Find research datasets worth reusing

opencc-by-4.0May 2023View details →

Data used to simulations in the GMD manuscript "Inter-comparison of multiple two-way coupled meteorology and air quality models (WRF v4.1.1-CMAQ v5.3.1, WRF-Chem v4.1.1 and WRF v3.7.1-CHIMERE v2020r1) in eastern China"

This dataset contains input data of simulations by WRF-CMAQ, WRF-Chem and WRF-CHIMERE in the GMD manuscript "Inter-comparison of multiple two-way coupled meteorology and air quality models (WRF v4.1.1-CMAQ v5.3.1, WRF-Chem v4.1.1 and WRF v3.7.1-CHIMERE v2020r1) in eastern China", as follows: 1. WRF-CMAQ input data including emission, ICs and lateral BCs of meteorology and air quality: YYYYMM.zip represents the input data for each month for simulations. Due to the large size of the compressed file containing input data each month, there may be interruptions when uploading it to Zenodo. Therefore, we will split each compressed file into 50MB. If users want to browse the file, they can download the segmented files, and then merge them into the YYYYMM.zip file using the Linux command line "unzip 'YYYYMM.zip.*' -d combined"

opencc-zeroJun 2023View details →

Data and code for: Optimal clutch size revisited: separating individual quality from the costs of reproduction

Life-history theory, central to our understanding of diversity in morphology, behaviour and senescence, describes how traits evolve through the optimisation of trade-offs in investment. Despite considerable study, there is only minimal support for trade-offs within species between the two traits most closely linked to fitness – reproduction and survival – questioning the theory's general validity. We used a meta-analysis to separate quality effects from the costs of reproduction using studies of parental investment and survival in birds. Experimental enlargement of broods caused reduced parental survival. However, the effect of experimental enlargements was small and opposite to the effect of phenotypic quality, where individuals that naturally produced larger clutches also survived better. The opposite effects on survival in experimental and observational studies of parental care provide the first meta-analytic evidence for theory suggesting that quality differences mask trade-offs. Fitness projections using the overall effect size revealed that reproduction presented negligible costs, except when reproductive effort was forced beyond the level observed within species, to that seen between species. We conclude that there is little support for the most fundamental life-history trade-off, between reproduction and longevity, operating within a population. We suggest that within species, the fitness landscape of the reproduction–survival trade-off is flat until it reaches the boundaries of the between-species fast-slow life-history continuum. Our interpretation explains why the costs of reproduction are not apparent and why variation in reproductive output persists within species.

opencc-by-4.0Jun 2023View details →

Data for "Upward migration of calanoid copepods is driven by high food quality in surface waters in an alpine lake"

In this study, we explored why zooplankton migrated to surface waters at night from the perspective of their physiological characteristics and adaptability to the environment. The calanoid Arctodiaptomus sp. accumulated large amounts of polyunsaturated fatty acids (PUFAs) and astaxanthin, which relieved oxidative stress to fatty acids. The concentrations of lutein, a precursor of astaxanthin synthesis, were highest in surface water, indicating the enhancement of ultraviolet radiation (UVR) to precursor synthesis, which was confirmed by our indoor experiment. The calanoids migrated to surface water at night to obtain high concentrations of lutein and PUFAs from their diets. Relevant data for this study include: the vertical distribution of Arctodiaptomus sp. during the day and at night; concentrations of total astaxanthin, free astaxanthin, astaxanthin esters in Arctodiaptomus sp. at night and during the day; fatty acid concentration and the ratio of SAFAs (saturated fatty acids), MUFAs (monounsaturated fatty acids), and PUFAs in Arctodiaptomus sp. during the day and at night; the carotenoid concentrations  in seston at different depth of Lake Heihai during the day and at night; the lutein concentration in seston under UVR and dark treatment; main characteristics of Lake Heihai; fatty acid concentrations and the ratio of SAFAs , MUFAs, and PUFAs of seston in Lake Heihai; the relative abundance of Chlorophytes with the size of greater than 5 μm and 0.2-5 μm in different layers of Lake Heihai; fatty acid concentrations of the calanoids in Fuxian Lake.

opencc-by-4.0Jun 2023View details →

Data for the manuscript 'Cover crop root morphology rather than quality controls the fate of root and rhizodeposition C into distinct soil C pools'

