Dane Badawcze UW University of Warsaw
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AI Readiness Scale – survey questionnaire
No full textThis file contains the full version of the survey questionnaire used to assess researchers’ readiness to use artificial intelligence (AI) tools in various phases of academic work. The questionnaire includes items related to editorial, conceptual, analytical, and interpretative tasks, as well as contextual and institutional conditions influencing AI adoption in research practices.File format: DOCX (Microsoft Word)Language: English and PolishUse:Self-administered survey (online or paper-based)For research and educational purposesAnonymity and ethics:The questionnaire does not collect personal identifiers. It was designed to ensure respondent anonymity while maintaining methodological transparency.Plik zawiera pełną wersję kwestionariusza ankiety służącej do oceny gotowości badaczy do wykorzystywania narzędzi sztucznej inteligencji (AI) na różnych etapach pracy naukowej. Kwestionariusz obejmuje stwierdzenia dotyczące zadań redakcyjnych, koncepcyjnych, analitycznych i interpretacyjnych, a także kontekstu sytuacyjnego i instytucjonalnego wpływającego na wykorzystanie AI w działalności badawczej.Format pliku: DOCX (Microsoft Word)Język: angielski i polskiZastosowanie:Ankieta do samodzielnego wypełnienia (online lub papierowa)Do zastosowania w celach badawczych i edukacyjnychAnonimowość i etyka:Kwestionariusz nie zawiera danych pozwalających na identyfikację osób badanych. Jego struktura została zaprojektowana z uwzględnieniem anonimowości respondentów przy zachowaniu przejrzystości metodologicznej.</p
Advancing dynamic quantum crystallography: enhanced models for accurate structures and thermodynamic properties - cif files
No full textCIF files for 5 molecules: alanine, xylitol, naphthalene and glycine polymorphs are stored here. In which file different models can be found. All of them were used to present the effectiveness of AAM_NoMoRe model and highlighting its the influence on the H-atom positions and shape of their ADPs, which are comparable with neutron data and described in manuscript Advancing dynamic quantum crystallography: enhanced models for accurate structures and thermodynamic properties. IUCrJ. 2025, 12, 123-136.Cif files can be opened by any text editor and/or by any version of crystallographic software, e.g. Mercury, Vesta.</p
Framing the war. Onet.pl and Wp.pl's coverage of the war in Ukraine in the first year of the conflict
No full textProjekt badawczy Ramowanie wojny. Sposób relacjonowania przez Onet.pl i Wp.pl wojny w Ukrainie w pierwszym roku konfliktu był badaniem jakościowym treści opublikowanych w polskich portalach informacyjnych w okresie luty 2022-luty 2023. Badanie przeprowadzone zostało w okresie od 1 września 2024 do lutego 2025. Projekt realizowany był bez wsparcia finansowego instytucji zewnętrznych, a przygotowany w ramach stosunku pracy pracowników Uniwersytetu Warszawskiego. Uzyskano dofinansowanie tłumaczenia artykułów naukowych na język angielski ze środków Uniwersytetu Warszawskiego w wysokości 6 tys. zł. w 2025 roku. Projektem kierowały i wykonawcami były Marta Jas-Koziarkiewicz i Ewa Stasiak-Jazukiewicz.Celem projektu było zidentyfikowanie ram interpretacyjnych, użytych w materiałach dziennikarskich w materiałach Onet.pl i Wp.pl. Realizacja tak wyznaczonego celu była możliwa dzięki uzyskaniu odpowiedzi na następujące pytania badawcze:- Jakie ramy interpretacyjne wykorzystywane były w materiałach publikowanych w analizowanych portalach?,- Jak często posługiwano się poszczególnymi ramami w materiałach publikowanych w analizowanych portalach?Cel badań oraz główne pytania badawcze zdeterminowały wybór metody badawczej - postawę metodologiczną artykułu stanowi analiza ramowa (framing analysis). Analizowano ramy zawarte w przekazach medialnych (media frames). W badaniu do wstępnej selekcji danych wykorzystano kwestionariusz kategorii ram opracowany na podstawie istniejących typologii ram tematycznych Holli A. Semetko oraz Patti