cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.25850/nioz/7b.b.hc
title: Viral lysis modifies seasonal phytoplankton dynamics and carbon flow in the Southern Ocean

description: Phytoplankton form the base of marine food webs and are a primary means for carbon export in the Southern Ocean, a key area for global pCO2 drawdown. Viral lysis and grazing have very different effects on microbial community dynamics and carbon export, yet, very little is known about the relative magnitude and ecological impact of viral lysis on natural phytoplankton communities, especially in Antarctic waters. Here, we report on the temporal dynamics and relative importance of viral lysis rates, in comparison to grazing, for Antarctic nano- and pico-sized phytoplankton of varied taxonomy and size over a full productive season. Our results show that viral lysis was a major loss factor throughout the season, responsible for roughly half (58%) of seasonal phytoplankton carbon losses. Viral lysis appeared critically important for explaining temporal dynamics and for obtaining a complete seasonal mass balance of Antarctic phytoplankton. Group-specific responses indicated a negative correlation between grazing and viral losses in Phaeocystis and picoeukaryotes, while for other phytoplankton groups losses were more evenly spread throughout the season. Cryptophyte mortality was dominated by viral lysis, whereas small diatoms were mostly grazed. Larger diatoms dominated algal carbon flow and a single ???lysis event??? directed &gt; 100% of daily carbon production away from higher trophic levels. This study highlights the need to consider viral lysis of key Antarctic phytoplankton for a better understanding of microbial community interactions and more accurate predictions of organic matter flux in this climate-sensitive region.
DOI: 10.6084/m9.figshare.23822784.v1
title: Niche and ecosystem preference of earliest diverging fungi in soils

description: Within the supergroup Rotosphaeromycetes, or “Holomycota”/“Nucletmycea”, there are several well-recognised unicellular clades in the earliest diverging fungi (EDF). However, we know little about their occurrence. Here, we investigated EDF in the rhizosphere and bulk soils from cropland, forest, orchard, and wetland ecosystems around the Beijing-Hebei area, China, to illustrate their niche and ecosystem preference. More than 500 new operational taxonomic units (OTUs) of EDF were detected based on the 18S rRNA genes. Microsporida and Aphelida constitute dominant groups, whereas Rozellosporida was quite rare. Although the EDF community was site-specific, the soil chemical characteristics, vegetation, and other eukaryotic microorganisms were the key factors driving the occurrence of EDF. Moreover, the stochastic process consisted the most of the EDF community assembly.
DOI: 10.25850/nioz/7b.b.nd
title: Vulnerable wildlife concentrations at the Mauritanian Shelf - Atlas of area sensitivity to surface pollutants. NIOZ Report 2022-04

description: Maritime transport associated with the Grand Tortue Ahmeyim (GTA) gas development project will increase risks for marine wildlife (seabirds and cetaeceans) of the existing threat for accidental spills by international maritime transport, or condensate spills or leakages due to for example ruptures of the wet gas pipeline as a result from fishing activities, accidents, or sabotage. When an accidental spill occurs, this vulnerability atlas will provide decision makers with easy to digest information on particularly sensitive area, enabling them to see, at a glance, and even before anything happened, when and where sea areas are at risk and where to prioritise clean-up/containment efforts in a crisis situation to protect marine wildlife and fishery resources. The vulnerability of seabirds to oil (or hydrocarbon) pollution in Mauritania was assessed by parameterising an Oil Vulnerability Index (OVI), used in combination with area specific spatial information on the distribution and density of marine birds (estimates of relative abundance based on state of the art, effort-corrected survey data). The resulting maps predict which areas are most at risk from hydrocarbon spills when they occur. Traditionally, vulnerability atlases for hydrocarbon pollution are based solely on (sensitive) seabird abundance data, while the presence and abundance of other megafauna is often put aside. Given the global importance of the Mauritanian slope and shelf area, sightings of cetaceans are added as exact plots, to integrate data and to highlight particular biodiversity hotspot areas.
DOI: 10.25850/nioz/7b.b.nf
title: Wadden Sea paper - R script

description: R-script for analysis of Cascabel data for Publication "Diel and seasonal methane dynamics in the shallow and turbulent Wadden Sea"
DOI: 10.25850/nioz/7b.b.pf
title: Wadden Sea manuscript available data

description: All data used for the Manuscript titled: Diel and seasonal methane dynamics in the shallow and turbulent Wadden Sea
DOI: 10.6084/m9.figshare.24166356
title: Ulopsin

