Find research datasets worth reusing

Quantum mechanical modeling of the on-grain formation of acetaldehyde on H2O:CO dirty ice surfaces

This Supporting Material contains: <ul> <li>Cartesian coordinates of HF-3c optimized minima and transition state for the reaction in gas phase, in .xyz format, computed using <a href="https://gaussian.com/">Gaussian16</a> code;</li> <li>Fractional coordinates of HF-3c optimized minima and trasition state structures for crystalline periodic models in <a href="https://www.moldraw.unito.it/_sgg/m1m1s43_1.htm">.mol</a> format, editable with <a href="http://www.moldraw.unito.it/">MOLDRAW</a>, computed using <a href="http://www.crystal.unito.it/">CRYSTAL17</a> computer code.</li> </ul>

Tailoring Ti Grade 2 and TNTZ alloy surfaces in a two-step mechanical-chemical modification

This record contains all files generated in the preparation process of the following publication: Agnieszka Kowalczyk, Donata Kuczyńska-Zemła, Agata Sotniczuk, Klaudia Anuszewska and Halina Garbacz, "Tailoring Ti Grade 2 and TNTZ alloy surfaces in a two-step mechanical-chemical modification", submitted to Surface Engineering. Designations: Ti alloy - Ti-29Nb-13Ta-4,6Zr alloy (TNTZ) G - sample grinded on #600 grit abrasive paper S_1,2 - sample shot peened with 90-150 µm shots, under pressure of 0.2 MPa S_1,3 - sample shot peened with 90-150 µm shots, under pressure of 0.3 MPa S_1,4 - sample shot peened with 90-150 µm shots, under pressure of 0.4 MPa S_1,5 - sample shot peened with 90-150 µm shots, under pressure of 0.5 MPa S_2,4 - sample shot peened with 150-250 µm shots, under pressure of 0.4 MPa S_2,5 - sample shot peened with 150-250 µm shots, under pressure of 0.5 MPa SE_1,2 - sample shot peened with 90-150 µm shots, under pressure of 0.2 MPa and etched in a solution of 3% hydrofluoric acid (HF) SE_1,3 - sample shot peened with 90-150 µm shots, under pressure of 0.3 MPa and etched in a solution of 3% hydrofluoric acid (HF) SE_1,4 - sample shot peened with 90-150 µm shots, under pressure of 0.4 MPa and etched in a solution of 3% hydrofluoric acid (HF) SE_1,5 - sample shot peened with 90-150 µm shots, under pressure of 0.5 MPa and etched in a solution of 3% hydrofluoric acid (HF) SE_2,4 - sample shot peened with 150-250 µm shots, under pressure of 0.4 MPa and etched in a solution of 3% hydrofluoric acid (HF) SE_2,5 - sample shot peened with 150-250 µm shots, under pressure of 0.5 MPa and etched in a solution of 3% hydrofluoric acid (HF) HV - Vickers hardness SEM - Scanning Electron Microscopy R - roughness W - wettability Folders content: Hardness - contains files with data obtained from hardness tests using a Falcon 500 hardness tester with a Vickers indenter at a load of 1.96 N (HV0.2) Roughness - contains files from topography analysis obtained using a Wyko NT9300 optical profilometer for various scan areas SEM - contains images of samples surfaces from Hitachi SU8000 and Hitachi SU70 Scanning Electron Microscopes   Wettability - contains files with data obtained from wettability tests using a DataPhysics OCA 25 goniometer with the sessile drop method This research was funded in part by National Science Centre, Poland [Grant no. 2022/45/B/ST5/03398].

opencc-zeroAug 2023View details →

Rapid sperm length divergence in a polygynandrous passerine: a mechanism of cryptic speciation?

