Dane Badawcze UW University of Warsaw
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Heteroplasmy selection and intermolecular mtDNA recombination in humans - analysis in a cell model
No full textBrief project description:As part of this project, human cybrid cell lines carrying a mixture of neutral mtDNA haplotypes differing in multiple nucleotide positions but not harboring pathogenic variants were generated. The aim of this study was to investigate the presence of heteroplasmy selection and intermolecular mtDNA recombination in humans in vitro.To generate cybrids containing a mixture of two mtDNA haplotypes, human 143B.TK- cells devoid of mtDNA (ρ0) were fused with enucleated cells serving as mitochondrial donors (cytoplasts). Six combinations of four mtDNA haplotypes (A, B, C, and D) were used, varying in genetic distance measured by the number of nucleotide differences. The nucleotide sequences of the studied mtDNA haplotypes were deposited in the GenBank database under accession numbers PQ468425 (A), PQ468426 (B), PQ468427 (C), and PQ468428 (D).Individual cell clones were screened for the presence and level of mtDNA heteroplasmy. mtDNA heteroplasmy was monitored over successive passages during cell culture to assess the occurrence of selection, its direction, and rate. Preliminary assessment was performed using Sanger sequencing of a selected mtDNA region (a fragment of the non-coding control region characterized by the highest variability). Detailed analysis of heteroplasmic cybrid lines was subsequently performed using high-throughput whole mtDNA sequencing using a method developed and implemented in our group's research on the MiSeq platform (Illumina) (https://doi.org/10.1016/j.exer.2018.10.004). The occurrence of intermolecular recombination in mtDNA in human cell culture in vitro was assessed by direct sequencing of native mtDNA molecules using Nanopore sequencing technology.The dataset consists of the following zip archives:Sanger_data.zip – DNA traces/chromatograms from Sanger sequencing (*.ab1) of selected mtDNA region for individual cybrid cell clones at different passages. The files can be opened using Sequencher software or any other similar bioinformatics software for Sanger data analysis.Illumina_FASTQ_files.zip – raw sequencing data as FASTQ files (*.fastq.gz) from next-generation sequencing (NGS) of mtDNA from heteroplasmic cybrid cell lines at different cell passage points. The files can be opened using CLC Genomics Workbench software, any other similar bioinformatics software, or open-source bioinformatics tools for NGS data analysis.Illumina_BAM_files.zip – mapped reads as BAM files and their corresponding index files (*.bam and *.bam.bai) generated from the bioinformatics analysis and mapping of mtDNA NGS data to the human mtDNA reference genome, rCRS (NC_012920). The files can be opened using CLC Genomics Workbench software, any other similar bioinformatics software, or open-source bioinformatics tools for NGS data analysis.Illumina_variant_lists.zip – Lists of mtDNA variants (SNVs and indels) identified from the bioinformatics analysis of mtDNA NGS data (*.xlsx). The files can be opened with MS Excel or any other spreadsheet software.ONT_data.zip – raw sequencing data as FASTQ files (*.fastq.gz) of long reads from direct sequencing of native mtDNA molecules using Oxford Nanopore Technology (ONT). The files can be opened using CLC Genomics Workbench software, any other similar bioinformatics software, or open-source bioinformatics tools for NGS/ONT data analysis.File naming instructions:Sanger files: e.g. F1_A_B_6_P0_M13_uni_21.ab1F1_ – Fusion experiment number (1–3)A_B_ – mtDNA haplotypes (A–D) = cybrid cell line6_ – Clone numberA3_ – Daughter line number (A3, E4, or F6)P0_ – Passage numberM13_uni_21 – Universal sequencing primer for Sanger sequencingIllumina files: e.g. 16_A_C_5_A3_P3_S17_L001_R1_001.fastq.gz, 16_A_C_5_A3_P3_S17_L001.bam, 16_A_C_5_A3_P3_S17_L001.bam.bai, 16_A_C_5_A3_P3_S17_L001.xlsx16_ – LR-PCR amplicon 16 kb or AB (for details, please see https://doi.org/10.1016/j.exer.2018.10.004)A_C_ – mtDNA haplotypes (A–D) = cybrid cell line5_ – Clone numberA3_ – Daughter line number (A3, E4, or F6)P3_ – Passage numberS17_ – Sample number based on the order of samples in the sample sheetL001_ – Flow cell lane numberR1_ – Read number in paired-end sequencing run (1 or 2)001 – Constant segment in FASTQ files.Nanopore files: e.g. mtDNA_A_C_5_A3_ont_2kb_q10.fastq.gzmtDNA_ – Mitochondrial DNAA_C_ – mtDNA haplotypes (A–D) = cybrid cell line5_ – Clone numberA3_ – Daughter line number (A3, E4, or F6)ont_ – Oxford Nanopore Technology2kb_ – Data were filtered to include reads longer than 2 kbq10_ – Data were filtered to include reads with a quality score greater than 10.</ul
Research data for article 'Ferroelectric nematogens containing a methylthio group'
