cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5281/zenodo.7616450
title: Ultrafine particle number concentration observations perpendicular to a main street in Berlin, Germany, in summer 2017

description: The data set was recorded in summer 2017 in Berlin, Germany. It was the basis of the paper: Fritz, S., Schubert, S., and Schneider, C. (2021). Measurements of spatial variability of sub-micron particle number concentrations perpendicular to a main road in a built-up area. metz. 30, 315–331. doi:10.1127/metz/2021/1058 The measurement setup, study site, and devices used are described more detailed in the paper. The data sets uploaded include observations of particle number concentrations, wind direction and wind speed at ground level as well as traffic count data. The time stamp is in local time for Berlin/Germany. The data sets: coordinates.csv contains the coordinates of the measurement points used in file obs_pnc_wind. The column ‘distance’ links these two files. The values in the column ‘distance’ are the distance from the curb of the main road. The distance ‘-10’ represents the measurement point on the central strip of the main road. The two columns ‘latitude’ and ‘longitude’ provide the coordinates of the measurement points. obs_pnc_wind contains the observation data for particle number concentration (PNC), wind speed, and wind direction. PNC was recorded in #/cm³ with a TSI 3007 CPC at a 1-second resolution. Wind speed `ws’ [m/s] was recorded with a KESTREL 5000 with a 2-second resolution. Wind direction ‘wdir’ [°] was manually recorded as the most prominent wind direction within the 3-minute measurements per measurement point in angles of 10°. Wind direction was changed to NA (wdir_comment &gt; 0), if it could not be determined either due to too calm wind (wdir_comment = 1) or with continuously changing wind direction (wdir_comment = 2). Along the measurement route, sometimes additional sources occurred and were recorded in the variable ‘source_type’ at the time they passed by the measurement device. Variable ‘source_comment’ provides additional information about ‘source_type’ where necessary. traffic_count contains the vehicles counted on the main street (Straße des 17. Juni) for each of the 72 runs. It was calculated as [vehicles/hour] based on 5-minute traffic counts. During the traffic counts, we differentiated between smaller (light duty) vehicles (&lt;3.5 t, cars, vans, motorcycles, scooters) and bigger (heavy duty) vehicles (&gt; 3.5 t, trucks and busses).
description: The study was carried out as part of the research programme Urban Climate under Change (UC2) within sub-project URBMOBI-GIS, grant No. 01LP1602B, as well as grant FKZ 01LP 1912B (Phase II, Module 3DO + M), funded by the German Federal Ministry of Research (BMBF) and Education (BMBF).
description: {"references": ["Fritz, S., Schubert, S., and Schneider, C. (2021). Measurements of spatial variability of sub-micron particle number concentrations perpendicular to a main road in a built-up area. metz. 30, 315\u2013331. doi:10.1127/metz/2021/1058"]}
DOI: 10.5281/zenodo.7616449
title: Ultrafine particle number concentration observations perpendicular to a main street in Berlin, Germany, in summer 2017

