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opencc-zeroApr 2022View details →

Source code for dynamic models and simulations of mate sampling behavior

Theory predicts that the strength of sexual selection (i.e., how well a trait predicts mating or fertilization success) should increase with population density, yet empirical support remains mixed. We explore how this discrepancy might reflect a disconnect between current theory and our understanding of the strategies individuals use to choose mates. We demonstrate that the density-dependence of sexual selection predicted by previous theory arises from the assumption that individuals automatically sample more potential mates at higher densities. We provide an updated theoretical framework for the density-dependence of sexual selection by (1) developing models that clarify the mechanisms through which density-dependent mate sampling strategies might be favored by selection and (2) using simulations to determine how sexual selection changes with population density when individuals use those strategies. We find that sexual selection may increase strongly with density if sampling strategies change adaptively in response to density-dependent sampling costs, whereas within-individual plasticity in sampling over time (e.g., due to adaptation to increasing sampling costs as the breeding season progresses) produces weaker density-dependent sexual selection. Our findings suggest that density-dependence of sexual selection depends on the ecological context in which mate sampling has evolved.

opencc-zeroDec 2020View details →

Reproductive strategies affect telomere dynamics across the life course

Because parental care has a heritable basis, the benefits of receiving increased parental provisioning early in life are genetically linked to the costs of providing increased parental provisioning at adulthood. Reproductive strategies thus result in distinct cost-benefit syndromes across the life course that may shape individual health and ageing trajectories. Here we used an artificial selection approach in Japanese quail (Coturnix japonica) to test how reproductive strategies affect telomere length, a biomarker of somatic state, at different life stages. We show that males, but not females, from lines selected for low maternal investment (i.e. developing in a relatively small egg) had shorter telomeres at birth. These patterns were still weakly present at the end of the juvenile growth period. In contrast, significantly shorter telomeres were found in reproductively active adult birds from the high investment lines, suggesting that telomere attrition was accelerated in these individuals once they had become reproductively active. Our study shows that reproductive strategies differentially affect telomere dynamics across the life course, highlighting the role of cross-generational constraints in shaping individual ageing trajectories.

opencc-zeroApr 2022View details →

Data from: Modeling spatiotemporal abundance and movement dynamics using an integrated spatial capture-recapture movement model

Animal movement is a fundamental ecological process affecting the survival and reproduction of individuals, the structure of populations, and the dynamics of communities. Methods to quantify animal movement and spatiotemporal abundances, however, are generally separate and thus omit linkages between individual-level and population-level processes. We describe an integrated spatial capture-recapture (SCR) movement model to jointly estimate (1) the number and distribution of individuals in a defined spatial region and (2) movement of those individuals through time. We applied our model to a study of polar bears (Ursus maritimus) in a 28,125 km2 survey area of the eastern Chukchi Sea, USA in 2015 that incorporated capture-recapture and telemetry data. In simulation studies, the model provided unbiased estimates of movement, abundance, and detection parameters using a bivariate normal random walk and correlated random walk movement process. Our case study provided detailed evidence of directional movement persistence for both male and female bears, where individuals regularly traversed areas larger than the survey area during the 36-day study period. Scaling from individual- to population-level inferences, we found that densities varied from < 0.75 bears/625 km2 grid cell/day in nearshore cells to 1.6–2.5 bears/grid cell/day for cells surrounded by sea ice. Daily abundance estimates ranged from 53–69 bears, with no trend across days. The cumulative number of unique bears that used the survey area increased through time due to movements into and out of the area, resulting in an estimated 171 individuals using the survey area during the study (95% credible interval 124–250). Abundance estimates were similar to a previous multi-year integrated population model using capture-recapture and telemetry data (2008–2016; Regehr et al. 2018). Overall, the SCR-movement model successfully quantified both individual- and population-level space use, including the effects of landscape characteristics on movement, abundance, and detection, while linking the movement and abundance processes to directly estimate density within a prescribed spatial region and temporal period. Integrated SCR-movement models provide a generalizable approach to incorporate greater movement realism into population dynamics and link movement to emergent properties including spatiotemporal densities and abundances.

