Ancient genomes reveal over two thousand years of dingo population structure.

Dingoes are culturally and ecologically important free-living canids whose ancestors arrived in Australia over 3,000 B.P., likely transported by seafaring people. However, the early history of dingoes in Australia-including the number of founding populations and their routes of introduction-remains uncertain. This uncertainty arises partly from the complex and poorly understood relationship between modern dingoes and New Guinea singing dogs, and suspicions that post-Colonial hybridization has introduced recent domestic dog ancestry into the genomes of many wild dingo populations. In this study, we analyzed genome-wide data from nine ancient dingo specimens ranging in age from 400 to 2,746 y old, predating the introduction of domestic dogs to Australia by European colonists. We uncovered evidence that the continent-wide population structure observed in modern dingo populations had already emerged several thousand years ago. We also detected excess allele sharing between New Guinea singing dogs and ancient dingoes from coastal New South Wales (NSW) compared to ancient dingoes from southern Australia, irrespective of any post-Colonial hybrid ancestry in the genomes of modern individuals. Our results are consistent with several demographic scenarios, including a scenario where the ancestry of dingoes from the east coast of Australia results from at least two waves of migration from source populations with varying affinities to New Guinea singing dogs. We also contribute to the growing body of evidence that modern dingoes derive little genomic ancestry from post-Colonial hybridization with other domestic dog lineages, instead descending primarily from ancient canids introduced to Sahul thousands of years ago.

Corrigendum: Translatability of findings from cynomolgus monkey to human suggests a mechanistic role for IL-21 in promoting immunogenicity to an anti-PD-1/IL-21 mutein fusion protein.

[This corrects the article DOI: 10.3389/fimmu.2024.1345473.].

An Anthropomorphic Diagnosis System of Pulmonary Nodules using Weak Annotation-Based Deep Learning.

Purpose: To develop an anthropomorphic diagnosis system of pulmonary nodules (PN) based on Deep learning (DL) that is trained by weak annotation data and has comparable performance to full-annotation based diagnosis systems. Methods: The proposed system uses deep learning (DL) models to classify PNs (benign vs. malignant) with weak annotations, which eliminates the need for time-consuming and labor-intensive manual annotations of PNs. Moreover, the PN classification networks, augmented with handcrafted shape features acquired through the ball-scale transform technique, demonstrate capability to differentiate PNs with diverse labels, including pure ground-glass opacities, part-solid nodules, and solid nodules. Results: The experiments were conducted on two lung CT datasets: (1) public LIDC-IDRI dataset with 1,018 subjects, (2) In-house dataset with 2740 subjects. Through 5-fold cross-validation on two datasets, the system achieved the following results: (1) an Area Under Curve (AUC) of 0.938 for PN localization and an AUC of 0.912 for PN differential diagnosis on the LIDC-IDRI dataset of 814 testing cases, (2) an AUC of 0.943 for PN localization and an AUC of 0.815 for PN differential diagnosis on the in-house dataset of 822 testing cases. These results demonstrate comparable performance to full annotation-based diagnosis systems. Conclusions: Our system can efficiently localize and differentially diagnose PNs even in resource-limited environments with good robustness across different grade and morphology sub-groups in the presence of deviations due to the size, shape, and texture of the nodule, indicating its potential for future clinical translation. Summary: An anthropomorphic diagnosis system of pulmonary nodules (PN) based on deep learning and weak annotation was found to achieve comparable performance to full-annotation dataset-based diagnosis systems, significantly reducing the time and the cost associated with the annotation. Key Points: A fully automatic system for the diagnosis of PN in CT scans using a suitable deep learning model and weak annotations was developed to achieve comparable performance (AUC = 0.938 for PN localization, AUC = 0.912 for PN differential diagnosis) with the full-annotation based deep learning models, reducing around 30%∼80% of annotation time for the experts.The integration of the hand-crafted feature acquired from human experts (natural intelligence) into the deep learning networks and the fusion of the classification results of multi-scale networks can efficiently improve the PN classification performance across different diameters and sub-groups of the nodule.