No full textThe synthesis and characterization of nematogens containing a terminal methylthio group is reported. The compounds are based on RM734 and differ in the number and position of fluorine substituents, and in the position of the lateral methoxy substituent. The phases are assigned based on observation of characteristic optical textures, measurements of dielectric properties, switching behaviour and optical birefringence, and the identification is confirmed with X-ray diffraction.The stored dataset includes: (i) manuscript of the publication in pdf format, (ii) results of X-ray diffraction experiments - gfrm files contain 2D detector images (native Bruker format, can be opened with gadds software), raw and txt files contained data reduced to 1D (binary Bruker and ASCI formats, respectively), (iii) txt files (ASCI) with results of electric polarization measurements performed in function of temperature, (iv) images (jpg) of optical textures of liquid crystalline phases taken with polarized light optical microscope, and (v) a txt file with numerical data (ASCI) for complex permittivity measured vs. frequency and temperature.</p
Influence of Pd precursor and reaction conditions on electrochemical properties of AB5-type alloy decorated with Pd nanoparticles
No full textThis dataset contains the results of studies on AB5-type hydrogen absorbing alloy decorated with Pd nanoparticles obtained from various Pd precursors. Files include SEM images, Raman spectra, XRD patterns and electrochemical measurements in 6 M KOH: cyclic voltammetry (CV), chronoamperometry (CA) and chronopotentiometry (CP).Please consult the Readme.txt file for additional information. </p
Content of the wolf-dog hybrid scats from Poland
No full textThe dataset contains a description of wolf-dog hybrid scat content used to assess the diet composition. Scats were collected in two study areas (Radomsko and Szubin). Scats were placed in paper envelopes and then dried in laboratory dryers for five days at 70°C. Afterward, scats were soaked and washed through a fine 0.5 mm mesh sieve. The dried remaining material was weighed. The food items were identified based on the presence of hair, fragments of bones, hooves, claws, teeth, and feathers, using specialist keys, as well as comparison with our reference material. The dataset contains the following columns:Species - wolf-dog hybridsRegion - name of the study areaDate - date when the sample was collectedMass_g - total mass of the washed scat sample in gramssmall_rodents - mass of small rodent remains within scats in gramshare - mass of European hare (Lepus europaeus) remains within scats in gramsbeaver - mass of Eurasian beaver (Castor fiber) remains within scats in gramsfallow_deer - mass of fallow deer (Dama dama) remains within scats in gramsmoose - mass of moose (Alces alces) remains within scats in gramswild_boar - mass of wild boar (Sus scrofa) remains within scats in gramsred_deer - mass of red deer (Cervus elaphus) remains within scats in gramsroe_deer - mass of roe deer (Capreolus capreolus) remains within scats in gramsCervidae_undetermined - mass of unidentified cervid remains within scats in gramscat - mass of domestic cat (Felis catus) remains within scats in gramsdog - mass of domestic dog (Canis familiaris) remains within scats in gramsbirds - mass of bird (Aves) remains within scats in gramsartificial - mass of artificial items (plastic, metal) within scats in gramsplants - mass of plant remains within scats in grams+ denotes mass <0.05 g</p
Public goods through private eyes. Exploring citizens' attitudes to public goods and the state in Central Eastern Europe
No full text“Public Goods through Private Eyes” Project. General information“Public Goods through Private Eyes” is a full-scale comparative public opinion survey carried out in 2013 and 2014 as a result of the 2009 ERC funding of 1.73 million Euro awarded to dr hab. Natalia Letki (project PI, University of Warsaw). The aim of the project was to collect high-quality survey data on attitudes and behaviour towards public goods and the state in 14 post-communist countries:Bulgaria, Croatia, Czech Republic, Estonia, Hungary, Latvia, Lithuania, Moldova, Poland, Romania, Serbia, Slovakia, Slovenia and Ukraine.PGPE QuestionnaireThe questionnaire was developed by the PGPE team with support from the Project’s Advisory Board: Rene Bekkers (VU University Amsterdam), Klarita Gërxhani (EUI), Erich Kirchler (University of Vienna), Stephan Muehlbacher (University of Vienna), Kristina Murphy (Griffith University), Pamela Paxton (The University of Texas at Austin) and Michael Wenzel (Flinders University). It contained 7 main modules:A. Local communityB. Social trust and social cohesionC. Personality and commitmentD. Public goodsE. Institutional qualityF. Tax behaviour and law complianceG. Green behaviourH. Political participationI. Socio-economic background.The survey also contains 4 vignettes – fully randomized