Orientador: Messias Modesto dos Passos / Banca: Antonio Cézar Leal / Banca: Wolmar Apparecida Carvalho / Banca: Sueli Ângelo Furlan / Banca: Maria Eugênia Moreira Costa / Banca: Helder Henrique de Faria / Resumo: Para muitos autores, as unidades de conservação da natureza, ou áreas protegidas, são ou serão os últimos baluartes da conservação estrita da biodiversidade, sendo esta razão, não excludente de outras, a principal motivadora para a existência de uma gestão verdadeiramente eficaz, que conduza ao alcance dos objetivos para os quais elas são criadas. A avaliação da eficácia de gestão através de procedimentos metodológicos estruturados com base na utilização de indicadores é uma importante ferramenta de suporte à gestão, pois possibilita a coleta periódica e sistemática sobre a qualidade da gestão, facilita a priorização de assistências e investimentos pontuais e a realimentação do sistema gerencial. Nesta pesquisa, verificou-se a eficácia de gestão de unidades de conservação de São Paulo adotando-se e adaptando-se um procedimento metodológico desenvolvido originalmente na Costa Rica, posteriormente adaptado à realidade das unidades de conservação de vários países da América Latina. Os princípios do procedimento são o uso de indicadores e critérios estritos para a qualificação, associados a uma escala de valoração geral. O universo do estudo envolveu 59 áreas gerenciadas pelo Instituto Florestal de São Paulo, sendo 41 do grupo de proteção integral e 18 do grupo de uso sustentável, totalizando 69% do total das UCs e quase 90% da superfície total sob a guarda da organização, representando 782.622,25ha. Para a coleta de dados utilizou-se a bibliografia disponível sobre o sistema em análise, oficinas de avaliação coletiva, entrevistas e visitas a áreas previamente selecionadas. A análise dos indicadores e das ameaças demonstraram as debilidades da organização e a fragilidade com que a gestão de muitas unidades de conservação é levada a termo... (Resumo completo clicar acesso eletrônico abaixo) / Abstract: For many authors, the conservation units (UCs) or protected areas are or will be the last bastions of the strict conservation of biodiversity, being this reason (not exculpatory of others) one of the main reasons for the existence of a truly effective management, that leads to the reach of the objectives for which they are created. The evaluation of the effectiveness management through structuralized procedures on the basis of the use of pointers is an important tool of support to the management, therefore it makes possible the periodic and systematic collection on the quality of the management, it makes easier and gives priority to help and prompt investments and the feedback of the management system. In this research adopting themselves developed methodological procedure from Costa Rica, later adapted to the reality of the protected areas of some countries from Latin America. The principles of the procedure are the strict use of indicators and criteria for the qualification, associates to a scale of general valuation. The universe of the study involved 59 protected areas managed for the Forest Institute of São Paulo, being 41 of the group of integral protection and 18 of the group of sustainable use, totalizing 69% of the total of UCs and almost 90% of the total surface under the guard of the organization, representing 782.622,25ha. For the data collection, has been used available bibliography on the system in analysis, workshops of collective evaluation, interviews and technical visits the areas previously selected. The indicators and the threats analysis had demonstrated to the debility of the organization and the fragility with that the management of many units of conservation is taken the term. The majority of the UCs had the management classified as inferior and medium standards of quality, demonstrating as many negative aspects as positive, unfortunately reigning the first ones... (Complete abstract, click electronic address below) / Doutor

Genome-wide studies are prone to false positives due to inherently low priors and statistical power. One approach to ameliorate this problem is to seek validation of reported candidate genes across independent studies: genes with repeatedly discovered effects are less likely to be false positives. Inversely, genes reported only as many times as expected by chance alone, while possibly representing novel discoveries, are also more likely to be false positives. We show that, across over 30 genome-wide studies that reported Drosophila and Daphnia genes with possible roles in thermal adaptation, the combined lists of candidate genes and orthologous groups are rapidly approaching the total number of genes and orthologous groups in the respective genomes. This is consistent with the expectation of high frequency of false positives. The majority of these spurious candidates have been identified by one or a few studies, as expected by chance alone. In contrast, a noticeable minority of genes have been identified by numerous studies with the probabilities of such discoveries occurring by chance alone being exceedingly small. For this subset of genes, different studies are in agreement with each other despite differences in the ecological settings, genomic tools and methodology, and reporting thresholds. We provide a reference set of presumed true positives among Drosophila candidate genes and orthologous groups involved in response to changes in temperature, suitable for cross-validation purposes. Despite this approach being prone to false negatives, this list of presumed true positives includes several hundred genes, consistent with the “omnigenic” concept of genetic architecture of complex traits.

