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opencc-by-4.0Apr 2022View details →

Limited stability of multi-component brines on the surface of Mars

This data package contains all the data used for the following publication:  Limited stability of multi-component brines on the surface of Mars Vincent F. Chevrier Alec Fitting Edgard G. Rivera-Valentín The data are evaporation simulations of multicomponent mixtures of composition as measured by the Phoenix Wet Chemistry Laboratory instrument at various temperatures and for three different models (described in the manuscript).  The organization and detailed description of the data is presented in the text file AAS35439R1_ReadMe.TXT

opencc-by-4.0Nov 2016View details →

Fig. 3 in Development Stability And Cytogenetic Homeostasis Of Perca Fluviatilis (Perciformes, Percidae) In The Rivers Of Rivne Region

Fig. 3. Comparison of Morphological and Cytogenetic Homeostasis Samples of P. fluviatilis in the Rivers of Rivne Region.

opencc-by-4.0Nov 2016View details →

Fig. 1 in Development Stability And Cytogenetic Homeostasis Of Perca Fluviatilis (Perciformes, Percidae) In The Rivers Of Rivne Region

Fig. 1. Frequency of Nuclear Damages of P. fluviatilis Peripheral Blood Erythrocytes in the Rivers in Rivne Region: 1 — Styr River; 2 — Sluch River; 3 — Horyn River; 4 — Ustia River; 5 — Zamchysko River; 6 — Stubelka River; 7 — Ikva River.

opencc-by-4.0Mar 2022View details →

MR Gradient System Long-Term Stability Investigation and Protocol Optimization for Quality Control using Gradient Impulse Response Function (GIRF)

The dataset of the abstract "MR Gradient System Long-Term Stability Investigation and Protocol Optimization for Quality Control using Gradient Impulse Response Function (GIRF)" for ISMRM 2022, London, UK. The data processing code with instructions could be found <a href="https://github.com/BRAIN-TO/girfISMRM2022">here</a>.   Meas1.zip and Meas2.zip contain the first and the second measurements of the raw T2* decay signal acquired with the phantom-based method. Note that the coil dimension has been averaged to save data volume for demonstration purposes. This will lead to a lower SNR of the calculated output gradient and GIRF.   CalculatedGIRF.zip provides the author's pre-calculated GIRFs using the data without coil averaging. This data is used for all the postprocessing (e.g. SNR and stability analysis, etc.) in the published abstract with the source code provided in the same Github repository.

opencc-by-4.0Apr 2022View details →

Data of curvature model for the study of nanoparticle size effects on amyloid fibril stability and molecular dynamics simulations data

The data provided refer to our published article: T. John, J. Adler, C. Elsner, J. Petzold, M. Krueger, L.L. Martin, D. Huster, H.J. Risselada, B. Abel, Mechanistic insights into the size-dependent effects of nanoparticles on inhibiting and accelerating amyloid fibril formation, J. Colloid Interface Sci. 622 (2022), 804–818. <a href="https://doi.org/10.1016/j.jcis.2022.04.134">https://doi.org/10.1016/j.jcis.2022.04.134</a> This article is accompanied by a 'Data in Brief' article that explains in more detail the use of the curvature model and our molecular dynamics (MD) simulations: T. John, L.L. Martin, H.J. Risselada, B. Abel, Curvature model for nanoparticle size effects on peptide fibril stability and molecular dynamics simulation data, Data Brief 45 (2022), 108598. <a href="https://doi.org/10.1016/j.dib.2022.108598">https://doi.org/10.1016/j.dib.2022.108598</a>

opencc-zeroMay 2022View details →

Spatial structure within root systems moderates stability of Arbuscular Mycorrhizal mutualism and plant-soil feedbacks

