MODISTools - downloading and processing MODIS remotely sensed data in R

Remotely sensed data – available at medium to high resolution across global spatial and temporal scales – are a valuable resource for ecologists. In particular, products from NASA's MODerate-resolution Imaging Spectroradiometer (MODIS), providing twice-daily global coverage, have been widely used for ecological applications. We present MODISTools, an R package designed to improve the accessing, downloading, and processing of remotely sensed MODIS data. MODISTools automates the process of data downloading and processing from any number of locations, time periods, and MODIS products. This automation reduces the risk of human error, and the researcher effort required compared to manual per-location downloads. The package will be particularly useful for ecological studies that include multiple sites, such as meta-analyses, observation networks, and globally distributed experiments. We give examples of the simple, reproducible workflow that MODISTools provides and of the checks that are carried out in the process. The end product is in a format that is amenable to statistical modeling. We analyzed the relationship between species richness across multiple higher taxa observed at 526 sites in temperate forests and vegetation indices, measures of aboveground net primary productivity. We downloaded MODIS derived vegetation index time series for each location where the species richness had been sampled, and summarized the data into three measures: maximum time-series value, temporal mean, and temporal variability. On average, species richness covaried positively with our vegetation index measures. Different higher taxa show different positive relationships with vegetation indices. Models had high R2 values, suggesting higher taxon identity and a gradient of vegetation index together explain most of the variation in species richness in our data. MODISTools can be used on Windows, Mac, and Linux platforms, and is available from CRAN and GitHub (https://github.com/seantuck12/MODISTools)

The database of the PREDICTS (Projecting Responses of Ecological Diversity In Changing Terrestrial Systems) project

The PREDICTS project—Projecting Responses of Ecological Diversity In Changing Terrestrial Systems (www.predicts.org.uk)—has collated from published studies a large, reasonably representative database of comparable samples of biodiversity from multiple sites that differ in the nature or intensity of human impacts relating to land use. We have used this evidence base to develop global and regional statistical models of how local biodiversity responds to these measures. We describe and make freely available this 2016 release of the database, containing more than 3.2 million records sampled at over 26,000 locations and representing over 47,000 species. We outline how the database can help in answering a range of questions in ecology and conservation biology. To our knowledge, this is the largest and most geographically and taxonomically representative database of spatial comparisons of biodiversity that has been collated to date; it will be useful to researchers and international efforts wishing to model and understand the global status of biodiversity

The PREDICTS database: a global database of how local terrestrial biodiversity responds to human impacts

Biodiversity continues to decline in the face of increasing anthropogenic pressures such as habitat destruction, exploitation, pollution and introduction of alien species. Existing global databases of species’ threat status or population time series are dominated by charismatic species. The collation of datasets with broad taxonomic and biogeographic extents, and that support computation of a range of biodiversity indicators, is necessary to enable better understanding of historical declines and to project – and avert – future declines. We describe and assess a new database of more than 1.6 million samples from 78 countries representing over 28,000 species, collated from existing spatial comparisons of local-scale biodiversity exposed to different intensities and types of anthropogenic pressures, from terrestrial sites around the world. The database contains measurements taken in 208 (of 814) ecoregions, 13 (of 14) biomes, 25 (of 35) biodiversity hotspots and 16 (of 17) megadiverse countries. The database contains more than 1% of the total number of all species described, and more than 1% of the described species within many taxonomic groups – including flowering plants, gymnosperms, birds, mammals, reptiles, amphibians, beetles, lepidopterans and hymenopterans. The dataset, which is still being added to, is therefore already considerably larger and more representative than those used by previous quantitative models of biodiversity trends and responses. The database is being assembled as part of the PREDICTS project (Projecting Responses of Ecological Diversity In Changing Terrestrial Systems – www.predicts.org.uk). We make site-level summary data available alongside this article. The full database will be publicly available in 2015.Keywords: Habitat destruction, Data sharing, Global change, Land us

Widespread winners and narrow-ranged losers: land use homogenizes biodiversity in local assemblages worldwide

Human use of the land (for agriculture and settlements) has a substantial negative effect on biodiversity globally. However, not all species are adversely affected by land use, and indeed, some benefit from the creation of novel habitat. Geographically rare species may be more negatively affected by land use than widespread species, but data limitations have so far prevented global multi-clade assessments of land-use effects on narrow-ranged and widespread species. We analyse a large, global database to show consistent differences in assemblage composition. Compared with natural habitat, assemblages in disturbed habitats have more widespread species on average, especially in urban areas and the tropics. All else being equal, this result means that human land use is homogenizing assemblage composition across space. Disturbed habitats show both reduced abundances of narrow-ranged species and increased abundances of widespread species. Our results are very important for biodiversity conservation because narrow-ranged species are typically at higher risk of extinction than widespread species. Furthermore, the shift to more widespread species may also affect ecosystem functioning by reducing both the contribution of rare species and the diversity of species’ responses to environmental changes among local assemblages

Prediction of infrared light emission from pi-conjugated polymers: a diagrammatic exciton basis valence bond theory

