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Different currencies for calculating resource phenology result in opposite inferences about trophic mismatches
<p>Shifts in phenology are among the key responses of organisms to climate change. When rates of phenological change differ between interacting species they may result in phenological asynchrony. Studies have found conflicting patterns concerning the direction and magnitude of changes in synchrony, which have been attributed to biological factors. A hitherto overlooked additional explanation is differences in the currency used to quantify resource phenology, such as abundance and biomass. Studying an insectivorous bird, Sanderling, and its prey, we show that the median date of cumulative arthropod biomass occurred, on average, 6.9 days after the median date of cumulative arthropod abundance. In some years this difference could be as large as 21 days. For 23 years, hatch dates of Sanderlings became less synchronized with the median date of arthropod abundance, but more synchronized with the median date of arthropod biomass. The currency-specific trends can be explained by our finding that mean biomass per arthropod specimen increased with date. Using a conceptual simulation, we show that estimated rates of phenological change for abundance and biomass can differ depending on temporal shifts in the size distribution of resources. We conclude that studies of trophic mismatch based on different currencies for resource phenology can be incompatible with each other.</p>
Fig. 8. Heat map resulting from the Species Distribution Model using MaxEnt, where 1 in A revision of the genus Armillipora Quate (Diptera: Psychodidae) with the descriptions of two new species
Fig. 8. Heat map resulting from the Species Distribution Model using MaxEnt, where 1 is equal to the highest probability of distribution, while 0 is the lowest probability.
External Stakeholders Survey Results - The Future of Aquaculture The impact of 4.0 technologies worldwide
<p>Aquaculture 4.0 technologies have landed and are very likely to stay, aiming to play a major role within the implementation of new Circular Bioeconomy approaches. In this context, European aquaculture has been recently applying innovative and disruptive technologies to transform fishery management strategies. The so-called “4th industrial revolution” is projected to allow a 15-20% increase in the sector by the year 2030. In addition to the growth the revolution can provide, the benefits of Industry 4.0 include improved productivity, efficiency and reduced costs. Companies will be able to produce more, in less time, while allocating resources more effectively, due to a smooth adoption of interconnectivity through the Internet of Things (IoT), access to real-time data, and the introduction of cyber-physical systems. According to FAO data, the estimated production volume of fish from European aquaculture in 2028 will increase to approximately 1.4 million tons, needing more circular, digitized solutions to cover end user demand.</p> <p>This data was collected from a survey investigating the Future of Aquaculture The impact of 4.0 technologies worldwide. The results of this survey were used to understand the main challenges faced within the Aquaculture 4.0 market concerning usage experience and level of awareness, in order to identify barriers for implementation and key drivers to encourage adoption of innovative technologies within their businesses. The insights gathered will help us to improve our concept and ultimately the whole value chain of the Aquaculture 4.0 market.</p>
Quantitative results of the analysis of novel ossicle particles used in mandible bone regeneration
<p>Dataset corresponding to the results of the characterization analysis of novel holothurian ossicle biomaterials. These biomaterials were evaluated at three levels:</p> <p>1) Ex vivo analysis to determine thr potential cytotoxic effects of these biomaterials on human fibroblasts using LIVE/DEAD and quantification of DNA released to the medium.</p> <p>2) In vivo analysis to determine the potential systemic effects of these biomaterials grafted subcutaneously in laboratory rats.</p> <p>3) Histochemical and immunohistochemical analysis to determine the potential effects of these biomaterials on mandible bone regeneration.</p> <p>These results correspond to the publication entitled "<span>EVALUATION OF HOLOTHURIAN OSSICLES AS A BIOLOGICAL BIOMATERIAL FOR MANDIBULAR BONE REGENERATION</span>".</p>
Quantitative results of the analysis of human native and bioengineered tissues corresponding to the work "Histological, histochemical and immunohistochemical characterization of NANOULCOR nanostructured fibrin-agarose human cornea substitutes generated by tissue engineering"
<p>Dataset containing the quantitative results of the histochemical and immunohistochemical analysis of the following human tissues:</p> <ul> <li>Control native cornea (CTR-C)</li> <li>Control native limbus (CTR-L)</li> <li>Artificial cornea generated by tissue engineering (HAC)</li> </ul> <p>Each tissue type was subjected to histochemical and immunohistochemical analyses and results were quantified using ImageJ software to determine average intensities and area fractions corresponding to positive staining signal for each marker.</p>
Operating diagram of IF incubator, two identical incubators were used for eggs that were already sorted. They are made up of an isothermal enclosure and contain three tiers (100 × 60 × 17 cm). The water circulating in each tier comes from the same filtration, cooling and sterilisation device. As a result, the eggs placed in the different tiers are subject to the same temperature regime. in Reproduction of Zingel asper (Linnaeus, 1758) in controlled conditions: an assessment of the experiences realized since 2005 at the Besançon Natural History Museum
Operating diagram of IF incubator, two identical incubators were used for eggs that were already sorted. They are made up of an isothermal enclosure and contain three tiers (100 × 60 × 17 cm). The water circulating in each tier comes from the same filtration, cooling and sterilisation device. As a result, the eggs placed in the different tiers are subject to the same temperature regime.