survey-embedded experiments.In each country respondents were clustered in 75 stratified sampling points (with the exception of Ukraine, where Russian annexation of Crimea interfered with fieldwork and only data in 74 sampling points were collected). The sampling points were designed to cover a spatially relatable area that respondents could refer to when contextualizing their survey responses. For details, see PGPE document on sampling procedure.ResultThe result of the project is a multi-level multi-component survey, comprising of:1. The main survey of 22039 respondents nested in 1049 SPs in 14 countries.2. The survey of interviewers (each interviewer had to complete the survey prior to commencing work for the project).3. Survey of ecological data for the PSU level in all countries.Surveys 2 and 3 can be linked to survey 1 to explore interviewer effects (survey 2) and contextual effects (survey 3). For confidentiality reasons, surveys 2 and 3 cannot be released.Sampling procedure was developed in cooperation with dr Matthias Ganninger, dr Sabine Haeder and dr Siegfried Gabler (GESIS Mannheim) (for details, see a document on PGPE sampling).Weights were prepared based on the ESS standards by Jan-Philipp Kolb (GESIS Mannheim). The following weight types are provided in the PGPE dataset: DWEIGHT (design weight), PSPWGHT (post-stratification weight), PWEIGHT (population weights) and PPSPWGHT (combination of post-stratication weights and population size weights).Main fieldwork was carried out by two companies and their subcontractors: in Poland it was carried out by CBOS, in all other countries - by IPSOS Strategic Marketing. PAPI and CAPI were used as data collection methods.QualityTo achieve as high a quality as possible the key following principles were applied:· Sampling was designed and carried out centrally, by the PGPE team in cooperation with sampling experts. · Pre-listing of address was verified centrally, by the PGPE team, on the basis of maps.· Questionnaire was translated following the ESS round 5 guidelines.· Questionnaire was tested qualitatively, and a quantitative pre-test on quota samples were carried in each country prior to the main survey.· Data was centrally checked and screened for inconsistencies and feedback was given to the fieldwork companies to be taken into account in the subsequent phases of fieldwork.· Post-survey control in most countries was carried out with the participation of the PGPE team members.Translation of the questionnaireTranslation guidelines were modeled after ESS round 5, with particular emphasis on keeping the equivalence of meaning and the symmetry and consistency of scales. Translation was carried out in three stages: i) questionnaire was translated by two independently working, experienced translators per language; ii) two versions were adjudicated by an experienced adjudicator; iii) language versions used as minority questionnaires in other countries were harmonized by country coordinatorsQuestionnaire testingThe PGPE Questionnaire was tested in two stages. First, a Qualitative pre-test was performed in Polish by GFK Polonia in 3 waves of question testing in a studio with a venetian mirror. Second, a Quantitative pilot was performed by fieldwork companies on a representative quota sample of N=80 in each country. The aims of both qualitative and quantitative pre-testing was to control the quality of translation and to shorten the questionnaire.</p
Precise determination of lead isotope ratios by MCICP- MS without matrix separation exemplified by unique samples of diverse origin and history
No full textAll data were obtained using MC-ICP-MS (Multi-Collector Inductively Coupled Plasma Mass Spectrometry). Measurements were performed with a Nu Instruments Plasma 3 mass spectrometer. The sample introduction system consisted of a Cetac Aridus 3 desolvating nebulizer, operated at a flow rate of 50 or 100 μL/min.The analyzed solutions included isotopic standard solutions of NIST SRM 981 with increasing concentrations of matrix elements (mainly Cu and Sn), as well as archaeological bronze samples with known Pb isotopic compositions reported in the literature.Measurements were conducted using two approaches: the internal standard method, in which samples were spiked with thallium standard solution (NIST SRM 997), and the ORM (Optimised Regression Model) method, where the analytes were individual lead isotope pairs, and the calibrator was a pair of thallium isotopes (NIST SRM 997).The file name corresponds to the name of the analyzed standard or sample. If an additional note in the format “XX ppb” appears in the name, it indicates the concentration of the analyte expressed in ng/mg. This makes it easy to distinguish files with the same base name but different applied concentrations (e.g., “nist981 20 ppb” vs. “nist981” – in the first case, it is a measurement of the NIST981 standard at a concentration of 20 ng/mg, while in the second, it is an analysis of the standard without an additional concentration note).</p
