AndreaBozzo/ceres-open-data-index huggingface dataset:
Supplementary data: Effects of time pressure and regional background on the peak alignment and scaling of nuclear rises in national Standard German varieties

R scripts and data frames to accompany the research article of the same name. The three R files contain the scripts on which the analyses in Pöhnlein, J. & Kleber, F. (2025). Effects of time pressure and regional background on the peak alignment and scaling of nuclear rises in national Standard German varieties are based. The four txt files contain the corresponding input data that needs to be loaded in R prior to run the respective analysis script.

Organization: open.bydata
Raw Data and R Script for the Association between the Body Mass Index, Chronic Obstructive Pulmonary Disease and SUV of the Non-Tumorous Lung in the Pretreatment [18F]FDG-PET/CT of Patients with Lung Cancer

This research project aimed to elucidate the association between clinical variables and lung standardized uptake value (SUV) in pretherapeutic [18F]FDG-PET/CT scans of lung cancer patients. The study examined SUV measurements in non-tumorous regions of the lungs from 240 lung cancer patients, comparing SUVMEAN, SUVMAX, SUV95, and ratios of lung tissue to liver tissue and blood pool SUV with various patient characteristics and comorbidities. The analyzed clinical variables included sex, age, BMI, smoking status, pack years, COPD, tumor stage, previous lung operation, previous lung radiation, pleural effusion (PE), pericardial effusion (PCE), diabetes mellitus type II, asthma, coronary heart disease (CHD) and blood hemoglobin level (Hb). This comprehensive analysis aimed to shed light on the interplay between these clinical factors and lung SUV in lung cancer patients, potentially informing more tailored and effective management strategies for the disease. This dataset comprises essential components for replicating the research findings presented in my dissertation. Included are a README file offering an overview of the dataset's contents and usage instructions, a cohort file containing the dataset used in the study, and R scripts facilitating the reproduction of the analyses outlined in the dissertation. These resources aim to enhance transparency and reproducibility, enabling fellow researchers to validate and build upon the findings of the original research article: https://doi.org/10.3390/diagnostics14111139

Tags: 610-medical-sciences-and-medicine, bmi, copd, lung-cancer, medicine, petct, suv
Organization: open.bydata
Data Repository for Schwintek et al. in "Prebiotic Gas Flow Environment Enables Isothermal Nucleic Acid Replication"

"Data Repository Schwintek et al." contains raw image and plot data from main figures of the article "Prebiotic Gas Flow Environment Enables Isothermal Nucleic Acid Replication" by Dr. Philipp Josef Schwintek, Emre Eren, Dr. Christof Mast, and Prof. Dieter Braun. The preprint is available at https://elifesciences.org/reviewed-preprints/100152.

Tags: 530-physics, 540-chemistry-and-allied-sciences, evolution, fret-microscopy, nucleic-acid, origin-of-life, prebiotic, strand-separation
Organization: open.bydata
Data to: First report on presence of mitochondrial introns in freshwater sponges, and pseudogenic evidence of their loss

Mitochondrial introns have a patchy distribution in sponges lineages. Here, we report on the finding of a group-II-intron in Eunapius rarus (Demospongiae, Spongillidae), which constitutes the first report of a mitochondrial intron in freshwater sponges. Group-II-introns are self-splicing ribozymes, and are particularly rare among sponge mitochondrial genomes. The intron contains complete open reading frames (ORFs), including typical intron-encoded proteins (IEPs). Phylogenetic analysis reveals that the intron is more closely related to those found in brown algae, and distant from other sponge group-II-introns, indicating an acquisition of this intron independent from other sponges. Remarkably, the congeneric E. fragilis does not possess this intron in their mitochondrial genome. However we found pseudogenic copies of the E. rarus group-II-intron in the nuclear genome of E. fragilis, which indicates patterns of group-II-intron presence and their pseudogene transposition into the nuclear genomes in sponges for the first time. Our results show that a group-II-intron must have been present in the last common ancestor of both Eunapius mt genomes, and subsequently lost in E. fragilis, rather than independent acquisition. Consequently, our findings provide an explanation for the patchy distribution of introns in sponges as a result of frequent losses, besides multiple acquisitions.

