1. High-resolution Pan-European forest structure maps : an integration of earth observation and national forest inventory dataJukka Miettinen, Patricia Adame, Radim Adolt, Iciar Alberdi, Oleg Antropov, Ólafur Arnarsson, Rasmus Astrup, Ambros Berger, Jón Bogason, Gherardo Chirici, Luka Krajnc, Mitja Skudnik, 2024, complete scientific database of research data Keywords: uneven-aged forest, lidar data, canopy height model, voxels, canopy height diversity Published in DiRROS: 13.08.2024; Views: 44; Downloads: 461 Full text (2,00 MB) This document has many files! More... |
2. Identifying even- and uneven-aged forest stands using low-resolution nationwide lidar dataAnže Martin Pintar, Mitja Skudnik, 2024, original scientific article Abstract: In uneven-aged forests, trees of different diameters, heights, and ages are located in a small area, which is due to the felling of individual trees or groups of trees, as well as small-scale natural disturbances. In this article, we present an objective method for classifying forest stands into even- and uneven-aged stands based on freely available low-resolution (with an average recording density of 5 points/m2) national lidar data. The canopy closure, dominant height, and canopy height diversity from the canopy height model and the voxels derived from lidar data were used to classify the forest stands. Both approaches for determining forest structural diversity (canopy height diversity—CHDCHM and CHDV) yielded similar results, namely two clusters of even- and uneven-aged stands, although the differences in vertical diversity between even- and uneven-aged stands were greater when using CHM. The first analysis, using CHM for the CHD assessment, estimated the uneven-aged forest area as 49.3%, whereas the second analysis using voxels estimated it as 34.3%. We concluded that in areas with low laser scanner density, CHM analysis is a more appropriate method for assessing forest stand height heterogeneity. The advantage of detecting uneven-aged structures with voxels is that we were able to detect shade-tolerant species of varying age classes beneath a dense canopy of mature, dominant trees. The CHDCHM values were estimated to be 1.83 and 1.86 for uneven-aged forests, whereas they were 1.57 and 1.58 for mature even-aged forests. The CHDV values were estimated as 1.50 and 1.62 for uneven-aged forests, while they were 1.33 and 1.48 for mature even-aged forests. The classification of stands based on lidar data was validated with data from measurements on permanent sample plots. Statistically significantly lower average values of the homogeneity index and higher values of the Shannon–Wiener index from field measurements confirm the success of the classification of stands based on lidar data as uneven-aged forests. Keywords: uneven-aged forest, lidar data, canopy height model, voxels, canopy height diversity Published in DiRROS: 13.08.2024; Views: 33; Downloads: 488 Full text (15,08 MB) This document has many files! More... |
3. Editorial : brain cancer pathogenesis and data integrationAndrea Comba, Xinzhong Li, Barbara Breznik, 2023, other scientific articles Abstract: Brain tumors are one of the most aggressive malignancies in humans. They can be classified as primary tumors, which arise in the brain, or secondary tumors, which arise elsewhere in the body and initially metastaze the brain. The morbidity and mortality of brain tumors is one of the highest among cancers (Siegel et al., 2023). Of particular concern is that mortality and incidence of brain tumors are increasing, especially in the population under 44 years of age. Brain tumor mortality in this population is 13.4%. For example, primary brain tumors are the most common cancer in children and the leading cause of death in pediatric cancer patients (Gould, 2018). Considering the low survival rate of adult and pediatric brain tumor patients and the detrimental impact on patient quality of life, economic costs, and mortality rates, there is an urgent need to develop more effective therapeutic approaches. Despite major research efforts, there are currently no effective treatment modalities or prevention strategies that would significantly improve the quality of life and disease outcome of brain tumor patients. Keywords: brain tumor, data integration, therapeutic resistance, biomarkers, liquid biopsies Published in DiRROS: 06.08.2024; Views: 74; Downloads: 48 Full text (513,58 KB) This document has many files! More... |
