Find research datasets worth reusing

opencc-by-4.0Apr 2022View details →

Data accompanying "Saildrone direct covariance wind stress in various wind and current regimes of the tropical Pacific"

Data used for creating figures in the draft article "Saildrone direct covariance wind stress in various wind and current regimes of the tropical Pacific". This includes: <ul> <li>1-minute average fields as broadcast in real time by Saildrone;</li> <li>10-minute average direct covariance fluxes (calculated by Jack Reeves Eyre);</li> <li>10-minute average bulk fluxes (calculated by Dongxiao Zhang using the COARE 3.5 algorithm).</li> </ul> Code used to calculate the direct covariance fluxes, and to create the plots, is in a Github repository (https://github.com/NOAA-PMEL/SaildroneCovarianceFlux). The repository is also archived on Zenodo (https://doi.org/10.5281/zenodo.6484795). The data are archived in a directory structure that should work with the code - only a simple edit of "src/config.py" should be required.    Version history: <ul> <li>v0.1.0 -- submission to PMEL internal review (goes with code v0.1.0, https://doi.org/10.5281/zenodo.6484796).</li> </ul>

opencc-zeroApr 2022View details →

Direct and indirect effects of fire on microbial communities in a pyrodiverse dry-sclerophyll forest

Fire is one of the predominant drivers of the structural and functional dynamics of forest ecosystems. In recent years, novel fire regimes have posed a major challenge to the management of pyrodiverse forests. While previous research efforts have focused on quantifying the impacts of fire on above-ground forest biodiversity, how microbial communities respond to fire is less understood, despite their functional significance. Here, we describe the effects of time since fire, fire frequency and their interaction on soil and leaf litter fungal and bacterial communities from the pyrodiverse, Eucalyptus pilularis forests of south-eastern Australia. Using structural equation models, we also elucidate how fire can influence these communities both directly and indirectly through biotic-abiotic interactions. Our results demonstrate that fire is a key driver of litter and soil bacterial and fungal communities, with effects most pronounced for soil fungal communities. Notably, recently burnt forest hosted lower abundances of symbiotic ectomycorrhizal fungi and Acidobacteria in the soil, and basidiomycetous fungi and Actinobacteriota in the litter. Compared with low fire frequencies, high fire frequency increased soil fungal plant pathogens, but reduced Actinobacteriota. The majority of fire effects on microbial communities were mediated by fire-induced changes in litter and soil abiotic properties. For instance, recent and more frequent fire was associated with reduced soil sulphur, which led to an increase in soil fungal plant pathogens and saprotrophic fungi in these sites. Pathogenic fungi also increased in recently burnt forests that had a low fire frequency, mediated by a decline in litter carbon and an increase in soil pH in these sites. Synthesis. Our findings indicate that predicted increases in the frequency of fire may select for specific microbial communities directly and indirectly through ecological interactions, which may have functional implications for plants (increase in pathogens, decrease in symbionts), decomposition rates (declines in Actinobacteriota and Acidobacteriota) and carbon storage (decrease in ectomycorrhizal fungi). In the face of predicted shifts in wildfire regimes, which may exacerbate fire-induced changes in microbial communities, adaptive fire-management and monitoring is required to address the potential functional implications of fire-altered microbial communities.

opencc-by-4.0Jul 2021View details →

Data for "Direct Observation of Ultrafast Exciton Localization in an Organic Semiconductor with Soft X-ray Transient Absorption Spectroscopy"

Underlying data for figures 1-3 and supplementary figures S1-S7 for the paper entitled 'Direct Observation of Ultrafast Exciton Localization in an Organic Semiconductor with Soft X-ray Transient Absorption Spectroscopy'.

opencc-zeroMay 2022View details →

Maternal and/or direct supplementation with a combination of a casein hydrolysate and yeast β-glucan on postweaning performance and intestinal health in the pig

