9,229 research outputs found

    Ordinal time series analysis with the R package otsfeatures

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    The 21st century has witnessed a growing interest in the analysis of time series data. Whereas most of the literature on the topic deals with real-valued time series, ordinal time series have typically received much less attention. However, the development of specific analytical tools for the latter objects has substantially increased in recent years. The R package otsfeatures attempts to provide a set of simple functions for analyzing ordinal time series. In particular, several commands allowing the extraction of well-known statistical features and the execution of inferential tasks are available for the user. The output of several functions can be employed to perform traditional machine learning tasks including clustering, classification or outlier detection. otsfeatures also incorporates two datasets of financial time series which were used in the literature for clustering purposes, as well as three interesting synthetic databases. The main properties of the package are described and its use is illustrated through several examples. Researchers from a broad variety of disciplines could benefit from the powerful tools provided by otsfeatures

    Potential application of endophytes in the management of olive fruit fly and anthracnose

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    Olive fruit fly, Bactrocera oleae (Rossi) (Diptera: Tephritidae), and olive anthracnose, mainly caused by Colletotrichum acutatum, are considered key biotic constrains of olive crop worldwide. Strategies employed for controlling this pest and disease are mostly based on the use of insecticides and copper-based pesticides, respectively, which is not compatible with sustainable production systems. This work aims to study the effect of two endophytes, previously isolated from olive tree, namely Aureobasidium pullulans and Sarocladium summerbellii on the behavior (i.e. attractiveness or repellence) and preference for oviposition of B. oleae, as well as on anthracnose infection, by using in vitro and in vivo (detached fruits) assays. Aureobasidium. pullulans-mediated changes in olive fruit volatile organic compounds (VOCs) and their consequences for anthracnose disease development were also evaluated. The tests performed by multi-choice olfactometer showed that both endophytes did not exert a repellent or attractive effect against mature gravid B. oleae female’s. Similarly, females did not showed preference to oviposit in olives inoculated with endophytes versus non-inoculated. Among the two endophytes tested, only A. pullulans inhibited significantly the growth (up to 1.3-fold), sporulation (up to 5.9-fold) and spore germination (up to 3.5-fold) of C. acutatum in relation to the control (C. acutatum). Similarly, in inoculated olive assays, only A. pullulans was able to reduced significantly progress curve for incidence (up to 10-fold) and severity (up to 35-fold) of anthracnose, as well as both sporulation (up to 90%) and germination (up to 70%) of C. acutatum, in comparison with olives inoculated solely with C. acutatum. Gas chromatography–mass spectrometry analysis of olives inoculated with A. pullulans+C. acutatum and controls (olives inoculated with C. acutatum, A. pullulans or tween) led to identification