Neural Networks and the Classification of Active Galactic Nucleus Spectra

The use of Artificial Neural Networks (ANNs) as a classifier of digital spectra is investigated. Using both simulated and real data, it is shown that neural networks can be trained to discriminate between the spectra of different classes of active galactic nucleus (AGN) with realistic sample sizes and signal-to-noise ratios. By working in the Fourier domain, neural nets can classify objects without knowledge of their redshifts.Comment: 11 pages, LaTeX, including two postscript figures, 41 kb. Accepted for publication in Publ. AS

Detecting Bias in Large-Scale Comparative Analyses: Methods for Expanding the Scope of Hypothesis-Testing with HormoneBase

To address large-scale questions in evolutionary biology, the compilation of data from a variety of sources is often required. This is a major challenge in the development of databases in organismal biology. Here, we describe the procedure we used to reconstruct the phylogeny of the 474 species represented in HormoneBase, including fish, amphibians, mammals, birds, and reptiles. We also provide the methodology used to compile vertebrate environmental, life history, and metabolic rate data for use in conjunction with the HormoneBase database to test hypotheses of the evolution of steroid hormone traits. We then report a series of analyses using these data to determine the extent to which field measures of circulating hormones and associated life history data exhibit taxonomic and geographic bias. By providing a detailed description of the approaches used to compile and evaluate these data and identifying potential biases in the collection of these data, we hope to make the HormoneBase database a more broadly useful resource for the scientific community to address a diversity of comparative questions

Sleep-wake disturbances in hospitalized patients with traumatic brain injury: association with brain trauma but not with an abnormal melatonin circadian rhythm.

STUDY OBJECTIVES: To test whether the sleep-wake cycle disruption in patients hospitalized with traumatic brain injury (TBI) (1) is also found in patients with traumatic injuries other than TBI (non-TBI) and (2) is associated with a weaker or abnormal circadian clock signal. METHODS: Forty-two non-mechanically ventilated and non-sedated patients hospitalized for moderate-to-severe TBI were compared to 34 non-TBI patients. They wore wrist actigraphs for 9.4 ± 4.2 days, starting 19.3 ± 12.6 days post-injury. Of these, 17 TBI and 14 non-TBI patients had their urine collected every hour for 25 hours, starting 18.3 ± 12.3 days post-injury. We calculated urinary 6-sulfatoxymelatonin concentration to obtain total 24-hour excretion, excretion onset, offset, duration, amplitude, and acrophase. Using Student's t-tests, we compared groups on actigraphy (daytime activity ratio, nighttime total sleep time, and fragmentation index) and melatonin variables. We investigated associations between melatonin and actigraphy variables using Pearson's correlations. RESULTS: TBI patients had poorer daytime activity ratio (TBI: 77.5 ± 9.4%; non-TBI: 84.6 ± 6.9%), shorter nighttime total sleep time (TBI: 353.5 ± 96.6 min; non-TBI: 421.2 ± 72.2 min), and higher fragmentation index (TBI: 72.2 ± 30.0; non-TBI: 53.5 ± 23.6) (all p-values < 0.01). A melatonin rhythm was present in both groups, and no group differences were found on melatonin variables. No associations were found between melatonin and actigraphy variables in TBI patients. CONCLUSION: Moderate-to-severe TBI patients have more serious sleep-wake disturbances than non-TBI patients hospitalized in the same environment, suggesting that the brain injury itself alters the sleep-wake cycle. Despite their deregulated 24-hour sleep-wake cycle, TBI patients have a normal circadian clock signal

Preliminary results of an earthquake early warning system in Costa Rica

We analyze the performance of a prototype earthquake early warning system deployed at the National Seismological Network of Costa Rica in collaboration with the Swiss Seismological Service by presenting the real-time performance during six earthquakes (Mw 5.1-6.4) that took place during 2018 and 2019. We observe that, despite only limited efforts to optimize the existing network of 158 stations, for EEW purposes, the network density allows fast determination of source parameters using both the Virtual Seismologist and the Finite Fault Rupture Detector algorithms. Shallow earthquakes on or near-shore are routinely identified within 11–20 s of their occurrence. The warning times for the capital city of San Jose are of 43 s for epicenters located at 220 km, like for the Mw 6.4 Armuelles earthquake. On the other hand, during the time analyzed, the EEW system did not provide positive warning times for earthquakes at distances less than 40 km from San Jose. Even though large (Mw > 7) distant historical earthquakes have not caused heavy damage in San Jose, there is potential for developing an EEW system for Costa Rica, especially for the purposes of rapid earthquake notifications, disaster response management, and seismic risk mitigation.Swiss Development Agency/[]/SDA/SuizaUniversidad de Costa Rica/[113-B5-704]/UCR/Costa RicaUniversidad de Costa Rica/[113-B9-911]/UCR/Costa RicaUCR::Vicerrectoría de Docencia::Ciencias Básicas::Facultad de Ciencias::Escuela Centroamericana de Geologí

