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Abstract 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.

The ongoing biodiversity crisis associated with anthropogenic global warming has especially severe effects on mountain and cold-adapted species. The lesson from the postglacial period can provide examples for future predictions, but scenarios of the range shift of mountain species are not fully explored. Different stories could happen if a species achieved long-distance dispersal and reached lowland locations or if survived only in mountains, during the ice age. In the case of grasses, a key role in range dynamics is played also by polyploidy. Due to their enhanced genetic and physiological plasticity, polyploids are thought to be less likely to become extinct during global changes.The present study explores the postglacial range shifts in two Festuca species, which differ in range size (endemic vs widespread) and in ploidy level (diploid vs mixed-ploidy). We used phylogeography and distribution models to analyze changes in potential range during global warming. We achieved a sophisticated prediction by using modeling based on climate and edaphic factors.Our findings indicate a low level of gene flow between populations, irrespective of variation in distance, range size and ploidy. Slightly shorter genetic distances were observed between the tetraploid populations compared to the diploids. Our data indicates that diploids adapted to cold conditions were restricted to mountains during glaciations, while polyploids spread more widely during cold periods. Nevertheless, since the LGM it appears that all studied ranges have been rather conservative, with maybe some local contractions and expansions, especially in tetraploids. Moreover, tetraploids demonstrated the most stable potential range during climate warming.The studied cases are characterized by individual and complex range dynamics dependent on local conditions and cytotype behaviour. However, generally speaking, studied mountain species demonstrate a conservative range, which places them at risk of extinction during global warming due to the lack of effective means of escape.

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.

The article presents an outline of the concept of a prototype system allowing for the optimization of inventory management in a diagnostic laboratory on the basis of patients results. The effectiveness of laboratory diagnostics depends largely on the appropriate management of resources and the quality of tests. A functional quality management system is an integral element of every diagnostic laboratory, ensuring reliability and appropriate work standards. This system includes maintaining correct and reliable analytical test results as well as the optimal use of the laboratory equipment’s processing capacity and the appropriate organization of the supply chain—both analytical material and reagents. It is extremely important to avoid situations in which tests cannot be performed due to a lack of reagents, the overloading of analyzers, or improper calibration. Therefore, the accurate prediction of the number of orders is crucial to optimize the laboratory’s operations, both in the short term—for the next few hours and minutes—and in the longer term, even monthly, which will allow for the appropriate planning of reagent stock. As part of the research presented in this article, machine learning methods were used to implement the above functionalities, which allowed for the development of a prototype of a laboratory optimization system using patient test results as a basis.

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.

This article presents for the first time a list of the possible archaeophytes from Iceland. In the present study, all the flowering plant taxa that are considered native/long established in Iceland were assessed against criteria designed to recognize possible archaeophytes. The assessment resulted in a list of 39 taxa meeting (or possibly meeting) at least one research criterion. Nineteen taxa were classified as possible archaeophytes, 10 were classified as non-natives of unknown age (due to the inability to classify them as neither archaeophytes nor neophytes using the available data), while the remaining 10 species were classified as uncertain (doubtfully native). The limitations of the present study in terms of both the methodology and the uncertainties connected with the classification of individual taxa are discussed.

Blechnum spicant var. fallax Lange is a fern taxon endemic to Iceland where it occurs in the vicinity of hot springs on geothermally heated soils. The taxon was first described by a Danish botanist Johan Martin Christian Lange in 1880 on the basis of plant material collected by Christian Grønlund in Iceland. Because its holotype was not designated in the protologue, we examined the extant original material including illustrations from Flora Danica and a single plant on sheet C10021769 (deposited in C) that was the basis for the respective plate. We select this specimen as the lectotype of Blechnum spicant var. fallax.

A morphometric study of the three species of Lepidium L. sect. Dileptium DC. is presented. Multivariate methods (cluster analysis and canonical discriminant analysis) were employed to investigate phenetic relations between examined individuals. As a result a set of quantitative characters useful in species determination was proposed and discussed.

The North American lodgepole pine (Pinus contorta) has been widely introduced globally and is now considered invasive in several countries. It was first planted in subarctic Iceland in the 1950s. Recently, the forestry sector has strongly promoted it as an attractive means of carbon capture to mitigate global climate change. It is now the most extensively planted tree species in Iceland. We describe the expansion of the lodgepole pine from a mid-20th-century plantation in Steinadalur, southeast Iceland, and decadal changes between 2010 and 2021. The extent of occurrence expanded nearly tenfold, with tree number and population density reflecting exponential growth patterns. The lodgepole pine colonised diverse habitats, including native birch woodlands and heathland, and was associated with significant reductions in vascular plant species richness and diversity. We conclude that lodgepole pine has the characteristics of an invasive species in Steinadalur and that this will also apply to many native ecosystems across most lowland regions of Iceland. Our study highlights the urgent need for management strategies to mitigate the long-term ecological impacts of lodgepole pine invasion in subarctic environments.

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.

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.

The improvement of health, safety and protection of workers at risk from explosive in the workplace is governed by the European ATEX Directives requiring the employer to carry out a risk assessment for possible explosion scenario. In order to determine explosion risk, the recently proposed methodology ExLOPA requires the identification of the explosion scenario and its structural elements, conventionally by applying different Process Hazard Analysis methods. This paper presents a novel strategy based on the combination of an expert system for explosion scenario identification (ExSys), with subsequent application of ExLOPA method. An expert system (ExSys) employs values from ad-hoc prepared engineering databases to identify the explosion loss event tailored for the selected target process and the given workplace. Subsequently, an explosion barrier model is developed, to provide data for a representative explosion scenario, which is finally used for explosion risk assessment by the ExLOPA methodology. The proposed technique supports and extends the application of the Layer of Protection Analysis especially for safety assurance assessment of risk-based determination for chemical, petrochemical, pharmaceutical, energy, food, wood and other process industries and related services.

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.

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.

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.

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.