Abstract. The Amazon rain forest experiences the combined pressures from human-made deforestation and progressing climate change, causing severe and potentially disruptive perturbations of the ecosystem's integrity and stability. To intensify research on critical aspects of Amazonian biosphere–atmosphere exchange, the Amazon Tall Tower Observatory (ATTO) has been established in the central Amazon Basin. Here we present a multi-year analysis of backward trajectories to derive an effective footprint region of the observatory, which spans large parts of the particularly vulnerable eastern basin. Further, we characterize geospatial properties of the footprint regions, such as climatic conditions, distribution of ecoregions, land cover categories, deforestation dynamics, agricultural expansion, fire regimes, infrastructural development, protected areas, and future deforestation scenarios. This study is meant to be a resource and reference work, helping to embed the ATTO observations into the larger context of human-caused transformations of Amazonia. We conclude that the chances to observe an unperturbed rain forest–atmosphere exchange at the ATTO site will likely decrease in the future, whereas the atmospheric signals from human-made and climate-change-related forest perturbations will increase in frequency and intensity.

Like a moth into the flame - Phototaxis is an iconic example for innate preferences. Such preferences likely reflect evolutionary adaptations to predictable situations and have traditionally been conceptualized as hard-wired stimulus-response links. Perhaps therefore, the century-old discovery of flexibility in Drosophila phototaxis has received little attention. Here we report that across several different behavioral tests, light/dark preference tested in walking is dependent on various aspects of flight. If we temporarily compromise flying ability, walking photopreference reverses concomitantly. Neuronal activity in circuits expressing dopamine and octopamine, respectively, plays a differential role in photopreference, suggesting a potential involvement of these biogenic amines in this case of behavioral flexibility. We conclude that flies monitor their ability to fly, and that flying ability exerts a fundamental effect on action selection in Drosophila . This work suggests that even behaviors which appear simple and hard-wired comprise a value-driven decision-making stage, negotiating the external situation with the animal’s internal state, before an action is selected.

For many decades, the hyperinflation of subscription prices for scholarly journals have concerned scholarly institutions. After years of fruitless efforts to solve this “serials crisis”, open access has been proposed as the latest potential solution. However, also the prices for open access publishing are high and are rising well beyond inflation. What has been missing from the public discussion so far is a quantitative approach to determine the actual costs of efficiently publishing a scholarly article using state-of-the-art technologies, such that informed decisions can be made as to appropriate price levels. Here we provide a granular, step-by-step calculation of the costs associated with publishing primary research articles, from submission, through peer-review, to publication, indexing and archiving. We find that these costs range from less than US$200 per article in modern, large scale publishing platforms using post-publication peer-review, to about US$1,000 per article in prestigious journals with rejection rates exceeding 90%. The publication costs for a representative scholarly article today come to lie at around US$400. We discuss the additional non-publication items that make up the difference between publication costs and final price.

For many decades, the hyperinflation of subscription prices for scholarly journals have concerned scholarly institutions. After years of fruitless efforts to solve this “serials crisis”, open access has been proposed as the latest potential solution. However, also the prices for open access publishing are high and are rising well beyond inflation. What has been missing from the public discussion so far is a quantitative approach to determine the actual costs of efficiently publishing a scholarly article using state-of-the-art technologies, such that informed decisions can be made as to appropriate price levels. Here we provide a granular, step-by-step calculation of the costs associated with publishing primary research articles, from submission, through peer-review, to publication, indexing and archiving. We find that these costs range from less than US$200 per article in modern, large scale publishing platforms using post-publication peer-review, to about US$1,000 per article in prestigious journals with rejection rates exceeding 90%. The publication costs for a representative scholarly article today come to lie at around US$400. We discuss the additional non-publication items that make up the difference between publication costs and final price.

Open source bioimage informatics tools for the analysis of DNA damage and associated biomarkers

Fast object tracking in real time allows convenient tracking of very large numbers of animals and closed-loop experiments that control stimuli for multiple animals in parallel. We developed MARGO, a real-time animal tracking suite for custom behavioral experiments. We demonstrated that MARGO can rapidly and accurately track large numbers of animals in parallel over very long timescales. We incorporated control of peripheral hardware, and implemented a flexible software architecture for defining new experimental routines. These features enable closed-loop delivery of stimuli to many individuals simultaneously. We highlight MARGO’s ability to coordinate tracking and hardware control with two custom behavioral assays (measuring phototaxis and optomotor response) and one optogenetic operant conditioning assay. There are currently several open source animal trackers. MARGO’s strengths are 1) robustness, 2) high throughput, 3) flexible control of hardware and 4) real-time closed-loop control of sensory and optogenetic stimuli, all of which are optimized for large-scale experimentation.