opencc-by-4.0Apr 2022View details →

Supplementary material for paper "Contribution of the wind and Loop Current Eddies to the circulation in the southern Gulf of Mexico" submitted to journal of Ocean Dynamics

Movie including the time evolution of the daily SSH and surface velocity vector fields in the BoC, the meridional  velocity in the CG zonal section, meridional velocity in the 22°N zonal section, the vq sections at 22°N, the time series of PVF2 and CPFV2 and the time series of daily transport through the CG western arm.

opencc-by-4.0Mar 2022View details →

Results of "Comparison of ice dynamics using full-Stokes and Blatter-Pattyn approximation: application to the Northeast Greenland Ice Stream"

This archive provides ice sheet model output produced as part of the publication: Rückamp, M., Kleiner, T., and Humbert, A.: Comparison of ice dynamics using full-Stokes and Blatter–Pattyn approximation: application to the Northeast Greenland Ice Stream, The Cryosphere, 16, 1675–1696, https://doi.org/10.5194/tc-16-1675-2022, 2022. About the data: The archive contains 2 zipped tar-files for the two 2 different regions 'icestream' and 'outlet'. Each tar-file contains ascii files for the different conducted scenarios. An exemplary filename looks like: FSvsBPlike_icestream_res12800m_E1_SlidingM1_isFS_P1P1GLS_BCstrong.txt 'FSvsBPlike' indicates the general study 'icestream' indicates the region (either icestream or outlet) 'res12800m' indicates the horizontal resolution (ranges from 12800 to 100 meter) 'E1' indicates the enhancement factor used (available values E=0.1, 1, 3 and 6) 'SlidingM1' indicates the employed sliding exponent (available values m=1 and 3) 'isFS' indicates that the full-Stokes equation was employed (either isFS or isBPlike) 'P1P1GLS' describes the employed finite element discretization (either P1P1GLS or P2P1) 'BCstrong' indicates that the strong basal boundary implementation was used (either BCstrong or BCweak) An exemplary file structure looks as follows: % Creation date:      03-May-2022 % Institution:            AWI (Bremerhaven-Germany), BADW (Munich-Germany) % Correspondence: Martin Rueckamp (martin.rueckamp@badw.de), Angelika Humbert (angelika.humbert@awi.de) % Source:                COMSOL version 5.6 (www.comsol.com) % Citation:               Rückamp et al. (2022): https://tc.copernicus.org/preprints/tc-2021-193/ % Projection:           EPSG:3413 (proj4 string: +init=epsg:3413) x(m) y(m) z_s(m) z_b(m) vx_s(m/a) vy_s(m/a) vz_s(m/a) p_s(Pa) vx_b(m/a) vy_b(m/a) vz_b(m/a) p_b(Pa)  301099.83  -1256559.78 1840.83  205.40  -0.031   0.028  -5.456  -157729.374  -2.312   2.076   0.012 14684584.911 ... The fields x, y contain x- and y coordinates of the grid nodes in EPSG:3413 projection. The fields z_s and z_b are the ice surface and ice base, respectively. The fields vx, vy, and vz are the ice velocities in horizontal (x,y) and vertical (z) direction. The field p is the pressure. The subscripts _s and _b indicate the surface and ice base, respectively.

opencc-by-4.0Apr 2022View details →

A Differentiable Dynamic Model for Musculoskeletal Simulation and Exoskeleton Control

An exoskeleton, a wearable device, was designed based on the user's physical and cognitive interactions. The control of the exoskeleton used biomedical signals reflecting user intention as input and its algorithm calculated an output to make the movement smooth. However, the process of transforming the input of biomedical signals, such as electromyography (EMG), into the output of adjusting the torque and angle of the exoskeleton is limited by a finite time lag and precision of trajectory prediction, which result in a mismatch between subject and exoskeleton. Here we propose an EMG-based single-joint exoskeleton system, merging a differentiable continuous system with a dynamic musculoskeletal model. The parameters of each muscle contraction were calculated and applied to the rigid exoskeleton system to predict the precise trajectory. The results revealed accurate torque and angle prediction for the knee exoskeleton and good performance of assistance during movement. Our method outperformed other models by rate of convergence and execution time. In conclusion, a differentiable continuous system merged with a dynamic musculoskeletal model supported effective and accurate performance of an exoskeleton controlled by EMG signals.

