CLUDE: An Efficient Algorithm for LU Decomposition Over a Sequence of Evolving Graphs

Session: Matrix Factorization, Clustering and Probabilistic DataIn many applications, entities and their relationships are represented by graphs. Examples include the WWW (web pages and hyperlinks) and bibliographic networks (authors and co-authorship). A graph can be conveniently modeled by a matrix from which various quantitative measures are derived. Some example measures include PageRank and SALSA (which measure nodes’ importance), and Personalized PageRank and Random Walk with Restart (which measure proximities between nodes). To compute these measures, linear systems of the form Ax = b, where A is a matrix that captures a graph’s structure, need to be solved. To facilitate solving the linear system, the matrix A is often decomposed into two triangular matrices (L and U). In a dynamic world, the graph that models it changes with time and thus is the matrix A that represents the graph. We consider a sequence of evolving graphs and its associated sequence of evolving matrices. We study how LU-decomposition should be done over the sequence so that (1) the decomposition is efficient and (2) the resulting LU matrices best preserve the sparsity of the matrices A’s (i.e., the number of extra non-zero entries introduced in L and U are minimized.) We propose a cluster-based algorithm CLUDE for solving the problem. Through an experimental study, we show that CLUDE is about an order of magnitude faster than the traditional incremental update algorithm. The number of extra non-zero entries introduced by CLUDE is also about an order of magnitude fewer than that of the traditional algorithm. CLUDE is thus an efficient algorithm for LU decomposition that produces high-quality LU matrices over an evolving matrix sequence.published_or_final_versio

Identification of Novel Small Organic Compounds with Diverse Structures for the Induction of Epstein-Barr Virus (EBV) Lytic Cycle in EBV-Positive Epithelial Malignancies

Phorbol esters, which are protein kinase C (PKC) activators, and histone deacetylase (HDAC) inhibitors, which cause enhanced acetylation of cellular proteins, are the main classes of chemical inducers of Epstein-Barr virus (EBV) lytic cycle in latently EBV-infected cells acting through the PKC pathway. Chemical inducers which induce EBV lytic cycle through alternative cellular pathways may aid in defining the mechanisms leading to lytic cycle reactivation and improve cells’ responsiveness towards lytic induction. We performed a phenotypic screening on a chemical library of 50,240 novel small organic compounds to identify novel class(es) of strong inducer(s) of EBV lytic cycle in gastric carcinoma (GC) and nasopharyngeal carcinoma (NPC) cells. Five hit compounds were selected after three successive rounds of increasingly stringent screening. All five compounds are structurally diverse from each other and distinct from phorbol esters or HDAC inhibitors. They neither cause hyperacetylation of histone proteins nor significant PKC activation at their working concentrations, suggesting that their biological mode of action are distinct from that of the known chemical inducers. Two of the five compounds with rapid lytic-inducing action were further studied for their mechanisms of induction of EBV lytic cycle. Unlike HDAC inhibitors, lytic induction by both compounds was not inhibited by rottlerin, a specific inhibitor of PKCδ. Interestingly, both compounds could cooperate with HDAC inhibitors to enhance EBV lytic cycle induction in EBV-positive epithelial cancer cells, paving way for the development of strategies to increase cells’ responsiveness towards lytic reactivation. One of the two compounds bears structural resemblance to iron chelators and the other strongly activates the MAPK pathways. These structurally diverse novel organic compounds may represent potential new classes of chemicals that can be used to investigate any alternative mechanism(s) leading to EBV lytic cycle reactivation from latency.published_or_final_versio

Mining Order-Preserving Submatrices from Data with Repeated Measurements

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Modelos de sobrevivência para o estudo dos fatores de prognóstico até à ocorrência da resposta ao tratamento de fisioterapia em utentes com dor lombar crónica

