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openother-openOct 2021View details →

DIAeT - Synthesizing Evidence from Clinical Trials with Dynamic Interactive Argument Trees

Synthesizing Evidence from Clinical Trials with Dynamic Interactive Argument Trees

opennotspecifiedOct 2021View details →

Figure 1 in Occupation dynamics and nesting behaviours of Xylocopa frontalis (Olivier) (Hymenoptera: Apidae) in artificial shelters

Figure 1. Temporal variation of the number of Xylocopa frontalis nesting females and the number of brood cells produced in the shelters at the Panga Ecological Station (PES) and at the Água Limpa Experimental Farm (ALEF) from April 2012 to March 2013.

opencc-by-4.0Dec 2020View details →

SARS-CoV-2 exposure in Malawian blood donors: an analysis of seroprevalence and variant dynamics between January 2020 and July 2021

Results of population-based age stratified seroepidemiological investigation in Malawi.

opencc-by-4.0Nov 2021View details →

Molecular Dynamics Study on the Shock Induced Spallation of Polyethylene

This repository contains the LAMMPS models (data files) we used in our recent work. More information and the required LAMMPS files to run shock simulations are available here: https://github.com/nuwan-d/shock_response_pe

opencc-by-4.0Nov 2021View details →

Typical & Extreme Meteorological Year and Heatwaves for Dynamic Building Simulations in Belgium based on MAR model Simulations

This dataset contains 3 types of files for 12 cities (v.1.0) in Belgium: <ul> <li>Typical Meteorological Year</li> <li>Extreme Meteorological Year</li> <li>Heatwave Events</li> </ul> These files were produced from simulations of the MAR model forced by the ERA5 reanalyses over the period 1980-2020 but also by 3 ESMs from the CMIP6 database, namely BCC-CSM2-MR, MPI-ESM.1.2, and MIROC6 over the period 1980-2100. The available data for version 1.0 concerns 12 cities in Belgium but may be increased in future versions of this dataset. A detailed description of the methods used has been submitted as an article in the ESSD journal (S. Doutreloup et al., Historical and Future Weather Data for Dynamic Building Simulations in Belgium using the MAR model: Typical & Extreme Meteorological Year and Heatwaves, Earth Syst. Sci. Data, 2021).

Patch size distribution affects species invasion dynamics in dendritic networks

<div class="page"> <div class="section"> <div class="layoutArea"> <div class="column"> Biological invasions are globally affecting ecosystems, causing local species loss and altering ecosystem functioning. Understanding how such biological invasions occur and succeed is thus of high priority. Both local properties and the spatial network structure have been shown to be determinants of invasion success, and the identification of spatial invasion hubs directly promoting invasion dynamics is gaining attention. Spatial dynamics, however, could also indirectly alter invasion success by shaping pre- invasion local community structure: in many ecosystems, such as riverine networks, regional properties such as patch size distribution are known drivers of local community structures, which themselves may affect the establishment success of invading species. Using microcosm experiments in dendritic networks, we disentangled how inherent patch size distribution and dispersal along specific network topologies shaped local resident communities, and, subsequently, affected the establishment success of invading species. After controlling for regional-scale effects of connectivity on pre-invasion diversity, we find that patch size distributions independently shaped pre-invasion community diversity and invasion success, with no direct effect of pre-invasion diversity on invasion success. Our results suggest that 1) landscape configuration plays an underestimated role in invasion success and that 2) invasion success should follow predictable landscape-scale patterns in riverine networks given non-random patch-size distribution. </div> </div> </div> </div>

Supplementary material 1 from: Mally R, Ward SF, Trombik J, Buszko J, Medzihorský V, Liebhold AM (2021) Non-native plant drives the spatial dynamics of its herbivores: the case of black locust (Robinia pseudoacacia) in Europe. NeoBiota 69: 155-175. https://doi.org/10.3897/neobiota.69.71949

Table S1. First record locations of Parectopa robiniella, Macrosaccus robiniella and Obolodiplosis robiniae from Europe.

Wildland-urban interface fire dynamics simulator input files for pyric tree spatial patterning interactions in historical and contemporary mixed conifer forests, California, USA

Tree spatial patterns in dry coniferous forests of the western US, and analogous ecosystems globally, were historically aggregated, comprising a mixture of single trees and groups of trees. Modern forests, in contrast, are generally more homogeneous and overstocked than their historical counterparts. As these modern forests lack regular fire, pattern formation and maintenance is generally attributed to fire. Accordingly, fires in modern forests may not yield historically analogous patterns. However, direct observations on how selective tree mortality among pre-existing forest structure shapes tree spatial patterns is limited. In this study, we (1) simulated fires in historical and contemporary counterpart plots in a Sierra Nevadan mixed-conifer forest, (2) estimated tree mortality, and (3) examined tree spatial patterns of live trees before and after fire, and of fire-killed trees. Tree mortality in the historical period was clustered and density-dependent, because trees were aggregated and segregated by tree size before fire. Thus, fires maintained an aggregated distribution of tree groups. Tree mortality in the contemporary period was widespread, except for dispersed large trees, because most trees were a part of large, interconnected tree groups. Thus, post-fire tree patterns were more uniform and devoid of moderately sized tree groups. Post-fire tree patterns in the historical period, unlike the contemporary period, were within the historical range of variability identified for the western US. This divergence suggests that decades of forest dynamics without significant disturbances has altered the historical means of pyric pattern formation. Our results suggest that ecological silvicultural treatments, such as forest restoration thinnings, which emulate qualities of historical forests may facilitate the reintroduction of fire as a means to reinforce forest structural heterogeneity.

