Dane Badawcze UW University of Warsaw
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Diversity in a drop: plant-pollinator interaction, flower and nectar traits shaping nectar mycobiome
No full textDataset description:Rows: Individual nectar samplesColumns:sample — Unique identifier of the nectar sample (string; e.g. G4O).species — Plant species name (string; binomial, underscores instead of spaces; e.g. Impatiens_walleriana).f__… — Columns prefixed with f__ represent fungal families (e.g. f__Aspergillaceae, f__Bartaliniaceae). Each contains integer read counts of ITS amplicon sequencing reads assigned to that family.Example: f__Aspergillaceae — read counts for family Aspergillaceae.Zero means no reads assigned.Pollinator visitation columns:bumblebee — Number of visits by bumblebees recorded for the given sample (integer).fly — Number of visits by non-hoverfly Diptera (integer).ant — Number of visits by ants (integer).hoverfly — Number of visits by Syrphidae (hoverflies) (integer).hymenoptera — Number of visits by non-bee Hymenoptera (integer).other — Number of visits by other insect groups (integer).Diversity indices (calculated from fungal community data):richness — Observed richness (number of fungal OTUs detected).sha_div — Shannon diversity index.invsimp — Inverse Simpson diversity index.chao — Chao1 richness estimator.Methods of obtaining statistical results:All analyses were performed in R (Team, 2024). To assess the alpha diversity of nectar-associated microbial communities, two complementary indices were calculated: Shannon diversity and the Chao1 richness estimator. Shannon diversity was used as the primary metric for statistical analysis and visualization, as it reflects both species richness and evenness, providing a comprehensive measure of community complexity. Chao1 was included to estimate total richness, including rare or undetected taxa, which is particularly relevant in systems with uneven sequencing depth or low detection rates. Both indices were calculated from taxon abundance tables derived from ITS amplicon sequencing using the vegan (VEGAN, 2003) and phyloseq packages (McMurdie and Holmes, 2013).</p
Research data for article 'Nematic and smectic phases with proper ferroelectric order'
No full textSynthesis and characterization of a new material showing a sequence of three ferroelectric liquid crystalline phases below the paraelectric nematic phase is reported.The stored dataset includes:1) publication in Advanced Science (manuscript and Supporting Information, pdf format ) - see also https://doi.org/10.1002/advs.2024097542) Data (numerical and plots) for chemical characterization (NMR, IR, HRMS) of the synthesised compounds (final and intermediates) 3) numerical data (ASCI) for optical birefringence measured vs. temperature for final compound (GJS_W22, 7509)4) numerical data (ASCI) for dielectric permittivity measured vs. temperature and frequency for final compound (GJS_W22, 7509)5) numerical data (binary Bruker .raw format) for small angle X-ray diffraction studies performed for final compound (GJS_W22, 7509)6) results of single crystal X-ray diffraction studies for final compound (GJS_W22, 7509)7) images of optical textures taken with polarized light optical microscope for compound 7509 in various geometries</p
Replication data for: Electric-field metrology of a terahertz frequency comb using Rydberg atoms
No full textThe dataset contains the replication data used for generating plots and tables in the associated article. It contains both the data itself, stored in netcdf4 and pickle format. The data is best analyzed using a Python based stack for data analysis. The following packages are recommended for its viewing and running the examples below:numpymatplotlibxarrayxrftarc-alkali-rydberg-calculatornetcdf4pinttabulateDue to the complexity of the data, analyzing them is best done based on the custom scripts below, developed while conducting the associated research. The structured nature of the netcdf format, as well as high level and quality code presented in the examples, serve as a documentation of its own. The code replicates all of the plots and values presented in the article.All photon counts were measured using a single photon avalanche photodiode, while the probe spectra were measured using a regular avalanche photodiode, where the probe laser was scanned in frequency.Contentsexamples.py contains a Python script to be run in interactive mode, for viewing all the plots that are part of the linked articlecomb_scan.nc contains broadband scans of the frequency comb showing photon counts with respect to the decoupling laser detuning, for 4 different atomic transitions. Used in Fig. 3-4comb_theory.pkl theoretical predictions of the aforementioned scan for the 126 GHz transition, obtained with the theoretical model from appendix A, used in Fig. 4map.nc conversion gain map, obtained from the aforementioned theoretical model. Used in Fig. 8-9 and to derive the theory in Fig. 5photon_counts.nc measured photon counts for maximum comb signal intensity, thermal background