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opencc-by-4.0Aug 2020View details →

Dataset_2020_Biogeosciences_Protists and collembolans alter microbial community composition, C dynamics and soil aggregation in simplified consumer - prey systems

Dataset associated to the publication: Erktan, A., Rillig, M.C., Carminati, A., Jousset, A., Scheu, S. (2020) Protists and collembolans alter microbial community composition, C dynamics and soil aggregation in simplified consumer - prey systems, Biogeosciences, accepted the 27/08/2020.

opencc-zeroAug 2020View details →

Disentangling the determinants of transposable elements dynamics in vertebrate genomes using empirical evidences and simulations

The interactions between transposable elements (TEs) and their hosts constitute one of the most profound co-evolutionary processes found in nature. The population dynamics of TEs depends on factors specific to each TE families, such as the rate of transposition and insertional preference, the demographic history of the host and the genomic landscape. How these factors interact has yet to be investigated holistically. Here we are addressing this question in the green anole ( Anolis carolinensis ) whose genome contains an extraordinary diversity of TEs (including non-LTR retrotransposons, SINEs, LTR-retrotransposons and DNA transposons). We observe a positive correlation between recombination rate and TEs frequencies and densities for LINEs, SINEs and DNA transposons. For these elements, there was a clear impact of demography on TE frequency and abundance, with a loss of polymorphic elements and skewed frequency spectra in recently expanded populations. On the other hand, some LTR-retrotransposons displayed patterns consistent with a very recent phase of intense amplification. To determine how demography, genomic features and intrinsic properties of TEs interact we ran simulations using SLiM3. We determined that i) short TE insertions are not strongly counter-selected, but long ones are, ii) neutral demographic processes, linked selection and preferential insertion may explain positive correlations between average TE frequency and recombination, iii) TE insertions are unlikely to have been massively recruited in recent adaptation. We demonstrate that deterministic and stochastic processes have different effects on categories of TEs and that a combination of empirical analyses and simulations can disentangle these mechanisms.

Data from: Why we should care about movements: Using spatially explicit integrated population models to assess habitat source-sink dynamics

1. Assessing the source-sink status of populations and habitats is of major importance for understanding population dynamics and for the management of natural populations. Sources produce a net surplus of individuals (per capita contribution to the metapopulation >1) and will be the main contributors for self-sustaining populations, whereas sinks produce a deficit (contribution < 1). However, making these types of assessments is generally hindered by the problem of separating mortality from permanent emigration, especially when survival probabilities as well as moved distances are habitat-specific. 2. To address this long-standing issue, we propose a spatial multi-event Integrated Population Model (IPM) that incorporates habitat-specific dispersal distances of individuals. Using information about local movements, this IPM adjusts survival estimates for emigration outside the study area. 3. Analyzing 24 years of data on a farmland passerine (the northern wheatear Oenanthe oenanthe) we assessed habitat-specific contributions, and hence the source-sink status and temporal variation of two key breeding habitats, while accounting for habitat- and sex-specific local dispersal distances of juveniles and adults. We then examined the sensitivity of the source-sink analysis by comparing results with and without accounting for these local movements. 4. Estimates of first-year survival, and consequently habitat-specific contributions, were higher when local movement data were included. The consequences from including movement data were sex specific, with contribution shifting from sink to likely source in one habitat for males, and previously noted habitat differences for females disappearing. 5. Assessing the source-sink status of habitats is extremely challenging. We show that our spatial IPM accounting for local movements can reduce biases in estimates of the contribution by different habitats, and thus reduce the overestimation of the occurrence of sink habitats. This approach allows combining all available data on demographic rates and movements, which will allow better assessment of source-sink dynamics and better informed conservation interventions.

opencc-zeroAug 2020View details →

Reactivation of latent infections with migration shapes population-level disease dynamics