A 2 × 2 factorial experiment was conducted to investigate the effect of maternal supplementation from day 83 of gestation and/or direct supplementation from weaning of a bovine casein hydrolysate plus a yeast β‑glucan (CH-YBG) on pig performance and intestinal health on day ten post‑weaning. Twenty cross bred gilts (Large White × Landrace) were randomly assigned to one of two dietary groups (n = 10 gilts/group): basal diet (basal sows) and basal diet supplemented with CH‑YBG (supplemented sows) from day 83 of gestation until weaning (2g/sow/day). At weaning, 120 pigs (6 pigs/sow) were selected. The two dam groups were further divided, resulting in four experimental groups (10 replicates/group; 3 pigs/pen) as follows: 1) BB (basal sows + basal pigs); 2) BS (basal sows + supplemented pigs); 3) SB (supplemented sows + basal pigs); 4) SS (supplemented sows + supplemented pigs). Supplemented pigs were offered 0.5g CH‑YBG/kg of feed for 10 days post-weaning. On day 10 post‑weaning, 1 pig/pen was humanely sacrificed and samples were taken from the gastrointestinal tract for analysis. Pigs weaned from supplemented sows (SS, SB) had reduced faecal scores and incidence of diarrhoea (P<0.05) compared to pigs weaned from basal sows (BB, BS), with SS pigs not displaying the transient rise in faecal scores seen in the other three groups from day 3 to day 10 post‑weaning (P<0.05). Pigs weaned from supplemented sows had reduced feed intake (P<0.05), improved feed efficiency (P<0.05), increased butyrate concentrations (P<0.05), increased abundance of Lactobacillus (P<0.05) and decreased abundance of Enterobacteriaceae and Campylobacteraceae (P<0.05) compared to pigs weaned from basal sows. In conclusion, maternal supplementation increased the abundance of Lactobacillus and decreased the abundance of Enterobacteriaceae and Campylobacteraceae while also increasing butyrate concentrations. The combination of maternal and direct supplementation led to pigs having the lowest faecal scores compared to all other groups.

opencc-by-4.0Jun 2022View details →

RNA modification detection using direct RNA sequencing and nanoDoc2

The core of nanoDoc2 includes a machine-learning algorithm in which a 6-mer segmented raw current signal is compared by Deep-One-Class classification using a Wavenet-based neural network. As an output, an RNA modification is detected by a statistical score in each candidate position. Herein, we describe the detailed instructions on how to use nanoDoc2 for signal segmentation, train/test the neural network and finally predict RNA modifications present in nanopore direct RNA sequence data.

opencc-zeroJun 2022View details →

Different functional networks underlying human walking with pulling force fields acting in forward or backward directions

Walking with pulling force fields acting at the body center of mass (in the forward or backward directions) is compatible with inclined walking and is used in clinical practice for gait training. From the perspective of known differences in the motor strategies that underlie walking with the respective force fields, the present study elucidated whether the adaptation acquired by walking on a split-belt treadmill with either one of the force fields affects subsequent walking in other directions. Walking with the force field induced an adaptive and de-adaptive behavior of the subjects, with the aspect evident in the anterior breaking and posterior propulsive impulses of the ground reaction force as parameters. In the parameters, the adaptation acquired during walking with a force field acting in one direction was transferred to that in the opposite direction only partially. Furthermore, the adaptation that occurred while walking in a force field in one direction was rarely washed out by subsequent walking in a force field in the opposite direction and thus was maintained independently of the other. These results demonstrated possible independence in the neural functional networks capable of controlling walking in each movement task with an opposing force field.

opencc-by-4.0Jun 2022View details →

In vivo characterization of antibodies directed against TREAT-AD target proteins in mouse model of AD pathology

In vivo characterization of antibodies directed against TREAT-AD target proteins (Moesin, CD44, Midkine, and SFRP1) in the 5xFAD mouse model

opencc-by-4.0May 2022View details →

Sustainable polyesters via direct functionalization of lignocellulosic sugars

Source data for the following publication: DOI: 10.1038/s41557-022-00974-5

opencc-by-4.0Jun 2022View details →

Direct prediction for carbapenemase-producing and colistin-resistant Klebsiella pneumoniae isolates from routine MALDI-TOF mass spectrum using machine learning

The emergence of carbapenem-nonsusceptible K. pneumoniae (CnSKP) leads a serious threat to patient survival and colistin resistance makes the treatment of CnSKP more difficultly. To make treatment strategy properly and quickly, we aimed to develop a rapid prediction method for CnSKP and colistin-resistant K. pneumoniae (ColRKP) based on the spectra of routine matrix-assisted laser desorption/ionization-time-of-flight mass spectrometry (MALDI–TOF MS). The machine learning (ML) model for differentiating CnSKP and carbapenem-susceptible K. pneumoniae (CSKP) showed accuracy of 0.8869 and AUC of 0.9551; the model for ColRKP and colistin-intermediate K. pneumoniae (ColIKP) showed accuracy of 0.8361 and the AUC of 0.8447.