IUCN Conservation Status Does Not Predict Glucocortoid Concentrations in Reptiles and Birds

Circulating glucocorticoids (GCs) are the most commonly used biomarkers of stress in wildlife. However, their utility as a tool for identifying and/or managing at-risk species has varied. Here, we took a very broad approach to conservation physiology, asking whether International Union for the Conservation of Nature (IUCN) listing status (concern versus no obvious concern) and/or location within a geographic range (edge versus non-edge) predicted baseline and post-restraint concentrations of corticosterone (CORT) among many species of birds and reptiles. Even though such an approach can be viewed as coarse, we asked in this analysis whether CORT concentrations might be useful to implicate species at risk. Indeed, our effort, relying on HormoneBase, a repository of data on wildlife steroids, complements several other large-scale efforts in this issue to describe and understand GC variation. Using a phylogenetically informed Bayesian approach, we found little evidence that either IUCN status or edge/non-edge location in a geographic distribution were related to GC levels. However, we did confirm patterns described in previous studies, namely that breeding condition and evolutionary relatedness among species predicted some GC variation. Given the broad scope of our work, we are reluctant to conclude that IUCN status and location within a range are unrelated to GC regulation. We encourage future more targeted efforts on GCs in at-risk populations to reveal how factors leading to IUCN listing or the environmental conditions at range edges impact individual performance and fitness, particularly in the mammals, amphibians, and fish species we could not study here because data are currently unavailable

\u3ci\u3eTrans\u3c/i\u3e-ancestry Fine Mapping and Molecular Assays Identify Regulatory Variants at the ANGPTL8 HDL-C GWAS Locus

Recent genome-wide association studies (GWAS) have identified variants associated with highdensity lipoprotein cholesterol (HDL-C) located in or near the ANGPTL8 gene. Given the extensive sharing of GWAS loci across populations, we hypothesized that at least one shared variant at this locus affects HDL-C. The HDL-C–associated variants are coincident with expression quantitative trait loci for ANGPTL8 and DOCK6 in subcutaneous adipose tissue; however, only ANGPTL8 expression levels are associated with HDL-C levels. We identified a 400-bp promoter region of ANGPTL8 and enhancer regions within 5 kb that contribute to regulating expression in liver and adipose. To identify variants functionally responsible for the HDL-C association, we performed fine-mapping analyses and selected 13 candidate variants that overlap putative regulatory regions to test for allelic differences in regulatory function. Of these variants, rs12463177-G increased transcriptional activity (1.5-fold, P = 0.004) and showed differential protein binding. Six additional variants (rs17699089, rs200788077, rs56322906, rs3760782, rs737337, and rs3745683) showed evidence of allelic differences in transcriptional activity and/or protein binding. Taken together, these data suggest a regulatory mechanism at the ANGPTL8 HDL-C GWAS locus involving tissue-selective expression and at least one functional variant

Metabolic Scaling of Stress Hormones in Vertebrates

Glucocorticoids (GCs) are stress hormones that can strongly influence physiology, behavior, and an organism’s ability to cope with environmental change. Despite their importance, and the wealth of studies that have sought to understand how and why GC concentrations vary within species, we do not have a clear understanding of how circulating GC levels vary within and across the major vertebrate clades. New research has proposed that much interspecific variation in GC concentrations can be explained by variation in metabolism and body mass. Specifically, GC concentrations should vary proportionally with mass-specific metabolic rates and, given known scaling relationships between body mass and metabolic rate, GC concentrations should scale to the -1/4 power of body mass and to the power of 1 with mass-specific metabolic rate. Here, we use HormoneBase, the newly compiled database that includes plasma GC concentrations from free-living and unmanipulated vertebrates, to evaluate this hypothesis. Specifically, we explored the relationships between body mass or mass-specific metabolic rate and either baseline or stress-induced GC (cortisol or corticosterone) concentrations in tetrapods. Our phylogenetically-informed models suggest that, whereas the relationship between GC concentrations and body mass across tetrapods and among mammals is close to -1/4 power, this relationship does not exist in amphibians, reptiles, and birds. Moreover, with the exception of a positive association between stress-induced GC concentrations and mass-specific metabolic rate in birds, we found little evidence that GC concentrations are linked to metabolic rate, although the number of species sampled was quite limited for amphibians and somewhat so for reptiles and mammals. Nevertheless, these results stand in contrast to the generally accepted association between the two and suggest that our observed positive association between body mass and GC concentrations may not be due to the well-established link between mass and metabolism. Large-scale comparative approaches can come with drawbacks, such as pooling and pairing observations from separate sources. However, these broad analyses provide an important counterbalance to the majority of studies examining variation in GC concentrations at the population or species level, and can be a powerful approach to testing both long-standing and new questions in biology

