Find research datasets worth reusing

opencc-by-4.0Nov 2023View details →

Engineering surgical face masks with photothermal and photodynamic plasmonic nanostructures for enhancing filtration and on-demand pathogen eradication_[photothermal properties]

Engineering surgical face masks with photothermal and photodynamic plasmonic nanostructures for enhancing filtration and on-demand pathogen eradication: photothermal properties

opencc-by-4.0Nov 2023View details →

Data regarding "Development and evaluation of RADA-PDGF2 self-assembling peptide hydrogel for enhanced skin wound healing"

Raw data for data published in Development and evaluation of RADA-PDGF2 self-assembling peptide hydrogel for enhanced skin wound healing, Front. Pharmacol. Sec. Experimental Pharmacology and Drug Discovery Volume 14 - 2023 | <a href="https://doi.org/10.3389/fphar.2023.1293647">doi: 10.3389/fphar.2023.1293647</a>

opencc-by-4.0Nov 2023View details →

Utilizing Creator Profiles for Predicting Valuable User Enhancement Reports

This is the dataset for paper "Utilizing Creator Profiles for Predicting Valuable User Enhancement Reports"

opencc-by-4.0Oct 2023View details →

ESSENCE-Dock: A Consensus-Based Approach to Enhance Virtual Screening Enrichment in Drug Discovery

All of the individual docking data and ESSENCE-Dock consensus results for 21 diverse DUD-E targets as presented in the paper "ESSENCE-Dock: A Consensus-Based Approach to Enhance Virtual Screening Enrichment in Drug Discovery". The data is sorted per DUD-E target. It contains the prepared data that was used for the docking calculations (in the Undocked directory), as well as our docking results. Finally, our ESSENCE-Dock Consensus results are included as well Docking calculations were performed using: <ul> <li><a href="https://github.com/bio-hpc/metascreener">Metascreener (V1.1)</a> (Gnina and LeadFinder Calculations; prefix VS_GN_ and VS_LF_ respectively)</li> <li><a href="https://github.com/Jnelen/DiffDockHPC/tree/DiffDockHPCv1.0">DiffDockHPC (v1.0)</a> (DiffDock calculations; prefix VS_DD_ )</li> </ul> The consensus calculations were performed using ESSENCE-Dock, available via <a href="https://github.com/bio-hpc/metascreener">Metascreener </a>as well. The whole methodology and all of the details are described in the ESSENCE-Dock paper: <a href="https://doi.org/10.1021/acs.jcim.3c01982">https://doi.org/10.1021/acs.jcim.3c01982</a> Paper Abstract Drug development is a complex, costly, and time-consuming endeavor. While high-throughput screening (HTS) plays a critical role in the discovery stage, it is one of many factors contributing to these challenges. In certain contexts, virtual screening can complement HTS, potentially offering a more streamlined approach in the initial stages of drug discovery. Molecular docking is an example of a popular virtual screening technique that is often used for this purpose, however, its effectiveness can vary greatly. This has led to the use of consensus docking approaches, which combine results from different docking methods to improve the identification of active compounds and reduce the occurrence of false positives. However, many of these methods do not fully leverage the latest advancements in molecular docking. In response, we present ESSENCE-Dock (Effective Structural Screening ENrichment ConsEnsus Dock), a new consensus docking workflow aimed at decreasing false positives and increasing the discovery of active compounds. By utilizing a combination of novel docking algorithms, we improve the selection process for potential active compounds. ESSENCE-Dock has been made to be user-friendly, requiring only a few simple commands to perform a complete screening, while also being designed for use in high-performance computing (HPC) environments.

More is not always better: Peat moss mixtures slightly enhance peatland stability