and dark counts. Each measurement is a 1s aggregation and there are 30 copies of each level measurement. Used in Fig. 2 and sensitivity derivations shown in Table 1rabi_fits.pkl experimental data showing Autler-Townes splitting, registered in the probe spectrum with a photodiode. Additionally, contains the resulting plots of the fitted theoretical model and estimated Rabi frequencies. Used in Fig. 7rabis.pkl fitted Rabi frequencies with respect to the half-waveplate angles used for attenuating the signal. Used in Fig. 2 and the calibration proceduretds.nc single frequency comb pulse spectrum, measured with a standard Time Domain Spectroscopy setup. Used in Fig. 3tra_da.nc measured photon counts of the converted TRA chip signal with respect to the attenuation induced by the half-waveplate angles and the selected chip power mode. Used in Fig. 2bandwidth.nc measured photon counts of the converted TRA chip signal with respect to its detuning, driven by a phase locked loop. Used as the conversion bandwidth for frequency comb mode number derivations presented in Table 2beat_histogram.nc measured photon counts with respect to time, used for observing beat notes and shown in Fig. 5This research was funded in whole or in part by National Science Centre, Poland grants No. 2021/43/D/ST2/03114 and No. 2024/53/N/ST7/02730. The "Quantum Optical Technologies" (FENG.02.01-IP.05-0017/23) project is carried out within the Measure 2.1 International Research Agendas programme of the Foundation for Polish Science co-financed by the European Union under the European Funds for Smart Economy 2021-2027 (FENG).</p
First-generation quark couplings
No full textDataset contains data and codes related to the study of the possible use of radiative processes for precise measurement of first-generation quark couplings at future electron-positron collider running at the Z-pole. Results of the study were summarized in the publication "Determination of the first-generation quark couplings at the Z-pole" published in J. High Energ. Phys. 11 (2025) 050.This research was part of the project "Realistic simulations of exotic processes at future e+e- colliders" funded by National Science Centre, Poland, under grant agreement nr 2021/43/B/ST2/01778.MethodologyThe study was based on large event samples of quark pair-production events for electron-positron collider running at the Z-pole. Samples were generated with the WHIZARD program and processed with the DELPHES framework to model detector performance. Event selection efficiencies and acceptance of the cut used to select events with final state radiation extracted from the Monte Carlo simulation were then used in the semi-analytical framework to extract quark pair-production cross sections and quark couplings. We present a method to extract the values of the Z couplings to light quarks based on up- and down-quarks’ different contributions to radiative and non-radiative Z boson decays. We show that systematic uncertainty in the heavy-flavour tagging performance is the key factor in the analysis, and that reducing it to the sub-permille level is crucial to fully profit from the high luminosity of future e+e− machines.Files:example Jupyter notebook (Python scripts) for studying coupling measurement precision as a function of the integrated collider luminosity, for different assumptions concerning systematic uncertainties in flavour tagging (Fig. 7 in the paper),input file with photon cut acceptance for radiative and non-radiative events, for different quark flavours (required by the Jupyter notebook)CSV files with final analysis results: expected uncertainties in the quark coupling extraction as a function of the analysis cut and collider luminosity, as presented in Figs. 4 and 7 of the paper.PDF and PNG files of the figuresSoftware tools usedWHIZARD Event Generator web page: https://whizard.hepforge.org/DELPHES: https://github.com/delphes/delphes</p
The role of TGFβ1 in regulating MMP-9 and MMP-2 activity during myoblast differentiation in vitro
No full textAlthough the role of TGFβ1 in the regulation of ECM protein synthesis is well established, its involvement in the regulation of enzymes, such as MMPs, is still not well understood. In this project, we investigated the relationship between TGFβ1 and MMP-9/MMP-2 in in vitro differentiating myoblasts isolated from rat slow-twitch Soleus or fast-twitch Extensor Digitorum Longus (EDL) muscles. Using siRNA to silence TβR1 expression, suramin as a competitive inhibitor of the TβR1 receptor, and inhibitors of both the canonical and non-canonical TGFβ signaling pathways, we characterized the role of TGFβ1 in regulating MMP-9 and MMP-2 during differentiation of myoblasts derived from slow-twitch and fast-twitch muscles in vitro.Chociaż rola TGFβ1 w regulacji syntezy białek ECM jest dobrze znana, jego zaangażowanie w regulację enzymów, takich jak MMP, wciąż nie jest w pełni zrozumiane. W projekcie zbadaliśmy zależność między TGFβ1 a MMP-9/MMP-2 w hodowanych in vitro mioblastach, izolowanych z mięśni wolno- (Soleus) lub mięśni szybko-kurczących się (Extensor Digitorum Longus-EDL) szczura. Używając siRNA do wyciszenia ekspresji TβR1, suraminy jako konkurencyjnego inhibitora receptora TβR1 oraz inhibitorów zarówno kanonicznych, jak i niekanonicznych szlaków sygnalizacyjnych TGFβ, scharakteryzowaliśmy rolę TGFβ1 w regulacji MMP-9 i MMP-2 podczas różnicowania in vitro mioblastów izolowanych z mięśni wolno- i szybko-kurczących się.</p