Figure 6. Most parsimonious result from a in Exploring phylogenetic relationships of Pteraspidiformes heterostracans (stem-gnathostomes) using continuous and discrete characters
Figure 6. Most parsimonious result from a phylogenetic analysis of discrete (1—64) and discretized continuous characters identified through gap coding (88—100). A, strict consensus of 30 most parsimonious trees with equally weighted characters (tree length 346). B, most parsimonious solution with implied weighted characters (k = 3) (tree length 27.86). Psammosteidae taxa in bold (for which quantitative characters have been treated as inapplicable, i.e. non-homologous).
Figure 4. Results from the phylogenetic analysis using discrete data only. A in Exploring phylogenetic relationships of Pteraspidiformes heterostracans (stem-gnathostomes) using continuous and discrete characters
Figure 4. Results from the phylogenetic analysis using discrete data only. A, strict consensus of 275 most parsimonious trees with equal character weights; length 276 steps, consistency index (CI) = 0.35, retention index (RI) = 0.59, and rescaled consistency index (RC) = 0.22. B, strict consensus of four most parsimonious trees with implied character weighting (k = 3) (tree length 23.11). Psammosteidae taxa in bold.
Software for optimizing treatment to slow the spatial propagation of invasive species: Code and results
<p>Slowing the spread of invasive species is a major challenge. How can we achieve this goal in the most cost-effective manner? This package includes the complete code and simulation results that help finding the optimal, most cost-effective treatment to slow the spread of a propagating species. This package accompanies the paper "Optimizing strategies for slowing the spread of invasive species" by Adam Lampert (PLOS Computational Biology, DOI: 10.1371/journal.pcbi.1011996). The file general_model_code.zip contains the code for the general model; the file spongy_moth_model_code.zip contains the code for the spongy moth model; and the file general_model_simulation_results.zip contains the results for the general model; and the file spongy_moth_model_simulation_results.zip contains the results for the spongy moth model.</p>
Modelling data and model results Tox21
<p>The data sets accompany the manuscript </p> <ul> <li><a href="https://doi.org/10.1101/2023.11.15.567095" target="_blank" rel="noopener">10.1101/2023.11.15.567095</a></li> </ul> <p>The data sets rely on previous work from </p> <p>M. Lovrić, "Razvoj i primjena modela za procjenu ekotoksikoloških rizika bioaktivnih kemijskih spojeva", Disertacija, Sveučilište u Zagrebu, Prirodoslovno-matematički fakultet, Zagreb, 2021. Dostupno na: https://urn.nsk.hr/urn:nbn:hr:217:730117</p> <p>and</p> <p>Lovrić M, Malev O, Klobučar G, Kern R, Liu JJ, Lučić B. Predictive Capability of QSAR Models Based on the CompTox Zebrafish Embryo Assays: An Imbalanced Classification Problem. Molecules. 2021 Mar 15;26(6):1617. doi: 10.3390/molecules26061617</p> <p>the original data was downloaded from the Tox21 challenge https://tripod.nih.gov/tox21/challenge/data.jsp </p> <p>The files comprise of:</p> <ol> <li>tox21_desc_p194.csv - descriptor data for the prepared Tox21 data set</li> <li>tox21_fp_all.csv - fingerprint and maccs data for the prepared Tox21 data set</li> <li>tox21_target_all.csv - 12 binary Tox21 target(labels) </li> <li>standardizer_pipeline.xml - structure standardizer pipeline for ChemAxon Standardizer </li> <li>tox21_models_metadata.json - model metadata such as sklearn hyperparameters and descriptor feature lists</li> </ol> <p> </p> <p> </p>
Fig. 1. a in First report on Phyllobothrium delphini infection and Crassicauda sp. parasitism resulting in osseous metaplasia in a Cuvier's beaked whale (Ziphius cavirostris) from the Brazilian region
Fig. 1. a Infected adipous tissue. Phyllobothrium delphini located in the center of the well-delimited parasitic cyst. Inset: Phyllobothrium delphini displaying a whitish coloration and shiny appearance. Bar, 2 cm b Thoracic aorta artery displaying bone metaplasia. Radiographic image highlighting the strong radiopacity, similar to bone radiopacity, observed along all the artery walls. Bar, 15 cm c Parasitic cyst located in adipose tissue. Proliferating and reacting fibrous tissue with a moderate number of lymphocytes and plasmocytes located along the parasitic cyst wall. Numerous activated macrophages and multinucleated giant cell (black arrow) are visible around the P. delphini specimen displaying a degenerated cuticle (red arrow). Insert: Hight power field of inflammatory infiltrate with lymphocytes (black arrow) and plasma cells (red arrow). d Thoracic aorta artery displaying bone metaplasia. Mature bone tissue is organized as circumferential lamellae and cement line (red arrow). Note the erythrocytes within the blood vessel and adipose tissue in the medullar region of the detected bone metaplasia. Inset: Hight power field of bone metaplasia with osteocytes allocated in lacunae (black arrow). e Parasitized kidney. Crassicauda sp. involved by reactive fibrous tissue associated with inflammatory infiltrate. f Parasitized Kidney. High power field of nephritis associated with Crassicauda sp. Note the fibrosis and inflammatory infiltrate formed by macrophages (red arrow) and plasma cells (black arrow).. (For interpretation of the references to color in this figure legend, the reader is referred to the Web version of this article.)