4. Challenges for sustained observing and forecasting systems in the Mediterranean SeaJoaquín Tintoré, Nadia Pinardi, Enrique Álvarez-Fanjul, Eva Aguiar, Diego Álvarez-Berastegui, Marco Bajo, Rosa Balbin, Roberto Bozzano, Bruno Buongiorno Nardelli, Vanessa Cardin, Vlado Malačič, 2019, review article Abstract: The Mediterranean community represented in this paper is the result of more than 30 years of EU and nationally funded coordination, which has led to key contributions in science concepts and operational initiatives. Together with the establishment of operational services, the community has coordinated with universities, research centers, research infrastructures and private companies to implement advanced multi-platform and integrated observing and forecasting systems that facilitate the advancement of operational services, scientific achievements and mission-oriented innovation. Thus, the community can respond to societal challenges and stakeholders needs, developing a variety of fit-for-purpose services such as the Copernicus Marine Service. The combination of state-of-the-art observations and forecasting provides new opportunities for downstream services in response to the needs of the heavily populated Mediterranean coastal areas and to climate change. The challenge over the next decade is to sustain ocean observations within the research community, to monitor the variability at small scales, e.g., the mesoscale/submesoscale, to resolve the sub-basin/seasonal and inter-annual variability in the circulation, and thus establish the decadal variability, understand and correct the model-associated biases and to enhance model-data integration and ensemble forecasting for uncertainty estimation. Better knowledge and understanding of the level of Mediterranean variability will enable a subsequent evaluation of the impacts and mitigation of the effect of human activities and climate change on the biodiversity and the ecosystem, which will support environmental assessments and decisions. Further challenges include extending the science-based added-value products into societal relevant downstream services and engaging with communities to build initiatives that will contribute to the 2030 Agenda and more specifically to SDG14 and the UN's Decade of Ocean Science for sustainable development, by this contributing to bridge the science-policy gap. The Mediterranean observing and forecasting capacity was built on the basis of community best practices in monitoring and modeling, and can serve as a basis for the development of an integrated global ocean observing system. Keywords: observing and forecasting systems, sustained observations, ocean variability, FAIR data, climate, operational services, science with and for society, SDG's Published in DiRROS: 06.08.2024; Views: 85; Downloads: 73 Full text (6,72 MB) This document has many files! More... |
5. Turbulence observations in the Gulf of Trieste under moderate wind forcing and different water column stratificationFrancesco Marcello Falcieri, Lakshmi Kantha, Alvise Benetazzo, Andrea Bergamasco, Davide Bonaldo, Francesco Barbariol, Vlado Malačič, Mauro Sclavo, Sandro Carniel, 2016, original scientific article Abstract: The oceanographic campaign CARPET2014 (Characterizing Adriatic Region Preconditionig EvenTs), (30 January–4 February 2014) collected the very first turbulence data in the Gulf of Trieste (northern Adriatic Sea) under moderate wind (average wind speed 10 m s−1) and heat flux (net negative heat flux ranging from 150 to 400 W m−2). Observations consisted of 38 CTD (Conductivity, Temperature, Depth) casts and 478 microstructure profiles (grouped into 145 ensembles) with three sets of yoyo casts, each lasting for about 12 consecutive hours. Averaging closely repeated casts, such as the ensembles, can lead to a smearing effect when in the presence of a vertical density structure with strong interfaces that can move up or down between subsequent casts under the influence of tides and internal waves. In order to minimize the smearing effect of such displacements on mean quantities, we developed an algorithm to realign successive microstructure profiles to produce sharper and more meaningful mean profiles of measured turbulence parameters.