of 29 VOCs, belonging to 10 different chemical classes, being alcohols the most diversified and abundant ones. The volatile profile of A. pullulans + C. acutatum revealed quali- and quantitatively differences from the controls, in particular due to the production of (z)-3-hexen-1-ol and acetic acid, hexyl ester. These findings provide new viable possibilities of controlling olive anthracnose using the endophyte A. pullulans and/or their VOCs. These volatile inhibitory metabolites should be further tested against anthracnose.A mosca da azeitona, Bactrocera oleae (Rossi) (Diptera: Tephritidae), e a gafa, causada principalmente por Colletotrichum acutatum, são consideradas inimigos chave da oliveira em todo o mundo. As estratégias de luta contra esta praga e doença baseiam-se principalmente no uso de inseticidas e pesticidas à base de cobre, respetivamente, o que não é compatível com sistemas de produção sustentáveis. O presente trabalho tem como objetivo estudar o efeito de dois endófitos, previamente isolados de oliveira, nomeadamente Aureobasidium pullulans e Sarocladium summerbellii, sobre o comportamento (atratividade ou repelência) e preferência de frutos para oviposição de B. oleae, bem como sobre o desenvolvimento de gafa, utilizando ensaios in vitro e in vivo (frutos destacados). A emissão de voláteis de azeitonas inoculadas com A. pullulans e o seu efeito no desenvolvimento da gafa, foi igualmente estudado. Os ensaios de escolha múltipla realizados no olfatómetro mostraram que nenhum dos endófitos exerceu um efeito repelente ou atraente sobre fêmeas grávidas de B. oleae. De igual modo, não foi detetada nenhuma preferência pelas fêmeas em colocar ovos em frutos não inoculados versus inoculados com endófitos. Dos dois endófitos testados, apenas A. pullulans inibiu significativamente o crescimento (até 1,3 vezes), esporulação (até 5,9 vezes) e germinação (até 3,5 vezes) de C. acutatum em relação ao controlo (C. acutatum). Nos ensaios de inoculação de azeitonas, foi também verificado que apenas A. pullulans reduziu significativamente a curva de progresso para incidência (até 10 vezes) e severidade (até 35 vezes) da gafa, bem como a esporulação (até 90%) e germinação (até 70%) de C. acutatum, face a azeitonas inoculadas apenas com C. acutatum. Análise por cromatografia gasosa de azeitonas inoculadas com A. pullulans + C. acutatum e controlos (azeitonas inoculadas com C. acutatum, A. pullulans ou tween) permitiram identificar 29 compostos voláteis, pertencentes a 10 classes químicas, tendo sido os álcoois os mais diversificados e abundantes. O perfil volátil de A. pullulans + C. acutatum revelou diferenças qualitativas e quantitativas em relação aos controlos, em particular devido à produção de (z) -3-hexen-1-ol e ácido acético, hexil éster. Apesar de preliminares, os resultados obtidos oferecem novas possibilidades para a luta da gafa pela exploração do endófito A. pullulans e / ou dos seus voláteis. A ação e potencial destes voláteis na luta contra a gafa deverá ser estudada no futuro.This work is supported by FEDER funds through the COMPETE (Operational Program for Competitiveness Factors) and by National funds through the FCT (Foundation for Science and Technology) in the scope of the project POCI-01-0145-FEDER-031133 “MicOlives - Exploiting plant induced resistance by beneficial fungi as a new sustainable approach to olive crop protection

