Find research datasets worth reusing

MicroED Characterization of a Robust Cationic σ-Alkane Complex Stabilized by the [B(3,5-(SF5)2C6H3)4]– Anion, via On-Grid Solid/Gas Single-Crystal to Single-Crystal Reactivity.

3DED/MicroED datasets collected using a Thermo Fisher Scientific Glacios microscope equipped with a Ceta-D Camera associated with the publication "MicroED Characterization of a Robust Cationic σ-Alkane Complex Stabilized by the [B(3,5- (SF5)2C6H3)4]– Anion, via On-Grid Solid/Gas Single-Crystal to Single-Crystal Reactivity." published in <a href="https://doi.org/10.1039/D2DT00335J">Dalton Transactions</a>.  Data collection details:  200kV, microprobe, gun lens 4, spot size 11, 30 µm C2 aperture. Illuminated area was ~4 µm and a 40 µm SA aperture was used. Under these conditions flux is ~0.01 e-/Å^2/s. Camera length calibrated from Al powder was 958.5 mm. Data acquired using EPU-D with following settings: 2x binning, 0.5 °/s, 2s exposure, rolling shutter, noise reduction mode enabled.  MRC format images can be processed with DIALS using the FormatMRC dxtbx format (distributed with DIALS from version 3.5 onwards), use goniometer.axes=1,0,0. Some processing notes for the σ-alkane Complex ([1-NBA][S-BArF4] in the paper) can be found <a href="https://github.com/huwjenkins/ed_scripts/wiki/Processing-%5BRh(NBA)(dcpe)%5D%5BB(ArSF5)4%5D-data-from-zenodo.org-record-5760938">here</a>.

Dataset and analyses for : Can foot placement during gait be trained? Adaptations in stability control when ankle moments are constrained

Here you'll find the dataset and analyses belonging to the publication "Can foot placement during gait be trained? Adaptations in stability control when ankle moments are constrained". Participants walked on a treadmill with and without shoes constraining ankle moment control. We evaluated whether participants improved their degree of foot placement control, during and after walking with ankle moment constraints. Ground reaction forces and full body kinematics have been collected. For more detail on the folders' contents please see "Read me - Can foot placement during gait be trained.docx".

Stability of a Mixed-Valence Hydrous Iron-Rich Oxide: Implications for Water Storage and Dynamics in the Deep Lower Mantle

The XRD datasets in Figure 1, Figure2A, Figure2B, Figure4A, Figure4B, Figure6A, and Figure6B.

opencc-by-4.0Mar 2022View details →

United Atom Parameters for United Atom Multiscale Modelling Of Bio-Nano Interactions Of Citrate Trianion Stabilized Nanoparticles

Short-range surface adsorption potentials of carbohydrates, lipid fragments, and amino acid side chains onto Cit(3-) stabilized surfaces (in tabulated form). Recovered from radial distribution functions Force Fields: adapted CHARMM36. Material: CIT(3-)

dryad32/100

Temporal stabilizing effects of species richness and seed arrangement on grassland biomass production

1. The extent to which individuals experience inter- and intraspecific interactions through their spatial arrangements within diverse plant communities, whether because of confounding effects of species richness, evenness, or direct changes in species patch sizes on their neighborhood relationships, could affect grassland biomass production and its stability at community scales. Elucidating the ways in which neighborhood effects and species richness contribute to such community responses has important implications for how practitioners establish grasslands to meet forage production and conservation goals. 2. We assessed the effects of altering plant species richness (3 levels: 2, 4, or 8 forage species per plot) and seed arrangements (4 levels: species mixed and seeded or seeded in 0.0625 m2, 0.25 m2, or 1.0 m2 single-species patches while maintaining plot-scale species evenness) on aboveground biomass production and its temporal stability in developing grasslands seeded with a suite of globally common forage species (three legumes, three cool-season grasses, two warm-season grasses). 3. Communities seeded with more species and those with their seeds arranged into smaller conspecific patches produced more biomass and were more temporally stable than those seeded with fewer species and larger conspecific patches. The effect of manipulating species arrangements is attributable to greater neighborhood scale interspecific interactions and stronger complementary effects. Furthermore, seeding species into conspecific patches resulted in communities that were 34% more productive, that were just as temporally stable, and that had similar diversity effects as those seeded with a species mixture, as is common in grassland reconstruction efforts. 4. Synthesis: In comparison with conventional mixed-seeding methods, seeding grasslands with high species richness and small, single-species patches may promote grassland reconstruction through increased biomass production, temporal stability, and complementarity effects. Our study highlights the importance of regulating intraspecific interactions within diverse communities for improving grassland biomass production and suggests that efforts to reevaluate methods used to establish forage and conservation grasslands could result in greater biomass production and stability in these systems.

