Network signatures based on gene pair expression ratios improve classification and the analysis of muscle-invasive urothelial cancer

Urothelial cancer (UC) is highly recurrent and can progress from non-invasive (NMIUC) to a more aggressive muscle-invasive (MIUC) subtype that invades the muscle tissue layer of the bladder. We present a proof of principle study that network-based features of gene pairs can be used to improve classifier performance and the functional analysis of urothelial cancer gene expression data. In the first step of our procedure each individual sample of a UC gene expression dataset is inflated by gene pair expression ratios that are defined based on a given network structure. In the second step an elastic net feature selection procedure for network-based signatures is applied to discriminate between NMIUC and MIUC samples. We performed a repeated random subsampling cross validation in three independent datasets. The network signatures were characterized by a functional enrichment analysis and studied for the enrichment of known cancer genes. We observed that the network-based gene signatures from meta collections of proteinprotein interaction (PPI) databases such as CPDB and the PPI databases HPRD and BioGrid improved the classification performance compared to single gene based signatures. The network based signatures that were derived from PPI databases showed a prominent enrichment of cancer genes (e.g., TP53, TRIM27 and HNRNPA2Bl). We provide a novel integrative approach for large-scale gene expression analysis for the identification and development of novel diagnostical targets in bladder cancer. Further, our method allowed to link cancer gene associations to network-based expression signatures that are not observed in gene-based expression signatures.

“CAPACITAR O DOENTE ONCOLÓGICO COM DOENÇA AVANÇADA E/OU O CUIDADOR PARA A GESTÃO DA DOR EM DOMICÍLIO” “EMPOWER THE ONCOLOGIC PATIENT WITH ADVANCED DISEASE AT HOME AND/OR THE CAREGIVER FOR THE MANAGEMENT OF PAIN”

