More effort — more results: recent advances in integrative ‘omics’ data analysis

The development of ‘omics’ technologies has progressed to address complex biological questions that underlie various plant functions thereby producing copious amounts of data. The need to assimilate large amounts of data into biologically meaningful interpretations has necessitated the development of statistical methods to integrate multidimensional information. Throughout this review, we provide examples of recent outcomes of ‘omics’ data integration together with an overview of available statistical methods and tools

Emergency Service of the University Hospital of Algarve in Faro: A Contribution of the DISTATIS Method to Classify and Prioritize its Main Issues and Challenges

Events occurring in hospital emergency services tend to be of a chaotic and complex nature, giving rise to unique challenges, mainly in the fields of finance management, equipment, workloads and human resources. The research here presented addresses the issue, first by determining the top ten problems and challenges facing the Emergency Service of the University Hospital of Algarve in Faro and second by underlining perceptions and associated levels of importance attributed by an in-house group of specialists that assist on the unit's management process. Data was collected in two phases a) a brainstorming exercise with work-shift leaders for generation of opinions and ideas regarding the evaluation of the top ten problems; b) presentation of the top ten issues to a panel of experts who, on an individual basis, classified, categorized and ranked them. Collected data was of a multidimensional nature and it was later analysed using an innovative three-way technique, the DISTATIS method (Abdi et al., 2005; Abdi et al., 2007). In our evaluation of the expert responses, we highlighted experts whose options were characterized by similarities and differences and others with stable and unstable opinions. Final results provided information on opposition and coherence among the experts, identifying common themes and problems relevant to the organization's management and decision processes

Multivariate Analysis of Mixed Data: The R Package PCAmixdata

Mixed data arise when observations are described by a mixture of numerical and categorical variables. The R package PCAmixdata extends standard multivariate analysis methods to incorporate this type of data. The key techniques/methods included in the package are principal component analysis for mixed data (PCAmix), varimax-like orthogonal rotation for PCAmix, and multiple factor analysis for mixed multi-table data. This paper gives a synthetic presentation of the three algorithms with details to help the user understand graphical and numerical outputs of the corresponding R functions. The three main methods are illustrated on a real dataset composed of four data tables characterizing living conditions in different municipalities in the Gironde region of southwest France

Multi-dimensional experimental and computational exploration of metabolism pinpoints complex probiotic interactions

Multi-strain probiotics are widely regarded as effective products for improving gut microbiota stability and host health, providing advantages over single-strain probiotics. However, in general, it is unclear to what extent different strains would cooperate or compete for resources, and how the establishment of a common biofilm microenvironment could influence their interactions. In this work, we develop an integrative experimental and computational approach to comprehensively assess the metabolic functionality and interactions of probiotics across growth conditions. Our approach combines co-culture assays with genome-scale modelling of metabolism and multivariate data analysis, thus exploiting complementary data- and knowledge-driven systems biology techniques. To show the advantages of the proposed approach, we apply it to the study of the interactions between two widely used probiotic strains of Lactobacillus reuteri and Saccharomyces boulardii, characterising their production potential for compounds that can be beneficial to human health. Our results show that these strains can establish a mixed cooperative-antagonistic interaction best explained by competition for shared resources, with an increased individual exchange but an often decreased net production of amino acids and short-chain fatty acids. Overall, our work provides a strategy that can be used to explore microbial metabolic fingerprints of biotechnological interest, capable of capturing multifaceted equilibria even in simple microbial consortia

Unique Aspects of Impulsive Traits in Substance Use and Overeating: Specific Contributions of Common Assessments of Impulsivity

Part of this work was supported by grants from NIDA for marijuana studies (K01 DA021632-01A1 to FMF) and The Mind Research Network for control, nicotine, and obesity studies (Institutional Grant to FMF). FMF and DB are currently supported by NIDA (R01 DA030344-01 and F31 DA035039-01A1, respectively). DB and HA createdRunning Head: UNIQUE IMPULSE IN SUBSTANCE USE AND OVEREATING 2 some of the open source software used for analysis in this manuscript (TExPosition and TInPosition). The authors have no other declarations of interest. The American Journal of Drug and Alcohol Abus

Structural Complexity is Negatively Associated with Brain Activity: A Novel Multimodal Test of Compensation Theories of Aging