The persistence of mutualisms is paradoxical, as there are fitness incentives for exploitation. This is particularly true for plant-microbe mutualisms like arbuscular mycorrhizae (AM), which are promiscuously, horizontally-transmitted. Preferential allocation by hosts to the best mutualist can stabilize horizontal mutualisms, however preferential allocation is imperfect, with its fidelity likely depending upon the spatial structure of symbionts in plant roots. In this study, we tested AM mutualisms' dependence on two dimensions of spatial structure: the initial dispersion of fungi and the ease of fungal dispersal, through three complementary experiments. We found that fitness of the beneficial AM fungus increased when fungi were initially separate, while initial spatial mixing benefited the fitness of the non-beneficial fungus. These effects were strongest when dispersal was limited, and hosts could discriminate. Additionally, we found that spatial structure moderated changes in AM fungal composition produced differential feedbacks on plant growth. Our results identify symbiont spatial structure within plant roots as an important modifier of plant preferential allocation and the dynamics of mycorrhizal mutualisms, with cascading effects on plant communities.

opencc-by-4.0Jun 2022View details →

Data from: Plant community stability is associated with a decoupling of prokaryote and fungal soil networks

Data from the manuscript Plant community stability is associated with a decoupling of prokaryote and fungal soil networks: https://doi.org/10.1101/2022.06.21.496867

opencc-by-4.0Jun 2022View details →

Frictional Properties of Opalinus Clay: Influence of Humidity, Normal Stress and Grain-size on Frictional Stability

We designed frictional experiments to characterize the effect exerted by humidity, grain size and normal stress on frictional behaviour of the Opalinus clay fault gouge. We explored a wide range of normal stresses, ranging from 5 to 70 MPa performing velocity up-steps from 1 to 300 μm/s and slide-hold-slide from 1 to 3000s. Our experiments confirms that the OPA clay is weak, with friction coefficients at steady-state of ~0.35 and ~0.41, for 100% RH and 25% RH experiments, respectively. The OPA clay is velocity strengthening over the entire range of applied normal stress. We observe a direct relationship between frictional parameter (a-b) and slip velocity up to 35 MPa where, from there on, (a-b) parameter seems to be velocity independent. As evidenced by the microstructural analysis, we suggest that this behaviour is due to the progressive transition with normal stress, from strain localization and grain size reduction to distributed deformation on well-developed phyllosilicate networks. The amount of relative humidity does not affect deformation mechanisms (i.e. localized or distributed), whereas decreases fault strength and increases fault stability. We hypothesize that this is due to a possible interplay of OPA clay swelling and lubrication, caused by the weakening of chemical bonds between phyllosilicate foliae.  Notably, the initial grain size (< 63 µm or 63 < g.s. < 125 µm) does not affect either the frictional strength or stability, with similar values of dilation upon velocity up-step. Collectively, our mechanical and microstructural observations have allowed us to build a conceptual model that summarizes the main mechanical features of the OPA clay fault gouge. In the context of deep geological repositories (DGR), our results confirm that slow aseismic slip is the most likely slip behaviour for a fault gouge hosted in the OPA clay, with similar mineralogical composition and clay fabric as our samples. Beyond the context of deep geological repositories, this study has also implications for carbon capture and geological storage in the deep subsurface. Indeed, OPA has the characteristics of a low permeability caprock, but faulted, and the integrity of a sealing caprock overlying a storage reservoir can evolve after fault reactivation, potentially generating undesired seismicity and new hydraulic pathways. The data are uploaded are structured as follow: 1) A .txt file of the datafile that is recorded from the machine (raw data) 2) A file in .txt format containing the elaborated data (data_rp)   The data are analyzed using rawPy that can be found at <a href="https://github.com/marcoscuderi/rawPy">https://github.com/marcoscuderi/rawPy</a> For any additional information please do not hesitate to contact the corresponding author Nico Bigaroni at nico.bigaroni@uniroma1.it