Relatório do Projeto de Investigação apresentado para cumprimento dos requisitos necessários à obtenção do grau de Mestre em Fisioterapia, área de especialização em Fisioterapia em Condições Músculo-EsqueléticasIntrodução: A recuperação, da função e/ou dor, é comummente utilizada em estudos relacionados com a dor lombar crónica não específica (DLCNE), contudo, os desenhos utilizados para medir a resposta ao tratamento não permitem saber quando, no decorrer da intervenção, é atingido um determinado critério de resposta ao tratamento, e consequentemente quais os fatores que aumentam o risco/ a probabilidade de obter esse critério de resposta ao tratamento ao longo do tempo. Objetivo: Este estudo pretendeu identificar fatores de prognóstico que influenciem significativamente o tempo até à ocorrência de um evento de interesse, definido como resposta ao tratamento multimodal de fisioterapia na intensidade da dor, incapacidade funcional e perceção de melhoria em indivíduos com DCLNE, recorrendo a avaliações repetidas semanalmente, durante 8 semanas. Metodologia: Estudo observacional de coorte prospetivo com 135 indivíduos com DLCNE referenciados para a fisioterapia, que foram avaliados no início da intervenção de fisioterapia e semanalmente desde a segunda até à oitava semana de intervenção. O “evento” definido foi a obtenção do critério de sucesso na resposta ao tratamento, estabelecido para cada outcome com base no valor da respetiva DCMI, definida como a diminuição ≥ 30% na escala numérica da dor (END) e na versão portuguesa da Quebec Back Pain Disability Scale (QBPDS-PT) e diferença mínima de 3 pontos para a versão portuguesa da Global Back Recovery Scale (GBRS-PT), mantidas durante um mínimo de 7 dias. Resultados: A proporção de utentes que alcançou a recuperação para a intensidade da dor e incapacidade funcional, no período de 8 semanas de tratamento, foi de 51.11% (n=69) e de 50.37% (n=68), respetivamente. A proporção de utentes que alcançou a recuperação na perceção de melhoria foi de 55.56% (n=75). A mediana do tempo de recuperação para os 3 outcomes ocorreu na 6ª semana de tratamento. Os indivíduos com maior intensidade de dor na baseline (HR:1.26, 95%IC: 1.12-1.43), que nunca ou raramente se sentiram “desamparados” (HR:2.09, 95%IC: 1.07-4.08), têm maior possibilidade de atingir o critério de recuperação para a dor, comparativamente aos utentes que não possuem estas características. Os indivíduos que vivem sozinhos (HR: 1.83, 95%IC: 1,05-3,19) têm maior possibilidade de atingir o critério de recuperação para a incapacidade funcional. Os utentes com inferior nível de ensino têm uma maior probabilidade de recuperação da perceção global de melhoria (IR:1.65; 95%IC: 1.02-2.67) comparativamente com utentes com mais formação. Conclusão: A recuperação da intensidade da dor e da incapacidade funcional ocorre nas primeiras 6 semanas de tratamento, sendo que aproximadamente metade dos utentes recuperados alcançaram o critério de resposta após as 2 primeiras semanas de tratamento. Maior intensidade da dor na baseline, baixos níveis de fatores psicossociais, viver sozinho e ter um nível educacional mais baixo, parece favorecer a probabilidade de recuperar destes utentes, ao longo do tempo.Introduction: The recovery from pain or function is usualy used in nonspecific chronic low back pain (NCLBP) studies. The designs to measure the response to treatment don’t allow to know when, whithin the intervention, the criteria of recovery is achieved and, therefore, which are the factors that increase the possibility of achieving the defined sucess along the time. Objective: The aim of this study is to identify prognosis factors that favour significantly the time until reaching the event of interest, defined as the response to the multimodal physiotherapy treatment for pain intensity, disability and global perception of recovery in patients with NCLBP, using repetitive assessments on a weekly basis for 8 weeks. Methodology: In this prospective cohort study were 135 NCLBP patients who were referred for physiotherapy and assessed 8 times (baseline and every week from 2nd to the 8th week) The event of interest was defined as the achievement of the recovery criteria on the treatment response, established for each outcome, considering the minimal important change (MIC) defined as a reduction of ≥ 30% on numeric rate scale (NRS) and portuguese version of Quebec Back Pain Disability Scale (QBPDS-PT) and a reduction of 3 points on the portuguese version of Global Back Recovery Scale (GBRS-PT), maintened for at least 7 days. Results: The proportion of patients that have acheived the recovery for pain intensity and disability, on the 8 weeks treatment was 51.11% (n=69) and 50.37% (n=68), respectivetly. The proportion of patiens that have acheived recovery for the global perception was 55.56% (n=75). The median of recovery time for the 3 outcomes occured on the 6th week. The NCLBP patients who have more pain intensity on baseline (HR: 1.26; 95%IC: 1.12-1.43) and who didn’t feel with support on the previous week (HR: 2.09; 95%IC: 1.07-4.08) have more possibility to achieve the recovery criteria for pain, compared with those that don’t have that caracteristics. The patients that live alone (HR: 1.83, 95%IC: 1,05-3,19) have more possibility of achieve the disability recovery, when compared with those who don´t. Patients with lower levels of education have more probability to recovery from global perception of recovery (IR:1.65; 95%IC: 1.02-2.67), compared with patients with higher levels of education. Conclusions: The recovery for pain intensity and disability occurs on the 6 first weeks of treatment, and approximetely half of the patients achieved the response criteria in the 2 first weeks. Higher levels of pain intensity on the baseline, lower levels for the psycosocial factors, living alone ad lower levels of education, seems to favour the probability or recovery on NCLBP patients, along the time

