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The Regional Coupled Suite (RCS): application of a flexible regional coupled modelling framework to the Indian region at km-scale

Supporting data for figures in GMD draft paper: The Regional Coupled Suite (RCS): application of a flexible regional coupled modelling framework to the Indian region at km-scale.

opencc-zeroJan 2022View details →

Community patch‐dynamics governs direct and indirect nutrient recycling by aggregated animals across spatial scales

Animals can have pervasive effects on ecosystems as they modify their biogeochemical and physical environments. In particular, when animals occur in high densities these effects can result in dramatic changes in the physical environment and biogeochemical hotspots or hot moments. While most research to date has focused on the direct role of animals in biogeochemical cycles, few have examined how animals indirectly influence biogeochemical cycles across scales. Freshwater mussels occur as spatially heterogeneous, dense and species-rich aggregations in many river ecosystems worldwide. Here we examined how mussel communities (1) directly influence the flux of particulate and dissolved nutrients and (2) indirectly effect the flux of N2 production, via denitrification, across a gradient of mussel biomass and differences in community composition at the patch- (0.25 m2) and stream reach-scales (60-80 m). We combined measurements of ammonia (N) and soluble reactive phosphorous (P) excretion and C, N, and P biodeposition rates for ten species with biomass and distribution estimates for seven mixed-species aggregations to quantify direct mussel contributions to biogeochemical cycling and the spatial heterogeneity of their impact. Additionally, we sampled sediments at a fine spatial scale to determine how mussel biomass and richness influence potential denitrification (indirect flux) rates at the patch- and reach-scales. We predicted that increasing mussel biomass would lead to greater direct and indirect fluxes of nutrients, manifesting in heterogeneous nutrient redistribution within and among stream reaches. We also predicted that variation in community composition would result in differential nutrient excretion and egestion stoichiometries. Our results indicate that mussel aggregations directly influence soluble and particulate nutrient fluxes with community composition, particularly phylogenetic tribe composition, controlling the stoichiometry. Mussel aggregations also indirectly influenced nutrient fluxes as greater mussel biomass and species richness resulted in higher denitrification rates as mediated by their interactions with the sediments and enhancement of nutrient availability. Our results underscore the importance of patchy communities in acting as biogeochemical control points.

Supplementary dataset and tables for "Carbon-negative production of acetone and isopropanol by gas fermentation at industrial pilot scale"

Supplementary dataset and tables for "Carbon-negative production of acetone and isopropanol by gas fermentation at industrial pilot scale" Supplementary Dataset and Tables listing identified acetone biosynthesis genes from mining of the DJ collection and gene and part sequences used for combinatorial library  and cell-free prototyping (Supplementary Tab. 1), combinatorial library combinations and results (Supplementary Tab. 2), gene KO predictions (Supplementary Tab. 3), cell-free prototyping combinations and results (Supplementary Tab. 4), proteomics results for wild-type strain plus acetone biosynthesis plasmid (Supplementary Tab. 5), proteomics results for strain Δ0553 plus select combinatorial library plasmids (Supplementary Tab. 6), Genbank accession numbers for 272 genomes (Supplementary Tab. 7). sequences of oligonucleotides (Supplementary Tab. 8) and emission factors used to calculate the GHG emissions of acetone (Supplementary Tab. 9) and IPA (Supplementary Tab. 10) in LCA.