M. Valkenburg: konfliktu (K), odpowiedzialności (O), konsekwencji ekonomicznych (E), moralną (M) i ludzkich spraw (L). W każdym z tekstów identyfikowano wszystkie występujące ramy. Kwalifikacji dokonywano na podstawie obecności treści przyporządkowanych do poszczególnych ram.Korpus badawczy artykułu stanowią materiały dziennikarskie zamieszczone w serwisach ogólnoinformacyjnych dwóch ogólnokrajowych portalach internetowych: Onet (wiadomości.onet.pl.) i Wirtualna Polska (wiadomości.wp.pl). Analizie poddano wszystkie materiały jako główny temat wojnę w Ukrainie.Jednostką analizy były materiał dziennikarski. Wszystkie pochodziły z 14 dni, które wybrano na podstawie próby losowej, warstwowej. Ich selekcji dokonano z wykorzystaniem koncepcji tygodnia komponowanego, która zakłada losowy wybór poszczególnych dni tygodnia ze wszystkich zidentyfikowanych w badanym okresie. Losowanie przeprowadzono w pierwszym roku konfliktu zbrojnego, tj. od 24 lutego 2022 roku do 23 lutego 2023 roku. Za pomocą programu Excel dla każdego dnia tygodnia (poniedziałek, wtorek itd.) wylosowano numer tygodnia roku, przy czym każdy tydzień mógł być brany pod uwagę tylko raz. Ponieważ pierwszy dzień konfliktu zbrojnego nie znalazł się w próbie postanowiono, że materiały dziennikarskie z 24 lutego 2022 zostaną dodatkowo poddane analizie.Analizie poddano pochodzące z 15 dni wszystkie materiały dziennikarskie (próba pełna), traktujące o konflikcie zbrojnym pomiędzy Rosją a Ukrainą, jego przyczynach, konsekwencjach i reakcji, jakie wywołał na arenie międzynarodowej. Pominięto te, które dotyczyły polityki wewnętrznej w państwach trzecich (w tym w Polsce), o ile nie odnosiły się one do działań podejmowanych na rzecz pojawiających się uchodźców z Ukrainy. Materiały dziennikarskie pobrano ze stron archiwalnych: https://wiadomosci.wp.pl/archive oraz https://wiadomosci.onet.pl/mapa-serwisu.WynikiDo ilościowej analizy zawartości zakwalifikowano 1.200 materiałów dziennikarskich, w tym 592 z Wirtualnej Polski i 608 z Onet-u. Analiza treści ujawniła obecność ram interpretacyjnych w 1.170 materiałach dziennikarskich, w tym w 563 z WP i w 607 z Onet-u. Najwięcej materiałów dziennikarskich o badanej tematyce oba portale informacyjne zamieściły pierwszego dnia wojny – Onet 174 a WP 133. W każdym przypadku kwalifikację do ramy interpretacyjnej poprzedzała pozytywna odpowiedź na co najmniej jedno z trzech wskazanych wcześniej pytań.Rama konfliktu okazała się najczęściej stosowaną. przy czym w Onecie sięgano po nią 261 razy a w WP znacznie częściej, bo 458 razy. Drugą chętnie wykorzystywaną ramą była rama ludzkich spraw. Onet używał jej 253 razy, zaledwie o kilka razy rzadziej niż ramy konfliktu. Natomiast w WP różnica między stosowaniami obu ram była bardziej wyraźna. Ramę ludzkich spraw zastosowano tam 120 razy.Analiza danych miała w większości charakter jakościowy. Skoncentrowano się w niej na analizie zakresu obecności ramy ludzkich spraw i ramy odpowiedzialności oraz moralności. W przypadku analizy sposobu wykorzystania ramy ludzkich spraw dokonano operacjonalizacji kategorii aktorów obecnych w tej ramie. Byli to: bohater wróg i ofiara.W ramie ludzkich spraw oba portale informacyjne pokazywały konkretne osoby, uwikłane w konflikt zbrojny. Z jednej strony był to wróg, Putin i jego zaplecze polityczne. Podejmowano wątek pobudek, jakimi kieruje się prezydent Federacji Rosyjskiej. Do kategorii wrogów zalicza się też bezwzględny i okrutny żołnierz rosyjski, źle wyposażony i niewyszkolony. Z drugiej strony prezentowano bohatera. Tak niewątpliwie przedstawiano prezydenta Ukrainy i innych ukraińskich polityków, na przykład burmistrza Kijowa. Bohaterem był żołnierz ukraiński z poświęceniem walczący o wolność swojej ojczyzny i Europy, także ratownicy medyczni, obrona cywilna, strażacy chroniący infrastrukturę i mieszkańców atakowanych ukraińskich miejscowości. Były też ofiary – wymordowani cywile w Irpieniu, ginący podczas bombardowań, pozbawieni pomocy humanitarnej mieszkańcy miejscowości odciętych od reszty kraju przez front i uchodźcy. Prezentowano i opozycjonistów