Tags: 500-natural-sciences-and-mathematics, 550-earth-sciences, 590-zoological-sciences, eunapius, freshwater-sponges, group-ii-intron, mitochondrial-intron, numt, porifera
Organization: open.bydata
Supplementary data to the Article: Proteasomal Activity and Disease-Outcome in Patients with Phenylketonuria, Carriers of a Structural SLC7A5 Variant

Treatment in phenylketonuria is aimed at protecting the brain from uncontrolled hyperphenylalaninemia. Although treatment methods are well established, clinical outcomes vary among patients. This may be due to alterations of phenylalanine transport mediated by the amino acid transporter LAT1, which also regulates the function of the mTORC1/proteasomal pathway. We explored the cellular mechanisms underlying potential phenotypic differences between carriers and noncarriers of the rs113883650 polymorphism – a marker of a structural variant of the SLC7A5 gene. For our experiments we used a model of hyperphenylalaninemia based on induced pluripotent stem cells (hiPSCs). We conducted a targeted analysis of the expression of peptides involved in the FOXO/proteasomal signaling pathway. We confirmed a statistically significant difference in FOXO pathway expression between the two groups of carriers and non carriers of the investigated variant (p = 0.005, t-test) under high Phe conditions. Notably, an increased abundance of CDK2 and ERK1 (MAPK1)—both known to downregulate FOXO1—was observed in carriers of rs113883650. We did not detect statistically significant differences between the tested groups under low Phe conditions.

Tags: 570-life-sciences, 610-medical-sciences-and-medicine, foxo, lat1, phenylketonuria, proteasome
Organization: open.bydata
Rotspektralanalysen von Herrscher- und Politikerbildern (1360-2014)

Tabelle mit Abbildungen, Metadaten, Angaben zur ikonographischen Tradition und formalen Kompositionsschemata sowie Rotspektralanalysen (Software Redcolor-Tool, HCI) von 50 Herrscher- und Politikerbildern (1360 - 2014). Angaben: Abkürzung, Abbildung, Künstler/Presseagentur, Dargestellte(r), Jahr, Material, Größe, Aufbewahrungsort/Publikationsort, Angaben zur ikonographischen Tradition, Angaben zu formalen Kompositionsschemata des Bildes mit besonderer Rücksicht auf die Rotwertdisposition, Angaben zur offiziellen/inoffiziellen Funktion des Bildes, der Auftragslage und des Entstehungskontextes, Daten zu Farbfrequenzen und zur statistischen Dispersion der Farben (Lab-Farbraum, 16 Farbklassen-Modell), Rotspektralanalysen (Software Redcolor-Tool, HCI) und Abbildungsnachweise. Farb-Key: Lab-Farbraum, 16 Farbklassen-Modell, Farbwert 1 (Rot) - Farbwert 16 (Dunkel). Euklidische Abstände zwischen den Farbwerten und sog. MacAdams-Ellipsoide approximieren mathematisch die menschliche Wahrnehmung und ermöglichen ein metrisches Skalenniveau. Der Lab-Farbraum ist ein geräteunabhängiger Farbraum und auf die Wahrnehmung des Menschen hin konzipiert. Software: Redcolor-Tool, Ommer Lab, Heidelberg Collaboratory for Image Processing (HCI). Anmerkung: Mein großer Dank gilt Guje Kroh von der Münchener Staatsbibliothek für die Übersetzungen aus dem Chinesischen (Renmin Ribao). Nicht genug danken kann ich Björn Ommer von der Computer Vision Group, Ruprecht-Karls-Universität Heidelberg, HCI, für die Entwicklung des Redcolor-Tools.

Tags: 004-data-processing-computer-science, 750-paintings-and-paintings-museums, 770-photography-and-photographs, digitale-bildanalyse, farbkomposition, herrschermalerei, malerei, medienwandel, pattern-detection, photographie, politikerdarstellungen, politische-ikonographie, rot, rotspektralanalyse, stilometrie
Organization: open.bydata
List of finds of AcrossBorders’ excavation in SAC5, Sai Island

Over the course of the ERC AcrossBorders project 2015–2017 campaigns in cemetery SAC5 on Sai Island in northern Sudan a considerable number of finds was made. The following list of finds illustrates the rich material discovered and is based on the original find lists created in the field.

Tags: archaeology, sudan
Organization: open.bydata
Supplementary Data: "An STM study on the diffusion of O atoms on a CO-covered Ru(0001) surface - The role of domain boundaries"

Supplementary data for the following publication: Ann-Kathrin Kügler, Hannah Illner, Joost Wintterlin, An STM study on the diffusion of O atoms on a CO-covered Ru(0001) surface—The role of domain boundaries, Surface Science, Volume 751, 2025, 122597, ISSN 0039-6028, https://doi.org/10.1016/j.susc.2024.122597

Organization: open.bydata
VerbaAlpina Version 23/2: SQL-Dump der zentralen MySQL-Datenbank

Bei den hier beschriebenen Daten handelt es sich um einen Dump der zentralen MySQL-Datenbank des DFG-Langfristvorhabens VerbaAlpina (http://gepris.dfg.de/gepris/projekt/253900505). Sie liefen zuletzt auf der MySQL-Serverversion 5.7.44-48-57-log. Der Dump kann in Installationen kompatibler MySQL- oder MariaDB-Versionen importiert und dort weiter verwendet werden.