Translatability of findings from cynomolgus monkey to human suggests a mechanistic role for IL-21 in promoting immunogenicity to an anti-PD-1/IL-21 mutein fusion protein.

AMG 256 is a bi-specific, heteroimmunoglobulin molecule with an anti-PD-1 antibody domain and a single IL-21 mutein domain on the C-terminus. Nonclinical studies in cynomolgus monkeys revealed that AMG 256 administration led to the development of immunogenicity-mediated responses and indicated that the IL-21 mutein domain of AMG 256 could enhance the anti-drug antibody response directed toward the monoclonal antibody domain. Anti-AMG 256 IgE were also observed in cynomolgus monkeys. A first-in-human (FIH) study in patients with advanced solid tumors was designed with these risks in mind. AMG 256 elicited ADA in 28 of 33 subjects (84.8%). However, ADA responses were only robust and exposure-impacting at the 2 lowest doses. At mid to high doses, ADA responses remained low magnitude and all subjects maintained exposure, despite most subjects developing ADA. Limited drug-specific IgE were also observed during the FIH study. ADA responses were not associated with any type of adverse event. The AMG 256 program represents a unique case where nonclinical studies informed on the risk of immunogenicity in humans, due to the IL-21-driven nature of the response.

A geometric morphometric analysis of variation in Australian frog ilia and taxonomic interpretations.

Anurans including frogs and toads exhibit an ilium that is often regarded as taxonomically diagnostic. The ilium, one of the three paired bones that make up the pelvic girdle, has been important in the fossil record for identifying anuran morphotypes. Osteological collections for Australian frogs are rare in herpetological museums, and skeletonizing whole-bodied specimens requires destroying soft tissue morphology which is valuable to anuran specialists working on living species. Computed tomography scans provide the opportunity to study anuran osteology without the loss of soft tissues. Our study, based on microcomputed tomography scans of extant Australian frogs from the public repository Morphosource and from museum collections focuses on the morphological differences between Australian frogs at the familial and generic levels using geometric morphometrics to compare the diagnostic shape of the ilium. Principal component analysis (PCA) and canonical variate analysis (CVA) were conducted to assess differences in the ilium between supraspecific groups of Australian frogs. The canonical variates analysis accurately predicted group membership (i.e., the correct family) with up to 76.2% success for cross-validated predictions and 100% of original group predictions. While the sample was limited to familial and generic level analyses, our research shows that ilial morphology in Australian frogs is taxonomically informative. This research provides a guide for identifying Australian anurans, including fossils, as well as new information relevant to considerations about their phylogenetic relationships, and the potential use of the fossil record to enhance efforts to conserve threatened living frog species.

Patterns of ontogenetic evolution across extant marsupials reflect different allometric pathways to ecomorphological diversity.

The relatively high level of morphological diversity in Australasian marsupials compared to that observed among American marsupials remains poorly understood. We undertake a comprehensive macroevolutionary analysis of ontogenetic allometry of American and Australasian marsupials to examine whether the contrasting levels of morphological diversity in these groups are reflected in their patterns of allometric evolution. We collate ontogenetic series for 62 species and 18 families of marsupials (n = 2091 specimens), spanning across extant marsupial diversity. Our results demonstrate significant lability of ontogenetic allometric trajectories among American and Australasian marsupials, yet a phylogenetically structured pattern of allometric evolution is preserved. Here we show that species diverging more than 65 million years ago converge in their patterns of ontogenetic allometry under animalivorous and herbivorous diets, and that Australasian marsupials do not show significantly greater variation in patterns of ontogenetic allometry than their American counterparts, despite displaying greater magnitudes of extant ecomorphological diversity.

Xenorhinos bhatnagari sp. nov., a new, nasal-emitting trident bat (Rhinonycteridae, Rhinolophoidea) from early Miocene forests in northern Australia.

