Unified Maxwell-Einstein and Yang-Mills-Einstein Supergravity Theories in Five Dimensions

Unified N=2 Maxwell-Einstein supergravity theories (MESGTs) are supergravity theories in which all the vector fields, including the graviphoton, transform in an irreducible representation of a simple global symmetry group of the Lagrangian. As was established long time ago, in five dimensions there exist only four unified Maxwell-Einstein supergravity theories whose target manifolds are symmetric spaces. These theories are defined by the four simple Euclidean Jordan algebras of degree three. In this paper, we show that, in addition to these four unified MESGTs with symmetric target spaces, there exist three infinite families of unified MESGTs as well as another exceptional one. These novel unified MESGTs are defined by non-compact (Minkowskian) Jordan algebras, and their target spaces are in general neither symmetric nor homogeneous. The members of one of these three infinite families can be gauged in such a way as to obtain an infinite family of unified N=2 Yang-Mills-Einstein supergravity theories, in which all vector fields transform in the adjoint representation of a simple gauge group of the type SU(N,1). The corresponding gaugings in the other two infinite families lead to Yang-Mills-Einstein supergravity theories coupled to tensor multiplets.Comment: Latex 2e, 28 pages. v2: reference added, footnote 14 enlarge

Microfluidic Synthesis of Microfibers for Magnetic-Responsive Controlled Drug Release and Cell Culture

This study demonstrated the fabrication of alginate microfibers using a modular microfluidic system for magnetic-responsive controlled drug release and cell culture. A novel two-dimensional fluid-focusing technique with multi-inlets and junctions was used to spatiotemporally control the continuous laminar flow of alginate solutions. The diameter of the manufactured microfibers, which ranged from 211 µm to 364 µm, could be well controlled by changing the flow rate of the continuous phase. While the model drug, diclofenac, was encapsulated into microfibers, the drug release profile exhibited the characteristic of a proper and steady release. Furthermore, the diclofenac release kinetics from the magnetic iron oxide-loaded microfibers could be controlled externally, allowing for a rapid drug release by applying a magnetic force. In addition, the successful culture of glioblastoma multiforme cells in the microfibers demonstrated a good structural integrity and environment to grow cells that could be applied in drug screening for targeting cancer cells. The proposed microfluidic system has the advantages of ease of fabrication, simplicity, and a fast and low-cost process that is capable of generating functional microfibers with the potential for biomedical applications, such as drug controlled release and cell culture

New genetic loci link adipose and insulin biology to body fat distribution.

Body fat distribution is a heritable trait and a well-established predictor of adverse metabolic outcomes, independent of overall adiposity. To increase our understanding of the genetic basis of body fat distribution and its molecular links to cardiometabolic traits, here we conduct genome-wide association meta-analyses of traits related to waist and hip circumferences in up to 224,459 individuals. We identify 49 loci (33 new) associated with waist-to-hip ratio adjusted for body mass index (BMI), and an additional 19 loci newly associated with related waist and hip circumference measures (P < 5 × 10(-8)). In total, 20 of the 49 waist-to-hip ratio adjusted for BMI loci show significant sexual dimorphism, 19 of which display a stronger effect in women. The identified loci were enriched for genes expressed in adipose tissue and for putative regulatory elements in adipocytes. Pathway analyses implicated adipogenesis, angiogenesis, transcriptional regulation and insulin resistance as processes affecting fat distribution, providing insight into potential pathophysiological mechanisms

Visual Microfossil Identification via Deep Metric Learning

We apply deep metric learning for the first time to the problem of classifying planktic foraminifer shells on microscopic images. This species recognition task is an important information source and scientific pillar for reconstructing past climates. All foraminifer CNN recognition pipelines in the literature produce black-box classifiers that lack visualization options for human experts and cannot be applied to open-set problems. Here, we benchmark metric learning against these pipelines, produce the first scientific visualization of the phenotypic planktic foraminifer morphology space, and demonstrate that metric learning can be used to cluster species unseen during training. We show that metric learning outperforms all published CNN-based state-of-the-art benchmarks in this domain. We evaluate our approach on the 34,640 expert-annotated images of the Endless Forams public library of 35 modern planktic foraminifera species. Our results on this data show leading 92% accuracy (at 0.84 F1-score) in reproducing expert labels on withheld test data, and 66.5% accuracy (at 0.70 F1-score) when clustering species never encountered in training. We conclude that metric learning is highly effective for this domain and serves as an important tool towards expert-in-the-loop automation of microfossil identification. Keycode, network weights, and data splits are published with this paper for full reproducibility