    Bayesian networks for disease diagnosis: What are they, who has used them and how?

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    A Bayesian network (BN) is a probabilistic graph based on Bayes' theorem, used to show dependencies or cause-and-effect relationships between variables. They are widely applied in diagnostic processes since they allow the incorporation of medical knowledge to the model while expressing uncertainty in terms of probability. This systematic review presents the state of the art in the applications of BNs in medicine in general and in the diagnosis and prognosis of diseases in particular. Indexed articles from the last 40 years were included. The studies generally used the typical measures of diagnostic and prognostic accuracy: sensitivity, specificity, accuracy, precision, and the area under the ROC curve. Overall, we found that disease diagnosis and prognosis based on BNs can be successfully used to model complex medical problems that require reasoning under conditions of uncertainty.Comment: 22 pages, 5 figures, 1 table, Student PhD first pape

    Pollution-induced community tolerance in freshwater biofilms – from molecular mechanisms to loss of community functions

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    Exposure to herbicides poses a threat to aquatic biofilms by affecting their community structure, physiology and function. These changes render biofilms to become more tolerant, but on the downside community tolerance has ecologic costs. A concept that addresses induced community tolerance to a pollutant (PICT) was introduced by Blanck and Wängberg (1988). The basic principle of the concept is that microbial communities undergo pollution-induced succession when exposed to a pollutant over a long period of time, which changes communities structurally and functionally and enhancing tolerance to the pollutant exposure. However, the mechanisms of tolerance and the ecologic consequences were hardly studied up to date. This thesis addresses the structural and functional changes in biofilm communities and applies modern molecular methods to unravel molecular tolerance mechanisms. Two different freshwater biofilm communities were cultivated for a period of five weeks, with one of the communities being contaminated with 4 μg L-1 diuron. Subsequently, the communities were characterized for structural and functional differences, especially focusing on their crucial role of photosynthesis. The community structure of the autotrophs was assessed using HPLC-based pigment analysis and their functional alterations were investigated using Imaging-PAM fluorometry to study photosynthesis and community oxygen profiling to determine net primary production. Then, the molecular fingerprints of the communities were measured with meta-transcriptomics (RNA-Seq) and GC-based community metabolomics approaches and analyzed with respect to changes in their molecular functions. The communities were acute exposed to diuron for one hour in a dose-response design, to reveal a potential PICT and uncover related adaptation to diuron exposure. The combination of apical and molecular methods in a dose-response design enabled the linkage of functional effects of diuron exposure and underlying molecular mechanisms based on a sensitivity analysis. Chronic exposure to diuron impaired freshwater biofilms in their biomass accrual. The contaminated communities particularly lost autotrophic biomass, reflected by the decrease in specific chlorophyll a content. This loss was associated with a change in the molecular fingerprint of the communities, which substantiates structural and physiological changes. The decline in autotrophic biomass could be due to a primary loss of sensitive autotrophic organisms caused by the selection of better adapted species in the course of chronic exposure. Related to this hypothesis, an increase in diuron tolerance has been detected in the contaminated communities and molecular mechanisms facilitating tolerance have been found. It was shown that genes of the photosystem, reductive-pentose phosphate cycle and arginine metabolism were differentially expressed among the communities and that an increased amount of potential antioxidant degradation products was found in the contaminated communities. This led to the hypothesis that contaminated communities may have adapted to oxidative stress, making them less sensitive to diuron exposure. Moreover, the photosynthetic light harvesting complex was altered and the photoprotective xanthophyll cycle was increased in the contaminated communities. Despite these adaptation strategies, the loss of autotrophic biomass has been shown to impair primary production. This impairment persisted even under repeated short-term exposure, so that the tolerance mechanisms cannot safeguard primary production as a key function in aquatic systems.:1. The effect of chemicals on organisms and their functions .............................. 1 1.1 Welcome to the anthropocene .......................................................................... 1 1.2 From cellular stress responses to ecosystem resilience ................................... 3 1.2.1 The individual pursuit for homeostasis ....................................................... 3 1.2.2 Stability from diversity ................................................................................. 5 1.3 Community ecotoxicology - a step forward in monitoring the effects of chemical pollution? ................................................................................................................. 6 1.4 Functional ecotoxicological assessment of microbial communities ................... 9 1.5 Molecular tools – the key to a mechanistic understanding of stressor effects from a functional perspective in microbial communities? ...................................... 12 2. Aims and Hypothesis ......................................................................................... 14 2.1 Research question .......................................................................................... 14 2.2 Hypothesis and outline .................................................................................... 15 2.3 Experimental approach & concept .................................................................. 16 2.3.1 Aquatic freshwater biofilms as model community ..................................... 16 2.3.2 Diuron as model herbicide ........................................................................ 