cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.25381/cput.25041329.v1
title: FIGURE 7 in Worming its way in-Polydora websteri (Annelida: Spionidae) increases the number of non-indigenous shell-boring polydorin pests of cultured molluscs in South Africa

description: FIGURE 7. Lectotype specimen of Polydora websteri (LACM-AHF POLY 1628) from oyster shells and deposited in the Los Angeles County Museum of Natural History (Radashevsky, 1999), stained with methyl-green. (A) dorsal anterior, scale bar: 1 mm, (B) dorsal anterior, scale bar: 0.25 mm, (C) ventral anterior, scale bar: 1 mm, (D) dorsal mid-body, scale bar: 1 mm, (E) latero-posterior; scale bar: 0.25mm (F) posterior; scale bar: 1 mm. Photographed by Adam Wall (Los Angeles County Museum of Natural History, August 2019).
DOI: 10.25381/cput.25041155
title: Data from: First circumglobal assessment of Southern Hemisphere humpback whale mitochondrial genetic variation and implications for management

description: The description of genetic population structure over a species' geographic range can provide insights into its evolutionary history and also support effective management efforts. Assessments for globally distributed species are rare, however, requiring significant international coordination and collaboration. The global distribution of demographically discrete populations for the humpback whale Megaptera novaeangliae is not fully known, hampering the definition of appropriate management units. Here, we present the first circumglobal assessment of mitochondrial genetic population structure across the species' range in the Southern Hemisphere and Arabian Sea. We combine new and existing data from the mitochondrial (mt)DNA control region that resulted in a 311 bp consensus sequence of the mtDNA control region for 3009 individuals sampled across 14 breeding stocks and subpopulations currently recognized by the International Whaling Commission. We assess genetic diversity and test for genetic differentiation and also estimate the magnitude and directionality of historic matrilineal gene flow between putative populations. Our results indicate that maternally directed site fidelity drives significant genetic population structure between breeding stocks within ocean basins. However, patterns of connectivity differ across the circumpolar range, possibly as a result of differences in the extent of longitudinal movements on feeding areas. The number of population comparisons observed to be significantly differentiated were found to diminish at the subpopulation scale when nucleotide differences were examined, indicating that more complex processes underlie genetic structure at this scale. It is crucial that these complexities and uncertainties are afforded greater consideration in management and regulatory efforts.
DOI: 10.25381/cput.25041155.v1
title: Data from: First circumglobal assessment of Southern Hemisphere humpback whale mitochondrial genetic variation and implications for management

description: The description of genetic population structure over a species' geographic range can provide insights into its evolutionary history and also support effective management efforts. Assessments for globally distributed species are rare, however, requiring significant international coordination and collaboration. The global distribution of demographically discrete populations for the humpback whale Megaptera novaeangliae is not fully known, hampering the definition of appropriate management units. Here, we present the first circumglobal assessment of mitochondrial genetic population structure across the species' range in the Southern Hemisphere and Arabian Sea. We combine new and existing data from the mitochondrial (mt)DNA control region that resulted in a 311 bp consensus sequence of the mtDNA control region for 3009 individuals sampled across 14 breeding stocks and subpopulations currently recognized by the International Whaling Commission. We assess genetic diversity and test for genetic differentiation and also estimate the magnitude and directionality of historic matrilineal gene flow between putative populations. Our results indicate that maternally directed site fidelity drives significant genetic population structure between breeding stocks within ocean basins. However, patterns of connectivity differ across the circumpolar range, possibly as a result of differences in the extent of longitudinal movements on feeding areas. The number of population comparisons observed to be significantly differentiated were found to diminish at the subpopulation scale when nucleotide differences were examined, indicating that more complex processes underlie genetic structure at this scale. It is crucial that these complexities and uncertainties are afforded greater consideration in management and regulatory efforts.
DOI: 10.6084/m9.figshare.25041389
title: assignment2

description: Artificial intelligence
DOI: 10.6084/m9.figshare.25041389.v1
title: assignment2

description: Artificial intelligence
DOI: 10.5281/zenodo.10551749
title: The supplementary for "Differential Expression of miRNA-769-5p and Smad2 in Patients with or without Oral cGVHD "
DOI: 10.5281/zenodo.10551750
title: The supplementary for "Differential Expression of miRNA-769-5p and Smad2 in Patients with or without Oral cGVHD "
DOI: 10.5281/zenodo.8233582
title: Hexanematic crossover in epithelial monolayers depends on cell adhesion and cell density.