Timing the Extant Avian Radiation: The Rise of Modern Birds, and the Importance of Modeling Molecular Rate Variation

Unravelling the phylogenetic relationships among the major groups of living birds has been described as the greatest outstanding problem in dinosaur systematics. Recent work has identified portions of the avian tree of life that are particularly challenging to reconstruct, perhaps as a result of rapid cladogenesis early in crown bird evolutionary history (specifically, the interval immediately following the end-Cretaceous mass extinction). At face value this hypothesis enjoys support from the crown bird fossil record, which documents the first appearances of most major crown bird lineages in the early Cenozoic-in line with a model of rapid postextinction niche-filling among surviving avian lineages. However, molecular-clock analyses have yielded strikingly variable estimates for the age of crown birds, and conflicting inferences on the impact of the end-Cretaceous mass extinction on the extant bird radiation. This uncertainty has often been ascribed to a patchy avian fossil record, but the possibility of model misspecification in molecular divergence-time analyses represents an important and relatively underexplored alternative hypothesis. Here, we highlight the necessity of further developing and using models that account for coordinated variation in rates of molecular evolution across a phylogeny (e.g., molecular early burst) as a means of assessing support for a rapid post-Cretaceous radiation of crown birds. We discuss how relationships between life history and substitution rates can mislead divergence-time studies that do not account for directional changes in substitution rates over time, and suggest that these effects might have caused some of the variation in existing molecular date estimates for birds. We suggest multiple paths forward that could help resolve this and similar conflicts within other major eukaryotic clades

Data from: The origin of snakes: revealing the ecology, behavior, and evolutionary history of early snakes using genomics, phenomics, and the fossil record

Background: The highly derived morphology and astounding diversity of snakes has long inspired debate regarding the ecological and evolutionary origin of both the snake total-group (Pan-Serpentes) and crown snakes (Serpentes). Although speculation abounds on the ecology, behavior, and provenance of the earliest snakes, a rigorous, clade-wide analysis of snake origins has yet to be attempted, in part due to a dearth of adequate paleontological data on early stem snakes. Here, we present the first comprehensive analytical reconstruction of the ancestor of crown snakes and the ancestor of the snake total-group, as inferred using multiple methods of ancestral state reconstruction. We use a combined-data approach that includes new information from the fossil record on extinct crown snakes, new data on the anatomy of the stem snakes Najash rionegrina, Dinilysia patagonica, and Coniophis precedens, and a deeper understanding of the distribution of phenotypic apomorphies among the major clades of fossil and Recent snakes. Additionally, we infer time-calibrated phylogenies using both new ‘tip-dating’ and traditional node-based approaches, providing new insights on temporal patterns in the early evolutionary history of snakes. Results: Comprehensive ancestral state reconstructions reveal that both the ancestor of crown snakes and the ancestor of total-group snakes were nocturnal, widely foraging, non-constricting stealth hunters. They likely consumed soft-bodied vertebrate and invertebrate prey that was subequal to head size, and occupied terrestrial settings in warm, well-watered, and well-vegetated environments. The snake total-group – approximated by the Coniophis node – is inferred to have originated on land during the middle Early Cretaceous (~128.5 Ma), with the crown-group following about 20 million years later, during the Albian stage. Our inferred divergence dates provide strong evidence for a major radiation of henophidian snake diversity in the wake of the Cretaceous-Paleogene (K-Pg) mass extinction, clarifying the pattern and timing of the extant snake radiation. Although the snake crown-group most likely arose on the supercontinent of Gondwana, our results suggest the possibility that the snake total-group originated on Laurasia. Conclusions: Our study provides new insights into when, where, and how snakes originated, and presents the most complete picture of the early evolution of snakes to date. More broadly, we demonstrate the striking influence of including fossils and phenotypic data in combined analyses aimed at both phylogenetic topology inference and ancestral state reconstruction

