Applications of Intuitionistic Logic in Answer Set Programming

We present some applications of intermediate logics in the field of Answer Set Programming (ASP). A brief, but comprehensive introduction to the answer set semantics, intuitionistic and other intermediate logics is given. Some equivalence notions and their applications are discussed. Some results on intermediate logics are shown, and applied later to prove properties of answer sets. A characterization of answer sets for logic programs with nested expressions is provided in terms of intuitionistic provability, generalizing a recent result given by Pearce. It is known that the answer set semantics for logic programs with nested expressions may select non-minimal models. Minimal models can be very important in some applications, therefore we studied them; in particular we obtain a characterization, in terms of intuitionistic logic, of answer sets which are also minimal models. We show that the logic G3 characterizes the notion of strong equivalence between programs under the semantic induced by these models. Finally we discuss possible applications and consequences of our results. They clearly state interesting links between ASP and intermediate logics, which might bring research in these two areas together.Comment: 30 pages, Under consideration for publication in Theory and Practice of Logic Programmin

Innovaciones poéticas en los espacios escénicos: S. M. de Tucumán (1967-1975)

El desarrollo del teatro moderno durante el siglo XX se caracterizó, entre otras múltiples cualidades, por los cuestionamientos, transformaciones e impugnaciones de las formas escénicas hegemónicas que fueron legitimadas durante los siglos XVII, XVIII y XIX en Europa Occidental. En este sentido, la arquitectura del teatro a la italiana constituyó un caso paradigmático, pues (como indicaremos a lo largo de este artículo) tuvo determinadas implicancias escenotécnicas y estéticas que los artistas, bajo sus objetivos de progreso y/o rechazo a la tradición, buscaron resignificar. Por consiguiente, nos proponemos indagar en los usos convencionales y/o prácticas innovadoras desplegadas por los agentes teatrales tucumanos a partir del espacio a la italiana, con el propósito de explicar y comprender algunas características de la modernización escénica local. Para lograr este objetivo, primero, seleccionamos (a partir del material fotográfico documentado) algunas puestas en escena, intentando describir y conceptualizar la gramática del espacio; segundo, determinamos ciertos núcleos semánticos de un texto dramático estratégico, con el fin de enunciar hipótesis heurísticas sobre los posibles ejes de lectura e interpretaciones que los escenógrafos desarrollaron, esto último, sin la intención de ahondar en otros ejes de teatralidad o de potencialidad literaria propios de dichas obras.Fil: Tossi, Mauricio Antonio. Universidad Nacional de Rio Negro; Argentina; Universidad Nacional de Tucumán; Argentina; Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Patagonia Norte; Argentina