Tags: 000-computers, 004-data-processing-computer-science, 400-language, 410-linguistics, 430-germanic-languages-german, 450-italian, alpen, alps, data-processing-computer-science, germanic-languages-german, high-german, information-and-general-reference, italian, language-geography, linguistic-map, linguistics, rhaeto-romatic, romanian, shifted-western-romance, sprachatlas, sprachgeografie, western-south-slavic
Organization: open.bydata
Supplementary data for the article "Metasurface of strongly coupled excitons and nanoplasmonic arrays"

Metasurfaces allow to manipulate light at the nanoscale. Integrating metasurfaces with transition metal dichalcogenide monolayers provides additional functionality to ultrathin optics, including tunable optical properties with enhanced light-matter interactions. In this work, we demonstrate the realization of a polaritonic metasurface utilizing the sizable light-matter coupling of excitons in monolayer WSe$_2$ and the collective lattice resonances of nanoplasmonic gold arrays. We developed a novel fabrication method to integrate gold nanodisk arrays in hexagonal boron nitride and thus simultaneously ensure spectrally narrow exciton transitions and their immediate proximity to the near-field of array surface lattice resonances. In the regime of strong light-matter coupling, the resulting van der Waals metasurface exhibits all key characteristics of lattice polaritons, with a directional and linearly-polarized far-field emission profile dictated by the underlying nanoplasmonic lattice. Our work can be straightforwardly adapted to other lattice geometries, establishing structured van der Waals metasurfaces as means to engineer polaritonic lattices.

Tags: 500-natural-sciences-and-mathematics, 530-physics, exciton-plasmon-polaritons, metasurface, nanoplasmonic-array, plasmonic-surface-lattice-resonance, strong-coupling, two-dimensional-semiconductors
Organization: open.bydata
Human remains from Tomb 26, Sai Island, AcrossBorders excavation. Supplementary data: age and sex determination

This is a detailed table listing all age and sex markers for individuals buried in Tomb 26 on Sai Island, Sudan. This tomb was excavated in the framework of Julia Budka's AcrossBorders project; the anthropological research was carried out for Julia Budka’s FWF START project Y615-G19, funded by the Austrian Science Fund.

Tags: 570-life-sciences, anthropology, archaeology, human-remains, sudan
Organization: open.bydata
Audioslide-Clip "Beekeeping in Gozo"

Dieser Audioslide-Clip entstand während eines Forschungsaufenthaltes im Rahmen des Workshops "Honeybee Culture in Gozo and Malta" der Anthropology Fieldschool Malta 2016. Der Clip ist eine audiovisuelle Ergänzung des Kapitels zur Imkerei in Malta der Promotionspublikation "Zwischen Staunen und Zweifeln - Motive, Haltungen und Dilemmata der zeitgenössischen imkerlichen Praxis aus ethnologischer Sicht und Konzeptvorschlag für eine solidarische Imkerei" von Peter Niedersteiner. Die Dissertation ist mit der ISBN 978-3-95925-158-7 für die Print-Version in der Reihe „Open Publishing in the Humanities“ der Universitätsbibliothek der LMU München erschienen (Online abrufbar unter der DOI: https://doi.org/10.5282/oph.7)

Organization: open.bydata
Supplementary material to "Cavity-enhanced photon indistinguishability at room temperature and telecom wavelengths"

Indistinguishable single photons in the telecom-bandwidth of optical fibers are indispensable for long-distance quantum communication. Solid-state single photon emitters have achieved excellent performance in key benchmarks, however, the demonstration of indistinguishability at room-temperature remains a major challenge. Here, we report room-temperature photon indistinguishability at telecom wavelengths from individual nanotube defects in a fiber-based microcavity operated in the regime of incoherent good cavity-coupling. The efficiency of the coupled system outperforms spectral or temporal filtering, and the photon indistinguishability is increased by more than two orders of magnitude compared to the free-space limit. Our results highlight a promising strategy to attain optimized non-classical light sources. Related article: https://doi.org/10.1038/s41467-024-48119-1

Tags: 530-physics, carbon-nanotubes-and-fullerenes-physical-sciences, nanoscale-materials, nanoscience-and-technology, optical-physics, optics-and-photonics, physical-sciences, physics, quantum-physics, single-photons-and-quantum, single-photons-and-quantum-effects-physical-sciences
Organization: open.bydata
Anhänge zur Forschungsarbeit „Community Music als pädagogisches Mittel im sonderpädagogischen Schulalltag“

