Algorithms for molecular geometry problems

Orientador: Carlile Campos LavorDissertação (mestrado) - Universidade Estadual de Campinas, Instituto de Matemática, Estatística e Computação CientíficaResumo: Neste trabalho, analisamos dois algoritmos da literatura para o "Molecular Distance Geometry Problem" (MDGP) e propomos um novo algoritmo que mantém a qualidade das soluções obtidas pelos dois anteriores e apresenta ganhos em termos de eficiência computacional. O MDGP consiste em determinar as posições dos átomos de uma molécula, no espaço tridimensional, a partir de um conjunto de distâncias entre eles. Quando todas as distâncias são conhecidas, o problema pode ser resolvido em tempo polinomial. Caso contrário, é um problema NP-difícilAbstract: In this work, we analyse two algorithms from the bibliography to solve the so-called "Molecular Distance Geometry Problem" (MDGP). Then, we propose a new algorithm that keeps the quality on the solutions obtained by both the previous ones and shows gains regarding computacional efficiency. The MDGP consists on the determination of positions of atoms in a molecule, on the tridimensional space, from a set containing distances among them. When all the distances are known, the problem might be solved in polynomial time. Otherwise, it is an NP-hard problemMestradoMatemática da ComputaçãoMestre em Matemática Aplicad

PhiKitA: Phishing Kit Attacks Dataset for Phishing Websites Identification

[En] Recent studies have shown that phishers are using phishing kits to deploy phishing attacks faster, easier and more massive. Detecting phishing kits in deployed websites might help to detect phishing campaigns earlier. To the best of our knowledge, there are no datasets providing a set of phishing kits that are used in websites that were attacked by phishing. In this work, we propose PhiKitA, a novel dataset that contains phishing kits and also phishing websites generated using these kits. We have applied MD5 hashes, fingerprints, and graph representation DOM algorithms to obtain baseline results in PhiKitA in three experiments: familiarity analysis of phishing kit samples, phishing website detection and identifying the source of a phishing website. In the familiarity analysis, we find evidence of different types of phishing kits and a small phishing campaign. In the binary classification problem for phishing detection, the graph representation algorithm achieved an accuracy of 92.50%, showing that the phishing kit data contain useful information to classify phishing. Finally, the MD5 hash representation obtained a 39.54% F1 score, which means that this algorithm does not extract enough information to distinguish phishing websites and their phishing kit sources properlySIInstituto Nacional de CiberseguridadThis work was supported by the framework agreement between the University of León and the Spanish National Cybersecurity Institute (INCIBE) under Addendum 01

Experiências internacionais de Community Land Trusts e lições para a implementação do modelo no Brasil

Community Land Trusts are a model of collective ownership of land that promotes tenure security, community strengthening and development for vulnerable populations. In this article, starting from the presentation of implemented experiences in the Global North and South, we analyze the organizational and conjunctural aspects that can contribute to its implementation in Brazil. After that, the Brazilian land tenure scenario is described, and also the first on-going experiment in Rio de Janeiro. The model, which still has few applications in the Global South, potentially represents an alternative to guaranteeing security of tenure and the right to housing in consolidated informal settlements. Inhabitants of these areas have their rights constantly violated and denied. Given the peculiarities of CLTs in the Global North and South, some lessons are suggested that can be drawn from the analyzed cases to facilitate the implementation of the model in Brazil.Os Community Land Trusts (CLTs) são um modelo de gestão coletiva da terra que promove a segurança da posse, assim como o fortalecimento e o desenvolvimento comunitário para populações vulnerabilizadas. Neste artigo, com base na apresentação de experiências consolidadas no Norte e Sul globais, analisam-se os aspectos organizativos e conjunturais que podem contribuir para sua implementação no Brasil. Em seguida, o cenário fundiário brasileiro é descrito, bem como a experiência pioneira em andamento na cidade do Rio de Janeiro. O modelo, ainda incipiente no Sul Global, apresenta potencial para aplicação em assentamentos informais consolidados com vistas a garantir a segurança da posse e o direito à moradia, constantemente negado e violado nesses contextos. Dadas as peculiaridades dos CLTs no Norte e Sul globais, são sugeridas algumas lições que podem ser retiradas dos casos analisados para facilitar a implementação do modelo no Brasil