Species-poor peatlands challenge biodiversity–ecosystem function theory, which generally links high species diversity to stable ecosystem functions. An open question in ecosystem ecology is whether assemblages of naturally co-occurring peat mosses contribute to the stability of peatland ecosystem processes. We used a replacement series mesocosm experiment with mixtures of Sphagnum cuspidatum and S. medium to assess resistance, resilience, and recovery rates of net ecosystem CO2 exchange (NEE) under a mild and a deep water table drawdown event. Our results show a positive effect of mild water table drawdown on NEE with no apparent role for the composition of the peat moss assemblage. Our study indicates that the carbon uptake capacity by peat moss assemblages is rather resilient to mild water table drawdown, but seriously affected by deeper drought conditions. Co-occurring peat moss species seem to enhance the resilience of the carbon uptake function – i.e. ability of NEE to return to pre-perturbation levels – of peat moss mixtures only slightly. These findings suggest that assemblages of co-occurring Sphagnum moss species do only marginally contribute to the stability of ecosystem functions in peatlands under drought conditions. We did find increased recovery with a larger share of S. cuspidatum in the mixtures, aiding in the ecosystem's role as carbon sink. Above all, our results highlight that predicted severe droughts can gravely affect the sink capacity of peatlands, with only a small extenuating role for peat moss mixtures.

opencc-by-4.0Dec 2023View details →

Enhanced performance of Pr_4Ni_3O_10+_\delta - Ce_0.75Gd_0.1Pr_0.15O_2-\delta composite electrode via particle size grading

The zipped file consists of original data of impedance for electrodes measured at 625 degrees and pO2 of 0.21 atm, and the corresponding DRT result, as well as peak fitting results based on DRT results. A txt file of specification is prepared for illustration.

Flow in fetoplacental-like microvessels in vitro enhances perfusion, barrier function, and matrix stability

Proper placental vascularization is vital for pregnancy outcomes, but assessing it with animal models and human explants has limitations. Here, we present a 3D in vitro model of human placenta terminal villi that includes fetal mesenchyme and vascular endothelium. By co-culturing HUVEC, placental fibroblasts, and pericytes in a macro-fluidic chip with a flow reservoir, we generate fully perfusable fetal microvessels. Pressure-driven flow is crucial for the growth and remodeling of these microvessels, resulting in early formation of interconnected placental-like vascular networks and maintained longevity. Computational fluid dynamics simulations predict shear forces, which increase microtissue stiffness, decrease diffusivity and enhance barrier function as shear stress rises. Mass-spec analysis reveals the deposition of numerous extracellular proteins, with flow notably enhancing the expression of matrix stability regulators, proteins associated with actin dynamics, and cytoskeleton organization. Our model provides a powerful tool for deducing complex in vivo parameters, such as shear stress on developing vascularized placental tissue, and holds promise for unraveling gestational disorders related to the vasculature.

opencc-by-4.0Dec 2023View details →

Behavioral data associated with "Passive exposure to task-relevant stimuli enhances categorization learning"

Behavioral data associated with Schmid et al. (2023) "Passive exposure to task-relevant stimuli enhances categorization learning", and example code for loading these data. See README.md for details.

Failure to mate enhances investment in behaviors that may promote mating reward and impairs the ability to cope with stressors via a subpopulation of Neuropeptide F receptor neurons

Living in dynamic environments such as the social domain, where interaction with others determines the reproductive success of individuals, requires the ability to recognize opportunities to obtain natural rewards and cope with challenges that are associated with achieving them. As such, actions that promote survival and reproduction are reinforced by the brain reward system, whereas coping with the challenges associated with obtaining these rewards is mediated by stress-response pathways, the activation of which can impair health and shorten lifespan. While much research has been devoted to understanding mechanisms underlying the way by which natural rewards are processed by the reward system, less attention has been given to the consequences of failure to obtain a desirable reward. As a model system to study the impact of failure to obtain a natural reward, we used the well-established courtship suppression paradigm in Drosophila melanogaster as means to induce repeated failures to obtain sexual reward in male flies. We discovered that beyond the known reduction in courtship actions caused by interaction with non-receptive females, repeated failures to mate induce a stress response characterized by persistent motivation to obtain the sexual reward, reduced male-male social interaction, and enhanced aggression. This frustrative-like state caused by the conflict between high motivation to obtain sexual reward and the inability to fulfill their mating drive impairs the capacity of rejected males to tolerate stressors such as starvation and oxidative stress. We further show that sensitivity to starvation and enhanced social arousal is mediated by the disinhibition of a small population of neurons that express receptors for the fly homologue of neuropeptide Y. Our findings demonstrate for the first time the existence of social stress in flies and offers a framework to study mechanisms underlying the crosstalk between reward, stress, and reproduction in a simple nervous system that is highly amenable to genetic manipulation.

