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opencc-zeroOct 2020View details →

Integrating univariate niche dynamics in species distribution models: a step forward for marine research on biological invasions

Aim The development of approaches to predict the distribution and potential expansion of invasive species is still an open challenge. Here our goal is to improve the modelling procedure for marine invaders by coupling Species Distribution Models (SDMs) with an analysis of their univariate niche dynamics. In particular, we tested for the first time whether choosing model predictors among the stable niche dimensions was effective in improving predictions of invasive species expansion. Location Mediterranean Sea Taxon Dusky spinefoot, Siganus luridus. Methods We analysed the univariate niche dynamics for S. luridus across its native and invaded ranges, by applying a standardized framework that allowed the identification of cases of niche stability or shift. We compared inter-range transferability of SDMs fitted with different combinations of labile or stable predictors. Finally, we evaluated interactions in SDM settings (calibration area, model technique and predictors set) on models' predictive ability, using independent data from the most recent phase of invasion. Results We detected a pattern of niche stability for several variables, especially salinity and bathymetry, which positively influenced model inter-ranges transferability: when the models calibrated in the native range include only stable niche axes, predictive ability is improved. We also identified a shift toward lower surface temperatures in the introduced range, which were almost never experienced by the species before invasion. The model calibrated within the combined ranges was the most ecologically congruent. Also, models calibrated in the invaded range allowed a correct prediction of range expansion, with the predicted suitable areas only slightly underestimated. Main conclusions We provide the first evidence that using conserved predictors in SDMs improves inter-range projections of expanding invasive species. Variable selection, calibration area and modelling technique all matter when modelling invasive species, with important interaction effects. We provide guidelines on how to improve SDMs applications in biological invasion research.

Dual DNA/protein tagging of open chromatin unveils dynamics of epigenomic landscapes in leukemia

The architecture of chromatin specifies eukaryotic cell identity by controlling transcription factor access to sites of gene regulation. Here we describe a dual transposase/peroxidase approach, integrative DNA And Protein Tagging (iDAPT), which detects both DNA (iDAPT-seq) and protein (iDAPT-MS) associated with accessible regions of chromatin. In addition to direct identification of bound transcription factors, iDAPT enables the inference of their gene regulatory networks, protein interactors, and regulation of chromatin accessibility. We applied iDAPT to profile the epigenomic consequences of granulocytic differentiation of acute promyelocytic leukemia, yielding previously undescribed mechanistic insights with potential therapeutic implications. Our findings demonstrate the power of iDAPT as a discovery platform for both the dynamic epigenomic landscapes and their transcription factor components associated with biological phenomena and disease.

opencc-zeroApr 2020View details →

Dynamic effects of insect herbivory and climate on tundra shrub growth: roles of browsing and ramet age

1. To predict shrub responses under climate change in tundra, we need to understand how thermal conditions and herbivory contribute to growth. We hypothesise that shrub growth increases with thermal conditions and precipitation, but that this increase is counteracted by insect herbivory, and that these climate-insect herbivory relationships are modified by both browsing and plant age. 2. We use empirical dynamic modelling (EDM) to analyse a 20-year time series on willow (Salix phylicifolia) shoot growth, growing degree days, summer precipitation and herbivory from an experiment at forest-tundra ecotone. The experiment includes manipulations of avian and mammal browsing (fences) and ramet age (pruning to rejuvenate willows). 3. Negative effects of insect herbivory on willow shoot growth were intensified during warmer years, whereas increasing precipitation led to reduced effects. Moreover, the effect of insect herbivores on shoot growth varied with ramet age and vertebrate browsing: Younger ramets generally experienced less negative insect herbivore effects, whereas Ptarmigan browsing was associated with more positive temperature effect on shoot growth, and reindeer browsing with more negative effects of insect herbivory and precipitation. 4. Synthesis. Our findings show that the negative effects of insect herbivory on shoot growth likely intensify under warmer thermal conditions, but that increasing precipitation can counteract these effects. Moreover, changing thermal conditions, precipitation and vertebrate browsers all have predictable, albeit complex and nonlinear, effects on shrub growth, highlighting the importance of long-term experimental data and flexible analytical methods such as EDM for characterizing climate and community interactions in artic systems.

opencc-zeroOct 2020View details →

Molecular dynamics trajectories for ionic conductors in: Paradigms of frustration in superionic solid electrolytes