17 2.3.3 Experimental design ................................................................................. 18 3. Structural and physiological changes in microbial communities after chronic exposure - PICT and altered functional capacity ................................................. 21 3.1 Introduction ..................................................................................................... 21 3.2 Methods .......................................................................................................... 23 3.2.1 Biofilm cultivation ...................................................................................... 23 3.2.2 Dry weight and autotrophic index ............................................................. 23 3.2.4 Pigment analysis of periphyton ................................................................. 23 3.2.4.1 In-vivo pigment analysis for community characterization ....................... 24 3.2.4.2 In-vivo pigment analysis based on Imaging-PAM fluorometry ............... 24 3.2.4.3 In-vivo pigment fluorescence for tolerance detection ............................. 26 3.2.4.4 Ex-vivo pigment analysis by high-pressure liquid-chromatography ....... 27 3.2.5 Community oxygen metabolism measurements ....................................... 28 3.3 Results and discussion ................................................................................... 29 3.3.1 Comparison of the structural community parameters ............................... 29 3.3.2 Photosynthetic activity and primary production of the communities after selection phase ................................................................................................. 33 3.3.3 Acquisition of photosynthetic tolerance .................................................... 34 3.3.4 Primary production at exposure conditions ............................................... 36 3.3.5 Tolerance detection in primary production ................................................ 37 3.4 Summary and Conclusion ........................................................................... 40 4. Community gene expression analysis by meta-transcriptomics ................... 41 4.1 Introduction to meta-transcriptomics ............................................................... 41 4.2. Methods ......................................................................................................... 43 4.2.1 Sampling and RNA extraction................................................................... 43 4.2.2 RNA sequencing analysis ......................................................................... 44 4.2.3 Data assembly and processing................................................................. 45 4.2.4 Prioritization of contigs and annotation ..................................................... 47 4.2.5 Sensitivity analysis of biological processes .............................................. 48 4.3 Results and discussion ................................................................................... 48 4.3.1 Characterization of the meta-transcriptomic fingerprints .......................... 49 4.3.2 Insights into community stress response mechanisms using trend analysis (DRomic’s) ......................................................................................................... 51 4.3.3 Response pattern in the isoform PS genes .............................................. 63 4.5 Summary and conclusion ................................................................................ 65 5. Community metabolome analysis ..................................................................... 66 5.1 Introduction to community metabolomics ........................................................ 66 5.2 Methods .......................................................................................................... 68 5.2.1 Sampling, metabolite extraction and derivatisation................................... 68 5.2.2 GC-TOF-MS analysis ............................................................................... 69 5.2.3 Data processing and statistical analysis ................................................... 69 5.3 Results and discussion ................................................................................... 70 5.3.1 Characterization of the metabolic fingerprints .......................................... 70 5.3.2 Difference in the metabolic fingerprints .................................................... 71 5.3.3 Differential metabolic responses of the communities to short-term exposure of diuron ............................................................................................................ 73 5.4 Summary and conclusion ................................................................................ 78 6. Synthesis ............................................................................................................. 79 6.1 Approaches and challenges for linking molecular data to functional measurements ...................................................................................................... 79 6.2 Methods .......................................................................................................... 83 6.2.1 Summary on the data ............................................................................... 83 6.2.2 Aggregation of molecular data to index values (TELI and MELI) .............. 83 6.2.3 Functional annotation of contigs and metabolites using KEGG ................ 83 6.3 Results and discussion ................................................................................... 85 6.3.1 Results of aggregation techniques ........................................................... 85 6.3.2 Sensitivity analysis of the different molecular approaches and endpoints 86 6.3.3 Mechanistic view of the molecular stress responses based on KEGG functions ............................................................................................................ 89 6.4 Consolidation of the results – holistic interpretation and discussion ............... 93 6.4.1 Adaptation to chronic diuron exposure - from molecular changes to community effects.............................................................................................. 93 6.4.2 Assessment of the ecological costs of Pollution-induced community tolerance based on primary production ............................................................. 94 6.5 Outlook ............................................................................................................ 9