RESUMO ABSTRACT Comunicações orais e Posters Oral communications and posters Este formulário, após preenchido, e aceites as condições descritas no regulamento das Comunicações orais e Posters deve ser enviado para isnr@porto.ucp.pt After complete this form and accept the conditions described in the oral communications and posters regulation, please sent to isnr@porto.ucp.pt Tipo de comunicação (comunicação oral ou poster): Comunicação oral Type of communication: (oral communication or poster): Oral comunication Título (Title): “CAPACITAR O DOENTE ONCOLÓGICO COM DOENÇA AVANÇADA E/OU O CUIDADOR PARA A GESTÃO DA DOR EM DOMICÍLIO” “EMPOWER THE ONCOLOGIC PATIENT WITH ADVANCED DISEASE AT HOME AND/OR THE CAREGIVER FOR THE MANAGEMENT OF PAIN” Autoria (Authors): CORREIA, Isabel* (doutoranda em Enfermagem na Universidade de Lisboa) LOPES, Manuel (orientador do projeto) Afiliação dos autores (Authors affiliation): – Professora adjunta na Universidade de Évora, Escola Superior de Enfermagem de São João de Deus de Évora, doutoranda em enfermagem Universidade de Lisboa - – Professor Doutor em Enfermagem, Diretor da Escola Superior de Enfermagem de São João de Deus de Évora, Universidade de Évora E-mail: icorreia@uevora.pt - 964078445 mjl@uevora.pt Resumo (3000 caracteres com espaços) INTRODUÇÃO Um dos sintomas mais frequentes no doente oncológico com doença avançada é a dor. Segundo Palliative Care in European, a dor oncológica, tem uma importância especial porque o cancro é a segunda causa de morte em Portugal e por existir dor moderada a intensa em mais de 90% dos doentes em situação oncológica terminal. O desenvolvimento de um programa estruturado de intervenção de enfermagem que vá de encontro às necessidades do doente oncológico com doença avançada e/ou cuidador, relativamente à gestão da dor, poderá ter um impacto muito significativo no controlo da dor e de outros sintomas. OBJETIVOS Avaliar o efeito de um programa de Intervenção de Enfermagem na capacidade de gestão da dor por parte do doente oncológico com doença avançada e/ou o cuidador em domicílio. MATERIAIS E MÉTODOS A implementação do programa tem a duração prevista para 6 semanas. Compreende duas sessões educativas, três telefonemas e uma sessão de avaliação final. O programa foi elaborado, após uma Revisão sistemática de Literatura, com base no programa “ THE PRO-SELF”, nas Orientações Genéricas preconizadas pelo Plano Nacional de Luta Contra a dor e na Intervenção de enfermagem “Controle da Dor” da Nursing Intervention Classification (NIC). RESULTADOS O projeto encontra-se na fase de implementação e avaliação do programa educativo. No início os doentes não apresentam informação relativamente à gestão da dor, no final demonstram capacidade para a monitorização da dor e de outros sintomas e para a gestão da terapêutica, realizando os registos num diário de bordo. A literacia, a situação clínica e a disponibilidade interferem na capacidade de gestão. A proximidade da morte e a alteração do estado de consciência interferem na autonomia e na tomada de decisão. CONCLUSÃO Em fase de colheita e análise de dados. REFERÊNCIAS BIBLIOGRÁFICAS 1. FREIXO, Manuel. Metodologia Cientifica - Fundamentos, Metodos e Tecnicas. s.l. : Piaget, 2011. 2. Bulechek, Gloria M. e etal. Classificaçaõ das Intervenções de Enfermagem (NIC). Rio de Janeiro : elsevier, 2010. 3. Tsigaroppoulos, T. e etal. Problems faced by relatives caring for cancer patients at home. International Journal Of Nursing Practice. 15, 2009, Vol. 1, Nursing Pratice. 4. west, C.:Dodd,M., et al. Pain Control Program-an effective approach for cancer pain management. Oncology Nursing Forum. 1, 2003, Vol. 30, Oncology Nursing. 5. NR/rdonlyres/6861126B-C57A-46E1-B065-316C0CF8DACD/0/ControlodaDor.pdf, . (2008). . Consultado em 30 de Novembro de 2012 a partir de. Direcção-Geral da Saúde . http://www.portaldasaude.pt. [Online] 2008. [Citação: 30 de Novembro de 2012.] http://www.portaldasaude.pt/NR/rdonlyres/6861126B-C57A-46E1-B065-316COCF8DACD/0/Controlodador.pdf . Abstract (3000 characters with spaces) INTRODUCTION One of the most frequent symptoms in oncological patient with advanced disease is pain. According to Palliative Care in European, oncological pain, has a special importance because the cancer is the second most common cause of death in Portugal and there is moderate to severe pain in more than 90 % of patients in oncological terminal situation. The development of a structured program of nursing intervention that will meet the needs of the oncological patient with advanced disease and/or caregiver at home on pain management, will be able to provide for the management of pain, increasing knowledge for the control of pain while minimizing the associated symptoms that influence the quality of life of the patient and the caregiver's anxiety. PURPOSE/GOAL/AIM To evaluate the effect of an educational program of Nursing Intervention on pain management by the oncological patient with advanced disease and/or caregiver. RESEARCH/PROBLEM What is the effect of a structured program of nursing intervention directed to the patient and/or oncological patient caregiver with advanced disease at home, in the management of pain? METHODOLOGY Almost experimental study, with assessment of the management capacity of the oncological patient pain with advanced disease at home and/or informal caregiver, before and after the intervention of nursing (educational program) and transverse evaluation throughout the study. Population: oncological patients with advanced disease at home, with more than 18 years, and or family caregiver, attending an Oncology Unit – Hospital during the day. RESULTS Made an application in an Oncology service in oncological patients with advanced disease at home, it was found that at the beginning the patients did not present information regarding pain management, at the end demonstrated capacity for monitoring of pain and other symptoms and therapeutic management, performing a logbook records. CONCLUSION In the process of collection and analysis of data. KEYWORDS Educational Program; oncological patient; oncological pain.