When populations become geographically isolated, they begin to diverge in various traits and at variable rates. The dynamics of such trait divergences are relevant for understanding evolutionary processes such as local adaptation and speciation. Here we examine divergences in sperm and body structures in a polygynandrous songbird, the alpine accentor (Prunella collaris) between two allopatric high-altitude populations, in Morocco and Spain. The populations diverged around 82,000 years ago, as estimated with a coalescence-based phylogenetic analysis of genome-wide single nucleotide polymorphisms. We found that birds in the two areas had non-overlapping sperm lengths. This suggests adaptation to divergent female reproductive tract environments. Sperm length also showed an exceptionally low coefficient of among-male variation, a signal of strong stabilizing selection imposed by sperm competition. The evolutionary rate of sperm length was almost twice the rates for the most divergent morphological traits, and more than three times higher than expected from literature data over a similar generational timescale. This rapid evolution of a key reproductive trait has implications for reproductive isolation and ultimately for speciation. Strong selection for different sperm length optima in allopatry predicts conspecific sperm precedence and disruptive selection in sympatry, hence a possible postcopulatory prezygotic barrier to gene flow.

The Role of Criptic Ancestral Symmetry In Histone Folding Mechanisms Across Eukarya and Archaea

The shown folders contain the molecular dynamics simulation data, used tools, and scripts for the study of "The Role of Criptic Ancestral Symmetry In Histone Folding Mechanisms Across Eukarya and Archaea". The simulation data includes the force field and simulation setup for both AWSEM-MD and atomistic MD in OpenMM, the data analyses that are presented in the related paper, and the representative conformations from each simulation. Due to the large file size, the original trajectory files are available upon separate request. The tools and scripts folder includes the specific version of the AWSEM model, implemented in the LAMMPS package, and the scripts used to analyze the simulations. For detailed instructions on using AWSEM model, please refer to our Github: <a href="https://github.com/adavtyan/awsemmd/wiki">https://github.com/adavtyan/awsemmd/wiki</a>. For detailed instructions on using the LAMMPS package, please refer to <a href="https://www.lammps.org/#gsc.tab=0">https://www.lammps.org/#gsc.tab=0</a>. For detailed instructions on using the OpenMM package, please refer to <a href="https://openmm.org/">https://openmm.org/</a>. For any questions about using this data repository, please feel free to contact the author.

Supplementary data for "Chamber studies of OH + dimethyl sulfoxide and dimethyl disulfide: insights into the dimethyl sulfide oxidation mechanism."

This page contains public data for the peer-reviewed publication: Matthew B. Goss and Jesse H. Kroll: "Chamber studies of OH + dimethyl sulfoxide and dimethyl disulfide: insights into the dimethyl sulfide oxidation mechanism." ACP, XX, XXXX–XXXX, 202X. Submitted. These data files are intended as additional supplementary information for this publication. If you would like to use any data herein in a publication, please contact the corresponding author (Matthew Goss, mgoss@mit.edu) first. Data files contain product concentration timeseries. Time is reported in seconds after UV lights were turned on. All data, except for ozone and NOx timeseries, have been corrected for chamber dilution. Product concentrations are reported in parts per billion. If you have any more questions, please contact the corresponding author, Matthew Goss at mgoss@mit.edu.

Sensorimotor mechanisms selective to numerosity: evidence from individual differences

This is the dataset related to the article:"Sensorimotor mechanisms selective to numerosity: evidence from individual differences" The file contains subjects Weber Fractions for all of the experiments presented in the paper sub_ID is the participant's identification number

Response mechanism of residual strength to meso-structure of shear surface in gravelly slip zone of ancient landslide

Response mechanism of residual strength to meso-structure of shear surface in gravelly slip zone of ancient landslide-Original data

opencc-zeroAug 2023View details →

Data from: Shallow moonquake mechanisms illuminated by rheologic characteristics of basaltic gouges

The projected evolutionary history of the Moon and observed occurrence of moonquakes suggest that brittle faulting is present in the shallow lunar crust. Chang'e 5 samples of lunar regolith show a mineral composition almost identical to basaltic bedrock. We measure the friction-stability characteristics of dry synthetic gouges representative of basaltic faults assumed to be present in the lunar crust. Frictional strengths are ~0.7 and exhibit overall velocity-strengthening response but transition to velocity-weakening at intermediate temperatures (100-300℃) and stresses (10-100 MPa). Bounding temperature profiles representative of the lunar crust suggest that moonquakes are feasible throughout the shallowest ~40-60 km of the crust. However, observations of unusually high stress drops (up to 210 MPa) are inconsistent with the measured frictional strengths – suggesting that high degrees of healing on preexisting faults or intact crust are present – to augment stress accumulation mechanisms due to tidal forcing or differential thermal cooling.

