cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5281/zenodo.8091305
title: Supplemental Files

description: Supplemental Tables 1 and 2 of the original manuscript entitled "<strong><em>Stenotrophomonas goyi </em>sp. nov., a novel bacterium associated with the alga <em>Chlamydomonas reinhardtii</em> </strong>" Supplemental Table 1: Tentative genome annotation of Stenotrophomonas goyi (derived from the RAST server) Supplemental Table 2: Orthology gene assignments of Stenotrophomonas goyi (derived from the BlastKOALA sever)
DOI: 10.6084/m9.figshare.22144223
title: Modelling of acetaldehyde and acetic acid combustion

description: Despite the beneficial impact of biofuels on most regulated pollutants and carbon dioxide emissions, their combustion results in the generation of undesired pollutants, such as acetaldehyde and acetic acid. To better understand the chemistry of these species, detailed chemical kinetic models deriving from two alternative strategies for mechanism generation were developed and validated against available data. The first model represents a semi-lumped mechanism comprising 89 species and 366 reactions, whereas the latter is automatically generated to aggregate elemental steps based on a rate-based algorithm, and it contains 541 species and 27,334 reactions. Under the studied conditions, the two kinetic models fairly predicted ignition delay times and laminar burning velocity data of acetic acid and acetaldehyde. Few discrepancies were observed for ignition delay time at temperatures lower than 1300 K. However, the overall agreement between experimental measurements and numerical estimations allowed for the use of the two kinetic models to unravel the chemistry of the investigated species. <b>Highlights</b>Identification of key primary reactions for acetic acid and acetaldehydeIntegration of an existing kinetic mechanism with selected reactionsDevelopment of a detailed kinetic mechanism through an automated algorithmComparison of experimental and numerical data for overall reactivityAnalysis of the chemistry of acetic acid and acetaldehyde Identification of key primary reactions for acetic acid and acetaldehyde Integration of an existing kinetic mechanism with selected reactions Development of a detailed kinetic mechanism through an automated algorithm Comparison of experimental and numerical data for overall reactivity Analysis of the chemistry of acetic acid and acetaldehyde
DOI: 10.6084/m9.figshare.22144223.v1
title: Modelling of acetaldehyde and acetic acid combustion

description: Despite the beneficial impact of biofuels on most regulated pollutants and carbon dioxide emissions, their combustion results in the generation of undesired pollutants, such as acetaldehyde and acetic acid. To better understand the chemistry of these species, detailed chemical kinetic models deriving from two alternative strategies for mechanism generation were developed and validated against available data. The first model represents a semi-lumped mechanism comprising 89 species and 366 reactions, whereas the latter is automatically generated to aggregate elemental steps based on a rate-based algorithm, and it contains 541 species and 27,334 reactions. Under the studied conditions, the two kinetic models fairly predicted ignition delay times and laminar burning velocity data of acetic acid and acetaldehyde. Few discrepancies were observed for ignition delay time at temperatures lower than 1300 K. However, the overall agreement between experimental measurements and numerical estimations allowed for the use of the two kinetic models to unravel the chemistry of the investigated species. <b>Highlights</b>Identification of key primary reactions for acetic acid and acetaldehydeIntegration of an existing kinetic mechanism with selected reactionsDevelopment of a detailed kinetic mechanism through an automated algorithmComparison of experimental and numerical data for overall reactivityAnalysis of the chemistry of acetic acid and acetaldehyde Identification of key primary reactions for acetic acid and acetaldehyde Integration of an existing kinetic mechanism with selected reactions Development of a detailed kinetic mechanism through an automated algorithm Comparison of experimental and numerical data for overall reactivity Analysis of the chemistry of acetic acid and acetaldehyde
DOI: 10.6084/m9.figshare.23141534
title: Supplementary Figure 13 from Mattila et al. 2023