opencc-zeroApr 2022View details →

opencc-by-4.0Apr 2022View details →

Gradual Enhancement of the Assemblage Stability of the Reed Rhizosphere Microbiome with Recovery Time

This is a supplementary material for the article of "Gradual Enhancement of the Assemblage Stability of the Reed Rhizosphere Microbiome with Recovery Time"

opencc-by-4.0Dec 2021View details →

Non-Invasive Rheo-MRI Study of Egg Yolk-Stabilized Emulsions: Yield Stress Decay and Protein Release

Raw data for our publication "Non-Invasive Rheo-MRI Study of Egg Yolk-Stabilized  Emulsions: Yield Stress Decay and Protein Release", including MRI (Paravision) and D-T2 maps (Topspin) datasets, rheological measurements (ASCII) and MATLAB scripts organised corresponding to each figure in the paper.

opencc-by-4.0May 2022View details →

The rehydration attributes and quality characteristics of 'Quick-cooking' dehydrated beans: Implications of glass transition on storage stability

The data set was used to generate the figures.

opencc-by-4.0May 2022View details →

Repository for the paper "Stability of the Jupiter southern polar vortices inspected through vorticity using Juno/JIRAM data"

This repository contains all the *img and *lbl files that have been used in the analysis reported in "Stability of the Jupiter southern polar vortices inspected through vorticity using Juno/JIRAM data". Please see the text for details.

dryad32/100

The influence of nutrient enrichment on riverine food web function and stability

Nutrient enrichment of rivers and lakes has been increasing rapidly over the past few decades, primarily because of agricultural intensification. Although nutrient enrichment is known to drive excessive algal and microbial growth, which can directly and indirectly change the ecological community composition, the resulting changes in food web emergent properties are poorly understood. We used ecological network analysis (ENA) to examine the emergent properties of 12 riverine food webs across a nutrient enrichment gradient in the Manawatu, New Zealand. We also derive Keystone Sensitivity Indices to explore whether nutrients change the trophic importance of species in a way that alters the resilience of the communities to further nutrient enrichment or floods. Nutrient enrichment resulted in communities composed of energy inefficient species with high community (excluding microbes) respiration. Community respiration was several times greater in enriched communities and this may drive hypoxic conditions even without concomitant changes in microbial respiration. Enriched communities exhibited weaker trophic cascades, which may yield greater robustness to energy flow loss. Interestingly, enriched communities were also more structurally and functionally affected by species sensitive to flow disturbance making these communities more vulnerable to floods.

opencc-zeroJul 2022View details →

Replication package for A Risk-based Theory of Exchange Rate Stabilization

The package contains the code necessary to reproduce Table 1, Figure 1 in the main text, and Table 2 in the Online Appendix in Hassan, Mertens and Zhang (2022) "A Risk-based Theory of Exchange Rate Stabilization." Review of Economic Studies. The package also includes a Mathematica notebook that derives the equations and propositions in the main text.

openother-openJul 2022View details →

Coexistence is stabilized by conspecific negative density dependence via fungal pathogens more than oomycete pathogens

No description provided.

opencc-by-4.0Jul 2022View details →

Postural stability metrics associated to the publication: Additive manufacturing of spinal braces: evaluation of production process and postural stability in patients with scoliosis

Data was collected for each condition (3D-printed brace, conventional brace, unbraced) for 60 seconds with patients in a standing posture, open eyes and both feet together.

Stability and electronic properties of CsK2Sb surface facets

This is the dataset for the identically named publication. In the framework of density-functional theory, we investigate stability and electronic properties of surface slabs of CsK2Sb.

