Find research datasets worth reusing

opencc-by-sa-4.0Nov 2023View details →

Synthetic dataset for end-to-end Relation Extraction of relationships between Organisms and Natural-Products with Vicuna-13b-v1.5

A new synthetic dataset (training/validation) for end-to-end Relation Extraction of relationships between Organisms and Natural-Products.The new dataset was generated using <a href="https://huggingface.co/lmsys/vicuna-13b-v1.5">Vicuna-13b-v1.5</a>, derived from LLaMA 2. Like the model, the produced synthetic data are also submitted to the License of the model used for generation, see the original <a href="https://github.com/facebookresearch/llama/blob/main/LICENSE">LLaMA 2 license</a>.The new dataset was created based on the top-1000 (per biological kingdom) LOTUS literature references extracted with the <a href="https://github.com/idiap/gme-sampler">GME-sampler</a>.The dataset contains 10,405 items in the training set and 547 items in the validation set.The dataset was generated using the same protocol as described in the <a href="https://github.com/idiap/gme-sampler">article</a>.

opencc-by-4.0Oct 2023View details →

Simulation dataset and plotting scripts used for journal article "Impact of acidity and surface modulated acid dissociation on cloud response to organic aerosol" by Sengupta et al. (2024)

Simulation data underlying all figures presented in "Impact of acidity and surface modulated acid dissociation on cloud response to organic aerosol" by Sengupta et al. (2024). DOI: 10.5194/acp-24-1467-2024 The data for each figure and the plotting scripts are included in a zip file labelled by the figure number as presented in the paper and accompanying supplement.

opencc-by-4.0Dec 2023View details →

Data for: Assessing hydrology, biogeochemistry and organic micropollutants in an urban stream-aquifer system: an interdisciplinary dataset

Accompanying data for data article "Assessing hydrology, biogeochemistry and organic micropollutants in an urban stream-aquifer system: a comprehensive dataset" of Popp et al., JGR:Biogeosciences. In this repository, all data described in Table 1 of the manuscript can be found, except for the data already published by Popp et al., 2020, ES&T, doi: 10.1021/acs.est.9b05393. These data can be freely accessed in ERIC (Eawag Research Data Institutional Collection): doi.org/10.25678/0001JD.  Data are structured the following way: 1_logger-data: time series of logger data (water temperature, water levels, electrical conductivity and pH [the latter only for the stream]) obtained at the stream Chriesbach and piezometers P1 and P4; 2_tracer-data: time series of nutrients, ions, and other tracer data obtained at the stream Chriesbach, the piezometers (P1, P4, P5) and the regional groundwater well (reg-gw);   3_micropollutant_data: time series of organic micropolluntants obtained at the stream Chriesbach, P1, P4, P5 and the regional groundwater well (reg-gw); 4_R-script: R script used for statistical analysis and to create the plots shown in the manuscript. Units, estimated uncertainties or other measures of uncertainty such as limits of quantification are provided in the respective files. Each subfolder contains its own readme file with relevant metadata.  Coordinates (WGS84):         Location    Latitude    Longitude Stream logger monitoring    47.404613    8.6113 Stream sampling    47.404459    8.607777 Piezometer 1 (P1)    47.4044    8.6080 Piezometer 4 (P4)    47.4044    8.6078 Piezometer 5 (P5)    47.404392    8.607619 Regional groundwater    47.40501    8.60822

opencc-zeroDec 2023View details →

Soil organic carbon loss decreases biodiversity but stimulates multitrophic interactions that promote belowground metabolism