Data for manuscript The data provided in the present document corresponds to the manuscript: Engedal, T., Magid, J., Hansen, V., Rasmussen, J., Sørensen, H., Jensen, L. S. (2023): Cover crop root morphology rather than quality controls the fate of root and rhizodeposition C into distinct soil C pools. Global Change Biology, in press.   Short abstract In order to investigate the fate of cover crop-derived belowground C as rhizodeposition and, over time, into the distinct soil organic carbon pools of particulate- and mineral-associated organic carbon (POC and MAOC), a column trial was esblished with 0.25 m top soil and 0.25 m sub soil. Four cover crops were grown for 3 months and 14CO2-labelled twice a week. Four out of eight replicate columns were destructively harvested to quantify root C and the carbon lost via rhizodeposition in absolute (qClvR) and relative terms (%ClvR) in bulk soil and rhizosphere soil from top- and subsoil (t1). The other four replicate columns were harvested for undisturbed incubation for one year, before final sampling (t2). Bulk soil from both sampling times were subject to a simple fractionation protocol by size, where particles larger from 50 microns were assigned to POC and smaller than 50 microns assigned to MAOC after dispersion in NaHMP. All fractions were dried, weighed and analyzed for 14C activity as disintegrations per minute (DPM).   Further details Column ID 1-16 refer to columns sampled at t1, while column ID 17-32 refer to columns sampled at t2. Underlying assumptions and detailed descriptions of the different fractions are to be found in the manuscript.

Data and R code for: "Global meta-analysis shows reduced quality of food crops under inadequate animal pollination"

R code, data, and metadata for the study "Global meta-analysis shows reduced quality of food crops under inadequate animal pollination"

opencc-zeroJul 2023View details →

Data from: Litter quality controls tradeoffs in soil carbon decomposition and replenishment in a subtropical forest

Species-rich forests can produce litter of varying carbon (C) and nitrogen (N) composition (i.e., quality), which can affect decomposition and play a central role in long-term soil organic carbon (SOC) accumulation. However, how differences in litter quality affect SOC decomposition and formation remains unclear over the full litter decomposition trajectory. We followed the in-situ complete decomposition of added 13C-labelled high- (low C:N) and low-quality (high C:N) leaf-litter and its effect on particulate (POM) and mineral-associated (MAOM) organic matter fractions over two years in a natural subtropical forest. We found that during early stages of decomposition, low-quality litter inputs decreased SOC via a positive priming effect (i.e., new C inputs favored decomposition of native SOC), but these SOC losses were offset by SOC gains observed via a negative priming effect during decomposition of high-quality litter. In contrast, this pattern reversed during late stages of decomposition—SOC losses via a positive priming effect induced by high-quality litter were offset by SOC gains via a negative priming effect induced by low-quality litter. Over the full decomposition of litter, both high- and low-quality litter stimulated microbial breakdown of SOC tied to POM, but also replenished more persistent SOC that associated with soil minerals (MAOM). Altogether, we observed that low-quality litter formed twice as much new SOC as high-quality litter (24% vs. 12% of added litter-C). We extend the notion of the priming effect from primarily a negative role promoting losses of native SOC, to a functional role that can replenish persistent SOC. Synthesis. Our measurements raise the possibility that, in species-rich forests, high- and low-quality litter decomposition play opposite but dynamically complementary roles in renewing POM—both by inducing its decomposition and formation—while exclusively favoring MAOM formation, which can help explain how differences in litter quality favor SOC accumulation and persistence. Global change factors that shift plant community composition may ultimately affect the fate of soil C, as changes in litter quality may force soil transitions from sinks to sources or sources to sinks of atmospheric CO2.

opencc-zeroJul 2023View details →

Data for: Water depth and transparency drive the quantity and quality of organic matter in sediments of Alpine lakes on the Tibetan Plateau

The primary objectives of the study were to: (i) determine OM quantity and quality in the sediments of alpine lakes on the Tibetan Plateau, (ii) identify the primary environmental regulators of OM quantity and quality, and (iii) reveal OM transformations in the water column and sediments. Firstly, we collected sediments and lake water from 20 lakes with diverse morphology and sizes across the entire Tibetan Plateau. Secondly, We analyzed the bulk sedimentary OM and two leachable pools of the sedimentary OM, i.e., water-soluble OM and alkaline-extracted OM combining elemental and stable isotopic analysis, optical measurements (i.e., absorbance and fluorescence spectroscopy), and ultrahigh-resolution molecular techniques (i.e., electrospray ionization-assisted Fourier transform-ion cyclotron resonance mass spectrometry, ESI FT-ICR MS). We also measured the lake water physicochemical characteristics (i.e., depth, transparency, salinity, turbidity, DO, pH, TN, TP and Chl a), as well as the composition of dissolved OM in water column via optical measurements. Thirdly, we performed statistical analysis to determine the primary environmental control and predictors of the spatial variability in sedimentary OM on the Tibetan Plateau. The statistical analysis included non-parametric Kruskal-Wallis with Dunn post hoc test, redundancy analysis, and linear regression models. Main results of the study are that (i) sedimentary water-soluble OM and alkaline-extracted OM were both dominated by low-molecular-weight, low-aromaticity compounds with low contributions of terrestrial humic substances, suggesting that sedimentary leachable OM was primarily regulated by in-lake sources and processes; (ii) water depth, water transparency, and total phosphorus concentration in water column explained ~50% variance of sedimentary bulk and leachable OM, substantiating the importance of autochthonous sources and primary productivity in regulating the quantity and quality of sedimentary OM; (iii) in comparison to lake surface water DOM, water-soluble OM and alkaline-extracted OM from sediments had higher proportions of terrestrial humic-like substances, suggesting preferential preservation of allochthonous materials in the sediments.