description: The data set was recorded in summer 2017 in Berlin, Germany. It was the basis of the paper: Fritz, S., Schubert, S., and Schneider, C. (2021). Measurements of spatial variability of sub-micron particle number concentrations perpendicular to a main road in a built-up area. metz. 30, 315–331. doi:10.1127/metz/2021/1058 The measurement setup, study site, and devices used are described more detailed in the paper. The data sets uploaded include observations of particle number concentrations, wind direction and wind speed at ground level as well as traffic count data. The time stamp is in local time for Berlin/Germany. The data sets: coordinates.csv contains the coordinates of the measurement points used in file obs_pnc_wind. The column ‘distance’ links these two files. The values in the column ‘distance’ are the distance from the curb of the main road. The distance ‘-10’ represents the measurement point on the central strip of the main road. The two columns ‘latitude’ and ‘longitude’ provide the coordinates of the measurement points. obs_pnc_wind contains the observation data for particle number concentration (PNC), wind speed, and wind direction. PNC was recorded in #/cm³ with a TSI 3007 CPC at a 1-second resolution. Wind speed `ws’ [m/s] was recorded with a KESTREL 5000 with a 2-second resolution. Wind direction ‘wdir’ [°] was manually recorded as the most prominent wind direction within the 3-minute measurements per measurement point in angles of 10°. Wind direction was changed to NA (wdir_comment &gt; 0), if it could not be determined either due to too calm wind (wdir_comment = 1) or with continuously changing wind direction (wdir_comment = 2). Along the measurement route, sometimes additional sources occurred and were recorded in the variable ‘source_type’ at the time they passed by the measurement device. Variable ‘source_comment’ provides additional information about ‘source_type’ where necessary. traffic_count contains the vehicles counted on the main street (Straße des 17. Juni) for each of the 72 runs. It was calculated as [vehicles/hour] based on 5-minute traffic counts. During the traffic counts, we differentiated between smaller (light duty) vehicles (&lt;3.5 t, cars, vans, motorcycles, scooters) and bigger (heavy duty) vehicles (&gt; 3.5 t, trucks and busses).
description: The study was carried out as part of the research programme Urban Climate under Change (UC2) within sub-project URBMOBI-GIS, grant No. 01LP1602B, as well as grant FKZ 01LP 1912B (Phase II, Module 3DO + M), funded by the German Federal Ministry of Research (BMBF) and Education (BMBF).
description: {"references": ["Fritz, S., Schubert, S., and Schneider, C. (2021). Measurements of spatial variability of sub-micron particle number concentrations perpendicular to a main road in a built-up area. metz. 30, 315\u2013331. doi:10.1127/metz/2021/1058"]}
DOI: 10.6084/m9.figshare.18059795
title: Efficient Estimation of the Efficacy and Safety Endpoints for Clinical Trials with Preplanned Dose Titrations

description: Preplanned dose titrations are sometimes used in clinical trials to improve patient tolerability to treatment. Such titrations often start from a low dose and gradually increase to the targeted dose, and therefore, the low-dose and high-dose arms may share the same dose for a certain period of time. Traditionally, the analysis has been performed according to the treatment arm, ignoring the fact that there are overlapping initial doses between arms. This article describes an alternative method of analysis that exploits the design feature on titrations to produce a more efficient estimation for the mean response over time for each treatment regimen as well as the comparison between treatment regimens for continuous, time-to-event, binary, and count variables. For continuous and count data, we used the (generalized) linear mixed model framework to construct the new estimators; for time-to-event data, we developed a novel logrank test; and for the binary variable, we derived the point and variance estimators based on the events that occurred in each study period. Simulation studies and the application to a real clinical dataset demonstrate the newly proposed approach is advantageous over the traditional approach.
DOI: 10.6084/m9.figshare.18059795.v1
title: Efficient estimation of the efficacy and safety endpoints for clinical trials with preplanned dose titrations

description: Preplanned dose titrations are sometimes used in clinical trials to improve patient tolerability to treatment. Such titrations often start from a low dose and gradually increase to the targeted dose, and therefore the low-dose and high-dose arms may share the same dose for a certain period of time. Traditionally, the analysis has been performed according to the treatment arm, ignoring the fact that there are overlapping initial doses between arms. This article describes an alternative method of analysis that exploits the design feature on titrations to produce a more efficient estimation for the mean response over time for each treatment regimen as well as the comparison between treatment regimens for continuous, time-to-event, binary, and count time-to-event variables. For continuous and count data, we used the (generalized) linear mixed model framework to construct the new estimators; for time-to-event data, we developed a novel logrank test; and for the binary variable, we derived the point and variance estimators based on the events that occurred in each study period. Simulation studies and the application to a real clinical dataset demonstrate the newly proposed approach is advantageous over the traditional approach.
DOI: 10.6084/m9.figshare.17148275
title: Optimal Spiking Experiment for Noninferiority of Qualitative Microbiological Methods on Accuracy With Multiple Microorganisms