Permeability and groundwater flow dynamics in deep-reaching orogenic faults estimated from regional-scale hydraulic simulations

Input file and porosity and permeability datasets to run the case in Figure 3a.

Carbon isotopic constraints on basin-scale vertical and lateral particulate organic carbon dynamics in the northern South China Sea

This dataset includes:(1) Table S1. Time-series of total mass fluxes, POC content, POC fluxes, Lithogeinic matter content,  lithogenic matter flux, C/N mole ratio,as well as the POC isotopic compositions (δ13C, Fm) for sediment trap intercepted sinking particles (n = 59) in the northern South China Sea basin . (2) Table S2. Time-series monthly dust deposition (dry+wet) at station SCS-N of northern South China Sea basin. (3) Table S3. POC content and radiocarbon isotopic compositions for sediment trap intercepted bulk organic carbon from the South China Sea supplementary to one-year time series (2014-2015) published in Blattmann, T.M. et al., 2018. Geophysical Research Letters, 45(17): 9077-9086. (4) Table S4. Time-series clay mineral content and compositions for sediment trap intercepted sinking particles from the South China Sea supplementary to one-year time series (2009-2010) published in Schroeder A. et al., 2015 . Earth Planet. Sci. Lett. 430: 30–42. The dataset is archived in .xlsx data format, consists of four data files with data size of 34 KB.

Data from: Hierarchical variation in phenotypic flexibility across timescales and associated survival selection shape the dynamics of partial seasonal migration

Population responses to environmental variation ultimately depend on within-individual and among-individual variation in labile phenotypic traits that affect fitness, and resulting episodes of selection. Yet, complex patterns of individual phenotypic variation arising within and between time periods, and associated variation in selection, have not been fully conceptualised or quantified. We highlight how structured patterns of phenotypic variation in dichotomous threshold traits can theoretically arise and experience varying forms of selection, shaping overall phenotypic dynamics. We then fit novel multistate models to ten years of band-resighting data from European shags to quantify phenotypic variation and selection in a key threshold trait underlying spatio-seasonal population dynamics: seasonal migration versus residence. First, we demonstrate substantial among-individual variation alongside substantial between-year individual repeatability in within-year phenotypic variation ('flexibility'), with weak sexual dimorphism. Second, we demonstrate that between-year individual variation in within-year phenotypes ('supraflexibility') is structured and directional, consistent with the threshold trait model. Third, we demonstrate strong survival selection on within-year phenotypes, and hence on flexibility, that varies across years and sexes, including episodes of disruptive selection representing costs of flexibility. By quantitatively combining these results, we show how supraflexibility and survival selection on migratory flexibility jointly shape population-wide phenotypic dynamics of seasonal movement.

Data set - Island area and historical geomorphological dynamics shape multifaceted diversity of barrier island floras