Thriving in the heat – Lysine acetylation stabilizes the quaternary structure of a Mega-Dalton hyperthermoactive PEP-synthase

Over time structural adaptations enabled proteins and enzymes to have sufficient stability and flexibility to perform the basic functions of life under various environmental conditions. The catalytic cores of key metabolic enzymes of hyperthermophilic archaea work at a temperature range of 80-120 °C, similar to the conditions wher the earliest life forms may have thrived. Here we characterize a key enzyme of the central carbon metabolism of Pyrococcus furious, through an integrative approach combining structural mass spectrometry, cryo-electron microscopy, mass photometry and molecular modelling with molecular dynamics simulations. From our investigation, we unveil the structural organization of phosphoenolpyruvate synthase (PPSA). Its 24-meric assembly - weighing over 2 MDa - harbors flexible distal domains, whose proper functioning and coordination depends on widespread chemical acetylation of lysine residues. This non-enzymatic post-translational modification, along with other types of lysine modifications, also occurs on most other major protein complexes of P. furiosus. These modifications likely originated in the chemically favorable primordial conditions and gradually became highly specialized and enzyme-driven in more distantly related mesophiles and Eukaryotes. Molecular dynamics simulations and analysis – The all-atom structures of the full c1(X4) 24-mer PPSA models, carrying highly acetylated sites at 14 positions (106, 120,185, 187, 427, 466, 492, 496, 557, 574, 641, 726, 737, 805) or unmodified lysines were coarse grained (CG), mapping their atoms to the SIRAH force field (ff), that uses a classical Hamiltonian common to most all-atom potentials to describe particle–particle interactions, and recently extended to support the PTMs most commonly found on proteins(Garay et al., 2020). Both starting structures contained a disulfide bond between Cys42-Cys189 as well as phosphorylation of Thr440. All starting structures, simulation boxes and parameters files used for the minimization, equilibration and production are provided (Supplementary Data 5). Simulation was conducted in GROMACS 2020.4(Hess et al., 2008), for which code can be found here: <a href="https://doi.org/10.5281/zenodo.5636522">https://doi.org/10.5281/zenodo.5636522</a>. The 24-aly system consisted of 94128 CG atoms for the protein representation, solvated with 179271 WT4 CG water beads (Garay et al., 2020). A neutral charge was achieved adding 6617 NaW (Na+) and 5633 ClW (Cl-), corresponding to a concentration of approximately 150 mM NaCl concentration. The 24-lys system was also prepared accordingly and consisted of 93456 CG atoms for the protein, 186690 WT4 CG water beads and neutralized with 6503 NaW (Na+) and 5855 ClW (Cl-). Solvation was done using the default radii of 0.105 nm for atoms not present in the VdW database (vdwradii.dat) and then removing the WT4 molecules within 0.3 nm from the solute. In all cases, eventual clashes were relaxed during the solute-restrained energy minimization. Due to the length of the loops connecting the 3 domains, an alternative configuration of the tetramers where the CD-NBD domains are sitting on top of the neighboring PPSA subunit is also possible (see Supplementary Note 1). This was named “alternative” (a) configuration, as opposed to the “original” (o), thus producing 4 starting models: a24-aly, o24-aly, a24-lys and o24-lys (Supplementary Data 5). All these configurations were subjected to a first round of production consisting of 125 ns in duplicate to define the stable configuration for further extension of the simulation time to 500 ns. The main stages of the simulation can be summarized as follows:1) solvent and side-chain relaxation by 2 stages of 20’000 steps of energy minimization, imposing positional restraints of 1000 kJ mol-1 nm-2 on the whole protein (stage 1) and only on backbone beads (GN and GO, stage 2); 2) solvent NVT ensemble equilibration with a first stage where the temperature was slowly increased from 303K to 363K in 7 steps of 4 ns each, and a second stage to equilibrate the protein by gradually releasing the positional restraints from 1000 kJ mol-1 nm-2  on the backbone beads (GN and GO) to 100 kJ mol-1 nm-2 on the C-terminus to compensate for the missing stabilization effect of the Met799-Fe cluster; 3) production simulation of an additional 80 ns in NPT ensemble at 363 K and 1 bar imposing positional restraints of 100 kJ mol-1 nm-2 on the C-terminus. Non-bonded interactions were treated with a 1.2 nm cutoff and PME for long-range electrostatics. An integration time-step of 15 fs was used during MD production runs. The system pressure was controlled by the Parrinello-Rahman barostat (Parrinello and Rahman, 1981) with a coupling time of 4 ps. The positional restraints during the production simulation were necessary to maintain the overall system at the high energy of the particles at 363 K (90 ˚C), the temperature mimicking the near-optimum temperature for PPSA catalytic activity. All simulations were run in duplicate. Although the simulations do not accurately reflect the possible dynamics of the protein in native conditions, the computational challenges of simulating >350000 atoms for the protein only drove us to use a CG representation of the system.  To analyze the trajectories, every functional module (tetramer) was extracted from the simulation of the full 24-mer for each replicate, resulting in two sets of 12 independent trajectories (6 for each 24-mer) either with and without acetylated Lysine residues. To produce morphed movies and analyze secondary structure and interfaces, the CG tetramers trajectories were back mapped to atomistic detail using SIRAH tools via VMD. A back mapped atomistic model was produced every 35.7 ns, and subjected to 100 cycles of energy minimization in AMBER, resulting in 14 atomistic models describing each trajectory of a given tetramer over the 500 ns of simulation, further interpolated in ChimeraX using the morph command to produce the atomistic representation of the dynamics (Supplementary Data 5). RMSD calculation and trajectory analysis were done with the MDanalysis suite(Michaud-Agrawal et al., 2011). Each probability density in Figure 5B and 5C is calculated over two independent coarse-grained molecular dynamics simulations of the last 250 ns of production of the PPSA 24-mer in the acetylated and non-acetylated form, using a snapshot frequency of 5 ns. In Figure 5B, the RMSD of the Cα atoms (equivalent to backbone GC beads in CG MD) of the NBD region (residues 1-365) in the tetramer form was calculated with respect to their conformation in the tetramer PPSA resting state. The six trajectories of all six tetramers included in the simulated PPSA complex, resulting in 3 μs ([250ns*6]*2) of accumulated tetramer simulation, were used in the probability density calculation. In Figure 5C, the RMSD of the Cα atoms (equivalent to backbone GC beads in CG MD) was calculated over the CD (residues 379-481) and PBD (residues 510-790) regions with respect to the modelled CD-PBD state of PPSA in the monomer form. All 24 PPSA monomers of which the simulated PPSA complex was composed were included in the probability density calculation, resulting in 12 μs ([250ns*24]*2) of accumulated PPSA monomer simulation.

