| 1. |
- Araza, Arnan, et al.
(författare)
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Past decade above-ground biomass change comparisons from four multi-temporal global maps
- 2023
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Ingår i: International Journal of Applied Earth Observation and Geoinformation. - 1569-8432. ; 118
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Tidskriftsartikel (refereegranskat)abstract
- Above-ground biomass (AGB) is considered an essential climate variable that underpins our knowledge and information about the role of forests in mitigating climate change. The availability of satellite-based AGB and AGB change (ΔAGB) products has increased in recent years. Here we assessed the past decade net ΔAGB derived from four recent global multi-date AGB maps: ESA-CCI maps, WRI-Flux model, JPL time series, and SMOS-LVOD time series. Our assessments explore and use different reference data sources with biomass re-measurements within the past decade. The reference data comprise National Forest Inventory (NFI) plot data, local ΔAGB maps from airborne LiDAR, and selected Forest Resource Assessment country data from countries with well-developed monitoring capacities. Map to reference data comparisons were performed at levels ranging from 100 m to 25 km spatial scale. The comparisons revealed that LiDAR data compared most reasonably with the maps, while the comparisons using NFI only showed some agreements at aggregation levels <10 km. Regardless of the aggregation level, AGB losses and gains according to the map comparisons were consistently smaller than the reference data. Map-map comparisons at 25 km highlighted that the maps consistently captured AGB losses in known deforestation hotspots. The comparisons also identified several carbon sink regions consistently detected by all maps. However, disagreement between maps is still large in key forest regions such as the Amazon basin. The overall ΔAGB map cross-correlation between maps varied in the range 0.11–0.29 (r). Reported ΔAGB magnitudes were largest in the high-resolution datasets including the CCI map differencing (stock change) and Flux model (gain-loss) methods, while they were smallest according to the coarser-resolution LVOD and JPL time series products, especially for AGB gains. Our results suggest that ΔAGB assessed from current maps can be biased and any use of the estimates should take that into account. Currently, ΔAGB reference data are sparse especially in the tropics but that deficit can be alleviated by upcoming LiDAR data networks in the context of Supersites and GEO-Trees.
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| 2. |
- Novotny, Andreas, 1991-, et al.
(författare)
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Niche partitioning between planktivorous fish in the pelagic Baltic Sea assessed by DNA metabarcoding, qPCR and microscopy
- 2022
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Ingår i: Scientific Reports. - : Springer Science and Business Media LLC. - 2045-2322. ; 12
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Tidskriftsartikel (refereegranskat)abstract
- Marine communities undergo rapid changes related to human-induced ecosystem pressures. The Baltic Sea pelagic food web has experienced several regime shifts during the past century, resulting in a system where competition between the dominant planktivorous mesopredatory clupeid fish species herring (Clupea harengus) and sprat (Sprattus sprattus) and the rapidly increasing stickleback (Gasterosteus aculeatus) population is assumed to be high. Here, we investigate diet overlap between these three planktivorous fishes in the Baltic Sea, utilizing DNA metabarcoding on the 18S rRNA gene and the COI gene, targeted qPCR, and microscopy. Our results show niche differentiation between clupeids and stickleback, and highlight that rotifers play an important role in this pattern, as a resource that is not being used by the clupeids nor by other zooplankton in spring. We further show that all the diet assessment methods used in this study are consistent, but also that DNA metabarcoding describes the plankton-fish link at the highest taxonomic resolution. This study suggests that rotifers and other understudied soft-bodied prey may have an important function in the pelagic food web and that the growing population of pelagic stickleback may be supported by the open feeding niche offered by the rotifers.
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| 3. |
- Tebaldini, S., et al.
(författare)
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THE TOMOSENSE EXPERIMENT: MONO- AND BISTATIC SAR TOMOGRAPHY OF FORESTED AREAS AT P-, L-, AND C-BAND
- 2021
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Ingår i: International Geoscience and Remote Sensing Symposium (IGARSS). ; 2021-July, s. 7955-7958
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Konferensbidrag (refereegranskat)abstract
- The TomoSense experiment comprises campaign and research activities in support of future Synthetic Aperture Radar (SAR) mission concepts at P-, L-, and C-band by the European Space Agency (ESA). The research is intended to provide a quantitative basis for the evaluation of single-pass interferometry over temperate forests at L- and C-band and investigate potential synergies between C-band convoy mission concepts and future P- and L-band missions. SAR acquisitions include P- L-, and C-band data acquired at the Eifel National Park in Germany by flying approximately 25 trajectories to provide tomographic imaging capabilities. L- and C-band data were acquired by simultaneously flying two aircraft to gather bistatic data with varying interferometric baselines. Field activities include forest census (dbh, tree height and species) at 80 plots and Terrestrial Laser Scanning (TLS). The dataset is complemented by small-footprint Airborne Lidar Scanning (ALS) and derived products. Preliminary results are here shown relative to polarimetric tomography at P-band and L-band imaging.
