Find research datasets worth reusing

Discovering cryptic pocket opening and binding of a stimulant derivative in a vestibular site of the 5-HT3A receptor

Raw MD simulation data of 4-Bromoamphetamine-5HT3A complex in two different forceeild, AMBER and CHARMM. Original paper title: "Discovering cryptic pocket opening and binding of a stimulant derivative in a vestibular site of the 5-HT3A receptor" Author list: Nandan Haloi, Emelia Karlsson, Marc Delarue, Rebecca J. Howard, Erik Lindahl

opencc-by-4.0Nov 2023View details →

Thermal conductivity analysis of polymer-derived nano-composite via image-base structure reconstruction, computational homogenization and machine learning

This dataset includes supplementary data and utilities for validating simulation results and training machine learning models as outlined in the publication titled "Thermal Conductivity Analysis of Polymer-Derived Nanocomposite via Image-Based Structure Reconstruction, Computational Homogenization, and Machine Learning" (<a href="https://doi.org/10.1002/adem.202302021">Fathidoost, 2024</a>). This dataset containes the microstructure images (identified by particle diameters size \(D_1\) and \(D_2\) volume fraction \(V_\mathrm{f}\) and aspect ratio \(A_\mathrm{r}\)) (see Table 1) and their corresponding homogenized thermal conductivity. these images resemble the microstructure of the monolithic \(\mathrm{(Hf,Ta)C/SiC}\) ceramic following FAST sintering, the material system of this work (<a href="https://doi.org/10.1002/adem.202302021">Fathidoost, 2024</a>). White and black colors within the images represent distinct regions of the material system,  respectively referring to former powder particles (FPPs) and sinter necks (SNs), which is explained in this work. Table 1. Parameterized descriptors extracted from the mesoscale SEM image analysis <table> <tbody> <tr> <td>Param.</td> <td>Mean [unit]</td> <td>Std.</td> </tr> <tr> <td>\(D_{1}\)</td> <td>40, 50, 60 [μm]</td> <td>20%</td> </tr> <tr> <td>\(D_{2}\)</td> <td>20, 25, 26, 30, 33, 40 [μm]</td> <td>30%</td> </tr> <tr> <td>\(V_\mathrm{f}\)</td> <td>1.5, 2.0</td> <td>-</td> </tr> <tr> <td>\(A_\mathrm{r}\)</td> <td>35, 40, 45, 55, 60 [%]</td> <td>-</td> </tr> </tbody> </table> This dataset contains: <ul> <li>dataset.csv: containing a summary of data including the names of microstructure images, their corresponding geometric details, as well as the first and third principal components of two-point statistics for all images, along with the effective thermal conductivity of the corresponding microstructures. Further details can be found in the associated publication.</li> <li>microstructures_images.zip: containing binary cross-section images of the RVEs from synthetic microstructures。</li> <li>results.zip: contains all the simulation results based on digitized diffuse-interface microstructures, which can be opened by the post-processing software, such as ParaView.</li> </ul>

opencc-zeroMar 2024View details →

Leech-derived iDNA complements traditional surveying methods, enhancing species detections for rapid biodiversity sampling in the tropics

Deforestation, exploitation, and other drivers of biodiversity loss in Madagascar leave its highly endangered and predominantly endemic wildlife at risk of extinction. Decreasing biodiversity threatens to compromise ecosystem functions and vital services provided to people. New, economical, and diverse methods of biodiversity monitoring can help to establish reliable baseline and long-term records of species richness. Metabarcoding with invertebrate-derived DNA (iDNA) has emerged as a promising new biosurveillance tool. An unexpected wet forest fragment tucked in the dry cliffs of Madagascar's southcentral plateau, the Ivohibory Protected Area (IPA), hosts a unique mosaic of species diversity, featuring both dry and wet forest species. Recently elevated to protected status, the IPA has been surveyed for flora and fauna with a range of inventory methods over three years and six expeditions (2016, 2017, & 2019). We collected 1,451 leeches over 12 days from the IPA to supplement known species richness and to compare results against current records. With iDNA, we pooled tissues, and isolated, and amplified bloodmeal DNA with five sets of primers. We detected 20 species of which four are species of frogs previously undetected and three of which are previously unknown to exist in this region. iDNA surveys can provide complementary data to traditional surveying methods like camera traps, line transects, and bioacoustic methods.

The Cannon-Re-derived Parameters and Abundances of GALAH DR3 Giants

Table 1 in Manea et al. 2023: Chemical Doppelgangers in GALAH DR3: the Distinguishing Power of Neutron-Capture Elements Among Milky Way Disk Stars (https://ui.adsabs.harvard.edu/abs/2023arXiv231015257M/abstract) These files contain the parameter and abundance results of our Cannon run on GALAH DR3 giants.  manea_et_al_2023.fits contains the results without censoring applied, and manea_et_al_2023_censoring.fits contains the results with censoring applied.  The latter file is provided solely for reader interest, but the former file is what we use for our measurement of the doppelganger rate in GALAH DR3.  We strongly urge users to only consider abundances with X_fe_cannon_chisq < 2 as these abundances are considered reliable (see Section 3.1.4).  Entries with empty abundance uncertainties correspond to extremely poorly-fit abundances and should be ignored by the user, and employing the X_fe_cannon_chisq < 2 will already remove these. Please see Table 1 in Manea et al. 2023 for the table schema.