opencc-zeroNov 2022View details →

Regionalized dynamic climate series for ecological climate impact research in modern controlled environment facilities

Modern controlled environment facilities (CEFs) enable the simulation of dynamic microclimates in controlled ecological experiments through their technical ability to precisely control multiple environmental parameters. However, few CEF studies exploit the technical possibilities of their facilities, as climate change treatments are frequently applied by static manipulation of an inadequate number of climate change drivers, ignoring intra-annual variability and co-variation of multiple meteorological variables. We present so called Test Reference Years (TRY) that consist of typical annual cycles of temperature, relative humidity, air pressure, global radiation, photosynthetically active photon flux density, tropospheric ozone concentration and CO2. The TRYs represent possible annual cycles of a reference period (1987-2016) and the two contrasting climate scenarios RCP2.6 and RCP8.5.

High resolution dynamic mapping of the C. elegans intestinal brush border

The intestinal brush border is made of an array of microvilli that increases the membrane surface area for nutrient processing, absorption, and host defense. Studies on mammalian cultured epithelial cells uncovered some of the molecular players and physical constrains required to establish this apical specialized membrane. However, the building and maintenance of a brush border in vivo has not been investigated in detail yet. Here, we combined super-resolution imaging, transmission electron microscopy and genome editing in the developing nematode C. elegans to build a high-resolution and dynamic localization map of known and new brush border markers. Notably, we show that microvilli components are dynamically enriched at the apical membrane during microvilli outgrowth and maturation but become highly stable once microvilli are built. This new toolbox will be instrumental to understand the molecular processes of microvilli growth and maintenance in vivo as well as the effect of genetic perturbations, notably in the context of disorders affecting brush border integrity.

Population dynamics of the glacial relict amphipod Monoporeia affinis in a subarctic lake

Seasonal and interannual (2002–2019) variations in the abundance (ind. m-2) and population structure of the glacial relict amphipod Monoporeia affinis in a small subarctic Lake Krivoe (North-West of the Russian Federation) are presented. The study site (66⁰ 20.774′ N and 33⁰ 37.77′ E) was situated in the sublittoral zone at the depth of 8.5 m. Materials were collected from June 2002 to December 2019 mainly during the ice-free period (late May – October) as a rule, 4–5 times a season. In addition, the next data sets used in interpretation of population dynamics are presented: (1) Changes in mean near- bottom (7–8 m) temperature (± range) and mean chlorophyll a (0–7 m) concentration (µg l-1) gat study site during open-water period (May – October) in 2002–2019. (2) Changes in mean annual abundance (ind. m-2) of main macrobenthic taxa at study site in 2002–2019.

A tangled web: comparing inter- and intraspecific mating dynamics in Anasa squash bugs

Reproductive interference, reproductive interactions between heterospecific individuals including mating, is commonly reported across taxa but its drivers are still unclear. Studying heterospecific matings in the context of their conspecific mating system— by relating an individual's conspecific mating behavior to its heterospecific interactions— offers a powerful approach to address this uncertainty. Here we compare inter- and intraspecific mating dynamics in the squash bug Anasa tristis and its close relative Anasa andresii under semi-natural conditions. Using replicated enclosures, we surveyed the mating behavior of individually marked A. tristis and A. andresii bugs (5 males and 5 females of each species per trial) at hourly intervals using a robotic camera system over a 14-day period. We uncovered high levels of reproductive interference (19% of individuals engaged in heterospecific matings) but the majority of mating activity took place between conspecifics. A. tristis females which engaged in heterospecific matings had comparable hatching success with those which did not. Therefore, in this system, relatively high levels of reproductive interference may emerge under semi-natural conditions as a byproduct of limited intraspecific pre-copulatory choice paired with limited fitness penalties for at least one of the species involved.