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| 4. |
- Tebaldini, S., et al.
(författare)
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TomoSense: A unique 3D dataset over temperate forest combining multi-frequency mono- and bi-static tomographic SAR with terrestrial, UAV and airborne lidar, and in-situ forest census
- 2023
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Ingår i: Remote Sensing of Environment. - : Elsevier BV. - 0034-4257. ; 290
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Tidskriftsartikel (refereegranskat)abstract
- The TomoSense experiment was funded by the European Space Agency (ESA) to support research on remote sensing of forested areas by means of Synthetic Aperture Radar (SAR) data, with a special focus on the use of tomographic SAR (TomoSAR) to retrieve information about the vertical structure of the vegetation at different frequency bands. The illuminated scene is the temperate forest at the Eifel National Park, North-West Germany. Dominant species are beech and spruce trees. Forest height ranges roughly from 10 to 30 m, with peaks up to over 40 m. Forest Above Ground Biomass (AGB) ranges from 20 to 300 Mg/ha, with peaks up to over 400 Mg/ha. SAR data include P-, L-, and C-band surveys acquired by flying up to 30 trajectories in two headings to provide tomographic imaging capabilities. L- and C-band data were acquired by simultaneously flying two aircraft to gather bistatic data along different trajectories. The SAR dataset is complemented by 3D structural canopy measurements made via terrestrial laser scanning (TLS), Unoccupied Aerial Vehicle lidar (UAV-L) and airborne laser scanning (ALS), and in-situ forest census. This unique combination of SAR tomographic and multi-scale lidar data allows for direct comparison of canopy structural metrics across wavelength and scale, including vertical profiles of canopy wood and foliage density, and per-tree and plot-level above ground biomass (AGB). The resulting TomoSense data-set is free and openly available at ESA for any research purpose. The data-set includes ALS-derived maps of forest height and AGB, forest parameters at the level of single trees, TLS raw data, and plot-average TLS vertical profiles. The provided SAR data are coregistered, phase calibrated, and ground steered, to enable a direct implementation of any kind of interferometric or tomographic processing without having to deal with the subtleties of airborne SAR processing. Moreover, the data-base comprises SAR tomographic cubes representing forest scattering in 3D both in Radar and geographical coordinates, intended for use by non-Radar experts. For its unique features and completeness, the TomoSense data-set is intended to serve as an important basis for future research on microwave scattering from forested areas in the context of future Earth Observation missions.
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| 5. |
- Gkekas, Ioannis, 1981-, et al.
(författare)
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Colon cancer patients with mismatch repair deficiency are more likely to present as acute surgical cases
- 2021
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Ingår i: European Journal of Cancer. - : Elsevier. - 0959-8049 .- 1879-0852. ; 157, s. 1-9
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Tidskriftsartikel (refereegranskat)abstract
- Background: The effect of the genetic imprint on the emergency presentation of colon cancer remains unclear. The disparity between tumours evolving along different carcinogenetic pathways has not been studied systematically. This retrospective multicenter cohort study evaluates the association between mismatch repair status and the risk for acute surgery of colon cancer.Patients and methods: A retrospective multicenter cohort study including in total 870 patients from three different countries. Scandinavian cohort (Finland and Sweden), including a total of 412 patients operated between January 1, 1995 and December 31, 2010, was validated against a cohort from the Czech Republic, including a total of 458 patients, operated between January 1, 2018 and December 31, 2019. The proficiency or deficiency of mismatch repair was determined by immunohistochemistry. Primary outcome was the risk for acute colon cancer surgery given as the Odds Ratio (OR) in the univariable and multivariable analyses. Acute colon cancer surgery was defined as surgery performed during the same hospital admission as when the diagnosis of colon cancer was made.Results: Of the 870 patients (399 females [46%]) included in the analyses, median age at surgery was 69 [interquartile range, 61–76] years, deficient Mismatch Repair (dMMR) status was found in 190 patients (22%), and 179 patients (21%) underwent acute surgery during the same hospital admission as when the diagnosis of colon cancer was made. In the Scandinavian cohort, a significant association between dMMR status and acute surgery was seen in both the univariable (OR 1.82, 95% CI 1.11–3.02, P = 0.017) and the multivariable (OR = 2.21, 95% CI 1.28–3.95, P = 0.005) analyses. This was confirmed in the Czech validation cohort in both the univariable (OR = 1.94, 95% CI 1.09–3.26, P = 0.022) and the multivariable (OR = 1.77, 95% CI 1.15–3.18, P = 0.021) analyses.Conclusion: This multicenter study reveals a strong association between acute colon cancer surgery and dMMR tumour status.
