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Abstract: In biomedical research, large-scale profiling of gene expression has become routine and offers a valuable means to evaluate changes in onset and progression of diseases, in particular cancer. An overwhelming amount of cancer genomics data has become publicly available, and the complexity of these data makes it a challenge to perform in silico data exploration, integration and analysis, in particular for scientists lacking a background in computational programming or informatics. Many web interface tools make these large datasets accessible but are limited to process large datasets. To accelerate the translation of genomic data into new insights, we provide a simple method to explore and select data from cancer genomic datasets to generate gene-expression profiles of subsets that are of specific genetic, biological or clinical interest.
Keywords: cancer genomics, cBioPortal, data mining, epigenetics, gene expression, in silico
Published in DiRROS: 24.07.2024; Views: 218; Downloads: 451
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Abstract: Harmonization of monitoring protocols and analytical methods is a crucial issue for transnational marine environmental status assessment, yet not the only one. Coherent data management and quality control become very relevant when environmental status is assessed at regional or subregional scale (e.g., for the Mediterranean or the Adriatic Sea), thus requiring data from different sources. Heavy metals are among the main targets of monitoring activities. Significant efforts have been dedicated to share best practices for monitoring and assessment of ecosystem status and to strengthen the network of national, regional and European large data infrastructures in order to facilitate the access to data among countries. Data comparability and interoperability depend not only on sampling and analytical protocols but also on how data and metadata are managed, quality controlled and made accessible. Interoperability is guaranteed by using common metadata and data formats, and standard vocabularies to assure homogeneous syntax and semantics. Data management of contaminants is complex and challenging due to the high number of information required on sampling and analytical procedures, high heterogeneity in matrix characteristics, but also to the large and increasing number of pollutants. Procedures for quality control on heterogeneous datasets provided by multiple sources are not yet uniform and consolidated. Additional knowledge and reliable long time-series of data are needed to evaluate typical ranges of contaminant concentration. The analysis of a coherent and harmonized regional dataset can provide the basis for a multi-step quality control procedure, which can be further improved as knowledge increases during data validation process.
Keywords: contaminants, data management, harmonization, Adriatic Sea, Ionian Sea, pollution, assessment, heavy metals
Published in DiRROS: 22.07.2024; Views: 135; Downloads: 119
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Abstract: Planetary extinction of biodiversity underscores the need for taxonomy. Here, we scrutinizespider taxonomy over the last decade (2008–2018), compiling 2083 published accounts of newlydescribed species. We evaluated what type of data were used to delineate species, whether data weremade freely available, whether an explicit species hypothesis was stated, what types of media wereused, the sample sizes, and the degree to which species constructs were integrative. The findings wereport reveal that taxonomy remains largely descriptive, not integrative, and provides no explicitconceptual framework. Less than 4% of accounts explicitly stated a species concept and over one-thirdof all new species described were based on 1–2 specimens or only one sex. Only ~5% of studies madedata freely available, and only ~14% of all newly described species employed more than one line ofevidence, with molecular data used in ~6% of the studies. These same trends have been discovered inother animal groups, and therefore we find it logical that taxonomists face an uphill challenge whenjustifying the scientific rigor of their field and securing the needed resources. To move taxonomyforward, we make recommendations that, if implemented, will enhance its rigor, repeatability, andscientific standards.
Keywords: taxonomy, taxonomic crisis, species concepts, data management, monographic research
Published in DiRROS: 16.07.2024; Views: 125; Downloads: 61
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Abstract: Considering the role of phytoplankton in the functioning and health of marine systems, it is important to characterize its responses to a changing environment. The central Adriatic Sea, as a generally oligotrophic area, is a suitable environment to distinguish between regular fluctuations in phytoplankton and those caused by anthropogenic or climatic influences. This study provides a long-term perspective of phytoplankton assemblage in the central eastern Adriatic Sea, with 14 years of continuous time series data collected at two coastal and two offshore stations. The predominant phytoplankton groups were diatoms and phytoflagellates, but their proportion varied depending on the vicinity of the coast, as evidenced also by the distribution of chlorophyll a. In the coastal environment, the phytoplankton biomass was substantially higher, with a higher proportion of microphytoplankton, while small phytoplankton accounted for the majority of biomass in the offshore area. In addition, a decreasing trend in diatom abundance was observed in the coastal waters, while such trend was not so evident in the offshore area. Using a neural gas algorithm, five clusters were defined based on the contribution of the major groups. The observed increase in diversity, especially in dinoflagellates, which outnumber diatom taxa, could be a possible adaptation of dinoflagellates to the increased natural solar radiation in summer and the increased sea surface temperature.
Keywords: phytoplankton community, long-term data, diversity, chlorophyll a, neural gas analysis, solar radiation, Adriatic Sea
Published in DiRROS: 11.07.2024; Views: 161; Downloads: 148
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Abstract: Background Among the diseases of oral mucosa, malignant tumors are the most dangerous, but not the most common lesions that might appear in the oral cavity. Since most of the studies are focused on the detection of cancer in the oral cavity, we were interested in detecting the frequency of benign changes of the oral mucosa in Slovene population. Oral mucosal lesions are important pointer of oral health and quality of life, especially in elderly. The prevalence of oral mucosal lesions, together with information on the risk habits associated with oral health, such as tobacco and alcohol use, can help in planning future oral health studies and screening programs. Patients and methods Survey upon oral mucosal lesions was conducted during the national project for oral cancer screening in spring 2017 in the Slovenia in which more than 50% of dentists participated and 2395 patients (904 men and 1491 women) were included. Results Clinical examination, which was conducted according to the WHO standards revealed that 645 patients (27%) had oral mucosal lesions. The ten most common oral lesions detected were fibroma, gingivitis, Fordyce spots, white coated tongue, cheek biting, linea alba, denture stomatitis, geographic tongue, recurrent aphthous ulcerations and lichen planus. Conclusions Overall, these epidemiological data suggest need for specific health policies for prevention, diagnosis and treatment of oral mucosal lesions.
Keywords: oral mucosa lesions, epidemiological data, malignant tumors
Published in DiRROS: 02.07.2024; Views: 188; Downloads: 87
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