Weather driven demography and population dynamics of an endemic perennial plant during a 34-year period

1. Increased anthropogenic influence on the environment has accentuated the need to assess how climate and other environmental factors drive vital rates and population dynamics of different types of organisms. However, to allow distinction between effects of multiple correlated variables, and to capture the effects of rare and extreme climatic conditions, studies extending over decades are often necessary. 2. In this study we used an individual-based dataset collected in three populations of Pulsatilla vulgaris subsp. gotlandica during 34 years, to explore the effects of variation in precipitation and temperature on vital rates and population dynamics. 3. Most of the observed conspicuous variation in flowering among years was associated with differences in precipitation and temperature in the previous summer and autumn with a higher incidence of flowering following summers with high precipitation and low temperatures. In contrast, climatic variables had no significant effects on individual growth or survival. 4. Although the weather-driven variation in flowering had only moderate absolute effects on the population growth rate, simulated persistent changes in average precipitation and temperature resulted in considerable reductions in population sizes compared with current conditions. Analyses carried out with with subsets of data consisting of 5 and 10 years yielded results that strongly deviated from those based on the full data set. 5. Synthesis: The results of this study illustrate the importance of long-term demographic monitoring to identify key climatic variables affecting vital rates and driving population dynamics in long-lived organisms.

Molecular Dynamics of HLA-A 02:01 with neoantigen and wild-type peptides from AKP6 and ASTN1 genes.

Molecular Dynamics simulations of 4 complexes : 1. Protein HLA-A*02:01 with the wild-type peptide WLIDMESLV from AKP6 gene. 2. Protein HLA-A*02:01 with the neoantigen peptide WLIDMKSLV from AKP6 gene. 3. Protein HLA-A*02:01 with the neoantigen peptide KLYGLDWAEL from ASTN1 gene. 4. Protein HLA-A*02:01 with the wild-type peptide KPYGLDWAEL from ASTN1 gene.

Data for "Modeling the short-term fire effects on vegetation dynamics and surface energy in southern Africa"

This is the data used for "Modeling the short-term fire effects on vegetation dynamics and surface energy in southern Africa using the improved SSiB4/TRIFFID-Fire model". The data includes two folders: fireon and fireoff representing the scenarios with the fire model turned on and off. Each folder includes 14 years of data from 2000-2013.

Supplementary material 2 from: Cook RT, Ward SF, Liebhold AM, Fei S (2021) Spatial dynamics of spotted lanternfly, Lycorma delicatula, invasion of the Northeastern United States. NeoBiota 70: 23-42. https://doi.org/10.3897/neobiota.70.67950

Figure S2. Distributions of anthropogenic predictor variables used in Cox proportional hazards moder development

opencc-by-4.0Oct 2021View details →

Data and output files for the paper, "Dynamical systems inference at scale reveals intrinsic instability in the dysbiotic microbiome"

The above files contain the output of the model, which we call MDSINE2, developed in the paper titled, "Dynamical systems inference at scale reveals intrinsic instability in the dysbiotic microbiome" (See https://github.com/gerberlab/MDSINE2_Paper for implementation details). More specifically, forward_sims.tgz contains the output of forward simulations in .npy format; mixed_prior_fixed.tgz contains the pickle files corresponding to the output of the MCMC simulations for fixed topology; mixed_prior_unfixed.tgz contains the pickle files corresponding to the output of the MCMC simulations for unfixed topology; other_files contains information on eigenvalues and cycles, results for Phylogenetic Neighborhood Analysis, Keystoneness Analysis and the output in .npy format for comparator methods; ASV_OTU_aggregate_and_plylogeneteic trees contains the plots of trajectories (relative abundance) of OTUS and their constituent ASVs, and of phylogenetic trees.

Neural dynamics model testing dataset

These datasets are used to reproduce the results of the neural dynamics model from the paper https://doi.org/10.1101/725382.

Population structure and dynamics, breeding activity and phenology of the blue-sided treefrog (Agalychnis annae)

Agalychnis annae is a species endemic to Costa Rica and Panama with populations shrinking or disappearing from several locations. We studied the reproduction of a relict population of A. annae in a 1,300 m2 natural pond in Costa Rica during 2007–2008. We marked adults with a visible implant alphanumeric tag injected in the thigh. We measured reproductive effort considering calling males per night and per hour, number of pairs in amplexus, and number of egg masses. We summed 366 individual observations: 57% juveniles, 39% adult males and 4% adult females. Average SVL was 29 mm (juveniles), 63 mm (males) and 78 mm (females). Sex ratio (males:females) was 4.85:1, while operational sex ratio varied between 1–6 males per female when both sexes were present at the pond. Maximum estimated census population size varied between 27 and 59 individuals, with a Ne = 43.11. Calling activity occurred mostly from 1800 h – 2000 h, and we counted 65 egg masses. Number of adults and calling males were positively correlated with accumulated rainfall and average temperature. Number of egg masses was positively correlated with the number of adults, accumulated rainfall, and average temperature. The causes of the long-term population decline must be identified to conserve A. annae and similar species, as well as establishing long-term monitoring programs. Required conservation actions include: translocation individuals from risky areas, creation of artificial ponds to increase ecological connectivity, elimination of introduced species, particularly in small habitat remnants, and establishment of ex situ conservation programs.

Neural dynamics model training dataset

These datasets are used to reproduce the results of the neural dynamics model from the paper https://doi.org/10.1101/725382.