Chitin/Metal‐Organic Framework Composites as Wide‐Range Adsorbent

Composites based on chitin (CH) biopolymer and metal-organic framework (MOF) microporous nanoparticles have been developed as broad-scope pollutant absorbent. Detailed characterization of the CH/MOF composites revealed that the MOF nanoparticles interacted through electrostatic forces with the CH matrix, inducing compartmentalization of the CH macropores that led to an overall surface area increase in the composites. This created a micro-, meso-, and macroporous structure that efficiently retained pollutants with a broad spectrum of different chemical natures, charges, and sizes. The unique prospect of this approach is the combination of the chemical diversity of MOFs with the simple processability and biocompatibility of CH that opens application fields beyond water remediation.Fil: Tovar Jimenez, Gabriel Ibrahin. Consejo Nacional de Investigaciones Científicas y Técnicas. Oficina de Coordinación Administrativa Houssay. Instituto de Química y Metabolismo del Fármaco. Universidad de Buenos Aires. Facultad de Farmacia y Bioquímica. Instituto de Química y Metabolismo del Fármaco; ArgentinaFil: Valverde, Ainara. Universidad del País Vasco; EspañaFil: Mendes Felipe, Cristian. Universidad del País Vasco; EspañaFil: Wuttke, Stefan. Universidad del País Vasco; EspañaFil: Fidalgo Marijuan, Arkaitz. University of the Basque Country ; EspañaFil: Larrea, Edurne S.. Loire Valley Institute for Advanced Studies, ; FranciaFil: Lezama, Luis. Universidad del País Vasco; EspañaFil: Zheng, Fangyuan. Universidad del País Vasco; EspañaFil: Reguera, Javier. Universidad del País Vasco; EspañaFil: Lanceros Méndez, Senentxu. Universidad del País Vasco; EspañaFil: Arriortua, María. Universidad del País Vasco; EspañaFil: Copello, Guillermo Javier. Consejo Nacional de Investigaciones Científicas y Técnicas. Oficina de Coordinación Administrativa Houssay. Instituto de Química y Metabolismo del Fármaco. Universidad de Buenos Aires. Facultad de Farmacia y Bioquímica. Instituto de Química y Metabolismo del Fármaco; ArgentinaFil: Luis, Roberto Fernández. Universidad del País Vasco; Españ

Association of melanoma with intraepithelial neoplasia of the pancreas in three patients

Melanoma and pancreatic cancer are two low frequency types of cancer. In this study, three patients who developed both melanoma and intraepithelial neoplasia of the pancreas were tested for CDKN2A mutations and deletions, and investigated for rare germline copy number variations (CNVs). The three patients were negative for CDKN2A point mutations and intragenic deletions. One of these patients carried two large (> 300 kb) germline CNVs, both genomic duplications affecting coding sequences that are not copy number variable in the population. A second patient exhibited loss of the entire Y chromosome, an event probably coincidental related to his advanced age (79 years-old). Our data pinpoint that rare germline CNVs harboring genes can contribute to the cancer predisposition of melanoma and intraepithelial neoplasia of the pancreas.This work was supported by the National Institute of Science and Technology in Oncogenomics (Grant 08/57887-9) and FAPESP (Grants 2012/21932-6 and 2013/07480-8)

Effectiveness of Chewing Gum Containing CPP-ACP for Remineralisation of Demineralised Enamel around Orthodontic Brackets: An in Situ Study

Objective: To evaluate the effectiveness of chewing gums containing CPP-ACP in remineralisation of demineralised enamel around orthodontic brackets. Material and Methods: Enamel blocks from 120 bovine incisors were used. The blocks were flattened and polished, followed by the development of incipient subsurface caries. The blocks have been subjected to a baseline microhardness analysis. Orthodontic brackets were bonded to the exposed area of the blocks, reserving an area for hardness analysis. An in situ crossover (three-way crossover phases of 21 days with an interval of one week between them), controlled, randomised and blind experimental model was used, with the participation of 12 volunteers divided into groups: G1 – negative control group, without chewing gum; G2 – conventional sugar-free chewing gum, without CPP-ACP (placebo); and G3 – sugar-free chewing gum with CPP-ACP. The following parameters were analysed: superficial linear (Ra), volumetric roughness (Sa), and superficial structural loss, which was indicated by Gap measurement (difference between the healthy and treated area). Statistical tests used were the Friedman, Wilcoxon and Shapiro-Wilk, Kruskal Wallis' nonparametric tests and ANOVA. Results: There was a significant reduction in enamel microhardness after demineralisation in all the groups (p<0.05). This deleterious effect was attenuated in the three groups after the final evaluation, although there were no statistical differences (p<0.05); however, the final values did not return to the baseline values (p<0.05). Conclusion: Chewing gum containing CPP-ACP did not promote in situ remineralisation of demineralised enamel around orthodontic brackets