Bryophytes enhance nitrogen content in decaying wood via biological interactions

An increase in the nitrogen (N) content in coarse woody debris (CWD) facilitates its decomposition, affecting the cycling of N and other nutrients in forest ecosystems. Bryophytes may increase the N content by transferring the N in bryophyte tissues to the underlying CWD. This study examined whether and how bryophytes increase N content in the underlying CWD using N-stable isotope ratios (δ15N) as tracers for N sources. The N content and δ15N values in CWD with bryophytes were significantly higher than those in CWD without bryophytes. However, the δ15N values in CWD with bryophytes differed significantly from those in bryophytes on CWD, demonstrating that the N in bryophytes did not cause the increase in N content in CWD. The analyses using δ15N further indicated that the high N content in CWD with bryophytes may be attributed to increased N supply from wood-decomposing fungi and N-fixing bacteria. This increase in N content may result from the enhanced moisture content in CWD beneath bryophytes, which facilitates the activity of wood-decomposing fungi and N-fixing bacteria. Notably, the influence of bryophytes on the N content in CWD differed between bryophyte life forms: bryophytes that form dense mats increased the N content in CWD, whereas those with loose mats decreased the N content. This difference can be explained by the greater humidity experienced by CWD with bryophytes forming dense mats than that experienced by CWD with bryophytes forming loose mats. Given that the N content in CWD affects the decay processes, the results highlight the importance of biological interactions associated with bryophytes in forest ecosystems.

opencc-by-4.0Dec 2022View details →

Dataset of "Experimental Implementation of Molecule Shift Keying for Enhanced Molecular Communication"

Molecular communication is a paradigm inspired by biological systems, where chemical signals encode and transmit information. MoSK (Molecule Shift Keying) is proposed as a modulation technique that utilizes different signaling molecules to encode digital information. MoSK mimics natural molecular communication by leveraging the diversity of signaling molecules and their specific roles. Experimental testbeds have been developed using microfluidic systems, droplet-based platforms, and biological cells to validate MoSK. A prototype platform for MoSK was implemented, including a transmitter with infusion and selection valves, and a fluorescence-based receiver. The receiver detects and decodes fluorescence signals emitted by Graphene Quantum Dots (GQDs), which are water-soluble and fluorescent molecular messengers. The receiver acquires the fluorescence signals of blue-GQDs and cyan-GQDs, and the performance of the system can be evaluated in terms of synchronization, detection threshold, and symbol recognition using the provided dataset. Each file contains the signal related to 5 molecular messenger releases consisting of blue-GQDs or cyan-GQDs. The sequence of successive releases is given in the file MoSK-sequence.txt. The first row of the file contains the value of the emission wavelength, expressed in nanometers. The first column of the file contains the receive time value, expressed in seconds. The other values represent the emission intensities, expressed in arbitrary units.   Please write to nunzio.tuccitto@unict.it for more information.

A distinct isoform of lymphoid enhancer binding factor 1 (LEF1) epigenetically restricts EBV reactivation to maintain viral latency

As a human tumor virus, EBV is present as a latent infection in its associated malignancies where genetic and epigenetic changes have been shown to impede cellular differentiation and viral reactivation. We reported previously that levels of the Wnt signaling effector, lymphoid enhancer binding factor 1 (LEF1) increased following EBV epithelial infection and an epigenetic reprogramming event was maintained even after loss of the viral genome. Elevated LEF1 levels are also observed in nasopharyngeal carcinoma and Burkitt lymphoma. To determine the role played by LEF1 in the EBV life cycle, we used in silico analysis of EBV type 1 and 2 genomes to identify over 20 Wnt-response elements, which suggests that LEF1 may bind directly to the EBV genome and regulate the viral life cycle. Using CUT&RUN-seq, LEF1 was shown to bind the latent EBV genome at various sites encoding viral lytic products that included the immediate early transactivator BZLF1 and viral primase BSLF1 genes. The LEF1 gene encodes various long and short protein isoforms. siRNA depletion of specific LEF1 isoforms revealed that the alternative-promoter derived isoform with an N-terminal truncation (∆N LEF1) transcriptionally repressed lytic genes associated with LEF1 binding. In addition, forced expression of the ∆N LEF1 isoform antagonized EBV reactivation. As LEF1 repression requires histone deacetylase activity through either recruitment of or direct intrinsic histone deacetylase activity, siRNA depletion of LEF1 resulted in increased histone 3 lysine 9 and lysine 27 acetylation at LEF1 binding sites and across the EBV genome. Taken together, these results indicate a novel role for LEF1 in maintaining EBV latency and restriction viral reactivation via repressive chromatin remodeling of critical lytic cycle factors.