Indiana University-Purdue University Indianapolis (IUPUI) / This dissertation proposes an approach to reduce the cost of manual inspections for as large a number of false positive warnings that are being reported by Static Code Analysis (SCA) tools as much as possible using Machine Learning (ML) techniques. The proposed approach neither assume to use the particular SCA tools nor depends on the specific programming language used to write the target source code or the application. To reduce the number of false positive warnings we first evaluated a number of SCA tools in terms of software engineering metrics using a highlighted synthetic source code named the Juliet test suite. From this evaluation, we concluded that the SCA tools report plenty of false positive warnings that need a manual inspection. Then we generated a number of datasets from the source code that forced the SCA tool to generate either true positive, false positive, or false negative warnings. The datasets, then, were used to train four of ML classifiers in order to classify the collected warnings from the synthetic source code. From the experimental results of the ML classifiers, we observed that the classifier that built using the Random Forests (RF) technique outperformed the rest of the classifiers. Lastly, using this classifier and an instance-based transfer learning technique, we ranked a number of warnings that were aggregated from various open-source software projects. The experimental results show that the proposed approach to reduce the cost of the manual inspection of the false positive warnings outperformed the random ranking algorithm and was highly correlated with the ranked list that the optimal ranking algorithm generated.

The goal of this research is to improve an IDS so that the percentage of true positives is high, an organisation can cut time and cost and use its resources in a more optimal way. This research goal was to prove that the precision of an intrusion detection system (IDS), in terms of producing lower rate of false positives or higher rate of true alerts, can be achieved by parsing indicators of compromise (IOC) to gather information, that combined with system-specific knowledge will be a solid base for manual fine-tuning of IDS-rules. The methodology used is Design Science Research Methodology (DSRM) because it is used for research that aims to answer an existing problem with a new or improved solution. A part of that solution is a proposed process for tuning of an arbitrary intrusion detection system. The implemented and formalized process Tuned Intrusion Detection System (TIDS) has been designed during this research work, aiding us in presenting and performing validation tests in a structured and robust way. The testbed consisted of a Windows 10 operating system and a NIDS implementation of Snort as an IDS. The work was experimental, evaluated and improved regarding IDS rules and tools over several iterations. With the use of recorded data traffic from the public dataset CTU-13, the difference between the use of tuned versus un-tuned rules in an IDS was presented in terms of precision of the alerts created by the IDS. Our contributions were that the concept holds; the precision can be improved by adding custom rules based on known parameters in the network and features of the network traffic and disabling rules that were out of scope. The second contribution is the TIDS process, as designed during the thesis work, serving us well during the process.