SPT results - Simulation of zonation-function relationships in the liver using coupled multiscale models: Application to drug-induced liver injury
<p>Results of the study "Simulation of zonation-function relationships in the liver using coupled multiscale models: Application to drug-induced liver injury"</p>
Source code and simulation results: Efficient rational approximation of optical response functions with the AAA algorithm
<p>This publication provides data published in the article "Efficient rational approximation of optical response functions with the AAA algorithm" [1] in tabulated form along with the Matlab scripts that have been used to produce them. These scripts interface the finite element method solver JCMsuite [2,3]. The article presents rational approximations of optical response functions based on an extended version of the AAA algorithm [4] that allows to efficiently reconstruct sensitivty spectra and gives access to sensitivities of poles, residues, and zeros. Furthermore, the rational approximation of a scalar observalbe is used to construct solutions of the source free Maxwell's equation, i.e., a nonlinear eigenvalue problem. </p> <p><strong>The physical Structure</strong></p> <p>The example is based on the chiral metasurface introduced in [5]. For the sake of simplicity we added infinite layers of SiO\(_2\) to the top and the bottom of the structure. The original structure has a SiO\(_2\) substrate and a layer of PMMA polymethyl methacrylate (PMMA) deposited on top. PMMA can be modelled with the same refractive index of 1.45 as SiO\(_2\). Furthermore, our simulations include the 13 nm indium tin oxide (ITO) coating which drastically reduces the Q-factor as it is slightly absorbing. The accuracy of the discrete model is verified by assessing reflection, transmission, and absorption at 241 evenly spaced points within the specified range. Energy conservation requires that the discrepancy between their sum and the energy entering the system is zero. The numerical discretization is chosen such that the maximum relative error is less than \(3\times10^{−5}\).</p> <p><strong>Dispersion</strong></p> <p>Tabulated data for ITO has been taken from the <a href="https://refractiveindex.info/?shelf=other&book=In2O3-SnO2&page=Konig">refractiveindex.info</a> database (T. A. F. König et al., 2014, https://doi.org/10.1021/nn501601e) and the data for TiO2 was kindly provided the authors of [5]. The permittivity \(\varepsilon = (n+ik)^2\) is locally approximated as a rational function, i.e., only data in a vicinity of the frequency range of interest is considered. As we aim for a function with the symmetry \(f^\ast(\omega) = f(-\omega^\ast)\) we add the complex conjugated data at negative frequencies and enforce the symmetry in a second step. The partial fraction decomposition of the required function is of the form: \(\varepsilon(\omega) = \varepsilon_\infty + \sum_{j=1}^{4}a_j/(\omega-\omega_j) - a_j^\ast/(\omega+\omega_j^\ast)\) with the residues \(a_j\) and the poles \(\omega_j\). We expect 4 pairs of poles to sufficiently approximate the data within the range of interest (4 with positive and 4 with negative real parts).</p> <h4><strong>Requirements</strong></h4> <ul> <li>JCMsuite (at least 6.2.0)</li> <li>MATLAB (tested with version R2023b)</li> </ul> <p>In order to run the simulations with JCMsuite you must replace corresponding place holders with a path to your installation of JCMsuite. Free trial licenses are available, please refer to the homepage of <a href="https://jcmwave.com/">JCMwave</a>.</p> <p><strong>Usage</strong></p> <p>With the content of 'spectra.zip' you can reproduce results presented in the paper. Running the script 'plots.m' will not start any expensive simulation but use the provided data. With 'dispersion.m' the fits to the material data can be reproduced. Additionally, tabulated data is contained in 'data/ascii'. The archive 'eigenmodes.zip' must be extracted in the same directory as 'spectra.zip'.</p> <p><strong>References</strong></p> <p>[1] Fridtjof Betz, Martin Hammerschmidt, Lin Zschiedrich, Sven Burger, Felix Binkowski: Efficient rational approximation of optical response functions<br>with the AAA algorithm, https://doi.org/10.48550/arXiv.2403.19404.