description: An R script and f-statistics datasets for plotting Supplementary Figure 19 from Mattila et al. 2023 showing evidence for Western and Eastern Hunter-Gatherers in West Eurasian hunter-gatherers.
DOI: 10.6084/m9.figshare.23097608
title: Conditional nucleotide diversity

description: Conditional nucleotide diversity (CND) calculated for a set of Mesolithic and Neolithic individual pairs as described in Skoglund et al. (2014). Skoglund, P. <em>et al.</em> Genomic diversity and admixture differs for stone-age Scandinavian foragers and farmers. <em>Science (80-. ).</em> <strong>344</strong>, 747–750 (2014).
DOI: 10.6084/m9.figshare.22843679
title: f3s and f4s from Mattila et al. 2023 Fig. 3

description: f3s and f4s from Fig. 3 plots from Mattila et al. 2023: Patterns of allele sharing in Mesolithic, Neolithic, and Eneolithic Central and Eastern Europeans.
DOI: 10.6084/m9.figshare.22843679.v1
title: f3s and f4s from Mattila et al. 2023 Fig. 3

description: f3s and f4s from Fig. 3 plots from Mattila et al. 2023: Patterns of allele sharing in Mesolithic, Neolithic, and Eneolithic Central and Eastern Europeans.
DOI: 10.6084/m9.figshare.22842185
title: Calibrated radiocarbon age 95,4 % range midpoint per sample (Fig. 3)

description: Calibrated radiocarbon age midpoint values per sample from Mattila et al. 2023 (Fig. 3, Supplementary Data 1) and Fernandes et al. (2018) (samples code N) and González-Fortes (2017) (sample codes OC & SC). <br> Fernandes, D. M. <em>et al.</em> A genomic Neolithic time transect of hunter-farmer admixture in central Poland. <em>Sci. Rep.</em> <strong>8</strong>, 1–11 (2018). <br> González-Fortes, G. <em>et al.</em> Paleogenomic evidence for multi-generational mixing between Neolithic farmers and Mesolithic hunter-gatherers in the Lower Danube Basin. <em>Curr. Biol.</em> <strong>27</strong>, 1801–1810 (2017).
DOI: 10.6084/m9.figshare.22842185.v1
title: Calibrated radiocarbon age 95,4 % range midpoint per sample (Fig. 3)

description: Calibrated radiocarbon age midpoint values per sample from Mattila et al. 2023 (Fig. 3, Supplementary Data 1) and Fernandes et al. (2018) (samples code N) and González-Fortes (2017) (sample codes OC & SC). <br> Fernandes, D. M. <em>et al.</em> A genomic Neolithic time transect of hunter-farmer admixture in central Poland. <em>Sci. Rep.</em> <strong>8</strong>, 1–11 (2018). <br> González-Fortes, G. <em>et al.</em> Paleogenomic evidence for multi-generational mixing between Neolithic farmers and Mesolithic hunter-gatherers in the Lower Danube Basin. <em>Curr. Biol.</em> <strong>27</strong>, 1801–1810 (2017).
DOI: 10.6084/m9.figshare.22822535
title: Evidence for admixture through time in Neolithic Romania and Poland

description: A dataset from Mattila et al. 2023 showing evince of genetic admixture through time in Neolithic Romania and Poland. The admixing lineages were European Neolithic (that derived from Anatolian Neolithic aka AN) and Western Hunter-Gatherers-Paleolithic Siberian/Eastern Hunter-Gatherers (WHG/EHG-mix).
DOI: 10.6084/m9.figshare.22822535.v1
title: Evidence for admixture through time in Neolithic Romania and Poland

description: A dataset from Mattila et al. 2023 showing evince of genetic admixture through time in Neolithic Romania and Poland. The admixing lineages were European Neolithic (that derived from Anatolian Neolithic aka AN) and Western Hunter-Gatherers-Paleolithic Siberian/Eastern Hunter-Gatherers (WHG/EHG-mix).
DOI: 10.6084/m9.figshare.22811516
title: Sampling site geographical coordiates