Patient classification for intelligent wheelchair adaptation

A importância e preocupação dedicadas à autonomia e independência das pessoas idosas e dos pacientes que sofrem de algum tipo de deficiência tem vindo a aumentar significativamente ao longo das últimas décadas. As cadeiras de rodas inteligentes (CRI) são tecnologias que podem ajudar este tipo de população a aumentar a sua autonomia, sendo atualmente uma área de investigação bastante ativa. Contudo, a adaptação das CRIs a pacientes específicos e a realização de experiências com utilizadores reais são assuntos de estudo ainda muito pouco aprofundados. A cadeira de rodas inteligente, desenvolvida no âmbito do Projeto IntellWheels, é controlada a alto nível utilizando uma interface multimodal flexível, recorrendo a comandos de voz, expressões faciais, movimentos de cabeça e através de joystick. Este trabalho teve como finalidade a adaptação automática da CRI atendendo às características dos potenciais utilizadores. Foi desenvolvida uma metodologia capaz de criar um modelo do utilizador. A investigação foi baseada num sistema de recolha de dados que permite obter e armazenar dados de voz, expressões faciais, movimentos de cabeça e do corpo dos pacientes. A utilização da CRI pode ser efetuada em diferentes situações em ambiente real e simulado e um jogo sério foi desenvolvido permitindo especificar um conjunto de tarefas a ser realizado pelos utilizadores. Os dados foram analisados recorrendo a métodos de extração de conhecimento, de modo a obter o modelo dos utilizadores. Usando os resultados obtidos pelo sistema de classificação, foi criada uma metodologia que permite selecionar a melhor interface e linguagem de comando da cadeira para cada utilizador. A avaliação para validação da abordagem foi realizada no âmbito do Projeto FCT/RIPD/ADA/109636/2009 - "IntellWheels - Intelligent Wheelchair with Flexible Multimodal Interface". As experiências envolveram um vasto conjunto de indivíduos que sofrem de diversos níveis de deficiência, em estreita colaboração com a Escola Superior de Tecnologia de Saúde do Porto e a Associação do Porto de Paralisia Cerebral. Os dados recolhidos através das experiências de navegação na CRI foram acompanhados por questionários preenchidos pelos utilizadores. Estes dados foram analisados estatisticamente, a fim de provar a eficácia e usabilidade na adequação da interface da CRI ao utilizador. Os resultados mostraram, em ambiente simulado, um valor de usabilidade do sistema de 67, baseado na opinião de uma amostra de pacientes que apresentam os graus IV e V (os mais severos) de Paralisia Cerebral. Foi também demonstrado estatisticamente que a interface atribuída automaticamente pela ferramenta tem uma avaliação superior à sugerida pelos técnicos de Terapia Ocupacional, mostrando a possibilidade de atribuir automaticamente uma linguagem de comando adaptada a cada utilizador. Experiências realizadas com distintos modos de controlo revelaram a preferência dos utilizadores por um controlo compartilhado com um nível de ajuda associado ao nível de constrangimento do paciente. Em conclusão, este trabalho demonstra que é possível adaptar automaticamente uma CRI ao utilizador com claros benefícios a nível de usabilidade e segurança.

Classification of incomplete feature vectors by radial basis function networks

The paper describes the use of radial basis function neural networks with Gaussian basis functions to classify incomplete feature vectors. The method uses the fact that any marginal distribution of a Gaussian distribution can be determined from the mean vector and covariance matrix of the joint distribution.

The PREDICTS database: a global database of how local terrestrial biodiversity responds to human impacts

Biodiversity continues to decline in the face of increasing anthropogenic pressures such as habitat destruction, exploitation, pollution and introduction of alien species. Existing global databases of species’ threat status or population time series are dominated by charismatic species. The collation of datasets with broad taxonomic and biogeographic extents, and that support computation of a range of biodiversity indicators, is necessary to enable better understanding of historical declines and to project – and avert – future declines. We describe and assess a new database of more than 1.6 million samples from 78 countries representing over 28,000 species, collated from existing spatial comparisons of local-scale biodiversity exposed to different intensities and types of anthropogenic pressures, from terrestrial sites around the world. The database contains measurements taken in 208 (of 814) ecoregions, 13 (of 14) biomes, 25 (of 35) biodiversity hotspots and 16 (of 17) megadiverse countries. The database contains more than 1% of the total number of all species described, and more than 1% of the described species within many taxonomic groups – including flowering plants, gymnosperms, birds, mammals, reptiles, amphibians, beetles, lepidopterans and hymenopterans. The dataset, which is still being added to, is therefore already considerably larger and more representative than those used by previous quantitative models of biodiversity trends and responses. The database is being assembled as part of the PREDICTS project (Projecting Responses of Ecological Diversity In Changing Terrestrial Systems – www.predicts.org.uk). We make site-level summary data available alongside this article. The full database will be publicly available in 2015.

Day 1. Free Communications – Psychology (Session 2): The influence of body language and expected competency on gaze behaviour while forming an initial impression of a tennis player.

D1.S3.4(4). BASES Conference 2015 (Burton-on-Trent), 1-2 December. British Association of Sport and Exercise Sciences

Neural network classification of cerebral embolic signals

The presence of circulating cerebral emboli represents an increased risk of stroke. The detection of such emboli is possible with the use of a transcranial Doppler ultrasound (TCD) system.