opencc-by-4.0May 2022View details →

Subdaily meteorological measurements of temperature, direction of the movement of the clouds, and cloud cover in the Late Maunder Minimum by Louis Morin in Paris

Supplementary dataset of the publication:  Pliemon, T., Foelsche, U., Rohr, C., and Pfister, C.: Subdaily meteorological measurements of temperature, direction of the movement of the clouds, and cloud cover in the Late Maunder Minimum by Louis Morin in Paris, Clim. Past, 2022 For more details see the file.

opencc-by-4.0Jul 2022View details →

Data for manuscript sumitted to Open Research Europe, entitled "Low-resistivity, high-resolution W-C electrical contacts fabricated by direct-write focused electron beam induced deposition"

These are the data obtained experimentally and used to draw the figures in the article submitted to Open Research Europe

opencc-by-4.0Jul 2022View details →

Finite-strain Visco-elastic Visco-plastic model identification of PA12 material printed along different directions

The data provide the identification of PA12 bulk material for a finite-strain visco-elastic-visco-plastic (VE-VP) model printed along two directions. Tests were conducted in L. Cobian, M. Rueda-Ruiz, J.P. Fernandez-Blazquez, V. Martinez, F. Galvez, F. Karayagiz, T. Lück, J. Segurado, M.A. Monclus, Micromechanical characterization of the material response in a PA12-SLS fabricated lattice structure and its correlation with bulk behaviour, Polymer Testing 110 (2022) 107556: <a href="https://doi.org/10.1016/j.polymertesting.2022.107556">https://doi.org/10.1016/j.polymertesting.2022.107556</a> (in Open access), see also <a href="http://dx.doi.org/10.5281/zenodo.6136935">http://dx.doi.org/10.5281/zenodo.6136935</a> (in Open access) Material model follows V. D. Nguyen, F. Lani, T. Pardoen, X. Morelle, L. Noels, A large strain hyperelastic viscoelastic-viscoplastic-damage constitutive model based on a multi-mechanism non-local damage continuum for amorphous glassy polymers. International Journal of Solids and Structures 96 (2016): 192-216; <a href="https://dx.doi.org/10.1016/j.ijsolstr.2016.06.008">https://dx.doi.org/10.1016/j.ijsolstr.2016.06.008</a>, Open access:  <a href="https://orbi.uliege.be/handle/2268/197898">https://orbi.uliege.be/handle/2268/197898</a>. The model <ul> <li>Is implemented as a cross platform UMAT subroutine that is openly available on <a href="https://gitlab.uliege.be/moammm/moammmpublic/-/tree/master/code/MaterialModels/FiniteStrain/Finite_VEVP">https://gitlab.uliege.be/moammm/moammmpublic/-/tree/master/code/MaterialModels/FiniteStrain/Finite_VEVP</a> (Licensed under the Creative Commons Attribution 4.0 International (CC BY 4.0) (<a href="https://creativecommons.org/licenses/by/4.0">https://creativecommons.org/licenses/by/4.0</a>).) and referenced on the project web-site <a href="https://www.moammm.eu/index.php/developed-code/">https://www.moammm.eu/index.php/developed-code/</a>.</li> <li>The model is also implemented at the cm3 laboratory, who provides efficient algorithms for homogenisation implemented in a parallel setting in the open source finite element code base on <a href="http://gmsh.info/">Gmsh</a>. In order to have access to the sources follows <a href="https://www.moammm.eu/index.php/developed-code/">https://www.moammm.eu/index.php/developed-code/</a>.</li> </ul> If you use these data or model, we would be grateful if you could cite the related papers: <ul> <li>L. Cobian, M. Rueda-Ruiz, J.P. Fernandez-Blazquez, V. Martinez, F. Galvez, F. Karayagiz, T. Lück, J. Segurado, M.A. Monclus, Micromechanical characterization of the material response in a PA12-SLS fabricated lattice structure and its correlation with bulk behaviour, Polymer Testing 110 (2022) 107556: https://doi.org/10.1016/j.polymertesting.2022.107556 (in Open access)</li> <li>Data of “. Cobian, M. Rueda-Ruiz, J.P. Fernandez-Blazquez, V. Martinez, F. Galvez, F. Karayagiz, T. Lück, J. Segurado, M.A. Monclus, Micromechanical characterization of the material response in a PA12-SLS fabricated lattice structure and its correlation with bulk behaviour, Polymer Testing 110 (2022) 107556” http://dx.doi.org/10.5281/zenodo.6136935 (in Open access)</li> <li>V. D. Nguyen, F. Lani, T. Pardoen, X. Morelle, L. Noels, A large strain hyperelastic viscoelastic-viscoplastic-damage constitutive model based on a multi-mechanism non-local damage continuum for amorphous glassy polymers. International Journal of Solids and Structures 96 (2016): 192-216; https://dx.doi.org/10.1016/j.ijsolstr.2016.06.008, Open access: https://orbi.uliege.be/handle/2268/197898</li> </ul> This project has received funding from the European Union’s Horizon 2020 research and innovation programme under grant agreement No 862015