HormoneBase, a Population-Level Database of Steroid Hormone Levels Across Vertebrates

Hormones are central regulators of organismal function and flexibility that mediate a diversity of phenotypic traits from early development through senescence. Yet despite these important roles, basic questions about how and why hormone systems vary within and across species remain unanswered. Here we describe HormoneBase, a database of circulating steroid hormone levels and their variation across vertebrates. This database aims to provide all available data on the mean, variation, and range of plasma glucocorticoids (both baseline and stress-induced) and androgens in free-living and un-manipulated adult vertebrates. HormoneBase (www.HormoneBase.org) currently includes \u3e6,580 entries from 476 species, reported in 648 publications from 1967 to 2015, and unpublished datasets. Entries are associated with data on the species and population, sex, year and month of study, geographic coordinates, life history stage, method and latency of hormone sampling, and analysis technique. This novel resource could be used for analyses of the function and evolution of hormone systems, and the relationships between hormonal variation and a variety of processes including phenotypic variation, fitness, and species distributions

Macroevolutionary Patterning in Glucocorticoids Suggests Different Selective Pressures Shape Baseline and Stress-Induced Levels

Glucocorticoid (GC) hormones are important phenotypic mediators across vertebrates, but their circulating concentrations can vary markedly. Here we investigate macroevolutionary patterning in GC levels across tetrapods by testing seven specific hypotheses about GC variation and evaluating whether the supported hypotheses reveal consistent patterns in GC evolution. If selection generally favors the “supportive” role of GCs in responding effectively to challenges, then baseline and/or stress-induced GCs may be higher in challenging contexts. Alternatively, if selection generally favors “protection” from GC-induced costs, GCs may be lower in environments where challenges are more common or severe. The predictors of baseline GCs were all consistent with supportive effects: levels were higher in smaller organisms and in those inhabiting more energetically demanding environments. During breeding, baseline GCs were also higher in populations and species with fewer lifetime opportunities to reproduce. The predictors of stress-induced GCs were instead more consistent with the protection hypothesis: during breeding, levels were lower in organisms with fewer lifetime reproductive opportunities. Overall, these patterns indicate a surprising degree of consistency in how some selective pressures shape GCs across broad taxonomic scales; at the same time, in challenging environments selection appears to operate on baseline and stress-induced GCs in distinct ways

Baseline and Stress-Induced Corticosterone Levels Across Birds and Reptiles Do Not Reflect Urbanication Levels

Rates of human-induced environmental change continue increasing with human population size, potentially altering animal physiology and negatively affecting wildlife. Researchers often use glucocorticoid concentrations (hormones that can be associated with stressors) to gauge the impact of anthropogenic factors (e.g. urbanization, noise and light pollution). Yet, no general relationships between human-induced environmental change and glucocorticoids have emerged. Given the number of recent studies reporting baseline and stress-induced corticosterone (the primary glucocorticoid in birds and reptiles) concentrations worldwide, it is now possible to conduct large-scale comparative analyses to test for general associations between disturbance and baseline and stress-induced corticosterone across species. Additionally, we can control for factors that may influence context, such as life history stage, environmental conditions and urban adaptability of a species. Here, we take a phylogenetically informed approach and use data from HormoneBase to test if baseline and stress-induced corticosterone are valid indicators of exposure to human footprint index, human population density, anthropogenic noise and artificial light at night in birds and reptiles. Our results show a negative relationship between anthropogenic noise and baseline corticosterone for birds characterized as urban avoiders. While our results potentially indicate that urban avoiders are more sensitive to noise than other species, overall our study suggests that the relationship between human-induced environmental change and corticosterone varies across species and contexts; we found no general relationship between human impacts and baseline and stress-induced corticosterone in birds, nor baseline corticosterone in reptiles. Therefore, it should not be assumed that high or low levels of exposure to human-induced environmental change are associated with high or low corticosterone levels, respectively, or that closely related species, or even individuals, will respond similarly. Moving forward, measuring alternative physiological traits alongside reproductive success, health and survival may provide context to better understand the potential negative effects of human-induced environmental change