Find research datasets worth reusing

opencc-by-4.0Jun 2023View details →

Spatial Mapping and Host Linking of Mobile Genetic Elements in Complex Microbiomes - Optimization of single molecule MGE FISH

We used Escherichia coli transformed with pJKR-H-tetR plasmids encoding an inducible GFP gene as a model system to assess and optimize MGE-FISH on a confocal microscope. We designed FISH probes for the non-coding strand of the GFP gene, used non-transformed E. coli as a negative control, and tested six different FISH protocols.

opencc-zeroJun 2023View details →

Data and code for: Optimal clutch size revisited: separating individual quality from the costs of reproduction

Life-history theory, central to our understanding of diversity in morphology, behaviour and senescence, describes how traits evolve through the optimisation of trade-offs in investment. Despite considerable study, there is only minimal support for trade-offs within species between the two traits most closely linked to fitness – reproduction and survival – questioning the theory's general validity. We used a meta-analysis to separate quality effects from the costs of reproduction using studies of parental investment and survival in birds. Experimental enlargement of broods caused reduced parental survival. However, the effect of experimental enlargements was small and opposite to the effect of phenotypic quality, where individuals that naturally produced larger clutches also survived better. The opposite effects on survival in experimental and observational studies of parental care provide the first meta-analytic evidence for theory suggesting that quality differences mask trade-offs. Fitness projections using the overall effect size revealed that reproduction presented negligible costs, except when reproductive effort was forced beyond the level observed within species, to that seen between species. We conclude that there is little support for the most fundamental life-history trade-off, between reproduction and longevity, operating within a population. We suggest that within species, the fitness landscape of the reproduction–survival trade-off is flat until it reaches the boundaries of the between-species fast-slow life-history continuum. Our interpretation explains why the costs of reproduction are not apparent and why variation in reproductive output persists within species.

Data from "Optimizing the baiting strategy for oral vaccine delivery to wild boar"

Data from the paper "Optimization of the baiting strategy for the administration of oral vaccines to wild boar". These data are from experiments done in field work based on the baiting preference of different animal species.

opencc-zeroJul 2023View details →

Increased initial task difficulty drives social foragers to develop sub-optimal conformity instead of adaptive diversity

The extent to which animal societies exhibit social conformity as opposed to behavioural diversity is commonly attributed to adaptive learning strategies. Less attention is given to the possibility that the relative difficulty of learning a task socially as opposed to individually can be critical for social learning dynamics. Here we show that by raising initial task difficulty, house sparrows previously shown to exhibit adaptive social diversity become predominantly conformists. The task we used required opening feeding well covers (easier to learn socially) and to choose the covers with the rewarding cues (easy to learn individually). We replicated a previous study where sparrows exhibited adaptive diversity, but did not pre-train the naive sparrows to open covers, making the task initially more difficult. In sharp contrast to the previous study results, most sparrows continued to conform to the demonstrated cue even after experiencing greater success with the alternative rewarding cue for which competition was less intense. Thus, our study shows that a task's cognitive demands, such as the initial dependency on social demonstration, can change the entire learning dynamics, causing social animals to exhibit sub-optimal social conformity rather than adaptive diversity under otherwise identical conditions.

Calibration Dataset - HPOSS: A hierarchical portfolio optimization stacking strategy to reduce the generalization error of ensembles of models

Calibration dataset for the study case presented in the paper "HPOSS: A hierarchical portfolio optimization stacking strategy to reduce the generalization error of ensembles of models". It encompasses a .h5 file with a dataset called "Calibrations_LHS", which consists of a 80x5 numpy array of float numbers corresponding to (d1(m),d2(m),d3(m),d4(m),zeta_max(Pa)), where d_i, i = 1,...,4 are dimensions (in meters) of the I-beam and zeta_max is the maximum bending stress (in Pascals) developed in a simply such supported beam with 1 m of length after a point load of 1000N is applied at its center.

opencc-by-4.0Feb 2023View details →

Logical and thermodynamical reversibility: optimized experimental implementation of the NOT operation