There is currently a great need for solid state lasers that emit in the infrared, as this is the operating wavelength regime for applications in telecommunications. Existing $\pi$--conjugated polymers all emit in the visible or ultraviolet, and whether or not $\pi$--conjugated polymers that emit in the infrared can be designed is an interesting challenge. On the one hand, the excited state ordering in trans-polyacetylene, the $\pi$--conjugated polymer with relatively small optical gap, is not conducive to light emission because of electron-electron interaction effects. On the other hand, excited state ordering opposite to that in trans-polyacetylene is usually obtained by chemical modification that increases the effective bond-alternation, which in turn increases the optical gap. We develop a theory of electron correlation effects in a model $\pi$-conjugated polymer that is obtained by replacing the hydrogen atoms of trans-polyacetylene with transverse conjugated groups, and show that the effective on-site correlation in this system is smaller than the bare correlation in the unsubstituted system. An optical gap in the infrared as well as excited state ordering conducive to light emission is thereby predicted upon similar structural modifications.Comment: 15 pages, 15 figures, 1 tabl

Turbulence in the Solar Atmosphere: Manifestations and Diagnostics via Solar Image Processing

Intermittent magnetohydrodynamical turbulence is most likely at work in the magnetized solar atmosphere. As a result, an array of scaling and multi-scaling image-processing techniques can be used to measure the expected self-organization of solar magnetic fields. While these techniques advance our understanding of the physical system at work, it is unclear whether they can be used to predict solar eruptions, thus obtaining a practical significance for space weather. We address part of this problem by focusing on solar active regions and by investigating the usefulness of scaling and multi-scaling image-processing techniques in solar flare prediction. Since solar flares exhibit spatial and temporal intermittency, we suggest that they are the products of instabilities subject to a critical threshold in a turbulent magnetic configuration. The identification of this threshold in scaling and multi-scaling spectra would then contribute meaningfully to the prediction of solar flares. We find that the fractal dimension of solar magnetic fields and their multi-fractal spectrum of generalized correlation dimensions do not have significant predictive ability. The respective multi-fractal structure functions and their inertial-range scaling exponents, however, probably provide some statistical distinguishing features between flaring and non-flaring active regions. More importantly, the temporal evolution of the above scaling exponents in flaring active regions probably shows a distinct behavior starting a few hours prior to a flare and therefore this temporal behavior may be practically useful in flare prediction. The results of this study need to be validated by more comprehensive works over a large number of solar active regions.Comment: 26 pages, 7 figure

Matrix metalloproteinase-3 (MMP-3)-mediated gene therapy for glaucoma.

Approximately 80 million people globally are affected by glaucoma, with a projected increase to over 110 million by 2040. Substantial issues surrounding patient compliance remain with topical eye drops, and up to 10% of patients become treatment resistant, putting them at risk of permanent vision loss. The major risk factor for glaucoma is elevated intraocular pressure, which is regulated by the balance between the secretion of aqueous humor and the resistance to its flow across the conventional outflow pathway. Here, we show that adeno-associated virus 9 (AAV9)-mediated expression of matrix metalloproteinase-3 (MMP-3) can increase outflow in two murine models of glaucoma and in nonhuman primates. We show that long-term AAV9 transduction of the corneal endothelium in the nonhuman primate is safe and well tolerated. Last, MMP-3 increases outflow in donor human eyes. Collectively, our data suggest that glaucoma can be readily treated with gene therapy-based methods, paving the way for deployment in clinical trials

Downscaling land-use data to provide global 30″ estimates of five land-use classes

Land‐use change is one of the biggest threats to biodiversity globally. The effects of land use on biodiversity manifest primarily at local scales which are not captured by the coarse spatial grain of current global land‐use mapping. Assessments of land‐use impacts on biodiversity across large spatial extents require data at a similar spatial grain to the ecological processes they are assessing. Here, we develop a method for statistically downscaling mapped land‐use data that combines generalized additive modeling and constrained optimization. This method was applied to the 0.5° Land‐use Harmonization data for the year 2005 to produce global 30″ (approx. 1 km2) estimates of five land‐use classes: primary habitat, secondary habitat, cropland, pasture, and urban. The original dataset was partitioned into 61 bio‐realms (unique combinations of biome and biogeographical realm) and downscaled using relationships with fine‐grained climate, land cover, landform, and anthropogenic influence layers. The downscaled land‐use data were validated using the PREDICTS database and the geoWiki global cropland dataset. Application of the new method to all 61 bio‐realms produced global fine‐grained layers from the 2005 time step of the Land‐use Harmonization dataset. Coarse‐scaled proportions of land use estimated from these data compared well with those estimated in the original datasets (mean R2: 0.68 ± 0.19). Validation with the PREDICTS database showed the new downscaled land‐use layers improved discrimination of all five classes at PREDICTS sites (P < 0.0001 in all cases). Additional validation of the downscaled cropping layer with the geoWiki layer showed an R2 improvement of 0.12 compared with the Land‐use Harmonization data. The downscaling method presented here produced the first global land‐use dataset at a spatial grain relevant to ecological processes that drive changes in biodiversity over space and time. Integrating these data with biodiversity measures will enable the reporting of land‐use impacts on biodiversity at a finer resolution than previously possible. Furthermore, the general method presented here could be useful to others wishing to downscale similarly constrained coarse‐resolution data for other environmental variables

Inselect: Automating the Digitization of Natural History Collections

Copyright: © 2015 Hudson et al. This is an open access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited. The attached file is the published version of the article