Topical levofloxacin, nepafenac and prednisolone acetate medication after cataract surgery in the biggest tertiary eye hospital in Finland during 2015-2018

Non peer reviewe

Spatio-temporal population dynamics of six phytoplankton taxa

Studying aquatic population dynamics using spatio-temporal monitoring data is associated with a number of challenges and choices. One can let several samples represent the same population over larger areas, or alternatively model the dynamics of each sampling location in continuous space. We analysed the spatio-temporal population dynamics of six phytoplankton taxa in the Baltic Sea applying multivariate state-space models with first-order density dependence. We compared three spatial scales and three models for spatial correlation between predefined subpopulations using information theoretic model selection. We hypothesised that populations close to each other display similar dynamic properties and spatial synchrony decreasing with the distance. We further hypothesize that intermediate-scale grouping of data into subpopulations may parsimoniously represent such dynamics. All taxa showed constant density dependence across space and strong spatial synchrony, consistently requiring a parameter for spatial correlation whenever models included several population states. The most parsimonious spatial structure varied between taxa, most often being one panmictic population or ten intercorrelated population states. Evidently, longer time-series, containing more information, provide more options for modelling detailed spatio-temporal patterns. With a few decade-long plankton time-series data, we encourage determining the appropriate spatial scale on biological grounds rather than model fit

Adverse prognostic impact of regulatory T-cells in testicular diffuse large B-cell lymphoma

Objectives Testicular diffuse large B-cell lymphoma (T-DLBCL) is a rare and aggressive extranodal lymphoma. We have previously shown that high content of tumor-infiltrating lymphocytes (TILs) and PD-1 expressing TILs associate with better survival in T-DLBCL. In this study, we have further characterized distinct TIL subtypes and their proportions in association with patient demographics and survival. Methods We used multiplex immunohistochemistry to characterize TIL phenotypes, including cytotoxic T-cells (CTLs; CD8(+), OX40(+), Granzyme B+, Ki-67(+), LAG-3(+), TIM-3(+), PD-1(+)), CD4(+)T-cells (CD3(+), CD4(+), TIM-3(+), LAG-3(+)), regulatory T-cells (Tregs; CD3(+), CD4(+), FoxP3(+)), and T helper 1 cells (Th1; CD3(+), CD4(+), T-bet(+)) in 79 T-DLBCLs, and correlated the findings with patient demographics and outcome. Results We observed a substantial variation in TIL phenotypes between the patients. The most prominent CD8(+)TILs were Ki-67(+)and TIM-3(+)CTLs, whereas the most prominent CD4(+)TILs were FoxP3(+)Tregs. Despite the overall favorable prognostic impact of high TIL content, we found a subpopulation of T-bet(+)FoxP3(+)Tregs that had a significant adverse impact on survival. Lower content of CTLs with activated or exhausted phenotypes correlated with aggressive clinical features. Conclusions Our results demonstrate significant variation in TIL phenotypes and emphasize the adverse prognostic impact of Tregs in T-DLBCL.Peer reviewe

Environmental variables driving species and genus level changes in annual plankton biomass

Abiotic variables subject to global change are known to affect plankton biomasses, and these effects can be species-specific. Here, we investigate the environmental drivers of annual biomass using plankton data from the Gulf of Finland in the northern Baltic Sea, spanning years 1993–2016. We estimated annual biomass time-series of 31 nanoplankton and microplankton species and genera from day-level data, accounting for the average phenology and wind. We found wind effects on day-level biomass in 16 taxa. We subsequently used state-space models to connect the annual biomass changes with potential environmental drivers (temperature, salinity, stratification, ice cover and inorganic nutrients), simultaneously accounting for temporal trends. We found clear environmental effects influencing the annual biomasses of Dinobryon faculiferum, Eutreptiella spp., Protoperidinium bipes, Pseudopedinella spp., Snowella spp. and Thalassiosira baltica and indicative effects in 10 additional taxa. These effects mostly concerned temperature, salinity or stratification. Together, these 16 taxa represent two-thirds of the summer biomass in the sampled community. The inter-annual variability observed in salinity and temperature is relatively low compared to scenarios of predicted change in these variables. Therefore, the potential impacts of the presented effects on plankton biomasses are considerable

