria N R Mobil real....pdf: 357343 bytes, checksum: 5e7279515aa41c01d0c75ed09a95c5b2 (MD5) Previous issue date: 2016-09-29University of Oxford. Department of Zoology. South Parks Road. Oxford, UK.University of Sao Paulo. Department of Infectious Diseases and Institute of Tropical Medicine. São Paulo, BrasilMinistry of Health. Evandro Chagas Institute. Center for Technological Innovation. Ananindeua, PA, Brasil / University of Texas Medical Branch. Department of Pathology. Galveston, USAFundação Gonçalo Moniz, Centro de Pesquisas Gonçalo Moniz. Salvador, BA, BrasilUniversity of Birmingham. Institute of Microbiology and Infection. Birmingham, UK.The World Health Organization has declared Zika virus an international public health emergency. Knowledge of Zika virus genomic epidemiology is currently limited due to challenges in obtaining and processing samples for sequencing. The ZiBRA project is a United Kingdom-Brazil collaboration that aims to improve this situation using new sequencing technologies

Tracking arboviruses, their transmission vectors and potential hosts by nanopore sequencing of mosquitoes

The risk to human health from mosquito-borne viruses such as dengue, chikungunya and yellow fever is increasing due to increased human expansion, deforestation and climate change. To anticipate and predict the spread and transmission of mosquito-borne viruses, a better understanding of the transmission cycle in mosquito populations is needed. We present a pathogen-agnostic combined sequencing protocol for identifying vectors, viral pathogens and their hosts or reservoirs using portable Oxford Nanopore sequencing. Using mosquitoes collected in São Paulo, Brazil, we extracted RNA for virus identification and DNA for blood meal and mosquito identification. Mosquitoes and blood meals were identified by comparing cytochrome c oxidase I (COI) sequences against a curated Barcode of Life Data System (BOLD). Viruses were identified using the SMART-9N protocol, which allows amplified DNA to be prepared with native barcoding for nanopore sequencing. Kraken 2 was employed to detect viral pathogens and Minimap2 and BOLD identified the contents of the blood meal. Due to the high similarity of some species, mosquito identification was conducted using blast after generation of consensus COI sequences using RACON polishing. This protocol can simultaneously uncover viral diversity, mosquito species and mosquito feeding habits. It also has the potential to increase understanding of mosquito genetic diversity and transmission dynamics of zoonotic mosquito-borne viruses.</p