High Concentration of Anti-SARS-CoV-2 Antibodies 2 Years after COVID-19 Vaccination Stems Not Only from Boosters but Also from Widespread, Often Unrecognized, Contact with the Virus.

This study follows 99 subjects vaccinated with Pfizer/BioNTech COVID-19 vaccines over two years, with particular focus on the last year of observation (between days 360 and 720). The response to the vaccination was assessed with Diasorin's SARS-CoV-2 TrimericSpike IgG. Screening for SARS-CoV-2 infection was performed with Abbott's SARS-CoV-2 Nucleocapsid IgG immunoassay. Data from questionnaires were also analyzed. Two years after the first vaccine dose administration, 100% of the subjects were positive for anti-spike SARS-CoV-2 IgG and the median antibody level was still high (3600 BAU/mL), dropping insignificantly over the last year. Simultaneously, a substantial increase in seropositivity in anti-nucleocapsid SARS-CoV-2 IgG was noted, reaching 33%. There was no statistically significant agreement between anti-N seropositivity and reported COVID-19. Higher anti-spike concentrations and lower COVID-19 incidence was seen in the older vaccinees. It was noted that only subjects boosted between days 360 and 720 showed an increase in anti-spike IgG concentrations. The higher antibody concentrations (median 7440 BAU/mL) on day 360 were noted in participants not infected over the following year. Vaccination, including booster administrations, and natural, even unrecognized, contact with SARS-CoV-2 entwined two years after the primary vaccination, leading to high anti-spike antibody concentrations.

Genome Size in the Arenaria ciliata Species Complex (Caryophyllaceae), with Special Focus on Northern Europe and the Arctic.

The main aim of the present study has been the completion of genome size data for the diverse arctic-alpine A. ciliata species complex, with special focus on the unexplored arctic taxon A. pseudofrigida, the north-European A. norvegica, and A. gothica from Gotland (Sweden). Altogether, 46 individuals of these three Nordic taxa have been sampled from seven different regions and their genome size estimated using flow cytometry. Three other alpine taxa in the A. ciliata complex (A. multicaulis, A. ciliata subsp. ciliata, and A. ciliata subsp. bernensis) were also collected and analyzed for standardization purposes, comprising 20 individuals from six regions. A mean 2c value of 1.65 pg of DNA was recorded for A. pseudofrigida, 2.80 pg for A. norvegica, and 4.14 pg for A. gothica, as against the reconfirmed 2c value of 1.63 pg DNA for the type taxon A. ciliata subsp. ciliata. Our results presenting the first estimations of genome sizes for the newly sampled taxa, corroborate ploidy levels described in the available literature, with A. pseudofrigida being tetraploid (2n = 4x = 40), A. norvegica possessing predominantly 2n = 8x = 80, and A. gothica with 2n = 10x = 100. The present study also reconfirms genome size and ploidy level estimations published previously for the alpine members of this species complex. Reflecting a likely complex recent biogeographic history, the A. ciliata species group comprises a polyploid arctic-alpine species complex characterized by reticulate evolution, polyploidizations and hybridizations, probably associated with rapid latitudinal and altitudinal migrations in the Pleistocene-Holocene period.

DiagSet: a dataset for prostate cancer histopathological image classification.

Cancer diseases constitute one of the most significant societal challenges. In this paper, we introduce a novel histopathological dataset for prostate cancer detection. The proposed dataset, consisting of over 2.6 million tissue patches extracted from 430 fully annotated scans, 4675 scans with assigned binary diagnoses, and 46 scans with diagnoses independently provided by a group of histopathologists can be found at https://github.com/michalkoziarski/DiagSet . Furthermore, we propose a machine learning framework for detection of cancerous tissue regions and prediction of scan-level diagnosis, utilizing thresholding to abstain from the decision in uncertain cases. The proposed approach, composed of ensembles of deep neural networks operating on the histopathological scans at different scales, achieves 94.6% accuracy in patch-level recognition and is compared in a scan-level diagnosis with 9 human histopathologists showing high statistical agreement.

Evolutionary imbalance, climate and human history jointly shape the global biogeography of alien plants.

Human activities are causing global biotic redistribution, translocating species and providing them with opportunities to establish populations beyond their native ranges. Species originating from certain global regions, however, are disproportionately represented among naturalized aliens. The evolutionary imbalance hypothesis posits that differences in absolute fitness among biogeographic divisions determine outcomes when biotas mix. Here, we compile data from native and alien distributions for nearly the entire global seed plant flora and find that biogeographic conditions predicted to drive evolutionary imbalance act alongside climate and anthropogenic factors to shape flows of successful aliens among regional biotas. Successful aliens tend to originate from large, biodiverse regions that support abundant populations and where species evolve against a diverse backdrop of competitors and enemies. We also reveal that these same native distribution characteristics are shared among the plants that humans select for cultivation and economic use. In addition to influencing species' innate potentials as invaders, we therefore suggest that evolutionary imbalance shapes plants' relationships with humans, impacting which species are translocated beyond their native distributions.

