cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5281/zenodo.6961545
title: ReSPack: A Large-Scale Rectilinear Steiner Tree Packing Benchmark for Wire Routing

description: Combinatorial optimization (CO) has been studied as a useful tool for modeling industrial problems, but it still remains a challenge in complex domains because of the NP-hardness. With recent advances in machine learning, the field of CO is shifting to the study of neural combinatorial optimization using a large amount of data, showing promising results in some CO problems. Rectilinear Steiner Tree Packing Problem (RSTPP) is a well-known CO problem and is widely used in modeling wiring problem among components in a printed circuit board and an integrated circuit design. Despite the importance for a design automation, the lack of availab le data has restricted to fully leverage machine learning approaches. In this paper, we present ReSPack, a large-scale synthetic RSTPP dataset and a benchmark for wire routing. ReSPack includes a source code for generating RSTPP problems of various types with different sizes, data instances generated for the benchmark testing, and implementations of several baseline algorithms. We believe that ReSPack can contribute to solving circuit design problems as well as the development of CO with machine learning.
DOI: 10.6084/m9.figshare.20438159
title: Additional file 2 of MOSCATO: a supervised approach for analyzing multi-Omic single-Cell data

description: Additional file 2 Gene and protein selections.
DOI: 10.6084/m9.figshare.20438159.v1
title: Additional file 2 of MOSCATO: a supervised approach for analyzing multi-Omic single-Cell data

description: Additional file 2 Gene and protein selections.
DOI: 10.6084/m9.figshare.14721791.v1
title: Additional file 1 of MetaVelvet-DL: a MetaVelvet deep learning extension for de novo metagenome assembly

description: Additional file 1.
DOI: 10.6084/m9.figshare.14721791
title: Additional file 1 of MetaVelvet-DL: a MetaVelvet deep learning extension for de novo metagenome assembly

description: Additional file 1.
DOI: 10.6084/m9.figshare.14721794
title: Additional file 2 of MetaVelvet-DL: a MetaVelvet deep learning extension for de novo metagenome assembly

description: Additional file 2.
DOI: 10.6084/m9.figshare.14721794.v1
title: Additional file 2 of MetaVelvet-DL: a MetaVelvet deep learning extension for de novo metagenome assembly

description: Additional file 2.
DOI: 10.6084/m9.figshare.20438189
title: Additional file 2 of SEMplMe: a tool for integrating DNA methylation effects in transcription factor binding affinity predictions

description: Additional file 2 Table S1 Data availability for ChIP-set, WGBS, and DNase-seq used in this study along with empirical p-value estimation for each ChIP-seq dataset (see Methods) Table S2. Starting PWM and cell type used to generate SEMs and all other data shown in figures in this paper.
DOI: 10.6084/m9.figshare.20438189.v1
title: Additional file 2 of SEMplMe: a tool for integrating DNA methylation effects in transcription factor binding affinity predictions

description: Additional file 2 Table S1 Data availability for ChIP-set, WGBS, and DNase-seq used in this study along with empirical p-value estimation for each ChIP-seq dataset (see Methods) Table S2. Starting PWM and cell type used to generate SEMs and all other data shown in figures in this paper.
DOI: 10.4119/unibi/2964881
title: Video Stimuli and Appendix to Stange & Kopp 2020 (Effects of a Social Robot's Self-Explanations on How Humans Understand and Evaluate Its Behavior)
DOI: 10.6084/m9.figshare.20438228.v1
title: Additional file 6 of Assessing cardiovascular parameters and risk factors in physical therapy practice: findings from a cross-sectional national survey and implication for clinical practice

description: Additional file 6. Raw dataset.
DOI: 10.6084/m9.figshare.20438228
title: Additional file 6 of Assessing cardiovascular parameters and risk factors in physical therapy practice: findings from a cross-sectional national survey and implication for clinical practice

description: Additional file 6. Raw dataset.
DOI: 10.6084/m9.figshare.20438285
title: Additional file 2 of Analysis of archaic human haplotypes suggests that 5hmC acts as an epigenetic guide for NCO recombination