rosyjskich, którzy uciekli przed reżimem Putina, dziennikarzy, literatów, intelektualistów. Nie zabrakło relacji o losach zwykłych Rosjan, matek żołnierzy wysłanych na front, mężczyzn ukrywających się przed powołaniem do wojska.Zdaniem twórców teorii ramowanie pełni trzy funkcje. Po pierwsze, diagnostyczną – polegająca na zdefiniowaniu problemu, ustaleniu jego przyczyn i atrybucji, czyli przypisaniu odpowiedzialności. Po drugie, prognostyczną, która wystawia ocenę moralną i proponuje rozwiązanie problemu. Po trzecie, motywacyjną – nakłaniającą do działania. Poszczególne ramy mogą pełnić wszystkie trzy funkcje albo żadnej. W niniejszym artykule nie analizowano efektów oddziaływania Onetu i WP. Dokonana analiza treści uprawnia jednak do konstatacji o potencjalnym pełnieniu przez badane materiały dziennikarskie wszystkich trzech funkcji.Pokazując aktorów konfliktu, w tym: idealizując postawę żołnierzy ukraińskich, okrucieństwo wroga, niewinność ofiar, los uchodźców, mobilizowały do wyrażania solidarności. Funkcję motywacyjną pełniły przykłady działań wolontariuszy z Polski i zagranicy – ratowników medycznych, kucharzy, kierowców – niosących pomoc humanitarną i na terenie objętej działaniami wojennymi Ukrainy i w Polsce.The research project Framing the War. The way Onet.pl and Wp.pl report on the war in Ukraine in the first year of the conflict was a qualitative study of the content published in Polish news portals in the period February 2022-February 2023. The study was conducted between 1 September 2024 and February 2025. The project was carried out without the financial support of external institutions, and prepared within the framework of the employment relationship of the employees of the University of Warsaw. Funding was obtained for the translation of scientific articles into English from the University of Warsaw funds in the amount of PLN 6,000. 2025. The project was managed and carried out by Marta Jas-Koziarkiewicz and Ewa Stasiak-Jazukiewicz.The aim of the project was to identify the interpretative frameworks used in journalistic materials on Onet.pl and Wp.pl. The realisation of such a goal was possible by obtaining answers to the following research questions: - What interpretative frameworks were used in materials published in the analysed portals?,- How often were particular frameworks used in materials published in the analysed portals?The aim of the research and the main research questions determined the choice of the research method - the methodological basis of the article is framing analysis. The frames contained in media messages (media frames) were analysed. The study used a framing category questionnaire developed on the basis of existing thematic framing typologies by Holli A. Semetko and Patti M. Valkenburg: conflict (K), responsibility (O), economic consequences (E), moral (M) and human affairs (L). In each text, all the frameworks present were identified. Qualifications were made on the basis of the presence of content assigned to each framework. The research corpus of the article consists of journalistic materials posted in the general information services of two national Internet portals: Onet (wiadomości.onet.pl.) and Wirtualna Polska (wiadomości.wp.pl). All materials were analysed with the war in Ukraine as the main topic.The unit of analysis was journalistic material. They all came from 14 days, which were selected on the basis of a random, stratified sample. Their selection was made using the concept of the composed week, which involves the random selection of individual days of the week from all those identified during the period under study. The randomisation was carried out in the first year of the armed conflict, i.e. from 24 February 2022 to 23 February 2023. As the first day of the armed conflict was not included in the sample, it was decided that journalistic material from 24 February 2022 would be analysed additionally.All journalistic material from 15 days (full sample) dealing with the armed conflict between Russia and Ukraine, its causes, consequences and reactions it