Micro-Evolutionary Processes in Armeria maritima at Metalliferous Sites.

Tolerance to heavy metals in plants is a model process used to study adaptations to extremely unfavorable environments. One species capable of colonizing areas with high contents of heavy metals is Armeria maritima (Mill.) Wild. A. maritima plants growing in metalliferous areas differ in their morphological features and tolerance levels to heavy metals compared to individuals of the same species growing in non-metalliferous areas. The A. maritima adaptations to heavy metals occur at the organismal, tissue, and cellular levels (e.g., the retention of metals in roots, enrichment of the oldest leaves with metals, accumulation of metals in trichomes, and excretion of metals by salt glands of leaf epidermis). This species also undergoes physiological and biochemical adaptations (e.g., the accumulation of metals in vacuoles of the root's tannic cells and secretion of such compounds as glutathione, organic acids, or HSP17). This work reviews the current knowledge on A. maritima adaptations to heavy metals occurring in zinc-lead waste heaps and the species' genetic variation from exposure to such habitats. A. maritima is an excellent example of microevolution processes in plants inhabiting anthropogenically changed areas.

Population structure and genetic variation of fragmented mountain birch forests in Iceland.

Betula pubescens Ehrh. (mountain birch) is the only forest-forming tree in Iceland. Since human settlement (874 AD), the continuous 25,000 to 30,000 km2 forest has shrunk to 1.200 km2 of fragmented patches, making it a good object to study population genetic consequences of habitat fragmentation and disturbance. Further, genetic studies have also shown that hybridization between the tetraploid (2n = 56) B. pubescens and the diploid (2n = 28) Betula nana L. (dwarf birch) occurs among Iceland's natural populations. This study assessed the genetic variation within and among 11 birch forests remaining across Iceland. Genotype-by-sequencing methodology provided a total of 24,585 single nucleotide polymorphisms (SNP´s), with a minor allele frequency >5% for genetic analyses. The analysis showed similar diversity within forests, suggesting that fragmentation and hybridization have had a limited effect on the genetic variation within sites. A clear genetic divergence is found among forests from the different regions of Iceland that may reflect historical isolation; the differentiation between forests increased with geographic distances reflecting isolation by distance. Information on the distribution of genetic variation of birch in Iceland is essential for its conservation and to establish genotype-phenotype associations to predict responses to new environmental conditions imposed by climate change and novel biotic/abiotic stressors.

Metals in Calluna vulgaris, Empetrum nigrum, Festuca vivipara and Thymus praecox ssp. arcticus in the geothermal areas of Iceland.

This investigation was conducted to identify the content of metals in Calluna vulgaris (family Ericaceae), Empetrum nigrum (family Ericaceae), Festuca vivipara (family Poaceae) and Thymus praecox subsp. arcticus (family Lamiaceae), as well as in the soils where they were growing in eight geothermal heathlands in Iceland. Investigation into the vegetation of geothermal areas is crucial and may contribute to their proper protection in the future and bring more understanding under what conditions the plants respond to an ecologically more extreme situation. Plants from geothermally active sites were enriched with metals as compared to the same species from non-geothermal control sites (at an average from about 150 m from geothermal activity). The enriched metals consisted of Cd, Co, Cu, Fe and Ni in C. vulgaris; Cd, Mn and Ti in E. nigrum; Hg and Pb in F. vivipara; and Cd, Fe and Hg in T. praecox. Notably, C. vulgaris, E. nigrum, F. vivipara and T. praecox had remarkably high concentrations of Ti at levels typical of toxicity thresholds. Cd and Pb (except for C. vulgaris and F. vivipara) were not accumulated in the shoots of geothermal plants. C. vulgaris from geothermal and control sites was characterised by the highest bioaccumulation factor (BF) of Ti and Mn; E. nigrum and F. vivipara by the highest BF of Ti and Cr; and T. praecox by the highest BF of Ti and Zn compared to the other elements. In comparison with the other examined species, F. vivipara from geothermal sites had the highest concentration of Ti in above-ground parts at any concentration of plant-available Ti in soil.

A new taxon within Biscutella laevigata L. (Brassicaceae) endemic to calamine areas in southern Poland.