opencc-by-4.0Apr 2022View details →

Thermodynamic stability of quinary alloys

This dataset describes the thermodynamic stability of over 65000 hypothetical quinary alloys from the combination of 40 metal elements: <pre><code>['Ag', 'Al', 'As', 'Au', 'Bi', 'Cd', 'Co', 'Cr', 'Cu', 'Fe', 'Ga', 'Ge', 'Hf', 'Hg', 'In', 'Ir', 'Mg', 'Mn', 'Mo', 'Nb', 'Ni', 'Os', 'Pb', 'Pd', 'Pt', 'Re', 'Rh', 'Ru', 'Sb', 'Sc', 'Si', 'Sn', 'Ta', 'Te', 'Ti', 'V', 'W', 'Y', 'Zn', 'Zr']</code></pre>   The stability is assessed through a binary solid solution model for which the enthalpy of mixing is calculated using density functional theory. The binary interaction parameters used for calculating the enthalpy of mixing are provided as a json file (omegas.json). The highest possible synthesis temperature at 90% of the melting point is considered. In addition to the thermodynamic stability, the dataset provides (inverse) energy above hull, enthalpy of mixing, and structure phase among other properties.

opencc-zeroSep 2022View details →

Stability of patch-turnover relationships under equilibrium and nonequilibrium metapopulation dynamics driven by biogeography

Two controversial tenets of metapopulation biology are whether patch quality and the surrounding matrix are more important to turnover (colonization and extinction) than biogeography (patch area and isolation) and whether factors governing turnover during equilibrium also dominate nonequilibrium dynamics. We tested both tenets using 18 years of surveys for two secretive wetland birds, black and Virginia rails, during (1) a period of equilibrium with stable occupancy and (2) after drought and arrival of West Nile Virus (WNV), which resulted in WNV infections in rails, increased extinction and decreased colonization probabilities modified by WNV, nonequilibrium dynamics for both species, and occupancy decline for black rails. Area (primarily) and isolation (secondarily) drove turnover during both stable and unstable metapopulation dynamics, greatly exceeding the effects of patch quality and matrix conditions. Moreover, slopes between turnover and patch characteristics changed little between equilibrium and nonequilibrium, confirming the overriding influences of biogeographic factors on turnover.

Examining the diversity, stability and functioning of marine fish communities across a latitudinal gradient

Aim: As anthropogenic stressors on the biosphere intensify, understanding how communities respond to disturbances is critical. Biodiversity is often thought to promote the stability of communities over time and enhance ecosystem functioning. However, results have been inconsistent, and the multifaceted linkages among diversity, stability, and functioning under acute disturbances remain poorly understood. We experimentally tested the responses of marine fish communities to disturbance (i.e., acute habitat loss) across a diversity gradient spanning 35º degrees of latitude in the western Atlantic Ocean to assess the diversity-stability relationship and the interplay between diversity, stability, and fish biomass recovery (as a proxy for function) in marine fish communities. Location: Western Atlantic Ocean (Maine, Massachusetts, North Carolina, Florida [USA], Belize, and Panama). Time period: 2016 – 2017 Major taxa studied: Small, bottom-dwelling ('cryptobenthic') fishes Results: Diversity showed a negative effect on community stability at both the regional (across docks) and local (within docks) scales. Similarly, local diversity was negatively correlated with ecosystem function. These effects are exacerbated by the habitat loss imposed via our experimental treatment. Main conclusions: Our results suggest that habitat loss may more intensively re-shuffle diverse, tropical communities, which impacts biomass recovery, our proxy of functioning. Contrary to ecological theory, in small-bodied, benthos-associated vertebrate communities, biodiversity may neither promote stability nor functioning, suggesting that human disturbances may be particularly impactful in tropical, high-diversity ecosystems.

opencc-by-4.0Oct 2022View details →

Data for "High-accuracy determination of Paul-trap stability parameters for electric-quadrupole-shift prediction", J. Appl. Phys. 132, 124401 (2022)