provoked in the international arena was analysed. Those that dealt with domestic politics in third countries (including Poland) were omitted unless they referred to actions taken in support of emerging refugees from Ukraine. Journalistic material was taken from the archive websites: https://wiadomosci.wp.pl/archive and https://wiadomosci.onet.pl/mapa-serwisu.Results1,200 journalistic materials were qualified for quantitative content analysis, including 592 from Wirtualna Polska and 608 from Onet. Content analysis revealed the presence of an interpretative framework in 1,170 journalistic materials, including 563 from WP and 607 from Onet. The largest number of journalistic materials on the examined topics was posted by both news portals on the first day of the war - Onet 174 and WP 133. In each case, qualification for an interpretative frame was preceded by a positive answer to at least one of the three questions indicated earlier.The conflict frame turned out to be the most frequently used. with OneT using it 261 times and WP using it much more frequently, 458 times. The second most frequently used frame was the human affairs frame. Onet used it 253 times, only a few times less frequently than the conflict frame. At WP, on the other hand, the difference between the uses of the two frames was more pronounced. The human affairs frame was used there 120 times.The data analysis was mostly qualitative. It focused on analysing the extent to which the human affairs frame and the responsibility and morality frame were present. When analysing how the human affairs frame was used, the categories of actors present in the frame were operationalised. These were: the hero the enemy and the victim.In the frame of human affairs, both news portals showed specific people caught up in the armed conflict. On one side was the enemy, Putin and his political base. The motives of the President of the Russian Federation were taken up. The ruthless and cruel Russian soldier, ill-equipped and untrained, also fell into the category of enemy. On the other hand, a hero was presented. This is undoubtedly how the Ukrainian President and other Ukrainian politicians, such as the mayor of Kyiv, were portrayed. The hero was the Ukrainian soldier, fighting sacrificially for the freedom of his homeland and Europe, also the paramedics, civil defence, firefighters protecting the infrastructure and inhabitants of the Ukrainian towns under attack. There were also casualties - the murdered civilians in Irpin, those dying in bombing raids, residents of towns cut off from the rest of the country by the front and refugees deprived of humanitarian aid. Russian oppositionists who fled Putin's regime, journalists, writers, intellectuals were also presented. There was no shortage of accounts of the fate of ordinary Russians, mothers of soldiers sent to the front, men hiding from being drafted.According to the developers of the theory, framing has three functions. First, diagnostic - which involves defining the problem, determining its causes and attributing responsibility. Second, prognostic - making a moral judgement and proposing a solution to the problem. Third, motivational - prompting action. A particular framework may perform all three functions or none. This article did not analyse the effects of Onet and WP. However, the analysis of the content entitles us to conclude that the studied journalistic materials potentially perform all three functions.By showing the actors of the conflict, including: idealising the attitude of Ukrainian soldiers, the cruelty of the enemy, the innocence of the victims, the fate of the refugees, they mobilised people to express solidarity. The motivational function was fulfilled by examples of the actions of volunteers from Poland and abroad - medical rescuers, cooks, drivers - bringing humanitarian aid and on the territory of Ukraine and Poland covered by warfare.</p
Lipid membrane systems and parameter and topology files used in molecular dynamics simulations concerning redistribution of cholesterol between lateral domains.