A new taxon Biscutella laevigata subsp. woycickii (Brassicaceae) is described from southern Poland. The taxon is similar to B. laevigata subsp. gracilis, but differs in having thin, light-green rosette leaves very densely covered by simple non-glandular trichomes, smaller seeds and the ability to tolerate and accumulate high amounts of heavy metals. This new taxon is supported by results of cultivation experiments, as well as genetic and paleobotanical evidence.

Vascular plant colonisation of Surtsey Island (1965-1990) - a dataset.

BACKGROUND: The process of ecosystem development over time that takes place on a new substrate devoid of biological activity (such as, for example, lava) is called primary succession. Research on primary succession is not easy, as it is limited to rare occasions when a piece of land totally lacking in any pre-existing life occurs. The emergence of volcanic islands is such an occasion; it is a unique event that allows a natural experiment in the study of colonisation processes and primary succession. Surtsey (located in the Vestmannaeyar archipelago off the southern coast of Iceland) is an iconic example of a place where primary succession has been studied for decades and where human disturbance has been minimised due to significant geographic isolation and early protection efforts. Here, we present a georeferenced dataset of vacular plant occurrences collected during the field studies carried out on Surtsey Island during the first three decades of its existence. NEW INFORMATION: To date, no dataset containing plant distribution data documenting the process of early stages of colonisation of Surtsey has been published. What is more, to our knowledge, there is no other dataset that can be compared with our Surtsey data that is readily available for researchers working on plant colonisation dynamics and primary succession processes. Here, we present a complete, geo-referenced dataset of all plant occurrences (10,094 in total) collected on Surtsey between 1965 and 1990.

The transferability of microsatellite loci from a homoploid to a polyploid hybrid complex: an example from fine-leaved Festuca species (Poaceae).

BACKGROUND: Microsatellite loci, or single sequence repeats (SSR), are widely used as powerful markers in population genetics. They represent an attractive tool for studying plants such as grasses, whose evolution is driven by hybridisation and polyploidization. However, the development of microsatellite markers has been challenging and time-consuming, especially for non-model organisms lacking available genome-wide sequence data. One straightforward and low-cost approach is to transfer the SSR loci developed for one species, or complex, to another closely-related one. This work evaluates the transferability of microsatellite loci from homoploid to allopolyploid complexes of fine-leaved Festuca species and to assess their use in two new species. The studied complex (F. amethystina-F. tatrae) is a useful model for research on the local adaptability of grasses with different ploidy levels. Since both species can be considered as rare or threatened (F. tatrae-as a mountain and narrow endemic species and F. amethystina-a mountain species with relict lowland populations), any tool enabling studies on genetic diversity and population genetics, such as SSR markers, could also be very useful in a conservation context. METHODS: The ploidy level within populations was estimated using flow cytometry. One diploid and one tetraploid population of F. amethystina and a diploid population of F. tatrae were chosen to test the transferability of SSR loci. Because our work describes the transfer of SSR nuclear markers designed originally for F. gautieri, a phylogenetic tree was prepared based on the ITS marker to assess the genetic distance between the studied complexes. The PCR products were separated on a high-resolution agarose gel, intended for SSR marker analysis. Appropriate solutions for the allotetraploid population and whole mixed-ploidy complex were implemented. RESULTS: Flow cytometry confirmed earlier data regarding DNA content in the investigated species and cytotypes. The phylogenetic ITS tree indicated a small genetic distance between F. gautieri complexes and the studied species. Ten microsatellite markers were successfully transferred. All markers were polymorphic. In total, 163 different alleles were scored from the 10 SSR loci. PCoA of accessions revealed well-separated groups corresponding to studied populations. Over 60% of the total variance is explained by differentiation within populations and one third among them. CONCLUSIONS: The transferred markers are valid tools for the study of population genetics and inheritance relationships within cytotypes and species and between them. The presented markers can be used to study inbreeding depression in the Festuca species, and variations in the degrees of genetic diversity between different cytotypes in mountain and lowland areas. Our findings can also be applied to study conservation strategies for ensuring biodiversity at the genetic level in polyploid complexes.

Arctic terrestrial biodiversity status and trends: A synopsis of science supporting the CBMP State of Arctic Terrestrial Biodiversity Report.

This review provides a synopsis of the main findings of individual papers in the special issue Terrestrial Biodiversity in a Rapidly Changing Arctic. The special issue was developed to inform the State of the Arctic Terrestrial Biodiversity Report developed by the Circumpolar Biodiversity Monitoring Program (CBMP) of the Conservation of Arctic Flora and Fauna (CAFF), Arctic Council working group. Salient points about the status and trends of Arctic biodiversity and biodiversity monitoring are organized by taxonomic groups: (1) vegetation, (2) invertebrates, (3) mammals, and (4) birds. This is followed by a discussion about commonalities across the collection of papers, for example, that heterogeneity was a predominant pattern of change particularly when assessing global trends for Arctic terrestrial biodiversity. Finally, the need for a comprehensive, integrated, ecosystem-based monitoring program, coupled with targeted research projects deciphering causal patterns, is discussed.