description: Raw data files concerning the publication,

Hexanematic crossover in epithelial monolayers depends on cell adhesion and cell densityJulia Eckert, Benoit Ladoux, Rene-Marc Mege, Luca Giomi and Thomas SchmidtNature Communications (2023) 14:5762.doi: https://doi.org/10.1038/s41467-023-41449-6Abstract:

Changes in tissue geometry during developmental processes are associated with collective migration of cells. Recent experimental and numerical results suggest that these changes could leverage on the coexistence of nematic and hexatic orientational order at different length scales. How this multiscale organization is affected by the material properties of the cells and their substrate is presently unknown. In this study, we address these questions in monolayers of Madin-Darby canine kidney cells having various cell densities and molecular repertoires. At small length scales, confluent monolayers are characterized by a prominent hexatic order, independent of the presence of E-cadherin, monolayer density, and underlying substrate stiffness. However, all three properties affect the meso-scale tissue organization. The length scale at which hexatic order transits to nematic order, the ”hexanematic” crossover scale, strongly depends on cell-cell adhesions and correlates with monolayer density. Our study demonstrates how epithelial organization is affected by mechanical properties, and provides a robust description of tissue organization during developmental processes.

 

Data description:

WT.zip  - zipped raw image data and extracted vertices of experiments on wild-type cellsKO.zip  - zipped raw image data and extracted vertices of experiments on eCad KO-cellsFigureData.zip  - zipped data referring to each of the figures in the paper

 

Software:

The software to analyze the data presented here is found on GitHub, [https://github.com/hexanematic/orientation tracker]
description: microscopy data, epithelial cell sheets
DOI: 10.5281/zenodo.10551751
title: Published version of the SSATD Dataset

description: The SSATD dataset curated for the paper "What Can Self-Admitted Technical Debt Tell Us About Security? A Mixed-Methods Study" Díaz Ferreyra, Nicolás E., Shahin, Mojtaba, Zahedi, Mansorreh, and Scandariato, Ricardo. Submitted to the 21th International Conference on Mining Software Repositories (MSR '24) 2024
DOI: 10.5281/zenodo.10551752
title: Published version of the SSATD Dataset

description: The SSATD dataset curated for the paper "What Can Self-Admitted Technical Debt Tell Us About Security? A Mixed-Methods Study" Díaz Ferreyra, Nicolás E., Shahin, Mojtaba, Zahedi, Mansorreh, and Scandariato, Ricardo. Submitted to the 21th International Conference on Mining Software Repositories (MSR '24) 2024
DOI: 10.5281/zenodo.10551783
title: Proteomic Files for individuals buried at Histria, Romania

description: This repository includes the proteomic files that were included in "Ancient DNA and paleoproteomic analysis on Roman Imperial-era individuals from Histria, Romania".
DOI: 10.5281/zenodo.10551784
title: Proteomic Files for individuals buried at Histria, Romania

description: This repository includes the proteomic files that were included in "Ancient DNA and paleoproteomic analysis on Roman Imperial-era individuals from Histria, Romania".
DOI: 10.6084/m9.figshare.25041491
title: 20240123_starrydata2

description: All data on Starrydata2, a database of experimental properties in the field of inorganic materials
DOI: 10.6073/pasta/47e34a5ccc6f9ece84b12b04bf79562e
title: Visual Counts of Tree Reproduction near NEON plots at Harvard Forest since 2020

description: Mast seeding, a resource pulse that has cascading effects in the environment, is a measure that can provide insight into forest dynamics. When masting data is collected in sequential years it can provide information on how tree populations are responding to climatic and environmental variables, and can also be used to relate to other indices, such as seed-eating animal species. The objective of this study is to quantify the yearly seed production of mast seeding tree species at Harvard Forest which are located near National Ecological Observatory Network (NEON) plots. This project is part of larger NEON-enabled project examining mast seeding on a continental scale at 25 NEON sites in the United States, which uses mast seeding records in conjunction with NEON collected data products like mammal box-trapping, tick drags, and bird point counts. Data collected on mast seeding can be linked to these other indices at regional and continental scales.
DOI: 10.6084/m9.figshare.25041491.v1
title: 20240123_starrydata2

description: All data on Starrydata2, a database of experimental properties in the field of inorganic materials
DOI: 10.5281/zenodo.5833782
title: Data on: Impact of neurite alignment on organelle motion

description: Impact of neurite alignment on organelle motion.