A new Old World trident bat (Rhinonycteridae) is described from an early Miocene cave deposit in the Riversleigh World Heritage Area, northwestern Queensland, Australia. Living rhinonycterids comprise a small family of insect-eating, nasal-emitting rhinolophoid bats from Africa, Madagascar, Seychelles, the Middle East, and northern Australia. The new fossil species is one of at least 12 rhinonycterid species known from the Oligo-Miocene cave deposits at Riversleigh. We refer the new species to the genus Xenorhinos (Hand, Journal of Vertebrate Paleontology, 18, 430-439, 1998a) because it shares a number of unusual cranial features with the type and only other species of the genus, X. halli, including a broad rostrum, very wide interorbital region, pronounced ventral flexion of the rostrum, very constricted sphenoidal bridge, and, within the nasal fossa, reduced bony division, and relatively well developed turbinals. Xenorhinos species lived in northern Australia during the global Miocene Climatic Optimum, in closed wet forests, unlike the drier habitats that trident bats largely inhabit today. Our phylogenetic analysis suggests that more than one dispersal event gave rise to the Australian rhinonycterid radiation, with two lineages having sister-group relationships with non-Australian taxa.

Secondary Degeneration Impairs Myelin Ultrastructural Development in Adulthood following Adolescent Neurotrauma in the Rat Optic Nerve.

Adolescence is a critical period of postnatal development characterized by social, emotional, and cognitive changes. These changes are increasingly understood to depend on white matter development. White matter is highly vulnerable to the effects of injury, including secondary degeneration in regions adjacent to the primary injury site which alters the myelin ultrastructure. However, the impact of such alterations on adolescent white matter maturation is yet to be investigated. To address this, female piebald-virol-glaxo rats underwent partial transection of the optic nerve during early adolescence (postnatal day (PND) 56) with tissue collection two weeks (PND 70) or three months later (PND 140). Axons and myelin in the transmission electron micrographs of tissue adjacent to the injury were classified and measured based on the appearance of the myelin laminae. Injury in adolescence impaired the myelin structure in adulthood, resulting in a lower percentage of axons with compact myelin and a higher percentage of axons with severe myelin decompaction. Myelin thickness did not increase as expected into adulthood after injury and the relationship between the axon diameter and myelin thickness in adulthood was altered. Notably, dysmyelination was not observed 2 weeks postinjury. In conclusion, injury in adolescence altered the developmental trajectory, resulting in impaired myelin maturation when assessed at the ultrastructural level in adulthood.

A swan-sized fossil anatid (Aves: Anatidae) from the early Miocene St Bathans Fauna of New Zealand.

A large fossil anserine-like anatid (Aves, Anatidae, Notochen bannockburnensis gen. et sp. nov.) is described based on a distal humerus from the lower Bannockburn Formation, early Miocene (1916 Ma), St Bathans Fauna from New Zealand. Its morphology and size suggest that this taxon represents an early swan rather than a goose. Extant anserines are split into Northern and Southern Hemisphere clades. The St Bathans Fauna is known to have the oldest anserines in the Southern Hemisphere, unnamed cereopsines perhaps ancestral to species of Cnemiornis (New Zealand geese). The elongate and flat morphology of the tuberculum supracondylare ventrale of the new species, however, preclude affinities with cereopsines. It is a rare taxon and the eighth anatid represented in the fauna and is the largest known anseriform from the Oligo-Miocene of Australasia. We also reassess other large anatid specimens from the St Bathans Fauna and identify Miotadorna catrionae Tennyson, Greer, Lubbe, Marx, Richards, Giovanardi Rawlence, 2022 as a junior synonym of Miotadorna sanctibathansi Worthy, Tennyson, Jones, McNamara Douglas, 2007.

Sheath-tailed bats (Chiroptera: Emballonuridae) from the early Pleistocene Rackham's Roost Site, Riversleigh World Heritage Area, and the distribution of northern Australian emballonurid species.

