Find research datasets worth reusing

opencc-by-4.0Dec 2018View details →

Code and Data to recreate figures from: Activation of immune receptor Rx1 triggers distinct immune-responses culminating in cell death after four hours.

Code and Data to recreate figures from: Activation of immune receptor Rx1 triggers distinct immune-responses culminating in cell death after four hours. <a href="https://doi.org/10.1111/mpp.12776">https://doi.org/10.1111/mpp.12776</a>   These files are also on Github: https://github.com/MolPlantPathology/PMID-30537296-

opencc-by-4.0Oct 2022View details →

All Data Used in "The effects of Time-Variable Absorption due to Gamma-Ray Bursts In Active Galactic Nuclei Accretion Disks"

This dataset submission contains the data necessary to reproduce any and all results presented in the paper "The effects of Time-Variable Absorption due to Gamma-Ray Bursts In Active Galactic Nuclei Accretion Disks", set to be submitted for publication in the coming days.

opencc-by-4.0Oct 2022View details →

All Data Used in "The effects of Time-Variable Absorption due to Gamma-Ray Bursts In Active Galactic Nuclei Accretion Disks"

These files contain all the data necessary to fully reproduce any and all results presented in the paper "The effects of Time-Variable Absorption due to Gamma-Ray Bursts In Active Galactic Nuclei Accretion Disks", set to be submitted to MNRAS in the coming days.

All data support the published articel "Loop-optimization of Trichoderma reesei endoglucanases for balancing the activity–stability trade-off through cross-strategy between machine learning and the B-factor analysis"

Trichoderma reesei endoglucanases (EGs) have limited industrial applications due to its low thermostability and activity. Here, we aimed to improve the thermostability of EGs from T.reesei without reducing its activity counteracting the activity-stability trade-off. A cross-strategy combination of machine learning and B-factor analysis was used to predict beneficial amino acid substitution in EG loop optimization. Experimental validation showed single-site mutated EG concomitantly improved enzymatic activity and thermal properties by 17.21%–18.06% and 49.85%–62.90%, respectively, compared with wild-type EGs. Furthermore, the mechanism explained mutant variants had lower RMSD values and a more stable overall structure than the wild type. According to this study, EGs loop optimization is crucial for balancing the activity-stability trade-off, which may provide new insights into how loop region function interacts with enzymatic characteristics. Moreover, the cross-strategy between machine learning and B-factor analysis improved superior enzyme activity-stability performance, which integrated structure-dependent and sequence-dependent information.

The dataset for the paper "Long-Lived and Continual Volcanic Eruptions, Tectonic Activity, Pit Chains Formation and Boulder Avalanches in Northern Tharsis Region: Implications for Late Amazonian Geodynamics and Seismo-Tectonic Processes on Mars" JGR: Planets.

This dataset pertains to the following paper in Journal of Geophysical Research: Planets. Krishnan, V., and Kumar, P.S. (2022), Long-Lived and Continual Volcanic Eruptions, Tectonic Activity, Pit Chains Formation and Boulder Avalanches in Northern Tharsis Region: Implications for Late Amazonian Geodynamics and Seismo-Tectonic Processes on Mars, Journal of Geophysical Research: Planets (for full citation, please see the journal). AGU Manuscript No. 2022JE007511.

Hypoxia preconditioned mesenchymal stem cells prevent cardiac fibroblast activation and collagen production via leptin

Aims: Activation of cardiac fibroblasts into myofibroblasts constitutes a key step in cardiac remodeling after myocardial infarction (MI), due to interstitial fibrosis. Mesenchymal stem cells (MSCs) have been shown to improve post-MI remodeling an effect that is enhanced by hypoxia preconditioning (HPC). Leptin has been shown to promote cardiac fibrosis. The expression of leptin is significantly increased in MSCs after HPC, but it is unknown whether leptin contributes to MSC therapy or the fibrosis process. The objective of this study was to determine whether leptin secreted from MSCs modulates cardiac fibrosis. Methods: Cardiac fibroblast (CF) activation was induced by hypoxia (0.5% O2). The effects of MSCs on fibroblast activation were analyzed by co-culturing MSCs with CFs and detecting the expression of a-SMA, SM22a, and collagen IaI in CFs by western blot, immunofluorescence and Sirius red staining. In vivo MSCs antifibrotic effects on left ventricular remodeling were investigated using an acute MI model involving permanent ligation of the left anterior descending coronary artery. Results: Co-cultured MSCs decreased fibroblast activation and HPC enhanced the effects. Leptin deficit MSCs from Ob/Ob mice did not decrease fibroblast activation. Consistent with this, H-MSCs significantly inhibited cardiac fibrosis after MI and mediated decreased expression of TGF-b/Smad2 and MRTF-A in CFs. These effects were again absent in leptin-deficient MSCs. Conclusion: Our data demonstrate that activation of cardiac fibroblast was inhibited by MSCs in a manner that was leptin-dependent. The mechanism may involve blocking TGF-b/Smad2 and MRTF-A signal pathway.