Annual migration is common across animal taxa and can dramatically shape the spatial and temporal patterns of infectious disease. Although migration can decrease infection prevalence in some contexts, these energetically costly long-distance movements can also have immunosuppressive effects that may interact with transmission processes in complex ways. Here we develop a mechanistic model for the reactivation of latent infections driven by physiological changes or energetic costs associated with migration (i.e., "migratory relapse") and its effects on disease dynamics. We determine conditions under which migratory relapse can amplify or reduce infection prevalence across pathogen and host traits (e.g., infectious periods, virulence, overwinter survival, timing of relapse) and transmission phenologies. We show that relapse at either the start or end of migration can dramatically increase prevalence across the annual cycle and may be crucial for maintaining pathogens with low transmissibility and short infectious periods in migratory populations. Conversely, relapse at the start of migration can reduce the prevalence of highly virulent pathogens by amplifying culling of infected hosts during costly migration, especially for highly transmissible pathogens and those transmitted during migration or the breeding season. Our study provides a mechanistic foundation for understanding the spatiotemporal patterns of relapsing infections in migratory hosts, with implications for zoonotic surveillance and understanding how infection patterns will respond to shifts in migratory propensity associated with environmental change. Further, our work suggests incorporating within-host processes into population-level models of pathogen transmission may be crucial for reconciling the range of migration–infection relationships observed across migratory species.

Supplementary material 2 from: Laini A, Beermann AJ, Bolpagni R, Burgazzi G, Elbrecht V, Zizka VMA, Leese F, Viaroli P (2020) Exploring the potential of metabarcoding to disentangle macroinvertebrate community dynamics in intermittent streams. Metabarcoding and Metagenomics 4: e51433. https://doi.org/10.3897/mbmg.4.51433

Table S1, Figures S1–S5

Supplementary material 1 from: Laini A, Beermann AJ, Bolpagni R, Burgazzi G, Elbrecht V, Zizka VMA, Leese F, Viaroli P (2020) Exploring the potential of metabarcoding to disentangle macroinvertebrate community dynamics in intermittent streams. Metabarcoding and Metagenomics 4: e51433. https://doi.org/10.3897/mbmg.4.51433

Raw data

opencc-zeroDec 2019View details →

Data from: Dynamic up- and down-regulation of the default (DMN) and extrinsic (EMN) mode networks during alternating task-on and task-off periods

Using fMRI, Hugdahl et al. (2015) reported the existence of a general-domain cortical network during active task-processing which was non-specific to the cognitive task being processed. They labelled this network the extrinsic mode network (EMN). The EMN would be predicted to be negatively, or anti-correlated with the classic default mode network (DMN), typically observed during periods of rest, such that while the EMN should be down-regulated and the DMN up-regulated in the absence of demands for task-processing, the reverse should occur when demands change from resting to task-processing. This would require alternating periods of task-processing and resting, and analyzing data continuously when demands change from active to passive periods and vice versa. We were particularly interested in how the networks interact in the critical transition points between conditions. For this purpose we used an auditory task with multiple cognitive demands in a standard fMRI block-design. Task-present (ON) blocks were alternated with an equal number of task-absent, or rest (OFF) blocks to capture network dynamics across time and changing environmental demands. To achieve this, we specified the onset of each block, and used a finite-impulse response function (FIR) as basis function for estimation of the fMRI-BOLD response. During active (ON) blocks, the results showed an initial rapid onset of activity in the EMN network, which remained throughout the period, and faded away during the first scan of the OFF-block. During OFF blocks, activity in the DMN network showed an initial time-lag where neither the EMN nor the DMN was active, after which the DMN was up-regulated. Studying network dynamics in alternating passive and active periods may provide new insights into brain network interaction and regulation.

Reconstruction of magnetospheric storm-time dynamics using cylindrical basis functions and multi-mission data mining

This zip file contains data used to create figures and tables, describing the results of the paper "Reconstruction of magnetospheric storm-time dynamics using cylindrical basis functions and multi-mission data mining", by N. A. Tsyganenko, V. A. Andreeva, and M. I. Sitnov.