Non-native vascular flora of the Arctic: Taxonomic richness, distribution and pathways.

We present a comprehensive list of non-native vascular plants known from the Arctic, explore their geographic distribution, analyze the extent of naturalization and invasion among 23 subregions of the Arctic, and examine pathways of introductions. The presence of 341 non-native taxa in the Arctic was confirmed, of which 188 are naturalized in at least one of the 23 regions. A small number of taxa (11) are considered invasive; these plants are known from just three regions. In several Arctic regions there are no naturalized non-native taxa recorded and the majority of Arctic regions have a low number of naturalized taxa. Analyses of the non-native vascular plant flora identified two main biogeographic clusters within the Arctic: American and Asiatic. Among all pathways, seed contamination and transport by vehicles have contributed the most to non-native plant introduction in the Arctic.

Infraspecific Variation of Huperzine A and B in Icelandic Huperzia selago Complex.

The alkaloids huperzine A and huperzine B were originally isolated from the Chinese club moss Huperzia serrata. They are known inhibitors of acetylcholinesterase, and especially huperzine A shows pharmaceutical potential for the treatment of Alzheimer's disease. Its supply heavily relies on natural plant sources belonging to the genus Huperzia, which shows considerable interspecific huperzine A variations. Furthermore, taxonomic controversy remains in this genus, particularly in the Huperzia selago group. With focus on Icelandic H. selago taxa, we aimed to explore the relatedness of Huperzia species using multi-locus phylogenetic analysis, and to investigate correlations between huperzine A contents, morphotypes, and genotypes. Phylogenetic analysis was performed with five chloroplastic loci (the intergenic spacer between the photosystem II protein D1 gene and the tRNA-His gene, maturase K, ribulose-1,5-bisphosphate carboxylase/oxygenase large subunit, tRNA-Leu, and the intergenic spacer region between tRNA-Leu and tRNA-Phe). Huperzine A and huperzine B contents were determined using an HPLC-UV method. The phylogenetic analysis suggests that previously proposed Huperzia appressa and Huperzia arctica should not be considered species, but rather subspecies of H. selago. Three genotypes of Icelandic H. selago were identified and presented in a haplotype networking diagram. A significantly (p < 0.05) higher amount of huperzine A was found in H. selago genotype 3 (264 - 679 µg/g) than genotype 1 (20 - 180 µg/g), where the former shows a typical green and reflexed "selago" morphotype. The huperzine A content in genotype 3 is comparable to Chinese H. serrata and a good alternative huperzine A source. Genotype 2 contains multiple morphotypes with a broad huperzine A content (113 - 599 µg/g). The content of huperzine B in Icelandic taxa (6 - 13 µg/g) is much lower than that in Chinese H. serrata (79 - 207 µg/g).

Invasion of a Legume Ecosystem Engineer in a Cold Biome Alters Plant Biodiversity.

Plant ecosystem engineers are widely used to combat land degradation. However, the ability of those plants to modulate limiting abiotic and biotic resources of other species can cause damage to ecosystems in which they become invasive. Here, we use Lupinus nootkatensis as example to estimate and project the hazardous potential of nitrogen fixing herbaceous plants in a sub-polar oceanic climate. L. nootkatensis was introduced to Iceland in the 1940s to address erosion problems and foster reforestation, but subsequently became a high-latitude invader. In a local field survey, we quantified the impact of L. nootkatensis invasion at three different cover levels (0, 10-50, and 51-100%) upon native plant diversity, richness, and community composition of heath-, wood-, and grasslands using a pairwise comparison design and comparisons of means. Afterward, we scaled impacts up to the ecosystem and landscape level by relating occurrences of L. nootkatensis to environmental and human-mediated variables across Iceland using a species distribution model. Plant diversity was significantly deteriorated under high lupine cover levels of the heath- and woodland, but not in the grassland. Plant species richness of the most diverse habitat, the heathland, linearly decreased with lupine cover level. The abundance of small rosettes, cushion plants, orchids, and small woody long-lived plants of the heath declined with invader presence, while the abundance of late successional species and widespread nitrophilous ruderals in wood- and grasslands increased. Distribution modeling revealed 13.3% of Iceland's land surface area to be suitable lupine habitat. Until 2061-2080, this area will more than double and expand significantly into the Central Highlands due to human mediation and increasingly favorable climatic conditions. Species-rich habitats showed a loss of plant species diversity and richness as well as a change in community composition even in low lupine cover classes. The future increase of suitable lupine habitat might lead to the displacement of cold-adapted native plant species and will certainly challenge conservation as well as restoration of ecosystems in the cold climate of Iceland, but also elsewhere. Lupine invasion speeds up succession, which may be additive with climate change effects, and accelerates ecological change in cold biomes.