Data from: navigating uncertainty: managing herbivore communities enhances savanna ecosystem resilience under climate change

Savannas are characterized by water scarcity and degradation, making them highly vulnerable to increased uncertainties in water availability resulting from climate change. This poses a significant threat to ecosystem services and rural livelihoods that depend on them. In addition, the lack of consensus among climate models on precipitation change makes it difficult for land managers to plan for the future. Therefore, savanna rangeland management needs to develop strategies that can sustain savanna resilience and avoid tipping points under an uncertain future climate. Our study aims to analyze the impacts of climate change and rangeland management on degradation in savanna ecosystems of southern Africa, providing insights for the management of semi-arid savannas under uncertain conditions worldwide. To achieve this, we simulated the effects of projected changes in temperature and precipitation, as predicted by ten global climate models, on water resources and vegetation (cover, functional diversity, tipping points (transition from grass-dominated to shrub-dominated vegetation)). We simulated three different rangeland management options (herbivore community dominated by grazers, by browser and by mixed-feeders), each with low and high animal densities using the ecohydrological model EcoHyD. Our results identified intensive grazing as the primary contributor to the increased risk of degradation in response to changing climatic conditions across all climate change scenarios. This degradation encompassed a reduction in available water for plant growth within the context of predicted climate change. It also entails a decline in the overall vegetation cover, the loss of functionally important plant species, and the inefficient utilization of available water resources, leading to earlier tipping points. Our findings underscore that in the face of climate uncertainty, farmers' most effective strategy for securing their livelihoods and ecosystem stability is to integrate browsers and apply management of mixed herbivore communities. This management approach not only significantly delays or averts tipping points but also maintained greater plant functional diversity, fostering a more robust and resilient ecosystem that acts as a vital buffer against adverse climatic conditions.

Data for: A novel and enhanced calibration of the tilting weir as a flow measurement structure

To achieve reliable and equitable water distribution it is necessary to accurately estimate the volumetric discharge of water flow through rivers and canals. One such method of accomplishing this is by using hydraulic structures, such as the tilting weir. This structure not only can be used to measure the discharge of water on a continuous basis, but also allows for regulating the water level upstream of the structure. Presently, tilting weirs are often used to control water levels, but the literature on their utilization as flow measurement structures has remained sparse. This study presents a thorough analysis of laboratory experiments on scaled models of tilting weirs, where the flow depth upstream of the structure (i.e., head) and the inclination angle are used to calibrate an equation to estimate the discharge to a high degree of accuracy. Operational guidelines to ensure minimum uncertainty in measurement are also given. The data published here include head and discharge measurements for all experiments conducted, including information on the experimental location, date, and model dimensions. Publication of this data is intended to allow other researchers to verify the calibration procedure laid out in the primary article, and as a comparative dataset for future calibrations.

Alibates Petroglyph - Anthropomorph Enhanced

A number of cupules and at least two petroglyphs on the boulder from Alibates National Monument. [The unenhanced version is here.](https://skfb.ly/6XSOx) Source: Objaverse 1.0 / Sketchfab

Alibates Petroglyph - Six toed foot - Enhanced

An unusual six toed petroglyph foot from Alibates National Moument. [The unehanced version is here.](https://skfb.ly/6XSOB) Source: Objaverse 1.0 / Sketchfab

Alibates Petroglyph - Quadruped - Enhanced

This one is hard to see but is a petroglyph of a four legged animal, probably a bison, from Alibates National Monument. You can also see a foot petroglyph and several cupules. [The unenhanced version is here.](https://skfb.ly/6XSP6) Source: Objaverse 1.0 / Sketchfab

opencc-byApr 2022View details →

Monk's Cave - Enhanced Petroglyphs

This is the enhanced version of the petroglyphs. The model is not visible to the public. Source: Objaverse 1.0 / Sketchfab

Alibates Petroglyph - Foot - Enhanced

An enhanced view of a foot petroglyph from Alibates National Monument. [Here is the unenhanced version.](https://skfb.ly/6XSOS) Source: Objaverse 1.0 / Sketchfab