Retinotopic localizer with embedded dynamic macaque faces and walking humans

Retinotopic localizer with embedded dynamic macaque faces and walking humans. From Zhu, Q., & Vanduffel, W. (2019). Submillimeter fMRI reveals a layout of dorsal visual cortex in macaques, remarkably similar to New World monkeys. Proceedings of the National Academy of Sciences of the United States of America, 116(6), 2306–2311. http://doi.org/10.1073/pnas.1805561116

Dataset to study "Social dynamics of values, taboos, and perceived threats around sacred groves in Kurdistan, Iran"

This dataset includes the raw data of a survey of 205 local residents in Kurdistan province, Iran. The "Dataset" sheet presents respondents' socio-demographic characteristics (distance to Baneh city, age group, gender, formal education, traditional lifestyle) and Likert-scale answers (ranging from 1 to 5) on agreement with several statements on values, taboos, and perceived threats around sacred groves in Kurdistan. The full statements are cited in the "Statements" sheet. The complete method is described in: Plieninger, T., Quintas-Soriano, C., Torralba, M., Samani, M.K. & Shakeri, Z. (2020): Social dynamics of values, taboos, and perceived threats around sacred groves in Kurdistan, Iran. People and Nature, in press.

Dissecting the structural dynamics of the nuclear pore complex

Raw mass spectrometry data files for the experiments included in the manuscript "Dissecting the structural dynamics of the nuclear pore complex" by Hakhverdyan et al.

Dynamic encoding of social threat and spatial context in the hypothalamus - calcium activity recordings and behavioural dataset

Social aggression and avoidance are defensive behaviors expressed by territorial animals in a manner appropriate to spatial context and experience. The ventromedial hypothalamus controls both social aggression and avoidance, suggesting that it may encode an general internal state of threat modulated by space and experience. Here we show that neurons in the mouse ventromedial hypothalamus are activated both by the presence of a social threat as well as by a chamber where social defeat previously occurred. Moreover, under conditions where the animal could move freely between a home and defeat chamber, firing activity emerged that predicted the animal's position, demonstrating the dynamic encoding of spatial context in the hypothalamus. Finally, we found that social defeat induced a functional reorganization of neural activity as optogenetic activation could elicit avoidance after, but not before social defeat. These findings reveal how the hypothalamus dynamically encodes spatial and sensory cues to drive social behaviors.

Species interactions across trophic levels mediate rainfall effects on dryland vegetation dynamics

Arid ecosystems are strongly limited by water availability, and precipitation plays a major role in the dynamics of all species in arid regions, as well as the ecosystem processes that occur there. However, understanding how biotic interactions mediate long-term responses of dryland ecosystems to rainfall remains very fragmented. We report on a unique large-scale field experiment spanning 25 years and three trophic levels (plants, small mammal herbivores, predators) in a dryland ecosystem in the northern Chilean Mediterranean Region where we assessed how biotic interactions influence the long-term plant community responses to precipitation. As the most persistent ecological changes in dryland systems may result from changes in the structure, cover, and composition of the perennial vegetation, we emphasized the interplay between bottom-up and top-down controls of perennial plants in our analyses. Rainfall was the primary factor affecting the dynamics of, and interactions among, plants and small mammals. Ephemeral plant cover dynamics closely tracked short-term annual rainfall, but seemed unaffected by top-down controls (herbivory). In contrast, the response of the perennial plant cover to precipitation was mediated by: (i) a complex interplay between subtle top-down (herbivory) controls that become more apparent in the long-term, (ii) competition with ephemeral plants during wet years, and (iii) an indirect effect of predators on subdominant shrubs and perennial herbs. This long-term field experiment highlights how climate-induced responses of arid perennial vegetation are influenced by interactions across trophic levels and temporal scales. In the face of global change, understanding how multi-trophic controls mediate dryland vegetation responses to climate is essential to properly managing the conservation of biodiversity in arid systems.

Landscape mosaic map archive for "Forest cover dynamics in the shifting landscape mosaic of the continental United States from 2001 to 2016"

This data archive contains two zipfiles, each containing a raster map of the continental United States showing the landscape mosaic classification at 30-meter resolution as described in the citing publication.