Maria Mytiliniou, Joeri A. J. Wondergem, Thomas Schmidt, Doris Heinrich.J. R. Soc. Interface 19:20210617.doi: https://doi.org/10.1098/rsif.2021.0617

Abstract

Intracellular transport is pivotal for cell growth and survival. Malfunctions in this process have been associated with devastating neurodegenerative diseases, posing a need for deeper understanding of the involved mechanisms. Here, we used an experimental methodology that lead neurites of differentiated PC12 cells in either of two configurations: an one-dimensional, where the neurites align along lines, or a two-dimensional configuration, where the neurites adopt a random orientation and shape on a flat substrate. We subsequently monitored the motion of functional organelles, the lysosomes, inside the neurites. Implementing a time-resolved analysis of the mean-squared displacement, we quantitatively characterized distinct motion modes of the lysosomes. Our results indicate that neurite alignment gives rise to faster diiffusive and super-diiffusive lysosomal motion in comparison to the situation where the neurites are randomly oriented. After inducing lysosome swelling through an osmotic challenge by sucrose, we confirmed the predicted slowdown in diffusive mobility. Surprisingly we found that the swelling-induced mobility change affected each of the (sub- /super-) diiffusive motion modes differently and depended on the alignment configuration of the neurites. Our findings imply that intracellular transport is significantly and robustly dependent on cell morphology, which might be in part controlled by the extracellular matrix.
DOI: 10.5281/zenodo.5833783
title: Data on: Impact of neurite alignment on organelle motion

description: Impact of neurite alignment on organelle motion.

Maria Mytiliniou, Joeri A. J. Wondergem, Thomas Schmidt, Doris Heinrich.J. R. Soc. Interface 19:20210617.doi: https://doi.org/10.1098/rsif.2021.0617

Abstract

Intracellular transport is pivotal for cell growth and survival. Malfunctions in this process have been associated with devastating neurodegenerative diseases, posing a need for deeper understanding of the involved mechanisms. Here, we used an experimental methodology that lead neurites of differentiated PC12 cells in either of two configurations: an one-dimensional, where the neurites align along lines, or a two-dimensional configuration, where the neurites adopt a random orientation and shape on a flat substrate. We subsequently monitored the motion of functional organelles, the lysosomes, inside the neurites. Implementing a time-resolved analysis of the mean-squared displacement, we quantitatively characterized distinct motion modes of the lysosomes. Our results indicate that neurite alignment gives rise to faster diiffusive and super-diiffusive lysosomal motion in comparison to the situation where the neurites are randomly oriented. After inducing lysosome swelling through an osmotic challenge by sucrose, we confirmed the predicted slowdown in diffusive mobility. Surprisingly we found that the swelling-induced mobility change affected each of the (sub- /super-) diiffusive motion modes differently and depended on the alignment configuration of the neurites. Our findings imply that intracellular transport is significantly and robustly dependent on cell morphology, which might be in part controlled by the extracellular matrix.
DOI: 10.25381/cput.25041467
title: Data from: Incorporating non-equilibrium dynamics into demographic history inferences of a migratory marine species

description: Understanding how dispersal and gene flow link geographically separated populations over evolutionary history is challenging, particularly in migratory marine species. In southern right whales (SRWs, Eubalaena australis), patterns of genetic diversity are likely influenced by the glacial climate cycle and recent history of whaling. Here we use a dataset of mitochondrial DNA (mtDNA) sequences (n=1,327) and nuclear markers (17 microsatellite loci, n=222) from major wintering grounds to investigate circumpolar population structure, historical demography, and effective population size. Analyses of nuclear genetic variation identify two population clusters that correspond to the South Atlantic and Indo-Pacific ocean basins that have similar effective breeder estimates. In contrast, all wintering grounds show significant differentiation for mtDNA, but no sex-biased dispersal was detected using the microsatellite genotypes. An approximate Bayesian computation (ABC) approac h with microsatellite markers compared scenarios with gene flow through time, or isolation and secondary contact between ocean basins, while modeling declines in abundance linked to whaling. Secondary-contact scenarios yield the highest posterior probabilities, implying that populations in different ocean basins were largely isolated and came into secondary contact within the last 25,000 years, but the role of whaling in changes in genetic diversity and gene flow over recent generations could not be resolved. We hypothesise that these findings are driven by factors that promote isolation, such as female philopatry, and factors that could promote dispersal, such oceanographic changes. These findings highlight the application of ABC approaches to infer connectivity in mobile species with complex population histories and currently low levels of differentiation.
DOI: 10.25381/cput.25041467.v1
title: Data from: Incorporating non-equilibrium dynamics into demographic history inferences of a migratory marine species

