Find research datasets worth reusing

opencc-by-4.0May 2023View details →

Data from: Integrated survey methodologies provide process-driven framework for marine renewable energy environmental impacts

Data from: Integrated survey methodologies provide process-driven framework for marine renewable energy environmental impacts

Example data and scripts for: Processing IMU signals to recreate sacral trajectory during treadmill walking

Example IMU data and scripts for reconstructing the trajectory of a sacral IMU and validation with motion capture data. Also contains example code of gait event detection and synchronization.

Sleep-like changes in neural processing emerge during sleep deprivation in early auditory cortex - Dataset

Dataset summarizing for every State X Unit the auditory response features + the statistical models for all the different figures. Variables: corticosteroneRawData:the corticosterone measures in 12 animals across the five conditions described in the paper. statistics: statistical models for every figure isUnitValidForAnalysis: Logical vector with n units length describing which units were included in every analysis. resultsPerUnit: auditory response features per unit for all the different states/conditions described in the paper (Vigilant, Tired, NREM, REM, Q-Wakefulness during recovery sleep, movement-controlled Vigilant and Tired conditions). Each state is a struct with 496 entries (496 units). the different field in the struct are: - session: animal and session identifiers. - isContext: is Auditory Paradigm A (with 2,10,20,30,40 Hz Click Trains) or B (just 40 Hz click trains. - ch: recording channel/microwire # (1-16) - clus: cluster number in channel - clusType: is single-unit / multi-unit - spikeShape: the average spike waveform - baseFr: unit's baseline firing rate - baseFanoFactor: fano factor of each unit's baseline firing rate (not used in paper). - baseIsiCv: baseline ISI (inter-spike interval) CV (coefficient of variation), not used in paper - basePopCoupling: baseline population coupling values - clicks40Hz: 40Hz click responses - clicksAll: responses to all click trains (2,10,20,30,40 Hz) - offState: post-onset and off-state analysis. - clicksSim: simulated click response to different click rates based on the onset+post onset responses as in Supp. Fig. 6. - PostOnsetYoked: Surrogate post-onset response following spontaneous bursts as in Fig. 5A-C - drc: responses to Dynamic random chords used to get tuning.

opencc-by-4.0Dec 2022View details →

LTEE-INSeq-processed-data

This repository contains processed data from transposon sequencing (INSeq) of the ancestral strain (REL606) and clones sampled at 2,000 and 15,000 generations for the Ara+2 and Ara-1 lineages from the Lenski's Long-Term Evolution Experiment (LTEE). Files contain the number of reads per data point for genome-wide insertion mutants that were subjected to bulk competition under similar conditions to those of the LTEE. Raw sequencing reads are available from the NCBI BioProject database (PRJNA979973). Scripts for analyses are available from GitHub (https://github.com/ACouce/LTEE2022).

Data from: Complex evolutionary processes maintain an ancient chromosomal inversion

Genome re-arrangements such as chromosomal inversions are often involved in adaptation. As such, they experience natural selection, which can erode genetic variation. Thus, whether and how inversions can remain polymorphic for extended periods of time remains debated. Here we combine genomics, experiments, and evolutionary modeling to elucidate the processes maintaining an inversion polymorphism associated with the use of a challenging host plant (Redwood trees) in Timema stick insects. We show that the inversion is maintained by a combination of processes, finding roles for life-history trade-offs, heterozygote advantage, local adaptation to different hosts, and gene flow. We use models to show how such multi-layered regimes of balancing selection and gene flow provide resilience to help buffer populations against the loss of genetic variation, maintaining the potential for future evolution. We further show that the inversion polymorphism has persisted for millions of years and is not a result of recent introgression. We thus find that rather than being a nuisance, the complex interplay of evolutionary processes provides a mechanism for the long-term maintenance of genetic variation.

opencc-by-4.0Mar 2023View details →

Comparing effects of food mechanical properties on oral processing behaviors in two sympatric lemur species - Dataset

Dataset for maximal random slope mixed models from manuscript "Comparing effects of food mechanical properties on oral processing behaviors in two sympatric lemur species". Column headers are described in the article and the key tab of the excel.