정확한 서열정렬기법과 인메모리 핵심 유전자 데이터베이스 기반의 향상된 메타유전체 분류법

학위논문 (박사) -- 서울대학교 대학원 : 자연과학대학 협동과정 생물정보학전공, 2020. 8. 천종식.샷건 메타지노믹스는 미생물과 숙주 또는 환경사이의 미치는 영향을 이해하는데 매우 중요한 역할을 하고 있다. 기술의 발달과 더불어 메타지노믹스를 통한 올바른 미생물 종의 동정과 각 종들의 분포는 마이크로바이옴 연구의 핵심 구성요소가 되었으며, 지난 10년간 샷건 메타지노믹스 분석을 위한 여러 알고리즘과 데이터베이스들이 개발되어져 왔다. 하지만 서로 다른 기준 데이터 혹은 알고리즘을 사용한 방법들은 서로 다른 분류 정보와 분석 파이프라인으로 인하여 편향된 결과를 나타내기도 하였는데, 이를 보완하고 보다 정확한 분류 동정을 위해 배양이 어려운 표준 균주와 같은 다양한 균주의 유전체 데이터를 포함하는 기준 데이터베이스의 중요성이 대두되고 있다. 샷건 메타지노믹스 분석에서 또 다른 중요한 요소는 분석에 소요되는 시간이라 할 수 있는데 대부분의 생물정보학적 프로그램들은 계산을 수행함에 있어 메모리와 알고리즘 최적화가 되어있지 않아 분석에 상당한 시간이 소요되는 문제점이 있다. 이러한 문제를 해결하기 위해, 본 연구에서는 exact match k-mer classification과 같은 방법을 사용하여 분석 속도를 향상시켰으며 Up-to-date Bacterial Core Gene (UBCG)를 기준 데이터베이스로 사용하여 보다 정확한 샷건 메타지노믹 분석을 수행할 수 있게 하였다. 분석의 효율성을 높이기 위해 두개의 기준 UBCG 데이터베이스가 만들어 졌으며 한 개는 박테리아의 분류체계에서 유효한 종명 (Valid names)만을 가지고 있는 데이터베이스와 다른 하나는 유효한 종명과 함께 EzBioCloud에 있는 genomospecies를 가지고 생성하였다. 검증을 위해 Streptococcus 종을 포함하는 (i) 합성된 메타지놈 샘플과 (ii) 만성 폐쇄성 폐질환(COPD) 환자의 임상 검체 (iii) 혈류 감염 환자의 임상 검체로 이루어진 세개의 데이터 셋을 이용하였으며 기존에 널리 알려진 샷것 파이프라인인 MetaPhlan2과 본 연구의 파이프라인을 비교 분석하였다. 위 검증 분석에서 UBCG를 기준 서열로 사용하기에 충분함을 검증하였으며, 빠르고 정확하게 기준 유전체에서 UBCG 서열을 뽑아 샷건 분석에 용이함을 증명하였다. 또한 genomospecies를 기준 데이터베이스에 추가함으로써, 보다 개선된 분류 정확도를 얻을 수 있음을 제시하였다. 마지막으로 비록 여러 파이프라인과 데이터베이스들이 존재하지만 보다 신뢰할 수 있는 분류결과를 얻기 위해선 기준 데이터베이스의 지속적인 업데이트와 분류 체계의 검증의 중요함을 강조하였다. 이후 본 연구에서 개발된 파이프라인을 이용하여 4,000개의 샷건 메타지놈 샘플에서 사람에 장내에 가장 많이 발견되는 Bacteroides 종에 대한 분석을 수행하였다. 많은 양의 데이터를 분석하여야 하기 때문에 기존에 많이 사용되는 MetaPhlAn2 과 같은 방법은 사용할 수 없었으며 분석 결과 Bacteroides는 도시화된 사람에게 많이 분포하는 반면 아프리카 혹은 남미지역에서 원시적 부족의 삶을 사는 사람에게서는 상대적으로 적게 분포함을 확인할 수 있었다. 또한 각 나라별 인구에서는 우점되는 Bacteroides 종이 다름을 확인할 수 있었는데 이는 각 연구의 샘플링 방법 혹은 위치에 따라 설명되어 질 수 있었다. 실험용 쥐의 결과에서는 가장 다양한 Bacteroides를 관찰할 수 있었으며 이는 많은 수의 기준 유전체가 생쥐에게서 나왔기 때문인 것으로 생각된다. 또한 고양이나 강아지 같은 반려동물의 샘플에서도 높은 상관관계를 발견할 수 있었는데 각 동물들의 생활양식과 먹이에 따른 결과인 것으로 보인다. 본 연구를 통해 보다 많은 메타지놈 데이터 분석의 필요성을 강조하고 있으며, 핵심 유전자들을 기준 데이터로 사용하는 방법의 실효성과 성능을 검증하였다. 이러한 핵심 유전자 기반의 기준 데이터베이스는 보다 정확하고 전체 미생물의 풍부도를 예측하는데 중요한 역할을 하는 것을 확인하였고 k-mer 방법을 통해 기존에 존재하던 다른 파이프라인 보다 더욱 빠른 결과를 도출할 수 있었다. 마지막으로 빠르게 기준 데이터베이스를 만들 수 있기 때문에 항상 최신의 데이터를 가지고 분석을 수행할 수 있으며 이는 궁극적으로 본 연구의 파이프라인을 실질적으로 연구나 진단 목적으로 이용하는 연구자들에게 큰 도움이 될 것이다.Shotgun metagenomics is of great importance to understand the microbial community composition of a sample and the impact it has on its host. The proper identification and quantification of bacterial species is a key component of any microbiome research that is based on metagenomic samples. In the last decade, several algorithms and databases have been developed, however the differences between references and the type of algorithm used for the classification makes the comparisons among themselves unfair and bias. The contents of the reference database, including genome sequences of type strains or reference genomes of uncultured species, have a great impact on the performance of the classification results of metagenomic samples. Another significant factor on shotgun metagenomics is the classification speed as most current bioinformatic tools lack computational and memory optimization. Here, I propose several enhancements to a well-known method, exact match k-mer classification in order to increase the overall speed of a metagenomic classification. This method was further improved by the use of Up-to-date Bacterial Core Gene (UBCG) sequences to provide better method for a faster and accurate shotgun metagenomic profiling classification. In order to prove the efficiency of our method, I built two UBCG-based reference databases: one containing UBCG sequences of valid named species, and the second one containing UBCG sequences of all valid named species and genomospecies in the EzBioCloud database. Three datasets containing Streptococcus species were used to evaluate the improved method against the MetaPhlan2 tool which is the most widely used open-source shotgun metagenomic classifier: (i) synthetic metagenomic samples, (ii) clinical sputum samples from patients with chronic obstructive pulmonary disease (COPD), and (iii) clinical samples of a blood stream infection. In this analysis, I demonstrated that UBCG sequences can be used as references for metagenomic classification, showing that they are easy to extract from genome sequences and accurate when predicting relative abundance. I also showed that the inclusion of genomospecies in the reference databases, significantly improves the classification accuracy of bacterial species