description: Understanding how dispersal and gene flow link geographically separated populations over evolutionary history is challenging, particularly in migratory marine species. In southern right whales (SRWs, Eubalaena australis), patterns of genetic diversity are likely influenced by the glacial climate cycle and recent history of whaling. Here we use a dataset of mitochondrial DNA (mtDNA) sequences (n=1,327) and nuclear markers (17 microsatellite loci, n=222) from major wintering grounds to investigate circumpolar population structure, historical demography, and effective population size. Analyses of nuclear genetic variation identify two population clusters that correspond to the South Atlantic and Indo-Pacific ocean basins that have similar effective breeder estimates. In contrast, all wintering grounds show significant differentiation for mtDNA, but no sex-biased dispersal was detected using the microsatellite genotypes. An approximate Bayesian computation (ABC) approac h with microsatellite markers compared scenarios with gene flow through time, or isolation and secondary contact between ocean basins, while modeling declines in abundance linked to whaling. Secondary-contact scenarios yield the highest posterior probabilities, implying that populations in different ocean basins were largely isolated and came into secondary contact within the last 25,000 years, but the role of whaling in changes in genetic diversity and gene flow over recent generations could not be resolved. We hypothesise that these findings are driven by factors that promote isolation, such as female philopatry, and factors that could promote dispersal, such oceanographic changes. These findings highlight the application of ABC approaches to infer connectivity in mobile species with complex population histories and currently low levels of differentiation.
DOI: 10.57745/v2weew
title: ANR_HEMERALD_101016joptmat2023114319_ReadMe_20230903_V0.txt

description: Read Me file
DOI: 10.57745/u5xri7
title: ANR_HEMERALD_101016joptmat2023114319_Fig3a_20230903_V0.jpg

description: Figure 3a
DOI: 10.57745/g11rco
title: ANR_HEMERALD_101016joptmat2023114319_Fig3_20230903_V0.jpg

description: Figure 3
DOI: 10.57745/iwrdla
title: ANR_HEMERALD_101016joptmat2023114319_Data_Fig3a_20230903_V0.opj

description: Data of Transmission spectra of Y3NbO7:Ho3+ transparent ceramics according to sintering conditions (HIP dwell time was 1 h)
DOI: 10.5281/zenodo.7689832
title: Ru(0001) surface phonon spectra

description: The file contains raw data of phonon spectra of a Ru(0001) surface and the DFT calculation used to interpret them.
DOI: 10.6084/m9.figshare.25041545
title: Supplementary Material for: Tattoo pigment biokinetics in vivo in a 28-day porcine model: elements undergo fast distribution to lymph nodes and reach steady state after 7 days