description: Latitude and longitude in decimal degrees for Stone Age ancient DNA samples from Mattila et al. (2023). Country codes Poland (P), Romania (R), Ukraine (U). "Verbose_population" column indicates simplified time period classification where "Mesolithic" indicates everything before European Neolithic (encompasses Mesolithic and potential Epipalaeolithic) and "Neolithic" everything after European Neolithic (encompasses Neolithic and Eneolithic).
DOI: 10.6084/m9.figshare.22811420
title: Calibrated radiocarbon age medians (Fig 1a)

description: Calibrated radiocarbon age medians (IntCal20 cal. median BP (=1950), reservoir effect corrected) per country from Mattila et al. (2023) Fig. 1a
DOI: 10.17909/8d57-1698
title: A Catalog Of Ultraviolet Variables Observed By GALEX With Sub-Minute Resolution ("GFCAT")

description: GFCAT is the result of a systematic search for intra-visit variability using calibrated GALEX photon events to construct lightcurves at 30-second time resolution.  Using the gPhoton2 software package, a semi-automated search for variable objects was conducted using calibrated photon events from every GALEX visit with at least 500 seconds of exposure time. This is equivalent to searching all visits from the Medium Image Survey ("MIS") or longer exposure lengths.  Source detection was run on the resultant time series of images, and aperture photometry applied in both FUV (where available) and NUV bands using five photometric apertures.  Variable objects were first identified through automated detection and then by-hand screening.  The final product consists of 1959 lightcurves from 1426 unique sources.  The lightcurves are constructed using five aperture sizes (9, 12.5, 17.5, 25, and 35 arcseconds), stored in separate FITS files.  Each GALEX eclipse is analyzed independently, thus, variable objects observed more than once will have more than one set of lightcurves created.  Four catalogs are also provided: an object catalog containing information about the unique objects, a visit catalog containing information about the vetted variable objects in each GALEX visit, an eclipse catalog containing those sources identified as looking like eclipsing objects through visual inspection, and a flare catalog containing those sources identified as looking like flares.  GFCAT should not be considered suitable for general population studies or statistics: the goal was to locate as many intra-visit variables as possible in the GALEX photon database, at the expense of analyzing selection effects.
DOI: 10.6084/m9.figshare.22954532.v1
title: Supplementary Material for: Long-term Safety and Efficacy of Eltrombopag for Advanced Myelodysplastic Syndromes or Acute Myeloid Leukemia and Severe Thrombocytopenia: Results of the ASPIRE Extension Study

description: ASPIRE, a three-part, international, phase II trial (ClinicalTrials.gov identifier: NCT01440374), investigated eltrombopag efficacy and safety in patients with advanced myelodysplastic syndrome or acute myeloid leukemia, and grade 4 thrombocytopenia (&lt;25 × 109 platelets/L). Approximately 30–65% of patients in this open-label extension phase experienced clinically relevant thrombocytopenic events; no conclusions could be made regarding long-term efficacy (non-randomized design, no placebo control), and survival rates may simply reflect advanced disease. Long-term safety was consistent with the double-blind phase and contrasted with earlier SUPPORT study findings in higher-risk patients, suggesting that eltrombopag may have a role in treating thrombocytopenia in patients with low-/intermediate-risk myelodysplastic syndrome.
DOI: 10.6084/m9.figshare.22926227.v1
title: Supplementary Material for: Optical genome mapping for a patient with a congenital disorder and chromosomal translocation