description: The European and United States Pharmacopoeia demand a noninferiority study on the detection of microorganisms when an alternate qualitative microbiological method is intended to replace the compendial microbiological method. However, without imposing any modeling assumptions or constraints, noninferiority studies require large numbers of test samples for a proposed noninferiority criterion of 0.7 or higher for each microorganism. When we can assume that the accuracy of the alternate method with respect to the compendial method is homogeneous across microorganisms, a joint statistical analysis of the data from all microorganisms can be used to help reduce the sample size dramatically. For this situation, we provide a test statistic for noninferiority, an optimal spiking experiment, and a sample size calculation approach under only mild modeling assumptions of the microorganism-specific detection proportions. We illustrate our approach on a real dataset and demonstrate good performance of our method using simulation studies.
DOI: 10.6084/m9.figshare.17148275.v2
title: Optimal Spiking Experiment for Noninferiority of Qualitative Microbiological Methods on Accuracy With Multiple Microorganisms

description: The European and United States Pharmacopoeia demand a noninferiority study on the detection of microorganisms when an alternate qualitative microbiological method is intended to replace the compendial microbiological method. However, without imposing any modeling assumptions or constraints, noninferiority studies require large numbers of test samples for a proposed noninferiority criterion of 0.7 or higher for each microorganism. When we can assume that the accuracy of the alternate method with respect to the compendial method is homogeneous across microorganisms, a joint statistical analysis of the data from all microorganisms can be used to help reduce the sample size dramatically. For this situation, we provide a test statistic for noninferiority, an optimal spiking experiment, and a sample size calculation approach under only mild modeling assumptions of the microorganism-specific detection proportions. We illustrate our approach on a real dataset and demonstrate good performance of our method using simulation studies.
DOI: 10.6084/m9.figshare.17148275.v1
title: Optimal spiking experiment for non-inferiority of qualitative microbiological methods on accuracy with multiple microorganisms

description: The European and United States Pharmacopoeia demand a non-inferiority study on the detection of microorganisms when an alternate qualitative microbiological method is intended to replace the compendial microbiological method. However, without imposing any modeling assumptions or constraints, non-inferiority studies require large numbers of test samples for a proposed non-inferiority criterion of 0.7 or higher for each microorganism. When we can assume that the accuracy of the alternate method with respect to the compendial method is homogeneous across microorganisms, a joint statistical analysis of the data from all microorganisms can be used to help reduce the sample size dramatically. For this situation, we provide a test statistic for non-inferiority, an optimal spiking experiment, and a sample size calculation approach under only mild modeling assumptions of the microorganism-specific detection proportions. We illustrate our approach on a real data set and demonstrate good performance of our method using simulation studies.
DOI: 10.5281/zenodo.7616885
title: heliconius_cydno_spades_01.fasta.gz

description: .
DOI: 10.5281/zenodo.7616884
title: heliconius_cydno_spades_01.fasta.gz

description: .
DOI: 10.5281/zenodo.7617107
title: DECIMER - Hand-drawn molecule images dataset

description: <strong>DECIMER - Hand-drawn molecule images dataset</strong> The translation of images of chemical structures into machine-readable representations of the depicted molecules is known as optical chemical structure recognition (OCSR). There has been a lot of progress over the last three decades in this field, but the development of systems for the recognition of complex hand-drawn structure depictions is still at the beginning. Currently, there is no data for the systematic evaluation of OCSR methods on hand-drawn structures available. Here we present DECIMER - Hand-drawn molecule images, a standardised, openly available benchmark dataset of 5088 hand-drawn depictions of diversely picked chemical structures. Every structure depiction in the dataset is mapped to a machine-readable representation of the underlying molecule. The dataset is openly available and published under the CC-BY 4.0 licence which applies very few limitations. We hope that it will contribute to the further development of the field.
DOI: 10.5281/zenodo.6456305
title: DECIMER - Hand-drawn molecule images dataset

description: <strong>DECIMER - Hand-drawn molecule images dataset</strong> The translation of images of chemical structures into machine-readable representations of the depicted molecules is known as optical chemical structure recognition (OCSR). There has been a lot of progress over the last three decades in this field, but the development of systems for the recognition of complex hand-drawn structure depictions is still at the beginning. Currently, there is no data for the systematic evaluation of OCSR methods on hand-drawn structures available. Here we present DECIMER - Hand-drawn molecule images, a standardised, openly available benchmark dataset of 5088 hand-drawn depictions of diversely picked chemical structures. Every structure depiction in the dataset is mapped to a machine-readable representation of the underlying molecule. The dataset is openly available and published under the CC-BY 4.0 licence which applies very few limitations. We hope that it will contribute to the further development of the field.
DOI: 10.5281/zenodo.7617090
title: pyrrhura_viridicata_spades_01.fasta.gz

