Find research datasets worth reusing

opencc-by-4.0May 2023View details →

Automated control and optimization of laser-driven ion acceleration: Data

This data repository contains python scripts that can recreate the plots from the article on 'Automated control and optimization of laser-driven ion acceleration'.

opencc-zeroMay 2023View details →

Coarse woody debris accelerates the decomposition of deadwood inputs across temperate forest

Wood decomposition is regulated by multiple controls, including climate and wood traits, that vary at local to regional scales. Yet decomposition rates differ dramatically when these controls do not. Fungal community dynamics are often invoked to explain these differences, suggesting that knowledge of ecosystem properties that influence fungal communities will improve understanding and projection of wood decomposition. We hypothesize that deadwood inputs decompose faster in forests with higher stocks of downed coarse woody material (CWM) because CWM is a resource from which lignocellulolytic fungi rapidly colonize new inputs. To test this hypothesis, we measure decomposition of 1,116 pieces of fine woody material (FWM) of five species, incubated for 13 to 49 months at five locations spanning 10°-latitude in eastern U.S. forest. We place FWM pieces near and far from CWM across observational transects and experimental common gardens. Soil temperature positively affects location-level mean decomposition rates, but these among-location differences are smaller than within-location variation in decomposition. Some of this variability is caused by CWM, where FWM pieces next to CWM decompose more rapidly. These effects are greater with time of incubation and lower initial wood density of FWM. The effect size of CWM is of the same relative magnitude as for the known controls of temperature, deadwood density and diameter. Abundance data for CWM is available for many forests and hence may be an ecosystem variable amenable for inclusion in decomposition models. Our findings suggest that conservation efforts to rebuild depleted CWM stocks in temperate forests may accelerate decomposition of fresh deadwood inputs.

opencc-by-4.0Jun 2023View details →

Emulator of PR-DNS: Accelerating Dynamical Fields with Neural Operators in Particle-Resolved Direct Numerical Simulation

The codes directory includes the various machine learning models, such as FNO, UNet and ResNet. R128_init1 and R128_init2 are the PR-DNS time step simulations at different initial conditions. R64_init2, R128_init2 and R256_init2 are the PR-DNS time step simulations at different resolutions.

opencc-by-4.0Jun 2023View details →

ICPP23 Scalable Incremental Checkpointing using GPU-Accelerated De-Duplication Input Graphs

Input graphs and checkpoints used for generating results in the ICPP 23 paper "Scalable Incremental Checkpointing using GPU-Accelerated De-Duplication".

opencc-zeroJul 2023View details →

Rapid acceleration offsets the costs of intermittent locomotion in lizards when turning

Intermittent locomotion is a common locomotor mode in small vertebrates. Pausing is thought to aid in locating a predator or prey, enhanced crypsis, lowering energy costs, and/or maneuvering around obstacles or towards a refuge. Many lizards flee predators by turning as they pass a potential refuge and subsequently pause, presumably to conceal themselves. Intermittent locomotion may be associated with turning by allowing an animal time to assess its surroundings and/or decreasing the likelihood of losing its footing before or after turning. In this study, we quantify locomotor performance and the use of intermittent locomotion in Florida Scrub Lizards (Sceloporus woodi) when navigating either a 45° or 90° turn. Lizards paused in 92% of all trials, and yet despite pausing, linear speed was not different prior to entering or when exiting the turn. This result suggests that turning comes at minimal cost to forward speed for lizards under these conditions. The angle of the turn had no effect on whether lizards paused, nor was there a relationship with pausing before or after the turn. Interestingly, the speed in the turn did not differ in trials with a pause before the turn vs. trials without a pause. We found that lizards increase peak acceleration following pauses to achieve similar speed, and hence explain both why, and how, intermittent locomotion is such a common strategy in predator escape.

opencc-by-4.0Jul 2023View details →

Accelerating medical education with ChatGPT: An implementation guide

This dataset is a collection of prompt examples of how ChatGPT has been used to accelerate medical education.

opencc-by-4.0Aug 2023View details →

Velocity and acceleration for the positions of the sun meridian declination, according to the geometric model

The data set gives the sun meridian declination for every day of the year, according to the geometric model for the sun declination. In the next columns, the velocity and acceleration of the sun meridian declination is also assessed. And the last column assesses the relative concentration of solar resources available per minute of latitude (arcmin), which is obtained by giving 100% to the 365 rotations of the planet, considering the velocity of the sun meridian declination.