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| 6. |
- Gkekas, Ioannis, 1981-
(författare)
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Mismatch repair deficiency in colorectal cancer : prognosis and prediction for basic treatment strategies
- 2021
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Doktorsavhandling (övrigt vetenskapligt/konstnärligt)abstract
- Colorectal cancer (CRC) remains a significant healthcare problem worldwide, being the third most common cancer and the fourth most frequent cause of cancer death. Environmental and dietary factors such as alcohol abuse, cigarette smoking, and genetic predisposition seem to constitute the main aetiologies.Two major distinct molecular genetic pathways have been recognised as models of transition from normal epithelium to adenoma and carcinoma. The first involves chromosomal instability (CIN) and the second involves microsatellite instability (MSI). The MSI pathway constitutes 2-4% of CRCs with a hereditary Mismatch Repair (MMR) defect (dMMR) and approximately 15% of sporadic MMR defects due to epigenetic silencing of the MutL homologue 1 (MLH1) promoter. Extracellular factors and spontaneous copy errors necessitate molecular systems to survey and repair human genetic information, and to protect it from chemical disruption. A complicated and entangled network of DNA damage response mechanisms, including multiple DNA repair pathways, damage tolerance processes, and cell cycle checkpoints safeguard genomic integrity. It has recently become apparent that key proteins contributing tocellular survival by taking part in DNA repair become executioners in the face of excess DNA damage. All prokaryotic and eukaryotic organisms have major DNA repair pathways. In each of these DNA repair pathways there are key proteins that have dual functions in DNA damage sensing/repair and apoptosis, taking advantage of the fact that DNA is a double helix with the same information present on both strands. Damages that affect one strand can easily be repaired by excision and replacement with newly synthesised DNA using the complementary strand as a template. MMR plays a critical role in the repair of errors that occur spontaneously during DNA replication, such as single base mismatches. dMMR increases the mutation frequency in an affected cell by approximately 1000 times, leading to MSI through the accumulation of short repetitive DNA sequences called microsatellites. Carcinogenesis in dMMR cases can present as hereditary cases (Lynch syndrome) due to germline mutation inin one of the main MMR genes – MLH1, MSH2, MSH6, and PMS2 or somatic/sporadic cases (epigenetic silencing or somatic inactivation of MLH1promoter. dMMR seems to have a favourable prognosis as these CRCs seems to be less prone to metastasising. This phenomenon is much more obvious for tumour stages II and III, while in advanced disease dMMR seems to lose its positive prognostic effect. Even if the underlying mechanism is not fully understood, some studies attribute the positive effect of dMMR tumours to their increased immunogenicity leading to a stronger more effective immune response. On the other hand, the predictive value of the dMMR mechanism isless well understood and has only gained attention in recent years. In general, dMMR seems to predict a poor response to 5-FU, the basis of gastrointestinal chemotherapy.The aims of this thesis were: 1. To review the latest publications on the role of MSI status as prognostic factor in stage II colon cancer (CC) patients (Study I); 2. To validate MMR status as a prognostic factor in patients with CC Stage II (Study II); 3. To verify MMR status as a predictive factor in relation to the administration of adjuvant chemotherapy in patients with stage II CC (Study III); 4. To investigate the potential role of MMR status as a risk factor for acute CC surgery (Study IV); and finally 5. To investigate the association between CRC with sporadic dMMR and non-colorectal malignancy (Study V).Study I, a meta-analysis reviewing recently published papers, revealed that MSI status in stage II CC patients does not seem to affect overall survival (OS)and disease-free survival (DFS). This lack of impact could be explained by selection bias and the extremely high proportion of patients receiving adjuvant chemotherapy in the studies included. This was the first meta-analysis specifically evaluating patients with colon cancer stage II. The optimal treatment algorithm for these patients remains unclear, and approximately 20% experience relapse and finally die from disseminated disease.Study II verified the prognostic role of MMR status in patients with stage II CC. Patients with a dMMR tumour have a significantly lower risk for cancer recurrence, a finding that is particularly important for CC treatment. This relationship does not correlate to a better OS