Data required to reproduce the key results in: "High-accuracy determination of Paul-trap stability parameters for electric-quadrupole-shift prediction", J. Appl. Phys. 132, 124401 (2022). <a href="https://doi.org/10.1063/5.0106633">https://doi.org/10.1063/5.0106633</a> <ul> <li>The file "sec_freq.dat" contains measured secular frequencies, the rf frequency, the applied bias voltages, and the MJD of the measurement: <ul> <li>Figures 4-5 use rows 31-33 of this data.</li> <li>Figure 6 uses all data corresponding to -1.1e-3 < ax < -0.6e-3.</li> <li>Figure 7(a) uses all the data.</li> </ul> </li> <li>The file "data2021-12-21_MJD.txt" contains the secular frequency data used to derive Eq. (16) and plot Figure 8.</li> <li>The file "RF_monitor_rectifier_1d.txt" contains the rectified monitor voltage used in Figure 8.</li> <li>The file "Temperature_108_1d.txt" contains the helical-resonator temperature used in Figure 8.</li> <li>The file "Fig9_EQS.dat" contains the measured electric quadrupole shift (EQS) used for Figure 9.</li> <li>The file "interleavedEQS.dat" contains the data from the interleaved EQS measurement used to determine a lower value of 1070 for the cancellation factor.</li> </ul>

Structure and stability constrained substitution models outperform traditional substitution models used for evolutionary inference

The current knowledge about how protein structures influence sequence evolution is rarely incorporated into substitution models adopted for phylogenetic inference, which are commonly based on independent with the same substitution process and ignore the known variation of the evolutionary rates across sites with different structural properties. In previous works, we presented site-specific substitution models of protein evolution based on selection on the folding stability of the native state (Stab-CPE), which predict more realistically the evolutionary variability across protein sites. However, those Stab-CPE present qualitative differences from observed data, probably because they ignore changes in the native structure, despite empirical studies suggesting that conservation of the native structure is a strong selective force. Here we present novel structurally constrained substitution models (Str-CPE) based on Julián Echave's model of the structural change due to a mutation as the linear response of the protein to a perturbation and on the explicit model of the perturbation generated by a specific amino-acid mutation. Compared to our previous Stab-CPE models, the novel Str-CPE models are more stringent (they predict lower sequence entropy and substitution rate), provide higher likelihood to multiple sequence alignments (MSA) of the wild-type protein, and better predict the observed substitution rates. Next, we combine Str-CPE and Stab-CPE models to obtain structure and stability constrained substitution models (SSCPE) that fit the empirical MSAs even better. Importantly, these SSCPE models present a relevant improvement of the phylogenetic likelihood for all ten protein families that we analyzed with the program RAxML-NG. We implemented the SSCPE models in the program Prot evol, freely available at <a href="https://github.com/ugobas/Prot_evol">https://github.com/ugobas/Prot_evol</a>.

opencc-by-4.0May 2022View details →

Supplementary Data for: Shifts in food webs and niche stability shaped survivorship and extinction at the end-Cretaceous

This compendium of files includes a list of statistical routines (Data S1) and cleaned fossil datasets from the Paleobiology Database (Data S2 to S3) for the Science Avances paper "Shifts in food webs and niche stability shaped survivorship and extinction at the end-Cretaceous". Data S1 and Data S2 can be opened in Microsoft Office and Data S3 can be imported in R using the load() command. Data S2 and S3 contain the same information (i.e., cleaned fossil datasets) but in different formats (xlsx vs. RData). Please, feel free to send an email to the maintainer Dr. Jorge García Girón (jogarg@unileon.es) if you face any trouble downloading, opening or using these files.

G-matrix stability of clinally diverging populations of an annual weed

How phenotypic and genetic divergence among populations is influenced by the genetic architecture of those traits, and how microevolutionary changes in turn affect the within-population patterns of genetic variation, are of major interest to evolutionary biology. Work on Ipomoea hederacea, an annual vine, has found genetic clines in the means of a suite of ecologically important traits, including flowering time, growth rate, seed mass, and corolla width. Here we investigate the genetic (co)variances of these clinally varying traits in two northern range-edge and two central populations of Ipomoea hederacea to evaluate the influence of the genetic architecture on divergence across the range. We find 1) limited evidence for clear differentiation between Northern and Southern populations in the structure of G, suggesting overall stability of G across the range despite mean trait divergence and 2) that the axes of greatest variation (gmax) were unaligned with the axis of greatest multivariate divergence. Together these results indicate the role of the quantitative genetic architecture in constraining evolutionary response and divergence among populations across the geographic range.