Non-native species in the vascular flora of highlands and mountains of Iceland.

The highlands and mountains of Iceland are one of the largest remaining wilderness areas in Europe. This study aimed to provide comprehensive and up-to-date data on non-native plant species in these areas and to answer the following questions: (1) How many non-native vascular plant species inhabit highland and mountainous environments in Iceland? (2) Do temporal trends in the immigration of alien species to Iceland differ between highland and lowland areas? (3) Does the incidence of alien species in the disturbed and undisturbed areas within Icelandic highlands differ? (4) Does the spread of non-native species in Iceland proceed from lowlands to highlands? and (5) Can we detect hot-spots in the distribution of non-native taxa within the highlands? Overall, 16 non-native vascular plant species were detected, including 11 casuals and 5 naturalized taxa (1 invasive). Results showed that temporal trends in alien species immigration to highland and lowland areas are similar, but it is clear that the process of colonization of highland areas is still in its initial phase. Non-native plants tended to occur close to man-made infrastructure and buildings including huts, shelters, roads etc. Analysis of spatio-temporal patterns showed that the spread within highland areas is a second step in non-native plant colonization in Iceland. Several statically significant hot spots of alien plant occurrences were identified using the Getis-Ord Gi* statistic and these were linked to human disturbance. This research suggests that human-mediated dispersal is the main driving force increasing the risk of invasion in Iceland's highlands and mountain areas.

Phylogeography of Arabidopsis halleri (Brassicaceae) in mountain regions of Central Europe inferred from cpDNA variation and ecological niche modelling.

The present study aimed to investigate phylogeographical patterns present within A. halleri in Central Europe. 1,281 accessions sampled from 52 populations within the investigated area were used in the study of genetic variation based on chloroplast DNA. Over 500 high-quality species occurrence records were used in ecological niche modelling experiments. We evidenced the presence of a clear phylogeographic structure within A. halleri in Central Europe. Our results showed that two genetically different groups of populations are present in western and eastern part of the Carpathians. The hypothesis of the existence of a glacial refugium in the Western Carpathians adn the Bohemian Forest cannot be rejected from our data. It seems, however, that the evidence collected during the present study is not conclusive. The area of Sudetes was colonised after LGM probably by migrants from the Bohemian Forest.

Distribution patterns in the native vascular flora of Iceland.

The aim of our study was to reveal biogeographical patterns in the native vascular flora of Iceland and to define ecological factors responsible for these patterns. We analysed dataset of more than 500,000 records containing information on the occurrence of vascular plants. Analysis of ecological factors included climatic (derived from WORLDCLIM data), topographic (calculated from digital elevation model) and geological (bedrock characteristics) variables. Spherical k-means clustering and principal component analysis were used to detect biogeographical patterns and to study the factors responsible for them. We defined 10 biotic elements exhibiting different biogeographical patterns. We showed that climatic (temperature-related) and topographic variables were the most important factors contributing to the spatial patterns within the Icelandic vascular flora and that these patterns are almost completely independent of edaphic factors (bedrock type). Our study is the first one to analyse the biogeographical differentiation of the native vascular flora of Iceland.

Nuclear microsatellite loci for Arabidopsis halleri (Brassicaceae), a model species to study plant adaptation to heavy metals.

PREMISE OF THE STUDY: Arabidopsis halleri is a model species to study the adaptation of plants to soils contaminated by zinc, cadmium, and lead. To provide a neutral genetic background with which adaptive genetic markers could be compared, we developed highly polymorphic neutral microsatellite markers. METHODS AND RESULTS: Using a microsatellite-enriched library method, we identified 120 microsatellite loci for quantitative trait locus (QTL) mapping analysis, of which eight primer pairs were developed in a single multiplex for population genetic studies. Analyses were performed on 508 individuals from 26 populations. All loci were polymorphic with six to 23 alleles per locus. Genetic diversity varied between 0.56 and 0.76. CONCLUSIONS: Our results demonstrated the value of these eight microsatellite markers to investigate neutral population genetic structure in A. halleri. To increase the resolution of population genetic analyses, we suggest adding them to the 11 markers previously developed independently.