within a metagenomic sample. Finally, I showed that while publicly available pipelines and databases are easily accessible, for accurate and reliable taxonomic classification, an updated database with proper taxonomic and genomic curation must be used. The method devised in this work is then applied to profile the Bacteroides species in over 4,000 shotgun metagenomic samples, which is one of most abundant members of the human gut microbiome. This task cannot be accomplished using conventional tools such as MetaPhlAn2 due to the high processing time they require. The results in this study showed that Bacteroides is high abundant in human samples from urban areas while being low abundant in humans from rural areas, particularly African and South American tribes. Countries showed dominance for a specific Bacteroides species, but this could also be explained by the type of study were the samples came from. Mice samples showed the most diversity of Bacteroides, this can be attributed by the number of bacterial references isolated from this organism. House cat and dog samples showed correlation between each other, this may be attributed to the similarities of their lifestyle and diet. This study shows the importance of having a great number of samples for any given metagenomic analysis, and even though, we have profiled thousands of samples, more might be needed in the future. The method proposed in this thesis demonstrates that core genes are reliable reference sequences for shotgun metagenomics. Their implementation as reference sequences in metagenomic databases improves the accuracy of the abundance prediction of any given sample. Additionally, with the use of a k-mer approach, this methods running time outperforms the most popular shotgun metagenomic tools. The work presented in this thesis aims to help microbial research by providing faster and accurate metagenomic taxonomic predictions. Finally, with the ability of updating a metagenomic database with ease, will help researchers to obtain the most up-to-date results to find potential diagnosis or treatments for diseases associated to human microbial communities.Chapter 1. General Introduction 1 1.1. Introduction to metagenomics 2 1.2. 16S rRNA sequencing 3 1.3. Shotgun metagenomic sequencing 5 1.3.1. History 5 1.3.2. Sample extraction 7 1.3.3. Library preparation 8 1.3.4. Sequencing 8 1.4. Shotgun metagenomic classification 9 1.4.1. Homology-based approaches 9 1.4.2. Exact match K-mer approaches 11 Chapter 2. An exact match k-mer algorithm 13 2.1. An exact match k-mer classification approach 14 2.1.1. Definition of the problem 14 2.1.2. Building a k-mer reference database 14 2.1.2.1. K-mer counting 14 2.1.2.2. K-mer mapping 16 2.1.3. Classification of a metagenomic read 16 2.1.3.1. K-mer search 19 2.1.3.2. Scoring a metagenomic read 20 2.1.4. Calculating the metagenome profile 20 2.1.4.1. Normalization for LCA-assigned reads 21 2.1.4.2. Normalization for cell count relative abundance 22 2.2. RAM memory usage 22 2.3. Quality Control 23 2.3.1. Read Trimming 23 2.3.2. Host read removal 24 Chapter 3. Revealing unrecognized species in the genus Streptococcus 28 3.1. A brief history of streptococcus in clinical metagenomics 29 3.2. Results and Discussion 32 3.2.1. Building a core gene reference database 32 3.2.2. Evaluation of Pipelines using Synthetic Metagenomes 36 3.2.3. Chronic obstructive pulmonary disease samples 44 3.2.3. Evaluating the value of genomospecies references in a metagenomic database 56 3.2.4. Identifying accurately a Streptococcal infection using clinical data 63 3.2.5. Effects of different ANI thresholds on the classification of genomospecies 69 3.3. Materials and Methods 76 3.3.1. Selecting the reference genomes 76 3.3.2. Average nucleotide identity and hierarchical clustering 76 3.3.3. Synthetic and Real metagenomic samples 77 3.3.4. Extracting the core genes 77 3.3.5. Taxonomic profiling 83 3.3.6. Biomarker discovery 84 3.4. Conclusions 85 Chapter 4. A large-scale shotgun metagenomic analysis on Bacteroides 86 4.1. Introduction 87 4.2. Bacteroides on the human gut 89 4.2.1. Collecting the samples 89 4.2.2. Methods 89 4.2.2.1. Reference Genomes 89 4.2.2.2. Metagenome profiling 90 4.2.3. Results 103 4.3. Bacteroides on Animal Species 128 4.3.1. Methods 128 4.3.2. Results 128 4.4. Discussion and conclusions 133 General Conclusion 135 References 139 Appendix I. A list of genomes from the genus Streptococcus used on Chapters 3 analysis. 146 국문초록 155Docto

