Ranking relations using analogies in biological and information networks

Analogical reasoning depends fundamentally on the ability to learn and generalize about relations between objects. We develop an approach to relational learning which, given a set of pairs of objects $\mathbf{S}=\{A^{(1)}:B^{(1)},A^{(2)}:B^{(2)},\ldots,A^{(N)}:B ^{(N)}\}$, measures how well other pairs A:B fit in with the set $\mathbf{S}$. Our work addresses the following question: is the relation between objects A and B analogous to those relations found in $\mathbf{S}$? Such questions are particularly relevant in information retrieval, where an investigator might want to search for analogous pairs of objects that match the query set of interest. There are many ways in which objects can be related, making the task of measuring analogies very challenging. Our approach combines a similarity measure on function spaces with Bayesian analysis to produce a ranking. It requires data containing features of the objects of interest and a link matrix specifying which relationships exist; no further attributes of such relationships are necessary. We illustrate the potential of our method on text analysis and information networks. An application on discovering functional interactions between pairs of proteins is discussed in detail, where we show that our approach can work in practice even if a small set of protein pairs is provided.Comment: Published in at http://dx.doi.org/10.1214/09-AOAS321 the Annals of Applied Statistics (http://www.imstat.org/aoas/) by the Institute of Mathematical Statistics (http://www.imstat.org

Low-dimensional affine synchronizing groups

Tese de mestrado em Matemática, apresentada à Universidade de Lisboa, através da Faculdade de Ciências, 2012The synchronization property emerged from finite state automata and transformation semigroup theory. Synchronizing permutation groups were introduced by Arnold and Steinberg to study the Cerný Conjecture. In this thesis we study the synchronization property in affine permutation groups of low-dimensions. J.E. Pin proved that one-dimensional affine groups are synchronizing. Hence our main results concern affine groups in dimension 2. We used the characterization given by Neumann of synchronization using graph theory, which relies on the study of the equality between the clique number and the chromatic number of certain graphs invariant under the actions of a group, called the suitability property. It turned out that some of such graphs for two-dimensional affine groups have an interesting geometry and are part of a widely studied class of graphs, the generalized Paley graphs. Further, we used the properties of the theta-function defined by Lovász connected to eigenvalues of a graph to obtain a necessary condition for the suitability in edge-transitive and vertex-transitive graphs. In this thesis we stated a criterion to decide if a generalized Paley graph is suitable. Then we used the tools referred to above and we presented conditions for twodimensional affine groups to be synchronizing.A propriedade de sincronização surgiu no contexto da teoria de autómatos e semigrupos de transformaçãoo. Arnold and Steinberg definiram os grupos de permutação sincronizantes com o objectivo de estudar a Conjectura de Cerný por outra perspectiva. Nesta tese estudamos a propriedade de sincronização em grupos afins de pequenas dimensões. Dado que J.E. Pin provou que os grupos afins de dimensão 1 são sempre sincronizantes, os resultados principais desta tese aplicam-se a grupos afins bidimensionais. Peter Neumann estudou os grupos sincronizantes usando teoria de grafos. Esta caracterização consiste no estudo de grafos invariantes sobre a acção de um grupo e em determinar se os seus números cromático e de clique coincidem. Descobrimos que alguns grafos invariantes sobre a acção de grupos afinns bidimensionais tinham uma geometria simétrica e que faziam parte de uma classe amplamente estudada de grafos, conhecidos como grafos de Paley generalizados. Como ferramenta extra, estudámos a função-teta, um número invariante num grafo, que foi definida por Lovász. Esta função possui uma caracterização que utiliza os valores próprios da matriz de adjacência do grafo e que nos permitiu concluir uma condição suficiente para a igualdade no número cromático e de clique em grafos cujo grupo de automorfismos é transitivo nas arestas e nos vértices. Nesta tese estabelecemos um critério para a igualdade no número cromático e de clique nos grafos de Paley generalizados e usámos esse resultado, bem como as ferramentas anteriormente referidas, para obter uma caracterização dos grupos afins bidimensionais sincronizantes

Fuzzy Authentication using Rank Distance

Fuzzy authentication allows authentication based on the fuzzy matching of two objects, for example based on the similarity of two strings in the Hamming metric, or on the similiarity of two sets in the set difference metric. Aim of this paper is to show other models and algorithms of secure fuzzy authentication, which can be performed using the rank metric. A few schemes are presented which can then be applied in different scenarios and applications.Comment: to appear in Cryptography and Physical Layer Security, Lecture Notes in Electrical Engineering, Springe

Copd Phenotypes On Computed Tomography And Its Correlation With Selected Lung Function Variables In Severe Patients