Data for: Associations between leaf developmental stability, canalization and phenotypic plasticity in an architectural perspective

Associations between developmental stability, canalization and phenotypic plasticity have been predicted, but rarely supported by direct evidence. Architectural analysis may provide a more powerful approach to finding correlations among these mechanisms in plants. To investigate the relationships among the three mechanisms in architectural perspective, we subjected plants of Abutilon theophrasti to three densities, measured and calculated fluctuating asymmetry (FA), coefficients of variation (CV) and plasticity (PI) of three leaf traits, to analyze the correlations among these variables. As density increased, mean leaf size, petiole length and angle of most layers and mean leaf FA of some layers decreased (at both stages), CV of petiole angle increased (at day 50), and PI of petiole length and angle across all layers decreased (at day 70); leaf FA and CV of traits generally increased with higher layers at all densities. At both stages, there were more positive correlations between FA and CV at lower vs. high densities; at day 50, little correlation of plasticity with FA or CV was found; at day 70, more positive correlations between FA and PI occurred for response to high vs. low density than for response to medium vs. low density, and more positive correlations between CV and PI occurred at lower vs. high densities. Results suggested that developmental instability, decreased canalization and plasticity can be cooperative and the relationships between decreased canalization and plasticity are more likely to be positive if decreased canalization is due to vibrant growth rather than stressful effects. The relationships of plasticity with developmental instability differed from its relationship with decreased canalization in the way of variation. Decreased canalization should be more beneficial for possible plasticity in the future, while canalization may result from already-expressed plasticity.

Figure 2 -UNDERSTANDING THE MIXING PHENOMENA-FROM STRUCTURAL STABILITY TO CHAOS

In order to assign some basic features of di®erent speci¯c qualitative anal- ysis, let us present in what follows some basic cases of the classic analysis of the 3D mixing model associated to the vortex technology presented above [4]. Since in the classic analysis the target is the study of the e±ciencies e¸ and e´ at successive moments, the analysis is a discrete one, which aims testing the special events that could appear at various, random, values of the versors Mi; Nj . Therefore, the factor (D : D)1=2 which in concrete cases has numerical values, has not an important signi¯cance in the numeric analysis.

Figure 1-UNDERSTANDING THE MIXING PHENOMENA-FROM STRUCTURAL STABILITY TO CHAOS

Starting from the importance of implementation of some optimized tech- nologies for processing the polluted °uids, the bene¯ts of this technology are both of scienti¯c and technologic type [6]. It concerns, one one-hand, ¯nd- ing new physic- mathematical models for describing at optimal parameters the turbulent mixing created by a vorticity structure, and from technologi- cal standpoint, developing the vortex technology for handling the polluting materials.

Figure 9- UNDERSTANDING THE MIXING PHENOMENA-FROM STRUCTURAL STABILITY TO CHAOS

Thus, for the non-periodic °ow, it must be noticed that a little perturbation has a consistent in°uence on the model, going into a far from equilibrium model. If there is annexed the irrationality of the length / surface versors values (an appliance used since the beginning of the mixing study [1,2,3,4]), a globally panel is obtained, with random distributed events. This space-time context consolidates the basic statement that the turbulent mixing °ows must be approached as chaotic systems. This is in fact regaining the idea of a system / model high sensitive to initial conditions.

Figure 6-UNDERSTANDING THE MIXING PHENOMENA-FROM STRUCTURAL STABILITY TO CHAOS

At a ¯rst sight of the graphics, it is obvious that both in discrete and continuous case, the phenomena is not linear; there are relatively linear cases { ¯g. 4,6,7 { but especially non-linear cases { the other pictures;