</p> <p>[2] Jan Pomplun, Sven Burger, Lin Zschiedrich, Frank Schmidt, Adaptive finite element method for simulation of optical nano structures, Physica Status Solidi B <strong>244</strong>, 3419 (2007), http://dx.doi.org/10.1002/pssb.200743192.</p> <p>[3] Fridtjof Betz, Felix Binkowski, Sven Burger, RPExpand: Software for Riesz projection expansion of resonance phenomena, SoftwareX <strong>15</strong>, 100763 (2021), https://doi.org/10.1016/j.softx.2021.100763.</p> <p>[4] Y. Nakatsukasa, O. Sète, and L. N. Trefethen, The AAA Algorithm for Rational Approximation, SIAM Journal on Scientific Computing <strong>40</strong>, A1494 (2018), http://dx.doi.org/10.1137/16M1106122.</p> <p>[5] X. Zhang, Y. Liu, J. Han, Y. Kivshar, and Q. Song, Chiral emission from resonant metasurfaces, Science <strong>377</strong>, 1215 (2022), http://dx.doi.org/%2010.1126/science.abq7870.</p>
Results for the paper "The impact of temporal hydrogen regulation on hydrogen exporters and their domestic energy transition"
<p>As global demand for green hydrogen rises, potential hydrogen exporters move into the spotlight. However, the large-scale installation of on-grid hydrogen electrolysis for<br>export can have profound impacts on domestic energy prices and energy-related emissions. Our investigation explores the interplay of hydrogen exports, domestic<br>energy transition and temporal hydrogen regulation, employing a sector-coupled energy model in Morocco. We find substantial co-benets of domestic climate change<br>mitigation and hydrogen exports, whereby exports can reduce domestic electricity prices while mitigation reduces hydrogen export prices. However, increasing hydrogen<br>exports quickly in a system that is still dominated by fossil fuels can substantially raise domestic electricity prices, if green hydrogen production is not regulated.<br>Surprisingly, temporal matching of hydrogen production lowers domestic electricity cost by up to 31% while the effect on exporters is minimal. This policy instrument can<br>steer the welfare (re-)distribution between hydrogen exporting firms, hydrogen importers, and domestic electricity consumers and hereby increases acceptance<br>among actors.</p>
Demonstration of "RO-Crate for Testbeds: Automated Packaging of Experimental Results"
<p>Demonstrative experiment data of the paper "RO-Crate for Testbeds: Automated Packaging of Experimental Results".</p> <p>Demonstrator shows experimental artifacts as a RO-Crate package.</p>
Common bunt in wheat: Results of the ECOBREED field trials, Austria and Czech Republic, 2021-2022
<p>Supplementary material to Lunzer et al. (2023) Front Plant Sci 14: 1264458 [https://doi.org/10.3389/fpls.2023.1264458]:</p> <ul> <li>Scheme for the marker-assisted selection for common bunt QTL</li> <li>Raw data of field and lab evaluations - Austria & Czech Republic 2021</li> <li>Raw data of field and lab evaluaitons - Austria & Czech Republic 2022</li> </ul> <p>Raw data files include the data on several spreadsheet sheets. Each file includes metadata and used abbreviations in the first two sheets.</p>
Seismic profiles, migration velocities and tomographic inversion results of the deep reflection profiles in the central South China
<h1><strong>Overview</strong></h1> <p>The following set of data and scripts are meant to accompany the paper:</p> <p>Jiang, W. B., Wang, Q., Zhang, Y.Q., Dong, S.W., Ruan, Y.Q., Cui, J.J., Kuang, Z.Y., Paleoproterozoic collision to Mesozoic crustal reworking in central South China: evidence from borehole data and seismic crustal structure, Submitted to JGR: Solid Earth</p> <p>The data and scripts are intended to reproduce seismic profiles, migration velocities, and tomographic inversion results shown in the paper.</p> <p>The repository contains five directories:</p> <p><strong>./01_Seismic_Profiles/</strong> -> Four seismic profiles shown in the manuscript. (1) psdm_line01.sgy (Figure 7a); (2) psdm_line02.sgy (Figure 7b); (3) SCB_PSDM.segy (Figure 9); (4) SCB_PSTM.segy (Figure S5a).