First-principles insights into the electronic, optical, thermophysical, and mechanical properties of lead-free cubic novel Ba3SbBr3 perovskite

Lead-free halide perovskites have emerged as a significant class of materials with immense potential for solar cell synthesis. Among these materials, Ba3SbBr3, a halide novel perovskite, exhibits remarkable efficiency and holds promise for solar cell applications. There are a lot of physical properties, including its elasticity, electrical composition, bonding, thermophysical, optoelectronic properties, and optical properties, that remain unexplored. In this study, we employ advanced density functional theory-based computations to investigate and unveil the previously unidentified physical properties of novel Ba3SbBr3. Our research encompasses a wide range of analyses, covering mechanical stability, phonon dispersion properties, thermophysical properties, elastic parameters, and bonding nature. By precisely analyzing the phonon dispersion properties and applying the Born-Huang criteria, we demonstrated it as mechanically stable. Moreover, our investigation demonstrates that Ba3SbBr3 exhibits favorable machinability and mechanical isotropy through the analysis of various elastic parameters. ELATE’s three- dimensional visualization and optical properties also show isotropic behavior in all directions. The electron charge density reveals the possession of the ionic bonding. Additionally, Ba3SbBr3 possesses a direct bandgap, which is essential for efficient optoelectronic performance. The study also encompasses an exploration of the thermophysical properties including the melting temperature, Debye temperature, Grüneisen parameter, and thermal expansion coefficient. The higher values observed in these properties highlight the material's enhanced mechanical stability, thermal stability, and overall suitability for optoelectronic device applications. A large range of photoconductivity and absorption coefficient indicates the suitability of its application in solar cells. The comprehensive investigation conducted in this study contributes novel insights into the unexplored physical properties of Ba3SbBr3, providing a solid foundation for future research endeavors. The findings presented here serve as a valuable reference and inspiration for further theoretical and experimental studies in this rapidly evolving field. The knowledge gained from this research holds great promise for advancing the development of solar engineering and device technologies.

opencc-by-4.0Sep 2023View details →

Dataset for "Disentangling mechanisms responsible for wind energy effects on European bats"

Data used in the study "Disentangling mechanisms responsible for wind energy effects on European bats". site = ID attributed to the studied site ; ID_Parc = ID attributed to the studied wind farm ; night = date of the sampling ; SM4 = ID attributed to the recorder ; NbWT_1500m = number of wind turbines in a 1500m buffer ; Dist_WT = distance to the nearest wind turbine ; Dist_water = distance to the nearest water body or water course ; Dist_forest = distance to the nearest forest ; avg_temp = average temperature of the night ; Prev_wind_mod1 = prevailing wind direction of the night ; count_prev_wind22.5 = number of hours during which the wind direction was close (± 22.5°) to the prevailing wind direction (mode) of the night ; angle = angle between the axis wind-turbine - detector and the north direction ; MES_year = year of commissioning of the nearest wind turbines ; Model = model of the nearest wind turbine ; Rotor_diameter = diameter of the rotor of the nearest wind turbine ; Hub_height = height of the hub of the nearest wind turbine ; ID_WT = ID attributed to the nearest wind turbine

opencc-zeroSep 2023View details →

Data for: Multiple mechanisms for inbreeding avoidance used simultaneously in a wild ape

Mating with close kin can have considerable negative fitness consequences, which are expected to result in selective pressure for inbreeding avoidance mechanisms, such as dispersal, mate choice and postcopulatory biases. Captive studies have suggested that inbreeding avoidance through mate choice is far less widespread than expected and may be absent where other mechanisms already limit inbreeding. However, few studies have examined multiple mechanisms of inbreeding avoidance simultaneously, particularly in the wild. We use 13 years of detailed dispersal, copulation, and paternity data from mountain gorillas to examine inbreeding avoidance. We find that partial dispersal of both sexes results in high kinship in multimale groups, but that copulations between close kin occur 40% less than expected. We find strong kin discrimination in mate choice, with significant avoidance of maternal kin but more limited avoidance of paternal kin. We find no evidence for post-copulatory inbreeding avoidance. Our analyses support familiarity-based mechanisms of kin identification and age-based avoidance that limits mating between fathers and daughters in their natal group. Our findings demonstrate that multiple complementary mechanisms for inbreeding avoidance can evolve in a single species and suggest that inbreeding avoidance through mate choice may enable more flexible dispersal systems to evolve.