No full textDataset for publication: "Dehydration of lipid membrane drives redistribution of cholesterol between lateral domains".Zip file contains folders (separate folders for systems of different lipid composition, eg. DRPC_CHOL for membrane composed of DRPC and CHOL molecules and PSM_CHOL for membrane composed of PSM and CHOL molecules) in which input files for molecular dynamics simulations of considered lipid systems can be found. In folders there are files that are needed to reproduce molecular dynamics simulations described in the related publication:files with simulated system structure (.gro file) - containing water and lipid membranefiles with molecular dynamics parameters (*mdp files) necessary to conduct MD simulations with a specifically curated parametersfiles containing information about topology of the simulated system in specific, chosen force field (toppar/ folder)index file (*ndx) with indexes of the atoms in the simulated systemsREADME file - with commands needed for execution of MD simulationsAll files can be opened using a text editor.</p
Efficient inference of quantum system parameters by approximate Bayesian computation - ABC libraries
No full textTrajectory libraries used in the cited publication to perform approximate Bayesian computation (ABC). With this library, ABC can be used to determine the posterior for the physical systems described in the publication for any given trajectory. As such, this database can be used to reproduce similar results as those presented in the manuscript, or as a library for performing quantum inference upon a new trajectory created by the reader. Information on the library's structure can be found in the readme file.</p
Data on the wolf road mortality in Poland, 2003-2023
No full textWe gathered information on wolves that were struck by vehicles on roads in Poland from 2003 to 2023, primarily individuals who were killed, but also those (several individuals) seriously wounded that would have died without the intensive help of veterinarians provided in the rehabilitation centers. Data were collected according to the protocol developed by the authors, which included a form to be completed and a checklist for detailed photo documentation. Reports have been provided by the staff of State Forests, officers of regional directorates for environmental protection, the Police, the regional branches of the General Directorates of National Roads and Motorways, Regional Veterinarian Inspections, the staff of companies removing carcasses of animals from roads for utilization, as well as car drivers who found dead wolves on roads. The photo documentation was sent to us to confirm the species recognition and estimate the individual's age based on the teeth wear. The provided reports contained information on the date and cause of death, the individual's sex, the geographic coordinates of the death site, and the road number and section. Breeding females were recognized based on the evidence of lactation, pregnancy, and nipple length. Reports were verified by the authors and co-workers in the field whenever possible. In cases when doubts appeared, the cause of death was also verified during a necropsy performed by veterinarians or experienced wildlife biologists to exclude instances where wolves were illegally shot and dropped off on the road to simulate an accident. To ensure that as many cases of mortality as possible were registered, we also used an Internet search engine to obtain information on wolves killed and/or injured by cars. Altogether, we collected data on 447 wolves struck by vehicles from 2003 to 2023; however, the exact locations were known for 441 of these. In six cases, the wolves were found between two neighboring roads; therefore, it was impossible to determine the precise location of the accident. We were able to distinguish between adults and juveniles for 436 individuals and assess their exact age based on tooth wear for 362 individuals. Additionally, we obtained information on sex for 403 individuals. We assigned every killed wolf to the Carpathian, Baltic, or Central European wolf management units/subpopulation (see Linnell et al., 2008, for the justification of management units’ delimitation), taking into consideration the results of a study on the wolf genetic structure (Szewczyk et al., 2019, 2021). For all individuals with known exact locations (n = 442), we obtained the habitat type (forest, watercourse, open land, or urbanized area) adjacent to the accident site and the average vehicle traffic on the