    Anuário científico da Escola Superior de Tecnologia da Saúde de Lisboa - 2021

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    É com grande prazer que apresentamos a mais recente edição (a 11.ª) do Anuário Científico da Escola Superior de Tecnologia da Saúde de Lisboa. Como instituição de ensino superior, temos o compromisso de promover e incentivar a pesquisa científica em todas as áreas do conhecimento que contemplam a nossa missão. Esta publicação tem como objetivo divulgar toda a produção científica desenvolvida pelos Professores, Investigadores, Estudantes e Pessoal não Docente da ESTeSL durante 2021. Este Anuário é, assim, o reflexo do trabalho árduo e dedicado da nossa comunidade, que se empenhou na produção de conteúdo científico de elevada qualidade e partilhada com a Sociedade na forma de livros, capítulos de livros, artigos publicados em revistas nacionais e internacionais, resumos de comunicações orais e pósteres, bem como resultado dos trabalhos de 1º e 2º ciclo. Com isto, o conteúdo desta publicação abrange uma ampla variedade de tópicos, desde temas mais fundamentais até estudos de aplicação prática em contextos específicos de Saúde, refletindo desta forma a pluralidade e diversidade de áreas que definem, e tornam única, a ESTeSL. Acreditamos que a investigação e pesquisa científica é um eixo fundamental para o desenvolvimento da sociedade e é por isso que incentivamos os nossos estudantes a envolverem-se em atividades de pesquisa e prática baseada na evidência desde o início dos seus estudos na ESTeSL. Esta publicação é um exemplo do sucesso desses esforços, sendo a maior de sempre, o que faz com que estejamos muito orgulhosos em partilhar os resultados e descobertas dos nossos investigadores com a comunidade científica e o público em geral. Esperamos que este Anuário inspire e motive outros estudantes, profissionais de saúde, professores e outros colaboradores a continuarem a explorar novas ideias e contribuir para o avanço da ciência e da tecnologia no corpo de conhecimento próprio das áreas que compõe a ESTeSL. Agradecemos a todos os envolvidos na produção deste anuário e desejamos uma leitura inspiradora e agradável.info:eu-repo/semantics/publishedVersio

    INVESTIGATING THE PERCEPTION OF EXPATRIATES TOWARDS IMMIGRATION SERVICE QUALITY IN SHARJAH, UNITED ARAB EMIRATES THROUGH MIXED METHOD APPROACH

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    The public sectors in UAE are under immense pressure to demonstrate that their services are customer-focused and that continuous performance improvement is being delivered. The United Arab Emirates is a favoured destination for expatriates due to its own citizens form a minority of the population and are barely represented in the private sector workforce. These highly unusual demographics confer high importance on the national immigration services. Recently, increased interest in international migration, specifically within the United Arab Emirates, has been shown both by government agencies and by the governments of industrialised countries. Given the importance of the expatriate labour force to economic stability and growth in the Emirates, this research investigates how immigration services are perceived, with the aim of contributing to their improvement, thus ultimately supporting economic growth. It proposes a service quality perception framework to improve understanding within SID of how to raise levels of service delivered to migrants and other persons directly or indirectly affected by SID services. Qualitative data were collected by means of semi-structured interviews and quantitative data by means of a questionnaire survey based on the abovementioned framework. The survey data, on the variables influencing participants’ experiences and perceptions of SID services, were subjected to statistical analysis. The framework was then used to evaluate quality of service in terms of general impressions, delivery, location, response, SID culture and behaviour. Numerical data were analysed using inferential and descriptive statistics. It was found that service quality positively influenced service behaviour and that this relationship was mediated by SID culture. This research makes an original contribution to knowledge as one of the few studies of immigration to the United Arab Emirates. By examining the workings of one immigration department, it adds to the literature on immigration departments and organisational development in developing countries. It illuminates the mechanics of immigration services and demonstrates their increasing importance to the world economy