Computed tomography (CT) phenotypic characterization helps in understanding the clinical diversity of chronic obstructive pulmonary disease (COPD) patients, but its clinical relevance and its relationship with functional features are not clarified. Volumetric capnography (VC) uses the principle of gas washout and analyzes the pattern of CO2 elimination as a function of expired volume. The main variables analyzed were end-tidal concentration of carbon dioxide (ETCO2), Slope of phase 2 (Slp2), and Slope of phase 3 (Slp3) of capnogram, the curve which represents the total amount of CO2 eliminated by the lungs during each breath. Objective: To investigate, in a group of patients with severe COPD, if the phenotypic analysis by CT could identify different subsets of patients, and if there was an association of CT findings and functional variables. Subjects and methods: Sixty-five patients with COPD Gold III-IV were admitted for clinical evaluation, high-resolution CT, and functional evaluation (spirometry, 6-minute walk test [6MWT], and VC). The presence and profusion of tomography findings were evaluated, and later, the patients were identified as having emphysema (EMP) or airway disease (AWD) phenotype. EMP and AWD groups were compared; tomography findings scores were evaluated versus spirometric, 6MWT, and VC variables. Results: Bronchiectasis was found in 33.8% and peribronchial thickening in 69.2% of the 65 patients. Structural findings of airways had no significant correlation with spirometric variables. Air trapping and EMP were strongly correlated with VC variables, but in opposite directions. There was some overlap between the EMP and AWD groups, but EMP patients had signicantly lower body mass index, worse obstruction, and shorter walked distance on 6MWT. Concerning VC, EMP patients had signicantly lower ETCO2, Slp2 and Slp3. Increases in Slp3 characterize heterogeneous involvement of the distal air spaces, as in AWD. Conclusion: Visual assessment and phenotyping of CT in COPD patients is feasible and may help identify functional and clinically different subsets of patients. VC may provide useful information about the heterogeneous involvement of lung structures in COPD.1150351

Erratum To: Functional And Evolutionary Analyses Of The Mir156 And Mir529 Families In Land Plants.

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Efeitos antiangiogênicos in vivo convalidam a atividade antineoplásica potencial do metiljasmonato

Molecular plant components have long been aimed at the angiogenesis and anti-angiogenesis pathways, and have been tested as sources for antineoplasic drugs with promising success. The present work deals with the anti-angiogenic effects of Methyl Jasmonate. Jasmonate derivatives were demonstrated to selectively damage the mitochondria of cancer cells. In vitro, 1-10 mM Methyl Jasmonate induced the cell death of the human umbilical vein endothelial cells (HUVEC) and the Murine melanoma cells (B16F10), while micromolar concentrations were ineffective. In vivo, comparable concentrations were toxic and reduced the vessel density of the Chorioallantoic Membrane of the Chicken Embryo (CAM). However, 1-10 µM concentrations produced a complex effect. There was increased capillary budding, but the new vessels were leakier and less organised than corresponding controls. It is suggested that not only direct toxicity, but also the drug effects upon angiogenesis are relevant to the antineoplasic effects of Methyl Jasmonate.Moléculas de origem vegetal são, há muito, conhecidas como substâncias ativas sobre as vias de angiogênese e antiangiogênese e foram testadas como fonte de drogas antineoplásicas com sucesso promissor. Este trabalho trata dos efeitos antiangiogênicos do Metiljasmonato, um protótipo da família dos derivados do ácido jasmônico, que danificam seletivamente a mitocôndria de células neoplásicas. In vitro, metiljasmonato 1-10 mM promoveu a morte celular de células endoteliais humanas de cordão umbilical (HUVEC) e de melanoma murino (B16F10); concentrações micromolares foram inócuas. In vivo, concentrações equivalentes foram tóxicas e reduziram a densidade de vasos em membranas corioalantoicas de embrião de galinha (CAM). Entretanto, concentrações entre 1-10 µM produziram um efeito complexo. Ocorreu aumento no brotamento capilar, mas os novos vasos apresentaram-se frágeis e menos organizados que os controles correspondentes. Sugere-se que, além da toxicidade direta contra as células tumorais, a ação do metiljasmonato sobre a angiogênese seja relevante para seu efeito antineoplásico

Phenotypic and genotypic distribution of ESBL, AmpC β-lactamase and carbapenemase-producing Enterobacteriaceae in community-acquired and hospital-acquired urinary tract infections in Sri Lanka