description: We performed optical genome mapping (OGM), a newly developed cytogenetic technique, for a patient with a disorder of sex development (DSD) and a 46,XX,t(9;11)(p22;p13) karyotype. The results of OGM were validated using other methods. OGM detected a 9;11 reciprocal translocation and successfully mapped its breakpoints to small regions of 0.9–12.3 kb. OGM identified 46 additional small structural variants, only three of which were detected by array-based comparative genomic hybridization. OGM suggested the presence of complex rearrangements on chromosome 10; however, these variants appeared to be artifacts. The 9;11 translocation was unlikely to be associated with DSD, while the pathogenicity of the other structural variants remained unknown. These results indicate that OGM is a powerful tool for detecting and characterizing chromosomal structural variations, although the current methods of OGM data analyses need to be improved.
DOI: 10.7934/x29201
title: Phylogenetic datasets for: A new lapillopsid from Antarctica and a re-appraisal of the phylogenetic relationships of early diverging stereospondyls [X29201] Baseline (new base matrix)
DOI: 10.7934/x29202
title: Phylogenetic datasets for: A new lapillopsid from Antarctica and a re-appraisal of the phylogenetic relationships of early diverging stereospondyls [X29202] Analysis 1 (matrix with only Lapillopsis changes, 360 characters listed)
DOI: 10.5281/zenodo.8058781
title: Data and R scrips for "Exposure to closed-loop scrubber washwater alters biodiversity, reproduction, and grazing of marine zooplankton"

description: Research data and scripts associated with the article "Exposure to closed-loop scrubber washwater alters biodiversity, reproduction, and grazing of marine zooplankton" by Jönander et al.
DOI: 10.7934/x29203
title: Phylogenetic datasets for: A new lapillopsid from Antarctica and a re-appraisal of the phylogenetic relationships of early diverging stereospondyls [X29203] Analysis 1 (matrix with only Lapillopsis changes, 358 characters listed)
DOI: 10.5281/zenodo.7547023
title: Data and R scrips for "Exposure to closed-loop scrubber washwater alters biodiversity, reproduction, and grazing of marine zooplankton"

description: Research data and scripts associated with the article "Exposure to closed-loop scrubber washwater alters biodiversity, reproduction, and grazing of marine zooplankton" by Jönander et al.
DOI: 10.7934/x29204
title: Phylogenetic datasets for: A new lapillopsid from Antarctica and a re-appraisal of the phylogenetic relationships of early diverging stereospondyls [X29204] Analysis 2 (all taxa and character changes, 360 characters listed)
DOI: 10.7934/x29205
title: Phylogenetic datasets for: A new lapillopsid from Antarctica and a re-appraisal of the phylogenetic relationships of early diverging stereospondyls [X29205] Analysis 2 (all taxa and character changes, 345 characters listed)
DOI: 10.7934/x29208
title: Phylogenetic datasets for: A new lapillopsid from Antarctica and a re-appraisal of the phylogenetic relationships of early diverging stereospondyls [X29208] Analysis 3 (modified matrix of Eltink et al., 2019, 222 characters listed)
DOI: 10.7934/x29209
title: Phylogenetic datasets for: A new lapillopsid from Antarctica and a re-appraisal of the phylogenetic relationships of early diverging stereospondyls [X29209] Analysis 3 (modified matrix of Eltink et al., 2019, 209 characters listed)
DOI: 10.6084/m9.figshare.23586924
title: Supplementary Material for: Quantifying the Variability Associated with Postoperative Localization of Deep Brain Stimulation Electrodes

description: <b><i>Introduction:</i></b> Computational models of deep brain stimulation (DBS) have become common tools in clinical research studies that attempt to establish correlations between stimulation locations in the brain and behavioral outcome measures. However, the accuracy of any patient-specific DBS model depends heavily upon accurate localization of the DBS electrodes within the anatomy, which is typically defined via co-registration of clinical CT and MRI datasets. Several different approaches exist for this challenging registration problem, and each approach will result in a slightly different electrode localization. The goal of this study was to better understand how different processing steps (e.g., cost-function masking, brain extraction, intensity remapping) affect the estimate of the DBS electrode location in the brain. <b><i>Methods:</i></b> No “gold standard” exists for this kind of analysis, as the exact location of the electrode in the living human brain cannot be determined with existing clinical imaging approaches. However, we can estimate the uncertainty associated with the electrode position, which can be used to guide statistical analyses in DBS mapping studies. Therefore, we used high-quality clinical datasets from 10 subthalamic DBS subjects and co-registered their long-term postoperative CT with their preoperative surgical targeting MRI using 9 different approaches. The distances separating all of the electrode location estimates were calculated for each subject. <b><i>Results:</i></b> On average, electrodes were located within a median distance of 0.57 mm (0.49–0.74) of one another across the different registration approaches. However, when considering electrode location estimates from short-term postoperative CTs, the median distance increased to 2.01 mm (1.55–2.78). <b><i>Conclusions:</i></b> The results of this study suggest that electrode location uncertainty needs to be factored into statistical analyses that attempt to define correlations between stimulation locations and clinical outcomes.
DOI: 10.6084/m9.figshare.23586924.v1
title: Supplementary Material for: Quantifying the Variability Associated with Postoperative Localization of Deep Brain Stimulation Electrodes