description: Additional file 2: Table S1. Summary of data sources.
DOI: 10.6084/m9.figshare.20438288
title: Additional file 3 of Analysis of archaic human haplotypes suggests that 5hmC acts as an epigenetic guide for NCO recombination

description: Additional file 3: Table S2. Details of the Mann-Whitney test statistics on the impact of epigenetic marks on the NCO recombination rate in genomic subregions (Fig. 3A). A description of all the columns in the table is provided in the worksheet "Description" of the ‘supplemental Table 2.xlsx’ file.
DOI: 10.6084/m9.figshare.20282149
title: Additional file 1 of Detecting multiscale periodicity from the secular effusive activity at Santiaguito lava dome complex (Guatemala)

description: Additional file 1: Appendix 1 Cumulative lava volume as calculated from MIROVA data from 2000 to 2021.
DOI: 10.6084/m9.figshare.20282149.v1
title: Additional file 1 of Detecting multiscale periodicity from the secular effusive activity at Santiaguito lava dome complex (Guatemala)

description: Additional file 1: Appendix 1 Cumulative lava volume as calculated from MIROVA data from 2000 to 2021.
DOI: 10.6084/m9.figshare.15128355
title: Additional file 21 of BREC: an R package/Shiny app for automatically identifying heterochromatin boundaries and estimating local recombination rates along chromosomes

description: Addtional file 21. This is a spreadsheet (.xlsx file). It includes accessible links to the genetic and physical maps for the 44 genomes mentioned in Additional file 20. Adapted from the Additional file named Table S1, published by [41].
DOI: 10.6084/m9.figshare.15128355.v1
title: Additional file 21 of BREC: an R package/Shiny app for automatically identifying heterochromatin boundaries and estimating local recombination rates along chromosomes

description: Addtional file 21. This is a spreadsheet (.xlsx file). It includes accessible links to the genetic and physical maps for the 44 genomes mentioned in Additional file 20. Adapted from the Additional file named Table S1, published by [41].
DOI: 10.6084/m9.figshare.20438400
title: Additional file 2 of Methylome decoding of RdDM-mediated reprogramming effects in the Arabidopsis MSH1 system

description: Additional file 2. Epi-line state 4 DMGs and GO enrichment.
DOI: 10.6084/m9.figshare.20438403.v1
title: Additional file 3 of Methylome decoding of RdDM-mediated reprogramming effects in the Arabidopsis MSH1 system

description: Additional file 3. Arabidopsis C24 and Ler F1 DMGs and network enrichments.
DOI: 10.6084/m9.figshare.20438400.v1
title: Additional file 2 of Methylome decoding of RdDM-mediated reprogramming effects in the Arabidopsis MSH1 system

description: Additional file 2. Epi-line state 4 DMGs and GO enrichment.
DOI: 10.6084/m9.figshare.20438406
title: Additional file 4 of Methylome decoding of RdDM-mediated reprogramming effects in the Arabidopsis MSH1 system

description: Additional file 4. Arabidopsis msh1 epi-line state 4 DEG and GO enrichment.
DOI: 10.6084/m9.figshare.20438409
title: Additional file 5 of Methylome decoding of RdDM-mediated reprogramming effects in the Arabidopsis MSH1 system

description: Additional file 5. 871 DMGs shared between four msh1 states.
DOI: 10.6084/m9.figshare.20438403
title: Additional file 3 of Methylome decoding of RdDM-mediated reprogramming effects in the Arabidopsis MSH1 system

description: Additional file 3. Arabidopsis C24 and Ler F1 DMGs and network enrichments.
DOI: 10.6084/m9.figshare.20438406.v1
title: Additional file 4 of Methylome decoding of RdDM-mediated reprogramming effects in the Arabidopsis MSH1 system

description: Additional file 4. Arabidopsis msh1 epi-line state 4 DEG and GO enrichment.
DOI: 10.6084/m9.figshare.20438409.v1
title: Additional file 5 of Methylome decoding of RdDM-mediated reprogramming effects in the Arabidopsis MSH1 system

description: Additional file 5. 871 DMGs shared between four msh1 states.
DOI: 10.6084/m9.figshare.20438412.v1
title: Additional file 6 of Methylome decoding of RdDM-mediated reprogramming effects in the Arabidopsis MSH1 system