Soil organic carbon (SOC) plays an essential role in mediating community structure and metabolic activities of belowground biota. Unraveling the evolution of belowground communities and their feedback mechanisms on SOC dynamics helps embed the ecology of soil microbiome into carbon cycling, which serves to improve biodiversity conservation and carbon management strategy under global change. Here, croplands with a SOC gradient were used to understand how belowground metabolisms and SOC decomposition were linked to the diversity, composition, and co-occurrence networks of belowground communities encompassing archaea, bacteria, fungi, protists, and invertebrates. As SOC decreased, the diversity of prokaryotes and eukaryotes also decreased, but their network complexity showed contrasting patterns: prokaryotes increased due to intensified niche overlap, while that of eukaryotes decreased possibly because of greater dispersal limitation owing to the breakdown of macro aggregates. Despite the decrease in biodiversity and SOC stocks, the belowground metabolic capacity was enhanced as indicated by increased enzyme activity and decreased enzymatic stoichiometric imbalance. This could, in turn, expedite carbon loss through respiration, particularly in the slow-cycling pool. The enhanced belowground metabolic capacity was dominantly driven by greater multitrophic network complexity and particularly negative (competitive and predator-prey) associations, which fostered the stability of the belowground metacommunity. Interestingly, soil abiotic conditions including pH, aeration, and nutrient stocks, exhibited a less significant role. Overall, this study reveals a greater need for soil C resources across multitrophic levels to maintain metabolic functionality as declining SOC results in biodiversity loss. Our researchers highlight the importance of integrating belowground biological processes into models of SOC turnover, to improve agroecosystem functioning and carbon management in the face of intensifying anthropogenic land-use and climate change.

opencc-zeroJan 2024View details →

Bridging length scales in organic mixed ionic-electronic conductors through internal strain and mesoscale dynamics

Understanding structural and dynamic properties of inherently disordered systems at the mesoscale is crucial. This is particularly important in organic mixed ionic-electronic conductors (OMIECs), which undergo significant and complex structural changes when operated in electrolyte. In this study, we investigate the mesoscale strain, reversibility, and dynamics of a model OMIEC material under external electrochemical potential using operando X-ray photon correlation spectroscopy. Our results reveal mesoscale strain and structural hysteresis that depend on the sample's cycling history, establishing a comprehensive kinetic sequence bridging the macroscopic and microscopic behaviors of OMIECs. Furthermore, we uncover equilibrium and non-equilibrium dynamics of charge carriers and material doping states, highlighting the unexpected coupling between charge carrier dynamics and mesoscale order. These findings advance our understanding of the structure-dynamics-function relationships in OMIECs, opening pathways for designing and engineering materials with improved performance and functionality in non-equilibrium states during device operation.

opencc-by-4.0Dec 2023View details →

Implications of the three-dimensional chromatin organization for genome evolution in a fungal plant pathogen

The spatial organization of eukaryotic genomes is linked to their biological functions, although it is not clear how this impacts the overall evolution of a genome. Here, we uncover the three-dimensional (3D) genome organization of the phytopathogen Verticillium dahliae, known to possess distinct genomic regions, designated adaptive genomic regions (AGRs), enriched in transposable elements and genes that mediate host infection. Short-range DNA interactions form clear topologically associating domains (TADs) with gene-rich boundaries that show reduced levels of gene expression and reduced genomic variation. Intriguingly, TADs are less clearly insulated in AGRs than in the core genome. At a global scale, the genome contains bipartite long-range interactions, particularly enriched for AGRs and more generally containing segmental duplications. Notably, the patterns observed for V. dahliae are also present in other Verticillium species. Thus, our analysis links 3D genome organization to evolutionary features conserved throughout the Verticillium genus.

opencc-zeroJan 2024View details →

Data from: Whole-brain spatial organization of hippocampal single-neuron projectomes

Mapping hippocampal single-neuron projections is essential for understanding brain-wide circuit organization and diverse functions of the hippocampus, a brain structure underlying episodic memory and cognition. Here, we reconstructed 10,100 single-neuron projectomes of the mouse hippocampus, identified rostral and caudal axon pathways that preferentially innervated cortical vs. subcortical areas, and classified 43 projectome subtypes with distinct axon targeting patterns. Notably, the soma locations along hippocampal longitudinal and transverse axes determined the number of their target areas and the spatial distribution and complexity of their axon arbors within the targets. We defined selective hippocampal subdomains based on spatial transcriptomic profiles and found that many projectome subtypes were enriched in specific subdomains. Next, we defined the wiring diagram for hippocampal neurons exclusively projecting to hippocampal formation (HPF) and those projecting to both intra- and extra-HPF targets with coordinated projection strengths. Furthermore, bi-hemispheric projecting hippocampal neurons generally projected to one pair of homologous targets with ipsilateral preference. These organization principles of single-neuron projectomes provide a structural basis for understanding diverse but coordinated functions of hippocampal neurons.