Global oceanic seamless POC concentration products derived from MODIS-Aqua

The dataset integrates seamless POC concentration daily products for the global ocean from 2011 to 2016, derived from MODIS-Aqua‘s XGBoost satellite retrieval products.  The POC concentration in the product used int32 to integer data, specifically, the raw POC concentration (mg m-3) is first multiplied by 10000 and then rounded using int32.

Global oceanic seamless POC concentration products derived from MODIS-Aqua

The dataset integrates seamless POC concentration daily products for the global ocean from 2003 to 2010, derived from MODIS-Aqua‘s XGBoost satellite retrieval products. It covers the time span from 2003 to 2010. The POC concentration in the product used int32 to integer data, specifically, the raw POC concentration (mg m-3) is first multiplied by 10000 and then rounded using int32.

Global oceanic seamless POC concentration products derived from MODIS-Terra

The dataset integrates seamless POC concentration daily products for the global ocean from 2001 to 2008, derived from MODIS-Terra‘s XGBoost satellite retrieval products.  The POC concentration in the product used int32 to integer data, specifically, the raw POC concentration (mg m-3) is first multiplied by 10000 and then rounded using int32.

opencc-zeroMar 2024View details →

Data underlying the publication: Gut bacteria-derived volatiles mediate the Drosophila melanogaster (Diptera: Drosophilidae) attraction

Bacteria-originated volatile molecules play a crucial role in chemical communications between insects, representing their promising application as odor bait traps in pest control. In this study, we investigated the behavioral preferences of the fruit fly Drosophila melanogaster (Diptera: Drosophilidae) towards the fermentation broth of seven gut-associated bacteria using trap choice assays. All seven bacterial fermentations significantly attracted adults and larvae compared to the medium control. We assessed the effects of bacterial fermentations on bayberry fruits' olfaction attractiveness to fly adults and found that the bayberry fruits sprayed with fermentation broth from seven bacteria were all significantly more attractive to insects than the non-sprayed fruits, resulting in increased egg numbers. We also compared the attractive effect of bacterial fermentations with a sugar-vinegar mixture and a commercial odor-bait. The commercial odor bait proved more enticing than the unconcentrated 5-day fermentation broths. However, out of the seven bacteria, 64-fold concentrated bacterial fermentation of Corynebacterium (Actinomycetota phylum) was significantly more attractive than commercial bait. Finally, we chemically identified the predominant compounds 2-methylpropanal and acetaldehyde, which are likely responsible for the behavioral preference of fruit flies. Our findings provide a deeper understanding of how gut microbes affect insect behavior and offer a potential bacteria-originated odor bait for fly control in the orchard.

Towards automatic derivation of geometry-based descriptors as surrogates for complex structural approaches in enzyme-substrate prediction

Dataset produced for the Project PRELUDIUM19 2020/37/N/NZ2/00967 entitled: "Towards automatic derivation of geometry-based descriptors as surrogates for complex structural approaches in enzyme-substrate prediction" The dataset counts with the three families of enzymes used: dehalogenase, aldehyde reductase and nitrilase. For each enzyme, the docked structures, docked parameters and scripts to analyze them further are present. Moreover, the protocol that derives geometric descriptors from docked structures is also present. This work was supported by the National Science Centre, Poland (grant no. 2020/37/N/NZ2/00967)

opencc-zeroApr 2024View details →

Data from: Phenotypic resources immortalized in a panel of wild-derived strains of five species of house mice