Palaeoparositological and bioarchaeological data from Lubelska 72A Street, Chełm
No full text[ENG:]This dataset comprises three interlinked tables containing both paleoparasitological and osteological data from the Early Modern Period cemetery located at Lubelska 72A Street in Chełm, Poland.Osteological_data_list: This table lists the graves from which soil samples were analyzed and provides information on the individuals buried in them, including age and sex. It also contains the raw osteological data used for sex determination. The osteological data were collected during the analysis of human remains carried out at the Faculty of Archaeology, University of Warsaw, Poland.Paleoparasitological_data_list: This table includes a list of graves with corresponding laboratory IDs for the analyzed soil samples. It provides detailed records of the parasite taxa identified in the samples, along with the total number of eggs discovered. These data were obtained through paleoparasitological analysis of soil samples collected from human bones prior to osteological examination. The paleoparasitological analyses were conducted at the Chrono-environnement Laboratory, Université Marie et Louis Pasteur, Besançon, France.Paleoparasitological_control_samples_data_list: This table lists graves for which control soil samples were analyzed, including results from samples collected via soil drilling. This dataset is the first large-scale collection of paleoparasitological data from the territory of Poland. Its uniqueness lies not only in the scope and scale of the paleoparasitological information but also in the integration with osteological data. This combination allows for sorting and analysis of parasite occurrence in relation to different age and sex groups, offering new possibilities for demographic and epidemiological reconstructions of past populations.[PL:]Zbiór danych składa się z trzech powiązanych tabel zawierających dane paleoparazytologiczne, jak i osteologiczne, pochodzące z cmentarza z okresu nowożytnego przy ulicy Lubelskiej 72A w Chełmie (Polska).Osteological_data_list: Tabela zawiera listę grobów, z których pobrano próbki ziemi do analizy, a także informacje o pochowanych w nich osobnikach, w tym ich wiek i płeć. Zawiera również surowe dane osteologiczne na podstawie, których określona została płeć. Dane osteologiczne zostały zebrane podczas analizy szczątków ludzkich przeprowadzonej na Wydziale Archeologii Uniwersytetu Warszawskiego.Paleoparasitological_data_list: Tabela zawiera listę grobów wraz z odpowiadającymi im laboratoryjnymi identyfikatorami próbek ziemi. Zawiera szczegółowe dane dotyczące zidentyfikowanych taksonów pasożytów oraz całkowitą liczbę znalezionych jaj. Dane te uzyskano w wyniku analizy paleoparazytologicznej próbek ziemi pobranych z kości ludzkich przed przeprowadzeniem analizy osteologicznej. Analizy paleoparazytologiczne przeprowadzono w laboratorium Chrono-environnement, Université Marie et Louis Pasteur w Besançon (Francja).Paleoparasitological_control_samples_data_list: Tabela zawiera listę grobów, dla których przeanalizowano próbki kontrolne gleby, w tym wyniki próbek z odwiertów.Jest to pierwszy tak duży zbiór danych paleoparazytologicznych z obszaru Polski. Jego unikalność polega nie tylko na skali i zakresie informacji paleoparazytologicznych, ale również na ich powiązaniu z danymi osteologicznymi. Połączenie to umożliwia sortowanie i analizę występowania pasożytów w zależności od grupy wiekowej i płci, otwierając nowe możliwości rekonstrukcji demograficznych i epidemiologicznych dawnych populacji.</p
Experimental research data for the article: "Electroactive and thermoresponsive hybrid microgel on gold surface for electrochemically controlled release of active substance"
No full textThe collection comprises experimental research data obtained during studies on a thermoresponsive and electroactive hybrid microgel immobilized on an electrode surface, developed as a platform for the electrochemically induced release of positively charged model compounds. The physical and chemical properties of the microgel were thoroughly characterized using dynamic light scattering (DLS), transmission electron microscopy (TEM), energy-dispersive X-ray spectroscopy (EDS), and electrochemical techniques. The processes of microgel immobilization and dye incorporation were monitored using quartz crystal microbalance with dissipation monitoring (QCM-D). The electrochemical properties were examined using cyclic voltammetry. The electrochemically triggered release of dye from the microgel monolayer on the electrode surface was monitored by UV-Vis spectroscopy.The dataset consists of files described in attached readme.txt file.</p
Liczba ofiar zabójstw i samobójstw w garnizonie stołecznym 2015-2022