Identifying heavy neutrinos at lepton colliders
No full textDataset contains data related to the study of the prospects for identifying the nature of the heavy neutral lepton (heavy neutrino) in future lepton collider experiments described in the publication "Discriminating Majorana and Dirac heavy neutrinos at lepton colliders" published in J. High Energ. Phys. 2024, 75 (2024).This research was part of the project "Realistic simulations of exotic processes at future e+e- colliders" funded by National Science Centre, Poland, under grant agreement nr 2021/43/B/ST2/01778.MethodologyThe study was based on large event samples of different particle scattering processes, which can be observed at future lepton collider experiments. Considered collider projects are International Linear Collider (ILC) running at 250 GeV, 500 GeV and 1 TeV centre-of-mass energy, Compact Linear Collider (CLIC) running at 3 TeV, and Muon Collider (MuC) running at 3 TeV and 10 TeV. Samples were generated with the WHIZARD program. Considered signal process of heavy neutral lepton production was simulated according to the HeavyN model. Outputs from the WHIZARD program (lists of produced particles with their parameters) were then processed with the DELPHES framework to model detector performance for considered experiments. Event samples from detector simulation were stored in root format.Signal samples used for the analysis are too large to be stored. Included in the dataset are example control scripts of the WHIZARD program which can be used to reproduce them. These are "pseudo-data" reflecting our current assumptions about how the future lepton collider experiment will perform. Also included are final numerical results on the analysis: expected 95% CL exclusion limits, expected 95% CL discrimination range between two neutrino nature hypotheses: Dirac and Majorana, and 5 σ discovery range.Files:example WHIZARD scripts for generating signal samples for production of heavy neutrino at ILC, CLIC and MuC,CSV files with final analysis results: expected exclusion limits on the heavy neutrino coupling parameter V2lN as a function of its mass, 95% CL discrimination limits between Dirac and Majorana netrino, and expected 5 σ discovery range.PDF and PNG files of the figures showing these limits (Fig. 1 and Fig. 5 from the paper).Software tools usedHeavyN model webpage: https://feynrules.irmp.ucl.ac.be/wiki/HeavyNWHIZARD Event Generator web page: https://whizard.hepforge.org/DELPHES: https://github.com/delphes/delphes</ul
Taming the wild…: Trainers as constructors of interspecies narratives in the horse-human relationship
No full textThis dataset is associated with the following paper: Sara Kruszona-Barełkowska. (2025). Taming the wild…: Trainers as constructors of interspecies narratives in the horse-human relationship. TRACE∴ Journal for Human-Animal Studies, 12, 4–27, https://doi.org/10.23984/fjhas.144515Dataset consists of:1) readme.txt2) Shy_boy.odt3) Taming_wild.odtThe Shy_boy.odt file contains a description of the film provided by its filmmakers, as well as notes made by the author of the study while watching the film. These notes include insights relevant to the study of interspecies relations and were an important part of the analysis presented in the publication.The Taming_Wild.odt file contains a description of the film provided by its filmmakers, along with notes made by the author of the study during the viewing. These notes include reflections significant to the exploration of interspecies relations and constituted a key element of the analysis discussed in the publication.</p
Enhancement of temozolomide stability and anticancer efficacy by loading in monopalmitolein-based cubic phase nanoparticles
No full textThe manuscript "Enhancement of Temozolomide Stability and Anticancer Efficacy by Loading in Monopalmitolein-Based Cubic Phase Nanoparticles" contains data from this dataset.In this study, temozolomide was incorporated into both monoolein (MO)- and monopalmitolein (MP)-derived cubic phases. Determination of the profile and kinetics of drug release was carried out. We concluded that likely the observed advantages in the release profile of MP might be related to the observed differences in the structural parameters of both systems, where the aqueous channel diameter is larger for the MP-derived formulation. Moreover, the biological studies revealed that the TMZ-loaded MP formulation presents stronger anticancer properties than the drug-loaded MO phase. What is crucial, the improved effectiveness of MP/TMZ was also observed during treatment of drug-resistant glioma-derived cells. As MP-based formulations present increased TMZ stability and