Superionic solid electrolytes have widespread use in energy devices, but the fundamental motivations for fast ion conduction are often elusive. Here, we draw upon atomistic simulations of a wide range of halide, oxide, sulfide, and closo-borate superionic conductors to illustrate some of the key features that enhance local cation mobility in these solids. We classify three types of frustration that create competition between different local atomic preferences, thereby flattening the diffusive energy landscape and enhancing entropy. These include chemical frustration, which derives from competing factors in the anion-cation interaction; structural frustration, which is connected to the lack of a clear site preference for mobile ion ordering; and dynamical frustration, which is associated with temporary fluctuations in the energy landscape due to anion orientations or cation reconfigurations. For each class of frustration, we provide detailed simulation analyses of multiple materials to show how ion mobility is facilitated, resulting in stabilizing factors that are both entropic and enthalpic in origin. Implications for identifying suitable descriptors for superionic conductivity are discussed.

opencc-zeroOct 2020View details →

Latent but not absent: the 'long tail' nature of rural special education and its dynamic correction mechanism

The 'long tail' nature of rural special education (RSE) suggests that it simultaneously possesses the private nature of discreteness and the public nature of externalities, which can easily cause provision insufficiency. However, this mismatch may have a dynamic intertemporal correction mechanism impacted by different expenditures of supply sectors (governments and other social sectors). This paper uses different models and data from 30 provinces in China from 2003-2014 to analyze this dynamic correction mechanism. This research finds that different kinds of expenditures from different suppliers have divergent effects on this correction. Capital expenses (especially infrastructure construction) have significantly positive effects on the correction, but administrative expenses have significant dual effects on the correction. These effects may be caused by the various governance efficiencies and motivations of all stakeholders in RSE. This paper concludes that we should pay more attention to the accurate recognition and effective satisfaction of RSE affected by the governance efficiency and motivation of different suppliers to achieve this dynamic correction.

Data from: Ocean warming affected faunal dynamics of benthic invertebrate assemblages across the Toarcian Oceanic Anoxic Event in the Iberian Basin (Spain)

The Toarcian Oceanic Anoxic Event (TOAE; Early Jurassic, ca. 182 Ma ago) represents one of the major environmental disturbances of the Mesozoic and is associated with global warming, widespread anoxia, and a severe perturbation of the global carbon cycle. Warming-related dysoxia-anoxia has long been considered the main cause of elevated marine extinction rates, although extinctions have been recorded also in environments without evidence for deoxygenation. We addressed the role of warming and disturbance of the carbon cycle in an oxygenated habitat in the Iberian Basin, Spain, by correlating high resolution quantitative faunal occurrences of early Toarcian benthic marine invertebrates with geochemical proxy data (δ18O and δ13C). We find that temperature, as derived from the δ18O record of shells, is significantly correlated with taxonomic and functional diversity and ecological composition, whereas we find no evidence to link carbon cycle variations to the faunal patterns. The local faunal assemblages before and after the TOAE are taxonomically and ecologically distinct. Most ecological change occurred at the onset of the TOAE, synchronous with an increase in water temperatures, and involved declines in multiple diversity metrics, abundance, and biomass. The TOAE interval experienced a complete turnover of brachiopods and a predominance of opportunistic species, which underscores the generality of this pattern recorded elsewhere in the western Tethys Ocean. Ecological instability during the TOAE is indicated by distinct fluctuations in diversity and in the relative abundance of individual modes of life. Local recovery to ecologically stable and diverse post-TOAE faunal assemblages occurred rapidly at the end of the TOAE, synchronous with decreasing water temperatures. Because oxygen-depleted conditions prevailed in many other regions during the TOAE, this study demonstrates that multiple mechanisms can be operating simultaneously with different relative contributions in different parts of the ocean.