Microevolutionary processes in a foundation tree inform macrosystem patterns of community biodiversity and structure

Despite an increased focus on multiscale relationships and interdisciplinary integration, few macroecological studies consider the contribution of genetic-based processes to landscape-scale patterns. We tested the hypothesis that tree genetics, climate, and geography jointly drive continental-scale patterns of community structure, using genome-wide SNP data from a broadly distributed foundation tree species (<a>Populus fremontii</a> S. Watson) and two dependent communities (leaf-modifying arthropods and fungal endophytes) spanning southwestern North America. Four key findings emerged: (1) Tree genetic structure was a significant predictor for both communities; however, the strength of influence was both scale- and community-dependent. (2) Tree genetics was the primary driver for endophytes, explaining 17% of variation in continental-scale community structure, whereas (3) climate was the strongest predictor of arthropod structure (24%). (4) Power to detect tree genotype<a>—</a>community phenotype associations changed with scale of genetic organization, increasing from individuals to populations to ecotypes, emphasizing the need to consider nonstationarity (i.e., changes in the effects of factors on ecological processes across scales) when inferring macrosystem properties. Our findings highlight the role of foundation tree species as drivers of macroscale community structure and provide macrosystems ecology with a theoretical framework for linking fine- and intermediate-scale genetic processes to landscape-scale patterns. Management of genetic diversity harbored within foundation species is a critical consideration for conserving and sustaining regional biodiversity.

Data from: Comparative LCA studies of simulated HMF-biorefineries from maize and miscanthus as an example of first- and second-generation biomass as a tool for process development

5-Hydroxymethylfurfural (HMF) is a versatile platform chemical for a fossil free, bio-based chemical industry. HMF can be produced by using fructose as a feedstock. Using edible, first-generation biomass to produce chemicals has been questioned in terms of potential competition with food supply. Second-generation biomass like miscanthus could be an alternative. However, there is a lack of information if second-generation lignocellulosic biomass is a more sustainable feedstock to produce HMF. Therefore, a life cycle assessment was performed in this study to determine the environmental impacts of HMF production from miscanthus and to compare it with HMF from high fructose corn syrup (HFCS). HFCS from either Hungary or Baden-Württemberg (Germany) was considered. Compared to the HFCS biorefineries the miscanthus concept is producing less emissions in all impact categories studied, except land occupation. Overall, the production and usage of second-generation biomass could be especially beneficial in areas where the use of N-fertilizers is restricted. Besides, conclusions for the further development of the on-farm-biorefinery concept were elaborated. For this purpose, process simulations from a previous study were used. Results of the previous study in terms of TEA and the current LCA study in terms of environmental sustainability indicate that the lignin depolymerization unit in the miscanthus biorefinery has to be improved. The scenario without lignin depolymerization performs better in all impact categories. The authors recommend to not further convert the lignin to products like phenol and other aromatic compounds. The results of the contribution analyses show that the major impact in the HMF production is caused by the auxiliary materials in the separation units and the required heat. Further technical development should focus on efficient heat as well as solvent use and solvent recovery. At this point further optimizations will lead to reduced emissions and costs at the same time. The presented data set is the used inventory to model the environmental impacts.

Improved dual-permeability model for characterizing the mass transfer process inside matrix blocks

The dual-permeability model (DPM) is highly efficient for describing bimodal transport in heterogeneous porous media. However, it uses only one domain to describe the matrix blocks, and it therefore ignores the impact of the mass transfer process inside the matrix blocks at the microscale. Therefore, in this study, to investigate the effect of the mass transfer process in dual-permeability media and the computational accuracy when considering it, the dual-permeability model with a transition domain (DPMTD) is proposed based on the DPM. Comparison of the DPMTD with the DPM by applying them to a sand column experiment with the same concept as the model reveals that the DPMTD captures the bimodal transport (especially the first peak) more effectively because it calculates the rapid exchange of solute in the early stage more accurately. Subsequently, the same conclusion is reached when both models are applied to a reported solute displacement experiment for an Andisol. In short, we suggest that the mass transfer process inside matrix blocks needs to be characterized in the model to achieve higher accuracy and provides a new approach for modeling the solute transport of preferential flow.

BIG DATA ANALYTICS IN DIGITAL HUMAN RESOURCES MANAGEMENT: IMPACT ON THE RECRUITMENT PROCESS

This study investigates how HR employees experience the big data phenomenon in the recruitment function of HRM and how their perceptions of the phenomenon have evolved. This study also examines how BD will affect organizational and HRM and how it can be improved in other functions of HR. In this exploratory study, which comprehensively addresses the BD phenomenon in HRM, the phenomenological design approach, one of the qualitative research methods, was applied to test the research questions and a semi-structured interview form was used for research data. Using the snowball sampling method, in-depth interviews were conducted with 10 HR employees working in large and semi-structured organizations in Turkey and the interviews were analyzed with MAXQDA 20. The findings show that HRM employees are aware of BD. On the other hand, it is understood that BD technologies provide easy accessibility in recruitment, offer a strategic competitive advantage, and enable more effective management of information management, which saves HR employees' work in a facilitating way. They benefit from technology as a decision support assistant. Finally, the research results provide theoretical and practical implications for future researchers and practitioners for the development and effective use of BD technology in the field of HRM.

processed single-cell data from "Cancer cell non-autonomous tumor progression from chromosomal instability"

The h5ad files can be used as processed scRNA-seq input to the ContactTracing code (https://zenodo.org/badge/latestdoi/625036312). There is one file for the highCIN/lowCIN comparison, and another for the highCIN/noSTING comparison.