high drug effectiveness, the MP/TMZ cubosomes may offer a new strategy to overcome the restrictions related to the blood-brain barrier.DATA & FILE OVERVIEWFile List: Scheme 1. Chemical structures of the used reagentsFig1A.csv Diffractograms of cubic phases prepared from monoolein (MO) and acetate buffer, doped with various concentrations of temozolomide (TMZ); Fig1B.csv Diffractograms for cubic phases prepared from monopalmitolein (MP) and temozolomide;Fig1C.csv Diffractograms of cubosomes prepared from MO or MP and acetate buffer, doped with TMZ. Fig2A.csv Cyclic voltammogram recorded on the glassy carbon electrode (GCE) for TMZ in an acetic buffer (pH of 5.0); scan rate 50 mV s–1; Fig2B.csv Differential pulse voltammograms recorded on the GCE for the MO and MP cubic phases; amplitude: ?E = 50 mV, pulse time: tp = 50 ms; Fig2C.csv Drug release profile for TMZ-loaded MO and MP cubic phases; D) TMZ release profile from cubic phase nanoparticles.Fig3.csv Ratio of the relaxation input (R) and the diffusion input according to Fick (F) (R/F ratio) for TMZ release from the MO- and MP-based A) cubic phase and B) cubosomes.Fig4A.csv Analysis of the survival rate of A-172 and T98G cells treated with free TMZ (TMZ) and TMZ-loaded MO or MP phases (MO/TMZ; MP/TMZ, respectively). The cell’s viability was measured using MTS assay. Data are presented as mean ± SD (standard deviation); (n = 8). Non-treated cells served as controls. * p < 0.05.Fig4B.csv Analysis of the survival rate of A-172 and T98G cells treated with free TMZ (TMZ) and TMZ-loaded MO or MP phases (MO/TMZ; MP/TMZ, respectively). The cell’s viability was measured using trypan blue exclusion assay. Data are presented as mean ± SD (standard deviation); (n = 8). Non-treated cells served as controls. * p < 0.05.Fig5.csv Flow cytometry analysis of A-172 and T98G cells treated with free TMZ and TMZ-loaded MO or MP phases. The light color bars show the number of viable cells (V), while the dark color bars refer to the number of apoptotic cells (A) in each of the tested samples. Data are presented as mean ± SD; (n = 10). Control?non-treated cells. * p < 0.05.Fig6.tiff Click-iT TUNEL Alexa Fluor 647 Imaging Assay of A-172 cells exposed to free TMZ, TMZ-loaded MO or TMZ-loaded MP phases for 24 h (representative images). Non-treated cells or cells treated with non-loaded MO or non-loaded MP particles served as controls. The intensity of the red signal (Alexa Fluor 647) refers to the apoptotic rate in the tested cells. The green signal (phalloidin-FITC) indicates the organization of the cell structure. Cell nuclei were counterstained with DAPI (blue signal). Objective: 63x/1.4 oil DIC M27. Panel A – standard confocal imaging; Panel B – Airyscan imaging.METHODOLOGICAL INFORMATIONDescription of methods used for collection/generation of data: small angle X-ray scattering, voltammetry.Instrument- or software-specific information needed to interpret the data: csv data can be opened with e.g. Excel, Origin, jpg (tiff) files contain images.</p
High speed camera videos used for preparation of fig. 6 presenting the impact of various flow rates of sorting oil on droplet sorting under microbial cultivation conditions
No full textHigh speed camera videos used for preparation of Fig. 6 presenting the impact of various flow rates of sorting oil on droplet sorting under microbial cultivation conditions.Detailed description can be found in the attached "Dataset_ZD2_README_Potenza et al_Analytical Chemistry_2024".</p
Multifunctional dynamic hydrogels crosslinked with boronic ester and disulfide bonds reinforced with oxidized cellulose nanofibers for self-healing, motion sensing, and controlled drug release
No full textThis study presents a novel multifunctional dynamic hydrogel, cross-linked with boronic ester and disulfide bonds, and incorporating oxidized bacterial cellulose nanofibers (OBCNF). The OBCNF content was optimized to achieve a material with optimal mechanical properties. The presence of dynamic boronic ester and disulfide bonds enabled efficient self-healing behavior. Moreover, the hydrogel proved to be highly effective as a flexible sensor for monitoring motion. It demonstrated stable changes in conductivity under mechanical deformation, making it suitable for applications in wearable electronics. The hydrogel also exhibited specific degradation behavior in acidic and oxidative environments, where disulfide bonds and boronic ester linkages were selectively cleaved, leading to controlled degradation of the material. Additionally, the hydrogels were shown to be cytocompatible and enable pH-dependent release of incorporated doxorubicin (DOX), with significantly higher release rates observed at lower pH, with an increase of total amount of DOX release from ~20% to ~70% when decreasing the pH from 7.4 to 5.1. These properties make the hydrogel promising from the point of view of biomedical applications. Altogether, we introduced a dynamic hydrogel based on dual dynamic covalent bond crosslinking as promising approach for development of multifaceted smart materials.</p