description: Additional file 6. TE and sRNA associations with 871 DMGs shared between four msh1 states.
DOI: 10.6084/m9.figshare.20438415
title: Additional file 7 of Methylome decoding of RdDM-mediated reprogramming effects in the Arabidopsis MSH1 system

description: Additional file 7. Cluster 11 and 18 with dcl2/3/4-sensitive DMPs.
DOI: 10.6084/m9.figshare.20438412
title: Additional file 6 of Methylome decoding of RdDM-mediated reprogramming effects in the Arabidopsis MSH1 system

description: Additional file 6. TE and sRNA associations with 871 DMGs shared between four msh1 states.
DOI: 10.6084/m9.figshare.20438415.v1
title: Additional file 7 of Methylome decoding of RdDM-mediated reprogramming effects in the Arabidopsis MSH1 system

description: Additional file 7. Cluster 11 and 18 with dcl2/3/4-sensitive DMPs.
DOI: 10.6084/m9.figshare.20438418
title: Additional file 8 of Methylome decoding of RdDM-mediated reprogramming effects in the Arabidopsis MSH1 system

description: Additional file 8. Cluster motifs within 67 core hub loci.
DOI: 10.6084/m9.figshare.20438418.v1
title: Additional file 8 of Methylome decoding of RdDM-mediated reprogramming effects in the Arabidopsis MSH1 system

description: Additional file 8. Cluster motifs within 67 core hub loci.
DOI: 10.6084/m9.figshare.20438433
title: Additional file 1 of Quantitative microbial population study reveals geographical differences in bacterial symbionts of Ixodes ricinus

description: Additional file 1: Table S1. Metadata for all of the locations including their full names and coordinates as well as information on vegetation and tick density. Table S2. Number of samples collected from different tick life stages at different locations. Table S3. Location and tick life stage per sample.
DOI: 10.6084/m9.figshare.20438433.v1
title: Additional file 1 of Quantitative microbial population study reveals geographical differences in bacterial symbionts of Ixodes ricinus

description: Additional file 1: Table S1. Metadata for all of the locations including their full names and coordinates as well as information on vegetation and tick density. Table S2. Number of samples collected from different tick life stages at different locations. Table S3. Location and tick life stage per sample.
DOI: 10.6084/m9.figshare.20438439
title: Additional file 3 of Quantitative microbial population study reveals geographical differences in bacterial symbionts of Ixodes ricinus

description: Additional file 3: Table S4. Read counts for different taxa, including taxonomy per sample. Negative control samples included. Figure S1. Ordination of community composition with uncorrected abundances. Figure S2. Rarefaction curve of samples coloured by quartile of total bacterial load. Figure S3. Abundances of bacterial phyla separated by quartiles of total bacterial load (16S rRNA content in ng/μL), unscaled (a) or scaled by total bacterial load (b). Table S5. Figure S4. Correlation of Shannon diversity of the unrarefied data to (a) sequencing depth and (b) total bacterial load. Figure S5. Correlation of total bacterial load to (a) sequencing depth and (b) uncorrected count of contaminant sequences. Figure S6. The top 10 genera of negative controls versus the 25% lowest biomass samples.
DOI: 10.6084/m9.figshare.20438439.v1
title: Additional file 3 of Quantitative microbial population study reveals geographical differences in bacterial symbionts of Ixodes ricinus

description: Additional file 3: Table S4. Read counts for different taxa, including taxonomy per sample. Negative control samples included. Figure S1. Ordination of community composition with uncorrected abundances. Figure S2. Rarefaction curve of samples coloured by quartile of total bacterial load. Figure S3. Abundances of bacterial phyla separated by quartiles of total bacterial load (16S rRNA content in ng/μL), unscaled (a) or scaled by total bacterial load (b). Table S5. Figure S4. Correlation of Shannon diversity of the unrarefied data to (a) sequencing depth and (b) total bacterial load. Figure S5. Correlation of total bacterial load to (a) sequencing depth and (b) uncorrected count of contaminant sequences. Figure S6. The top 10 genera of negative controls versus the 25% lowest biomass samples.
DOI: 10.6084/m9.figshare.20438442
title: Additional file 4 of Quantitative microbial population study reveals geographical differences in bacterial symbionts of Ixodes ricinus