Mecanização agrícola - Transmissões mecânicas em máquinas agrícolas

Este trabalho destina-se a apoiar a aprendizagem de estudantes do ramo das ciências agrárias sobre aspectos relevantes das transmissões mecânicas nas máquinas agrícolas. A transmissão mecânica, formada normalmente por uma cadeia de componentes, constitui um dos modos possíveis para efectuar a transmissão de potência desde uma fonte (exemplo: a tomada-de-força do tractor) para diversos órgãos dos equipamentos agrícolas. São apresentadas as diferentes soluções de transmissão mecânica presentes nos equipamentos agrícolas, com a preocupação focada nos aspectos de manutenção, regulações permitidas e protecção do operador. O texto não está vocacionado para aspectos de dimensionamento de transmissões; contudo, faz-se a apresentação dos princípios de cinemática e dinâmica das transmissões que constitui a ferramenta necessária para se entenderem as transmissões susceptíveis de regulação por parte do operador. Será dada especial ênfase às transmissões mecânicas passíveis de regulação de semeadores de linhas e de plantadores, para efeitos de regulação da densidade de sementeira/plantação/adubação. São apresentados problemas de aplicação. Este trabalho reúne textos de anteriores edições do mesmo autor: Transmissões mecânicas (2012, 2007, 2004, 2002, 1998; 1994; 1990; 1988; 1986); Transmissões mecânicas – Equipamentos agrícolas com regulação da transmissão – Grade rotativa (2008); Transmissões mecânicas – Equipamentos agrícolas com regulação da transmissão – Semeadores de linhas monogrão e plantadores (2012, 2008); Transmissões mecânicas – Equipamentos agrícolas com regulação da transmissão – Semeadores de linhas de fluxo contínuo (2011, 2009); Transmissões mecânicas – Equipamentos agrícolas com regulação da transmissão – Semeadores de linhas, de fluxo contínuo, com transporte de sementes em corrente de ar (2012, 2008). Os textos acima indicados foram publicados periodicamente no contexto de disciplinas em cursos da Universidade de Évora, nomeadamente: - Mecânica Aplicada (1983/84 a 2003/04) - disciplina obrigatória do 3º semestre os cursos de Engenharia Agrícola e Engenharia Zootécnica; - Fundamentos de Engenharia nas Máquinas Agrícolas – (2004/05 e 2005/06) – disciplina obrigatória do 3º semestre de Engenharia Agrícola; - Tecnologia dos Equipamentos Agrícolas – (2004/05 e 2005/06) – disciplina obrigatória do 3º semestre de Engenharia Zootécnica; - Mecanização Agrícola (2006/07 até ao presente) – unidade curricular obrigatória do 3º semestre da licenciatura em Agronomia; - Princípios de Engenharia Aplicados à Ciência Animal (2006/07 até ao presente) – unidade curricular obrigatória do 1º ciclo em Ciência e Tecnologia Animal

A comparison of hepatitis B viral markers of patients in different clinical stages of chronic infection

Hepatitis B viral markers may be useful for predicting outcomes such as liver-related deaths or development of hepatocellular carcinoma. We determined the frequency of these markers in different clinical stages of chronic hepatitis B infection. We compared baseline hepatitis B viral markers in 317 patients who were enrolled in a prospective study and identified the frequency of these tests in immune-tolerant (IT) patients, in inactive carriers , and in patients with either hepatitis B e antigen ( HBeAg)- positive or HBeAg-negative chronic hepatitis or cirrhosis. IT patients were youngest (median age 27 years) and HBeAg- negative patients with cirrhosis were oldest (median age 58 years) (p = 0.03 to < 0.0001). The male to female ratio was similar both in IT patients and in inactive carriers, but there was a male preponderance both in patients with chronic hepatitis and in patients with cirrhosis (p < 0.0001). The A1896 precore mutants were most prevalent in inactive carriers (36.4%) and HBeAg- negative patients with chronic hepatitis (38.8%; p < 0.0001), and the T 1762/A1764 basal core promoter mutants were most often detected in HBeAg- negative patients with cirrhosis (65.1%; p = 0.02). Genotype A was detected only in 5.3% of IT patients, and genotype B was least often detected in both HBeAg-Positive patients with chronic hepatitis and cirrhosis (p = 0.03). The hepatitis B viral DNA levels were lowest in inactive carriers (2.69 log(10) IU/mL) and highest in IT patients (6. 80 log(10) IU/mL; p = 0.02 to < 0.0001). At follow-up, HBeAg-positive and HBeAg-negative patients with cirrhosis accounted for 57 of 64 (89.1%) liver-related deaths (p < 0. 0001). Differences in baseline hepatitis B viral markers were detected in patients in various clinical stages of hepatitis B virus infection. HBeAg-positive and HBeAg- negative patients with cirrhosis accounted for the majority of the liver-related fatalities