Guidelines for using environmental DNA in Finnish marine phytoplankton monitoring – Improved biodiversity assessment through method complementation

This document is a methodological guide for using a genomic ecosystem survey technique (eDNA metabarcoding) to supplement conventional phytoplankton monitoring of the Finnish marine monitoring program. The guidelines describe the detection of eukaryotic and prokaryotic phytoplankton with 18S and 16S rDNA gene primers, using high-throughput sequencing. The document includes information on sampling, sample processing, molecular biological work, quality control, and bioinformatics so that the method can be applied in addition to standardized light microscopy. The guidelines are based on a first pilot project testing the integration of eDNA metabarcoding in Finnish marine phytoplankton monitoring and will be developed further, according to evolving genetic methods and international guidelines and standards. Suggestions on steps towards introducing eDNA methodology in phytoplankton monitoring are included in the guidelines. Using eDNA metabarcoding to complement standardized light microscopy advances conventional monitoring and research of phytoplankton communities to assess biodiversity and the status of the marine environment. Menetelmäohje DNA-viivakoodaustekniikan käyttöön meren kasviplanktonseurannassa Tässä julkaisussa kuvataan menetelmäohje DNA-viivakoodeihin perustuvan eDNA (ympäristö-DNA) -metaviivakoodaustekniikan käytöstä Suomen merenhoidon seurantaohjelmaan kuuluvan kasviplanktonseurannan tukena. Aitotumaisen kasviplanktonin (mikrolevät) tunnistamiseen soveltuvan 18S rDNA -menetelmän lisäksi ohjeessa kuvataan esitumaisten syanobakteerien (sinilevät) analysointi 16S rDNA -menetelmällä käyttäen korkean käsittelytehon sekvensointia (high-throughput sequencing). Ohje sisältää yksityiskohtaiset tiedot eDNA -näytteiden keräämisestä, näytteiden käsittelystä, molekyylibiologisista työvaiheista, bioinformatiikka-analyyseistä ja laadunvarmennuksesta. Ohje perustuu ympäristöministeriön rahoittaman hankkeen tuloksiin. Ohjeistusta tullaan kehittämään jatkossa sitä mukaa, kun uusia tutkimustuloksia, kansainvälisiä ohjeita ja standardeja julkaistaan. Ohjeistus sisältää ehdotuksen etenemisvaiheista, jotka kannattaa huomioida, kun eDNA-menetelmää ryhdytään ottamaan mukaan kasviplanktonseurantaan. eDNA-menetelmää voidaan käyttää valomikroskopointimenetelmän ohella tarkentamaan ja tehostamaan kasviplanktonyhteisöjen biodiversiteetin seurantaa ja tutkimusta meriympäristön tilan arvioita varten

Climate change and eutrophication induced shifts in Northern summer plankton communities

Marine ecosystems are undergoing substantial changes due to human-induced pressures. Analysis of long-term data series is a valuable tool for understanding naturally and anthropogenically induced changes in plankton communities. In the present study, seasonal monitoring data were collected in three sub-basins of the northern Baltic Sea between 1979 and 2011 and statistically analysed for trends and interactions between surface water hydrography, inorganic nutrient concentrations and phyto- and zooplankton community composition. The most conspicuous hydrographic change was a significant increase in late summer surface water temperatures over the study period. In addition, salinity decreased and dissolved inorganic nutrient concentrations increased in some basins. Based on redundancy analysis (RDA), warming was the key environmental factor explaining the observed changes in plankton communities: the general increase in total phytoplankton biomass, Cyanophyceae, Prymnesiophyceae and Chrysophyceae, and decrease in Cryptophyceae throughout the study area, as well as increase in rotifers and decrease in total zooplankton, cladoceran and copepod abundances in some basins. We conclude that the plankton communities in the Baltic Sea have shifted towards a food web structure with smaller sized organisms, leading to decreased energy available for grazing zooplankton and planktivorous fish. The shift is most probably due to complex interactions between warming, eutrophication and increased top-down pressure due to overexploitation of resources, and the resulting trophic cascades

