Cyber-Physical System for Environmental Monitoring Based on Deep Learning.

Cyber-physical systems (CPS) constitute a promising paradigm that could fit various applications. Monitoring based on the Internet of Things (IoT) has become a research area with new challenges in which to extract valuable information. This paper proposes a deep learning classification sound system for execution over CPS. This system is based on convolutional neural networks (CNNs) and is focused on the different types of vocalization of two species of anurans. CNNs, in conjunction with the use of mel-spectrograms for sounds, are shown to be an adequate tool for the classification of environmental sounds. The classification results obtained are excellent (97.53% overall accuracy) and can be considered a very promising use of the system for classifying other biological acoustic targets as well as analyzing biodiversity indices in the natural environment. The paper concludes by observing that the execution of this type of CNN, involving low-cost and reduced computing resources, are feasible for monitoring extensive natural areas. The use of CPS enables flexible and dynamic configuration and deployment of new CNN updates over remote IoT nodes.

GeMSTONE: orchestrated prioritization of human germline mutations in the cloud.

Integrative analysis of whole-genome/exome-sequencing data has been challenging, especially for the non-programming research community, as it requires simultaneously managing a large number of computational tools. Even computational biologists find it unexpectedly difficult to reproduce results from others or optimize their strategies in an end-to-end workflow. We introduce Germline Mutation Scoring Tool fOr Next-generation sEquencing data (GeMSTONE), a cloud-based variant prioritization tool with high-level customization and a comprehensive collection of bioinformatics tools and data libraries (http://gemstone.yulab.org/). GeMSTONE generates and readily accepts a shareable 'recipe' file for each run to either replicate previous results or analyze new data with identical parameters and provides a centralized workflow for prioritizing germline mutations in human disease within a streamlined workflow rather than a pool of program executions.

Relying on Incomplete Information Can Lead to the Wrong Conclusions. Comment on van Hassel, F.; Bovenkerk, B. How Should We Help Wild Animals Cope with Climate Change? The Case of the Iberian Lynx. Animals 2023, 13, 453.

In their recent paper, Van Hassel and Bovenkerk [...].

Niche models at inter- and intraspecific levels reveal hierarchical niche differentiation in midwife toads.

Variation and population structure play key roles in the speciation process, but adaptive intraspecific genetic variation is commonly ignored when forecasting species niches. Amphibians serve as excellent models for testing how climate and local adaptations shape species distributions due to physiological and dispersal constraints and long generational times. In this study, we analysed the climatic factors driving the evolution of the genus Alytes at inter- and intraspecific levels that may limit realized niches. We tested for both differences among the five recognized species and among intraspecific clades for three of the species (Alytes obstetricans, A. cisternasii, and A. dickhilleni). We employed ecological niche models with an ordination approach to perform niche overlap analyses and test hypotheses of niche conservatism or divergence. Our results showed strong differences in the environmental variables affecting species climatic requirements. At the interspecific level, tests of equivalence and similarity revealed that sister species were non-identical in their environmental niches, although they neither were entirely dissimilar. This pattern was also consistent at the intraspecific level, with the exception of A. cisternasii, whose clades appeared to have experienced a lower degree of niche divergence than clades of the other species. In conclusion, our results support that Alytes toads, examined at both the intra- and interspecific levels, tend to occupy similar, if not identical, climatic environments.

Extensive disruption of protein interactions by genetic variants across the allele frequency spectrum in human populations.

Each human genome carries tens of thousands of coding variants. The extent to which this variation is functional and the mechanisms by which they exert their influence remains largely unexplored. To address this gap, we leverage the ExAC database of 60,706 human exomes to investigate experimentally the impact of 2009 missense single nucleotide variants (SNVs) across 2185 protein-protein interactions, generating interaction profiles for 4797 SNV-interaction pairs, of which 421 SNVs segregate at > 1% allele frequency in human populations. We find that interaction-disruptive SNVs are prevalent at both rare and common allele frequencies. Furthermore, these results suggest that 10.5% of missense variants carried per individual are disruptive, a higher proportion than previously reported; this indicates that each individual's genetic makeup may be significantly more complex than expected. Finally, we demonstrate that candidate disease-associated mutations can be identified through shared interaction perturbations between variants of interest and known disease mutations.

Synthetic rainfall vibrations evoke toad emergence.

Toads occupy underground refugia during periods of daily or seasonal inactivity, emerging only during rainfall [1]. We test the hypothesis that rainfall-induced vibrations in soil are the cues that trigger the emergence of toads from underground. Using playback experiments in the absence of natural rainfall in native habitats, we observed that two Iberian toad species (Pelobates cultripes and Bufo calamita) emerged significantly earlier than controls when exposed to low-frequency soil vibrations that closely mimic those of rainfall. Our results suggest that detection of abiotic seismic events are biologically relevant and widespread in arid-zone anurans. These findings provide insights into the evolutionary role played by the two low-frequency-tuned inner-ear organs in anuran amphibians - the amphibian papilla and sacculus, both detectors of weak environmental vibrational cues.

Subsymmetries predict auditory and visual pattern complexity.

A mathematical measure of pattern complexity based on subsymmetries possessed by the pattern, previously shown to correlate highly with empirically derived measures of cognitive complexity in the visual domain, is found to also correlate significantly with empirically derived complexity measures of perception and production of auditory temporal and musical rhythmic patterns. Not only does the subsymmetry measure correlate highly with the difficulty of reproducing the rhythms by tapping after listening to them, but also the empirical measures exhibit similar behavior, for both the visual and auditory patterns, as a function of the relative number of subsymmetries present in the patterns.

Calling behaviour under climate change: geographical and seasonal variation of calling temperatures in ectotherms.

Calling behaviour is strongly temperature-dependent and critical for sexual selection and reproduction in a variety of ectothermic taxa, including anuran amphibians, which are the most globally threatened vertebrates. However, few studies have explored how species respond to distinct thermal environments at time of displaying calling behaviour, and thus it is still unknown whether ongoing climate change might compromise the performance of calling activity in ectotherms. Here, we used new audio-trapping techniques (automated sound recording and detection systems) between 2006 and 2009 to examine annual calling temperatures of five temperate anurans and their patterns of geographical and seasonal variation at the thermal extremes of species ranges, providing insights into the thermal breadths of calling activity of species, and the mechanisms that enable ectotherms to adjust to changing thermal environments. All species showed wide thermal breadths during calling behaviour (above 15 °C) and increases in calling temperatures in extremely warm populations and seasons. Thereby, calling temperatures differed both geographically and seasonally, both in terrestrial and aquatic species, and were 8-22 °C below the specific upper critical thermal limits (CTmax ) and strongly associated with the potential temperatures of each thermal environment (operative temperatures during the potential period of breeding). This suggests that calling behaviour in ectotherms may take place at population-specific thermal ranges, diverging when species are subjected to distinct thermal environments, and might imply plasticity of thermal adjustment mechanisms (seasonal and developmental acclimation) that supply species with means of coping with climate change. Furthermore, the thermal thresholds of calling at the onset of the breeding season were dissimilar between conspecific populations, suggesting that other factors besides temperature are needed to trigger the onset of reproduction. Our findings imply that global warming would not directly inhibit calling behaviour in the study species, although might affect other temperature-dependent features of their acoustic communication system.