Fractal dimensionality (FD) measures the complexity within the folds and ridges of cortical and subcortical structures. We tested the degree that FD might provide a new perspective on the atrophy-compensation hypothesis: age or disease-related atrophy causes a compensatory neural response in the form of increased brain activity in prefrontal cortex (PFC) to maintain cognition. Brain structural and functional data were collected from 63 middle-aged and older adults and 18 young-adult controls. Two distinct patterns of FD were found that separated cortical from subcortical structures. Subcortical FD was more strongly negatively correlated with age than cortical FD and cortical FD was negatively associated with brain activity during memory retrieval in medial and lateral parietal cortices uniquely in middle-aged and older adults. Multivariate analyses revealed that the lower FD/higher brain activity pattern was associated with poorer cognition—patterns not present in young adults, consistent with compensation. Bayesian analyses provide further evidence against the modal interpretation of the atrophy-compensation hypothesis in the PFC—a key principle found in some neurocognitive theories of aging

Contribuciones a los métodos STASIS basados en técnicas de aprendizaje no supervisado

[ES] 1. La revisión bibliográfica ha mostrado que los métodos STATIS se han desarrollado ampliamente, sobre todo a partir del año 2000. Desde la propuesta original de L’Hermier des Plantes en 1976 con STATIS y STATIS-dual(L’Hermier des Plantes, 1976), y la de Jaffrenou en 1978 con X-STATIS o PTA, no se habían presentado nuevos métodos de esta familia. A partir del año 2004 se presentan 17 nuevas propuestas, de las cuales las más recientes son: Sir-STATIS, HiDiSTATIS , DiDiSTATIS, CATATIS y CLUSTATIS. 2. De la exhaustiva revisión bibliográfica realizada, hemos encontrado que los métodos sparse, se han aplicado a técnicas de análisis de datos de tres vías como lo son el Candecomp/Parafac y más recientemente a los métodos Tucker. 3. No se ha encontrado en la literatura referencias que implementen técnicas de restricción en los métodos STATIS. Es así, que nuestro principal aporte es una nueva propuesta de STATIS (Sparse STATIS-dual), basado en las restricciones Elastic Net. Al combinar las normas 1 y 2 , en la penalización, tiende a dar menos cargas establecidas en cero que un ajuste en un valor de la norma 1, y una mayor contracción de los otros coeficientes. 4. Consideramos que el uso de las técnicas de regularización sparse en el STATIS, permite obtener soluciones eficientes a problemas de alta dimensionalidad de los datos. 5. Para dar soporte al nuevo método del Sparse STATIS-dual planteado, se ha implementado una librería en el lenguaje de programación R, facilitando su aplicación a cualquier conjunto de datos mediante funciones específicas. El software desarrollado en R, llamado SparseSTATISdual, permite aplicar la propuesta teórica de esta tesis doctoral. 6. Se han desarrollado dos librerías más para los métodos STATIS (clásico) y STATIS-dual. 7. Se han comparado los resultados obtenidos mediante el STATIS-dual y el Sparse STATIS-dual, aplicados a datos sobre indicadores ambientales a nivel mundial, compilados en el Environmental Performance Index de la Universidad de Yale. De esta manera, se ha demostrado que al pasar del STATIS-dual a los resultados del Sparse STATIS-dual se ha reducido el número de variables, lo que hace más obtener una mejor interpretación de las variables. 8. Esta contribución abre las puertas para el desarrollo de nuevas aplicaciones de las Sparse en otras técnicas de la familia STATIS

A gestão do risco clínico e do risco não clínico no serviço de urgência da unidade de Faro do Centro Hospitalar Universitário do Algarve: a segurança do doente no processo contínuo de melhoria