An Inherited Small Microdeletion at 15q13.3 in a Patient\ud with Early- Onset Obsessive-Compulsive Disorder

Copy number variations (CNVs) have been previously associated with several different neurodevelopmental psychiatric\ud disorders, such as autism, schizophrenia, and attention deficit hyperactivity disorder (ADHD). The present study consisted of\ud a pilot genome-wide screen for CNVs in a cohort of 16 patients with early-onset obsessive-compulsive disorder (OCD) and\ud 12 mentally healthy individuals, using array-based comparative genomic hybridization (aCGH) on 44K arrays. A small rare\ud paternal inherited microdeletion (,64 kb) was identified in chromosome 15q13.3 of one male patient with very early onset\ud OCD. The father did not have OCD. The deletion encompassed part of the FMN1 gene, which is involved with the\ud glutamatergic system. This finding supports the hypothesis of a complex network of several genes expressed in the brain\ud contributing for the genetic risk of OCD, and also supports the glutamatergic involvement in OCD, which has been\ud previously reported in the literature.We wish to thank the patients and heathy controls who volunteered to participate in this study.This study was supported by grants to Dras Cappi and Brentani from the Foundation for Research Support of the State of São Paulo (FAPESP); grant number: 2008/11537-7, and from the Brazilian National Council for Scientific and Technological Development (CNPq; protocol number MCT/CNPq 14/2008). The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript

Implantación tecnológica y metodológica de una plataforma institucional de SPOC (Small Private Online Courses) en la Universidad de Salamanca

Memoria ID-074. Ayudas de la Universidad de Salamanca para la innovación docente, curso 2019-2020.[ES]El objetivo principal de este proyecto es sentar las bases tecnológicas, metodológicas y pragmáticas de una política institucional sobre los SPOC (Small Private Online Courses) en la Universidad de Salamanca

Treatment variability and its relationships to outcomes among patients with Wernicke's encephalopathy: A multicenter retrospective study

Background: Despite guidelines and recommendations, Wernicke's encephalopathy (WE) treatment lacks evidence, leading to clinical practice variability.Aims: Given the overall lack of information on thiamine use for WE treatment, we analyzed data from a large, well-characterized multicenter sample of patients with WE, examining thiamine dosages; factors associated with the use of different doses, frequencies, and routes; and the influence of differences in thiamine treatment on the outcome.Methods: This retrospective study was conducted with data from 443 patients from 21 centers obtained from a nationwide registry of the Spanish Society of Internal Medicine (from 2000 to 2012). Discharge codes and Caine criteria were applied for WE diagnosis, and treatment-related (thiamine dosage, frequency, and route of administration) demographic, clinical, and outcome variables were analyzed.Results: We found marked variability in WE treatment and a low rate of high-dose intravenous thiamine administration. Seventy-eight patients out of 373 (20.9%) received > 300 mg/day of thiamine as initial dose. Patients fulfilling the Caine criteria or presenting with the classic WE triad more frequently received parenteral treatment. Delayed diagnosis (after 24 h hospitalization), the fulfillment of more than two Caine criteria at diagnosis, mental status alterations, and folic acid deficiency were associated significantly with the lack of complete recovery. Malnutrition, reduced consciousness, folic acid deficiency, and the lack of timely thiamine treatment were risk factors for mortality.Conclusions: Our results clearly show extreme variability in thiamine dosages and routes used in the management of WE. Measures should be implemented to ensure adherence to current guidelines and to correct potential nutritional deficits in patients with alcohol use disorders or other risk factors for WE