opencc-by-4.0Feb 2022View details →

Supplementary Materials: Developers Activity Satisfaction and Performance during the COVID-19 Pandemic

Following the onset of the COVID-19 pandemic and subsequent lockdowns, the daily lives of software engineers were heavily disrupted as they were abruptly forced to work remotely from home. To better understand and contrast typical working days in this new reality with work in pre-pandemic times, we conducted one exploratory ($N$ = 192) and one confirmatory study ($N$ = 290) with software engineers recruited remotely. Specifically, we build on self-determination theory to evaluate whether and how specific activities are associated with software engineers' satisfaction and productivity. To explore the subject domain, we first ran a two-wave longitudinal study. We found that the time software engineers spent on specific activities (e.g., coding, bugfixing, helping others) while working from home was similar to pre-pandemic times. Also, the amount of time developers spent on each activity was unrelated to their general well-being, perceived productivity, and other variables such as basic needs. Our confirmatory study found that activity-specific variables (e.g., how much autonomy software engineers had during coding) do predict activity satisfaction and productivity but not by activity-independent variables such as general resilience or a good work-life balance. Interestingly, we found that satisfaction and autonomy were significantly higher when software engineers were helping others and lower when they were bugfixing. Finally, we discuss implications for software engineers, management, and researchers. In particular, active company policies to support developers' need for autonomy, relatedness, and competence appear particularly effective in a WFH context.

Raw data for the paper "Cobalamin co-limits phytoplankton and bacterial biomass and activity in Eastern Mediterranean coastal waters"

Raw data for the paper "Cobalamin co-limits phytoplankton and bacterial biomass and activity in Eastern Mediterranean coastal waters".

Larger body size leads to greater female beluga whale ovarian reproductive activity at the southern periphery of their range

Identification of phenotypic characteristics in reproductively successful individuals provides important insights into the evolutionary processes that cause range shifts due to environmental change. Female beluga whales (Delphinapterus leucas) from the Baffin Bay region (BB) of the Canadian Arctic in the core area of the species' geographic range have larger body size than their conspecifics at the southern range periphery in Hudson Bay (HB). We investigated the mechanism for this north and south divergence as it relates to ovarian reproductive activity (ORA = total corpora) that combines morphometric data with ovarian corpora counted from female reproductive tracts. Our study aim was to assess the relative influence of age and body size of female beluga whale on ovarian reproductive activity in the two populations. Female beluga whale ORA increased more quickly with age (63% partial variation explained) in BB than in HB (41%). In contrast, body length in HB female beluga whales accounted for considerably more of the total variation (12 vs 1%) in ORA compared to BB whales. We speculate that female HB beluga whale ORA was more strongly linked with body length due to higher population density resulting in food competition that favors the energetic advantages of larger body size during seasonal food limitations. Understanding the evolutionary mechanism of how ORA varies across a species' range will assist conservation efforts in anticipating and mitigating future challenges associated with a warming planet.

Insecticidal activity of Beauveri bassiana ERL1170-egfp against Tribolium castaneum

Background Beauveria bassiana is one of the commercially available entomopathogenic fungi (EPF), and a number of isolates with high virulence and broad host spectrum have been used to control agricultural and forest pests. Although the functional importance of genes in EPFs' pathogenesis have been extensively studied, the precise ultrastructural mechanism of the fungal infection, particularly penetration of the host insect cuticles, is not well understood. Results In this study, we investigated the morphology and ultrastructure of the larval cuticle of the red flour beetle, Tribolium castaneum, after treatment with B. bassiana ERL1170 expressing an enhanced green fluorescent protein (Bb-eGFP). The Bb-eGFP showed high virulence against the larvae, with approximately 90% mortality at 48 h after treatment (HAT) and 100% at 72 HAT under our infection conditions. In these larvae, the regions of the body wall with flexible cuticles, such as the ventral and ventrolateral thorax and abdomen, became darkly melanized, but there was little to none melanization in the rigid dorsal cuticular structures. Confocal microscopy and transmission electron microscopy (TEM) indicated that germinated conidia on the surface of the larval cuticle were evident at 6 HAT, which formed penetration pegs and began to penetrate the several cuticle layers/laminae by 12 HAT. The penetration pegs then developed invading hyphae, some of which passed through the cuticle and reached the epidermal cells by 24 HAT. The larval cuticle was aggressively and extensively disrupted by 48 HAT, and a number of outgrowing hyphae were observed at 72 HAT.