description: <b><i>Introduction:</i></b> Computational models of deep brain stimulation (DBS) have become common tools in clinical research studies that attempt to establish correlations between stimulation locations in the brain and behavioral outcome measures. However, the accuracy of any patient-specific DBS model depends heavily upon accurate localization of the DBS electrodes within the anatomy, which is typically defined via co-registration of clinical CT and MRI datasets. Several different approaches exist for this challenging registration problem, and each approach will result in a slightly different electrode localization. The goal of this study was to better understand how different processing steps (e.g., cost-function masking, brain extraction, intensity remapping) affect the estimate of the DBS electrode location in the brain. <b><i>Methods:</i></b> No “gold standard” exists for this kind of analysis, as the exact location of the electrode in the living human brain cannot be determined with existing clinical imaging approaches. However, we can estimate the uncertainty associated with the electrode position, which can be used to guide statistical analyses in DBS mapping studies. Therefore, we used high-quality clinical datasets from 10 subthalamic DBS subjects and co-registered their long-term postoperative CT with their preoperative surgical targeting MRI using 9 different approaches. The distances separating all of the electrode location estimates were calculated for each subject. <b><i>Results:</i></b> On average, electrodes were located within a median distance of 0.57 mm (0.49–0.74) of one another across the different registration approaches. However, when considering electrode location estimates from short-term postoperative CTs, the median distance increased to 2.01 mm (1.55–2.78). <b><i>Conclusions:</i></b> The results of this study suggest that electrode location uncertainty needs to be factored into statistical analyses that attempt to define correlations between stimulation locations and clinical outcomes.
DOI: 10.5281/zenodo.7766790
title: Data files for manuscript "Elucidating the clinical and molecular spectrum of SMARCC2-associated NDD in a cohort of 65 affected individuals"

description: # 2023-06-28<br> # Data files for manuscript "Elucidating the clinical and molecular spectrum of SMARCC2-associated NDD in a cohort of 65 affected individuals"<br> # Summary<br> This ZIP-file contains the supplementary files of our SMARCC2 study "Elucidating the clinical and molecular spectrum of SMARCC2-associated NDD in a cohort of 65 affected individuals". <br> Suppl. File S2 contains comprehensive clinical data<br> Suppl. File S3 contains comprehensive genetic data<br> Suppl. File S4 contains files of the SMARCC2 N-terminal homology model # Folder structure<br> ./ (parent directory containing this README file and all subfolders)<br> ./Files/ (contains Excel Suppl. File S2 and Suppl.File S3, and ZIP Suppl.File S4) # Files and checksums<br> Algorithm Hash Path<br> --------- ---- ----<br> MD5 003A879AA75CF8B5C4E3E05F76C4EB4C SMARCC2-Supplementary\Files\FileS2_cases_clinical-table.xlsx<br> MD5 73B4F9E83419A8404345101CAA4D2205 SMARCC2-Supplementary\Files\FileS3_variants-and-domains.xlsx<br> MD5 B0A12F36B4801EB6C4D21BA02B4270BB SMARCC2-Supplementary\Files\FileS4_SMARCC2 N-terminal homology model.zip
DOI: 10.5281/zenodo.7766791
title: Data files for manuscript "Elucidating the clinical and molecular spectrum of SMARCC2-associated NDD in a cohort of 65 affected individuals"