Tree diversity effects on litter decomposition are mediated by litterfall and microbial processes

Forest ecosystems are critical for their carbon sequestration potential. Increasing tree diversity was shown to enhance both forest productivity and litter decomposition. Litter diversity increases litter decomposability by increasing the diversity of substrates offered to decomposers. However, the relative importance of litter decomposability and decomposer community in mediating tree diversity effects on decomposition remains unknown. Moreover, tree diversity modulation of litterfall spatial distribution, consequently, litter decomposition has rarely been tested. We studied tree diversity effects on leaf litter decomposition and its mediation by the amount of litterfall, litter species richness and decomposability, and soil microorganisms in a large-scale tree diversity experiment in subtropical China. Furthermore, we examined how litter functional identity and diversity affect leaf litter decomposability. Finally, we tested how leaf functional traits, tree biomass, and forest spatial structure drive the litterfall spatial distribution. We found evidence that tree species richness increased litter decomposition by increasing litter species richness and the amount of litterfall. We showed that soil microorganisms in this subtropical forest perform 84–87% of litter decomposition. Moreover, changes in the amount of litterfall and microbial decomposition explained 19–37% of the decomposition variance. Additionally, up to 20% of the microbial decomposition variance was explained by litter decomposability, while litter decomposability itself was determined by litter functional identity, diversity, and species richness. Tree species richness increased litter species richness and the amount of litterfall (+200% from monoculture to 8-species neighborhood). We further demonstrated that the amount of species-specific litterfall increased with increasing tree proximity and biomass and was modulated by leaf functional traits. These litterfall drivers increased the spatial heterogeneity of litter distribution, thus, litter decomposition. We highlighted multiple biomass- and diversity-mediated effects of tree diversity on ecosystem properties driving forest nutrient cycling. We conclude that considering spatial variability in biotic properties will improve our mechanistic understanding of ecosystem functioning.

Reproducibility Report for the paper "Vibration signal-assisted endpoint detection for long-stretch, ultraprecision polishing processes"

This reproducibility report includes the datasets and computer code used for reproducing the results in the paper, Jin, Bukkapatnam, Hayes, and Ding, 2023, “Vibration signal-assisted endpoint detection for long-stretch, ultraprecision polishing processes,” ASME Transactions, Journal of Manufacturing Science and Engineering, Vol.145, pp. 061007.

Spatial controls on eco-evolutionary processes in microbial communities

<div> Microorganisms are the most biodiverse life forms on our planet, yet we know little about the spatial processes underlying their ecology and evolution. Here, we highlight the importance of two spatial processes that act on individual cells – spatial intermixing of different populations and mechanical cell shoving during growth – to improve our understanding of microbial eco-evolutionary dynamics. Using an individual-based model, we show that the coexistence between slow- and fast-growing populations becomes highly constrained under two conditions: when the slow- and fast-growing populations are highly spatially intermixed and when the ability to shove other cells (both conspecific and heterospecific) is weak. The potential for evolution through plasmid-mediated horizontal gene transfer between slow- and fast- growing populations also becomes restricted in the same scenario. Our modeling highlights that ecological constraints can dampen evolutionary opportunities within microbial communities due to variation in spatial intermixing and mechanical shoving at the cellular scale. </div>

SUPPLIMANTRY [Vacuum Ohmic Heating: A Promising Technology for the Improvement of Tomato Paste Processing, Safety, Quality and Storage Stability]

Abstract: Ohmic heating (OH) is an electrothermal technology used to inactivate enzyme and microbial activities. This work aimed to study the impact of Ohmic Heating Under Vacuum (OHUV) which compared to conventional heating (CH) as well as storage stability at 5°C and 25 °C on microbial safety, and nutritional quality. The evaluation parameters were pH, titratable acidity, TSS, lycopene, ascorbic acid, PME, HMF, and microbiological activity. The obtained results showed that tomato paste samples that were treated by OHUV are significantly superior to CH in terms of all physicochemical and microbiological characteristics, as well as being the least harmful during storage in both transparent and dark packages. The results showed the changes in ascorbic acid, lycopene, and HMF values that were treated by OHUV at 25 °C and filled in transparent package are most affected compared to other treated samples. On the other hand, tomato paste samples stored in dark packages at 5 °C performed significantly better than those subjected to CH under the same conditions and activated PME the most had higher ascorbic acid and lycopene and fewer changes in HMF during storage time for 90 days. OHUV found to be a good alternative treatment in the production of tomato paste.