Les inconvénients associés à l’application des traitements thermiques élevés lors de la conservation des aliments sont nombreux, allant des coûts énergétiques élevés jusqu’à la détérioration de la valeur nutritive et organoleptique des aliments transformés. La tendance des consommateurs se dirige de plus en plus vers la consommation des aliments peu transformés, salubres et de haute valeur nutritive et sensorielle. Ainsi, afin de répondre à leurs besoins et pour minimiser les effets néfastes dus aux traitements thermiques élevés, le recours à de nouvelles techniques de conservation des aliments est devenu nécessaire. Ainsi, l’objectif principal de ce projet de doctorat était de trouver une nouvelle alternative aux traitements thermiques élevés afin de produire des aliments peu transformés ayant deux caractéristiques : une haute valeur nutritionnelle et organoleptique tout en étant salubre. Pour atteindre cet objectif, la technologie de l’électro-activation en solution, en combinaison avec des traitements thermiques modérés et de la nisine, a été mise à l’étude dans ce projet. Pour cela, huit solutions aqueuses (acétate et citrate de potassium avec et sans KCl) ont été électro-activées dans un réacteur d’électro-activation modulé avec des membranes échangeuses d’anions et de cations. Une fois électro-activées, ces solutions ont été combinées avec des températures modérées, entre 25 et 95 C, et d’une bactériocine de source naturelle, la nisine. Ainsi, l’activité synergique de différentes combinaisons impliquant ces trois facteurs a été testée dans des conditions modèles, ainsi qu’avec une matrice alimentaire végétale, sur l’inactivation des spores de Clostridium sporogenes PA 3679 utilisé comme un substitut non pathogène de Clostridium botulinum. Dans un premier temps, des solutions aqueuses d’acétate de potassium et de citrate de potassium, avec ou sans ajout de chlorure de potassium dans les deux cas, ont été électro-activées sous différentes intensités de courant électrique (100, 200, 300 et 400 mA) pendant une heure. Pour chaque type de solution, seules celles qui avaient le plus bas pH et le plus haut potentiel d’oxydoréduction (POR) ont été retenues pour la suite du projet. Par la suite, les solutions électro-activées retenues ont été testées, seules et combinées avec différents traitements thermiques modérés, pour leur effet d’inactivation des spores de C. sporogenes PA 3679 dans des conditions modèles. L’effet sporicide détecté a été validé par observation sous microscope électronique à transmission. Également, l’efficacité des traitements avec des solutions électro-activées, combinées avec la nisine à différentes concentrations, a été testée contre les spores de C. sporogenes PA 3679 dans une purée des haricots verts. Il a été démontré que ces solutions électro-activées induisaient une réduction significative des populations de spores de C. sporogenes PA 3679, mais le pouvoir tampon du milieu, induit par les matières organiques des haricots verts, a provoqué une baisse significative du degré d’inactivation des spores de C. sporogenes PA 3679 par rapport à celui détecté dans des conditions modèles. La combinaison de la nisine avec les solutions électro-activées et les traitements thermiques modérés était capable de récupérer une partie de l’activité sporicide initiale (obtenues dans des conditions modèles). L’activité sporicide finale obtenue a été validée par observation sous microscope électronique à transmission. Finalement, testée dans un milieu contenant des tiges intactes (entières) des haricots verts, une augmentation significative de l’activité sporicide a été détectée en combinant les solutions électro-activées d’acétate de potassium et de citrate de potassium avec la nisine et un traitement thermique modéré représentant le barème thermique utilisé pour le blanchiment des légumes (95 C). Ainsi, le pouvoir protecteur de la purée des haricots pour les spores de C. sporogenes PA 3679 a été mis en évidence. En conclusion, deux combinaisons permettant un traitement efficace contre les spores de C. sporogenes PA 3679 ont été suggérées. La première est une combinaison d’une solution d'acétate de potassium électro-activée à 400 mA pendant 60 minutes combinée avec de la nisine à une concentration de 1000 UI/mL et un traitement thermique modéré de 95 °C pendant 15 minutes. La seconde consiste à combiner une solution de citrate de potassium électro-activée à 400 mA pendant 60 minutes avec la nisine à une concentration de 1000 UI/ml et un traitement thermique de 115 °C pendant 15 minutes. / The severe heat treatments used for the preservation of foods, especially the canned, is associated with different disadvantages ranging from high energy costs of the process to the deterioration of the nutritional and organoleptic value of the processed foods. Currently, consumers are increasingly turning their attention to the consumption of safe, low-processed foods with high nutritional value and organoleptic value. Thus, in order to meet their needs (requirements) and to minimize the negative effects of the processing technologies, due to the high heat treatments, the search of new food preservation techniques is necessary. Thus, the main aim of this work was to find an alternative method of food preservation in order to produce low-processed foods with respect to two main