Laser-equipped gas reaction chamber for probing environmentally sensitive materials at near atomic scale

Five atom probe datasets as featured in the PLOSone journal concerning the methodology of laser-assisted thermochemical gas treatments of atom probe needles, two comparing the deuterium charged and uncharged states of a steel and comparing various early states of direct hydrogen reduction of FeO.

opencc-zeroJan 2022View details →

Data from: How to date a crocodile – estimation of neosuchian clade ages and a comparison of four time-scaling methods

Clade ages within the crocodylomorph clade Neosuchia have long been debated. Molecular and morphological studies have yielded remarkably divergent results. Despite recent advances, there has been no comprehensive relative comparison of the major time calibration methods available to estimate clade ages based on morphological data. We used four methods (cal3, Extended Hedman [EH], smoothed Ghost-Lineage-Analysis [sGLA] and the Fossilised Birth-Death model [FBD]) to date clade ages derived from a published crocodylomorph supertree and a new neosuchian phylogeny. All time-scaling methods applied here agree on the origination of Neosuchia during the Late Triassic/Early Jurassic, and the presence of the major extant eusuchian groups (Crocodyloidea, Gavialoidea, Alligatoroidea, and Caimaininae) by the end of the Late Cretaceous. The number of distinct lineages present before the K/Pg boundary is less certain, with support for two competing scenarios in which Crocodylinae, Tomistominae and Diplocynodontinae either: 1) diverged from other eusuchian lineages before the K/Pg boundary; or 2) evolved during a 'burst' of diversification after the K/Pg event. Cal3 and FBD are identified as the most suitable methods for time-scaling phylogenetic trees dominated by fossil taxa. Extended Hedman estimates are substantially older than the others, with larger standard deviations and a strong vulnerability to taxon sampling and topological changes. sGLA has similar problems and cannot be recommended either. We conclude that a detailed understanding of phylogenetic relationships, tree reconstruction methods, and good taxonomic coverage (in particular the inclusion of the oldest taxon in each clade) is essential when evaluating the results of such dating analyses.

A dataset of proton kinetic-scale current sheets selected at 1 AU using Wind spacecraft measurements

This is a dataset of proton kinetic-scale current sheets selected at 1 AU using 11 Samples/s magnetic field measurements aboard Wind spacecraft. The current sheets were selected using Partial Variance Increments method.  The detailed analysis of this dataset can be found at https://arxiv.org/abs/2112.15256v1 The first column gives a CS index number, the second panel gives a date in the year/month/day format, the last two columns give  temporal positions of the left and right boundaries of a CS. These moments of times are in seconds from the beginning of the day indicated in the second column.

Microswimmers in turbulent fluid flow of Taylor-scale Reynolds number Re = 21 dataset

The data includes the trajectories and the swimming velocities of individual microswimmers embedded in a turbulent fluid flow of Taylor-scale Reynolds number $Re_{\lambda} = 21$ . The net swimming velocity of a microswimmer is the sum of the intrinsic swimming velocity and the fluid velocity. The intrinsic swimming velocity is dictated by the swimming parameters, that is, the swimming speed $v_s$ and the reorientation time $B$. Different values of swimming parameters are explored. <table> <tbody> <tr> <td>Item</td> <td>$v_s$</td> <td>$B$</td> </tr> <tr> <td>R1</td> <td>2.20</td> <td>10</td> </tr> <tr> <td>R2</td> <td>0</td> <td>0</td> </tr> <tr> <td>R3</td> <td>2.20</td> <td>30</td> </tr> <tr> <td>R4</td> <td>2.20</td> <td>50</td> </tr> <tr> <td>R5</td> <td>1.10</td> <td>10</td> </tr> <tr> <td>R6</td> <td>0.22</td> <td>10</td> </tr> <tr> <td>R7</td> <td>4.39</td> <td>10</td> </tr> <tr> <td>R8</td> <td>1.76</td> <td>10</td> </tr> <tr> <td>R9</td> <td>2.85</td> <td>10</td> </tr> <tr> <td>R10</td> <td>6.58</td> <td>10</td> </tr> <tr> <td>R11</td> <td>2.20</td> <td>20</td> </tr> <tr> <td>R12</td> <td>5.49</td> <td>10</td> </tr> <tr> <td>R13</td> <td>3.29</td> <td>10</td> </tr> <tr> <td>R14</td> <td>3.60</td> <td>10</td> </tr> </tbody> </table> Each column in the file corresponds to the position and net velocity of particles, the fluid vorticity at particle location, particle id, and time step. <table> <tbody> <tr> <td>column number</td> <td>item</td> </tr> <tr> <td>0</td> <td>x - position</td> </tr> <tr> <td>1</td> <td>y - position</td> </tr> <tr> <td>2</td> <td>z - position</td> </tr> <tr> <td>3</td> <td>x - velocity</td> </tr> <tr> <td>4</td> <td>y - velocity</td> </tr> <tr> <td>5</td> <td>z - velocity</td> </tr> <tr> <td>15</td> <td>x - vorticity</td> </tr> <tr> <td>16</td> <td>y - vorticity</td> </tr> <tr> <td>17</td> <td>z - vorticity</td> </tr> <tr> <td>19</td> <td>particle id</td> </tr> <tr> <td>20</td> <td>time step</td> </tr> </tbody> </table>