opencc-by-4.0Aug 2023View details →

Harnessing genotype-phenotype nonlinearity to accelerate biological prediction

Description: We are sharing phenotypic data sets used in the pub <a href="http://doi.org/10.57844/arcadia-5953-995f">“Harnessing genotype-phenotype nonlinearity to accelerate biological prediction”</a>. Contained within are a set of publicly available empirical phenotype data sets, synthetic phenotypes we generated, and the output of an autoencoder model trained on them. Walkthroughs for all analyses using these data are available on <a href="http://doi.org/10.5281/zenodo.8371249">GitHub</a>. Files:  <ul> <li>“ail_cleaned_phenos.RDS”: .RDS file of mouse phenotypes from Bogue et al. 2015</li> <li>“all_autoencoder_phenotype_predictions.csv“: .csv file containing accuracy statistics for all phenotype-phenotype autoencoder models analyzed in the pub</li> <li>“arapheno_cleaned_phenos.RDS“: .RDS file of Arabidopsis phenotypes from Exposito-Alonso et al. 2019</li> <li>“autoencoder_phenos.zip“: directory of synthetic phenotype sets used to train the autoencoder models</li> <li>“dgrp_cleaned_phenos.RDS”: .RDS file of DGRP fruit fly phenotypes compiled from multiple sources, originally reported in Mackay et al. 2012</li> <li>“jax_cleaned_phenos.RDS”: .RDS file of mouse phenotypes from Gonzales et al. 2018</li> <li>“nematode_cleaned_phenos.RDS”: .RDS file of nematode phenotypes from Snoek et al. 2019</li> <li>“phen_pleio_int_01_0_1.pk”: pickle of all synthetic phenotypes analyzed in the pub</li> <li>“yeast_cleaned_phenos.RDS”: .RDS file of yeast phenotypes from Bloom et al. 2019</li> </ul> A full description of how the synthetic phenotypes and autoencoder predictions were generated is available in the associated <a href="http://doi.org/10.57844/arcadia-5953-995f">pub</a>.

opencc-by-4.0Aug 2023View details →

Data collected from questionnaires to collect feedback on the services' performance / accelerator programme and outcomes

Results of the immediate satisfaction surveys deployed to:  (i) all participants of the syncronous induction training [Tab: 2.InductionTrainingSync];  (ii) all participants of the asyncrhous induction training - [Tab: 3.InductionTrainingAsync];  (iii) makerpsace admins, consultants,mentors that participated in the delivery of the entire PMCA programme [Tab: 4.PCMA - Admins] and  (iv) to maker teams that succesfully finished the Mentoring stage of the PCMA programme [Tab: 5.PCMA - Makers] with a view to capture their impressions of programme and recommendations for further improvements.  The present spreadsheet is also accompanied by four (4) documents (.pdf) that present the surveys deployed for collecting the above responses. In particular:  1.InductionTrainingAsyncSatisfactionSurvey_Questions.pdf 2.InductionTrainingSyncSatisfactionSurvey_Questions.pdf 3.PCMASatisfactionSurveyMakerpace_Questions.pdf 4.PCMASatisfactionSurveyMakers_Questions.pdf

opencc-by-4.0Sep 2023View details →

Global LAke Surface water Temperature (GLAST): Global lakes are warming slower than surface air temperature due to accelerated evaporation

This repository houses a dataset, known as the Global LAke Surface water Temperature (GLAST), which provides both temporal and spatial details at high resolution for 92,245 lakes worldwide during the period of 1981-2099, with 36% of them situated in Arctic regions. The dataset was established based on four decades (1982-2020) of Landsat satellite images and a physical model (FLake). For a comprehensive overview of the dataset's production methodology, please refer to the paper titled 'Global lakes are warming slower than surface air temperature due to accelerated evaporation' (Tong et al., 2023, Nature Water). Detailed information regarding each data file can be found in the 'readme.docx' file.

opencc-zeroSep 2023View details →

Experimental evidence that network topology can accelerate the spread of beneficial mutations

Whether and how the spatial arrangement of a population influences adaptive evolution has puzzled evolutionary biologists. Theoretical models make conflicting predictions about the probability a beneficial mutation will become fixed in a population for certain topologies like stars, in which "leaf" populations are connected through a central "hub." To date, these predictions have not been evaluated under realistic experimental conditions. Here, we test the prediction that topology can change the dynamics of fixation both in vitro and in silico by tracking the frequency of a beneficial mutant under positive selection as it spreads through networks of different topologies. Our results provide empirical support that metapopulation topology can increase the likelihood that a beneficial mutation spreads, broadens the conditions under which this phenomenon is thought to occur, and points the way towards using network topology to amplify the effects of weakly favored mutations under directed evolution in industrial applications.

opencc-zeroSep 2023View details →

Accelerated discovery and mapping of block copolymer phase diagrams

Block copolymers are widely used in many applications due to their spontaneous self-assembly into a variety of nanoscale morphologies. However, a grand challenge in navigating this diverse and ever-growing array of possible structures is the accelerated discovery, design, and implementation of new materials. Here, we report a versatile and efficient strategy to accelerate materials discovery by rapidly building expansive, high-quality, and detailed block copolymer libraries through a combination of controlled polymerization and chromatographic separation. To illustrate the potential of this approach, a family of 16 parent diblock copolymers was synthesized and separated, leading to over 300 distinct and well-defined samples at the multigram scale. The resulting materials span a wide range of compositions with exceptional resolution in volume fraction and domain spacing that allows for the impact of monomer design on polymer self-assembly to be elucidated. Phase behavior that can be gleaned from these libraries includes the precise location of order–order boundaries and the identification of morphologies with extremely narrow windows of stability. This user-friendly, scalable, and automated approach to discovery significantly increases the availability of well-defined block copolymers with tailored molecular weights, molar-mass dispersities, compositions, and segregation strengths, accelerating the study of structure–property relationships in advanced soft materials.