Sheath-tailed bats (Family Emballonuridae) from the early Pleistocene Rackham's Roost Site cave deposit in the Riversleigh World Heritage Area, north-western Queensland are the oldest recorded occurrence for the family in Australia. The fossil remains consist of maxillary and dentary fragments, as well as isolated teeth, but until now their precise identity has not been assessed. Our study indicates that at least three taxa are represented, and these are distinguished from other Australian emballonurids based on morphometric analysis of craniodental features. Most of the Rackham's Roost Site emballonurid remains are referrable to the modern species Taphozous georgianus Thomas, 1915, but the extant species T. troughtoni Tate, 1952 also appears to be present, as well as a very large, as-yet undetermined species of Saccolaimus Temminck, 1838. We identify craniodental features that clearly distinguish T. georgianus from the externally very similar T. troughtoni. Results suggest that the distributions of T. georgianus and T. troughtoni may have overlapped in north-western Queensland since at least the early Pleistocene.

Natural Compound α-PGG and Its Synthetic Derivative 6Cl-TGQ Alter Insulin Secretion: Evidence for Diminishing Glucose Uptake as a Mechanism.

PURPOSE: Previously we showed that natural compound α-penta-galloyl-glucose (α-PGG) and its synthetic derivative 6-chloro-6-deoxy-1,2,3,4-tetra-O-galloyl-α-D-glucopyranose (6Cl-TGQ) act to improve insulin signaling in adipocytes by increasing glucose transport. In this study, we investigated the mechanism of actions of α-PGG and 6Cl-TGQ on insulin secretion. METHODS: Mouse islets and/or INS-1832/13 beta-cells were used to test the effects of our compounds on glucose-stimulated insulin secretion (GSIS), intracellular calcium [Ca2+]i using fura-2AM, glucose transport activity via a radioactive glucose uptake assay, intracellular ATP/ADP, and extracellular acidification (ECAR) and mitochondrial oxygen consumption rates (OCAR) using Seahorse metabolic analysis. RESULTS: Both compounds reduced GSIS in beta-cells without negatively affecting cell viability. The compounds primarily diminished glucose uptake into islets and beta-cells. Despite insulin-like effects in the peripheral tissues, these compounds do not act through the insulin receptor in islets. Further interrogation of the stimulus-secretion pathway showed that all the key metabolic factors involved in GSIS including ECAR, OCAR, ATP/ADP ratios, and [Ca2+]i of INS-1832/13 cells were diminished after the compound treatment. CONCLUSION: The compounds suppress glucose uptake of the beta-cells, which consequently slows down the rates of glycolysis and ATP synthesis, leading to decrease in [Ca2+]i and GSIS. The difference between adipocytes and beta-cells in effects on glucose uptake is of great interest. Further structural and functional modifications could produce new compounds with optimized therapeutic potentials for different target cells. The higher potency of synthetic 6Cl-TGQ in enhancing insulin signaling in adipocytes but lower potency in reducing glucose uptake in beta-cells compared to α-PGG suggests the feasibility of such an approach.

Global elongation and high shape flexibility as an evolutionary hypothesis of accommodating mammalian brains into skulls.

Little is known about how the large brains of mammals are accommodated into the dazzling diversity of their skulls. It has been suggested that brain shape is influenced by relative brain size, that it evolves or develops according to extrinsic or intrinsic mechanical constraints, and that its shape can provide insights into its proportions and function. Here, we characterize the shape variation among 84 marsupial cranial endocasts of 57 species including fossils, using three-dimensional geometric morphometrics and virtual dissections. Statistical shape analysis revealed four main patterns: over half of endocast shape variation ranges from elongate and straight to globular and inclined; little allometric variation with respect to centroid size, and none for relative volume; no association between locomotion and endocast shape; limited association between endocast shape and previously published histological cortex volumes. Fossil species tend to have smaller cerebral hemispheres. We find divergent endocast shapes in closely related species and within species, and diverse morphologies superimposed over the main variation. An evolutionarily and individually malleable brain with a fundamental tendency to arrange into a spectrum of elongate-to-globular shapes-possibly mostly independent of brain function-may explain the accommodation of brains within the enormous diversity of mammalian skull form.

Does Tweeting Improve Citations? One-Year Results From the TSSMN Prospective Randomized Trial.