opencc-zeroSep 2023View details →

Introduction pathways and evolutionary mechanisms of the spread of alien species of Lolium on sandy coasts in Japan

1. Estimating the role of specific processes in the spread of alien species necessitates the determination of introduction pathways and source populations of invaded areas. Alien grasses in the genus Lolium that have become widely invasive in Japan provide provides a unique opportunity to estimate the expansion process through a direct comparison between source and naturalised populations because the introduction pathways, contaminants in grain commodities and commercial cultivars for fodder crops or revegetation materials are well-known. Therefore, by directly comparing between source and naturalised populations, we estimated the introduction pathways and whether adaptative evolution occurred in Lolium species on sandy coasts in Japan. 2. Lolium individuals sampled from naturalised populations in croplands, seaports and sandy coasts were compared with those from two introduction sources for morphological and genetic variations based on a genome-wide single nucleotide polymorphism analysis and a common garden experiment. Furthermore, we conducted a reciprocal sowing experiment between a cropland and sandy coast. 3. Populations naturalized in croplands were closely related to the cultivars, whereas those naturalized in seaports and sandy coasts were associated with contaminants. This pattern is common in western Japan. Therefore, these results indicate that the cropland and sandy coast populations are derived from cultivars and contaminants, respectively. The reciprocal transplant experiment clearly demonstrated the home site advantage; populations derived from croplands yielded higher floret numbers than those derived from other habitats at the cropland site; however, such an advantage was not detected with the coastal site population. Sandy coast populations had higher survival rates than those from croplands at coastal sites. Port populations exhibited a similar tendency as sandy coast populations, indicating that contaminants may be originally adapted to salty and dry environments, such as that in sandy coasts. 4. Synthesis. We demonstrated that two congeneric species with different ecological characteristics were introduced through multiple introduction pathways and spread into different habitats. A direct comparison between source and naturalised populations can greatly advance our understanding of the patterns and processes of biological invasions.

opencc-by-4.0Oct 2023View details →

Computational Data Archive in Support of the Ping-Pong Mechanism for Peptide Bond Formation and Hydrolysis

In search for the goldilocks zone in the chemical space for amino acid oligomerization that is relevant to the emergence of protein-based metabolism, we identified a significant gap in our understanding about how peptide bond is formed and hydrolyzed under ambient aqueous conditions. We identified a six-step mechanism that reproduces the experimentally known experimental barriers. By careful evaluation of a comprehensive set of levels of theory, modelling of solvation effect, and calculation of thermochemical parameters, we established a robust computational model to expand the bulk water focus to interfacial phenomena of atmospheric/hydrospheric and litospheric/hydrospheric boundaries.  While we cannot travel back in time billions of years to witness the "birth" of the first macromolecule with pre-biotic relevance, we present the dataset and the corresponding publication in RSC Organic and Biomolecular Chemistry (July 26, 2023 issue) our attempt to establish an unbiased computational platform where we can evaluate experiments and generate experimentally testable ideas.

opencc-zeroOct 2023View details →

Molecular mechanisms of seasonal brain shrinkage and regrowth in Sorex araneus

<div class="page"> <div class="layoutArea"> <div class="column"> Human brains typically grow through development, then remain the same size in adulthood, and often shrink through age-related degeneration that induces cognitive decline and impaired functionality. In most cases, however, the neural and organismal changes that accompany shrinkage, especially early in the process, remain unknown. Paralleling neurodegenerative phenotypes, the Eurasian common shrew Sorex araneus, shrinks its brain in autumn through winter, but then reverses this process by rapidly regrowing the brain come spring. To identify the molecular underpinnings and parallels to human neurodegeneration of this unique brain size change, we analyzed multi-organ, season-specific transcriptomics and metabolomic data. Simultaneous with brain shrinkage, we discovered system-wide metabolic shifts from lipid to glucose metabolism, as well as neuroprotection of brain metabolic homeostasis through reduced cholesterol efflux. These mechanisms rely on a finely tuned brain-liver crosstalk that results in changes in expression of human markers of aging and neurodegeneration in Parkinson's disease and Huntington's disease. We propose metabolic shifts with signals that cross the brain-blood barrier are central to seasonal brain size changes in S. araneus, with potential implications for therapeutic treatment of human neurodegeneration. </div> </div> </div>

opencc-zeroOct 2023View details →

Data from: Divergent mechanisms of reduced growth performance in Betula ermanii saplings from high-altitude and low-latitude range edges