Scaling of activity space in marine organisms across latitudinal gradients

Unifying models have shown that the amount of space used by animals (e.g., activity space, home range) scales allometrically with body mass for terrestrial taxa; however, such relationships are far less clear for marine species. We compiled movement data from 1,596 individuals across 79 taxa collected using a continental passive acoustic telemetry network of acoustic receivers to assess allometric scaling of activity space. We found that ectothermic marine taxa do exhibit allometric scaling for activity space, with an overall scaling exponent of 0.64. However, body mass alone explained only 35% of the variation with the remaining variation best explained by trophic position for teleosts and latitude for sharks, rays, and marine reptiles. Taxon-specific allometric relationships highlighted weaker scaling exponents among teleost fish species (0.07) than sharks (0.96), rays (0.55), and marine reptiles (0.57). The allometric scaling relationship and scaling exponents for the marine taxonomic groups examined were lower than those reported from studies that had collated both marine and terrestrial species data derived using various tracking methods. We propose that these disparities arise because previous work integrated summarised data across many studies that used differing methods for collecting and quantifying activity space, introducing considerable uncertainty into slope estimates. Our findings highlight the benefit of using large-scale, coordinated animal biotelemetry networks to address cross-taxa evolutionary and ecological questions.

Knowledge-driven design and optimization of potent symmetric anticancer molecules: A case study on PKM2 activators

All the raw data files including 3D structures of all the 200 virtually designed palindromic and non-palindromic activators, 3D structures of top 5 palindromic and non-palindromic activators in complex with PKM2 protein, starting and ending conformations of MD simulation structures with the .tpr files for all six simulations for PDA116 and NPDA4 are available in this dataset.

Locomotor activity pattern of the olive fruit fly

LAM_data_repository: Locomotor activity data of olive fruit flies (Bactrocera oleae)  recorded with the LAM25H device. Both sexes, virgin and mated, and wild and artificially reared flies were monitored. data_repository: Raw LAM data were analyzed in MATLAB with SCAMP and sleep (inactivity) parameters of olive fruit flies were calculated. Number of sleep episodes and their mean duration during the light and the dark period are given.

opencc-by-nc-nd-4.0Nov 2022View details →

Radicals as Exceptional Electron-Withdrawing Groups: Nucleo-philic Aromatic Substitution of Halophenols via Homolysis-Enabled Electronic Activation

This dataset contains machine-readable files of the graphs in the main text of "Radicals as Exceptional Electron-Withdrawing Groups: Nucleophilic Aromatic Substitution of Halophenols via Homolysis-Enabled Electronic Activation" in J. Am. Chem. Soc. 2022, 144, 47, 21783–21790

opencc-zeroDec 2022View details →

Optogenetic activation of visual thalamus generates artificial visual percepts

The lateral geniculate nucleus (LGN), a retinotopic relay center where visual inputs from the retina are processed and relayed to the visual cortex, has been proposed as a potential target for artificial vision. At present, it is unknown whether optogenetic LGN stimulation is sufficient to elicit behaviorally relevant percepts, and the properties of LGN neural responses relevant for artificial vision have not been thoroughly characterized. Here, we demonstrate that tree shrews pre-trained on a visual detection task can detect optogenetic LGN activation using an AAV2-CamKIIα-ChR2 construct and readily generalize from visual to optogenetic detection. Simultaneous recordings of LGN spiking activity and primary visual cortex (V1) local field potentials (LFP) during optogenetic LGN stimulation show that LGN neurons reliably follow optogenetic stimulation at frequencies up to 60 Hz, and uncovered a striking phase locking between the V1 local field potential (LFP) and the evoked spiking activity in LGN. These phase relationships were maintained over a broad range of LGN stimulation frequencies, up to 80 Hz, with spike field coherence values favoring higher frequencies, indicating the ability to relay temporally precise information to V1 using light activation of the LGN. Finally, V1 LFP responses showed sensitivity values to LGN optogenetic activation that were similar to the animal's behavioral performance. Taken together, our findings confirm the LGN as a potential target for visual prosthetics in a highly visual mammal closely related to primates.