opencc-zeroJul 2023View details →

Data from: Cover cropping history affects cotton boll distribution, lint yields, and fiber quality

This is digital research data corresponding to a published manuscript, Cover cropping history affects cotton boll distribution, lint yields, and fiber quality, in Crop Science, Vol. 63 p. 1209–1220. There has been limited introduction of new cover crop species into cotton (Gossypium hirsutum L.) production within the last 30 years. Mounting evidence shows that traditional cover cropping species may be detrimental to cotton production, either by depleting soil fertility with crop removal, immobilizing minerals from high carbon residue, or excessive quantity of residue remaining at planting. The objective of this study was to determine the effects of growing a novel cover crop species, carinata (Brassica carinata A. Braun), as a winter annual cover crop for cotton rotation in the southeastern Coastal Plain. Over a 2-year period, carinata, winter wheat (Triticum aestivum L.), and fallow covers were maintained over winter months, then rotated into cotton. Each year, seedcotton and lint yields were collected, along with subsamples for ginning and subsequent fiber quality analyses. Additionally, end-of-season plant mapping was conducted on plants from 1-m of row per plot to determine cover crop effects on boll formation, retention, and distribution, as well as canopy architecture.

Research Data Quality Assurance – an intellectual property perspective

The presentation summarizes the intellectual property issues, regarding the second Demonstrator in the FAIR Data Spaces project, Research Data Quality Assurance. It will especially outline the specific copyright law paragraphs, which may be and are important for this demonstrator and the participants in the project.

Automated Data Quality Assurance with GitLab pipelines and Docker

<ul> <li>The Data Validation and Quality Assurance demonstrator is a tool designed to assist with collaborative research projects, ensuring that collected data complies with established schemas and monitoring these files for unusual or unexpected values. This demonstrator attempts to show how a task of this nature can be attempted in a scalable, cloud based infrastructure, while maintaining compatibility with existing frameworks. In this presentation we will cover a brief use case, showing the results of the demonstrator on an example dataset that contains some intentionally added data quality items</li> </ul>

Data from Preliminary estimates of genetic parameters and familial selection for non-native poplars show good potential for genetic gains on growth, cold hardiness, trunk quality and Sphaerulina musiva susceptibility

Data from Preliminary estimates of genetic parameters and familial selection for non-native poplars show good potential for genetic gains on growth, cold hardiness, trunk quality and Sphaerulina musiva susceptibility Abstract Genetic parameters for growth, trunk quality and susceptibility to frost and Sphaerulina musiva attack was estimated from 34 half-sib families of hybrid poplar from the crossing of non-native parents, Populus maximowiczii A. Henry and Populus trichocarpa Torr. & Gray, 3 and 6 years after planting. The use of spatial analysis proved to be the best method for quantitative growth data. The proportion of the among-family variance to the total (phenotypic) variance as well as the high heritabilities of growth and susceptibility to frost and Spaherulina musiva showed a high potential for selection for these traits while the quality traits were under low genetic control. Some families showed gains for several traits, suggesting the possibility of developing a selection index to obtain superior families that show gain for not only growth but quality and adaptive traits as well. Type B correlations were high, suggesting that families responded in the same way regardless of the site. High type A correlation between growth traits at 3 and 6 years showed early selection potential, although these relationships should be confirmed with future measurements to evaluate this effect at maturity. These results can be integrated into the strategy for improving hybrid poplar parental populations and, in the longer term, will make it possible to optimize the selection of individuals with traits of interest for the operational deployment of hybrid poplar clones.

Incorporating real-time traffic data into air quality mapping uncovers more severe exposure disparities at the community level

Data and codes for the XGBoost model training in our manuscript titled "Incorporating real-time traffic data into air quality mapping uncovers more severe exposure disparities at the community level"

opencc-zeroAug 2023View details →

Data for: Leveraging spatio-temporal genomic breeding value estimates of dry matter yield and herbage quality in ryegrass via random regression models