description: Pigments of tattoo inks may over time migrate to other parts of the body. Inks kinetics are still poorly understood and little studied. The aim of this first study was to investigate the kinetics of tattoo inks pigment in tattooed porcine skin, which is closer to human skin than mouse skin studied in the past. Three animals were tattooed on the inner thigh and one animal served as untreated control. Skin biopsies were taken on days 7, 14, and 28 after tattooing. Animals were sacrificed on day 28 and homogenate samples of the liver, spleen, kidney, and brain, as well the local lymph nodes were prepared. All samples were analyzed for ink components using inductively coupled plasma-mass spectrometry (ICP-MS). The ink itself was characterized by dynamic light scattering (DLS) and matrix assisted laser desorption-Ionization (MALDI) mass analysis. Titanium (212 g/kg), copper (6 mg/kg), aluminum (1 mg/kg), zirconium (1 mg/kg) and chromium (3 mg/kg) were found in the ink. Significant deposits of ink elements were detected in the tattooed skin when compared to non-tattooed skin from the same animal (mean±standard deviation: titanium 24081 mg/kg, copper 95  39 mg/kg, aluminum 11563 mg/kg, zirconium 2312 mg/kg, and chromium 1.00.2 mg/kg; p &lt; 0.05). Lymph node concentrations of titanium, copper, aluminum, zirconium, and chromium were 422 mg/kg, 6925 mg/kg, 4918 mg/kg, 0.30.2 mg/kg, 0.50.2 mg/kg, respectively. Deposits in skin were unchanged from day 7-28 indicating no redistribution or elimination. No significant deposits of ink elements were found in the liver, spleen, kidney, and brain. In conclusion, our findings confirmed distribution of elements from tattoos to regional lymph nodes, but neither to excretory organs, e.g. liver and kidney, nor to spleen and brain. Thus systemic internal organ exposure was not found.
DOI: 10.5281/zenodo.7041600
title: Automatically Reproducing Timing-Dependent Flaky-Test Failures

description: This artifact contains the source code for FlakeRake, a tool for automatically reproducing timing-dependent flaky-test failures. It also includes raw and processed results produced in the evaluation of FlakeRake Contents: Timing-related APIs that FlakeRake considers adding sleeps at: timing-related-apis Anonymized code for FlakeRake (not runnable in its anonymized state, but included for reference; we will publicly release the non-anonymized code under an open source license pending double-blind review): flakerake.tgz Failure messages extracted from the FlakeFlagger dataset: 10k_reruns_failures_by_test.csv.gz Output from running isolated reruns on each flaky test in the FlakeFlager dataset: 10k_isolated_reruns_all_results.csv.gz (all test results summarized into a CSV), 10k_isolated_reruns_failures_by_test.csv.gz (CSV including just test failures, including failure messages), 10k_isolated_reruns_raw_results.tgz (includes all raw results from reruns, including the XML files output by maven) Output from running the FlakeFlagger replication study (non-isolated 10k reruns):flakeFlaggerReplResults.csv.gz (all test results summarized into a CSV), 10k_reruns_failures_by_test.csv.gz (CSV including just failures, including failure messages), flakeFlaggerRepl_raw_results.tgz (includes all raw results from reruns, including the XML files output by maven - this file is markedly larger than the 10k isolated reruns results because we ran *all* tests in this experiment, whereas the 10k isolated rerun experiment only re-ran the tests that were known to be flaky from the FlakeFlagger dataset). Output from running FlakeRake on each flaky test in the FlakeFlagger dataset: For bisection mode: results-bis.tgz For one-by-one mode: results-obo.tgz Scripts used to execute FlakeRake using an HPC cluster: execution-scripts.tgz<br> Scripts used to execute rerun experiments using an HPC cluster: flakeFlaggerReplScripts.tgz<br> Scripts used to parse the "raw" maven test result XML files in this artifact into the CSV files contained in this artifact: parseSurefireXMLs.tgz Output from running FlakeRake in “reproduction” mode, attempting to reproduce each of the failures that matched the FlakeFlagger dataset (collected for bisection mode only): results-repro-bis.tgz Analysis of timing-dependent API calls in the failure inducing configurations that matched FlakeFlagger failures: bis-sleepyline.cause-to-matched-fail-configs-found.csv
DOI: 10.17638/datacat.liverpool.ac.uk/1989
title: Superionic lithium transport via multiple coordination environments defined by two anion packing

description: Fast cation transport in solids underpins energy storage. Materials design has focused on structures that can define transport pathways with minimal cation coordination change, restricting attention to a small part of chemical space. Motivated by the greater structural diversity of binary intermetallics than that of the metallic elements, we use two anions to build a pathway for three-dimensional superionic lithium ion conductivity that exploits multiple cation coordination environments. Li7Si2S7I is a pure lithium ion conductor created by an ordering of sulphide and iodide that combines elements of hexagonal and cubic close-packing analogously to the structure of NiZr. The resulting diverse network of lithium positions with distinct geometries and anion coordination chemistries affords low barriers to transport, opening a large structural space for high cation conductivity.
description: README files are provided within separate data folders.