opencc-zeroFeb 2024View details →

Data for: Dissolved organic matter (DOM) offsets the detrimental effects of climate change in the nitrogen fixing cyanobacterium Crocosphaera

<div> <div> <div> <div> Diazotrophs provide a significant reactive nitrogen source in the ocean. Increased warming and stratification may decrease nutrient availability in the future, forcing microbial communities to use dissolved organic matter (DOM). Not depending on reactive nitrogen availability, diazotrophs may be "winners" in a nutrient depleted ocean. However, their ability to exploit DOM may influence this success. We exposed cultures of the widespread Crocosphaera to low (26°C, pH 8.1), moderate (28°C, pH 8.0), and extreme (30°C, pH 7.9) climate change scenarios, under control or DOM-amended conditions. Growth was suboptimal in the low and extreme treatments, and favoured in the moderate treatment. DOM was preferred as a carbon source regardless of the treatment, and promoted N2 fixation in extreme conditions. This was reflected in the increased expression of photosynthesis genes to obtain energy. DOM provides Crocosphaera with a key ecological advantage, possibly dictating diazotroph-derived nitrogen inputs in the future ocean. </div> </div> </div> </div>

opencc-zeroFeb 2024View details →

Data from: The effect of drainage on the fine root biomass, production, and turnover in hemiboreal old-growth forests on organic soils

Information on the capacity of organic soils to capture and store carbon in old-growth forests in the hemiboreal forest zone is scarce and fragmented. However, fine root data can provide valuable insights into soil carbon fluxes. Thus, the aim of the current study was to provide estimates of the fine root biomass (FRB), fine root production (FRP), and fine root turnover (FRT) rate by tree species and other functional groups in old-growth (stand age 131–179 years) forests on mesotrophic organic soils dominated by Scots pine (Pinus sylvestris L.), with (drained mesotrophic organic soil) and without (undrained mesotrophic organic soil) the effects of forest drainage. The sequential soil coring method was used to estimate the FRB and FRP. The total FRB (sum of the FRB of all functional groups) was significantly higher in the undrained sites (6.8±0.3 t ha 1) than in the drained sites (3.97±0.1 t ha 1). The FRB of Scots pine in the undrained forest was significantly higher (1.7±0.1 t ha 1) than in the drained forest (0.5±0.1 t ha 1), supporting an extensive foraging strategy. The significantly higher mean FRB of Norway spruce (Picea abies [L.] Karst.) (1.4±0.1 t ha 1) in the drained sites than the undrained sites (0.7±0.2 t ha-1) can be explained by there being a higher proportion of spruce in the stand compositions, thus a higher standing volume (cubic meters per hectare) of this species and an increased FRB. The FRB of dwarf shrubs (2.43±0.2 t ha-1) formed the largest part of the total FRB in the undrained sites and the second largest (1.16±0.1 t ha-1), following Norway spruce, in the drained sites. The total FRP was similar between the undrained (2.05±0.31 t ha-1 yr-1) and drained (1.82±0.26 t ha-1 yr-1) stands. However, considerable variability in the FRP was observed between different sites of the same forest site type. The FRT rate of Scots pine was twice as high in the drained sites than the undrained sites, suggesting faster nutrient and carbon input into the drained soil compared to the undrained soil. Estimates of FRB, FRP, and FRT rate for different functional groups can be used in carbon-cycle modeling and in further calculations to estimate the carbon budget (balance) in forests on organic soils.

opencc-zeroFeb 2024View details →

Putative photosensitivity in internal light organs (organs of Pesta) of deep-sea sergestid shrimps