Supervised molecular dynamics for exploring the druggability of the SARS-CoV-2 spike protein (Topology and .xtc files)

ABSTRACT. The recent outbreak of the respiratory syndrome-related coronavirus (SARS-CoV-2) is stimulating an unprecedented scientific campaign to alleviate the burden of the coronavirus disease (COVID-19). One line of research has focused on targeting SARS-CoV-2 proteins fundamental for its replication by repurposing drugs approved for other diseases. The first interaction between the virus and the host cell is mediated by the spike protein on the virus surface and the human angiotensin-converting enzyme (ACE2). Small molecules able to bind the receptor-binding domain (RBD) of the spike protein and disrupt the binding to ACE2 would offer an important tool for slowing, or even preventing, the infection. Here, we screened 2421 approved small molecules in silico and validated the docking outcomes through extensive molecular dynamics simulations. Out of six drugs characterized as putative RBD binders, the cephalosporin antibiotic cefsulodin was further assessed for its effect on the binding between the RBD and ACE2, suggesting the importance of considering the dynamic formation of the heterodimer when judging any potential candidate.

opengpl-2.0Oct 2020View details →

Data and code from: Long-term effects of colonization-extinction dynamics of generalist versus specialist wodd-decaying fungi

Data and scripts required to fit colonization-extinction models and to run simulations presented in Moor et al. 2020 J Ecol. Scripts use RData files; data is also available i CSV file format.

opencc-by-4.0May 2020View details →

Evolution and lineage dynamics of a transmissible cancer in Tasmanian devils

Devil facial tumour 1 (DFT1) is a transmissible cancer clone endangering the Tasmanian devil. The expansion of DFT1 across Tasmania has been documented, but little is known of its evolutionary history. We analysed genomes of 648 DFT1 tumours collected throughout the disease range between 2003 and 2018. DFT1 diverged early into five clades, three spreading widely and two failing to persist. One clade has replaced others at several sites, and rates of DFT1 co-infection are high. DFT1 gradually accumulates copy number variants (CNVs) and its telomere lengths are short but constant. Recurrent CNVs reveal genes under positive selection, sites of genome instability and repeated loss of a small derived chromosome. Cultured DFT1 cell lines have increased CNV frequency and undergo highly reproducible convergent evolution. Overall, DFT1 is a remarkably stable lineage whose genome illustrates how cancer cells adapt to diverse environments and persist in a parasitic niche.

Simulation of Systems-of-Systems Dynamic Architectures

Video presentation of the paper entitled "Simulation of Systems-of-Systems Dynamic Architectures"  of the Undergraduate Research on Software Engineering Competition in the context of  the Brazilian Symposium on Software Engineering

opencc-zeroOct 2020View details →

Multi year social stability and social information use in reef sharks with diel fission-fusion dynamics: Raw acoustic detection

Animals across vertebrate taxa form social communities and often exist as fission-fusion societies. Central place foragers (CPF) may form social groups, from which they will predictably disperse to forage, either individually or in smaller groups, before returning to fuse with the larger group. However, the function and stability of social associations in predatory fish acting as CPFs is unknown, as individuals do not need to return to a shelter, yet show fidelity to core areas. Using dynamic social networks generated from acoustic tracking data, we document spatially structured sociality in CPF grey reef sharks at a Pacific Ocean atoll. We show that sharks form stable, social groups over multi-year periods, with some dyadic associations consistent for up to four years. Groups primarily formed during the day, increasing in group size before sharks dispersed from the reef to forage at night. Our simulations suggest that multiple individuals sharing a central place and using social information while foraging (i.e. local enhancement), will outperform non-CPF social foragers. We show multiyear social stability in sharks and suggest that social foraging with information transfer could provide a generalisable mechanism for the emergence of sociality with group central place foraging.

Dataset for "Unsupervised Learning of Lagrangian Dynamics from Images for Prediction and Control"

Dataset to reproduce results of "Unsupervised Learning of Lagrangian Dynamics from Images for Prediction and Control"   Abstract: Recent approaches for modelling dynamics of physical systems with neural networks enforce Lagrangian or Hamiltonian structure to improve prediction and generalization. However, when coordinates are embedded in high-dimensional data such as images, these approaches either lose interpretability or can only be applied to one particular example. We introduce a new unsupervised neural network model that learns Lagrangian dynamics from images, with interpretability that benefits prediction and control. The model infers Lagrangian dynamics on generalized coordinates that are simultaneously learned with a coordinate-aware variational autoencoder (VAE). The VAE is designed to account for the geometry of physical systems composed of multiple rigid bodies in the plane. By inferring interpretable Lagrangian dynamics, the model learns physical system properties, such as kinetic and potential energy, which enables long-term prediction of dynamics in the image space and synthesis of energy-based controllers.