Abstract
AbstractUsing a dataset of somatic Structural Variants (SVs) in cancers from 2658 patients—1220 with corresponding gene expression data—we identified hundreds of genes for which the nearby presence (within 100kb) of an SV breakpoint was associated with altered expression. For the vast majority of these genes, expression was increased rather than decreased with corresponding SV event. Well-known up-regulated cancer-associated genes impacted by this phenomenon included TERT, MDM2, CDK4, ERBB2, CD274, PDCD1LG2, and IGF2. SVs upstream of TERT involved ~3% of cancer cases and were most frequent in liver-biliary, melanoma, sarcoma, stomach, and kidney cancers. SVs associated with up-regulation of PD1 and PDL1 genes involved ~1% of non-amplified cases. For many genes, SVs were significantly associated with either increased numbers or greater proximity of enhancer regulatory elements near the gene. DNA methylation near the gene promoter was often increased with nearby SV breakpoint, which may involve inactivation of repressor elements.AbbreviationsPCAWGthe Pan-Cancer Analysis of Whole Genomes projectSVStructural Variant

Abstract
Demand response (DR) implementations have recently found wide application areas in the context of smart grids. The effectiveness of these implementations is primarily based on the willingness of end-users to be involved in such programs. In this paper, an interactive and user-friendly interface is presented in order to facilitate and accordingly to increase the participation of end-users in DR programs. The proposed interface has the capability of providing the targeted information about the DR events to end-users and system operators, as well as allowing end-users to interactively monitor and control the progress of their appliances. In addition to its benefits to system operators and thus to the improved operation of power systems, the proposed interface particularly aims to exploit the potential energy-related cost savings by providing the required information and resources to end-users via mobile phone. A separate interface apart from the mentioned end-user oriented interface has also been developed for the system operator to more effectively check the status of DR applications in detail. The capabilities of the proposed concept are evaluated in a real smart home in terms of various aspects.

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
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).