Many marine species can regulate the intensity of bioluminescence from their ventral photophores in order to counterilluminate, a camouflage technique whereby animals closely match the intensity of the downwelling illumination blocked by their bodies, thereby hiding their silhouettes. Recent studies on autogenic cuticular photophores in deep-sea shrimps indicate that the photophores themselves are light-sensitive. Here, our results further suggest photosensitivity in a second type of autogenic photophore, the internal organs of Pesta, found in deep-sea sergestid shrimps. Experiments were conducted ship-board on live specimens, exposing the animals to bright light, which resulted in ultrastructural changes that matched those seen in crustacean eyes during the photoreceptor membrane turnover, a process that is crucial for the proper functioning of photosensitive components. In addition, RNA-seq studies demonstrated the expression of visual opsins and phototransduction genes in organs of Pesta tissue that are known to play a role in light detection, and electrophysiological measurements indicated that the light organs are responding to light received by the eyes. The long-sought-after mechanism of counterillumination remains unknown, but evidence of photosensitivity in photophores may indicate a dual functionality of light detection and emission.

opencc-by-4.0Feb 2024View details →

Data archive for: Resting cells of Skeletonema marinoi assimilate organic compounds and respire by dissimilatory nitrate reduction to ammonium in dark, anoxic conditions

Data archive for: “Resting cells of Skeletonema marinoi assimilate organic compounds and respire by dissimilatory nitrate reduction to ammonium in dark, anoxic conditions” <a href="https://doi.org/10.1111/1462-2920.16625">https://doi.org/10.1111/1462-2920.16625</a>   Dataset of single cell assimilation of organic/inorganic C/N by resting cells of the marine diatom Skeletonema marinoi captured using secondary ion mass spectrometry (SIMS) and stable isotopic tracers. The dataset also contains POC/PON changes over time during dormancy, DNRA (15N-NH4+ production), denitrification (15N-N2 production) and a germination assay to determine survival rate, most probable number analysis (MPN).   Two strains (GF04 and R05) were incubated in dark and anoxic conditions in two different incubation experiments. Incubation 1: Diatoms treated with antibiotics before entering dormancy compared to a control not treated with antibiotics then given 15N-NO3- in dark anoxic conditions. Incubation 2: Diatoms treated with antibiotics given, 15N & 13C urea, 15N & 13C urea + 14N-NO3-, 13C-acetate, 13C-acetate + 15N-NO3-, or 15N-NO3-. See the main manuscript for a extensive experimental setup.   Each file is uploaded as both a .CSV and .XLSX, so that you can choose which you prefer. DNRA_and_denitrification.csv/xlsx: DRNA and denitrification depending on volume (Incubation 1) DNRA_per_cell.csv/xlsx: DNRA per cell (Incubation 1 & 2) MPN_data.csv/xlsx: Most probable number analysis (Incubation 1 & 2) POC_PON.csv/xlsx: POC and PON per cell and volume (Incubation 1 & 2) SIMS_data.csv/xlsx: SIMS data (Incubation 1 & 2)

Strong uptake of gas-phase organic peroxy radical (ROO•) by solid surfaces driven by redox reactions

This repository contains publicly available data supporting the article *Strong uptake of gas-phase organic peroxy radical (ROO•) by solid surfaces driven by redox reactions*, Durif et al. (2024)

opencc-by-4.0Dec 1953View details →

Alaimus elegans de Man. α, anterior r i end, 1/ 12, ok. 3, x 600. b, tail obj. 7, ok. 3, x 360. c, region of the female organs obj. 7, ok. 3, x 3 6 0. in Terrestrial nematodes from Jan Mayen

Alaimus elegans de Man. α, anterior r i end, 1/ 12, ok. 3, x 600. b, tail obj. 7, ok. 3, x 360. c, region of the female organs obj. 7, ok. 3, x 3 6 0.