description: Evolution
DOI: 10.6084/m9.figshare.24171246
title: My data_FEJ.xlsx

description: This data contains socio-demographic clinical and behavioural characteristics of children living with disability who attend three specific special needs institution in Cameroon.
DOI: 10.25850/nioz/7b.b.zc
title: Waddenmozaiek cruise report bemonstering sublitoraal Nederlandse Waddenzee 2019

description: Cruise report with some preliminary results of the first subtidal sampling campaign covering the entire Dutch Wadden Sea. The results presented in this cruise report are based on field data.
DOI: 10.6084/m9.figshare.24171411
title: Global metabolomic profiling of congenital heart defects and controls

description: Patients were enrolled into biobank programs at two separate institutions. A small volume of blood (1 mL) was collected in EDTA-coated tubes in the first month of the NICU hospitalization and prior to any cardiac surgery for CHD cases. EDTA tubes were centrifuged within six hours of collection at 1,850 g for 10 minutes at 4⁰C. Approximately 100 to 200 μL of plasma was extracted without disturbing the buffy coat and stored at -80⁰C. Patients from both institutions were selected and divided into three groups based on cardiac phenotype: cyanotic CHD, non-cyanotic (normoxic) CHD, and normoxic controls without CHD. Inclusion criteria for control patients were the absence of cardiopulmonary anomalies, gestational age greater than 32 weeks, absent or minimal respiratory support, as defined as non-invasive respiratory support with fractional inspired oxygen (FiO<sub>2</sub>) of 21% (room air) with maintained normal oxygen saturations. Exclusion criteria were syndromic genetic conditions, mechanical ventilation, or requirement of supplemental oxygen (FiO<sub>2</sub> &gt; 21%). Global plasma metabolite profiling (UPLC-MS/MS) was performed on cyanotic CHD patients (n = 27), non-cyanotic CHD (n = 11), and normoxic controls without CHD (n = 12).
DOI: 10.6084/m9.figshare.24171411.v1
title: Global metabolomic profiling of congenital heart defects and controls

description: Patients were enrolled into biobank programs at two separate institutions. A small volume of blood (1 mL) was collected in EDTA-coated tubes in the first month of the NICU hospitalization and prior to any cardiac surgery for CHD cases. EDTA tubes were centrifuged within six hours of collection at 1,850 g for 10 minutes at 4⁰C. Approximately 100 to 200 μL of plasma was extracted without disturbing the buffy coat and stored at -80⁰C. Patients from both institutions were selected and divided into three groups based on cardiac phenotype: cyanotic CHD, non-cyanotic (normoxic) CHD, and normoxic controls without CHD. Inclusion criteria for control patients were the absence of cardiopulmonary anomalies, gestational age greater than 32 weeks, absent or minimal respiratory support, as defined as non-invasive respiratory support with fractional inspired oxygen (FiO<sub>2</sub>) of 21% (room air) with maintained normal oxygen saturations. Exclusion criteria were syndromic genetic conditions, mechanical ventilation, or requirement of supplemental oxygen (FiO<sub>2</sub> &gt; 21%). Global plasma metabolite profiling (UPLC-MS/MS) was performed on cyanotic CHD patients (n = 27), non-cyanotic CHD (n = 11), and normoxic controls without CHD (n = 12).
DOI: 10.6084/m9.figshare.24279211
title: Gap-free genome assembly of hybrid poplar "84K"

description: We applied a trio-binning design and Pacific Bioscience High-Fidelity long-read sequencing to obtain haplotype-phased telomere-to-telomere genome assemblies for the two parents of the well-studied F<sub>1</sub> hybrid “84K”, <i>Populus alba</i> × <i>P. tremula</i> var. <i>glandulosa</i>. Almost the entire telomeres and centromeres were assembled for each haplotype subgenome, leaving only two small gaps for one chromosome.
DOI: 10.6084/m9.figshare.24279211.v1
title: Gap-free genome assembly of hybrid poplar "84K"

description: We applied a trio-binning design and Pacific Bioscience High-Fidelity long-read sequencing to obtain haplotype-phased telomere-to-telomere genome assemblies for the two parents of the well-studied F<sub>1</sub> hybrid “84K”, <i>Populus alba</i> × <i>P. tremula</i> var. <i>glandulosa</i>. Almost the entire telomeres and centromeres were assembled for each haplotype subgenome, leaving only two small gaps for one chromosome.
DOI: 10.6084/m9.figshare.24421024.v1
title: lanius