BACKGROUND: The Thoracic Surgery Social Media Network (TSSMN) is a collaborative effort of leading journals in cardiothoracic surgery to highlight publications via social media. This study aims to evaluate the 1-year results of a prospective randomized social media trial to determine the effect of tweeting on subsequent citations and nontraditional bibliometrics. METHODS: A total of 112 representative original articles were randomized 1:1 to be tweeted via TSSMN or a control (non-tweeted) group. Measured endpoints included citations at 1 year compared with baseline, as well as article-level metrics (Altmetric score) and Twitter analytics. Independent predictors of citations were identified through univariable and multivariable regression analyses. RESULTS: When compared with control articles, tweeted articles achieved significantly greater increase in Altmetric scores (Tweeted 9.4 ± 5.8 vs Non-tweeted 1.0 ± 1.8, P < .001), Altmetric score percentiles relative to articles of similar age from each respective journal (Tweeted 76.0 ± 9.1 percentile vs Non-tweeted 13.8 ± 22.7 percentile, P < .001), with greater change in citations at 1 year (Tweeted +3.1 ± 2.4 vs Non-Tweeted +0.7 ± 1.3, P < .001). Multivariable analysis showed that independent predictors of citations were randomization to tweeting (odds ratio [OR] 9.50; 95% confidence interval [CI] 3.30-27.35, P < .001), Altmetric score (OR 1.32; 95% CI 1.15-1.50, P < .001), open-access status (OR 1.56; 95% CI 1.21-1.78, P < .001), and exposure to a larger number of Twitter followers as quantified by impressions (OR 1.30, 95% CI 1.10-1.49, P < .001). CONCLUSIONS: One-year follow-up of this TSSMN prospective randomized trial importantly demonstrates that tweeting results in significantly more article citations over time, highlighting the durable scholarly impact of social media activity.

Evaluation of Residues in Hen Eggs After Exposure of Laying Hens to Water Containing Per- and Polyfluoroalkyl Substances.

Per- and polyfluoroalkyl substances (PFAS) have been used in aqueous film-forming foams used in firefighting, resulting in soil and groundwater contamination and leading to human exposure via animal products grown in contaminated areas. The present study reports the relationship between PFAS intake by hens and the PFAS concentrations in the edible parts of eggs. Laying hens were exposed via drinking water to different concentrations of 4 PFAS compounds (perfluorooctane sulfonate [PFOS], perfluorohexane sulfonate [PFHxS], perfluorooctanoic acid [PFOA], and perfluorohexanoic acid) over 61 d. Egg PFAS residues were assessed for a further 30 d after exposure ceased. The target concentrations of PFAS were 0, 0.3, 3, 30, and 300 µg/L for the treatment groups T1-T5, respectively; and PFAS residues were determined from the eggs collected every second day. There was a linear correlation between the PFAS concentrations in the drinking water of hens and those detected in the egg, which could be useful in estimating PFAS concentrations in the egg by measuring water concentrations. Exposure of hens to drinking water with PFAS concentrations below the Australian Government Department of Health limits (PFOS and PFHxS, 0.07 µg/L; PFOA, 0.56 µg/L), and with no other sources of PFAS exposure, is unlikely to result in egg PFAS concentrations that would exceed the 10% limit set by Food Standards Australia New Zealand for human consumption. Environ Toxicol Chem 2021;40:735-743. © 2020 SETAC.

Siderophore-Assisted Dissolution of Iron(III) Hydroxide Oxides from Iron-Rich Fossil Matrices.

Current paleontological techniques to separate vertebrate fossils from encasing iron-rich cements by chemical means are limited by the low solubility of common iron(III) hydroxide oxides such as hematite and goethite. This study examines novel geochemical extractions capable of selectively dissolving iron(III) hydroxide oxides, in aqueous solutions of pH 9-11, without damaging fossilised bones or teeth (hydroxidecarbonate-apatite). This involves the siderophore ligands pyridoxal isonicotinoyl hydrazone (PIH), salicylaldehyde isonicotinoyl hydrazone (SIH), and acetohydroxamic acid (aHA), whose coordination complexes with iron(III) show exceptionally high formation stability constants. The methods have been tested on natural hematite and fossil containing samples from the Riversleigh World Heritage Area in Australia. Both 0.01 mol dm-3 aHA and 0.001 mol dm-3 PIH at pH 9.7 were able to dissolve over 0.1 mmol dm-3 of the goethite coating bone fragments.