Microswimmers in turbulent fluid flow of Taylor-scale Reynolds number Re = 59 dataset

The data includes the trajectories and the swimming velocities of individual microswimmers embedded in a turbulent fluid flow of Taylor-scale Reynolds number $Re_{\lambda} = 59$ . The net swimming velocity of a microswimmer is the sum of the intrinsic swimming velocity and the fluid velocity. The intrinsic swimming velocity is dictated by the swimming parameters, that is, the swimming speed $v_s$ and the reorientation time $B$. Different values of swimming parameters are explored. <table> <tbody> <tr> <td>Item</td> <td>$v_s$</td> <td>B</td> </tr> <tr> <td>Tr</td> <td>0</td> <td>0</td> </tr> <tr> <td>T13</td> <td>1</td> <td>10</td> </tr> <tr> <td>T16</td> <td>3</td> <td>10</td> </tr> <tr> <td>T18</td> <td>5</td> <td>10</td> </tr> <tr> <td>T19</td> <td>10</td> <td>0.3</td> </tr> <tr> <td>T25</td> <td>10</td> <td>1</td> </tr> <tr> <td>T27</td> <td>10</td> <td>3</td> </tr> <tr> <td>T29</td> <td>10</td> <td>10</td> </tr> <tr> <td>T30</td> <td>30</td> <td>10</td> </tr> <tr> <td>T31</td> <td>10</td> <td>30</td> </tr> <tr> <td>T33</td> <td>10</td> <td>50</td> </tr> <tr> <td>T38</td> <td>20</td> <td>10</td> </tr> <tr> <td>T43</td> <td>15</td> <td>10</td> </tr> <tr> <td>T50</td> <td>25</td> <td>10</td> </tr> <tr> <td>T56</td> <td>8</td> <td>10</td> </tr> </tbody> </table> Each column in the file corresponds to the position and net velocity of particles, the fluid vorticity at particle location, particle id, and time step.   <table> <tbody> <tr> <td>column number</td> <td>item</td> </tr> <tr> <td>0</td> <td>x - position</td> </tr> <tr> <td>1</td> <td>y - position</td> </tr> <tr> <td>2</td> <td>z - position</td> </tr> <tr> <td>3</td> <td>x - velocity</td> </tr> <tr> <td>4</td> <td>y - velocity</td> </tr> <tr> <td>5</td> <td>z - velocity</td> </tr> <tr> <td>15</td> <td>x - vorticity</td> </tr> <tr> <td>16</td> <td>y - vorticity</td> </tr> <tr> <td>17</td> <td>z - vorticity</td> </tr> <tr> <td>19</td> <td>particle id</td> </tr> <tr> <td>20</td> <td>time step</td> </tr> </tbody> </table>

Large-scale conformational changes of FhaC provide insights into the two-partner secretion mechanism

This dataset contains raw and processed data and analyses related to the manuscript "Large-scale conformational changes of FhaC provide insights into the two-partner secretion mechanism" by the authors. A preprint of this manuscript is available on bioRxiv (https://doi.org/10.1101/2021.11.09.467682).