<div> The influence of island dynamics and characteristics on taxonomic diversity, particularly species richness, are well studied. Yet, our knowledge on the influence of island dynamics and characteristics on other facets of diversity, namely functional and phylogenetic diversity, is limited, constraining our understanding of assembly processes on islands (e.g., biogeographic history, dispersal and environmental filtering, and species interactions). Using barrier islands, a highly dynamic and so far, understudied island type, we investigate how multiple facets of vascular plant diversity (functional, phylogenetic and taxonomic diversity) are shaped by island geomorphology, modern and historic area, and habitat heterogeneity. In line with our expectation, historical dynamics in island geomorphology affected phylogenetic and taxonomic diversity via habitat heterogeneity. However, island area was the best predictor across all facets of diversity. Specifically, larger islands had higher functional and phylogenetic diversity than expected by chance while most of the smaller islands had lower diversity. The influence of area on functional diversity acted via habitat heterogeneity, with habitat heterogeneity influencing negatively functional diversity. Our results suggest that larger islands accumulate functionally and phylogenetically unique species. Further, results for functional diversity pointed towards potential area-heterogeneity trade-offs, with these trade-offs likely resulting from increased interspecific competition favoring a specific set of trait values (of stronger competitors), particularly on smaller islands. Together, these results demonstrate that going beyond taxonomic diversity contributes to identifying underlying processes shaping diversity-area relationships. </div>

opencc-by-4.0Apr 2022View details →

Chanalyzer: a computational geometry approach for the analysis of protein channel shape and dynamics

Dataset of molecular dynamics trajectories described in the "Chanalyzer: a computational geometry approach for the analysis of protein channel shape and dynamics" work. Trajectories of differently functionalized MscL channel forms.  The *_xyzr.tar.gz files contain the processed frames in the xyzr format, which is a compatible input for NanoShaper The conf.prm file is the parameter file that has been used for the NanoShaper tool

All-atom molecular dynamics simulations of synaptic vesicle fusion I: a glimpse at the primed Synaptotagmin-SNARE-complexin complex

Synaptic vesicles are primed into a state that is ready for fast neurotransmitter release upon Ca2+-binding to Syt1. This state likely includes trans-SNARE complexes between the vesicle and plasma membranes that are bound to Syt1 and complexins. However, the nature of this state and the steps leading to membrane fusion are unclear, in part because of the difficulty of studying this dynamic process experimentally. To shed light into these questions, we performed all-atom molecular dynamics simulations of systems containing trans-SNARE complexes between two flat bilayers or a vesicle and a flat bilayer with or without fragments of Syt1 and/or complexin-1. Our results need to be interpreted with caution because of the limited simulation times and the absence of key components, but suggest mechanistic features that may control release and help visualize potential states of the primed Syt1-SNARE-complexin-1 complex. In particular, the simulations suggest that SNAREs alone induce formation of extended membrane-membrane contact interfaces that may fuse slowly, and that the primed state contains macromolecular assemblies of trans-SNARE complexes bound to the Syt1 C2B domain and complexin-1 in a spring-loaded configuration that prevents premature membrane merger and formation of extended interfaces but keeps the system ready for fast fusion upon Ca2+ influx.

Data and source code from: Contingency and selection in mitochondrial genome dynamics

Eukaryotic cells contain numerous copies of mitochondrial DNA (mtDNA), allowing for the coexistence of mutant and wild-type mtDNA in individual cells. The fate of mutant mtDNA depends on their relative replicative fitness within cells and the resulting cellular fitness within populations of cells. Yet the dynamics of the generation of mutant mtDNA and features that inform their fitness remain unaddressed. Here we utilize long read single-molecule sequencing to track mtDNA mutational trajectories in Saccharomyces cerevisiae. We show a previously unseen pattern that constrains subsequent excision events in mtDNA fragmentation. We also provide evidence for the generation of rare and contentious non-periodic mtDNA structures that lead to persistent diversity within individual cells. Finally, we show that measurements of relative fitness of mtDNA fit a phenomenological model that highlights important biophysical parameters governing mtDNA fitness. Altogether, our study provides techniques and insights into the dynamics of large structural changes in genomes that may be applicable in more complex organisms.