description: .
DOI: 10.5281/zenodo.7617089
title: pyrrhura_viridicata_spades_01.fasta.gz

description: .
DOI: 10.6084/m9.figshare.22041587
title: Supplementary Data - Diet-induced obesity alters intestinal monocyte-derived and tissue-resident macrophages and increases intestinal permeability in female mice independent of TNF - Breznik et al. 2023

description: Supplementary Data for the AJP-GI article 'Diet-induced obesity alters intestinal monocyte-derived and tissue-resident macrophages and increases intestinal permeability in female mice independent of TNF' - Breznik et al. 2023
DOI: 10.6084/m9.figshare.22040780
title: Glacial geomorphology of the northwest Laurentide Ice Sheet on the northern Interior Plains and western Canadian Shield, Canada

description: The majority of the Northwest Territories of mainland Canada was covered by the northwest sector of the Laurentide Ice Sheet during the Last Glacial Maximum. The increasing coverage of high resolution remotely sensed data, and in particular, digital elevation models provides new opportunities to map the glacial geomorphology and study the glacial history of this remote location. Here we present a comprehensive map of glacial landforms within the northern Interior Plains and adjacent areas of the Canadian Shield, east of the Mackenzie and Richardson mountains, between 60˚N and the Beaufort Sea/Amundsen Gulf, comprising around 6% of the Laurentide Ice Sheet bed. Twelve landform types were identified and mapped from the high resolution ArcticDEM: ice flow parallel lineations, subglacial ribs, crevasse-squeeze ridges, major and minor moraine crests, hummocky terrain complexes and ridges, shear margin moraines, major, minor and lateral and submarginal meltwater channels, esker ridges and complexes, glaciofluvial complexes, perched deltas, raised shorelines and aeolian dunes. Together, these landforms provide a record of the highly dynamic behaviour of the northwest sector of the Laurentide Ice Sheet.
DOI: 10.5281/zenodo.7617219
title: tyrannus_couchii_spades_01.fasta.gz

description: .
DOI: 10.5281/zenodo.7617218
title: tyrannus_couchii_spades_01.fasta.gz

description: .
DOI: 10.5281/zenodo.7616991
title: Requirements elicitation (ReqElic) in my company

description: Questionnaire (online survey) about requirements elicitation (ReqElic) in my company, PDF generated from &lt;https://docs.google.com/forms/d/1RH_oMgpreDCvHexh4dKe40EVhsoBXPaXbbOYMITQDlQ/edit&gt;
DOI: 10.5281/zenodo.7616990
title: Requirements elicitation (ReqElic) in my company

description: Questionnaire (online survey) about requirements elicitation (ReqElic) in my company, PDF generated from &lt;https://docs.google.com/forms/d/1RH_oMgpreDCvHexh4dKe40EVhsoBXPaXbbOYMITQDlQ/edit&gt;
DOI: 10.3886/e184602
title: Civic Online Reasoning Across the Curriculum

description: Given the current threat posed by toxic digital content, preparing students to evaluate online sources cannot be relegated to a single subject area. This instruction should happen across the curriculum. This article focuses on materials designed to teach students to evaluate online information across subject areas. Ninth grade biology and world geography teachers taught a series of curriculum-embedded lessons based on the following design principles: (1) Focus on a core question and strategy; (2) engage students in evaluating real online content; (3) feature cognitive apprenticeship and formative assessment; (4) support teacher learning. We examined whether these lessons helped students become more skilled evaluators of online content. Pretest/posttest data (N =574) showed statistically significant growth in students’ ability to evaluate the credibility of online content. We analyze the role played by the curriculum design principles in this interdisciplinary intervention and explore implications for future initiatives.
DOI: 10.3886/e184602v1
title: Civic Online Reasoning Across the Curriculum

