Leibniz Data Manager – An adaptive Research Data Management System

The increasing demand of researchers to make the underlying research data openly accessible, in addition to the classic publication forms, can improve the reproducibility of scientific findings, whether voluntarily or due to the institution’s or research funders’ requirements. As a result, researchers depend on expressive descriptions of research data for reusability. These descriptions are in the form of comprehensive metadata stored in heterogeneous formats in research data repositories. However, finding the appropriate data is arduous, as there is a growing amount of research data stored in various places and only a few repositories offer the function of displaying a preview of the data. Research work efficiency can benefit from data previews whenever researchers can explore portions of a dataset before deciding on the relevance of the data for accessing and downloading the whole dataset. The Leibniz Data Manager (LDM) is a research data management system that resorts to Semantic Web technologies to empower FAIR principles. LDM supports searching and exploring research data across various repositories. LDM provides an additional (meta-)data management layer for data collected from existing research data repositories based on the webbased data catalog software CKAN (Comprehensive Knowledge Archive Network). The primary purpose of LDM is to preview research data, e.g., tables, audio-visual material like AutoCAD files or 2D and 3D data, or live programming code via Jupyter Notebook(s) so that their potential for reuse can be easily evaluated. Since LDM is available as a Docker container, anyone can install a local LDM distribution to assist research data management in different phases of the data lifecycle. LDM is accessible at https://service.tib.eu/ldmservice/. LDM empowers researchers by supporting them in preserving their research data as open and FAIR as possible. With LDM, researchers can check whether their data is displayed correctly and whether it is available in suitable and preferably open data formats before publication. In addition, humans and computational programs can access machine-readable metadata, which can be exported in various schemas (DCAT, DataCite, and DublinCore) and RDF serializations. This enables automated searching and processing by various data bases and tools. More importantly, DataCite DOIs and ORCIDs ensure the persistence and findability of LDM (meta-)data. At the poster session we will demonstrate how scientists can be supported in searching for datasets and preserving their research data. We are also interested in collecting ideas about future requirements to be implemented in upcoming versions of the LDM

Microbiome and colorectal cancer : Roles in carcinogenesis and clinical potential

Altres ajuts: Instituto Nacional de Bioinformatica (INB, grant PT17/0009/0023 - ISCIII-SGEFI/ERDF)The gastrointestinal tract harbors most of the microbiota associated with humans. In recent years, there has been a surge of interest in assessing the relationships between the gut microbiota and several gut alterations, including colorectal cancer. Changes in the gut microbiota in patients suffering colorectal cancer suggest a possible role of host-microbe interactions in the origin and development of this malignancy and, at the same time, open the door for novel ways of preventing, diagnosing, or treating this disease. In this review we survey current knowledge on the healthy microbiome of the gut and how it is altered in colorectal cancer and other related disease conditions. In describing past studies we will critically assess technical limitations of different approaches and point to existing challenges in microbiome research. We will have a special focus on host-microbiome interaction mechanisms that may be important to explain how dysbiosis can lead to chronic inflammation and drive processes that influence carcinogenesis and tumor progression in colon cancer. Finally, we will discuss the potential of recent developments of novel microbiota-based therapeutics and diagnostic tools for colorectal cancer

As Repercussões Jurídicas do Teletrabalho e os Reflexos de Eficiência na Administração Pública