opencc-zeroJan 2022View details →

Data and code from: Traits and phylogenies modulate the environmental responses of wood-inhabiting fungal communities across spatial scales

Identifying the spatial scales at which community assembly processes operate is fundamental for gaining a mechanistic understanding of the drivers shaping ecological communities. In this study, we examined whether and how traits and phylogenetic relationships structure fungal community assembly across spatial scales. We applied joint species distribution modelling to a European-scale dataset on 215 wood-inhabiting fungal species, which includes data on traits, phylogeny and environmental variables measured at the local (log-level) and regional (site-level) scales. At the local scale, wood-inhabiting fungal communities were mostly structured by deadwood decay stage, and the trait and phylogenetic patterns along this environmental gradient suggested the lack of diversifying selection. At regional scales, fungal communities and their trait distributions were influenced by climatic and connectivity-related variables. The fungal climatic niches were not phylogenetically structured, suggesting that diversifying selection or stabilizing selection for climatic niches has played a strong role in wood-inhabiting communities. In contrast, we found a strong phylogenetic signal in the responses to connectivity-related variables, revealing phylogenetic homogenization in small and isolated forests. Altogether, our results show that species-level traits and phylogenies modulate the responses of wood-inhabiting fungi to environmental processes acting at different scales. This result suggests that the evolutionary histories of fungal traits diverge along different environmental axes.

Large-scale temporal graph datasets

Large scale datasets used for evaluation in the article: `Optimizing the Interval-centric Distributed Computing Model for Temporal Graph Algorithms` to appear in `EuroSys 2022`.

Example data and scripts for the paper: Team maturity and reorganization during a very large-scale agile transformation in the automotive industry

Example data and scripts for the paper: Team maturity and reorganization during a very large-scale agile transformation in the automotive industry.

100 Hz ROCS microscopy correlated with fluorescence reveals cellular dynamics on different spatiotemporal scales

Image Datasets to 100 Hz ROCS microscopy correlated with fluorescence reveals cellular dynamics on different spatiotemporal scales

Data set for the article 'Temporal scaling in C. elegans larval development'

This directory contains all analyzed data and data analysis scripts to create all figures for the article Filina et al., Temporal scaling in C. elegans larval development, PNAS 2022 119:e2123110119

On the scale dependence in the dynamics of frictional rupture: constant fracture energy versus size-dependent breakdown work

<pre>Potential energy stored during the inter-seismic period by tectonic loading around faults is released during earthquakes as radiated energy, frictional dissipation and fracture energy. The latter is of first importance since it is expected to control the nucleation, the propagation and the arrest of the seismic rupture. On one side, the seismological fracture energy estimated for natural earthquakes (commonly called breakdown work) ranges between 1 $\mathrm{J/m^2}$ and tens of $ \mathrm{MJ/m^2} $ for the largest events, and shows a clear slip dependence. On the other side, recent experimental studies highlighted that, concerning rupture experiments, fracture energy is a material property (energy required to break the fault interface) independently of the size of the event, i.e. of the seismic slip. </pre> <pre>To reconcile these contradictory observations and definitions, we performed stick-slip experiments, as analog for earthquakes, in a bi-axial shear configuration. We estimated fracture energy through both Linear Elastic Fracture Mechanics (LEFM) and a Cohesive Zone Model (CZM) and through the integration of the near-fault stress-slip evolution. We show that, at the scale of our experiments, fault weakening is divided into a near-tip weakening, corresponding to an energy of few $ \mathrm{J/m^2} $, consistent with the one estimated through LEFM and CZM, and a long-tailed weakening corresponding to a larger energy not localized at the rupture tip, increasing with slip.</pre> <pre>Through numerical simulations, we demonstrate that only near-tip weakening controls the rupture initiation and that long-tailed weakening can enhance slip during rupture propagation and allow the rupture to overcome stress heterogeneity along the fault. We conclude that the origin of the seismological estimates of breakdown work could be related to the energy dissipated in the long-tailed weakening rather than to the one dissipated near the tip.</pre>

