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)

Buying Years to Extinction: Is Compensatory Mitigation for Marine Bycatch a Sufficient Conservation Measure for Long-Lived Seabirds?

Along the lines of the ‘polluter pays principle’, it has recently been proposed that the local long-line fishing industry should fund eradication of terrestrial predators at seabird breeding colonies, as a compensatory measure for the bycatch caused by the fishing activity. The measure is economically sound, but a quantitative and reliable test of its biological efficacy has never been conducted. Here, we investigated the demographic consequences of predator eradication for Cory's shearwater Calonectris diomedea, breeding in the Mediterranean, using a population model that integrates demographic rates estimated from individual life-history information with experimental measures of predation and habitat structure. We found that similar values of population growth rate can be obtained by different combinations of habitat characteristics, predator abundance and adult mortality, which explains the persistence of shearwater colonies in islands with introduced predators. Even so, given the empirically obtained values of survival, all combinations of predator abundance and habitat characteristics projected a decline in shearwater numbers. Perturbation analyses indicated that the value and the sensitivity of shearwater population growth rates were affected by all covariates considered and their interactions. A decrease in rat abundance delivered only a small increase in the population growth rate, whereas a change in adult survival (a parameter independent of rat abundance) had the strongest impact on population dynamics. When adult survival is low, rat eradication would allow us to “buy” years before extinction but does not reverse the process. Rat eradication can therefore be seen as an emergency measure if threats on adult survival are eliminated in the medium-term period. For species with low fecundity and long life expectancy, our results suggest that rat control campaigns are not a sufficient, self-standing measure to compensate the biological toll of long-line fisheries

The development and validation of a scoring tool to predict the operative duration of elective laparoscopic cholecystectomy

Background: The ability to accurately predict operative duration has the potential to optimise theatre efficiency and utilisation, thus reducing costs and increasing staff and patient satisfaction. With laparoscopic cholecystectomy being one of the most commonly performed procedures worldwide, a tool to predict operative duration could be extremely beneficial to healthcare organisations. Methods: Data collected from the CholeS study on patients undergoing cholecystectomy in UK and Irish hospitals between 04/2014 and 05/2014 were used to study operative duration. A multivariable binary logistic regression model was produced in order to identify significant independent predictors of long (> 90 min) operations. The resulting model was converted to a risk score, which was subsequently validated on second cohort of patients using ROC curves. Results: After exclusions, data were available for 7227 patients in the derivation (CholeS) cohort. The median operative duration was 60 min (interquartile range 45–85), with 17.7% of operations lasting longer than 90 min. Ten factors were found to be significant independent predictors of operative durations > 90 min, including ASA, age, previous surgical admissions, BMI, gallbladder wall thickness and CBD diameter. A risk score was then produced from these factors, and applied to a cohort of 2405 patients from a tertiary centre for external validation. This returned an area under the ROC curve of 0.708 (SE = 0.013, p  90 min increasing more than eightfold from 5.1 to 41.8% in the extremes of the score. Conclusion: The scoring tool produced in this study was found to be significantly predictive of long operative durations on validation in an external cohort. As such, the tool may have the potential to enable organisations to better organise theatre lists and deliver greater efficiencies in care

Guidelines for the use and interpretation of assays for monitoring autophagy (3rd edition)

In 2008 we published the first set of guidelines for standardizing research in autophagy. Since then, research on this topic has continued to accelerate, and many new scientists have entered the field. Our knowledge base and relevant new technologies have also been expanding. Accordingly, it is important to update these guidelines for monitoring autophagy in different organisms. Various reviews have described the range of assays that have been used for this purpose. Nevertheless, there continues to be confusion regarding acceptable methods to measure autophagy, especially in multicellular eukaryotes. For example, a key point that needs to be emphasized is that there is a difference between measurements that monitor the numbers or volume of autophagic elements (e.g., autophagosomes or autolysosomes) at any stage of the autophagic process versus those that measure fl ux through the autophagy pathway (i.e., the complete process including the amount and rate of cargo sequestered and degraded). In particular, a block in macroautophagy that results in autophagosome accumulation must be differentiated from stimuli that increase autophagic activity, defi ned as increased autophagy induction coupled with increased delivery to, and degradation within, lysosomes (inmost higher eukaryotes and some protists such as Dictyostelium ) or the vacuole (in plants and fungi). In other words, it is especially important that investigators new to the fi eld understand that the appearance of more autophagosomes does not necessarily equate with more autophagy. In fact, in many cases, autophagosomes accumulate because of a block in trafficking to lysosomes without a concomitant change in autophagosome biogenesis, whereas an increase in autolysosomes may reflect a reduction in degradative activity. It is worth emphasizing here that lysosomal digestion is a stage of autophagy and evaluating its competence is a crucial part of the evaluation of autophagic flux, or complete autophagy. Here, we present a set of guidelines for the selection and interpretation of methods for use by investigators who aim to examine macroautophagy and related processes, as well as for reviewers who need to provide realistic and reasonable critiques of papers that are focused on these processes. These guidelines are not meant to be a formulaic set of rules, because the appropriate assays depend in part on the question being asked and the system being used. In addition, we emphasize that no individual assay is guaranteed to be the most appropriate one in every situation, and we strongly recommend the use of multiple assays to monitor autophagy. Along these lines, because of the potential for pleiotropic effects due to blocking autophagy through genetic manipulation it is imperative to delete or knock down more than one autophagy-related gene. In addition, some individual Atg proteins, or groups of proteins, are involved in other cellular pathways so not all Atg proteins can be used as a specific marker for an autophagic process. In these guidelines, we consider these various methods of assessing autophagy and what information can, or cannot, be obtained from them. Finally, by discussing the merits and limits of particular autophagy assays, we hope to encourage technical innovation in the field