No full textZbiór zawiera uporządkowane dane pozyskane w trybie dostępu do informacji publicznej w ramach realizacji projektu “Dane o śmierci osób doświadczających bezdomności w Polsce” (Narodowe Centrum Nauki OPUS – 2022/45/B/HS6/00322). W tabelach znajdują się informacje o liczbie śmiertelnych ofiar zabójstw oraz samobójstw zebrane przez Komendę Stołeczną Policji (na terenie garnizonu stołecznego) w latach 2015-2022. KSP nie wyróżnia ofiar, które doświadczały bezdomności. Dane na temat liczby samobójstw podane są w podziale na lata, wiek i płeć zmarłej osoby, rodzaj samobójstwa oraz powiat w obrębie garnizonu stołecznego. Dane na temat liczby ofiar zabójstw również w podziale na rok, wiek i płeć zmarłej osoby oraz rodzaj zabójstwa.Pliki w formacie xlsx i ods.</p
When methods matter: solvent effects on pollinator responses to quantum‐dot–labelled pollen
No full textIn our study we ask whether, and how, insect pollinators respond to flowers whose anthers have been treated with quantum dots (QDs) and their solvent carrier. Using a common-garden experiment with genetically uniform Brassica napus, we compared pollinator visitation and foraging behaviour among flowers bearing QD–solvent treatments, solvent-only controls, and untreated controls. The experiment was conducted on 160 Brassica napus plants grown under controlled conditions. Five treatments were applied: (1) control, (2) pollen treated with hexane only, and (3–5) pollen labeled with QDs inducing radiation of three lengths: 530, 590, or 700 nm. Freshly opened flowers were labeled each morning by applying hexane or a QDs-hexane solution to anthers. Pollinator activity was recorded between 09:30 and 13:00 using digital cameras for 1.5 h per plant on two consecutive days, resulting in a total sampling effort of 480 h. In the laboratory, videos were reviewed for frequency of pollinator visits, time of the visit and the number of visited flowers. Visit frequency (visits/h) was computed as the number of visits per 90-min recording multiplied by 2/3. Visitors were assigned to morphogroups: honeybees (Apis mellifera), solitary bees, bumblebees (Bombus), hoverflies (Syrphidae), muscoid flies (Muscoidea), and butterflies.To assess whether hexane altered optical properties, reflectance of anthers (350–700 nm) was measured with a Jaz spectrometer for untreated and hexane-treated samples.Dataset descriptionThe dataset includes three primary data files covering pollinator visit frequency, visit duration, and the number of flowers visited. An additional file contains the results of spectral reflectance measurements of anthers."Frequency.csv" fileColumns:date – date in format YYYYMMDDplant – unique identifier of the planttreatment – experimental treatment (control, hexane, 530, 590, 700)hour – time when plant was recorded (HH:MM)n.of.flowers – number of flowers on the plantfreq.syrphidae – frequency of hoverfly (Syrphidae) visits (number of visits per hour)freq.beetle – frequency of beetle (Coleoptera) visits (number of visits per hour)freq.others – frequency of unidentified pollinator visits (number of visits per hour)freq.butterfly – frequency of butterfly visits (number of visits per hour)freq.fly – frequency of fly (Diptera) visits (number of visits per hour)freq.honeybee – frequency of honeybee (Apis mellifera) visits (number of visits per hour)freq.solitarybee – frequency of solitary bee visits (number of visits per hour)freq.bumblebee – frequency of bumblebee visits (number of visits per hour)freq.all – frequency of all pollinator visits (number of visits per hour)"Number_of_flowers_visited.csv" fileColumns:date – date in format YYYYMMDDplant – unique identifier of the planttreatment – experimental treatment (control, hexane, 530, 590, 700)hour – time when plant was recorded (HH:MM)n.of.flowers – number of flowers on the plantpollinator – identifier of the pollinator visiting the plantpollinator.morphogroup – pollinator’s assigned morphogroup ("0" means no visits to the plant)n.of.flowers.visited – number of flowers visited by the pollinator"Time_of_visit.csv" fileColumns:date – date in format YYYYMMDDplant – unique identifier of the planttreatment – experimental treatment (control, hexane, 530, 590, 700)hour – time when plant was recorded (HH:MM)n.of.flowers – number of flowers on the plantpollinator.id – identifier of the pollinator visiting the flowerpollinator.morphogroup – pollinator’s assigned morphogroup (0 means no visits to the flower)flower.visited – sequence number of the flower visited by the pollinator on a given planttime.of.visit – time of pollinator visit in seconds [s]"Hexane_test.csv" fileColumns:wavelength_nm – wavelength of light at which the measurement was taken by the spectrophotometer [nm]processed_signal – processed signal from the spectrophotometeranther – identifier of the anther measuredtype – sample treatment: "hexane" (anthers treated with hexane) or "control" (untreated anthers)</p