characteristics: high nutritional value and microbial safety. To reach this objective, four aqueous solutions; namely potassium acetate and potassium citrate with or without KCl added, were electro-activated in an electro-activation reactor composed of three section separated by anion and cation exchange membranes. Once electro-activated, these solutions were combined with moderate heat treatments and nisin at different concentrations. The synergistic activity of all these factors (hurdles) was tested under model conditions and in a food matrix on the inactivation of Clostridium sporogenes PA 3679 spores, used as a non-pathogenic surrogate of Clostridium botulinum. First, the selected aqueous solutions were electro-activated at different current intensities (100, 200, 300 and 400 mA) during one hour. For each type of solution, only solutions with the lowest pH and highest oxido-reduction potential (ORP) were selected to be used in the present study. After that, the selected electro-activated solutions were tested, alone and in combination with moderate heat treatments, for their inactivation effect towards C. sporogenes PA 3679 spores under model conditions (direct contact between the electro-activated solutions and the spores). The obtained results showed high effectiveness of these solutions and the detected sporicidal effect was validated by observation under transmission electron microscope. Finally, the efficacy of the combined treatments was tested against C. sporogenes PA 3679 spores in a green bean puree. The obtained results showed some buffering capacity induced by the organic matter of the puree which was able to significantly decrease the degree of inactivation of C. sporogenes PA 3679 spores compared to the effect we detected in the model conditions. The combination of nisin with the electro-activated solutions and moderate heat treatments was able to recover the initial sporicidal activity which was obtained under the model conditions. The final sporicidal activity detected was validated under transmission electron microscopy. Moreover, this study showed that when tested in intact stems of green beans, the sporicidal activity was very high. These results permitted to validate the protective effect induced by the bean puree to the C. sporogenes PA 3679 spores. In conclusion, two combinations that can be successfully used as effective hurdle were selected. The first one is a combination of an electro-activated potassium acetate solution under 400 mA during 60 min, nisin at a concentration of 1000 IU/mL and a moderate heat treatment of 95 °C applied during 15 minutes. The second hurdle consists of combining an electro-activated solution of potassium citrate under 400 mA during 60 min with 1000 IU/ ml of nisin and a heat treatment of 115 °C applied during 15 minutes. Thus, according to the obtained results, it can be suggested that under appropriate canning conditions, the process can be limited to the blanching step which be conducted at 95 °C.

This thesis investigates the integration of State-of-the-Art (SOTA) Large Language Models (LLMs) into the process of reassessing security findings generated by Static Application Security Testing (SAST) tools. The primary objective is to determine whether LLMs are able to detect false positives (FPs) while maintaining a high true positive (TP) rate, thereby enhancing the efficiency and effectiveness of security assessments. Four consecutive experiments were conducted, each addressing specific research questions. The initial experiment, using a dataset of security findings extracted from the OWASP Bench- mark, identified the optimal combination of context items provided by the SAST tool Spot- Bugs, which, when used with GPT-3.5 Turbo, reduced FPs while minimizing the loss of TPs. The second experiment, conducted on the same dataset, demonstrated that advanced prompting techniques, particularly few-shot Chain-of-Thought (CoT) prompting combined with Self-Consistency (SC), further improved the reassessment process. The third experiment compared both proprietary and open-source LLMs on an OWASP Benchmark dataset about one-fourth the size of the previously used dataset. GPT-4o achieved the highest performance, detecting 80 out of 128 FPs without missing any TPs, resulting in a perfect TPR of 100% and a decrease in FPR by 41.27 percentage points. Meanwhile, Llama 3.1 70B detected 112 out of the 128 FPs but missed 10 TPs, resulting in a TPR of 94.94% and a reduction in FPR by 56.62 percentage points. To validate these findings in a real-world context, the approach was applied to a dataset generated from the open-source project Mnestix using multiple SAST tools. GPT-4o again emerged as the top performer, detecting 26 out of 68 FPs while only missing one TP, resulting in a TPR decreased by 2.22 percentage points but simultaneously an FPR decreased 37.57 percentage points.:Table of Contents IV List of Figures VI List of Tables VIII List of Source Codes IX List of Abbreviations XI 1. Motivation 1 2. Background 3 3. Related Work 17 4. Concept 31 5. Preparing a Security Findings Dataset 39 6. Implementing a Workflow 51 7. Identifying Context Items 67 8. Comparing Prompting Techniques 85 9. Comparing Large Language Models 101 10.Evaluating Developed Approach 127 11.Discussion 141 12.Conclusion 145 A. Appendix: Figures 147 A.1. Repository Directory Tree 148 A.2. Precision-Recall Curve of Compared Large Language Models 149 A.3. Performance Metrics Self-Consistency on Mnestix Dataset 150 B. Appendix: Tables 151 B.1. Design Science Research Concept 151 C. Appendix: Code 153 C.1. Pydantic Base Config Documentation 153 C.2. Pydantic LLM Client Config Documentation 155 C.3. LLM BaseClient Class 157 C.4. Test Cases Removed From Dataset 158