Dataset for the article: Logical and thermodynamical reversibility: optimized experimental implementation of the NOT operation to be published in PRE Files description:  .fig: Matlab Figures used to create the figures of the article Analysis.mat: mat file storing the analysis of 4538 bitflip protocols. <ul> <li>dQall: average infinitesimal heat evolution along a protocol</li> <li>dt: sampling rate</li> <li>dW: average infinitesimal work evolution along a protocol</li> <li>f0: resonance frequency of the cantilever</li> <li>Klist: average kinetic energy evolution along a protocol</li> <li>N: number of protocols</li> <li>Qhisto: array of the average heat released for the N protocols</li> <li>sigma_m: position variance implemented in the FPGA at the beginning of the N protocols</li> <li>sigmalist: position variance recalibrated for each protocol </li> <li>tau1: duration of the bitflip</li> <li>Teq: duration of the equlivration step</li> <li>trelax: time between protocols</li> <li>Ulist: average potential energy evolution along a protocol</li> <li>Vplot: protocol driving for the plot</li> <li>Whisto: array of the average work released for the N protocols</li> <li>x0plot: protocol driving for the plot</li> <li>xplot: position signal for plotting </li> </ul> bitflip.m:  Analysis code to obtain the Analysis.mat type of files from the dataset of N protocols. bitflip_01.mat to bitflip_1000.mat Experimental data of bitflip protocols. The driving and the system position are stored, and some acquisition parameters. These files are designed to be analysed by bitflip.m .

opencc-zeroJul 2023View details →

Data from: Drop it all: Extraction-free detection of non-indigenous marine species through optimized direct-droplet digital PCR

Molecular biosecurity surveillance programs increasingly use environmental DNA (eDNA) for detecting marine non-indigenous species (NIS). However, the current molecular detection workflow is cumbersome, prone to errors and delays, and is limited in providing knowledge about eDNA beyond the spatial and temporal extent of the sampling. These limitations can hinder management efforts and restrict the "opportunity window" for a rapid response to new marine NIS incursions. Emerging innovative field-deployable digital droplet PCR (ddPCR) systems offer improved workflow efficiency by autonomously analyzing targeted free-floating extra-cellular eDNA (free-eDNA) signals. Despite their potential, these systems have not been tested in marine environments. Thus, an aquarium study was conducted with three distinct marine NIS: the Mediterranean fanworm Sabella spallanzanii, the ascidian clubbed tunicate Styela clava, and the brown bryozoan Bugula neritina to evaluate the detectability of free-eDNA in seawater. The detectability of targeted free-eDNA was assessed by directly analyzing aquarium water samples using an optimized species-specific ddPCR assay, without filtration or DNA extraction, so-called, "direct-ddPCR". The results demonstrated the consistent detection of Sabella spallanzanii and Bugula neritina free-eDNA when these organisms were present in high abundance. Once organisms were removed, the free-eDNA signal exponentially declined, noting that free-eDNA persisted between 24-72 hours. Results indicate that organism biomass, specimen characteristics (e.g., stress and viability), and species-specific biological differences may influence free-eDNA detectability. These results are critical for implementing in-situ nucleic acid automated continuous sensing systems for marine biosurveillance, enabling point-of-need detection and rapid management response to biosecurity threats.

opencc-by-4.0Jun 2023View details →

Topology optimization dataset

Dataset of topology optimization problems in 50x140 2D meshes. It was used to train machine learning models to accelerate topology optimization. Each sample contains: <ol> <li>Binary definition of supports</li> <li>Sparse definitions of position and components of two point loads</li> <li>Volume fraction</li> <li>Von Mises and strain energy density fields of initial FEA solution</li> <li>Final topology</li> </ol> Other than the dataset, contains files related to data filtering, and checkpoints of the trained generative adversarial networks.

The Optimal Climate Intervention Scenario for Crop Production Varies by Nation

Abstract. Stratospheric aerosol intervention (SAI) is a proposed strategy to reduce the effects of anthropogenic climate change. As it would not directly counteract the increased forcing from CO2, its impacts on national crop production need to be analyzed, as SAI regionally modifies variables such as surface temperature, precipitation, humidity, total solar radiation, diffuse radiation, ultraviolet radiation, and surface ozone. In this work, we analyze impacts to crop production by looking at output from 11 different SAI scenarios carried out with a fully coupled Earth System Model coupled to a crop model. Higher latitude nations tend to produce the most calories under unabated climate change, while midlatitude nations maximize calories under moderate temperature limitation, and equatorial nations prefer large levels of climate intervention to produce the most calories from crops. Our results highlight the challenges in defining “globally optimal” SAI strategies, even if such definitions are based on just one metric.