This study analyzes the legal repercussions of telework and the reflexes of efficiency in public administration. With the advancement in legislation, telework has gained even more space in establishments and in the public administration sectors. The use of telework can have several benefits for workers who use this type of work and also for companies that choose to adopt, in whole or in part, this type of work. For the use of telework in the Public Administration it must be proved that the use of this type of work does not infringe any Administration principle, which being proven, it is important to highlight the benefits caused by this type of work, among them the economy with space, energy and water as well as being a way to increase worker productivity. The worker also benefits from the use of teleworking, as he can save on transportation, as well as having greater flexibility in his working time.O presente estudo analisa as repercussões jurídicas do teletrabalho e os reflexos de eficiência na administração pública. Com o avanço na legislação, o teletrabalho ganhou ainda mais espaço nos estabelecimentos e, também, nos setores da administração pública. A utilização do teletrabalho pode causar uma série de benefícios para os trabalhadores que se utilizam dessa modalidade laboral e também para as empresas que optam por adotar, no todo ou em parte, essa modalidade de trabalho. Para a utilização do teletrabalho na Administração Pública é preciso comprovar que o uso dessa modalidade de trabalho não fere nenhum principio da Administração, sendo esse comprovado, é importante destacar os benefícios causados por essa modalidade de trabalho, dentre eles a economia com espaço, energia e água, além de ser uma forma de aumentar a produtividade do trabalhador. O trabalhador também é beneficiado com o uso da modalidade teletrabalho, tendo em vista que ele pode economizar com transporte, além de ter uma flexibilidade maior no seu tempo de trabalho

Interactions between local and global drivers determine long-term trends in boreal forest understorey vegetation

Aim Global change effects on forest ecosystems are increasingly claimed to be context dependent, indicated by interactions between global and local environmental drivers. Most examples of such context dependencies originate from temperate systems, while limited research comes from the boreal biome. Here we set out to test if interactions between climate warming, nitrogen deposition, land-use change resulting in increasing forest density, and soil pH drive long-term changes in understorey vegetation in boreal forests. Location Sweden. Time period 1953-2012. Major taxa studied Vascular plants. Methods We used long-term (50 years) National Forest Inventory data on forest understorey vegetation in Sweden to model the combined effects of climate warming, nitrogen deposition, increase in forest density (tree basal area), and soil pH. Results Our results identify increasing temperature, nitrogen deposition and denser, shadier forest conditions as the main drivers of understorey vegetation changes during this time period. More importantly, we found that these effects varied with local conditions, that is, that the change towards a more nitrophilic understorey vegetation was more pronounced at low than high soil pH. Forest density was an important modulator of nitrogen deposition and temperature increase, with effects generally decreasing with density. Decreased cover of ericaceous dwarf shrubs was driven by both forest density and nitrogen deposition, with a stronger effect at low than at high pH. Main conclusions Our results highlight that to understand forest ecosystems' response to global change, and to make adequate management decisions to mitigate the effects of global change, we need to understand how changes in local environmental factors (forest density and soil pH) interact with global-scale drivers (nitrogen deposition and climate warming). Neglecting such interactions will lead to incorrect estimations of effects. In our case, we would for example, have underestimated the eutrophication effects on acid soils, which constitute a considerable part of the boreal biome

Long Non-Coding RNAs As Potential Novel Prognostic Biomarkers in Colorectal Cancer

Colorectal cancer (CRC) is the fourth most common cause of death worldwide. Surgery is usually the first line of treatment for patients with CRC but many tumors with similar histopathological features show significantly different clinical outcomes. The discovery of robust prognostic biomarkers in patients with CRC is imperative to achieve more effective treatment strategies and improve patient's care. Recent progress in next generation sequencing methods and transcriptome analysis has revealed that a much larger part of the genome is transcribed into RNA than previously assumed. Collectively referred to as non-coding RNAs (ncRNAs), some of these RNA molecules such as microRNAs (miRNAs) and long non-coding RNAs (lncRNAs) have been shown to be altered and to play critical roles in tumor biology. This discovery leads to exciting possibilities for personalized cancer diagnosis, and therapy. Many lncRNAs are tissue and cancer-type specific and have already revealed to be useful as prognostic markers. In this review, we focus on recent findings concerning aberrant expression of lncRNAs in CRC tumors and emphasize their prognostic potential in CRC. Further studies focused on the mechanisms of action of lncRNAs will contribute to the development of novel biomarkers for diagnosis and disease progression