corresponding section of the road. In Poland, traffic data are measured every five years and are publicly available on the Polish General Directorate for National Roads and Motorways website (https://www.gov.pl/web/gddkia/generalny-pomiar-ruchu).The dataset contains the following columns:Species: common name of the grey wolf Canis lupus, i.e. wolfN: number of individuals (every entry is for single individual)Age_category: pup (1-12 months-year-old); adult (≥1 year-old)Sex: male, femaleBreeder: indicates females with visible singns of pregnancy (presence of fetuses) or lactation (extended nipples)Age: for pups age is given in months, for adults age is given in yearsDate: date in format DD.MM.YYYYLongitude: longitude - a geographical coordinate in format 00.00000Latitude: latitude - a geographical coordinate in format 00.00000Population: name of the wolf population, i.e. Baltic, Central European, CarpathianRoad_Category: general category of the road, i.e. forest_road, lokal_road, regional_road, national_road, express_road, motorway</p
Elucidating the nature of the interactions of oseltamivir with the 2D model of influenza A virus lipid envelope
No full textThis study investigates the molecular interactions of the antiviral agent oseltamivir phosphate (OSL) with a two-dimensional (2D) Langmuir monolayer model of the influenza A (AH1N1) virus lipid envelope. The model consists of a ternary lipid mixture (DOPE:DMPS:SM 50:35:15), prepared at the air-water interface and characterized using surface-sensitive techniques including Brewster angle microscopy (BAM), grazing incidence X-ray diffraction (GIXD), and polarization modulation infrared reflection absorption spectroscopy (PM-IRRAS). The dataset contains files (text, csv and tiff files) showing the experimental results included in the publication. Please consult the readme.txt file for additional information and a more detailed description of each csv and tiff file.</p
Free-standing lipidic mesophase film hosting Gramicidin A – membrane ion transport study
No full textThe study presents a free-standing lipid mesophase film within an H-cell as an effective model for electrochemical investigations of ion transport through lipid membranes. This setup, which mimics a biological membrane with aqueous solutions on both sides, was used to examine the incorporation of gramicidin A, a potassium channel peptide, into a lipidic cubic phase membrane. The results show that gramicidin enhances the conductivity of the lipid structure by connecting aqueous channels, facilitating ion transport. Additionally, the study reveals that the divalent ion Ca2+ inhibits gramicidin's ion channel function. This lipidic platform is proposed as a valuable tool for studying ion-transport proteins and their modulators.In the described repository, we have deposited files (mainly text files) that present representative results of the experiments shown in the publication. A more detailed description of each file can be found in the readme.txt file. The set includes characterization of the mesophases and electrochemical experiments based on electrochemical impedance spectroscopy.</p
Dynamics of PsaA and Representative Plastid Proteins in Selected Angiosperm Species During Etiolation and Greening
No full textThis dataset contains results from experiments on plastid protein composition, plastid complexes, and gene expression comparing several plant species (Arabidopsis thaliana, Phaseolus coccineus, Pisum sativum, Avena sativa) during a 10-day etiolation process at selected time points and under reference greening and illumination conditions.File name: species_western_blot.zip – compressed archive containing Western blot scans (.tif, .png) of etioplast and chloroplast proteins (PsaA, PsaB, Alb3, Ycf4, Lhca2) in samples of Arabidopsis thaliana, Phaseolus coccineus, Pisum sativum, and Avena sativa collected after 10 days of etiolation – 0d, and 20 days of long day conditions (16 h light/8 h darkness) – 20dL. Additional Coomassie Briliant Blue R-250 (CBB)-stained gels represent total protein loading controls. The archive includes a README.txt file with lane annotations and specifications. File naming convention: Species_Protein_ReplicateNumber.File name: Avena_western_blot.zip – compressed archive containing Western blot scans (.tif, .png) of etioplast and chloroplast proteins (PsaA, PsaB, PsaC, PsaD, Lhca2) in samples of Avena sativa collected during 10 days of etiolation – (-10d – 0 days of etiolation, -7d - 3 days of etiolation, -5d – 5 days of etiolation, -3d - 7 days of