Dataset for: On the Nature of Hydrophobic Organic Compound Adsorption to Smectite Minerals Using the Example of Hexachlorobenzene-Montmorillonite Interactions

This dataset contains all data obtained from first principle DFT calculations at the PBE-D3 DFT level by the program VASP  for the paper published in the journal "Minerals". Please cite this article when using the dataset. Title: "On the Nature of Hydrophobic Organic Compound Adsorption to Smectite Minerals Using the Example of Hexachlorobenzene-Montmorillonite Interactions." Authors: Peter Grancic, Leonard Böhm, Martin H. Gerzabek, and Daniel Tunega  DOI10.3390/min13020280.   The model systems are Ca-montmorillonite (Ca-Mt) models with varying layer charge from the Mg/Al substitutions. Calculated are interaction energies of hexachlorobenzene (HCB) with Ca-Mt models in various configurations. QE.dat file is file with collected energies of all models, Collect_QE.py is a selfmade python file for the collection of energies. The structure of all directories is as following: HCBCaxxx directories contain optimized  HCB-CaMt complexes HCBCaxxx_Clay directories contain  pure CaMt models HCBCaxxx_HOC  directories contain only HOC molecule Each directory contains: -input geometry data (POSCAR file) -optimized geometries (CONTCAR.norm file) -input parameters for VASP (INCAR file) -k-points (KPOINTS file) -complete output files (OUTCAR.norm and vasprun.xml.norm files) POTCAR file with pseudopotentials are not provided due to copyright rights. Their type can be found in OUTCAR or vasprun.xml files. Funding: This work has been supported by German Research Foundation (Deutsche Forschungsgemeinschaft, DFG), grant number 443637168, BO5388/1–1 and Austrian Science Fund (Fonds zur Förderung der Wissenschaftlichen Forschung, FWF), grant number I 4876–N in the bilateral project ”Clay minerals as sorbents for hydrophobic organic chemicals – ClayHOC”.  The results presented have been achieved using the Vienna Scientific Cluster (VSC), project number 70544. Terms of use: These data are provided "as is", without any warranty. This dataset is provided under the Creative Commons Attribution 4.0 International license.

opencc-zeroDec 2023View details →

Data for: Spillover effects of organic agriculture on pesticide use on nearby fields

The environmental impacts of organic agriculture are only partially understood and whether such practices have spillover effects on pests or pest control activity on nearby fields remains unknown. Using roughly 13,000 field observations per year from 2013-2019 in Kern County, CA , we estimate that organic crop producers benefit from surrounding organic fields, decreasing overall pesticide use and pesticides targeting insect pests. Conventional fields, in contrast, tend to increase pesticide use as the area of surrounding organic production increases.

Dataset for article: Adsorption of the hydrophobic organic pollutant hexachlorobenzene to phyllosilicate minerals

This repository contains data obtained from first principle DFT calculations at the PBE-D3 DFT level by the program VASP  for the research article  Title: "Adsorption of the hydrophobic organic pollutant hexachlorobenzene to phyllosilicate minerals" published in Environmental Science and Pollution Research (2023) 30:36824–36837. Authors: Leonard Böhm, Peter Grančič, Eva Scholtzová, Benjamin Justus Heyde, Rolf-Alexander Düring, Jan Siemens, Martin H. Gerzabek & Daniel Tunega. Please cite that article when using this dataset. The systems in the dataset are models of Me-montmorillonite layers (Me = Li, Na, K, Rb, Cs, Mg, Ca, Sr, Ba) interacting with hexachlorobenzene (HCB) molecule. Calculated are interaction energies of optimized geometries of HCB...Me-Mnt complexes. Dateset contains tables with collected calculated adsorption energies and main geometrical paramters. The structure of dataset is following: Rep_Ads_I directory contains directories for HCB molecule, and for complexes of HCB with Li-Mnt to Rb-Mnt. Each directory of complexes contains corresponding directory of isolated Me-Mnt layer. The second directory, Rep_ads_II has the same structure as Rep_Ads_I directory for Me=Mg, Ca, Sr, and Ba. In each directory are the main files for VASP calculations: input geometry data (POSCAR.norm file) optimized geometry  (CONTCAR.norm file) input parameters for VASP (INCAR file) k-points (KPOINT file) complete output files (OUTCAR.norm and vasprun.xml.norm files) POTCAR file with pseudopotentials are not provided due to copyright restrictions. Their type can be found in OUTCAR file or vasprun.xml file. Funding: This work has been supported by German Research Foundation (Deutsche Forschungsgemeinschaft, DFG), grant number 443637168, BO5388/1–1 and Austrian Science Fund (Fonds zur Förderung der Wissenschaftlichen Forschung, FWF), grant number I 4876–N in the bilateral project ”Clay minerals as sorbents for hydrophobic organic chemicals – ClayHOC”.  The results presented have been achieved using the Vienna Scientific Cluster (VSC), project number 70544. Terms of use: These data are provided "as is", without any warranty. This dataset is provided under the Creative Commons Attribution 4.0 International license.