A segurança do doente, intimamente relacionada com a gestão do risco, revela-se uma das componentes estruturantes e essenciais da qualidade dos cuidados de saúde (Thomas, Studdert, Burstin et al., 2000). Este trabalho aborda esta temática no serviço de urgência (SU), que se caracteriza por um ambiente complexo e desafiador devido às características dos doentes, à elevada afluência e à pressão que existe sobre os profissionais. Esta investigação procura abordar estas questões, utilizando um conjunto de problemas e desafios colocados à gestão do risco diretamente ligada à segurança do doente no SU polivalente da unidade de Faro do Centro Hospitalar Universitário do Algarve (CHUA), considerados prioritários segundo um painel de especialistas internos que intervêm no processo de gestão do serviço. Os dados utilizados neste trabalho, foram recolhidos no SU em dois momentos distintos e foi utilizada uma técnica exploratória para a análise de dados de Três Vias, neste caso o método DISTATIS (Abdi et al., 2005; Abdi et al., 2007). A análise dos resultados desta investigação sobre as avaliações dos especialistas, permitiu caracterizar as semelhanças e as diferenças nas opiniões manifestadas, bem como possibilitaram avaliar a estabilidade e/ou instabilidade das mesmas. Por fim, e tendo por base a informação sobre a coerência e a discordância manifestadas pelos especialistas, foi possível identificar os problemas/desafios de segurança do doente no SU prioritários no processo de tomada de decisão para uma gestão do risco mais eficiente do SU.Patient safety, closely related to risk management, is one of the structuring and essential components of the quality of healthcare (Thomas, Studdert, Burstin et al., 2000). This study addresses this theme in the emergency unit (EU), which is characterized by a complex and challenging environment due to the characteristics of patients, the high affluence and the pressure that exists on professionals. This research seeks to address these issues, using a set of problems and challenges faced by the risk management and directly linked to patient safety, in the general emergency unit of the Faro University Hospital Center of the Algarve (CHUA), considered as a priority according to a panel of internal experts involved in the service management process. The data used in this work were collected in the EU at two different moments and a three-way data exploratory technique was used to analyze the data, in this case the DISTATIS method (Abdi et al., 2005; Abdi et al., 2007). The analysis of the results of this investigation on the experts' evaluations allowed to characterize the similarities and differences in the opinions expressed, as well as to assess their stability and/or instability. Finally, and based on the information on the consistency and disagreement expressed by the experts, it was possible to identify the priority problems/challenges of patient safety in the EU in the decisionmaking process for more efficient risk management in the E

Serviço de urgência de ginecologia/obstetrícia da Unidade de Faro do Centro Hospitalar e Universitário do Algarve um contributo do método DISTATIS para a melhoria da gestão do serviço

Num contexto de incontornável exigência a nível da gestão de serviços de saúde, as unidades hospitalares, e em particular os Serviços de Urgência (SU), deparam-se com decisões críticas para manter a sua sustentabilidade financeira e operacional. Com base nos desafios e objetivos definidos no PNS e no Roteiro de Intervenção em Cuidados de Emergência e Urgência (RICEU), esta investigação parte de uma listagem dos 10 principais problemas/desafios identificados nos SUGO-CHUA da Unidade de Faro por um painel interno e institucional de especialistas que lhes atribui importância de forma a produzir resultados cruciais no auxílio do processo de gestão. O período de recolha dos dados incidiu entre abril e maio de 2021, com recurso à técnica de Brainstorming em especialistas do serviço e chefes de equipa, de forma a obter um Top 10 dos problemas/desafios associados a este serviço. Posteriormente, foram submetidos a apreciação, recorrendo à perceção da similitude através de Sorting Tasks por parte de um painel de especialistas com atividade direta com o serviço, de acordo com as diferentes dimensões de integração funcionais. Por último, a informação recolhida foi estruturada em matrizes de distância de Três-Vias, de forma a viabilizar uma análise de dados através do método DISTATIS (Abdi et al., 2005; Abdi et al., 2007a; Abdil et al.,2012; Gómez-Corona, 2017). Dos resultados obtidos, foi possível esclarecer as intervenções para as quais a perspetiva dos especialistas é mais concordante/influente, assim como as áreas suscetíveis de desenvolvimento, com ações de gestão de melhoria do serviço.The pursuit of ideal health service management imposed hospital units, and in particular Emergency Services, to face critical decisions to maintain their financial and operational sustainability. Based on the challenges and objectives defined in the PNS and in the Roadmap for Intervention in Emergency and Urgent Care, this investigation was established from a list of the 10 main problems/challenges identified in the SUGO-CHUA of the Faro Unit, considered as fundamental by an internal and institutional panel of specialists that scored them in order to produce results that could help in the management process. Data collection took place between April and May 2021 using the Brainstorming technique with specialists and team leaders in order to obtain a Top 10 of the problems/challenges from the service, and subsequently, were submitted for consideration using the perception of similarity through Sorting Tasks by a panel of experts. Finally, the information collected was structured in Three-Way distance matrices in order to enable data analysis using the DISTATIS method (Abdi et al., 2005; Abdi et al., 2007a; Abdil et al., 2012; Gómez-Corona, 2017). From the results, it was possible to clarify the interventions that from the perspective of the specialists are more consistent/influential, as well as the areas susceptible to enhancement, with management actions to improve the service