Abstract
Retinal vessel caliber changes are associated with several major diseases, such as diabetes and hypertension. These caliber changes can be evaluated using eye fundus images. However, the clinical assessment is tiresome and prone to errors, motivating the development of automatic methods. An automatic method based on vessel crosssection intensity profile model fitting for the estimation of vessel caliber in retinal images is herein proposed. First, vessels are segmented from the image, vessel centerlines are detected and individual segments are extracted and smoothed. Intensity profiles are extracted perpendicularly to the vessel, and the profile lengths are determined. Then, model fitting is applied to the smoothed profiles. A novel parametric model (DoG-L7) is used, consisting on a Difference-of-Gaussians multiplied by a line which is able to describe profile asymmetry. Finally, the parameters of the best-fit model are used for determining the vessel width through regression using ensembles of bagged regression trees with random sampling of the predictors (random forests). The method is evaluated on the REVIEW public dataset. A precision close to the observers is achieved, outperforming other state-of-the-art methods. The method is robust and reliable for width estimation in images with pathologies and artifacts, with performance independent of the range of diameters.

Abstract
Aim of study: The study aims to evaluate the maximum potential stocking level in cork oak (Quercus suber L.) woodlands, using the ecologically-based size-density relationship of the self-thinning law. Area of study: The study area refers to cork oak forests in mainland Portugal, distributed along its 18 districts from north to south. Material and Methods: A dataset with a total of 2181 observations regarding pure cork oak stands was collected from the Portuguese Forest Inventory (NFI) databases and from research plots. The dataset was subjected to two filtering procedures, one more restrictive than the other, to select the stands presenting the higher stocking values. The two resulting subsets, with 116 and 36 observations, from 16 and 10 districts of mainland Portugal, respectively, were then used to assess and describe the allometric relationship between tree number and their mean diameter. Main results: The allometric relationship was analysed and modelled using the log transformed variables. A slightly curvilinear trend was identified. Thus, a straight line and a curve were both fitted for comparison purposes. Goodness-of-fit statistics point out for a good performance when the data is set to the uppermost observed stocking values. A self-thinning line for cork oak was projected from the estimated relationship. Research highlights: The self-thinning model can be used as an ecological approach to develop density guidelines for oak woodlands in a scenario of increasing cork demands. The results indicate that the recommendations being applied in Portugal are far below the maximal potential stocking values for the species. It is therefore of the utmost importance to review the traditional silvicultural guidelines and endorse new ones.

Abstract
Conflict-free Data Types (CRDTs) were designed to automatically resolve conflicts in eventually consistent systems. Different CRDTs were designed in both operation-based and state-based flavors such as Counters, Sets, Registers, Maps, etc. In a previous paper [2], Baquero et al. presented the problem with embedded CRDT counters and a solution, covering state-based counters that can be embedded in maps, but needing an ad-hoc extension to the standard counter API. Here, we present a resettable operation-based counter design, with the standard simple API and small state, through a causal-stability-based state compaction.

Abstract
Este volume pretende abarcar algumas das evoluções atuais e devido à transformação digital. O mundo está em constante mutação e devido à verdadeira revolução e transformação digital esta mudança tem ocorrido a passos muito rápidos e de forma imprevisível – o que faz com que seja difícil fazer previsões a cinco anos e sobre como estarão certas indústrias afetadas pela tecnologia, no futuro. As redes sociais online modificaram a forma como nos expomos e apresentamos. Os smartphones tornaram tudo mais móvel – temos grandes computadores, muito potentes, no nosso bolso e connosco todos os dias. O negócio das apps e do software mudou de paradigma – o que conta são os seguidores e muito do software agora é grátis. Vejamos o caso do Facebook, do Instagram, e até do WhatsApp – plataformas grátis. Querem é utilizar os utentes como receptáculos de publicidade e para fins comerciais que outrora eram muito diferentes e até impensáveis. Em tal ambiente a pressão sobre os gestores e os agentes na sociedade, com poder de decisão, está em níveis nunca antes vistos. Por um lado, são exigidas empresas competitivas e que façam uso da tecnologia, tecnologia que muitas das vezes é nova e tem custos assim como perigos. A privacidade da informação, quer de adultos, quer de crianças, é fundamental. Nunca antes os nossos jovens tiveram acesso a tanta informação e de forma praticamente grátis. A Internet mudou radicalmente como acedemos à informação e ao conhecimento e os pais deixaram de ser a resposta para tudo e para todas as questões dos seus filhos – tendo sido substituídos, em muitos casos, por motores de busca como o Google, e outros (dependendo também da geografia do consumidor, sendo a China uma região grande e preponderante, mas que tem regras e instituições muito próprias). Também na sala de aula os educadores, em especial no ensino superior, se deparam com esta nova realidade em que, se fazem perguntas às quais o Google tem resposta, terão dificuldade em assegurar salas cheias de alunos. Os alunos querem adquirir conhecimento tácito sobre o qual o Google não informa. Este é somente um exemplo dos desafios que a tecnologia coloca. Fica também o desafio ao leitor para nos ajudar a cocriar um futuro cada vez mais igual e não cada vez mais desigual. Mandem-nos, por favor, as vossas sugestões sobre como acompanhar a revolução no meio da qual vivemos hoje em dia. Por último, gostaríamos de agradecer encarecidamente aos autores dos diversos capítulos do livro, pela sua dedicação aos temas, pela sua originalidade, e pela sua paciência e cooperação na revisão dos materiais submetidos.

Abstract
The huge amount of genomic and transcriptomic data obtained to characterize human diversity can also be exploited to indirectly gather information on the human microbiome. Here we present the pipeline QmihR designed to identify and quantify the abundance of known microbiome communities and to search for new/rare pathogenic species in RNA-seq datasets. We applied QmihR to 36 RNA-seq tumor tissue samples from Ukrainian gastric carcinoma patients available in TCGA, in order to characterize their microbiome and check for efficiency of the pipeline. The microbes present in the samples were in accordance to published data in other European datasets, and the independent BLAST evaluation of microbiome-aligned reads confirmed that the assigned species presented the highest BLAST match-hits. QmihR is available at GitHub (https://github.com/ Pereira-lab/QmihR). © Springer International Publishing AG 2017.

Abstract
Motivation: The exponential growth of publicly available RNA-sequencing (RNA-Seq) data poses an increasing challenge to researchers wishing to discover, analyse and store such data, particularly those based in institutions with limited computational resources. EMBL-EBI is in an ideal position to address these challenges and to allow the scientific community easy access to not just raw, but also processed RNA-Seq data. We present a Web service to access the results of a systematically and continually updated standardized alignment as well as gene and exon expression quantification of all public bulk (and in the near future also single-cell) RNA-Seq runs in 264 species in European Nucleotide Archive, using Representational State Transfer. Results: The RNASeq-er API (Application Programming Interface) enables ontology-powered search for and retrieval of CRAM, bigwig and bedGraph files, gene and exon expression quantification matrices (Fragments Per Kilobase Of Exon Per Million Fragments Mapped, Transcripts Per Million, raw counts) as well as sample attributes annotated with ontology terms. To date over 270 00 RNA-Seq runs in nearly 10 000 studies (1PB of raw FASTQ data) in 264 species in ENA have been processed and made available via the API.