opencc-by-4.0Feb 2022View details →

Organizing the fragmented landscape of multidisciplinary product development: A mapping of approaches, processes, methods and tools from the scientific literature - Searchable cartographies

This document gathers cartographies for the development of mechatronic products, cyber-physical systems and smart products. The three cartographies presented are associated with an open-access article – see the citation box below – and differ from the ones provided in the article in that they are searchable, which makes it easier to pinpoint references, concepts and techniques. This document comprises a legend, the cartographies and a list of associated references.  To contextualize the cartographies, the integration of digital and connectivity technologies in new products can invite companies to adapt their development. Organizing the fragmented landscape of multidisciplinary product development to help companies navigate the dense scientific literature corpus is a first step in supporting them in doing so. Multidisciplinary product development can be investigated by analyzing specific types of products that deal with both software and hardware development and can be referred to as cyber-physical systems, mechatronics, and smart products and systems in the literature. To support their development, 236 “concepts and techniques” (an expression that encompasses approaches, processes, methods and tools) were identified from 167 scientific papers through an extensive literature review and organized based on a four-level model paired with a decision tree. The mapping of the sorted concepts and techniques made it possible to generate graphical representations called “cartographies.” These cartographies represent a database of concepts and techniques for multidisciplinary product development and serve to support companies in their transformation from the product development perspective by providing them with a general overview of the related literature.

opencc-by-4.0Dec 2023View details →

Data from: Mechanisms underpinning the net removal rates of dissolved organic carbon in the global ocean

With almost 700 Pg of carbon, marine dissolved organic carbon (DOC) stores more carbon than all living biomass on Earth combined. However, the environmental controls behind the persistence and the spatial patterns of DOC concentrations on basin scale remain largely unknown, precluding quantitative assessments of the fate of this large carbon pool in a changing climate. We present the first global dynamic DOC model in agreement with more than 40,000 DOC observations, in which a feedback between DOC and picoheterotrophs is explicitly included (model of MICrobial-DOC interactions, MICDOC). This dataset contains model output and related information for a global model simulation in which a colimitation of macronutrients and organic carbon on microbial DOC uptake is implemented and explains >70% of the global variation of observed DOC concentrations. It provides the model output, source code and meta data for the simulations performed for the publication (doi: 10.1029/2023GB007912) "Mechanisms Underpinning the Net Removal Rates of Dissolved Organic Carbon in the Global Ocean" by Lennartz et al.

opencc-by-4.0Jul 2020View details →

Figure 1 in Lessons from the WBF2020: extrinsic and intrinsic value of soil organisms

Figure 1. (A) The World Biodiversity Forum was held high up in the snowy Alps in Davos. Credit: Marianne Darbi. (B) Participants of the House of Commons style debate. Participants discussed whether they thought biodiversity was declining. Credit: Marten Winter

Simulation dataset and plotting scripts used for journal article "Surface modulated dissociation of organic aerosol acids and bases in different atmospheric environments" by Sengupta and Prisle (2024)

Simulation data underlying all figures presented in "Surface modulated dissociation of organic aerosol acids and bases in different atmospheric environments" by Sengupta and Prisle (2024) <a href="http://dx.doi.org/10.1080/02786826.2024.2323641" target="_blank" rel="noopener noreferrer">http://dx.doi.org/10.1080/02786826.2024.2323641</a>.  The data for each figure and the plotting scripts are included in a zip file labelled by the figure number as presented in the paper and accompanying supplement.