Quantitatively assessing mekosuchine crocodile locomotion by geometric morphometric and finite element analysis of the forelimb.

Morphological shifts observed in the fossil record of a lineage potentially indicate concomitant shifts in ecology of that lineage. Mekosuchine crocodiles of Cenozoic Australia display departures from the typical eusuchian body-plan both in the cranium and postcranium. Previous qualitative studies have suggested that these crocodiles had a more terrestrial habitus than extant crocodylians, yet the capacity of mekosuchine locomotion remains to be tested. Limb bone shape, such as diaphyseal cross-section and curvature, has been related to habitual use and locomotory function across a wide variety of taxa. Available specimens of mekosuchine limbs, primarily humeri, are distinctly columnar compared with those of extant crocodylians. Here we apply a quantitative approach to biomechanics in mekosuchine taxa using both geomorphic morphometric and finite element methods to measure bone shape and estimate locomotory stresses in a comparative context. Our results show mekosuchines appear to diverge from extant semi-aquatic saltwater and freshwater crocodiles in cross-sectional geometry of the diaphysis and generate different structural stresses between models that simulate sprawling and high-walk gaits. The extant crocodylians display generally rounded cross-sectional diaphyseal outlines, which may provide preliminary indication of resistance to torsional loads that predominate during sprawling gait, whereas mekosuchine humeri appear to vary between a series of elliptical outlines. Mekosuchine structural stresses are comparatively lower than those of the extant crocodylians and reduce under high-walk gait in some instances. This appears to be a function of bending moments induced by differing configurations of diaphyseal curvature. Additionally, the neutral axis of structural stresses is differently oriented in mekosuchines. This suggests a shift in the focus of biomechanical optimisation, from torsional to axial loadings. Our results lend quantitative support to the terrestrial habitus hypothesis in so far as they suggest that mekosuchine humeri occupied a different morphospace than that associated with the semi-aquatic habit. The exact adaptational trajectory of mekosuchines, however, remains to be fully quantified. Novel forms appear to emerge among mekosuchines during the late Cenozoic. Their adaptational function is considered here; possible applications include navigation of uneven terrain and burrowing.

A new family of diprotodontian marsupials from the latest Oligocene of Australia and the evolution of wombats, koalas, and their relatives (Vombatiformes).

We describe the partial cranium and skeleton of a new diprotodontian marsupial from the late Oligocene (~26-25 Ma) Namba Formation of South Australia. This is one of the oldest Australian marsupial fossils known from an associated skeleton and it reveals previously unsuspected morphological diversity within Vombatiformes, the clade that includes wombats (Vombatidae), koalas (Phascolarctidae) and several extinct families. Several aspects of the skull and teeth of the new taxon, which we refer to a new family, are intermediate between members of the fossil family Wynyardiidae and wombats. Its postcranial skeleton exhibits features associated with scratch-digging, but it is unlikely to have been a true burrower. Body mass estimates based on postcranial dimensions range between 143 and 171 kg, suggesting that it was ~5 times larger than living wombats. Phylogenetic analysis based on 79 craniodental and 20 postcranial characters places the new taxon as sister to vombatids, with which it forms the superfamily Vombatoidea as defined here. It suggests that the highly derived vombatids evolved from wynyardiid-like ancestors, and that scratch-digging adaptations evolved in vombatoids prior to the appearance of the ever-growing (hypselodont) molars that are a characteristic feature of all post-Miocene vombatids. Ancestral state reconstructions on our preferred phylogeny suggest that bunolophodont molars are plesiomorphic for vombatiforms, with full lophodonty (characteristic of diprotodontoids) evolving from a selenodont morphology that was retained by phascolarctids and ilariids, and wynyardiids and vombatoids retaining an intermediate selenolophodont condition. There appear to have been at least six independent acquisitions of very large (>100 kg) body size within Vombatiformes, several having already occurred by the late Oligocene.