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  1. Abstract

    Using sequences from 2,615 ultraconserved element (UCE) loci and multiple methodologies we inferred phylogenies for the largest genetic data set of New World bats in the genus Myotis to date. The resulting phylogenetic trees were populated with short branch lengths and widespread conflict, hallmarks consistent with rapid adaptive radiations. The degree of conflict observed in Myotis has likely contributed to difficulties disentangling deeper evolutionary relationships. Unlike earlier phylogenies based on 1 to 2 gene sequences, this UCE data set places M. brandtii outside the New World clades. Introgression testing of a small subset of our samples revealed evidence of historical but not contemporary gene flow, suggesting that hybridization occurs less frequently in the Neotropics than the Nearctic. We identified several instances of cryptic lineages within described species as well as several instances of potential taxonomic oversplitting. Evidence from Central and South American localities suggests that diversity in those regions is not fully characterized. In light of the accumulated evidence of the evolutionary complexity in Myotis and our survey of the taxonomic implications from our phylogenies, it is apparent that the definition of species and regime of species delimitation need to be reevaluated for Myotis. This will require substantial collaboration and sample sharing between geneticists and taxonomists to build a system that is both robust and applicable in a genus as diverse as Myotis.

     
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  2. Abstract

    Here we investigate possible carryover effects of experimentally increased incubation temperatures for postnatal growth, metabolism, and parental care within and among 6 north temperate and one tropical songbird species. Increased temperatures during embryonic development consistently caused higher postnatal resting metabolism compared to control nests, among but not within the 7 species studied. The effects of the experiment on growth were species specific and depended on the morphometric considered. Size before the fledge date was positively correlated with feeding rate, and metabolism was lower in larger broods. Our experiment did not elicit changes in parental food delivery rates or brooding effort during the postnatal stage, and higher brooding effort was associated with nestlings of smaller mass and faster metabolism independently from treatment. Consequently, parental care seemed unlikely to be the cause of the differences in growth rates between treatments. Instead, physiological mechanisms triggered by our heating treatment appear to be responsible for the observed variation in growth. These intrinsic changes unmatched by adjustments in parental effort may contribute to longer-term consequences for individual quality and survival that deserve further attention.

     
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  3. HorologionValentine, one of the rarest and most enigmatic carabid beetle genera in the world, was until now known only from the holotype ofHorologion speokoitesValentine, discovered in 1931 in a small cave in West Virginia. A single specimen of a new species from Virginia was collected in 1991, but overlooked until 2018. DNA sequence data from specimens of this new species,Horologion hubbardisp. nov., collected in 2022 and 2023, as well as a critical examination of the external morphology of both species, allow us to confidently placeHorologionin the supertribe Trechitae, within a clade containing Bembidarenini and Trechini. A more specific placement as sister to the Gondwanan Bembidarenini is supported by DNA sequence data. Previous hypotheses placingHorologionin or near the tribes Anillini, Tachyini, Trechini, Patrobini, and Psydrini are rejected. The existence of two species ofHorologionon opposite sides of the high mountains of the middle Appalachians suggests that these mountains are where the ancestralHorologionpopulations dispersed from, and predicts the discovery of additional populations and species. All specimens ofH. hubbardiwere collected in or near drip pools, and most were found dead, suggesting that the terrestrial epikarst, rather than caves, is the true habitat ofHorologion, which explains their extreme rarity since epikarst has not been directly sampled. We recognize the tribe Horologionini, a relict lineage without any close relatives known in the Northern Hemisphere, and an important part of Appalachian biodiversity.

     
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    Free, publicly-accessible full text available January 8, 2025
  4. Abstract

    Real-world computers have operational constraints that cause nonzero entropy production (EP). In particular, almost all real-world computers are ‘periodic’, iteratively undergoing the same physical process; and ‘local’, in that subsystems evolve whilst physically decoupled from the rest of the computer. These constraints are so universal because decomposing a complex computation into small, iterative calculations is what makes computers so powerful. We first derive the nonzero EP caused by the locality and periodicity constraints for deterministic finite automata (DFA), a foundational system of computer science theory. We then relate this minimal EP to the computational characteristics of the DFA. We thus divide the languages recognised by DFA into two classes: those that can be recognised with zero EP, and those that necessarily have non-zero EP. We also demonstrate the thermodynamic advantages of implementing a DFA with a physical process that is agnostic about the inputs that it processes.