Emission-Constrained Optimization of Gas Networks: Input-Convex Neural Network Approach

# Emission-Aware Optimization of Gas Networks   This repository collects the Belgium gas network dataset, details on the training procedure, and codes to replicate the results reported in the following paper:   *Emission-Constrained Optimization of Gas Networks: Input-Convex Neural Network Approach *   accepted for presentation at the 62nd IEEE Conference on Decision and Control, Dec. 13-15, 2023, Singapore.   Materials are released with the Attribution 4.0 International (CC BY 4.0) license.   The repository contains two folders: * ```operation_planning``` folder containing data and codes for neural network training and operation planning optimization  * ```long_term_planning``` folder containing data and codes for neural network training and long-term planning optimization    The models are implemented in ```Julia-1.6``` Language, using ```JuMP.jl``` using ```Flux.jl``` library for machine learning and JuMP.jl library for mathematical programming. Before running the code, make sure to activate the virtual environment from ```Project.toml``` files stored in each folder, e.g., by running  ``` julia> ] (@v1.6) pkg> activate . (operation_planning) pkg> instantiate ``` For experiment settings, refer to ```exp_settings``` dictionary in file ```main.jl```. For network data, refer to ```.../data/case_BE```.

Dataset for 'Optimized strategies for the quantum-state preparation of single trapped nitrogen molecular ions'

Raw data and scripts to produce figures and tables from the article 'Optimized strategies for the quantum-state preparation of single trapped nitrogen molecular ions.'

opencc-zeroAug 2023View details →

Angiosperms follow a convex trade-off to optimize hydraulic safety and efficiency

Intervessel pits are considered to function as valves that avoid embolism spreading and optimize efficient transport of xylem sap across neighbouring vessels. Hydraulic transport between vessels would therefore follow a safety-efficiency trade-off, which is directly related to the total intervessel pit area (Ap), inversely related to the pit membrane thickness (TPM), and driven by a pressure difference. To test this hypothesis, we modelled the relative transport rate of gas (ka) and water (Q) at the intervessel pit level for 23 angiosperm species, and correlated these parameters with the water potential at which 50% of embolism occurs (Ψ50). We also measured ka for 10 species using pneumatic measurements. The pressure difference across adjacent vessels, and estimated values of ka and Q were related to Ψ50, following a convex safety-efficiency trade-off based on modelled and experimental data. Minor changes in TPM and Ap exponentially affected the pressure difference and flow, respectively. Our results provide clear evidence that a xylem safety-efficiency trade-off is not linear, but convex due to flow across intervessel pit membranes, which represent mesoporous media within microporous conduits. Moreover, the convex nature of long-distance xylem transport may contribute to an adjustable fluid balance of plants, depending on environmental conditions.

opencc-zeroAug 2023View details →

Optimal thermal conditions for corals extend poleward with oceanic warming

The capacity for poleward range expansions beyond the tropics in corals hinges on ecophysiological constraints and resulting responses to climatic variability. We applied thermal physiological constraints of corals adapted to extreme seasonality in Hong Kong, specifically the minimum annual temperature and the proportion of time annually spent at seasonal extremes, to ask how warming will affect habitat suitability at the poleward range edges of these foundational species in the Northwest Pacific. Climate model projections reveal an easing of thermal constraints on the leading edge of coral ecophysiological limits with an expansion of thermally suitable habitat poleward by 2-7 degrees in latitude depending on the coral species and model considered. We also highlight a potential divergence of present and future thermal regimes that may lead to a mismatch in suitability for corals currently inhabiting high-latitude reefs. Understanding the thermal constraints on coral range expansions and defining the potential range of corals is critical for adaptive management that focuses on coral conservation and ensuring ecosystem function of existing subtropical and temperate ecosystems.