Diese Datei stellt den Anhang des Dissertationsprojektes „Community Music als pädagogisches Mittel im sonderpädagogischen Schulalltag. Eine empirische Studie zum Einfluss des gemeinsamen Sambatrommelns auf aggressives Verhalten, Gruppendynamik und Musikalität“ dar. So werden zu Beginn Auszüge aus dem Konzept der Unterrichtssequenz „Samba in Brasilien“ dargestellt. Anschließend folgt die Präsentation der individuellen Verläufe der einzelnen Testpersonen sowie die Berechnung der Effekt- und Teststärken für die Hypothesenpaare 1-3. Für das Hypothesenpaar 2 gibt es zudem eine deskriptive Darstellung und für das Hypothesenpaar 3 werden die Differenzindexwerte angegeben. Für die Hypothesenpaare 3 und 6 werden die ausführlichen Berechnungen des U-Tests dargestellt. Auch für die Vorstudie werden die genauen Berechnungen zu den einzelnen Hypothesen aufgezeigt. Dazu gehören unter anderem die Berechnungen der Zeitreihenanalysen sowie die Berechnungen der Effekt- und Teststärken. Abschließend wird die Berechnung der optimalen Stichprobengröße aus den Ergebnissen der Vorstudie dargestellt. Die Dissertation ist mit der ISBN 978-3-95925-148-8 für die Print-Version in der Reihe „Open Publishing in the Humanities“ der Universitätsbibliothek der LMU München erschienen (Online abrufbar unter der DOI: https://doi.org/10.5282/oph.6)

Tags: 300-social-sciences, 700-arts-and-recreation, empirische-studie, musikpädagogik, pädagogik-bei-verhaltensstörungen, sonderpädagogik, zeitreihenanalysen
Organization: open.bydata
Lateral root primordia development of wild type and pip mutants of Arabidopsis thaliana

The experiment was performed on Arabidopsis thaliana wild type (Col) and aquaporin single mutants, pip2;1-2 and pip2;8-2, labeled with a marker for plasma membrane (UBQ10pro::PIP1;4-3xGFP) and nuclei of LRP cells (GATA23pro::H2B:3xmCHERRY) in a culture medium with ½ Murashige-Skoog and 0.8% Phytoagar. The plants were grown vertically for four days, and the gravitropic stimulus (pgi) was applied by rotating the plates at 180 °. At 17 hours pgi, the seedlings were transferred to a light-sheet microscope, and the LRP development was recorded every 30 min from 18 h to 39 h pgi. Images were processed, drift corrected, and cropped using the BigDataProcessor (Tischer et al. 2019) in Fiji (Schindelin et al. 2012). Max Projection was applied after imaging processing.

Organization: open.bydata
Responsible Automation: Exploring Potentials and Losses Through Automation in Human-Computer Interaction from a Psychological Perspective. (Study 1 and Study 2)

Robots and smart technologies become part of everyday life and private households. While this automation of mundane tasks typically creates pragmatic benefits (e.g., efficiency, accuracy, time savings), it may also come with psychological losses, such as in meaning, competence, or re-sponsibility. Depending on the domain (e.g., AI-assisted surgery, automated decision making), especially the user's felt responsibility could have far-reaching consequences. The present re-search systematically explores such effects, building a more structured base for responsible au-tomation in Human-Computer Interaction (HCI). Based on a framework of seven dimensions, study 1 (N=122) evaluates users' reflections on automating five mundane tasks (e.g., gardening, paperwork) and identifies reasons for or against automation in different domains (e.g., creativi-ty, care work, decision making). Study 2 (N=57) provides deeper insights into effects of automa-tion on responsibility perceptions. Based on the example of a vacuum cleaner robot, an experi-mental laboratory study contrasted a non-robotic manual vacuum cleaner to a robot, whereby the user's perceptions of device agency (higher for the robot) and own competence (higher for the manual device) were central mediator for the perceived responsibility for the result. We po-sition our findings as part of a broader idea of responsible design and automation from a us-er-centered design perspective. Data to: Diefenbach, S., Ullrich, D., Lindermayer, T., & Isaksen, K.-L. (2024). Responsible Automation: Exploring Potentials and Losses through Automation in Human–Computer Interaction from a Psychological Perspective. Information, 15(8), 460. doi:10.3390/info15080460

Organization: open.bydata
Supplementary data: Scalable Distributed Memory Implementation of the Quasi-Adiabatic Propagator Path Integral