etiolation, 0d - 10 days of etiolation), 3 hours of light illumination after 10 days od etiolation – 0d3hL, and 20 days of long day conditions (16 h light/8 h darkness) – 20dL. Additional Coomassie Briliant Blue R-250 (CBB)-stained gels represent total protein loading controls. The archive includes a README.txt file with lane annotations and specifications. File naming convention: Species_Protein_ReplicateNumber. Sample order on the membranes: Avena_sativa_-10d, Avena_sativa_-7d, Avena_sativa_-5d, Avena_sativa_-3d, Avena_sativa_0d, Avena_sativa_0d3hL, Avena_sativa_20dL/3, Avena_sativa_20dL.File name: Pisum_western_blot.zip– compressed archive containing Western blot scans (.tif, .png) of etioplast and chloroplast proteins (PsaA, PsaB, PsaC, PsaD, Lhca2) in samples of Pisum sativum collected during 10 days of etiolation – (-10d – 0 days of etiolation, -7d - 3 days of etiolation, -5d – 5 days of etiolation, -3d - 7 days of etiolation, 0d - 10 days of etiolation), 3 hours of light illumination after 10 days of etiolation – 0d3hL, and 20 days of long day conditions (16 h light/8 h darkness) – 20dL. Additional Coomassie Briliant Blue R-250 (CBB)-stained gels represent total protein loading controls. The archive includes a README.txt file with lane annotations and specifications. File naming convention: Species_Protein_ReplicateNumber. Sample order on the membranes: Pisum_sativum_-10d, Pisum_sativum_-7d, Pisum_sativum_-5d, Pisum_sativum_-3d, Pisum_sativum_0d, Pisum_sativum_0d3hL, Pisum_sativum_20dL/3, Pisum_sativum_20dL.File name: species_BN.zip – compressed archive containing Western blot scans (.tif, .png) of etioplast and chloroplast proteins within native protein complexes (PsaA) in samples of Pisum sativum and Avena sativa collected after 10 days of etiolation – 0d, and 20 days of long day conditions (16 h light/8 h darkness) – 20dL. Additional Blue Native PAGE gels represent total protein complexes resolving controls. The archive includes a README.txt file with lane annotations and specifications. File naming convention: Species_Protein_ BN_ReplicateNumber. Sample order on the membranes: Pisum_sativum_0d, Avena_sativa_0d, Pisum_sativum_20dL, Avena_sativa_20dL.File name: Pisum_BN_western_blot.zip – compressed archive containing Western blot scans (.tif, .png) of etioplast proteins within native protein complexes (PsaA, PsaB, FNR, POR, Chlorophyll synthase) in samples of Pisum sativum collected after 10 days of etiolation – 0d. Additional Blue Native PAGE gels represent total protein complexes resolving controls. The archive includes a README.txt file with lane annotations and specifications. File naming convention: Species_Protein_ BN_ReplicateNumber.File name: species_RT-qPCR.zip – . archive containing raw RT-qPCR (.txt format) results for plastid genes (psaA, psaB, atpB, Lhca2) and reference genes (TUBB, PP2A, HNR, ARF) from Pisum sativum and Avena sativa samples during 10 days of etiolation – (-10d – 0 days of etiolation, -7d - 3 days of etiolation, -5d – 5 days of etiolation, -3d - 7 days of etiolation, 0d - 10 days of etiolation) and 20 days of long day conditions (16 h light/8 h darkness) – 20dL. Columns: well – position on the qPCR plate, sample ID, sample type, target gene, target type (reference vs. target of interest), dye, Cq value. Additional columns represent raw fluorescence values across PCR cycles. The archive includes a README.txt file with annotations and specifications. File naming convention: OrderNumberOfSeries_Plate_RT-qPCR_ Replicate.File name: Avena_77K.tab – File (.csv format) contains raw data for low-temperature (77 K) chlorophyll or protochlorophyllide fluorescence emission spectra of Avena sativa first leaf tissue samples collected during 10 days of etiolation – (-10d – 0 days of etiolation, -7d - 3 days of etiolation, -5d – 5 days of etiolation, -3d - 7 days of etiolation, 0d - 10 days of etiolation), 3 hours of light illumination after 10 days of etiolation – 0d3hL and baseline in manner: OrderNumber_species_ ReplicateNumber | OrderNumber_baseline.File name: Pisum_77K.tab – File (.csv format) contains raw data for low-temperature (77 K) chlorophyll or protochlorophyllide fluorescence emission spectra of Pisum sativum first leaf tissue samples collected during 10 days of etiolation – (-10d – 0 days of etiolation, -7d - 3 days of etiolation, -5d – 5 days of etiolation, -3d - 7 days of etiolation, 0d - 10 days of etiolation), 3 hours of light illumination after 10 days of etiolation – 0d3hL and baseline in manner: OrderNumber_species_ ReplicateNumber | OrderNumber_baseline.File name: Pisum_densitometry.tab – File (.csv format) contains densitometric analysis of immunodetection of etioplast and chloroplast proteins (PsaA, PsaB, PsaC, PsaD, Lhca2) in samples of Pisum sativum collected during 10 days of etiolation – (-10d – 0 days of etiolation, -7d - 3 days of etiolation, -5d – 5 days of etiolation, -3d - 7 days of etiolation, 0d - 10 days of etiolation), 3 hours of light illumination after 10 days of etiolation – 0d3hL, and 20 days of long day conditions (16 h light/8 h darkness) – 20dL. Column A – lane_no, column B – sample_description (naming convention: species_GrowthStage; columns C-Q – Adjusted Volume Intensity data with naming convention: Protein_ ReplicateNumber.File name: Avena_ densitometry.tab – File (.csv format) contains densitometric analysis of immunodetection of etioplast and chloroplast proteins (PsaA, PsaB, PsaC, PsaD, Lhca2) in samples of Avena sativa collected during 10 days of etiolation – (-10d – 0 days of etiolation, -7d - 3 days of etiolation, -5d – 5 days of etiolation, -3d - 7 days of etiolation, 0d - 10 days of etiolation), 3 hours of light illumination after 10 days of etiolation – 0d3hL, and 20 days of long day conditions (16 h light/8 h darkness) – 20dL. Column A – lane_no, column B – sample_description (naming convention: species_GrowthStage; columns C-Q – Adjusted Volume Intensity data with naming convention: Protein_ ReplicateNumber.File name: species_densitometry.tab – File (.csv format) contains densitometric analysis of immunodetection of etioplast and chloroplast proteins (PsaA, PsaB, Ycf4, Alb3, Lhca2) in samples of Arabidopsis thaliana, Phaseolus coccineus, Pisum sativum, and Avena sativa collected after 10 days of etiolation – 0d, and 20 days of long day conditions (16 h light/8 h darkness) – 20dL. Column A – lane_no, column B – sample_description (naming convention: species_GrowthStage; columns C-Q – Adjusted Volume Intensity data wth naming convention: Protein_ ReplicateNumber.</p
Genetic insights into multiple sclerosis: exploring mitochondrial DNA and nuclear POLG gene variation in Polish patients
No full textBrief project description:Background:Mitochondrial dysfunction is increasingly implicated in the pathogenesis of multiple sclerosis (MS), yet its precise role remains unclear. This study aimed to evaluate the contribution of mitochondrial DNA (mtDNA) variation and POLG mutations to disease susceptibility and course in the Polish relapsing–remitting MS (RRMS) population.Methods:Whole mtDNA was sequenced in 100 RRMS patients and 212 healthy controls using NGS. We assessed the presence of pathogenic variants, distribution of haplogroups, rare variants, and heteroplasmy. Absolute mtDNA copy number was measured by real-time PCR. Additionally, patient group was screened for four common POLG mutations (p.Gly268Ala, p.Ala467Thr, p.Pro587Leu, and p.Trp748Ser).Results:No pathogenic variants were detected in mtDNA or the POLG gene. However, several mtDNA variants were associated with relapse occurrence, disability level, and age at symptom onset. Certain mitochondrial variants appeared protective in female patients. No significant associations were found for mtDNA haplogroups, copy number, heteroplasmy, or rare variants with MS risk or progression.Conclusions:Although mtDNA alterations are unlikely to be a primary causative factor of MS, they may influence disease expression and progression in the Polish population.The dataset consists of the following zip archives and files:_FASTQ_.zip – raw sequencing data as FASTQ files (*.fastq.gz) from next-generation sequencing (NGS) of mtDNA from persons with multiple sclerosis (MS_FASTQ_a/b/c) and control individuals (Control_group_A_FASTQ_a/b/c and Control_group_IMDIK_FASTQ_a/b). The files can be opened using CLC Genomics Workbench software, any other similar bioinformatics software, or open-source bioinformatics tools for NGS data analysis._SNV.xlsx – lists of mtDNA variants (SNVs and indels) identified from the bioinformatics analysis of mtDNA NGS data. The files can be opened with MS Excel or any other spreadsheet software.File naming instructions:FASTQ files: e.g. 16-SM001_S43_L001_R1_001.fastq.gz, 16-K1-56_S34_L001_R1_001.fastq.gz, AB-K6_S85_L001_R1_001.fastq.gz16- or AB- – LR-PCR amplicon 16 kb or AB (for details, please see https://doi.org/10.1016/j.exer.2018.10.004)SM001_ or K1-56_ or K6_ – MS subject ID or control group A subject ID or control group IMDiK subject IDS43_ – 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.</ul