Optimizing Continuous Integration by Dynamic Test Selection

Continuous integration (CI) is widely used in modern software engineering. However, it is  an expensive practice. Some proposed approaches only focus on either intra- or inter-build cost reduction. In this paper, we propose an adaptive technique for dynamic test selection DTS, which combines intra- and inter-build cost reduction techniques. DTS uses build features to construct machine learning models to predict the probability of a specific build failure and transform the probability into the necessary test proportion, with respect to a selected test case prioritization technique. Based on the output of prediction model, it thus selects a prioritized test suite and a variable proportion of test cases with respect to a build. We constructed a large-scale dataset with approximately 115,000 builds, and conducted a controlled experiment using the dataset. The experiment shows that DTS outperforms existing techniques significantly. It detects 19.9% to 32.5% more failed test cases, compared with state-of-the-art techniques evaluated in the experiment. At the same time, DTS performs better than all three existing peer techniques on approximately 47% of projects. Moreover, the experiment also shows that our failure prediction model has an improvement of 0.15 in Area Under Curve (AUC), compared to prior machine learning  models.

Bed topography of the large-scale meandering rivers at dynamic equilibrium state

The simulation results for the bed topography of the 42 large-scale testbed rivers at dynamic equilibrium (along with instantaneous bed shear stress distributions) are presented.

Data Availability - DRAFT - 'Process-based similarity' revealed by discharge-dependent relative submergence dynamics of thousands of large bed elements

Datasets and R code related to confidential manuscript submission entitled "‘Process-based similarity’ revealed by discharge-dependent relative submergence dynamics of thousands of large bed elements". Restrictions apply to the availability of the 2014 DTM and 2D model results, which were used under contractual agreement from the project sponsor. These are available from the senior author with the permission of Yuba Water Agency. Restrictions apply to the availability of the 2014 DTM and 2D model results, which were used under contractual agreement from the project sponsor. These are available from the senior author with the permission of Yuba Water Agency.

opencc-by-4.0Mar 2022View details →

Determination of sub-ps lattice dynamics in FeRh thin films

Open Access Data for "Determination of sub-ps lattice dynamics in FeRh thin films" published in Scientific Reports 12, 8584 (2022) https://doi.org/10.1038/s41598-022-12602-w   Raw data from the XFEL experiment are accessible at https://doi.psi.ch/detail/10.16907%2F85ff2f32-f561-4413-a02a-74abc65cc82b

Transcription feedback dynamics in the wake of cytoplasmic mRNA degradation shutdown

In the last decade, multiple studies demonstrated that cells maintain a balance of mRNA production and degradation, but the mechanisms by which cells implement this balance remain unknown. Here, we monitored cells’ total and recently-transcribed mRNA profiles immediately following an acute depletion of Xrn1—the main 5′-3′ mRNA exonuclease—which was previously implicated in balancing mRNA levels. We captured the detailed dynamics of the adaptation to rapid degradation of Xrn1 and observed a significant accumulation of mRNA, followed by a delayed global reduction in transcription and a gradual return to baseline mRNA levels. We found that this transcriptional response is not unique to Xrn1 depletion; rather, it is induced earlier when upstream factors in the 5′-3′ degradation pathway are perturbed. Our data suggest that the mRNA feedback mechanism monitors the accumulation of inputs to the 5′-3′ exonucleolytic pathway rather than its outputs.

Raw data for: Dynamic instability of dendrite tips generates the highly branched morphologies of sensory neurons

The highly ramified arbors of neuronal dendrites provide the substrate for the high connectivity and computational power of the brain. Altered dendritic morphology is associated with neuronal diseases. Many molecules have been shown to play crucial roles in shaping and maintaining dendrite morphology. Yet, the underlying principles by which molecular interactions generate branched morphologies are not understood. To elucidate these principles, we visualized the growth of dendrites throughout larval development of Drosophila sensory neurons and discovered that the tips of dendrites undergo dynamic instability, transitioning rapidly and stochastically between growing, shrinking, and paused states. By incorporating these measured dynamics into a novel, agent-based computational model, we showed that the complex and highly variable dendritic morphologies of these cells are a consequence of the stochastic dynamics of their dendrite tips. These principles may generalize to branching of other neuronal cell types, as well as to branching at the subcellular and tissue levels.