Data on individual PCR efficiency values as quality control for circulating miRNAs

AbstractThis data article contains data related to the research article entitled “Variability in microRNA recovery from plasma: Comparison of five commercial kits, doi:10.1016/j.ab.2015.07.018” Brunet-Vega (2015) [1]. PCR efficiency, along with RNA and cDNA quality, are the most important factors affecting the quality of qPCR results. Constant amplification efficiency in all compared samples is indispensable when relative quantification is used to measure changes in gene expression. An easy way to measure PCR efficiency, without the need of a standard curve, is LinRegPCR software. Individual PCR efficiency can be determined as a part of qPCR quality control. This is especially important when the initial RNA quantity is so low that cannot be accurately quantified, such as in circulating RNA extractions. This data article reports the Cqs and PCR efficiencies of 5 miRNAs quantified in RNA isolated from 4 patients with colorectal cancer (CRC) and 4 healthy donors using five commercially available kits

Estructuras geométricas jerárquicas para la modelización de escenas 3D

This work surveys on the principal hierarchical geometric structures used to represent 3D scenes. We also present the basic algorithms to work with them, an overview on some recent works and a comparative discussion. This work has been the outcomes of the graduate coursePostprint (published version

Testing lowered isothermal models with direct N-body simulations of globular clusters

Several self-consistent models have been proposed, aiming at describing the phase space distribution of stars in globular clusters. This study explores the ability of the recently proposed LIMEPY models (Gieles & Zocchi) to reproduce the dynamical properties of direct N-body models of a cluster in a tidal field, during its entire evolution. These dynamical models include prescriptions for the truncation and the degree of radially-biased anisotropy contained in the system, allowing us to explore the interplay between the role of anisotropy and tides in various stages of the life of star clusters. We show that the amount of anisotropy in an initially tidally underfilling cluster increases in the pre-collapse phase, and then decreases with time, due to the effect of the external tidal field on its spatial truncation. This is reflected in the correspondent model parameters, and the best-fit models reproduce the main properties of the cluster at all stages of its evolution, except for the phases immediately preceding and following core collapse. We also notice that the best-fit LIMEPY models are significantly different from isotropic King models, especially in the first part of the evolution of the cluster. Our results put limits on the amount of radial anisotropy that can be expected for clusters evolving in a tidal field, which is important to understand other factors that could give rise to similar observational signatures, such as the presence of an intermediate-mass black hole.Comment: 20 pages, 11 figures. Accepted for publication in MNRA

High Performance of a Dominant/X-Linked Gene Panel in Patients with Neurodevelopmental Disorders

Neurodevelopmental disorders (NDDs) affect 2-5% of the population and approximately 50% of cases are due to genetic factors. Since de novo pathogenic variants account for the majority of cases, a gene panel including 460 dominant and X-linked genes was designed and applied to 398 patients affected by intellectual disability (ID)/global developmental delay (GDD) and/or autism (ASD). Pathogenic variants were identified in 83 different genes showing the high genetic heterogeneity of NDDs. A molecular diagnosis was established in 28.6% of patients after high-depth sequencing and stringent variant filtering. Compared to other available gene panel solutions for NDD molecular diagnosis, our panel has a higher diagnostic yield for both ID/GDD and ASD. As reported previously, a significantly higher diagnostic yield was observed: (i) in patients affected by ID/GDD compared to those affected only by ASD, and (ii) in females despite the higher proportion of males among our patients. No differences in diagnostic rates were found between patients affected by different levels of ID severity. Interestingly, patients harboring pathogenic variants presented different phenotypic features, suggesting that deep phenotypic profiling may help in predicting the presence of a pathogenic variant. Despite the high performance of our panel, whole exome-sequencing (WES) approaches may represent a more robust solution. For this reason, we propose the list of genes included in our customized gene panel and the variant filtering procedure presented here as a first-tier approach for the molecular diagnosis of NDDs in WES studies