Supplementary videos for "Transient wave activity in snow avalanches is controlled by entrainment and topography"

Movie 1. Field avalanche happened at the Vallée de la Sionne test site on 3 February 2015. Movie 2. Numerical simulation of the 2015 VdlS avalanche. The color in the video shows the flow velocity, and the colorbar can be found in Fig. 3 of the manuscript. Movie 3. Roll-waves in the simulated avalanche, where the particles ahead of the wave are eroded and the particles at the wave tail are not deposited. The color in the video shows the flow velocity, and the colorbar can be found in Fig. 3 of the manuscript. Movie 4. Erosion-deposition waves in the simulated avalanche, where the particles ahead of the wave are eroded and the particles at the wave tail are deposited. The color in the video shows the flow velocity, and the colorbar can be found in Fig. 3 of the manuscript.

Recently fixed carbon fuels microbial activity several meters below the soil surface

This data file (Scheibe_2022.xlsx) contains radiocarbon data of bulk soil carbon and CO2 respired in incubations from soil profiles in three climate zones (arid, mediterranean, and humid) of the Costal Cordillera of Chile down to a depth of six meters. Variable descriptions are provided in Template Info File. The data are part of a study, which investigates how soil microbial carbon cycling affects soil formation especially in the critical zone by understanding the carbon source of microbial activity in deep soil. The study was conducted within the framework of the Deep EarthShape priority program funded by the German Science Foundation (DFG-SPP 1803).

Genome graphs detect human polymorphisms in active epigenomic states during influenza infection: validation

Sanger sequencing and qPCR validation data for "Genome graphs detect human polymorphisms in active epigenomic states during influenza infection" manuscript.

opencc-by-4.0Sep 2022View details →

Supplementary material for Impact of past steel-making activities on lanthanides and Y (REY) fractionation and potential mobility in riverbank sediments

Database related to the results that are presented in the manuscript Hissler et al. that will be submitted as research paper in the journal Frontiers in Earth Science on the research topic: "Further Rare Earth Elements Environmental Dissemination: Observation, Analysis and Impacts". Title of the submission: Impact of past steel-making activities on lanthanides and Y (REY) fractionation and potential mobility in riverbank sediments. Authorship:  Christophe Hissler1*, Emmanuelle Montarges-Pelletier2,3, Hussein J. Kanbar 2,3, Mathieu Le Meur2,3,4, Christophe Gauthier2,3 1CAT/ENVISION/ERIN Research Group, Luxembourg Institute of Science and Technology, L-4422 Belvaux, Luxembourg 2Université de Lorraine, CNRS, LIEC, F-54000 Nancy, France 3LTSER FRANCE Zone atelier Moselle 4SUBATECH UMR 6457/IMT Atlantique, CNRS, F-44307 Nantes, France   *Corresponding author: <a href="mailto:christophe.hissler@list.lu">christophe.hissler@list.lu</a>

The cosmic web of X-ray active galactic nuclei seen through the eROSITA Final Equatorial Depth Survey (eFEDS)

Which galaxies in the general population turn into active galactic nuclei (AGN) is a keystone of galaxy formation and evolution. Thanks to SRG/eROSITA’s contiguous 140 square degrees pilot survey field, we constructed a large, complete, and unbiased soft X-ray flux-limited AGN sample at low redshift 0.05 < z < 0.55. Two summary statistics, the clustering using spectra from SDSS-V and galaxy-galaxy lensing with imaging from HSC, are measured and interpreted with halo occupation distribution and abundance matching models. Both models successfully account for the observations. We obtain an exceptional complete view of the AGN  12 halo occupation distribution. The population of AGN is broadly distributed among halos with a mean mass of 3.9+2.0−2.4 × 10 M⊙ . +0.08. This corresponds to a large-scale halo bias of b(z = 0.34) = 0.99−0.10 . The central occupation has a large  transition parameter σlog10 (M) = 1.28 ± 0.2. The satellite occupation distribution is characterized by a shallow slope αsat = 0.73 ± 0.38. We find that AGNs in satellites are rare, with fsat < 20%. Most soft X-ray-selected AGNs are hosted by central galaxies in their dark matter halo. A weak correlation between soft X-ray luminosity and large-scale halo bias is confirmed (3.3σ). We discuss the implications of environmental-dependent AGN triggering. This study paves the way towards fully charting, in the coming decade, the co-evolution of X-ray AGN, their host galaxies, and dark matter haloes by combining eROSITA with SDSS-V, 4MOST, DESI, LSST, and Euclid.