Gene expression dynamics during rapid organismal diversification of African cichlid fishes

Changes in gene expression play a fundamental role in phenotypic evolution. Transcriptome evolutionary dynamics have so far mainly been compared among distantly related species and remain largely unexplored during rapid organismal diversification, in which gene regulatory changes have been suggested as particularly effective drivers of phenotypic divergence. Here, we studied gene expression evolution in a model system of adaptive radiation, the cichlid fishes of African Lake Tanganyika. By comparing gene expression profiles of six different organs in 74 cichlid species representing all subclades of this radiation, we demonstrate that the rate of gene expression evolution varies among organs, transcriptome parts, and the subclades of the radiation, indicating different strengths of selection. We found that the non-coding part of the transcriptome evolved more rapidly than the coding part, and that the gonadal transcriptomes evolved more rapidly than the somatic ones, with the exception of liver. We further show that the rate of gene-expression change was not constant over the course of the radiation but accelerated at its later phase. Finally, we show that – at the per-gene level – the evolution of expression patterns is dominated by stabilizing selection.

Effect of space diffuser on flow characteristics of a centrifugal pump by computational fluid dynamic analysis

Achieving an optimal configuration of the diffuser is indispensable for high pump performances. In this work, a numerical study on diffuser configuration is conducted for a high pump performance using a computational fluid dynamics code, and the effects of the wrap angle and the relative position of the diffuser vane to the impeller on pump performances are included. The results indicate that the modified diffuser with a suitable wrap angle may improve the pump hydraulic efficiency and the head by approximately 4% and 8%, respectively, while a suitable position of the diffuser vane can enhance the pump head by more than 4%. Meanwhile, the pressure recovery coefficient and the local Euler head of the diffuser are adopted to evaluate the diffuser performance. For a high pump performance, the local Euler head of the diffuser has a peak value at the leading edge with the change rate of zero along the meridian streamline, meaning that no blade loading at the leading edge of the diffuser guarantees a better match between the impeller and the diffuser.

opencc-zeroSep 2021View details →

The dynamic trophic niche of an island bird of prey

Optimal Foraging Theory predicts an inverse relationship between the availability of preferred prey and niche width in animals. Moreover, when individuals within a population have identical prey preferences and preferred prey is scarce, a nested pattern of trophic niche is expected if opportunistic and selective individuals can be identified. Here, we examined intraspecific variation in the trophic niche of a resident population of striated caracara (Phalcoboenus australis) on Isla de los Estados (Staten Island), Argentina, using pellet and stable isotope analyses. While this raptor specializes on seabird prey, we assessed this population's potential to forage on terrestrial prey, especially invasive herbivores as carrion, when seabirds are less accessible. We found that the isotopic niche of this species varies with season, age, breeding status and, to a lesser extent, year. Our results were in general consistent with classic predictions of the Optimal Foraging Theory, but we also explore other possible explanations for the observed pattern. Isotopic niche was broader for groups identified a priori as opportunistic (i.e., non-breeding adults during the breeding season and the whole population during the non-breeding season) than it was for individuals identified a priori as selective. Results suggested that terrestrial input was relatively low, and invasive mammals accounted for no more than 5% of the input. The seasonal pulse of rockhopper penguins likely interacts with caracara's reproductive status by constraining the spatial scale on which individuals forage. Niche expansion in spatially flexible individuals did not reflect an increase in terrestrial prey input, rather it may be driven by a greater variation in the types of marine prey items consumed.

Data associated to the manuscript "Structural and dynamic properties of soda-lime-silica in the liquid phase"

Contains input files and data used to generate the figures of the article: Structural and dynamic properties of soda-lime-silica in the liquid phase Alessandra Serva, Allan Guerault, Yoshiki Ishii, Emmanuelle Gouillart, Ekaterina Burov, and Mathieu Salanne, arXiv, 2009.07198, 2020 https://arxiv.org/abs/2009.07198 The folder *DATA_ASCII_FIGURES* contains the processed data used to plot all the figures of the article.

Spatial variation in early-winter snow cover determines local dynamics in a network of alpine butterfly populations

Snow cover is an extremely variable but critical component of alpine environments. We use long term population data on multiple small populations of the alpine butterfly Parnassius smintheus, combined with high-resolution satellite imagery of meadows, to show a strong link between fine-scale spatial and temporal variation in early-winter snow cover and annual change in butterfly population size, accounting for up to 80 percent of the variation in annual population change. Snow cover in early winter for each meadow is the best predictor of annual adult population change, despite being estimated for a relatively short time-window in late November. We identify a means by which subpopulation response to a local, short-term weather variable can be assessed over a large spatial extent, but also at a resolution relevant to the biology and local dynamics of this alpine species.