Structural and chemical characterization of corals grown under present day and naturally elevated pCO2 conditions in Papua New Guinea - a window into the future

Dissertação de mestrado, Biologia Marinha, Faculdade de Ciências e Tecnologia, Universidade do Algarve, 2015

Automatic classification of scientific records using the German Subject Heading Authority File (SWD)

The following paper deals with an automatic text classification method which does not require training documents. For this method the German Subject Heading Authority File (SWD), provided by the linked data service of the German National Library is used. Recently the SWD was enriched with notations of the Dewey Decimal Classification (DDC). In consequence it became possible to utilize the subject headings as textual representations for the notations of the DDC. Basically, we we derive the classification of a text from the classification of the words in the text given by the thesaurus. The method was tested by classifying 3826 OAI-Records from 7 different repositories. Mean reciprocal rank and recall were chosen as evaluation measure. Direct comparison to a machine learning method has shown that this method is definitely competitive. Thus we can conclude that the enriched version of the SWD provides high quality information with a broad coverage for classification of German scientific articles.

Cornerstone Baptist Church 100th Anniversary Day

This proclamation from Governor Mark Sanford proclaims October 30, 2005 as Cornerstone Baptist Church 100th Anniversary Day.

An address delivered in the Indigo Hall, Georgetown, South Carolina, on the fourth day of May, 1860, the 105th anniversary of the Winyaw Indigo Society

This pamphlet presents the text of the address given by Plowden C.J. Weston on May 4, 1860 to the Winyaw Indigo Society on their 105th anniversary.

A 30-Day-Ahead Forecast Model for Grass Pollen in North London, United Kingdom

A 30-day ahead forecast method has been developed for grass pollen at north London. The total period of the grass pollen season is covered by eight multiple regression models, each covering a 10-day period running consecutively from 21st May to 8th August. This means that three models were used for each 30-day forecast. The forecast models were produced using grass pollen and environmental data from 1961-1999 and tested on data from 2000 and 2002. Model accuracy was judged in two ways: the number of times the forecast model was able to successfully predict the severity (relative to the 1961-1999 dataset as a whole) of grass pollen counts in each of the eight forecast periods on a scale of one to four; and the number of times the forecast model was able to predict whether grass pollen counts were higher or lower than the mean. The models achieved 62.5% accuracy in both assessment years when predicting the relative severity of grass pollen counts on a scale of one to four, which equates to six of the eight 10-day periods being forecast correctly. The models attained 87.5% and 100% accuracy in 2000 and 2002 respectively when predicting whether grass pollen counts would be higher or lower than the mean. Attempting to predict pollen counts during distinct 10-day periods throughout the grass pollen season is a novel approach. The models also employed original methodology in the use of winter averages of the North Atlantic Oscillation to forecast 10-day means of allergenic pollen counts.

Constructing a 7-day Ahead Forecast Model for Grass Pollen at North London, United Kingdom

A number of media outlets now issue medium-range (~7 day) weather forecasts on a regular basis. It is therefore logical that aerobiologists should attempt to produce medium-range forecasts for allergenic pollen that cover the same time period as the weather forecasts. The objective of this study is to construct a medium-range (< 7 day) forecast model for grass pollen at north London. The forecast models were produced using regression analysis based on grass pollen and meteorological data from 1990-1999 and tested on data from 2000 and 2002. The modelling process was improved by dividing the grass pollen season into three periods; the pre-peak, peak and post peak periods of grass pollen release. The forecast consisted of five regression models. Two simple linear regression models predicting the start and end date of the peak period, and three multiple regression models forecasting daily average grass pollen counts in the pre-peak, peak and post-peak periods. Overall the forecast models achieved 62% accuracy in 2000 and 47% in 2002, reflecting the fact that the 2002 grass pollen season was of a higher magnitude than any of the other seasons included in the analysis. This study has the potential to make a notable contribution to the field of aerobiology. Winter averages of the North Atlantic Oscillation were used to predict certain characteristics of the grass pollen season, which presents an important advance in aerobiological work. The ability to predict allergenic pollen counts for a period between five and seven days will benefit allergy sufferers. Furthermore, medium-range forecasts for allergenic pollen will be of assistance to the medical profession, including allergists planning treatment and physicians scheduling clinical trials.

The Day Roads Became Rivers: A GIS-Based Assessment of Flash Floods in Worcester

In the last 4 years Worcester, UK has been hit by several intense convective rainstorms, which caused flash floods outside of existing surface drainage networks. This paper addresses two questions related to such events: Firstly to what extent can the occurrence of flash flood flow accumulation can be determined using only commonly available data and tools, assuming the rainfall events caused mainly surface runoff due to their tropical intensity and the relatively impermeable urban catchment surface? Secondly, are the flood in-cidents in Worcester aggravated by roads serving as preferential flow paths under these conditions? The as-sessment results indicated that roads do not have an influence on the flow path of flash flood rainfall in Worcester. Flow accumulation calculated with a 10m DEM, corresponds well with reported flood incidents. This basic assessment method can be used to inform the implementation of non structural flood mitigation and public awareness.