py4DSTEM: a software package for multimodal analysis of four-dimensional scanning transmission electron microscopy datasets

Scanning transmission electron microscopy (STEM) allows for imaging, diffraction, and spectroscopy of materials on length scales ranging from microns to atoms. By using a high-speed, direct electron detector, it is now possible to record a full 2D image of the diffracted electron beam at each probe position, typically a 2D grid of probe positions. These 4D-STEM datasets are rich in information, including signatures of the local structure, orientation, deformation, electromagnetic fields and other sample-dependent properties. However, extracting this information requires complex analysis pipelines, from data wrangling to calibration to analysis to visualization, all while maintaining robustness against imaging distortions and artifacts. In this paper, we present py4DSTEM, an analysis toolkit for measuring material properties from 4D-STEM datasets, written in the Python language and released with an open source license. We describe the algorithmic steps for dataset calibration and various 4D-STEM property measurements in detail, and present results from several experimental datasets. We have also implemented a simple and universal file format appropriate for electron microscopy data in py4DSTEM, which uses the open source HDF5 standard. We hope this tool will benefit the research community, helps to move the developing standards for data and computational methods in electron microscopy, and invite the community to contribute to this ongoing, fully open-source project

Response of native versus exotic plant guilds to cattle and elk herbivory in forested rangeland

Questions: Are exotic plant species favoured by non-native ungulate herbivores and disadvantaged by native herbivores in forested rangelands? Do the impacts of ungulates on exotic vs native plants depend on forest management activities such as prescribed fire and stand thinning? Location: Northeastern Oregon, USA. Methods: We recorded changes in richness and cover of different exotic and native plant life forms in experimental plots that were grazed only by cattle (a non-native herbivore), only by elk (a native herbivore) or not grazed by any ungulate over a 7-yr period at both managed (recently burned and thinned) and unmanaged (where no fire and thinning has occurred in >40 yr) forest stands. Results: There was a general decrease in exotic plant species richness and cover across all treatments. However, the decrease in exotic richness, particularly of exotic annual forbs, was slightly lower in plots grazed by elk than in ungrazed plots at managed stands. Managed stands also displayed a larger increase in native annual forb richness and exotic graminoid richness, and a larger decrease in native perennial graminoid cover with cattle grazing than elk grazing. At unmanaged stands, cover of woody native plants such as shrubs, sub-shrubs and trees as well as native perennial forbs decreased or remained relatively constant with elk grazing while increasing strongly at plots that were ungrazed or grazed by cattle. Conclusions: Cattle and elk have variable effects on different plant guilds at managed vs unmanaged forest stands. Overall, cattle grazing tends to have a larger impact on herbaceous plant guilds at managed stands, while elk grazing tends to have a larger impact on woody plant guilds at unmanaged stands. However, in contrast to findings from other ecosystems, grazing only has a minor impact on exotic plant dynamics in our study area, and cattle grazing does not favour exotic plants any more than grazing by elk or ungulate exclusion.Keywords: Non-Native Species, Conditioned Correspondence Analysis, Conifer Forest Management, Grazing, Ungulates, Stand Thinning, Prescribed Burnin

Ungulate Browsing Maintains Shrub Diversity in the Absence of Episodic Disturbance in Seasonally-Arid Conifer Forest

Ungulates exert a strong influence on the composition and diversity of vegetation communities. However, little is known about how ungulate browsing pressure interacts with episodic disturbances such as fire and stand thinning. We assessed shrub responses to variable browsing pressure by cattle and elk in fuels treated (mechanical removal of fuels followed by prescribed burning) and non-fuels treated forest sites in northeastern Oregon, US. Seven treatment paddocks were established at each site; three with cattle exclusion and low, moderate and high elk browsing pressure, three with elk exclusion and low, moderate and high cattle browsing pressure, and one with both cattle and elk exclusion. The height, cover and number of stems of each shrub species were recorded at multiple plots within each paddock at the time of establishment and six years later. Changes in shrub species composition over the six year period were explored using multivariate analyses. Generalized Linear Mixed Models were used to determine the effect of browsing pressure on the change in shrub diversity and evenness. Vegetation composition in un-browsed paddocks changed more strongly and in different trajectories than in browsed paddocks at sites that were not fuels treated. In fuels treated sites, changes in composition were minimal for un-browsed paddocks. Shrub diversity and evenness decreased strongly in un-browsed paddocks relative to paddocks with low, moderate and high browsing pressure at non-fuels treated sites, but not at fuels treated sites. These results suggest that in the combined absence of fire, mechanical thinning and ungulate browsing, shrub diversity is reduced due to increased dominance by certain shrub species which are otherwise suppressed by ungulates and/or fuels removal. Accordingly, ungulate browsing, even at low intensities, can be used to suppress dominant shrub species and maintain diversity in the absence of episodic disturbance events

Impact of ungulate exclusion on understorey succession in relation to forest management in the Intermountain Western United States