opencc-by-4.0Jul 2022View details →

Optical motion capturing of change of direction motions reconstructed with inverse kinematics and dynamics and optimal control simulation

This is the data belonging to the publication "Change the direction: 3D optimal control simulation by directly tracking marker and ground reaction force data". This study investigated the feasibility and accuracy of reconstructing, especially change of direction motions with a 3D full-body musculoskeletal model by tracking marker and ground reaction force (GRF) data in optimal control simulations. We recorded in total 30 trials with optical motion capture. Using this data, we compared inverse methods (inverse kinematics and dynamics) to coordinate tracking simulations and marker tracking simulations. Please see the README and the publication for further details.

Direct observational evidence of an oceanic dual kinetic energy cascade and its seasonality

Codes for the analysis and figure generation for drifter data

GPI-anchored protein homolog IcFBR1 functions directly in morphogenesis of Isaria cicadae

Isaria cicadae is a famous edible and medicinal fungus in China and Asia. The molecular basis of morphogenesis and synnemal formation needs to be understood in more detail, because this is the main source of biomass production in I. cicadae. In the present study, a fruiting body formation-related gene with a glycosylphosphatidylinositol (GPI) anchoring protein (GPI-Ap) gene homolog, IcFBR1, was identified by screening random insertion mutants. Targeted deletion of IcFBR1 resulted in abnormal, non-formation of synnemata, impairing aerial hyphae growth and sporulation. The IcFBR1 mutants were defective in utilization of carbon sources with reduced polysaccharide contents and in the regulation of amylase and protease activities. Transcriptome analysis of ΔIcfbr1 showed that IcFBR1 deletion influenced 49 gene ontology terms, including 23 biological processes, nine molecular functions, and 14 cellular components. IcFBR1 is therefore necessary for regulating synnemal development, secondary metabolism, and nutrient utilization in this important edible and medicinal fungus. This is the first report illustrating that the function of IcFBR1 is associated with the synnemata in I. cicadae.

Audio Examples for "Directional Frequency Filtering of Recordings in Spherical Harmonics Domain for Innovative Noise Reduction Strategies"

This is a collection of audio examples of the processing corresponding to the master thesis "Directional Frequency Filtering of Recordings in Spherical Harmonics Domain for Innovative Noise Reduction Strategies" The examples (ambisonics and binaural) contain recordings of moving sources in an anechoic chamber, which were made within different scenes partly containing noise barriers. Furthermore the simulation of noise barriers was implemented using directional filtering within a plane wave decomposition of the signals in sh domain.

opencc-zeroAug 2022View details →

Data from: Disentangling direct from indirect effects of habitat disturbance on multiple components of biodiversity