description: Nesting in territories of Lanius minor and number of farm and modern houses
DOI: 10.6084/m9.figshare.24421024.v2
title: lanius

description: Nesting in territories of Lanius minor and number of farm and modern houses. R code for calculation of home-ranges and GLM models.
DOI: 10.6084/m9.figshare.24473197.v1
title: Supporting Error Chains in Static Analysis for Precise Evaluation Results and Enhanced Usability

description: Abstract<b>Context:</b> Static analyses are well-established to aid in understanding bugs or vulnerabilities during the development process or in large-scale studies. A low false positive rate is essential for the adaption in practice and for precise results of empirical studies. Unfortunately, static analyses tend to report where a vulnerability manifests rather than the fix location. This can cause presumed false positives or imprecise results.<b> </b><b>Method:</b> To address this problem, we designed an adaption of an existing static analysis algorithm that can distinguish between a manifestation and fix location and reports error chains. Each error chain presents the dependency between the fix location with at least one manifestation location. We used our tool for a case study of 471 GitHub repositories and conducted an expert interview to investigate usability implications of the change. Further, we benchmarked both analysis versions to compare the runtime impact.<b> Result:</b> We found that 50% of the projects with a report had at least one error chain. During our expert interview, all participants required fewer executions of the static analysis if they used our adapted version. Our performance benchmark demonstrated that our improvement caused only a minimal runtime overhead of less than 4%.<b> </b><b>Conclusion:</b> Our results indicate that error chains occur frequently in real-world projects and ignoring them can lead to imprecise evaluation results. The performance benchmark indicates that our tool is a feasible and efficient solution for detecting error-chains in real-world projects. Further, our results indicate that the usability of static analyses benefits from supporting error chains.<br>DataThis artefact as of now contains information about the expert interview, see <code>expertinterview.md</code> for more details. Further, we include the graphics for the runtime evaluation. <br>
DOI: 10.6084/m9.figshare.24494605
title: Raw data from Boultby et al 2024, published in the Royal Society Open Science

description: Raw data from the study Boultby et al 2024, published in the Royal Society Open Science. The paper is entitled: Using isotopic fingerprints in gastropod shells to validate commercial production pathway and geographic provenance
DOI: 10.6084/m9.figshare.24502210.v1
title: The first demonstration of entirely roll-to-roll fabricated perovskite solar cell modules under ambient room conditions

description: XRD of printed perovskite
Device performance data of roll-to-roll fabricated perovskite solar cells and a module
DOI: 10.6084/m9.figshare.24502210
title: The first demonstration of entirely roll-to-roll fabricated perovskite solar cell modules under ambient room conditions

description: XRD of printed perovskite
Device performance data of roll-to-roll fabricated perovskite solar cells and a module
DOI: 10.6084/m9.figshare.24518593
title: Full-spectrum metabolism-LCMS raw data and Supplemental Table

description: Full-spectrum metabolism-LCMS raw data of the article
DOI: 10.6084/m9.figshare.24518593.v1
title: Full-spectrum metabolism-LCMS raw data

description: Full-spectrum metabolism-LCMS raw data of the article
DOI: 10.6084/m9.figshare.24518593.v2
title: Full-spectrum metabolism-LCMS raw data

description: Full-spectrum metabolism-LCMS raw data of the article
DOI: 10.6084/m9.figshare.24518593.v3
title: Full-spectrum metabolism-LCMS raw data and Supplemental Table

description: Full-spectrum metabolism-LCMS raw data of the article
DOI: 10.6084/m9.figshare.24518593.v4
title: Full-spectrum metabolism-LCMS raw data and Supplemental Table

description: Full-spectrum metabolism-LCMS raw data of the article
DOI: 10.6084/m9.figshare.24599430
title: Building <i>in vitro</i> tools for livestock genomics: chromosomal variation within the PK15 cell line

description: Data from "Building <i>in vitro</i> tools for livestock genomics: chromosomal variation within the PK15 cell line"<b>Coverage files from whole-genome sequencing</b>The coverage textfiles are <i>bedtools coverage</i> output from whole-genome sequencing of two PK15 samples (university laboratory and ATCC), and of fibroblasts.<b>Variants called from whole-genome sequencing</b>A vcf file of variants called from whole-genome sequencing of two PK15 samples (university laboratory and ATCC), and of fibroblasts. The "_AD.txt" files contain allelic coverage depth extracted from these variants by means of bcftools query.<b>Variants called from RNA sequencing</b>A vcf file of SNPs called from publicly available PK15 sequencing.Also, allelic coverage depth file extracted from these variants by means of <i>bcftools query</i>.
DOI: 10.6084/m9.figshare.24599430.v1
title: Building <i>in vitro</i> tools for livestock genomics: chromosomal variation within the PK15 cell line