Joint modeling of correlated multi-environment and multi-harvest data of perennial crop species may offer advantages in prediction schemes and a better understanding of the underlying dynamics in space and time. The goal of the present study was to investigate the relevance of incorporating the longitudinal dimension of within-season multiple measurements of forage perennial ryegrass traits in a reaction norm model setup that additionally accounts for genotype-environment interactions (G×E). Genetic parameters and accuracy of genomic breeding value (gEBV) predictions were investigated by fitting three random regression models (gRRM) using Legendre polynomial functions to the data. Genomic DNA sequencing of family pools of diploid perennial ryegrass was performed using DNA nanoball-based technology and yielded 56,645 single nucleotide polymorphisms which were used to calculate the allele frequency-based genomic relationship matrix. Biomass yield's estimated additive genetic variance and heritability values were higher in later harvests. The additive genetic correlations were moderate to low in early measurements and peaked at intermediates, with fairly stable values across the environmental gradient, except for the initial harvest data collection. This led to the conclusion that complex (G×E) arises from spatial and temporal dimensions in the early season, with lower re-ranking trends thereafter. In general, modeling the temporal dimension with a second-order orthogonal polynomial improved the accuracy of gEBV prediction for nutritive quality traits, but no gain in prediction accuracy was detected for dry matter yield. This study leverages the flexibility and usefulness of gRRM models for perennial ryegrass breeding and can be readily extended to other multi-harvest crops.

opencc-by-4.0Jun 2023View details →

Data analysis for "Wellbeing, loneliness, health-related quality of life and perception of technology of older adults in Slovenian senior homes"

We present datasets data analysis conducted in R for the article"Wellbeing, loneliness, health-related quality of life and perception of technology of older adults in Slovenian senior homes".

opencc-zeroSep 2023View details →

Data from: Novel methods to define invasive procedures at the end-of-life were developed to improve quality of end of life care research: A population-based cohort study in colorectal cancer

Background Understanding the use of invasive procedures (IPs) at the end-of-life (EoL) is important to avoid under- and overtreatment, but epidemiologic analysis is hampered by limited methods to define treatment intent and EoL phase. This study applied novel methods to report IPs at the EoL using a colorectal cancer (CRC) case study. Methods An English population-based cohort of adult patients diagnosed between 2013 and 2015 was used with follow-up to 2018. Procedure intent (curative, non-curative, diagnostic) by cancer site and stage at diagnosis was classified by two surgeons independently. Joinpoint regression modelled weekly rates of IPs for 36 sub-cohorts of patients with incremental survival of 0-36 months. EoL phase was defined by a significant IP rate change before death. Zero-inflated Poisson regression explored associations between IP rates and clinical/sociodemographic variables. Results Of 87,731 patients included, 41,972 (48%) died. 9,492 procedures were classified by intent (interrater agreement 99.8%). Patients received 502,895 IPs (1.39 and 3.36 per person year for survivors and decedents). Joinpoint regression identified significant increases in IPs four weeks before death in those living 3-6 months, and eight weeks before death in those living 7–36 months from diagnosis. 7,908 (18.8%) patients underwent IPs at the EoL, with stoma formation the most common major procedure. Younger age, early-stage disease, men, lower comorbidity, those receiving chemotherapy and living longer from diagnosis were associated with IPs. Conclusions Methods to identify and classify IPs at the EoL were developed and tested within a CRC population. This approach can be now extended and validated to identify potential under- and overtreatment.

opencc-zeroSep 2023View details →

Data from: Male size does not affect the strength of male mate choice for high-quality females in Drosophila melanogaster

Theory predicts that the strength of male mate choice should vary depending on male quality when higher-quality males receive greater fitness benefits from being choosy. This pattern extends to differences in male body size, with larger males often having stronger pre- and post-copulatory preferences than smaller males.We sought to determine whether large males and small males differ in the strength (or direction) of their preference for large, high-fecundity females using the fruit fly, Drosophila melanogaster. We measured male courtship preferences and mating duration to show that male body size had no impact on the strength of male mate choice; all males, regardless of their size, had equally strong preferences for large females. To understand the selective pressures shaping male mate choice in males of different sizes, we also measured the fitness benefits associated with preferring large females for both large and small males. Male body size did not affect the benefits that males received: large and small males were equally successful at mating with large females, received the same direct fitness benefits from mating with large females, and showed similar competitive fertilization success with large females. These findings provide insight into why the strength of male mate choice was not affected by male body size in this system. Our study highlights the importance of evaluating the benefits and costs of male mate choice across multiple males to predict when differences in male mate choice should occur.

ClinicalTrials.gov36/100

Using Data-Driven Implementation Strategies to Improve the Quality of Cirrhosis Care

ClinicalTrials.gov study NCT04178096. IPD Sharing: NO. Countries: 1. Publications: 4.

closedIPD-NOFeb 2026View details →

publicJan 2023View details →

Flow virometry for water-quality assessment: Protocol optimization for a model virus and automation of data analysis

Open the record for dataset details and reuse information.

publicDec 2020View details →

Littoral macroinvertebrate and water quality data for 32 lakes across the boreal-tundra transition in the Northwest Territories

Open the record for dataset details and reuse information.