Nexus file - genetic data only

Genetic data compiled from NCBI GenBank database (see Additional file 9 for accession numbers) for 21 nuclear loci and one mitochondrial locus. Generated using TextWrangler v. 4.0.1 (build 3152)

Data from: The origin of snakes: revealing the ecology, behavior, and evolutionary history of early snakes using genomics, phenomics, and the fossil record

Background: The highly derived morphology and astounding diversity of snakes has long inspired debate regarding the ecological and evolutionary origin of both the snake total-group (Pan-Serpentes) and crown snakes (Serpentes). Although speculation abounds on the ecology, behavior, and provenance of the earliest snakes, a rigorous, clade-wide analysis of snake origins has yet to be attempted, in part due to a dearth of adequate paleontological data on early stem snakes. Here, we present the first comprehensive analytical reconstruction of the ancestor of crown snakes and the ancestor of the snake total-group, as inferred using multiple methods of ancestral state reconstruction. We use a combined-data approach that includes new information from the fossil record on extinct crown snakes, new data on the anatomy of the stem snakes Najash rionegrina, Dinilysia patagonica, and Coniophis precedens, and a deeper understanding of the distribution of phenotypic apomorphies among the major clades of fossil and Recent snakes. Additionally, we infer time-calibrated phylogenies using both new ‘tip-dating’ and traditional node-based approaches, providing new insights on temporal patterns in the early evolutionary history of snakes. Results: Comprehensive ancestral state reconstructions reveal that both the ancestor of crown snakes and the ancestor of total-group snakes were nocturnal, widely foraging, non-constricting stealth hunters. They likely consumed soft-bodied vertebrate and invertebrate prey that was subequal to head size, and occupied terrestrial settings in warm, well-watered, and well-vegetated environments. The snake total-group – approximated by the Coniophis node – is inferred to have originated on land during the middle Early Cretaceous (~128.5 Ma), with the crown-group following about 20 million years later, during the Albian stage. Our inferred divergence dates provide strong evidence for a major radiation of henophidian snake diversity in the wake of the Cretaceous-Paleogene (K-Pg) mass extinction, clarifying the pattern and timing of the extant snake radiation. Although the snake crown-group most likely arose on the supercontinent of Gondwana, our results suggest the possibility that the snake total-group originated on Laurasia. Conclusions: Our study provides new insights into when, where, and how snakes originated, and presents the most complete picture of the early evolution of snakes to date. More broadly, we demonstrate the striking influence of including fossils and phenotypic data in combined analyses aimed at both phylogenetic topology inference and ancestral state reconstruction

4-sq example for Automorph

4-sq is an example image and dataset created to be used as part of the Automorph tutorials. Automorph software and tutorials can be accessed here: https://github.com/HullLab These files include unprocessed images from an automatic scanning microscope and various output from the Automorph modules including segmented images, and 2D and 3D data extractions

Measurement verification data for AutoMorph vs. hand measurements

These data include comparisons between 2D and 3D measurements automatically extracted by the AutoMorph software (https://github.com/HullLab/AutoMorph) and those collected manually (i.e., using calipers, ImageJ, or VGSStudio Max for the 2D measurements, or using CT scans for the 3D measurements). These measurements are intended to demonstrate the breadth of AutoMorph's applicability, and help users determine whether the accuracy of AutoMorph is suitable for their needs. 2D measurements (specifically major and minor axis length and/or squared area) have been collected and presented here for fossil patellogastropods (limpets), extant bivalves, and ichthyoliths (i.e., fish teeth). 3D volume and surface area data have been collected for a sample of planktonic foraminifera. More information about how these data were collected, and discussion about the measurement comparisons, can be found in the manuscript describing AutoMorph, to be published in Methods in Ecology and Evolution (in press; DOI pending)