description: Data from "Building <i>in vitro</i> tools for livestock genomics: chromosomal variation within the PK15 cell line"<b>Coverage files from whole-genome sequencing</b>The coverage textfiles are <i>bedtools coverage</i> output from whole-genome sequencing of two PK15 samples (university laboratory and ATCC), and of fibroblasts.<b>Variants called from whole-genome sequencing</b>A vcf file of variants called from whole-genome sequencing of two PK15 samples (university laboratory and ATCC), and of fibroblasts. The "_AD.txt" files contain allelic coverage depth extracted from these variants by means of bcftools query.<b>Variants called from RNA sequencing</b>A vcf file of SNPs called from publicly available PK15 sequencing.Also, allelic coverage depth file extracted from these variants by means of <i>bcftools query</i>.
DOI: 10.6084/m9.figshare.24679305.v2
title: Supporting Information for "Transfer Learning across Different Chemical Domains: Virtual Screening of Organic Materials with Deep Learning Models Pretrained on Small Molecule and Chemical Reaction Data"

description: Supporting Information for "Transfer Learning across Different Chemical Domains: Virtual Screening of Organic Materials with Deep Learning Models Pretrained on Small Molecule and Chemical Reaction Data"
DOI: 10.6084/m9.figshare.24679305.v3
title: Supporting Information for "Transfer Learning across Different Chemical Domains: Virtual Screening of Organic Materials with Deep Learning Models Pretrained on Small Molecule and Chemical Reaction Data"

description: Supporting Information for "Transfer Learning across Different Chemical Domains: Virtual Screening of Organic Materials with Deep Learning Models Pretrained on Small Molecule and Chemical Reaction Data"
DOI: 10.6084/m9.figshare.24679305.v4
title: Supporting Information for "Transfer Learning across Different Chemical Domains: Virtual Screening of Organic Materials with Deep Learning Models Pretrained on Small Molecule and Chemical Reaction Data"

description: Supporting Information for "Transfer Learning across Different Chemical Domains: Virtual Screening of Organic Materials with Deep Learning Models Pretrained on Small Molecule and Chemical Reaction Data"
DOI: 10.6084/m9.figshare.24742845
title: 255bins

description: Metagenome-assembled genomes (MAGs) obtained from the Okinawa Trough cold seep sediments.
DOI: 10.6084/m9.figshare.24760251
title: Wide climatic niche breadth and traits associated with climatic tolerance facilitate eucalypt occurrence in cities worldwide

description: AimEucalypts are important and popular urban tree species across cities worldwide. However, little is known about how their climatic niche breadth (CNB) and functional traits predict their success, and vulnerability, to current climate change in cities. We assessed the relationship between the CNB of eucalypts and key traits to understand their tolerance to climate change.LocationGlobal urban areas, 66 cities in 21 countries.Time period1981 to 2022.Major species studiedFifty ‘eucalypt’ species belonging to the genera <i>Eucalyptus</i>, <i>Angophora</i> and <i>Corymbia</i>.MethodsWe used the species' safety margin concept to determine cities where eucalypts were planted outside the limits of their CNB, as defined from the native range, considering two extreme variables, maximum temperature of the warmest month (MTWM) and precipitation of the driest month (PDM). We assessed correlations between functional traits (leaf δ<sup>13</sup>C, leaf dry mass, leaf length, leaf N per dry mass, wood density) and negative safety margins, indicative of tolerance to non-native conditions.ResultsIn total, 42 species planted in 40 cities exceeded their safety margins for MTWM, while 43 species in 38 cities exceeded their safety margins for PDM. Within 24 cities, all species exceeded their native CNB for both MTWM and PDM. The cities of Atakpame (Togo), Chennai (India), Chongqing (China) and the US cities of Phoenix and Riverside had the highest richness of eucalypt species growing outside their native CNB. Broadly, species with wide CNB, small leaves, high δ<sup>13</sup>C, high leaf N per dry mass and high wood density were more likely to persist in cities where climatic conditions exceeded their native CNB.Main conclusionsEucalypts occupy many cities experiencing climatic conditions outside their native CNB. Species with traits characteristic of heat and drought tolerance are more often planted in cities where climatic conditions may exceed their CNB native limits.
DOI: 10.6084/m9.figshare.24760251.v1
title: <b>Range expansion of eucalypts in urban spaces worldwide</b>