QUESTIONS: Do successional trajectories in plant diversity, heterogeneity and dominance respond differently to ungulate exclusion in unmanaged forests vs managed forests that are thinned and burned? Is vegetation in recently thinned and burned stands more sensitive to changes in the grazing regime? LOCATION: Northeast OR, USA. METHODS: We evaluated changes in plant community composition, diversity, heterogeneity and dominance under herbivory by multiple ungulates (cattle, elk, deer) vs ungulate exclusion at sites where trees were recently thinned and a prescribed burn was applied (managed), and in sites that were not thinned or burned in over 40 yr (unmanaged). Plant species diversity was calculated with the Simpsons index and richness as the total number of plant species. We estimated changes in plant community heterogeneity using a measure of taxonomic dissimilarity. Plant dominance was measured as the relative evenness among different plant functional groups (annual and perennial forbs and graminoids, and shrubs, subshrubs and trees). RESULTS: As expected, managed sites displayed more early succession species, such as annual forbs and annual graminoids,while unmanaged sites were dominated by late-succession species such as shrubs, subshrubs and trees. Species richness, particularly of annuals, was strongly reduced when ungulates were excluded from managed sites, and to a lesser extent from unmanaged sites for some perennial plant species. Species diversity decreased to a slightly greater extent with ungulate exclusion at managed sites. Species dominance was not influenced by ungulate exclusion. The effect of ungulate exclusion on plant heterogeneity also depended on forest management. Heterogeneity increased at managed sites and decreased in unmanaged sites with ungulate exclusion. Overall, the change in vegetation composition over time increased with the exclusion of ungulates, particularly at managed sites. CONCLUSIONS: The strength and direction of specific vegetation and diversity responses to ungulate exclusion vary with forest management, and the influence of ungulate exclusion on plant succession is more pronounced in recently thinned and burned sites. Management of wild and domestic ungulates thus needs to account for forest management activities that alter vegetation seral stage and increase the sensitivity of vegetation to the ungulate grazing regime.Keywords: Grazing, Stand thinning, Cattle, Conifer forest, Elk and deer herbivory, Prescribed burning, Taxonomic dissimilarityKeywords: Grazing, Stand thinning, Cattle, Conifer forest, Elk and deer herbivory, Prescribed burning, Taxonomic dissimilarit

Author correction : a global database for metacommunity ecology, integrating species, traits, environment and space

Correction to: Scientific Data https://doi.org/10.1038/s41597-019-0344-7, published online 08 January 202

Author correction : a global database for metacommunity ecology, integrating species, traits, environment and space

Correction to: Scientific Data https://doi.org/10.1038/s41597-019-0344-7, published online 08 January 202

Evolutionary potential and adaptation of Banksia attenuata (Proteaceae) to climate and fire regime in southwestern Australia, a global biodiversity hotspot

Substantial climate changes are evident across Australia, with declining rainfall and rising temperature in conjunction with frequent fires. Considerable species loss and range contractions have been predicted; however, our understanding of how genetic variation may promote adaptation in response to climate change remains uncertain. Here we characterized candidate genes associated with rainfall gradients, temperatures, and fire intervals through environmental association analysis. We found that overall population adaptive genetic variation was significantly affected by shortened fire intervals, whereas declining rainfall and rising temperature did not have a detectable influence. Candidate SNPs associated with rainfall and high temperature were diverse, whereas SNPs associated with specific fire intervals were mainly fixed in one allele. Gene annotation further revealed four genes with functions in stress tolerance, the regulation of stomatal opening and closure, energy use, and morphogenesis with adaptation to climate and fire intervals. B. attenuata may tolerate further changes in rainfall and temperature through evolutionary adaptations based on their adaptive genetic variation. However, the capacity to survive future climate change may be compromised by changes in the fire regime

Land-use effects on local biodiversity in tropical forests vary between continents

The file attached is the Published/publisher’s pdf version of the article

The Digital MIQE Guidelines Update: Minimum Information for Publication of Quantitative Digital PCR Experiments for 2020

Digital PCR (dPCR) has developed considerably since the publication of the Minimum Information for Publication of Digital PCR Experiments (dMIQE) guidelines in 2013, with advances in instrumentation, software, applications, and our understanding of its technological potential. Yet these developments also have associated challenges; data analysis steps, including threshold setting, can be difficult and preanalytical steps required to purify, concentrate, and modify nucleic acids can lead to measurement error. To assist independent corroboration of conclusions, comprehensive disclosure of all relevant experimental details is required. To support the community and reflect the growing use of dPCR, we present an update to dMIQE, dMIQE2020, including a simplified dMIQE table format to assist researchers in providing key experimental information and understanding of the associated experimental process. Adoption of dMIQE2020 by the scientific community will assist in standardizing experimental protocols, maximize efficient utilization of resources, and further enhance the impact of this powerful technology

The study of atmospheric ice-nucleating particles via microfluidically generated droplets

Ice-nucleating particles (INPs) play a significant role in the climate and hydrological cycle by triggering ice formation in supercooled clouds, thereby causing precipitation and affecting cloud lifetimes and their radiative properties. However, despite their importance, INP often comprise only 1 in 10³–10⁶ ambient particles, making it difficult to ascertain and predict their type, source, and concentration. The typical techniques for quantifying INP concentrations tend to be highly labour-intensive, suffer from poor time resolution, or are limited in sensitivity to low concentrations. Here, we present the application of microfluidic devices to the study of atmospheric INPs via the simple and rapid production of monodisperse droplets and their subsequent freezing on a cold stage. This device offers the potential for the testing of INP concentrations in aqueous samples with high sensitivity and high counting statistics. Various INPs were tested for validation of the platform, including mineral dust and biological species, with results compared to literature values. We also describe a methodology for sampling atmospheric aerosol in a manner that minimises sampling biases and which is compatible with the microfluidic device. We present results for INP concentrations in air sampled during two field campaigns: (1) from a rural location in the UK and (2) during the UK’s annual Bonfire Night festival. These initial results will provide a route for deployment of the microfluidic platform for the study and quantification of INPs in upcoming field campaigns around the globe, while providing a benchmark for future lab-on-a-chip-based INP studies