Human habitat disturbance affects both species diversity and intraspecific genetic diversity, leading to correlations between these two components of biodiversity (termed species - genetic diversity correlation, SGDC). However, whether SGDC predictions extend to host-associated communities, such as the intestinal parasite and gut microbial diversity, remains largely unexplored. Additionally, the role of dominant generalist species is often neglected despite their importance in shaping the environment experienced by other members of the ecological community, and their role as source, reservoir and vector of zoonotic diseases. New analytical approaches (e.g., structural equation modelling, SEM) can be used to assess SGDC relationships and distinguish among direct and indirect effects of habitat characteristics and disturbance on the various components of biodiversity. With six concrete and biologically sound models in mind, we collected habitat characteristics of 22 study sites from four distinct landscapes located in central Panama. Each landscape differed in the degree of human disturbance and fragmentation measured by several quantitative variables, such as canopy cover, canopy height and understory density. In terms of biodiversity, we estimated on the one hand, 1) small mammal species diversity, and, on the other hand, 2) genome-wide diversity, 3) intestinal parasite diversity and 4) gut microbial heterogeneity of the most dominant generalist species (Tome's spiny rat, Proechimys semispinosus). We used SEMs to assess the links between habitat characteristics and biological diversity measures. The best supported SEM suggested that habitat characteristics directly and positively affect the richness of small mammals, the genetic diversity of P. semispinosus and its gut microbial heterogeneity. Habitat characteristics did not, however, directly impact intestinal parasite diversity. We also detected indirect, positive effects of habitat characteristics on both host-associated assemblages via small mammal richness. For microbes, this is likely linked to cross species transmission, particularly in shared and/or anthropogenically altered habitats, whereas host diversity mitigates parasite infections. The SEM revealed an additional indirect but negative effect on intestinal parasite diversity via host genetic diversity. Our study showcases that habitat alterations not only affect species diversity and host genetic diversity in parallel, but also species diversity of host-associated assemblages. The impacts from human disturbance are therefore expected to ripple through entire ecosystems with far reaching effects felt even by generalist species.

Original data for publications: Direct solution–based synthesis of the Na4(B12H12)(B10H10) solid electrolyte, Experimental investigation of Mg(B3H8)2 dimensionality, materials for energy storage applications, Thermal Conversion of Unsolvated Mg(B3H8)2 to BH4– in the Presence of MgH2

Original data for the following papers (Only part of University of Geneva, synthesis part): Direct solution–based synthesis of the Na4(B12H12)(B10H10) solid electrolyte Gigante, A.; Duchêne, L.; Moury, R.; Pupier, M.; Remhof, A.; Hagemann, H. ChemSusChem 2019, 12, 4832-4837 Experimental investigation of Mg(B3H8)2 dimensionality, materials for energy storage applications Romain Moury, Angelina Gigante, Arndt Remhof, Elsa Roedern  and  Hans Hagemann Dalton Trans., 2020,49, 12168-12173, https://doi.org/10.1039/D0DT02170A Thermal Conversion of Unsolvated Mg(B3H8)2 to BH4– in the Presence of MgH2 Angelina Gigante, Noemi Leick, Andrew S. Lipton, Ba Tran, Nicholas A. Strange, Mark Bowden, Madison B. Martinez, Romain Moury, Thomas Gennett, Hans Hagemann, and Tom S. Autrey ACS Appl. Energy Mater. 2021, 4,3737-3747.   https://doi.org/10.1021/acsaem.1c00159

opencc-zeroAug 2022View details →

Cognitive experience alters cortical involvement in goal-directed navigation

Neural activity in the mammalian cortex has been studied extensively during decision tasks, and recent work aims to identify under what conditions cortex is actually necessary for these tasks. We studied whether cognitive experience, beyond sensory or motor learning, affects cortical involvement in goal-directed navigation. To this aim, we first trained different cohorts of mice on either a simple goal-directed navigation task ("simple task"), or one of two complex tasks involving delay periods ("delay task") or rule reversals ("switching task") in virtual reality. After task learning, we optogenetically inhibited various cortical areas on a subset of trials while mice performed a given task to assess the necessity of each area for task performance. We found overall minor cortical necessity for the simple task, but large necessity of cortical association areas (specifically of posterior parietal cortex and retrosplenial cortex) for each complex task. We then permanently transitioned mice with complex task experience to the simple task, again inhibiting cortical areas on a subset of trials. Crucially, we found that these mice heavily relied on cortical association areas for simple task performance, unlike mice without prior complex task experience. Therefore, past experience is a key factor in determining whether cortical areas have a causal role in goal-directed navigation. In this dataset, we include both behavioral data for the initial task training period, as well as behavioral data for all subsequent optogenetic inhibition experiments. Details about the data structure are available in the accompanying Readme.txt files.