description: # 2023-03-24<br> # Data files for manuscript "Elucidating the clinical and molecular spectrum of SMARCC2-associated NDD in a cohort of 65 affected individuals"<br> # Summary<br> This ZIP-file contains the supplementary files of our SMARCC2 study "Elucidating the clinical and molecular spectrum of SMARCC2-associated NDD in a cohort of 65 affected individuals". <br> Suppl. File S2 contains comprehensive clinical data<br> Suppl. File S3 contains comprehensive genetic data<br> Suppl. File S4 contains files of the SMARCC2 N-terminal homology model # Folder structure<br> ./ (parent directory containing this README file and all subfolders)<br> ./Files/ (contains Excel Suppl. File S2 and Suppl.File S3, and ZIP Suppl.File S4) # Files and checksums<br> Algorithm Hash Path<br> --------- ---- ----<br> MD5 4D3FCC655A9B27A533BCE873601360A3 SMARCC2-Supplementary\README.txt<br> MD5 794D379C2658179475259C0619EB0EE9 SMARCC2-Supplementary\Files\FileS2_cases_clinical-table.xlsx<br> MD5 73B4F9E83419A8404345101CAA4D2205 SMARCC2-Supplementary\Files\FileS3_variants-and-domains.xlsx<br> MD5 B0A12F36B4801EB6C4D21BA02B4270BB SMARCC2-Supplementary\Files\FileS4_SMARCC2 N-terminal homology model.zip
DOI: 10.5281/zenodo.8091569
title: Data files for manuscript "Elucidating the clinical and molecular spectrum of SMARCC2-associated NDD in a cohort of 65 affected individuals"

description: # 2023-06-28<br> # Data files for manuscript "Elucidating the clinical and molecular spectrum of SMARCC2-associated NDD in a cohort of 65 affected individuals"<br> # Summary<br> This ZIP-file contains the supplementary files of our SMARCC2 study "Elucidating the clinical and molecular spectrum of SMARCC2-associated NDD in a cohort of 65 affected individuals". <br> Suppl. File S2 contains comprehensive clinical data<br> Suppl. File S3 contains comprehensive genetic data<br> Suppl. File S4 contains files of the SMARCC2 N-terminal homology model # Folder structure<br> ./ (parent directory containing this README file and all subfolders)<br> ./Files/ (contains Excel Suppl. File S2 and Suppl.File S3, and ZIP Suppl.File S4) # Files and checksums<br> Algorithm Hash Path<br> --------- ---- ----<br> MD5 003A879AA75CF8B5C4E3E05F76C4EB4C SMARCC2-Supplementary\Files\FileS2_cases_clinical-table.xlsx<br> MD5 73B4F9E83419A8404345101CAA4D2205 SMARCC2-Supplementary\Files\FileS3_variants-and-domains.xlsx<br> MD5 B0A12F36B4801EB6C4D21BA02B4270BB SMARCC2-Supplementary\Files\FileS4_SMARCC2 N-terminal homology model.zip
DOI: 10.5517/ccdc.csd.cc2f7hjq
title: CCDC 2241533: Experimental Crystal Structure Determination

description: Related Article: Anita Lazić, Lidija Radovanović, Jelena Rogan, Nataša Valentić, Goran Janjić, Ivana Đorđević, Nemanja Trišović|2023|CrystEngComm|25|3637|doi:10.1039/D3CE00213F
description: An entry from the Cambridge Structural Database, the world’s repository for small molecule crystal structures. The entry contains experimental data from a crystal diffraction study. The deposited dataset for this entry is freely available from the CCDC and typically includes 3D coordinates, cell parameters, space group, experimental conditions and quality measures.