The accurate simulation of dissipative quantum dynamics subject to a non-Markovian environment poses persistent numerical challenges, in particular for structured environments where sharp mode resonances induce long-time system bath correlations. We present a scalable distributed memory implementation of the Mask Assisted Coarse Graining of Influence Coefficients (MACGIC) - Quasi-Adiabatic Propagator Path Integral (-QUAPI) method that exploits the memory resources of multiple compute nodes and mitigates the memory bottleneck of the method via a new pre-merging algorithm and a hash-based look-up (hMACGIC-QUAPI) while preserving numerical accuracy. The distributed memory implementation spreads the paths over the computing nodes by means of the MPI protocol and efficient high level path management is achieved via the hash map-based implementation with constant access time. The efficiency of the implementation is demonstrated in large-scale dissipative quantum dynamics simulations that account for the coupling to a structured non-Markovian environment containing a sharp resonance, a setup for which convergence properties are investigated in depth. Broad applicability and the non-perturbative nature of the simulation method is illustrated via the tuning of the mode resonance frequency of the structured environment with respect to the characteristic system frequency. The simulations reveal a splitting of resonances due to strong system-environment interaction and the emergence of sidebands due to multi-excitations of the bosonic mode that are not accounted for in perturbative approaches. The simulations demonstrate the versatility of the new hMACGIC-QUAPI method in the presence of strong non-Markovian system bath correlations. Data to: R. Ovcharenko and B. P. Fingerhut, Scalable Distributed Memory Implementation of the Quasi-Adiabatic Propagator Path Integral, submitted to JCTC (2025) Available under: https://doi.org/10.48550/arXiv.2506.03127

Tags: 530-physics, 540-chemistry-and-allied-sciences, non-markovian-dynamics, open-quantum-systems, path-integral-methods
Organization: open.bydata
Kinetic measurements and product studies used to determine the nucleophilicity of α-aryl vinyl azides

The zip file contains (1) a folder named "kinetics", which contains txt files with absorbance vs. time data; exp files used for the k(obs) determination; pdf files with results of the k(obs) determination. Folder and file names CGxxx and PTxxx refer to individual experiments and are identical to those in the Supporting Information (docx/rtf/pdf). (2) a folder named "products" which contains analytical data (NMR, IR, and HRMS) used to characterize the synthetically prepared vinyl azides as well as the amides isolated from the reactions of vinyl azides with benzhydrylium ions. Folder and file names CGxxx and PTxxx for the characterized chemical compounds are identical to those in the Supporting Information (docx/rtf/pdf).

Tags: 540-chemistry-and-allied-sciences, kinetics, nucleophiles, product-characterization, time-resolved-spectroscopy
Organization: open.bydata
Additional Files: Mitochondrial RNA processing in absence of tRNA punctuations in octocorals

Background: Mitogenome diversity is staggering among early branching animals with respect to size, gene density and content, gene orders, and number of tRNA genes, especially in cnidarians. This last point is of special interest as tRNA cleavage drives the maturation of mitochondrial mRNAs and is a primary mechanism for mt-RNA processing in animals. Mitochondrial RNA processing in non-bilaterian metazoans, some of which possess a single tRNA gene in their mitogenomes, is essentially unstudied despite its importance in understanding the evolution of mitochondrial transcription in animals. Results: We characterized the mature mitochondrial mRNA transcripts in a species of the octocoral genus Sinularia (Alcyoniidae: Octocorallia), and defined precise boundaries of transcription units using different molecular methods. Most mt-mRNAs were polycistronic units containing two or three genes and 5' and/or 3' untranslated regions (UTRs) of varied length. The octocoral specific, mtDNA-encoded mismatch repair gene, mtMutS, was found to undergo alternative polyadenylation (APA), and exhibited differential expression of alternate transcripts suggesting a unique regulatory mechanism for this gene. In addition, a long noncoding RNA complementary to the ATP6 gene (lncATP6) potentially involved in antisense regulation was detected. Conclusions: Mt-mRNA processing in octocorals bearing a single mt-tRNA is complex. Considering the variety of mitogenome arrangements known in cnidarians, and in general among non-bilaterian metazoans, our findings provide a first glimpse into the complex mtDNA transcription, mt-mRNA processing, and regulation among early branching animals and represents a first step towards understanding its functional and evolutionary implications.

Tags: 570-life-sciences, 590-zoological-sciences, alternative-polyadenylation-apa, cnidaria, long-noncoding-rna-lncrna, mitochondrial-rna, mitogenome, non-bilaterian, octocorals, polycistronic-transcripts, trna-punctuation
Organization: open.bydata