Le phénomène de multirésistance aux antibiotiques chez les bactéries à Gram positif causant des infections sévères du sang est un problème mondial grandissant. La détection du niveau de sensibilité aux antibiotiques avec des tests phénotypiques requière un minimum de 48 h avant l'obtention des résultats. Il est donc nécessaire de développer des tests de diagnostic rapides, sensibles, spécifiques et ubiquitaires pour améliorer le traitement des septicémies. Ce mémoire de maîtrise présente le développement d'un test de diagnostic moléculaire permettant la détection rapide des gènes de résistance aux antibiotiques cliniquement importants associés aux bactéries à Gram positif causant des septicémies. Ce test comprend 4 essais PCR multiplex combinés à une hybridation microfluidique sur puces à ADN intégrées à un disque compact. Les corrélations obtenues entre les résultats génotypiques et phénotypiques étaient de 98% pour les P-lactamines et de 100% pour la vancomycine, la clindamycine et la gentamicine. Cette approche moléculaire pourrait éventuellement être utilisée pour le diagnostic clinique afin de guider l'antibiothérapie des patients atteints d'une septicémie.

L’étude utilise la méthode des différences entre jumeaux monozygotes pour analyser le lien entre les pratiques parentales positives ou hostiles-réactives de la mère à 29 mois et la qualité des relations d’amitié des enfants à 6 ans, tout en contrôlant une série de facteurs confondants tels le sexe, le revenu familial, le tempérament et le poids à la naissance. Un effet modérateur du sexe est aussi testé. La méthodologie nouvelle et particulière de cette recherche permet de contrôler de possibles corrélations gènes-environnement. Les résultats ne concordent pas tous avec les hypothèses et démontrent que 1) le jumeau ayant reçu le plus de pratiques parentales positives de la mère est celui dont l’ami évalue le plus négativement sa relation d’amitié à 6 ans et 2) le jumeau ayant reçu le plus de pratiques parentales hostiles-réactives de la mère est celui dont l’ami évalue le moins positivement sa relation d’amitié à la maternelle. Différentes pistes d’explications sont proposées pour comprendre les résultats et pour guider les études futures. / This study used the monozygote twin differences method to analyze the links between positive or hostile maternal practices by the mother at 29 months and children’s friendship quality at 6 years of age. This new methodology can control for any possible genes-environment correlations. We also controlled for temperament, weight at birth, gender and socioeconomic status and we tested whether gender moderated the link between variables. Results are unexpected: 1) the twin who received the most positive maternal practices had the friend who evaluated the most negatively their friendship, 2) the twin who received the most hostile practices from his mother had the friend who evaluated the less positively their friendship. We propose different explanations to understand the results and we make suggestions for future studies.

L’étude utilise la méthode des différences entre jumeaux monozygotes pour analyser le lien entre les pratiques parentales positives ou hostiles-réactives de la mère à 29 mois et la qualité des relations d’amitié des enfants à 6 ans, tout en contrôlant une série de facteurs confondants tels le sexe, le revenu familial, le tempérament et le poids à la naissance. Un effet modérateur du sexe est aussi testé. La méthodologie nouvelle et particulière de cette recherche permet de contrôler de possibles corrélations gènes-environnement. Les résultats ne concordent pas tous avec les hypothèses et démontrent que 1) le jumeau ayant reçu le plus de pratiques parentales positives de la mère est celui dont l’ami évalue le plus négativement sa relation d’amitié à 6 ans et 2) le jumeau ayant reçu le plus de pratiques parentales hostiles-réactives de la mère est celui dont l’ami évalue le moins positivement sa relation d’amitié à la maternelle. Différentes pistes d’explications sont proposées pour comprendre les résultats et pour guider les études futures. / This study used the monozygote twin differences method to analyze the links between positive or hostile maternal practices by the mother at 29 months and children’s friendship quality at 6 years of age. This new methodology can control for any possible genes-environment correlations. We also controlled for temperament, weight at birth, gender and socioeconomic status and we tested whether gender moderated the link between variables. Results are unexpected: 1) the twin who received the most positive maternal practices had the friend who evaluated the most negatively their friendship, 2) the twin who received the most hostile practices from his mother had the friend who evaluated the less positively their friendship. We propose different explanations to understand the results and we make suggestions for future studies.