During the campaign, the water column in the gulf evolved from well-mixed to stratified conditions due to Adriatic waters intruding at the bottom along the gulf's south-eastern coast. We show that during the warm and relatively dry winter, the water column in the Gulf of Trieste, even under moderate wind forcing, was not completely mixed due to the influence of bottom waters intruding from the open sea. Inside the gulf, two types of water intrusions were found during yoyo casts: one coming from the northern coast of the Adriatic Sea (i.e. cooler, fresher and more turbid) and one coming from the open sea in front of the Po Delta (i.e. warmer, saltier and less turbid). The two intrusions had different impacts on turbulence kinetic energy dissipation rate profiles. The former, with high turbidity, acted as a barrier to wind-driven turbulence, while the latter, with low sediment concentrations and a smaller vertical density gradient, was not able to suppress downward penetration of turbulence from the surface. Keywords: hydrology, oceanographic data, numerical modelling, wind forcing, turbulence Published in DiRROS: 01.08.2024; Views: 121; Downloads: 135 Full text (2,99 MB) This document has many files! More... |
6. On the occurrence of the wreckfish Polyprion americanus in the Gulf of Trieste (northern Adriatic Sea)Nicola Bettoso, Lisa Faresi, Alessandro Felluga, Lovrenc Lipej, 2020, original scientific article Abstract: On 3rd June 2018 three juvenile specimens of Polyprion americanus were captured in the Gulf of Trieste. The wreckfish is a long-lived deep-water demersal species characterized by an extended pelagic juvenile phase. The juvenile forms are recurrently recorded in the northern Adriatic and due to data deficiency for this species, original morphometric data are shown. The occurrence of P. americanus in the Gulf of Trieste is not a typical case of thermophilic species moving northward due to Mediterranean tropicalization, rather its recurrent appearance could be investigated for specific hydrological conditions coupled to its peculiar life span.
Keywords: Polyprion americanus, morphometric data, pelagic phase, Gulf of Trieste, Adriatic Sea Published in DiRROS: 31.07.2024; Views: 117; Downloads: 70 Full text (1,06 MB) This document has many files! More... |
7. BioMinerJoachim Selbig, Kristina Gruden, Michal Or-Guil, Christian Schichor, Chris Bauer, Karol Stec, Alexander Glintschert, Johannes Schuchhardt, 2015, original scientific article Abstract: Personalized medicine is promising a revolution for medicine and human biology in the 21st century. The scientific foundation for this revolution is accomplished by analyzing biological high-throughput data sets from genomics, transcriptomics, proteomics, and metabolomics. Currently, access to these data has been limited to either rather simple Web-based tools, which do not grant much insight or analysis by trained specialists, without firsthand involvement of the physician. Here, we present the novel Web-based tool “BioMiner,” which was developed within the scope of an international and interdisciplinary project (SYSTHER†) and gives access to a variety of high-throughput data sets. It provides the user with convenient tools to analyze complex cross-omics data sets and grants enhanced visualization abilities. BioMiner incorporates transcriptomic and cross-omics high-throughput data sets, with a focus on cancer. A public instance of BioMiner along with the database is available at http://systherDB.microdiscovery.de/, login and password: “systher”; a tutorial detailing the usage of BioMiner can be found in the Supplementary File. Keywords: data mining, multiomics data integration, biomarker detection, pathway visualization, personalized medicine, cancer Published in DiRROS: 26.07.2024; Views: 114; Downloads: 105 Link to full text This document has many files! More... |
8. Real-life long-term outcomes of upfront surgery in patients with resectable stage I-IIIA non-small cell lung cancerMarko Bitenc, Tanja Čufer, Izidor Kern, Martina Miklavčič, Sabrina Petrovič, Vida Groznik, Aleksander Sadikov, 2022, original scientific article Abstract: Treatment of early-stage non-small cell lung cancer (NSCLC) is rapidly evolving. When introducing novelties, real-life data on effectiveness of currently used treatment strategies are needed. The present study evaluated outcomes of stage I–IIIA NSCLC patients treated with upfront radical surgery in everyday clinical practice, between 2010–2017. Data of 539 consecutive patients were retrieved from a prospective hospital-based registry. All diagnostic, treatment and follow-up procedures were performed at the same thoracic oncology centre according to the valid guidelines. The primary outcome was overall survival (OS) analysed by clinical(c) and pathological(p) TNM (tumour, node, metastases) stage. The impact of clinicopathological characteristics on OS was