description: Additional file 4: Table S5. Results of PERMANOVA testing an effect of tick life stage on community variation, and the analysis of variance. Table S6. Results of models of stage explaining Rickettsia and Rickettsiella abundance. Table S7. Prevalence (%) of tick symbionts in larvae, nymphs and adults of I. ricinus collected in two locations (ST and AW) indicating primary transmission mode (vertical or horizontal). Table S8. Prevalence (%) of tick symbionts in nymphs of I. ricinus collected in 19 forest sites in the Netherlands. Table S9. A list of all haplotypes used in relative occurrence analyses.
DOI: 10.6084/m9.figshare.20438442.v1
title: Additional file 4 of Quantitative microbial population study reveals geographical differences in bacterial symbionts of Ixodes ricinus

description: Additional file 4: Table S5. Results of PERMANOVA testing an effect of tick life stage on community variation, and the analysis of variance. Table S6. Results of models of stage explaining Rickettsia and Rickettsiella abundance. Table S7. Prevalence (%) of tick symbionts in larvae, nymphs and adults of I. ricinus collected in two locations (ST and AW) indicating primary transmission mode (vertical or horizontal). Table S8. Prevalence (%) of tick symbionts in nymphs of I. ricinus collected in 19 forest sites in the Netherlands. Table S9. A list of all haplotypes used in relative occurrence analyses.
DOI: 10.34740/kaggle/dsv/4714649
title: BBC News
DOI: 10.5281/zenodo.7430529
title: Processing code and data for ERA5 analysis

description: Data, processing code, and instructions for ERA5 analysis
DOI: 10.34740/kaggle/dsv/4714688
title: OntoUML/UFO Catalog
DOI: 10.5281/zenodo.7405904
title: Data Extraction table for the study Machine-based Stereotypes: How Machine Learning Algorithms Evaluate Ethnicity from Face Data

description: This table contains the data extraction results for the study Machine-based Stereotypes: How Machine Learning Algorithms Evaluate Ethnicity from Face Data. It contains 24 columns and 74 rows.
DOI: 10.5281/zenodo.7405905
title: Data Extraction table for the study Machine-based Stereotypes: How Machine Learning Algorithms Evaluate Ethnicity from Face Data

description: This table contains the data extraction results for the study Machine-based Stereotypes: How Machine Learning Algorithms Evaluate Ethnicity from Face Data. It contains 24 columns and 74 rows.
DOI: 10.5281/zenodo.7430540
title: Data Extraction table for the study Machine-based Stereotypes: How Machine Learning Algorithms Evaluate Ethnicity from Face Data

description: This table contains the data extraction results for the study Machine-based Stereotypes: How Machine Learning Algorithms Evaluate Ethnicity from Face Data. It contains 24 columns and 74 rows.
DOI: 10.6084/m9.figshare.20290587
title: Increased nighttime oxidants over China despite widespread decrease across the globe

description: Datasets that support the findings of the study "Increased nighttime oxidants over China despite widespread decrease across the globe"
DOI: 10.6084/m9.figshare.20290587.v3
title: Increased nighttime oxidants over China despite widespread decrease across the globe

description: Datasets that support the findings of the study "Global Production and Trends in Nighttime Oxidants – Increases in China, Decreases Elsewhere"
DOI: 10.5441/001/1.mn019k4d
title: Data from: Study "Movements of the Christmas Island flying fox, Australia"