Diazotrophic cyanobacteria in planktonic food webs

Blooms of cyanobacteria are recurrent phenomena in coastal estuaries. Their maximum abundance coincides with the productive period of zooplankton and pelagic fish. Experimental studies indicate that diazotrophic, i.e. dinitrogen (N2)-fixing cyanobacterial (taxonomic order Nostocales) blooms affect zooplankton, as well as other phytoplankton. We used multidecadal monitoring data from one archipelago station (1992–2013) and ten open sea stations (1979–2013) in the Baltic Sea to explore the potential bottom-up connections between diazotrophic and non-diazotrophic cyanobacteria and phyto- and zooplankton in natural plankton communities. Random forest regression, combined with linear regression analysis showed that the biomass of cyanobacteria (both diazotrophic and non-diazotrophic) was barely connected to any of the phytoplankton and zooplankton variables examined. Instead, physico-chemical variables (salinity, temperature, total phosphorus), as well as spatial and temporal variability seemed to have more significant connections to both phytoplankton and zooplankton variables. Zooplankton variables were also connected to the biomass of phytoplankton groups other than cyanobacteria (such as chrysophytes, cryptophytes and prymnesiophytes), and phytoplankton variables had connections with the biomass of different zooplankton groups, especially copepods. Overall, negative relationships between cyanobacteria and other plankton taxa were scarcer than expected based on previous experimental studies.​​​​​​​</ul

Diazotrophic cyanobacteria in planktonic food webs

Blooms of cyanobacteria are recurrent phenomena in coastal estuaries. Their maximum abundance coincides with the productive period of zooplankton and pelagic fish. Experimental studies indicate that diazotrophic, i.e. dinitrogen (N2)-fixing cyanobacterial (taxonomic order Nostocales) blooms affect zooplankton, as well as other phytoplankton. We used multidecadal monitoring data from one archipelago station (1992–2013) and ten open sea stations (1979–2013) in the Baltic Sea to explore the potential bottom-up connections between diazotrophic and non-diazotrophic cyanobacteria and phyto- and zooplankton in natural plankton communities. Random forest regression, combined with linear regression analysis showed that the biomass of cyanobacteria (both diazotrophic and non-diazotrophic) was barely connected to any of the phytoplankton and zooplankton variables examined. Instead, physico-chemical variables (salinity, temperature, total phosphorus), as well as spatial and temporal variability seemed to have more significant connections to both phytoplankton and zooplankton variables. Zooplankton variables were also connected to the biomass of phytoplankton groups other than cyanobacteria (such as chrysophytes, cryptophytes and prymnesiophytes), and phytoplankton variables had connections with the biomass of different zooplankton groups, especially copepods. Overall, negative relationships between cyanobacteria and other plankton taxa were scarcer than expected based on previous experimental studies

Approach for Supporting Food Web Assessments with Multi-Decadal Phytoplankton Community Analyses—Case Baltic Sea

Combining the existing knowledge on links between functional characteristics of phytoplankton taxa and food web functioning with the methods from long-term data analysis, we present an approach for using phytoplankton monitoring data to draw conclusions on potential effects of phytoplankton taxonomic composition on the next trophic level. This information can be used as a part of marine food web assessments required by the Marine Strategy Framework Directive of the European Union. In this approach, both contemporary taxonomic composition and recent trends of changes are used to assess their potential consequences for food web functioning. The approach consists of four steps: (1) long-term trend analysis of class-level and total phytoplankton biomass using generalized additive models (GAMs) and calculating average biomass share of each phytoplankton class from the total phytoplankton biomass, (2) comparing the current phytoplankton community composition and its long-term changes with non-metric ordination analysis (NMDS) of genus-level biomass, (3) describing which taxa (the most accurate taxonomic level) are primarily responsible for forming the biomass and for causing the possible changes, and (4) interpretation of the phytoplankton results to assess the potential effects on the next trophic level. Within step 4, special attention is given to the following characteristic of taxa: potential suitability or quality as food for grazers, harmfulness, size, and trophy. These characteristics are selected based on existing scientific knowledge on their relevance to the higher trophic levels. In this article, we present the concept of the suggested approach and demonstrate the phytoplankton analyses with multi-decadal monitoring data from the northern Baltic Sea. We also discuss the future development of the approach toward a food web index by combining or replacing the taxonomic analyses with functional trait-based approaches