evaluated using univariable (UVA) and multivariable regression analysis (MVA). With a median follow-up of 53.9 months, median OS and 5-year OS rate in the overall population were 90.4 months and 64.4%. Five-year OS rates by pTNM stage I, II and IIIA were 70.2%, 60.21%, and 49.9%, respectively. Both cTNM and pTNM stages were associated with OS; but only pTNM retained its independent prognostic value (p = 0.003) in MVA. Agreement between cTNM and pTNM was 69.0%. Next to pTNM, age (p = 0.001) and gender (p = 0.004) retained their independent prognostic value for OS. The study showed favourable outcomes of resectable stage I–IIIA NSCLC treated with upfront surgery in real-life. Relatively low agreement between cTNM and pTNM stages and independent prognostic value of only pTNM, observed in real-life data, suggest that surgery remains the most accurate provider of the anatomical stage of disease and important upfront therapy. Keywords: resectable NSCLC, upfront surgery, real-life data, overall survival, prognostic factors Published in DiRROS: 25.07.2024; Views: 132; Downloads: 103 Full text (747,28 KB) This document has many files! More... |
9. A European multi lake survey dataset of environmental variables, phytoplankton pigments and cyanotoxinsEvanthia Mantzouki, Špela Remec-Rekar, Tina Eleršek, 2018, original scientific article Abstract: Under ongoing climate change and increasing anthropogenic activity, which continuously challenge ecosystem resilience, an in-depth understanding of ecological processes is urgently needed. Lakes, as providers of numerous ecosystem services, face multiple stressors that threaten their functioning. Harmful cyanobacterial blooms are a persistent problem resulting from nutrient pollution and climate-change induced stressors, like poor transparency, increased water temperature and enhanced stratification. Consistency in data collection and analysis methods is necessary to achieve fully comparable datasets and for statistical validity, avoiding issues linked to disparate data sources. The European Multi Lake Survey (EMLS) in summer 2015 was an initiative among scientists from 27 countries to collect and analyse lake physical, chemical and biological variables in a fully standardized manner. This database includes in-situ lake variables along with nutrient, pigment and cyanotoxin data of 369 lakes in Europe, which were centrally analysed in dedicated laboratories. Publishing the EMLS methods and dataset might inspire similar initiatives to study across large geographic areas that will contribute to better understanding lake responses in a changing environment. Keywords: biological pigments, cyanotoxins, ecology, hydrobiology, data, datasets Published in DiRROS: 24.07.2024; Views: 104; Downloads: 190 Full text (1,32 MB) This document has many files! More... |
10. DiNAR: revealing hidden patterns of plant signalling dynamics using Diferential Network Analysis in RMaja Zagorščak, Andrej Blejec, Živa Ramšak, Marko Petek, Tjaša Stare, Kristina Gruden, 2018, original scientific article Abstract: Background
Progress in high-throughput molecular methods accompanied by more complex experimental designs demands novel data visualisation solutions. To specifically answer the question which parts of the specifical biological system are responding in particular perturbation, integrative approach in which experimental data are superimposed on a prior knowledge network is shown to be advantageous.
Results
We have developed DiNAR, Differential Network Analysis in R, a user-friendly application with dynamic visualisation that integrates multiple condition high-throughput data and extensive biological prior knowledge. Implemented differential network approach and embedded network analysis allow users to analyse condition-specific responses in the context of topology of interest (e.g. immune signalling network) and extract knowledge concerning patterns of signalling dynamics (i.e. rewiring in network structure between two or more biological conditions). We validated the usability of software on the Arabidopsis thaliana and Solanum tuberosum datasets, but it is set to handle any biological instances.
Conclusions
DiNAR facilitates detection of network-rewiring events, gene prioritisation for future experimental design and allows capturing dynamics of complex biological system. The fully cross-platform Shiny App is hosted and freely available at https://nib-si.shinyapps.io/DiNAR. The most recent version of the source code is available at https://github.com/NIB-SI/DiNAR/ with a DOI 10.5281/zenodo.1230523 of the archived version in Zenodo. Keywords: biological networks, clustering, gene expression, time series, dynamic network analysis, dynamic data visualisation, web application, multi-conditional datasets, background knowledge Published in DiRROS: 24.07.2024; Views: 152; Downloads: 131 Full text (1,63 MB) This document has many files! More... |