SOUTHTRAC-GW: An airborne field campaign to explore gravity wave 1 dynamics at the world's strongest hotspot

This contains the information on the zonal winds measured by the meteor radar at Tierra del Fuego in Argentina during July - December, 2019. Please contact the author for more information.

opencc-zeroDec 2018View details →

Multi-decadal shifts in fish community diversity across a dynamic biogeographic transition zone

Aim: A 21-year fisheries-independent monitoring dataset was used to explore fish community diversity across a latitudinal gradient to quantify how diversity has changed and relate those changes in diversity to changes in the abiotic environment. Additionally, this study spans a biogeographic transition zone, providing insight into future species assemblages across regions of relatively high species diversity. Location: Indian River Lagoon, Florida, USA Methods: Spatial and temporal beta diversity was quantified latitudinally with "best derived breaks" determined by using chronological cluster analyses. Multiple indices of alpha diversity were quantified, including species richness, Shannon diversity, Simpson diversity, and Pielou's evenness. AIC model selection and environmental fit tests were performed to link patterns of diversity and species assemblages with the abiotic environment. Results: Evidence of a biogeographic transition zone was supported by data spanning the entire study period; the largest break in species assemblage occurred near 28°N. Fine scale analyses using small and large seine catches were noisier than broad analyses but indicated a northern shift in location of the biogeographic transition zone. Beta-diversity was generally dominated by species turnover/balance versus nestedness/gradient components, implying that changes were driven by species sorting associated with the physical environment. Excluding the summation of all environmental variables, temperature and dissolved oxygen best describe patterns of diversity and species composition. Main Conclusions: Over years less affected by disturbances, large and small seine catch data suggest the fish community assemblage and location of the biogeographic transition zone has shifted 9 km and 21 km to the north. If the trends observed in these years were to continue from 1999 until the year 2100, a 111 km to 243 km shift in fish communities could be expected. Variation in rates of movement based on gear type suggest novel species assemblages could ensue.

opencc-by-4.0Sep 2020View details →

Dataset related to article "Control of Cytoskeletal Dynamics by β-Arrestin1/Myosin Vb Signaling Regulates Endosomal Sorting and Scavenging Activity of the Atypical Chemokine Receptor ACKR2"

This record contains raw data related to article "Control of Cytoskeletal Dynamics by β-Arrestin1/Myosin Vb Signaling Regulates Endosomal Sorting and Scavenging Activity of the Atypical Chemokine Receptor ACKR2" The atypical chemokine receptor ACKR2, formerly named D6, is a scavenger chemokine receptor with a non-redundant role in the control of inflammation and immunity. The scavenging activity of ACKR2 depends on its trafficking properties, which require actin cytoskeleton rearrangements downstream of a β-arrestin1-Rac1-PAK1-LIMK1-cofilin-dependent signaling pathway. We here demonstrate that in basal conditions, ACKR2 trafficking properties require intact actin and microtubules networks. The dynamic turnover of actin filaments is required to sustain ACKR2 constitutive endocytosis, while both actin and microtubule networks are involved in processes regulating ACKR2 constitutive sorting to rapid, Rab4-dependent and slow, Rab11-dependent recycling pathways, respectively. After chemokine engagement, ACKR2 requires myosin Vb activity to promote its trafficking from Rab11-positive recycling endosomes to the plasma membrane, which sustains its scavenging activity. Other than cofilin phosphorylation, induction of the β-arrestin1-dependent signaling pathway by ACKR2 agonists also leads to the rearrangement of microtubules, which is required to support the myosin Vb-dependent ACKR2 upregulation and its scavenging properties. Disruption of the actin-based cytoskeleton by the apoptosis-inducing agent staurosporine results in impaired ACKR2 internalization and chemokine degradation that is consistent with the emerging scavenging-independent activity of the receptor in apoptotic neutrophils instrumental for promoting efficient efferocytosis during the resolution of inflammation. In conclusion, we provide evidence that ACKR2 activates a β-arrestin1-dependent signaling pathway, triggering both the actin and the microtubule cytoskeletal networks, which control its trafficking and scavenger properties.

opencc-by-4.0Dec 2019View details →

DNA methylation regulates transcription factor specific neurodevelopmental but not sexually dimorphic gene expression dynamics in zebra finch telencephalon

Supplementary Information for the manuscript: "DNA methylation regulates transcription factor specific neurodevelopmental but not sexually dimorphic gene expression dynamics in zebra finch telencephalon"

Data from: Spatial dynamics of alpine treelines under global warming: what explains the mismatch between tree densification and elevational upward shifts at the treeline ecotone?