opencc-zeroOct 2023View details →

Climate change accelerates ecosystem restoration in the mountain forests of Central Europe

<ol> <li>Restoring degraded forest ecosystems is an important element in the ongoing challenge to sustain the integrity and functioning of the biosphere. However, the evaluation of restoration success is hampered by long lead times of management measures in forests. Moreover, forest change is accelerating in the absence of management because of ongoing climate change. Yet, because a counterfactual is frequently missing, it remains unclear whether restoration measures are aided or impeded by climate change. </li> <li>Here, we analyzed the pace and success of forest restoration under climate change, combining field data and simulation modelling. We focused on the management zone of Berchtesgaden National Park (BGNP), Germany, where restoration aims to restore homogeneous Norway spruce (Picea abies) forests to structurally diverse mixed mountain forests. We evaluated three alternative restoration strategies: Two active strategies focused on planting the currently underrepresented silver fir (Abies alba) and European beech (Fagus sylvatica) but differing in the creation of gap-cuts, and a third passive restoration strategy without interventions. Strategies were simulated with the forest landscape model iLand from 2020 to 2100 under different climate scenarios (historic, RCP 2.6, 4.5, and 8.5).</li> <li>The forests of BGNP developed into structurally diverse and mixed forests under all evaluated management strategies, and differences between active and passive restoration were generally small. While restoration goals for forest structure were largely met by 2100, forest composition remained far from target in all strategies. Climate change aided restoration by significantly increasing the prevalence of silver fir and European beech (+104.2 % to +258.6 %). Field data on short-term restoration effects were in line with simulated long-term trajectories.</li> <li> Synthesis and applications. We here show that forest restoration efforts in Central European mountain forests will likely be accelerated by climate change. Nonetheless, the slow pace of restoration underscores the need for taking action. Our study highlights that active restoration measures such as tree planting can bring the system closer to restoration targets. However, it also demonstrates that passive restoration (no intervention) is a viable option for management, highlighting the need to evaluate restoration measures against the counterfactual of a no-intervention strategy.</li> </ol>

opencc-zeroOct 2023View details →

A whole-genome reference panel of 14,393 individuals for East Asian populations accelerates discovery of rare functional variants

Underrepresentation of non-European populations hinders growth of global precision medicine. Resources such as imputation reference panels that match the study population are necessary to find low-frequency variants with substantial effects. We created a reference panel consisting of 14,393 whole-genome sequences including more than 11,000 Asian individuals. Genome-wide association studies were conducted using the reference panel and a population-specific genotype array of 72K subjects for eight phenotypes. This panel yields improved imputation accuracy of rare and low-frequency variants within East Asian populations compared with the largest reference panel. Thirty-nine previously unidentified associations were found, and more than half of the variants were East-Asian-specific. We discovered genes with rare protein-altering variants, including LTBP1 for height and GPR75 for body mass index, as well as putative regulatory mechanisms for rare noncoding variants with cell-type-specific effects. We suggest this data set will add to the potential value of Asian precision medicine.

opencc-by-4.0Oct 2023View details →

Source data: Negative Membrane potential accelerates sugar uptake by stabilizing the outward-facing conformation of the Na+/glucose symporter vSGLT

Galactose uptake source data.Excel file (annotated and color coded). Double electron-electron resonance (DEER) source data.File name indicates Figure number, construct  and conditions. First column: Time in microseconds. Second Column: Magnitude dipolar evolution data (phase corrected and normalized). Information for associated MD simulations under <a href="http://dx.doi.org/10.5281/zenodo.10000256">10.5281/zenodo.10000256.</a>

Accelerated rTMS for Post-Stroke Apathy

ClinicalTrials.gov study NCT05878457. IPD Sharing: NO. Countries: 1. Publications: 11.

Accelerated Invisalign Therapy in Conjunction With Acceledent Aura

ClinicalTrials.gov study NCT02868554. IPD Sharing: NO. Countries: 1. Publications: 12.

Accelerated Theta Burst in Treatment-Resistant Depression: A Dose Finding and Biomarker Study

ClinicalTrials.gov study NCT03680781. IPD Sharing: NO. Countries: 1. Publications: 6.

'TOTAL' (Tracheal Occlusion To Accelerate Lung Growth) Trial

ClinicalTrials.gov study NCT02875860. IPD Sharing: NO. Countries: 1. Publications: 15.

UARK 2012-02 Trial For High-Risk Myeloma Evaluating Accelerating and Sustaining Complete Remission

ClinicalTrials.gov study NCT02128230. IPD Sharing: NO. Countries: 1. Publications: 2.