The reduced growth performance of individuals from range edges is a common phenomenon in various taxa, and considered to be an evolutionary factor that limits the species' range. However, most studies did not distinguish between two mechanisms that can lead to this reduction: genetic load and adaptive selection to harsh conditions. This study investigated the climatic and genetic factors underlying the growth performance of Betula ermanii saplings transplanted from 11 populations including high-altitude edge and low-latitude edge population using RAD-seq analysis. For 11 B. ermanii populations in wide-latitude range of Japan, we estimated gene diversity, nucleotide diversity, the coefficients of linkage disequilibrium, genetic differentiation between populations, population structure as well as the relatedness coefficient from SNPs. As a result, the low-latitude edge population exhibited a high level of linkage disequilibrium, low genetic diversity, a distinct genetic composition from the other populations, and a high relatedness coefficient. This data contains two SNPs datas (vcf files) used in these analysis. We analyzed SNPs data separately for 8 planting sites. Then each tarball contains 8 separate vcf files. One tarball named "vcfAfterFiltering" contains vcf files after SNP filtering steps used for the calculation of the coefficients of linkage disequilibrium. Another tarball named "vcfAfterLDPruning" contains vcf files after SNP filtering and before LD-based pruning used for the calculation of other genetic parameters.

opencc-by-4.0Dec 2022View details →

Dataset for: A marine cryptochrome with an inverse photo-oligomerization mechanism

Raw data for all sequence analysis, SEC runs, MD simulations, and UV/Vis absorbance readings supporting the findings of the study 'A marine cryptochrome with an inverse photo-oligomerization mechanism'

opencc-by-4.0Oct 2023View details →

Exploring the anti-glioma mechanism of the active components of Cortex Periplocae based on network pharmacology and iTRAQ proteomics in vitro

Hierarchical clustering analysis of candidate proteins was illustrated in heat map, which showed obvious differences between CP-induced cells and controls (Fig. 6). Each column is a sample and each rowindicates a differentially expressed protein. Log values (log2expression) of significantly differentially expressed proteins in different samples are displayed in heat maps in different colors. GreenandRedrepresent up-regulation and down-regulation, respectively. The gray part represents no quantitative information of the proteins. T1, T2 and T3 means the CP-treated U251 cells group and C2, C2 and C3 means control group (n=3).

opencc-zeroOct 2023View details →

Data from: competition for time: evidence for an overlooked, diversity-maintaining competitive mechanism

Understanding how diversity is maintained in plant communities requires that we first understand the mechanisms of competition for limiting resources. In ecology, there is an underappreciated, but fundamental distinction between systems in which the depletion of limiting resources reduces the growth rates of competitors versus systems in which resource depletion reduces the time available for competitors to grow, a mechanism we call "competition for time." Importantly, modern community ecology, and our framing of the coexistence problem are built on the implicit assumption that competition reduces the growth rate. However, recent theoretical work suggests competition for time may be the predominant competitive mechanism in a broad array of natural communities, a significant advance given coexistence follows naturally when species compete for time. In this study we first introduce competition for time conceptually using a simple model of interacting species. Then, we perform an experiment in a Mediterranean annual grassland to determine whether competition for time is an important competitive mechanism in a field system. Indeed, we find that species respond to increased competition through reductions in their lifespan rather than their rate of growth. In total, our study suggests competition for time may be overlooked as a mechanism of biodiversity maintenance.

opencc-by-4.0Oct 2023View details →

Numerical data for research paper titled "Physical mechanism for a temporal decrease of the Gutenberg-Richter b-value prior to a large earthquake"

Numerical data used to make Figures in the manuscript entitled "Physical mechanism of the temporal decrease of a Gutenberg-Richter b-value prior to a large earthquake". We provide the data used to create Figures 2 to 13 from the main text, and Figures S2, S3 and S6 from the supplementary information. We also provide Python scripts to plot them.