3D kinematics and kinetics of change of direction motions reconstructed from virtual inertial sensor data through optimal control simulation

This is the data belonging to the publication "Estimating 3D kinematics and kinetics from inertial sensor data through musculoskeletal movement simulations". This study investigated the feasibility and accuracy of reconstructing, especially change of direction motions, with a 3D full-body musculoskeletal model by tracking virtual inertial sensor data in optimal control simulations. We used the recordings of 90 trials with optical motion capture to generate marker tracking simulations from which we computed virtual inertial sensor data. Using this data, we compared inertial tracking simulations and marker tracking simulations. Please see the README and the publication for further details.

Data used for modeling in Energy-water-land-CCUS nexus model: carbon dioxide opportunities based on optimized regional development

In this dataset, the data used for modeling technologies in an energy-water-land-CCUS nexus model in Khark Island in Iran, and the main sources for gathering them are presented.

Dataset for PNAS: Adiabatic computing for optimal thermodynamic efficiency of information processing

Data set for the article to be published in PNAS "Adiabatic computing for optimal thermodynamic efficiency of information processing" This data set contains: <ul> <li>optimal_1ms.zip : raw data files of the response to an optimal erasure protocol of characteristic duration 1ms. This Matlab file includes all necessary quantitites to compute the average work and heat during the procedure ( ie position trajectory and driving parameters).</li> <li>optimal_3ms_part1 & _part2.zip: same for optimal protocols of 3ms.</li> <li>Analysis_code_optimal.m: Analysis Matlab code to be run on the mat files above. The code run the full analysis and output the work, heat, kinetic and potential energy and some calibration parameters. The processed data is saved in optimal_1 & 3ms_result.mat.</li> <li>Fast_erasure_v1_0.3 & _0.12.zip: same for basic protocol at v1=0 & v1=0.12. The processed data is saved in Fast_erasure_v1_0.3 & _0.12.mat. This data corresponds tp the two speeds used to draw the heating kinetic energy curves of Fig.4</li> <li> BasicAndOptimalTranslations.mat: Mat file containing the data used to create Fig. 3: <ul> <li> tprotocol (ms), x1basprotocol and x1optprotocol (sigma) define the ramps of the well center for the basic and optimal protocols (time and value of x1 for each ramp). </li> <li> t (ms), xbas and xopt (sigma) are the recording from the experiment (time, and arrays corresponding to 2000 measurements with 10ms of data sampled at 2Mhz each). The data is post processed with a low pass filter at 8kHz (filtfilt function in Matlab, using a 4th order butterworth filter). Fig. 3 correspond to the average of those 2000 trajectories. </li> <li> f0 (Hz) is the resonance frequency of the cantilever. </li> </ul> </li> <li>FigX.fig: Matlab format figure source used to draw all of the plots of the article, embedding the all data.</li> </ul>

opencc-by-4.0Sep 2023View details →

Galindo-Carvajal Optimized Truss

Structural Analysis of Optimized Truss

opencc-by-4.0Oct 2023View details →

Optimal SNR grids

Optimal single-detector signal-to-noise ratios evaluated on a regular grid of detector frame masses and fixed distance. To be used for interpolation when calculating semi-analytical sensitivity estimates.

opencc-zeroOct 2023View details →

Data from: Optimal control pulses for the 1.2 GHz (28.2 T) NMR spectrometers

The ability to measure NMR spectra with a large sample volume is crucial for concentration limited biological samples in order to attain adequate signal-to-noise (S/N) ratio. The possibility to measure with a 5 mm cryoprobe is currently absent at the 1.2 GHz NMR instruments due to the exceedingly high radio frequency power demands, which is four times compared to a 600 MHz instruments. Here, we overcome the high power demands by designing optimal control (OC) pulses with up to 20 times lower power requirements than currently necessary at a 1.2 GHz spectrometer. We show that multidimensional biomolecular NMR experiments constructed using these OC pulses can bestow improvement in the S/N ratio of up to 26%. With the expected power limitations of a 5 mm cryoprobe, we observe an enhancement in the S/N ratio of more than 240% using our OC sequences. This motivates the development of a cryoprobe with a larger volume than the current 3 mm cryoprobes.