since these patients are older and often die from other causes. Debate on the best postoperative strategy in stage II CC continues. What this study contributes is the idea that determination of MMR status can have prognostic value in these patients.Study III also verified the predictive role of MMR status in patients with stageII CC, only this time in relation to treatment with adjuvant chemotherapy. Patients with proficient MMR (pMMR) status receiving adjuvant chemotherapy have a significantly better OS than those not receiving adjuvant treatment. This relationship was not seen in patients with a dMMR tumour. Furthermore, patients with a pMMR tumour receiving adjuvant treatment have a significantly longer survival time after the first relapse compared to those not receiving adjuvant treatment.Study IV revealed the higher probability of dMMR tumours to present as a surgical emergency. Stage III and IV tumours were also associated with acute surgery. This association was significant regardless of the potential bias due toretrospective methodology and possible heterogeneity between the differentcohorts. Further research is required before our conclusions can be applied in clinical practice due to the multicomplex relationship and interactions between variables that influence the oncologic outcome of acute CC surgery.Study V revealed that patients with sporadic, non-hereditary dMMR CRC run a greater risk for having non-colorectal cancer prior to or after the diagnosis ofCRC. This implies that patients with a dMMR tumour should be screened for other non-colorectal cancer, more so than in the the general population.Conclusion: CRC continues to be a significant healthcare problem worldwide, and treatment algorithms for patients with different genomic backgrounds can vary significantly. This thesis supports the idea of using MMR status as a prognostic and predictive factor in everyday clinical practice, especially in stage II CC and acute cases.
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| 7. |
- Gkekas, Ioannis, et al.
(författare)
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Mismatch repair status predicts survival after adjuvant treatment in stage II colon cancer patients.
- 2020
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Ingår i: Journal of Surgical Oncology. - : John Wiley & Sons. - 0022-4790 .- 1096-9098. ; 121:2, s. 392-401
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Tidskriftsartikel (refereegranskat)abstract
- BACKGROUND AND OBJECTIVES: Stage II colon cancer is primarily a surgical disease. Only a still not well-defined subset of patients may benefit from postoperative adjuvant chemotherapy. The relationship between adjuvant chemotherapy and survival after relapse is furthermore still not definitely explored in this group of patients. A number of reports suggest some association between defective mismatch repair (dMMR) and colorectal cancer stage II prognosis, but due to contradictory results from existing studies, the exact predictive role is still not fully understood.METHODS: Retrospective multicenter study including 451 stage II colon cancer patients. The proficiency or deficiency of mismatch repair was tested using immunohistochemistry and analyzed in relationship to two survival outcomes: overall survival (OS) and postrelapse survival.RESULTS: Patients with dMMR (20.4%) derived no OS benefit from adjuvant chemotherapy (hazard ratio [HR], 1.05; 95% confidence interval [CI], 0.47-2.38; P = .897). Patients with proficient mismatch repair (pMMR) tumors receiving adjuvant chemotherapy had the significantly better OS in comparison to those not receiving chemotherapy (HR, 0.54; 95% CI, 0.35-0.82; P = .004). This relationship remained significant in multivariable analysis (HR, 0.42; 95% CI, 0.22-0.78; P = .007). Patients with pMMR relapsing after adjuvant treatment lived significantly longer than those relapsing without previous adjuvant treatment (HR, 0.55; 95% CI, 0.32-0.96; P = .033) and this result remained significant in the multivariable model (HR, 0.49; 95% CI, 0.26-0.93; P = .030).CONCLUSION: In stage II CC patients, adjuvant chemotherapy improves therapeutic outcomes only in patients with pMMR tumors. Survival after relapse in patients having received adjuvant chemotherapy is significantly longer for patients with pMMR. No survival benefit from adjuvant chemotherapy was seen among patients with dMMR tumors.
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| 8. |
- Gkekas, Ioannis, 1981-, et al.
(författare)
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Sporadic deficient mismatch repair in colorectal cancer increases the risk for non-colorectal malignancy : a European multicenter cohort study
- 2024
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Ingår i: Journal of Surgical Oncology. - : John Wiley & Sons. - 0022-4790 .- 1096-9098.