Intelligent Knowledge Retrieval from Industrial Repositories

Actually, a large amount of information is stored in the industrial repositories. Accessing this information is complicated, and the techniques currently used in metadata and the material chosen by the user do not scale efficiently in large collections. The semantic Web provides a frame of reference that allows sharing and reusing knowledge efficiently. In our work, we present a focus for discovering information in digital repositories based on the application of expert system technologies, and we show a conceptual architecture for a semantic search engine. We used case-based reasoning methodology to create a prototype that supports efficient retrieval knowledge from digital repositories. OntoEnter is a collaborative effort that proposes a new form of interaction between users and digital enterprise repositories, where the latter are adapted to users and their surroundings

REVISIÓN DE LA LITERATURA DEL PROBLEMA DE RUTEO DE VEHÍCULOS EN UN CONTEXTO DE TRANSPORTE VERDE

In the efficient management of the supply chain the optimal management of transport of consumables and finished products appears. The costs associated with transport have direct impact on the final value consumers must pay, which in addition to requiring competitive products also demand that they are generated in environmentally friendly organizations. Aware of this reality, this document is intended to be a starting point for Master's and Doctoral degree students who want to work in a line of research recently proposed: green routing. The state of the art of the vehicle routing problem is presented in this paper, listing its variants, models and methodologies for solution. Furthermore, the proposed interaction between variants of classical routing problems and environmental effects of its operations, known in the literature as Green-VRP is presented. The goal is to generate a discussion in which mathematical models and solution strategies that can be applied within organizations that consider within their objectives an efficient and sustainable operation are posed. En el gerenciamiento eficiente de la cadena de suministro aparece la gestión óptima del transporte de insumos y productos terminados. Los costos asociados al transporte tienen impacto directo sobre el valor final que deben pagar los consumidores, que además de requerir productos competitivos también exigen que los mismos sean generados en organizaciones amigables con el medioambiente. Consientes de esa realidad este documento pretende ser un punto de partida para estudiantes de maestría y doctorado que quieran trabajar en una línea de investigación propuesta recientemente: el ruteo verde. En este trabajo se muestra un estado del arte del problema de ruteo de vehículos, enumerando sus variantes, modelos y metodologías de solución. Además, se presenta la interacción que se ha propuesto entre variantes clásicas de los problemas de ruteo y los efectos ambientales de su operación, denominados en la literatura como Green-VRP. El objetivo es generar una discusión donde se planteen modelos matemáticos y estrategias de solución que puedan ser aplicadas en organizaciones que consideren dentro de sus objetivos una operación eficiente y sustentable. Document type: Articl