description: <b>Aim</b>: Eucalypts are an important and popular urban tree species across cities worldwide. However, little is known about which aspects of their climatic niche and which functional traits predict their success, and vulnerability, to current climate change in urban environments. We assessed the relationship between climatic tolerance limits of eucalypts and key traits to classify species resilience and vulnerability.<b>Location</b>: Global urban areas, 66 cities in 21 countries.<b>Time period</b>: 1981 to 2022.<b>Major species</b> <b>studied</b>: Fifty ‘eucalypt’ species belonging to the genera <i>Eucalyptus, Angophora</i> and <i>Corymbia</i>.<b>Methods</b>: We used the species’ safety margin concept — an index of potential tolerance — to determine cities where eucalypts were planted outside their native climatic tolerance (i.e., a negative safety margin) considering two extreme climate variables, maximum temperature of the warmest month (MTWM) and precipitation of the driest month (PDM). We assessed which functional traits (leaf δ<sup>13</sup>C, leaf dry mass, leaf length, leaf N per dry mass, wood density) were correlated with species’ safety margins.<b>Results</b>: In total, 42 species planted in 40 cities exceeded their MTWM safety margins, while 43 species in 38 cities exceeded their PDM safety margins. Within 24 cities, all species were predicted to be experiencing conditions outside their native climatic tolerances for both MTWM and PDM. The cities of Atakpame (Togo), Chennai (India), Chongqing (China) and the US cities of Phoenix and Riverside had the highest richness of species growing outside their native climatic tolerances. Broadly, species with wide climate niche breadth, small leaves, high δ<sup>13</sup>C, high leaf N per dry mass, and high wood density were more likely to be persisting in cities outside their climate tolerance.<b>Main conclusions</b>: Eucalypts occupy many cities with conditions outside their native climatic ranges. Species with traits characteristic of heat and drought tolerance are more often planted, and successful, in cities that exceed the climatic tolerances in their native range.
DOI: 10.6084/m9.figshare.24765105
title: Sdh1 43-96 DMS pilot

description: WT-normalized log2-Effect Scores for pilot DMS analysis of yeast Sdh1 variants.
DOI: 10.6084/m9.figshare.24765240
title: HAP1 SDHA<sup>KO </sup>variant functional data

description: Functional data for SDHA variants in SDHA-knockout cell line
DOI: 10.6084/m9.figshare.24772905.v1
title: D1-P0-SensorConsistencyTest

description: This is the data that was used for consistency testing. ML is used to code the air, tap water and distilled water. 0 = Air, 2001 = Tap Water, 3001 = Distilled water
DOI: 10.6084/m9.figshare.24796689
title: Source Data, Tanner et al PLOSone

description: Source Data for Figures 3 and 5 of Tanner et al PLOSone
DOI: 10.6084/m9.figshare.24846498.v1
title: Complete separation of benzene-cyclohexene-cyclohexane mixtures via temperature-dependent molecular sieving by a flexible chain-like coordination polymer

description: Raw data for Figure 2.
DOI: 10.6084/m9.figshare.24846498
title: Complete separation of benzene-cyclohexene-cyclohexane mixtures via temperature-dependent molecular sieving by a flexible chain-like coordination polymer

description: Raw data for Figure 2.
DOI: 10.6084/m9.figshare.24865530
title: MA Project Docs

description: This study explores the peer feedback process with first-year undergraduate business students at an Irish University. This research explicitly examines (1) student attitudes to peer feedback (pre and post-process), (2) the impact of feedback quality on performance, (3) the association between training and feedback quality. A mixed methods approach was adopted where the data gathered included engagement with in-class training, draft and final assignment grades, ratings and content analysis of peer feedback and responses to student attitude and perception questionnaires. Participants overwhelmingly perceived in-class peer feedback training as a valuable resource and this was statistically related to peer feedback quality. Results indicate that the quality of participants’ initial draft along with the quality of peer feedback provided have a statistically significant impact on students’ final grades. Together with positive attitudes, these findings suggest that there is more scope to support and encourage students’ role as assessor in higher education.