31st Annual Meeting and Associated Programs of the Society for Immunotherapy of Cancer (SITC 2016) : part two

Background The immunological escape of tumors represents one of the main ob- stacles to the treatment of malignancies. The blockade of PD-1 or CTLA-4 receptors represented a milestone in the history of immunotherapy. However, immune checkpoint inhibitors seem to be effective in specific cohorts of patients. It has been proposed that their efficacy relies on the presence of an immunological response. Thus, we hypothesized that disruption of the PD-L1/PD-1 axis would synergize with our oncolytic vaccine platform PeptiCRAd. Methods We used murine B16OVA in vivo tumor models and flow cytometry analysis to investigate the immunological background. Results First, we found that high-burden B16OVA tumors were refractory to combination immunotherapy. However, with a more aggressive schedule, tumors with a lower burden were more susceptible to the combination of PeptiCRAd and PD-L1 blockade. The therapy signifi- cantly increased the median survival of mice (Fig. 7). Interestingly, the reduced growth of contralaterally injected B16F10 cells sug- gested the presence of a long lasting immunological memory also against non-targeted antigens. Concerning the functional state of tumor infiltrating lymphocytes (TILs), we found that all the immune therapies would enhance the percentage of activated (PD-1pos TIM- 3neg) T lymphocytes and reduce the amount of exhausted (PD-1pos TIM-3pos) cells compared to placebo. As expected, we found that PeptiCRAd monotherapy could increase the number of antigen spe- cific CD8+ T cells compared to other treatments. However, only the combination with PD-L1 blockade could significantly increase the ra- tio between activated and exhausted pentamer positive cells (p= 0.0058), suggesting that by disrupting the PD-1/PD-L1 axis we could decrease the amount of dysfunctional antigen specific T cells. We ob- served that the anatomical location deeply influenced the state of CD4+ and CD8+ T lymphocytes. In fact, TIM-3 expression was in- creased by 2 fold on TILs compared to splenic and lymphoid T cells. In the CD8+ compartment, the expression of PD-1 on the surface seemed to be restricted to the tumor micro-environment, while CD4 + T cells had a high expression of PD-1 also in lymphoid organs. Interestingly, we found that the levels of PD-1 were significantly higher on CD8+ T cells than on CD4+ T cells into the tumor micro- environment (p < 0.0001). Conclusions In conclusion, we demonstrated that the efficacy of immune check- point inhibitors might be strongly enhanced by their combination with cancer vaccines. PeptiCRAd was able to increase the number of antigen-specific T cells and PD-L1 blockade prevented their exhaus- tion, resulting in long-lasting immunological memory and increased median survival

Tucketal2013_MetaAnalysisData

Data set for the publication associated with this Dryad data package, on a meta-analysis on the effects of organic vs conventional farming on biodiversity. This data set contains data collected from the literature, including data necessary for calculating effect sizes, data on taxa and crop type subgroups among effect sizes, and descriptive data giving context of the studies. The data set also includes data collected from Google Earth on the surrounding landscape complexity and heterogeneity for each effect size. The method used to collect these data are described in the associated publication. The data set CSV file was created using Microsoft Excel 2013. See README for more details and metadata

Data from: Land-use intensity and the effects of organic farming on biodiversity: a hierarchical meta-analysis