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Tidskriftsartikel (refereegranskat)abstract
- Background and Objectives: Disparities between tumors arising via different sporadic carcinogenetic pathways have not been studied systematically. This retrospective multicenter cohort study evaluated the differences in the risk for non-colorectal malignancy between sporadic colorectal cancer (CRC) patients from different DNA mismatch repair status.Methods: A retrospective European multicenter cohort study including in total of 1706 CRC patients treated between 1996 and 2019 in three different countries. The proficiency (pMMR) or deficiency (dMMR) of mismatch repair was determined by immunohistochemistry. Cases were analyzed for tumor BRAFV600E mutation, and BRAF mutated tumors were further analyzed for hypermethylation status in the promoter region of MLH1 to distinguish between sporadic and hereditary cases. Swedish and Finish patients were matched with their respective National Cancer Registries. For the Czech cohort, thorough scrutiny of medical files was performed to identify any non-colorectal malignancy within 20 years before or after the diagnosis of CRC. Poisson regression analysis was performed to identify the incidence rates of non-colorectal malignancies. For validation purposes, standardized incidence ratios were calculated for the Swedish cases adjusted for age, year, and sex.Results: Of the 1706 CRC patients included in the analysis, 819 were female [48%], median age at surgery was 67 years [interquartile range: 60–75], and sporadic dMMR was found in 188 patients (11%). Patients with sporadic dMMR CRC had a higher incidence rate ratio (IRR) for non-colorectal malignancy before and after diagnosis compared to patients with a pMMR tumor, in both uni- (IRR = 2.49, 95% confidence interval [CI] = 1.89–3.31, p = 0.003) and multivariable analysis (IRR = 2.24, 95% CI = 1.67–3.01, p = 0.004). This association applied whether or not the non-colorectal tumor developed before or after the diagnosis of CRC in both uni- (IRR = 1.91, 95% CI = 1.28–2.98, p = 0.004), (IRR = 2.45, 95% CI = 1.72–3.49, p = 0.004) and multivariable analysis (IRR = 1.67,95% CI = 1.05–2.65, p = 0.029), (IRR = 2.35, 95% CI = 1.63–3.42, p = 0.005), respectively.Conclusion: In this retrospective European multicenter cohort study, patients with sporadic dMMR CRC had a higher risk for non-colorectal malignancy than those with pMMR CRC. These findings indicate the need for further studies to establish the need for and design of surveillance strategies for patients with dMMR CRC.
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| 9. |
- Novotny, Andreas, 1991-, et al.
(författare)
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DNA metabarcoding highlights cyanobacteria as the main source of primary production in a pelagic food web model
- 2023
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Ingår i: Science Advances. - 2375-2548. ; 9:17
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Tidskriftsartikel (refereegranskat)abstract
- Models that estimate rates of energy flow in complex food webs often fail to account for species-specific prey selectivity of diverse consumer guilds. While DNA metabarcoding is increasingly used for dietary studies, methodological biases have limited its application for food web modeling. Here, we used data from dietary metabarcoding studies of zooplankton to calculate prey selectivity indices and assess energy fluxes in a pelagic resource-consumer network. We show that food web dynamics are influenced by prey selectivity and temporal match-mismatch in growth cycles and that cyanobacteria are the main source of primary production in the investigated coastal pelagic food web. The latter challenges the common assumption that cyanobacteria are not supporting food web productivity, a result that is increasingly relevant as global warming promotes cyanobacteria dominance. While this study provides a method for how DNA metabarcoding can be used to quantify energy fluxes in a marine food web, the approach presented here can easily be extended to other ecosystems.
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| 10. |
- Serandour, Baptiste, 1995-, et al.
(författare)
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Opportunistic vs selective feeding strategies of zooplankton under changing environmental conditions
- 2023
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Ingår i: Journal of Plankton Research. - : Oxford University Press (OUP). - 0142-7873 .- 1464-3774. ; 45:2, s. 389-403
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Tidskriftsartikel (refereegranskat)abstract
- The plankton community consists of diverse interacting species. The estimation of species interactions in nature is challenging. There is limited knowledge on how plankton interactions are influenced by environmental conditions because of limited understanding of zooplankton feeding strategies and factors affecting trophic interactions. In this study, we used DNA-metabarcoding to investigate trophic interactions in mesozooplankton predators and the influence of prey availability on their feeding behavior. We found that mesozooplankton feeding strategies vary within species across an environmental gradient. Some species, such as Temora longicornis consistently used a selective strategy, while diets of Centropages hamatus and Acartia spp. varied between stations, showing a trophic plasticity with the prey community. We found a dominance of Synechococcales reads in Temora’s gut content and a high prey diversity for the cladoceran Evadne nordmanni. Our study shows the wide range of prey species that supports mesozooplankton community and helps to understand the spatial and temporal complexity of plankton species interactions and discriminate the selectivity ability of four zooplankton key species. Due to the central role of plankton in marine waters, a better comprehension of the spatiotemporal variability in species interactions helps to estimate fluxes to benthic and pelagic predators.
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