The house mouse, Mus musculus, is a widely used animal model in biomedical research, with classical laboratory strains (CLS) being the most frequently employed. However, the limited genetic variability in CLS hinders their applicability in evolutionary studies. Wild-derived strains (WDS), on the other hand, provide a suitable resource for such investigations. To assess the proportion of variation added by wild progenitors, we estimated phenotypic variation in 84 WDS representing 5 species (M. musculus, M. spretus, M. spicilegus, M. macedonicus, M. caroli), 3 subspecies (M. m. musculus, M. m. domesticus, M. m. castaneus), and compared it with 5 CLS. The spectrum of WDS captures long-term mouse evolution, estimated to be over 5 million years ago since the split of M. caroli from the remaining mouse species. All mice are housed in a conventional breeding facility (without a nanofilter barrier or specific-pathogen free condition) at the Institute of Vertebrate Biology, Czech Academy of Sciences, in Studenec. They are maintained under standard conditions: light/dark regime of 14/10 hours, temperatures of 23 ± 1 °C during summer (April-September) and 22 ± 1 °C during winter (October-March), respectively, and relative humidity within 40-70 %. Mice have access to food pellets and tap water ad libitum. Further data on this mouse repository and WDS can be obtained at <a href="https://housemice.cz/en/strains/">https://housemice.cz/en/strains/</a>. Morphological traits were measured in 4335 mice and include body weight, spleen weight, body length, tail length, weight of both ovaries, sperm count, the weight of testes, left epididymis, and seminal vesicles. Reproductive ability was estimated in 87 WDS and 8 CLS. This dataset was obtained from 90,077 offspring born to 8,298 mothers in 17,049 litters recorded in Studenec studbooks between 2000 and 2023. Reproductive performance was characterized by litter size, newborn mortality (calculated as the proportion of stillborn or cannibalized mice across all litters), and the number of generations produced per year. We also estimated the time since a WDS was established from wild progenitors until completing 20 generations of strict brother-sister mating, i.e., the generation at which a strain of mice can be considered inbred. Although CLS resemble M. m. domesticus and M. m. musculus WDS, they differ from them in 8 and 11 out of 15 phenotypic traits, respectively. The data suggest that WDS can be a useful tool in evolutionary studies, providing a basis for comparative analyses with other mammal taxa, particularly classical laboratory mice. The detected stunning phenotypic variation supplemented by genetic variation have great potential for medical applications.

opencc-by-4.0Nov 2022View details →

F I G U R E 4 in Genetic characteristics and growth patterns of the hybrid grouper derived from the hybridization of Epinephelus fuscoguttatus (female) Epinephelus polyphekadion (male)

F I G U R E 4 Examples of functional secondary structures of the 5S gene

opencc-by-4.0Apr 2024View details →

Photophysics of Benzoxazole and Dicyano Functionalised Diketopyrrolopyrrole Derivatives: Insights into Ultrafast Processes and the Triplet State - Experimental data

Experimental data supporting the manuscript "Photophysics of Benzoxazole and Dicyano Functionalised Diketopyrrolopyrrole Derivatives: Insights into Ultrafast Processes and the Triplet State" published in ChemPhysChem (https://doi.org/10.1002/cphc.202300872). Details in the "Read me.txt" For more information please contact Tuhin Khan (khan [AT] imc.cas.cz)

opencc-by-4.0Apr 2024View details →

Derived Protein Sequence Data From Kaggle

It is the dataset containing protein sequence and its associated go-terms, used for priliminary training process

opencc-by-4.0Apr 2024View details →

Surface science and liquid phase investigations of oxanorbornadiene/oxaquadricyclane ester derivatives as molecular solar thermal energy storage systems on Pt(111) [doi: 10.1063/5.0158124]

Primary data, meta data, and corresponding lists of figures & tables are included. [doi: 10.1063/5.0158124]

Dataset for publication "Sol-gel derived silicate-phosphate glass SiO2–P2O5–CaO–TiO2: the effect of titanium isopropoxide on porosity and thermomechanical stability"

In this work, sol-gel silica-phosphate glasses (30 mol.% P2O5) with defined porosity from 2.5 to 7.5 mol.% TiO2 modifications were synthesized. Thee dimensional stability with respect to the thermal stability of porous silica-phosphate glasses modified by titanium dioxide (TiO2) through titanium isopropoxide (TTIP) precursor was studied. The data of thermomechanical and thermogravimetric analysis, X-ray diffraction, SEM -EDX, mercury intrusion porosimetry, N2 physisorption, micro-computed tomography, ultra-small-angle X-ray scattering are published.

opencc-zeroApr 2024View details →

Preliminary GNET-derived mass variations for Greenland

Monitoring the Greenland mass balance (GMB) is crucial in the context of global sea level rise. Currently, three main methods are used to measure GMB, with the primary source of uncertainty arising from the glacial isostatic adjustment (GIA) contribution. Here, we propose a novel approach based on a simple methodology that uses the entire Greenland GNSS network (GNET) as an instrument to monitor the present-day mass changes. Our method is validated against GRACE-derived GMB, and we find a very good agreement. This leads to an independent methodology for estimating present-day mass changes from GNSS, bridging the gap between GRACE and GRACE-FO in GMB estimates.

opencc-by-4.0Nov 2024View details →

Plasticizer Content by TGA datasets - Mass loss curves of PVB grades and derivative TGA curves

Datasets obtained for the Plasticizer Content by TGA analysis, from the paper "An Integrated Characterization Strategy on Board for Recycling of poly(vinyl butyral) (PVB) from Laminated Glass Wastes"

opencc-by-4.0Dec 2024View details →

Dataset for article: Dizocilpine derivatives as neuroprotective NMDA receptor antagonists without psychomimetic side effects

Open the record for dataset details and reuse information.

opencc-by-4.0Sep 2024View details →

data and codes for paper "Deriving mobility-lifetime products in halide perovskite films from spectrally- and time-resolved photoluminescence"

These are the data and Matlab codes used in the paper "Deriving mobility-lifetime products in halide perovskite films from spectrally- and time-resolved photoluminescence".