</p> <p><strong>./02_Tomographic_Data_Velocity/</strong> -> picked_traveltimes.tt, picked traveltime for the normal shots (Figure 6a). The file contains location of shots and receivers, picked traveltimes; Tomo_inv.mdl, P-wave velocity model derived from first-arrival traveltime tomography (Figure 8a); Tomo_Fx1_Fz1_ray.mdl, Ray density distribution calculated using the Vp model (Figure 8b); traveltime_data_FILE_FORMAT.pdf, this pdf file describes the format of *.tt file; mdl_data_FILE_FORMAT.pdf, this pdf file describes the format of *.mdl file.</p> <p><strong>./03_Migration_Velocity_Models/ </strong>-> Migration velocity models to produce prestack time migration profile and prestack depth migration profile. VEL_RMS.mdl, RMS velocity field used in prestack time migration (Figure S4a); VEL_INTERVAL.mdl, Interval velocity field used in prestack depth migration (Figure S4b).</p> <p><strong>./04_Bouguer_Gravity_Anomaly/ </strong>-> gravity_data.grv, the Bouguer gravity anomaly data used in 2-D gravity modelling; gravity_data_FILE_FORMAT.pdf, this pdf file describes the format of *.grv file.</p> <p><strong>./05_Scripts/</strong> -> Matlab scripts to reproduce seismic profiles, migration velocities, and tomography inversion results shown in the paper. </p>
Dataset for DFT and one-step model results used in publication "Persistence of Structural Distortion and Bulk Band Rashba Splitting in SnTe above Its Ferroelectric Critical Temperature" in Nano Letters, 2024, 24, 1, 82–88
<p>Dataset for DFT and one-step model results used in publication DOI 10.1021/acs.nanolett.3c03280, "Persistence of Structural Distortion and Bulk Band Rashba Splitting in SnTe above Its Ferroelectric Critical Temperature" in Nano Letters, 2024, 24, 1, 82–88.</p> <p>Description of dataset is in the ReadMe.txt file in subdirectories.</p>
APPENDIX 2. — BLASTN results for the 16S in Morphological and molecular characterization of Goleter sp. (Nostocales, Nostocaceae) isolated from freshwater in Iran
APPENDIX 2. — BLASTN results for the 16S rRNA gene of the isolate Goleter sp. against the standard nucleotide database.
Greg Kolodziejzyk's 13-year associative remote viewing experiment results
<p>The research that created this data is described in:</p> <ul> <li>Kolodziejzyk, G. (2012). Greg Kolodziejzyk's 13-year associative remote viewing experiment results. <em>The Journal of Parapsychology, 76</em>(2), 349.</li> </ul> <p>Five files are included:</p> <ul> <li>GregsARVdata2.txt - This is the raw data provided by Greg Kolodziejzyk</li> <li>Code book_0.txt - Code book (raw data)</li> <li>GregsARVdata2-dates-fixed.csv - Cleaned data (date formats standardised)</li> <li>Code book (cleaned data).pdf - Code book (cleaned data)</li> <li>Cleaning procedure_0.zip - Procedure for transforming from raw data to cleaned data.</li> </ul>
ScienceDex guides
Understand access before you commit
These curated guides explain access requirements, typical timelines, costs, and reuse considerations for widely used research datasets.
Allen Brain Atlas
Allen Brain Atlas is an Allen Institute collection of brain map atlases, datasets, APIs, and analysis tools covering mouse, human, and non-human primate brain resources.
Annotated Behaviour and Observability Dataset (ABODe)
ABODe is a University of Edinburgh DataShare dataset for behavior classification in group-housed mice using home-cage video, identities, bounding boxes, ground-plate positions, and annotator labels.
DANDI Archive for NWB datasets
DANDI is a BRAIN Initiative archive for publishing and sharing neurophysiology data, including electrophysiology, optophysiology, and behavioral data packaged as NWB and related standards.
International Brain Laboratory public data
The International Brain Laboratory public data releases expose standardized mouse decision-making experiments, including Neuropixels recordings, widefield calcium imaging, behavior, and session metadata accessed through the ONE API.
OpenNeuro
OpenNeuro is a free, open platform for sharing neuroimaging datasets, with public search, dataset pages, and download paths for web, S3, DataLad, and the OpenNeuro CLI.