Aim Most studies focusing on the alpine treeline responses to climate warming have used either the tree densification within the ecotone or its elevational upshift as indicators. However, it is acknowledged that the relation between densification and upshift is spatially heterogeneous, making inferences and comparability among studies tricky. The lack of consistent empirical evidence on this potential mismatch and its drivers leads us to focus on this issue in this study. The aim was twofold: (i) to quantify the mismatch between the two processes at a regional scale, and (ii) to identify its site-specific determinants. Location French eastern Pyrenees Time period 1953-2015 Major taxa studied Pinus uncinata (Ramond ex DC) Methods An object-oriented supervised classification procedure was performed on historical (1953) and current (2015) air-photos. Based on the resulting rasters, densification of the treeline ecotone and upward shift of the treeline were estimated at the two dates in 191 sites, then standardized, before finally being compared. Three site clusters were derived (no mismatch, densification prevalence, upshift prevalence). After having characterized their spatial patterns through join count statistics, a multinomial logistic regression model was computed to identify the correlates of these clusters among a list of site variables. Results No spatial pattern among the categories of responses emerges at a local scale, but buffers with no mismatch tend to aggregate at a larger scale. Changes in minimum air temperatures, site elevation, mean slope, slope morphometry and lithology appear as significant drivers of the observed mismatch, implying that the relation between densification and elevational upshift is context-specific. Main conclusions <a name="_Hlk17817327">Our findings suggest that both </a><a name="_Hlk17816517">densification and upshift </a>should be considered in quantitative analyses of treeline spatial dynamics, since these two ecological processes are not controlled by the same drivers.

Supporting data used in the paper: Xi Chen, 2020, The LMARS based shallow-water dynamical core on generic gnomonic cubed-sphere geometry

# Simulation results of the unstaggered shallow water model This repository contains the supporting data used in the paper: Xi Chen, 2020, The LMARS based shallow‐water dynamical core on generic gnomonic cubed‐sphere geometry, DOI: 10.1029/2020MS002280 Organization of the repository: The tar archive with this data submission has a: doc directory contains a README.md with information regarding naming conventions to label the model configurations for a shallow water test simulation. Additional information can also be found in README.md. Table 4 in the paper provides additional details. The data directory contains the supporting data files (NetCDF format).

Blood test dynamics in hospitalized COVID-19 patients: potential utility of D-dimer for pulmonary embolism diagnosis

SPSS dataset with metadata of the published article in PlosOne and MedRxIv

opencc-by-nd-4.0Nov 2020View details →

The impact of phenotypic heterogeneity of tumour cells on treatment and relapse dynamics - Dataset

This is the dataset used in the manuscript "The impact of phenotypic heterogeneity of tumour cells on treatment and relapse dynamics" by Raatz et al. The code used to generate the data and figures can be found at https://doi.org/10.5281/zenodo.4461667.

WRF data for downscaling, used in Learned multi-resolution dynamical downscaling for precipitation

This study uses regional climate model (RCM) simulated precipitation at low and high spatial resolution, to develop convolution neural network (CNN) based approaches, that can emulate high resolution modeled data using low resolution modeled data with cheaper computational resource than running dynamical downscaling at the high spatial resolution. Specifically, we  define two types of CNNs, one that stacks variables directly and one that encodes each variable before stacking, and train each CNN type both with a conventional loss function, such as  Mean Square Error (MSE), and with a conditional generative adversarial network (CGAN), for a total of four CNN variants. We compare the four new CNN-derived high resolution precipitation with precipitation generated from a bi-linear interpolater and the state-of-the-art CNN-based super-resolution (SR) technique, using the original high resolution precipitation from the RCM as ground truth. We find that SR technique produces similar results to the interpolator with smoother spatial and temporal distributions and smaller data variabilities and extremes than ground truth shows. While the new CNNs trained by MSE generate better results over some regions than the interpolator and SR technique, their predictions are still not as close as ground truth. The CNNs trained by CGAN generate more realistic and physically reasonable results. This advanced technique improves not only the data variability in time and space, and but also the extremes, such as intense and long-lasting events, based on event-feature tracking algorithm.