     
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  5. After successfully diversifying during the Paleocene, the descendants of the first wave of mammals that survived the end‐Cretaceous mass extinction waned throughout the Eocene. Competition with modern crown clades and intense climate fluctuations may have been part of the factors leading to the extinction of these archaic groups. Why these taxa went extinct has rarely been studied from the perspective of the nervous system. Here, we describe the first virtual endocasts for the archaic order Tillodontia. Three species from the middle Eocene of North America were analyzed: Trogosus hillsii, Trogosus grangeri, and Trogosus castoridens. We made morphological comparisons with the plaster endocast of another tillodont,Tillodon fodiens, as well as groups potentially related to Tillodontia: Pantodonta, Arctocyonidae, and Cimolesta. Trogosus shows very little inter‐specific variation with the only potential difference being related to the fusion of the optic canal and sphenorbital fissure. Many ancestral features are displayed by Trogosus, including an exposed midbrain, small neocortex, orbitotemporal canal ventral to rhinal fissure, and a broad circular fissure. Potential characteristics that could unite Tillodontia with Pantodonta, and Arctocyonidae are the posterior position of cranial nerve V3 exit in relation to the cerebrum and the low degree of development of the subarcuate fossa. The presence of large olfactory bulbs and a relatively small neocortex are consistent with a terrestrial lifestyle. A relatively small neocortex may have put Trogosus at risk when competing with artiodactyls for potentially similar resources and avoiding predation from archaic carnivorans, both of which are known to have had larger relative brain and neocortex sizes in the Eocene. These factors may have possibly exacerbated the extinction of Tillodontia, which showed highly specialized morphologies despite the increase in climate fluctuations throughout the Eocene, before disappearing during the middle Eocene. 
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    Free, publicly-accessible full text available January 1, 2025
  6. Abstract

    Medical digital twins are computational models of human biology relevant to a given medical condition, which are tailored to an individual patient, thereby predicting the course of disease and individualized treatments, an important goal of personalized medicine. The immune system, which has a central role in many diseases, is highly heterogeneous between individuals, and thus poses a major challenge for this technology. In February 2023, an international group of experts convened for two days to discuss these challenges related to immune digital twins. The group consisted of clinicians, immunologists, biologists, and mathematical modelers, representative of the interdisciplinary nature of medical digital twin development. A video recording of the entire event is available. This paper presents a synopsis of the discussions, brief descriptions of ongoing digital twin projects at different stages of progress. It also proposes a 5-year action plan for further developing this technology. The main recommendations are to identify and pursue a small number of promising use cases, to develop stimulation-specific assays of immune function in a clinical setting, and to develop a database of existing computational immune models, as well as advanced modeling technology and infrastructure.

     
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  7. Due to its refractory properties and higher oxidation resistance, iridium (Ir) exhibits great potential for applications such as thermophotovoltaic emitters or contamination sensing. However, the lack of its temperature-dependent optical data prevents accurate modeling of Ir-based optical devices operating at higher temperatures. In this work, refractive indices of as-deposited and annealed Ir films, sputter-deposited, are characterized at between room temperature and 550°C over 300 nm to 15 µm of wavelength. The extinction coefficients of both as-deposited and annealed Ir films tend to decrease as temperature increases, with the exception of as-deposited Ir at 550°C due to significant grain growth. Under 530°C, optical constants of as-deposited Ir are less sensitive to temperature than those of annealed Ir. These characteristics of Ir films are correlated with their microstructural changes.

     
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  8. Free, publicly-accessible full text available May 16, 2024
  9. Free, publicly-accessible full text available October 1, 2024