Plasticity reveals hidden resistance to extinction under climate change in the global hotspot of salamander diversity

Extinction rates are predicted to rise exponentially under climate warming, but many of these predictions ignore physiological and behavioral plasticity that might buffer species from extinction. We evaluated the potential for physiological acclimatization and behavioral avoidance of poor climatic conditions to lower extinction risk under climate change in the global hotspot of salamander diversity, a region currently predicted to lose most of the salamander habitat due to warming. Our approach integrated experimental physiology and behavior into a mechanistic species distribution model to predict extinction risk based on an individual’s capacity to maintain energy balance with and without plasticity. We assessed the sensitivity of extinction risk to body size, behavioral strategies, limitations on energy intake, and physiological acclimatization of water loss and metabolic rate. The field and laboratory experiments indicated that salamanders readily acclimatize water loss rates and metabolic rates in ways that could maintain positive energy balance. Projections with plasticity reduced extinction risk by 72% under climate warming, especially in the core of their range. Further analyses revealed that juveniles might experience the greatest physiological stress under climate warming, but we identified specific physiological adaptations or plastic responses that could minimize the lethal physiological stress imposed on juveniles. We conclude that incorporating plasticity fundamentally alters ecological predictions under climate change by reducing extinction risk in the hotspot of salamander diversity

complementary_resid_data

The following dataset is from the complementary experiment, and it contains the data for the trade-off between skin resistance to water loss and metabolic rate

energy_figure_simuation

These data were generated using our biophysical modeling approach. The mean_energy column represents data that includes the trade-off whereas the mean_J_notrade represents data without the trade-off

heart_rate_data

The following data was collected from the complementary experiment on the thermal sensitivity of heart rates before and after the exposure to the temperature and humidity treatments

activity_figure_simuation

These data were used to generate the activity figure (Fig 4), and it contains estimates of average nightly activity (mean column) over the year assuming conditions are 25% drier than average conditions (roughly what salamanders experience during the driest conditions associated with activity)

CSAR data set release 2012: Ligands, affinities, complexes, and docking decoys

A major goal in drug design is the improvement of computational methods for docking and scoring. The Community Structure Activity Resource (CSAR) has collected several data sets from industry and added in-house data sets that may be used for this purpose

Advanced radiometry measurements and Earth science applications with the Airborne Prism Experiment (APEX)

We present the Airborne Prism Experiment (APEX), its calibration and subsequent radiometric measurements as well as Earth science applications derived from this data. APEX is a dispersive pushbroom imaging spectrometer covering the solar reflected wavelength range between 372 and 2540 nm with nominal 312 (max. 532) spectral bands. APEX is calibrated using a combination of laboratory, in-flight and vicarious calibration approaches. These are complemented by using a forward and inverse radiative transfer modeling approach, suitable to further validate APEX data. We establish traceability of APEX radiances to a primary calibration standard, including uncertainty analysis. We also discuss the instrument simulation process ranging from initial specifications to performance validation. In a second part, we present Earth science applications using APEX. They include geometric and atmospheric compensated as well as reflectance anisotropy minimized Level 2 data. Further, we discuss retrieval of aerosol optical depth as well as vertical column density of NOx, a radiance data-based coupled canopy–atmosphere model, and finally measuring sun-induced chlorophyll fluorescence (Fs) and infer plant pigment content. The results report on all APEX specifications including validation. APEX radiances are traceable to a primary standard with 625 for all spectral bands. Radiance based vicarious calibration is traceable to a secondary standard with ≤ 6.5% uncertainty. Except for inferring plant pigment content, all applications are validated using in-situ measurement approaches and modeling. Even relatively broad APEX bands (FWHM of 6 nm at 760 nm) can assess Fs with modeling agreements as high as R2 = 0.87 (relative RMSE = 27.76%). We conclude on the use of high resolution imaging spectrometers and suggest further development of imaging spectrometers supporting science grade spectroscopy measurements.ISSN:0034-425

CSAR Data Set Release 2012: Ligands, Affinities, Complexes, and Docking Decoys

A major goal in drug design is the improvement of computational methods for docking and scoring. The Community Structure Activity Resource (CSAR) has collected several data sets from industry and added in-house data sets that may be used for this purpose (www.csardock.org). CSAR has currently obtained data from Abbott, GlaxoSmithKline, and Vertex and is working on obtaining data from several others. Combined with our in-house projects, we are providing a data set consisting of 6 protein targets, 647 compounds with biological affinities, and 82 crystal structures. Multiple congeneric series are available for several targets with a few representative crystal structures of each of the series. These series generally contain a few inactive compounds, usually not available in the literature, to provide an upper bound to the affinity range. The affinity ranges are typically 3–4 orders of magnitude per series. For our in-house projects, we have had compounds synthesized for biological testing. Affinities were measured by Thermofluor, Octet RED, and isothermal titration calorimetry for the most soluble. This allows the direct comparison of the biological affinities for those compounds, providing a measure of the variance in the experimental affinity. It appears that there can be considerable variance in the absolute value of the affinity, making the prediction of the absolute value ill-defined. However, the relative rankings within the methods are much better, and this fits with the observation that predicting relative ranking is a more tractable problem computationally. For those in-house compounds, we also have measured the following physical properties: logD, logP, thermodynamic solubility, and p<i>K</i>_a. This data set also provides a substantial decoy set for each target consisting of diverse conformations covering the entire active site for all of the 58 CSAR-quality crystal structures. The CSAR data sets (CSAR-NRC HiQ and the 2012 release) provide substantial, publically available, curated data sets for use in parametrizing and validating docking and scoring methods

Driven-dissipative non-equilibrium Bose-Einstein condensation of less than ten photons

In a Bose–Einstein condensate, bosons condense in the lowest-energy mode available and exhibit high coherence. Quantum condensation is inherently a multimode phenomenon, yet understanding of the condensation transition in the macroscopic limit is hampered by the difficulty in resolving populations of individual modes and the coherences between them. Here, we report non-equilibrium Bose–Einstein condensation of 7 ± 2 photons in a sculpted dye-filled microcavity, where the extremely small particle number and large mode spacing of the condensate allow us to measure occupancies and coherences of the individual energy levels of the bosonic field. Coherence of the individual modes is found to generally increase with increasing photon number. However, at the break-down of thermal equilibrium we observe phase transitions to a multimode condensate regime wherein coherence unexpectedly decreases with increasing population, suggesting the presence of strong intermode phase or number correlations despite the absence of a direct nonlinearity. Experiments are well-matched to a detailed non-equilibrium model. We find that microlaser and Bose–Einstein statistics each describe complementary parts of our data and are limits of our model in appropriate regimes, providing elements to inform the debate on the differences between the two concepts1,2