Assessment of dizziness among older patients at a family practice clinic: a chart audit study

BACKGROUND: Dizziness is a common complaint among the elderly with a prevalence of over 30% in people over the age of 65. Although it is a common problem the assessment and management of dizziness in the elderly is challenging for family physicians. There is little published research which assesses the quality of dizziness assessment and management by family physicians. METHODS: We conducted a retrospective, chart audit study of patients with dizziness attending the Sunnybrook Family Practice Center of Sunnybrook and Women's College Health Sciences Center (SWCHSC) in Toronto. We audited a random sample of 50 charts of patients from 310 eligible charts. Quality indicators across all dizziness subtypes were assessed. These quality indicators included: onset and course of symptoms; symptoms in patients' own words; number of medications used; postural blood pressure changes; symptoms of depression or anxiety; falls; syncope; diagnosis; outcome; specialty referrals. Quality indicators specific to each dizziness subtype were also audited. RESULTS: 310 charts satisfied inclusion criteria with 20 charts excluded and 50 charts were randomly generated. Documentation of key quality indicators in the management of dizziness was sub-optimal. Charts documenting patients' dizziness symptoms in their own words were more likely to have a clinical diagnosis compared to charts without (P = 0.002). CONCLUSIONS: Documentation of selected key quality indicators could be improved, especially that of patients' symptoms in their own words

Hepatitis B virus: molecular genotypes and HBeAg serological status among HBV-infected patients in the southeast of Brazil

<p>Abstract</p> <p>Background</p> <p>Knowledge of HBV genotype is very important for clinical treatment. Studies have suggested possible pathogenic and therapeutic differences among HBV genotypes. The aim of this study was to determine HBV subtypes and genotypes in HBV-infected patients in our region (southeast Brazil) and to correlate results with clinical and histopathological data.</p> <p>Methods</p> <p>One hundred and thirty-nine HBsAg-positive patients were included in the study. All patients were anti-HCV and anti-HIV negative (64% male; mean age 42 ± 14.5 years; range 7-80 years; 84% Caucasian) and were followed up at the University Hospital. A method for genotyping and subtyping HBV by partial HBsAg gene sequencing with primers common to all known genotypes was used. The viral load was measured by Amplicor Monitor assay (Roche).</p> <p>Results</p> <p>HBV genotype A was the most prevalent (55%), while genotypes C, D and F were found in 3%, 38% and 4% of HBV-infected patients, respectively. Among the patients infected by genotype A, 18.3% (14/76) were African descendents and, among the patients infected by genotype D, 11.3% (6/53) were also African descendents. In the four patients infected with genotype C, 2 were Asian descendents and 2 were Caucasians. All (7) genotype F infected patients were Caucasians. Seventy percent of our HBsAg-positive patients were HBeAg negative (62% genotypes A; 26.2% D; 7.1% C and 4.7%F). The viral load of HBV-DNA was about 5 times higher in HBeAg-positive than in HBeAg-negative patients. About 40% of these patients had alanine aminotransferase of up to 1.5 times the normal level. The mean stage of fibrosis in genotype A patients (2.8) was significantly higher than the mean stage of fibrosis in genotype D patients (2.0) (P = 0.0179).</p> <p>Conclusion</p> <p>The genotypes encountered in our HBV-infected patients were apparently a consequence of the types of immigration that occurred in our region, where European and African descendents predominate. The HBeAg-negative status predominated, possibly due to the length of time of infection. The viral load in HBeAg-positive patients was higher than in HBeAg-negative individuals. The fibrosis grade in genotype A-infected patients was more advanced than genotype D-infected patients.</p

Lattice Boltzmann simulations of soft matter systems

This article concerns numerical simulations of the dynamics of particles immersed in a continuum solvent. As prototypical systems, we consider colloidal dispersions of spherical particles and solutions of uncharged polymers. After a brief explanation of the concept of hydrodynamic interactions, we give a general overview over the various simulation methods that have been developed to cope with the resulting computational problems. We then focus on the approach we have developed, which couples a system of particles to a lattice Boltzmann model representing the solvent degrees of freedom. The standard D3Q19 lattice Boltzmann model is derived and explained in depth, followed by a detailed discussion of complementary methods for the coupling of solvent and solute. Colloidal dispersions are best described in terms of extended particles with appropriate boundary conditions at the surfaces, while particles with internal degrees of freedom are easier to simulate as an arrangement of mass points with frictional coupling to the solvent. In both cases, particular care has been taken to simulate thermal fluctuations in a consistent way. The usefulness of this methodology is illustrated by studies from our own research, where the dynamics of colloidal and polymeric systems has been investigated in both equilibrium and nonequilibrium situations.Comment: Review article, submitted to Advances in Polymer Science. 16 figures, 76 page