The benefits of organic farming to biodiversity in agricultural landscapes continue to be hotly debated, emphasising the importance of precisely quantifying the effect of organic vs. conventional farming. We conducted an updated hierarchical meta-analysis of studies that compared biodiversity under organic and conventional farming methods, measured as species richness. We calculated effect sizes for 184 observations garnered from 94 studies, and for each study we obtained three standardised measures reflecting land-use intensity. We investigated the stability of effect sizes through time, publication bias due to the ‘file-drawer’ problem, and consider whether the current literature is representative of global organic farming patterns. On average, organic farming increased species richness by about 30%. This result has been robust over the last 30 years of published studies and shows no sign of diminishing. Organic farming had a greater effect on biodiversity as the percentage of the landscape consisting of arable fields increased; i.e. it is higher in intensively farmed regions. The average effect size and the response to agricultural intensification depend on taxonomic group, functional group, and crop type. There is some evidence for publication bias in the literature; however, our results are robust to its impact. Current studies are heavily biased towards Northern and Western Europe and North America, while other regions with large areas of organic farming remain poorly investigated. Synthesis and recommendations. Our analysis affirms that organic farming has large positive effects on biodiversity compared with conventional farming, but that the effect size varies with the organism group and crop studied, and is greater in landscapes with higher land-use intensity. Decisions about where to site organic farms to maximise biodiversity will, however, depend on the costs as well as the potential benefits. Current studies have been heavily biased towards agricultural systems in the developed world. We recommend that future studies pay greater attention to other regions, in particular, areas with tropical, subtropical and Mediterranean climates, in which very few studies have been conducted

PublicationAnalysisScript

R code (using R 3.0.1) used for the analysis of the data set for the associated publication. See README for information on how to run the code

Data from: The value of biodiversity for the functioning of tropical forests: insurance effects during the first decade of the Sabah biodiversity experiment

One of the main environmental threats in the tropics is selective logging, which has degraded large areas of forest. In southeast Asia, enrichment planting with seedlings of the dominant group of dipterocarp tree species aims to accelerate restoration of forest structure and functioning. The role of tree diversity in forest restoration is still unclear, but the ‘insurance hypothesis’ predicts that in temporally and spatially varying environments planting mixtures may stabilize functioning owing to differences in species traits and ecologies. To test for potential insurance effects, we analyse the patterns of seedling mortality and growth in monoculture and mixture plots over the first decade of the Sabah biodiversity experiment. Our results reveal the species differences required for potential insurance effects including a trade-off in which species with denser wood have lower growth rates but higher survival. This trade-off was consistent over time during the first decade, but growth and mortality varied spatially across our 500 ha experiment with species responding to changing conditions in different ways. Overall, average survival rates were extreme in monocultures than mixtures consistent with a potential insurance effect in which monocultures of poorly surviving species risk recruitment failure, whereas monocultures of species with high survival have rates of self-thinning that are potentially wasteful when seedling stocks are limited. Longer-term monitoring as species interactions strengthen will be needed to more comprehensively test to what degree mixtures of species spread risk and use limited seedling stocks more efficiently to increase diversity and restore ecosystem structure and functioning

The value of biodiversity for the functioning of tropical forests: Insurance effects during the first decade of the sabah biodiversity experiment

One of the main environmental threats in the tropics is selective logging, which has degraded large areas of forest. In southeast Asia, enrichment planting with seedlings of the dominant group of dipterocarp tree species aims to accelerate restoration of forest structure and functioning. The role of tree diversity in forest restoration is still unclear, but the ‘insurance hypothesis’ predicts that in temporally and spatially varying environments planting mixtures may stabilize functioning owing to differences in species traits and ecologies. To test for potential insurance effects, we analyse the patterns of seedling mortality and growth in monoculture and mixture plots over the first decade of the Sabah biodiversity experiment. Our results reveal the species differences required for potential insurance effects including a trade-off in which species with denser wood have lower growth rates but higher survival. This trade-off was consistent over time during the first decade, but growth and mortality varied spatially across our 500 ha experiment with species responding to changing conditions in different ways. Overall, average survival rates were extreme in monocultures than mixtures consistent with a potential insurance effect in which monocultures of poorly surviving species risk recruitment failure, whereas monocultures of species with high survival have rates of self-thinning that are potentially wasteful when seedling stocks are limited. Longer-term monitoring as species interactions strengthen will be needed to more comprehensively test to what degree mixtures of species spread risk and use limited seedling stocks more efficiently to increase diversity and restore ecosystem structure and functioning.ISSN:0962-8452ISSN:1471-295