Dissociable Multi-scale Patterns of Development in Personalized Brain Networks

The brain is organized into networks at multiple resolutions, or scales, yet studies of functional network development typically focus on a single scale. Here, we derived personalized functional networks across 29 scales in a large sample of youths (n=693, ages 8-23 years) to identify multi-scale patterns of network re-organization related to neurocognitive development. We found that developmental shifts in inter-network coupling systematically adhered to and strengthened a functional hierarchy of cortical organization. Furthermore, we observed that scale-dependent effects were present in lower-order, unimodal networks, but not higher-order, transmodal networks. Finally, we found that network maturation had clear behavioral relevance: the development of coupling in unimodal and transmodal networks are dissociably related to the emergence of executive function. These results demonstrate that the development of functional brain networks align with and refine a hierarchy linked to cognition

opencc-zeroFeb 2022View details →

Data from: Scale-dependence of landscape heterogeneity effects on plant invasions

Invasive alien species are amongst the most concerning threats to native biodiversity worldwide, and the level of landscape heterogeneity is considered to affect spatial patterns of their occurrence and spread. However, as previous studies on these associations report contrasting results, the role of landscape heterogeneity on its susceptibility to invasions remains poorly understood. Landscape heterogeneity is usually described by two measures: configuration and composition. Both measures may differently affect invasive species and these impacts may be additionally scale-dependent. Nevertheless, their relative contribution to invasion patterns is poorly known. We investigated the effect of two landscape heterogeneity components: configuration (edge density) and composition (number and evenness of land-cover types) measured at different spatial scales (from within 0.25 km to 5 km of the studied localities) on the local abundance of one of the most invasive alien plant species in Europe, the North American goldenrods (Solidago canadensis and S. gigantea). Using publicly available geospatial environmental data and a novel method based on remote analysis of Google Street View images, we collected and analyzed large dataset on goldenrod occurrence along 1347 roadside transects in agricultural landscapes of Poland. Both the compositional and configurational heterogeneity were positively associated with the local abundance of goldenrods, however the effect size of these relationships was dependent on spatial scale. While abundance-heterogeneity associations were most pronounced at the largest spatial scale for compositional heterogeneity, the pattern was the opposite for configurational heterogeneity. Landscape heterogeneity is a clear correlate of plant invasion potential, with occurrences of invasive plants generally higher in more heterogeneous landscapes. However, scale-dependence of this association means that researchers and practitioners may miss the association if only concentrating on a single spatial scale. While increasing heterogeneity of rural landscapes is widely introduced as a way to promote farmland biodiversity, we show that it may also support invasive plants and thus conflict with original goals of biodiversity-oriented strategies. Therefore, we suggest implementing regular management and eradication schemes in most heterogeneous landscapes. Finally, we demonstrate how remote analysis of plant invasions using existing imagery can advance our understanding of invasion biology.

Large-scale dataset for the analysis of outdoor-to-indoor propagation for 5G mid-band operational networks

We present a comprehensive dataset of channel measurements, performed to analyze outdoor-to-indoor propagation characteristics in the mid-band spectrum identified for the operation of 5th Generation (5G) cellular systems. The dataset includes measurements of channel power delay profiles from two 5G networks operating in Band n78, i.e., 3.3--3.8 GHz. Such measurements were collected at multiple locations in a large office building in the city of Rome, Italy, by using the Rohde & Schwarz (R&S) network scanner TSMA6 for several weeks in 2020 and 2021. A primary goal of the dataset is to provide an opportunity for researchers to investigate a large set of 5G channel measurements, aiming at analyzing the corresponding propagation characteristics towards the definition and refinement of empirical channel propagation models.

openother-openMar 2022View details →

Data and Code for: Validating ATLAS: a regional-scale high-throughput tracking system

Data and code for the manuscript: Validating ATLAS: a regional-scale high-throughput tracking system