Objectives: Although Sri Lanka belongs to a region with a high prevalence of extended-spectrum β-lactamase (ESBL), AmpC β-lactamase and carbapenemase-producing Enterobacteriaceae, data regarding antimicrobial resistance (AMR) is limited. We studied the prevalence and diversity of β-lactamases produced by Enterobacteriaceae urinary pathogens from two hospitals in the Western Province of Sri Lanka. Methods: ESBL, AmpC β-lactamase and carbapenemase production was detected by phenotypic testing followed by genotyping. Results: The species responsible for urinary tract infections (UTI) were Escherichia coli (69%), Klebsiella pneumoniae (16%) and Enterobacter sp (6%). The prevalence of ESBL (50%), AmpC β-lactamase (19%) and carbapenemase (11%) phenotypes was high, and greater in hospital-acquired (HA-UTI) (75%) than in community-acquired UTI (CA-UTI) (42%). Identification of CA-UTI caused by carbapenemase-producing Enterobacteriaceae (5%) is alarming. Only one ESBL gene, blaCTX- M-15, was detected. AmpC β-lactamase genes found in E. coli and K. pneumoniae were blaCMY-2, blaCMY-42 and blaDHA-1, while Enterobacter sp. carried blaACT-1. Carbapenemase genes were blaNDM-1, blaNDM-4, blaOXA-181 and blaOXA-232, while blaKPC, blaIMP and blaVIM were absent. Co-occurrence of multiple bla genes, with some isolates harbouring six different bla genes, was common. Carbapenem-resistant isolates without carbapenemase genes displayed mutations in the outer membrane porin genes, ompF of E. coli and ompK36 of K. pneumoniae. Factors associated with UTI with β-lactamase-producing Enterobacteriaceae were age ≥50 years, previous hospitalization, presence of an indwelling urinary catheter, history of diabetes mellitus or other chronic illness and recurrent urinary tract infections. Conclusion: This study adds to the currently scarce data on AMR in Sri Lanka

A System for Accessible Artificial Intelligence

While artificial intelligence (AI) has become widespread, many commercial AI systems are not yet accessible to individual researchers nor the general public due to the deep knowledge of the systems required to use them. We believe that AI has matured to the point where it should be an accessible technology for everyone. We present an ongoing project whose ultimate goal is to deliver an open source, user-friendly AI system that is specialized for machine learning analysis of complex data in the biomedical and health care domains. We discuss how genetic programming can aid in this endeavor, and highlight specific examples where genetic programming has automated machine learning analyses in previous projects.Comment: 14 pages, 5 figures, submitted to Genetic Programming Theory and Practice 2017 worksho

TREATMENT OF MILKING PARLOR EFFLUENT: STABILIZATION PONDS FOLLOWED BY CONSTRUCTED WETLAND

One of the major concerns in dairy cattle lodging management is the great amount of manure produced daily in a reduced area that can be an excellent fertilizer option or an enormous pollutant potential, depending on the disposal procedures. In Brazil, the destination of raw effluent of lodged dairy cattle was in the past and continues nowadays being the water courses using the conventional and condemned method of the dilution, as the only form to eliminate the residues of the installations which is one of the reasons for eutrophication of rivers, streams, lakes and ponds. A pilot plant was installed to treat 10% of the effluent produced in the dairy parlor installations of the EAFI/MG. The pilot plant was designed with three units: an anaerobic lagoon followed by a facultative pond and a subsurface constructed wetland. The pilot plant presented the following average removal: phosphorus, 80%; nitrate, 88%; COD, 89%; total solids, 67%; and turbidity, 60%. The pH during the whole operation maintained around 6.2. The study concluded that the system presented a great potential for treatment of dairy parlor effluent.301677

Development of Cork Biocomposites Enriched with Chitosan Targeting Antibacterial and Antifouling Properties

The demand for bio-based and safer composite materials is increasing due to the growth of the industry, human population, and environmental concerns. In this framework, sustainable and safer cork-polymer composites (CPC), based on green low-density polyethylene (LDPE) were developed using melt-based technologies. Chitosan and polyethylene-graft-maleic anhydride (PE-g-MA) were employed to enhance the CPC's properties. The morphology, wettability, mechanical, thermal, and antibacterial properties of the CPC against Pseudomonas putida (P. putida) and Staphylococcus aureus (S. aureus) were examined. The CPC showed improved stiffness when compared with that of the LDPE matrix, preferably when combined with chitosan and PE-g-MA (5 wt. %), reinforcing the stiffness (58.8%) and the strength (66.7%). Chitosan also increased the composite stiffness and strength, as well as reduced the surface hydrophilicity. The CPCs' antibacterial activity revealed that cork significantly reduces the biofilm on the polymer matrix. The highest biofilm reduction was found with CPC containing cork and 5 wt. % chitosan for both P. putida (54% reduction) and S. aureus (36% reduction), confirming their potential to extend the lifespan of products for packaging and healthcare, among other applications. This work leads to the understanding of the factors that influence biofilm formation in cork composites and provides a strategy to reinforce their behavior using chitosan