Dataset of paper "Removal of diclofenac by UV-B and UV-C light-emitting diodes (LEDs) driven advanced oxidation processes (AOPs): Wavelength dependence, kinetic modelling and energy consumption"

Dataset of paper "Removal of diclofenac by UV-B and UV-C light-emitting diodes (LEDs) driven advanced oxidation processes (AOPs): Wavelength dependence, kinetic modelling and energy consumption" <ul> <li>Molar absorption coefficient of the DCF (pH 7.2), FC (pH 8.5), and H2O2 (pH 6.5) in the wavelength range of 200-400 nm. </li> <li>Time-based and UV fluence-based kinetic constant and synergy factor for the DCF degradation.</li> <li>Diclofenac degradation fitted by the proposed models (UV/H2O2 and UV/FC).</li> <li>Oxidant degradation fitted by the proposed models (UV/H2O2 and UV/FC).</li> </ul>

opencc-by-4.0Jul 2023View details →

Processing load, and not stimulus evidence, determines the duration of unconscious visual feature integration

Data and MATLAB analysis script for the paper "Processing load, and not stimulus evidence, determines the duration of unconscious visual feature integration"

opencc-by-4.0Jul 2023View details →

Acc_tcga_2018_processed

This dataset is the final result gotten from preprocessing the Acc_tcga_2018 gotten from the cBio portal and integrating it with the nodes gotten from pathway commons. It contains the edge index, the patients' information and survival time. It is to be used with Pytorch geometric for building GNNs

opencc-zeroJul 2023View details →

Data from: Diversification processes in Gerp's mouse lemur demonstrate the importance of rivers and altitude as biogeographic barriers in Madagascar's humid rainforests

Madagascar exhibits exceptionally high levels of biodiversity and endemism. Models to explain the diversification and distribution of species in Madagascar stress the importance of historical variability in climate conditions which may have led to the formation of geographic barriers by changing water and habitat availability. The relative importance of these models for the diversification of the various forest-adapted taxa of Madagascar has yet to be understood. Here, we reconstructed the phylogeographic history of Gerp's mouse lemur (Microcebus gerpi) to identify relevant mechanisms and drivers of diversification in Madagascar's humid rainforests. We used restriction site associated DNA (RAD) markers and applied population genomic and coalescent-based techniques to estimate genetic diversity, population structure, gene flow and divergence times among M. gerpi populations and its two sister species M. jollyae and M. marohita. Genomic results were complemented with ecological niche models to better understand the relative barrier function of rivers and altitude. We show that M. gerpi diversified during the late Pleistocene. The inferred ecological niche, patterns of gene flow and genetic differentiation in M. gerpi suggest that the potential for rivers to act as biogeographic barriers depended on both size and elevation of headwaters. Populations on opposite sides of the largest river in the area with headwaters that extend far into the highlands show particularly high genetic differentiation, whereas rivers with lower elevation headwaters have weaker barrier functions, indicated by higher migration rates and admixture. We conclude that M. gerpi likely diversified through repeated cycles of dispersal punctuated by isolation to refugia as a result of paleoclimatic fluctuations during the Pleistocene. We argue that this diversification scenario serves as a model of diversification for other rainforest taxa that are similarly limited by geographic factors. In addition, we highlight conservation implications for this critically endangered species, which faces extreme habitat loss and fragmentation.

Land cover maps: End-to-end Learning for Land Cover Classification using Irregular and Unaligned SITS by Combining Attention-Based Interpolation with Sparse Variational Gaussian Processes

Land cover maps obtained with mTAN-GP, mTAN-MLP, mTAN-LTAE and raw-LTAE models for the year 2018 with Sentinel-2 acquisitions. For further details see the pre-print article "End-to-end Learning for Land Cover Classification using Irregular and Unaligned SITS by Combining Attention-Based Interpolation with Sparse Variational Gaussian Processes ". This article is available : <a href="https://hal.science/hal-04112115">here</a>.