description: Todd CM, Westcott DA, Martin JM, Rose K, McKeown A, Hall J, Welbergen JA. 2022. Body-size dependent foraging strategies in the Christmas Island flying-fox: implications for seed and pollen dispersal within a threatened island ecosystem. Mov Ecol. 10:19. doi:10.1186/s40462-022-00315-8
description: Background: Animals are important vectors for the dispersal of a wide variety of plant species, and thus play a key role in maintaining the health and biodiversity of natural ecosystems. On oceanic islands, flying-foxes are often the only seed dispersers or pollinators. However, many flying-fox populations are currently in decline, particularly those of insular species, and this has consequences for the ecological services they provide. Knowledge of the drivers and the scale of flying-fox movements is important in determining the ecological roles that flying-foxes play on islands. This information is also useful for understanding the potential long-term consequences for forest dynamics resulting from population declines or extinction, and so can aid in the development of evidence-based ecological management strategies. To these ends, we examined the foraging movements, floral resource use, and social interactions of the Critically Endangered Christmas Island flying-fox (Pteropus natalis). Methods: Utilization distributions, using movement-based kernel estimates (MBKE) were generated to determine nightly foraging movements of GPS-tracked P. natalis (n = 24). Generalized linear models (GLMs), linear mixed-effect models (LMMs), and Generalized linear mixed-effects model (GLMMs) were constructed to explain how intrinsic factors (body mass, skeletal size, and sex) affected the extent of foraging movements. In addition, we identified pollen collected from facial and body swabs of P. natalis (n = 216) to determine foraging resource use. Direct observations (n = 272) of foraging P. natalis enabled us to assess the various behaviors used to defend foraging resources. Results: Larger P. natalis individuals spent more time foraging and less time traveling between foraging patches, traveled shorter nightly distances, and had smaller overall foraging ranges than smaller conspecifics. Additionally, larger individuals visited a lower diversity of floral resources. Conclusions: Our findings suggest that smaller P. natalis individuals are the primary vectors of long-distance dispersal of pollen and digested seeds in this species, providing a vital mechanism for maintaining the flow of plant genetic diversity across Christmas Island. Overall, our study highlights the need for more holistic research approaches that incorporate population demographics when assessing a species’ ecological services.
DOI: 10.5441/001/1.mn019k4d/1
title: Movements of the Christmas Island flying fox Australia

description: Todd CM, Westcott DA, Martin JM, Rose K, McKeown A, Hall J, Welbergen JA. 2022. Body-size dependent foraging strategies in the Christmas Island flying-fox: implications for seed and pollen dispersal within a threatened island ecosystem. Mov Ecol. 10:19. doi:10.1186/s40462-022-00315-8
description: Background: Animals are important vectors for the dispersal of a wide variety of plant species, and thus play a key role in maintaining the health and biodiversity of natural ecosystems. On oceanic islands, flying-foxes are often the only seed dispersers or pollinators. However, many flying-fox populations are currently in decline, particularly those of insular species, and this has consequences for the ecological services they provide. Knowledge of the drivers and the scale of flying-fox movements is important in determining the ecological roles that flying-foxes play on islands. This information is also useful for understanding the potential long-term consequences for forest dynamics resulting from population declines or extinction, and so can aid in the development of evidence-based ecological management strategies. To these ends, we examined the foraging movements, floral resource use, and social interactions of the Critically Endangered Christmas Island flying-fox (Pteropus natalis). Methods: Utilization distributions, using movement-based kernel estimates (MBKE) were generated to determine nightly foraging movements of GPS-tracked P. natalis (n = 24). Generalized linear models (GLMs), linear mixed-effect models (LMMs), and Generalized linear mixed-effects model (GLMMs) were constructed to explain how intrinsic factors (body mass, skeletal size, and sex) affected the extent of foraging movements. In addition, we identified pollen collected from facial and body swabs of P. natalis (n = 216) to determine foraging resource use. Direct observations (n = 272) of foraging P. natalis enabled us to assess the various behaviors used to defend foraging resources. Results: Larger P. natalis individuals spent more time foraging and less time traveling between foraging patches, traveled shorter nightly distances, and had smaller overall foraging ranges than smaller conspecifics. Additionally, larger individuals visited a lower diversity of floral resources. Conclusions: Our findings suggest that smaller P. natalis individuals are the primary vectors of long-distance dispersal of pollen and digested seeds in this species, providing a vital mechanism for maintaining the flow of plant genetic diversity across Christmas Island. Overall, our study highlights the need for more holistic research approaches that incorporate population demographics when assessing a species’ ecological services.