    Computing Interpretable Representations of Cell Morphodynamics

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    Shape changes (morphodynamics) are one of the principal ways cells interact with their environments and perform key intrinsic behaviours like division. These dynamics arise from a myriad of complex signalling pathways that often organise with emergent simplicity to carry out critical functions including predation, collaboration and migration. A powerful method for analysis can therefore be to quantify this emergent structure, bypassing the low-level complexity. Enormous image datasets are now available to mine. However, it can be difficult to uncover interpretable representations of the global organisation of these heterogeneous dynamic processes. Here, such representations were developed for interpreting morphodynamics in two key areas: mode of action (MoA) comparison for drug discovery (developed using the economically devastating Asian soybean rust crop pathogen) and 3D migration of immune system T cells through extracellular matrices (ECMs). For MoA comparison, population development over a 2D space of shapes (morphospace) was described using two models with condition-dependent parameters: a top-down model of diffusive development over Waddington-type landscapes, and a bottom-up model of tip growth. A variety of landscapes were discovered, describing phenotype transitions during growth, and possible perturbations in the tip growth machinery that cause this variation were identified. For interpreting T cell migration, a new 3D shape descriptor that incorporates key polarisation information was developed, revealing low-dimensionality of shape, and the distinct morphodynamics of run-and-stop modes that emerge at minute timescales were mapped. Periodically oscillating morphodynamics that include retrograde deformation flows were found to underlie active translocation (run mode). Overall, it was found that highly interpretable representations could be uncovered while still leveraging the enormous discovery power of deep learning algorithms. The results show that whole-cell morphodynamics can be a convenient and powerful place to search for structure, with potentially life-saving applications in medicine and biocide discovery as well as immunotherapeutics.Open Acces

    CITIES: Energetic Efficiency, Sustainability; Infrastructures, Energy and the Environment; Mobility and IoT; Governance and Citizenship

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    This book collects important contributions on smart cities. This book was created in collaboration with the ICSC-CITIES2020, held in San José (Costa Rica) in 2020. This book collects articles on: energetic efficiency and sustainability; infrastructures, energy and the environment; mobility and IoT; governance and citizenship

    Echinoderms Metabolites: Structure, Functions and Biomedical Perspectives

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    The materials published in the Special Issue reflect the real diversity of echinoderm metabolites and cover most of their specific classes and biomedical potential as antioxidant, antiviral, anticancer, and even anticoagulant preparations. The metabolites include sea urchin naphtoquinoid pigments and their semi-synthetic derivatives, sea cucumber triterpene glycosides, esters of polyhydroxysteroids from starfish, sea urchins free sterols, and sea cucumber fucosylated chondroitin sulfates. This Special Issue, “Echinoderm Metabolites: Structure, Functions, and Biomedical Perspectives”, is a collection of articles about different scientific aspects concerning low molecular weight and biopolymer metabolites from echinoderms, including their isolation and chemical structures, biological activities, biosynthesis and evolution, biological functions, and obtaining of semi-synthetic derivatives of biologically active natural products. This Special Issue includes materials about sea urchin naphtoquinoid pigments and their semi-synthetic derivatives, sea cucumber triterpene glycosides, esters of polyhydroxysteroids from starfish, sea urchin free sterols, and sea cucumber fucosylated chondroitin sulfates

    Technologies and Applications for Big Data Value

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    This open access book explores cutting-edge solutions and best practices for big data and data-driven AI applications for the data-driven economy. It provides the reader with a basis for understanding how technical issues can be overcome to offer real-world solutions to major industrial areas. The book starts with an introductory chapter that provides an overview of the book by positioning the following chapters in terms of their contributions to technology frameworks which are key elements of the Big Data Value Public-Private Partnership and the upcoming Partnership on AI, Data and Robotics. The remainder of the book is then arranged in two parts. The first part “Technologies and Methods” contains horizontal contributions of technologies and methods that enable data value chains to be applied in any sector. The second part “Processes and Applications” details experience reports and lessons from using big data and data-driven approaches in processes and applications. Its chapters are co-authored with industry experts and cover domains including health, law, finance, retail, manufacturing, mobility, and smart cities. Contributions emanate from the Big Data Value Public-Private Partnership and the Big Data Value Association, which have acted as the European data community's nucleus to bring together businesses with leading researchers to harness the value of data to benefit society, business, science, and industry. The book is of interest to two primary audiences, first, undergraduate and postgraduate students and researchers in various fields, including big data, data science, data engineering, and machine learning and AI. Second, practitioners and industry experts engaged in data-driven systems, software design and deployment projects who are interested in employing these advanced methods to address real-world problems
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