description: Given the current threat posed by toxic digital content, preparing students to evaluate online sources cannot be relegated to a single subject area. This instruction should happen across the curriculum. This article focuses on materials designed to teach students to evaluate online information across subject areas. Ninth grade biology and world geography teachers taught a series of curriculum-embedded lessons based on the following design principles: (1) Focus on a core question and strategy; (2) engage students in evaluating real online content; (3) feature cognitive apprenticeship and formative assessment; (4) support teacher learning. We examined whether these lessons helped students become more skilled evaluators of online content. Pretest/posttest data (N =574) showed statistically significant growth in students’ ability to evaluate the credibility of online content. We analyze the role played by the curriculum design principles in this interdisciplinary intervention and explore implications for future initiatives.
DOI: 10.6084/m9.figshare.21801268
title: Concurrent testing paper

description: Data for concurrent testing via HPV DNA and visual inspection (VIA or EVA colposcopy)
DOI: 10.6084/m9.figshare.21801268.v2
title: Concurrent testing paper

description: Data for concurrent testing via HPV DNA and visual inspection (VIA or EVA colposcopy)
DOI: 10.6084/m9.figshare.21801268.v1
title: Concurrent testing paper

description: Data for concurrent testing via HPV DNA and visual inspection (VIA or EVA colposcopy)
DOI: 10.17909/bwwe-4a42
title: JWST dataset Abell 2744 from Morishita et al. 2023

description: This dataset includes NIRCam imaging, NIRISS imaging, NIRSpec MSA data in the line of sight of the cluster Abell 2744 that are used in Morishita et al. 2023. ("Early results from GLASS-JWST. XVIII: A spectroscopically confirmed protocluster 650 million years after the Big Bang")
DOI: 10.5281/zenodo.7617290
title: mesocentrotus_franciscanus_spades_01.fasta.gz

description: .
DOI: 10.5281/zenodo.7617289
title: mesocentrotus_franciscanus_spades_01.fasta.gz

description: .
DOI: 10.6084/m9.figshare.21313125
title: Fatigue Study Dataset 2022

description: All data points used in the study and the results of the correlation calculations are included in the two Microsoft Excel files.
DOI: 10.6084/m9.figshare.21313125.v1
title: Fatigue Study Dataset 2022

description: All data points used in the study and the results of the correlation calculations are included in the two Microsoft Excel files.
DOI: 10.5281/zenodo.7617277
title: ReqElic In My Company Responses Anonymized

description: The anonymized collected responses from the survey at &lt;doi: 10.5281/zenodo.7616991&gt; in .xlsx form
DOI: 10.5281/zenodo.7617207
title: Germinal Center and Cultured B cell expression libraries

description: Comparison of gene expression profiles between in vitro mitogen-activated spleen B lymphocytes and FACS-sorted Germinal Center B lymphocytes isolated from intestinal PeyerPatches of C57BL/6 mice. In order to explore gene expression signatures that may be orchestrating somatic hypermutation (SHM, also known as affinity maturation) during antigen-induced B lymphocyte differentiation in Germinal Centers (GC), we profiled whole transcriptome gene expression of ex vivo, commensal microflora-activated GC B-cells that exhibit efficient SHM, with in vitro activated B-cell blasts, which fail to undergo SHM. In In particular, we examine our hypothesis that differential expression or the DNA endonucleases apex1 and apex2 regulate SHM. Using Templated Oligo Sequencing (TempO-Seq®) in conjunction with conventional intracellular FACS staining and B lymphocyte cell sorting, we compare gene expression profiles of in vitro mitogen-activated (LPS and anti-IgD-dextran), short-term (48h) cultured B cell blasts with Germinal Center B-cells isolated from intestinal Peyer Patches (PP, identified by surface staining B220+, CD95+, GL7+), compared to each other and to naive PP B-cells (B220+, CD95-, GL7-). We find that unique, distinct transcriptional signatures dominate the DNA repair processes in GC B-cells or in vitro B-cell blast, shedding light on genomic processes that orchestrate efficient affinity maturation of B-cells during GC differentiation. We use Templated Oligo Sequencing (TempO-Seq), a RNA motif-specific short tandem Oligo DNA hybridization technique to quantitatively measure whole transcriptome mRNA in conjunction with conventional surface membrane, fixable live/dead discriminator dye, and intracytoplasmic fluorescence antibody staining followed by FACS to isolate B cell populations of interest.
description: Funded by NIH grants AI26122, AI023283, AI099988, and SBIR Phase II grant 2R44HG008917 to BioSypder