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Word2Vec embedding model trained on Czech legislation (from April 2020) corpus using gensim implementation with the following parameters in addition to default settings: vector dimension = \(400\), window size = \(10\), word minimum count = \(10\), sample = \(10^{-5}\). This work was supported by the Czech Science Foundation (GAČR),grant number 19-01641S.

Additional file 3. Data S3 Detailed information of selected variants from discovery phase.

Supplementary Material 23

Thesis reference: STEINER, Ludvík. DOI Assignment Practice of Czech Scientific Journal Publishers [online]. Praha, 2021[cit. 2021-05-07]. Bachelor thesis. Charles University. Faculty of Arts. Institute of Information Studies and Librarianship. This dataset contains data about scholarly journals published in the Czech Republic and about DOIs, which these journals assign. It was used to explore common patterns of DOIs and for assessment of quality of the associated metadata. It also contains data about editiorial systems of the journals and the DOI registration workflow. The thesis and this dataset are in Czech language only.

Collection simulations of small pure bilayers (max 128 phospholipids) with cholesterol in gromacs using the charmm36 force field. The list of systems describing their particular simulation conditions can be found below: DPPC_128_CHL1_32_310K For further information read the Readme file provided for each simulation.

Abstract Background Programmed cell death 1 (PD-1) belongs to immune checkpoint proteins ensuring negative regulation of the immune response. In non-small cell lung cancer (NSCLC), the sensitivity to treatment with anti-PD-1 therapeutics, and its efficacy, mostly correlated with the increase of tumor infiltrating PD-1+ lymphocytes. Due to solid tumor heterogeneity of PD-1+ populations, novel low molecular weight anti-PD-1 high-affinity diagnostic probes can increase the reliability of expression profiling of PD-1+ tumor infiltrating lymphocytes (TILs) in tumor tissue biopsies and in vivo mapping efficiency using immune-PET imaging. Methods We designed a 13 kDa β-sheet Myomedin scaffold combinatorial library by randomization of 12 mutable residues, and in combination with ribosome display, we identified anti-PD-1 Myomedin variants (MBA ligands) that specifically bound to human and murine PD-1-transfected HEK293T cells and human SUP-T1 cells spontaneously overexpressing cell surface PD-1. Results Binding affinity to cell-surface expressed human and murine PD-1 on transfected HEK293T cells was measured by fluorescence with LigandTracer and resulted in the selection of most promising variants MBA066 (hPD-1 KD = 6.9 nM; mPD-1 KD = 40.5 nM), MBA197 (hPD-1 KD = 29.7 nM; mPD-1 KD = 21.4 nM) and MBA414 (hPD-1 KD = 8.6 nM; mPD-1 KD = 2.4 nM). The potential of MBA proteins for imaging of PD-1+ populations in vivo was demonstrated using deferoxamine-conjugated MBA labeled with 68Galium isotope. Radiochemical purity of 68Ga-MBA proteins reached values 94.7–99.3% and in vitro stability in human serum after 120 min was in the range 94.6–98.2%. The distribution of 68Ga-MBA proteins in mice was monitored using whole-body positron emission tomography combined with computerized tomography (PET/CT) imaging up to 90 min post-injection and post mortem examined in 12 mouse organs. The specificity of MBA proteins was proven by co-staining frozen sections of human tonsils and NSCLC tissue biopsies with anti-PD-1 antibody, and demonstrated their potential for mapping PD-1+ populations in solid tumors. Conclusions Using directed evolution, we developed a unique set of small binding proteins that can improve PD-1 diagnostics in vitro as well as in vivo using PET/CT imaging. Graphical Abstract

The role of chromosome changes in speciation remains a debated topic, although demographic conditions associated with divergence should promote their appearance. We tested a potential relationship between chromosome changes and speciation by studying two Lake Whitefish (Coregonus clupeaformis) lineages that recently colonized postglacial lakes following allopatry. A dwarf limnetic species evolved repeatedly from the normal benthic species, becoming reproductively isolated. Lake Whitefish hybrids experience mitotic and meiotic instability, which may result from structurally divergent chromosomes. Motivated by this observation, we test the hypothesis that chromosome organization differs between Lake Whitefish species pairs using cytogenetics. While chromosome and fundamental numbers are conserved between the species (2n = 80, NF = 98), we observe extensive polymorphism of subtle karyotype traits. We describe intrachromosomal differences associated with heterochromatin and repetitive DNA, and test for parallelism among three sympatric species pairs. Multivariate analyses support the hypothesis that differentiation at the level of subchromosomal markers mostly appeared during allopatry. Yet we find no evidence for parallelism between species pairs among lakes, consistent with colonization effect or postcolonization differentiation. The reported intrachromosomal polymorphisms do not appear to play a central role in driving adaptive divergence between normal and dwarf Lake Whitefish. We discuss how chromosomal differentiation in the Lake Whitefish system may contribute to the destabilization of mitotic and meiotic chromosome segregation in hybrids, as documented previously. The chromosome structures detected here are still difficult to sequence and assemble, demonstrating the value of cytogenetics as a complementary approach to understand the genomic bases of speciation. Macrogen_sequence_filesFile produced during the sequencing of the PCR products used for FISH of 5S and 28S rDNA. File names contain "5S" or "28S" depending on what product they refer to.C-BandCMA3GiemsaFISH_rDNAFISH_rDNA

The BeechCOSTe52 includes phenotypic trait measurements from individual trees measured in an international network of provenance tests compiled by the COST Action E52 (2006 – 2010). It comprises 39 trial sites and 217 provenances covering the distribution of European beech (Fagus sylvatica L.). The BeechCOSTe52 database provides individual tree phenotypic measurements of height, diameter at breast height, basal diameter, mortality, spring and autumn leaf phenology. The following files are included: Fsylvatica.csv: individual tree measurements by trial and provenance of origin. Trials_coords.csv: geographical coordinates of the trials Prov_coords.cvs: geographical coordinates of the provenances BeechCOSTe52_metadata_descriptor.docx: description of the fields of Fsylvatica.csv, Trials_coords.csv and Prov_coords.cvs databases. Subset_by_trial.R: R script to subset the original database (Fsylvatica.csv) by trial Merge_trial_prov-coords_individualmeasurements.R: R script to merge the coordinates of trials and provenances (Trials_coords.csv and Prov_coords.cvs) with the phenotypic measurements (Fsylvatica.csv). Plot_Trial-Prov_locations.R: R script to map trial and provenance locations. Hplot.R: R script to map tree height variation across provenances and trials. Fagus_sylvatica_EUFORGEN.X: Shape files containing the distribution of Fagus sylvatica from EUFORGEN (http://www.euforgen.org)