Rhodococcus fascians is a Gram-positive phytopathogenic bacterium which induces the development of leafy galls, local amplifications of multiple buds, on most infected plants. This process is linked to the production of phytohormones along with the presence of essential virulence-associated genes like the plasmid loci att and fas and the chromosomal gene vicA. However, the presence of these genes is not sufficient to ensure the infection phenotype development, indicating that other genes play a role in R. fascians pathogenicity. In this work, we studied the metabolic modifications occurring when the bacterium interacts with its host using a proteomic approach. A comparison between virulent and avirulent strains showed variations in the expression of catalases. In the virulent strain, besides the transitory induction of the att locus expression, the bacterium changes its metabolism from the Krebs cycle to the glyoxylate shunt, a process which is frequently observed in bacteria confronted to a hostile environment. The expression of the shunt-specific enzyme isocitrate lyase increased, while expression of fumarate hydratase and pyruvate dehydrogenase decreased. Hence, we focused on the link between the glyoxylate shunt and virulence. A screening of a R. fascians mutant library based on the capacity of bacteria to use acetate as the sole carbon source, a metabolic pathway depending on the glyoxylate shunt, resulted in the identification of a new gene essential for R. fascians pathogenicity. This gene encodes a glycosyl transferase, an enzyme known to be involved in the bacterial cell wall biosynthesis but possibly also implicated in cytokinin secretion. A mutant in this gene harboured an altered colony phenotype and could not induce malformations on infected plants. Accordingly, our results were integrated in the leafy gall pathology model recently presented by Stes et al. (2011). Finally, the several questions that are raised by this work, allowed us to suggest further research perspectives in order to unveil a little more of the R. fascians mysterious ways to interact with the plant./Rhodococcus fascians est une bactérie Gram-positive phytopathogène qui induit le développement de galles feuillées, des amplifications locales de multiples bourgeons, sur la plupart des plantes infectées. Ce processus est lié à la production de phytohormones ainsi qu’à la présence de gènes essentiels associés à la virulence tels que les loci plasmidiques att et fas et le gène chromosomique vicA. Cependant, la présence de ces gènes ne suffit pas à garantir le développement du phénotype d’infection, indiquant que d’autres gènes jouent un rôle dans la pathogénicité de R. fascians. Dans ce travail, nous avons étudié les modifications métaboliques qui se produisent lorsque la bactérie interagit avec son hôte par une approche protéomique. Une comparaison entre les souches virulente et avirulente a mis en évidence des variations d’expression au niveau des catalases. Dans la souche virulente, outre l’induction transitoire de l’expression du locus att, la bactérie change son métabolisme pour passer du cycle de Krebs au shunt du glyoxylate, un processus fréquemment observé chez les bactéries confrontées à un environnement hostile. L’expression de l’isocitrate lyase, enzyme spécifique au shunt, augmente, tandis que celle de la fumarate hydratase et de la pyruvate déhydrogénase diminue. Nous nous sommes donc intéressés au lien entre le shunt du glyoxylate et la virulence. Le screening d’une banque de mutants de R. fascians basé sur la capacité de la bactérie à utiliser l’acétate comme seule source de carbone, une voie métabolique dépendant du shunt du glyoxylate, a permis d’identifier un nouveau gène essentiel pour la pathogénicité de R. fascians. Ce gène code pour une glycosyl transferase, une enzyme impliquée dans la biosynthèse de la paroi bactérienne mais également dans la sécrétion des cytokinines. Un mutant dans ce gène présente un phénotype de colonie altéré et ne peut induire de malformations chez les plantes infectées. Finalement, nos résultats et les pistes d’interprétations que nous avons émisent nous permettent de compléter le modèle de l’interaction R. fascians-plante proposé récemment par Stes et al. (2011). Des perspectives de recherches visant une meilleure compréhension de ce pathosystème sont proposées. / Doctorat en Sciences / info:eu-repo/semantics/nonPublished