Analyses for: The effect of external lateral stabilization on ankle moment control during steady-state walking

Here you'll find the analyses for the short communication published as : "The effect of external lateral stabilization on ankle moment control during steady-state walking" (Journal of Biomechanics). Participants walked on a treadmill, with and without external lateral stabilization. Kinematics (thorax and feet) and ground reaction forces were measured. The analysis focuses on ankle moment control as a stability control mechanism during steady-state walking. The "Read me" file in the zipped folder will help you through its contents.

Data from: Negative effects of phosphorus addition override positive effects of arbuscular mycorrhizal fungi on grassland temporal stability

The temporal stability of a plant community in a native grassland ecosystem is affected substantially by soil nitrogen (N) and phosphorus (P) enrichment. However, the interactions between N and P inputs and arbuscular mycorrhizal fungi (AMF) and their effects on the temporal stability of plant productivity have not yet been clarified. In this study, we combined a three-year in situ field experiment with a worldwide meta-analysis to assess the effects of soil fertilisation and AMF on the temporal stability of plant productivity. The addition of P decreased the stability of plant productivity as the standard deviation of plant productivity was increased directly and the temporal stability of C3 grasses was decreased. However, there was no relationship between species richness and the stability, and of plant productivity, rather the stability of the dominant functional group and asynchrony among functional groups were the main drivers changing the stability of change in plant productivity. In both the site-specific experimental data analysis and worldwide meta-analysis, the negative effects of P addition overrode the positive effects of AMF on the temporal stability of plant communities. Overall, our study highlights the importance of soil nutrient availability over AMF in terms of shaping the temporal stability of a plant community. Our results also suggest that anthropogenic soil nutrient enrichment might reduce the temporal stability of plant communities in grassland environments regardless of the existence of AMF.

opennotspecifiedSep 2021View details →

Fig. 1 in Is Phylogeographic Congruence Predicted by Historical Habitat Stability, or Ecological Co-associations?

Fig. 1. Ecological niche models (ENMs) estimated for each of the five species from present-day to Last Glacial Maximum, and climatic stability based on the ENM time series. Color coding uses "warm" colors to indicate areas of highest probability of occurrence, or highest climatic stability. Species names are abbreviated as follows: C.p. (Cryptocercus punctulatus), R.f. (Reticulitermes flavipes), O.d. (Odontotaenius disjunctus), S.s. (Scolopocryptops sexspinosus), and N.a. (Narceus americanus).

opennotspecifiedSep 2021View details →

Fig. 4 in Is Phylogeographic Congruence Predicted by Historical Habitat Stability, or Ecological Co-associations?

Fig. 4. Assessment of phylogeographic structure via comparison of FST (grey bars) versus Φ ST (black bars). All values represent mean differentiation across all pairs of BAPS clusters per species (i.e., "global" values). Species names are abbreviated as in Fig. 1.