Applying 3D Models of Giant Salamanders to Explore Form-function Relationships in Early Digit-bearing Tetrapods.

Extant salamanders are used as modern analogs of early digit-bearing tetrapods due to general similarities in morphology and ecology but the study species have been primarily terrestrial and relatively small when the earliest digit-bearing tetrapods were aquatic and an order of magnitude larger. Thus, we created a 3D computational model of underwater walking in extant Japanese giant salamanders (Andrias japonicus) using 3D photogrammetry and open-access graphics software (Blender) to broaden the range of testable hypotheses about the incipient stages of terrestrial locomotion. Our 3D model and software protocol represent the initial stages of an open-access pipeline that could serve as a "one-stop-shop" for studying locomotor function, from creating 3D models to analyzing the mechanics of locomotor gaits. While other pipelines generally require multiple software programs to accomplish the different steps in creating and analyzing computational models of locomotion, our protocol is built entirely within Blender and fully customizable with its Python scripting so users can devote more time to creating and analyzing models instead of navigating the learning curves of several software programs. The main value of our approach is that key kinematic variables (e.g., speed, stride length, elbow flexion) can be easily altered on the 3D model, allowing scientists to test hypotheses about locomotor function and conduct manipulative experiments (e.g., lengthening bones) that are difficult to perform in vivo. The accurate 3D meshes (and animations) generated through photogrammetry also provide exciting opportunities to expand the abundance and diversity of 3D digital animals available for researchers, educators, artists, conservation biologists, etc. to maximize societal impacts.

Developments and applications of the OPTIMADE API for materials discovery, design, and data exchange.

The Open Databases Integration for Materials Design (OPTIMADE) application programming interface (API) empowers users with holistic access to a growing federation of databases, enhancing the accessibility and discoverability of materials and chemical data. Since the first release of the OPTIMADE specification (v1.0), the API has undergone significant development, leading to the v1.2 release, and has underpinned multiple scientific studies. In this work, we highlight the latest features of the API format, accompanying software tools, and provide an update on the implementation of OPTIMADE in contributing materials databases. We end by providing several use cases that demonstrate the utility of the OPTIMADE API in materials research that continue to drive its ongoing development.

The Generation of an ocular anti-inflammatory biotherapeutic to enhance wound healing.

Microbes exist at and colonize mucosal surfaces striking a balance with the host immune system, so that these microbes can thrive on host tissues without causing pathology. Because of this, mucosal barrier-colonizing bacteria can be leveraged to act as long-term delivery vehicles for naturally derived therapeutics. Here, we use a mouse model of corneal wound healing to show that the eye-colonizing bacterium, Corynebacterium mastitidis (C. mast) can be engineered to produce and secrete bioactive murine anti-inflammatory interleukin (mIL)-10. Specifically, we used transposon mutagenesis to identify a native C. mast-specific secretion signal that was used to direct C. mast to secrete mIL-10. Mini-transposons were generated to deliver secretion capable mIL-10 to the bacterial genome. After screening, two isolates were identified that can: 1) colonize the eye, 2) produce and secrete mIL-10, and 3) enhance wound healing in an IL-10-dependent manner. This proof of concept illustrates that eye-colonizing bacteria can be engineered to deliver therapeutics to the ocular surface for the alleviation of ocular surface disease(s).

Absolute pitch in involuntary musical imagery.

Memory for isolated absolute pitches is extremely rare in Western, English-speaking populations. However, past research has found that people can voluntarily reproduce well-known songs in the original key much more often than chance. It is unknown whether this requires deliberate effort or if it manifests in involuntary musical imagery (INMI, or earworms). Participants (N = 30, convenience sample) were surveyed at random times over a week and asked to produce a sung recording of any music they were experiencing in their heads. We measured the "pitch error" of each recording to the nearest semitone by comparing participants' recordings to the original song. We found that 44.7% of recordings had a pitch error of 0 semitones, and 68.9% of recordings were within ± 1 semitone of the original song. Our results provide novel evidence that a large proportion of the population has access to absolute pitch, as revealed in their INMI.

Development of an initial training and evaluation programme for manual lower limb muscle MRI segmentation.

BACKGROUND: Magnetic resonance imaging (MRI) quantification of intramuscular fat accumulation is a responsive biomarker in neuromuscular diseases. Despite emergence of automated methods, manual muscle segmentation remains an essential foundation. We aimed to develop a training programme for new observers to demonstrate competence in lower limb muscle segmentation and establish reliability benchmarks for future human observers and machine learning segmentation packages. METHODS: The learning phase of the training programme comprised a training manual, direct instruction, and eight lower limb MRI scans with reference standard large and small regions of interest (ROIs). The assessment phase used test-retest scans from two patients and two healthy controls. Interscan and interobserver reliability metrics were calculated to identify underperforming outliers and to determine competency benchmarks. RESULTS: Three experienced observers undertook the assessment phase, whilst eight new observers completed the full training programme. Two of the new observers were identified as underperforming outliers, relating to variation in size or consistency of segmentations; six had interscan and interobserver reliability equivalent to those of experienced observers. The calculated benchmark for the Sørensen-Dice similarity coefficient between observers was greater than 0.87 and 0.92 for individual thigh and calf muscles, respectively. Interscan and interobserver reliability were significantly higher for large than small ROIs (all p < 0.001). CONCLUSIONS: We developed, implemented, and analysed the first formal training programme for manual lower limb muscle segmentation. Large ROI showed superior reliability to small ROI for fat fraction assessment. RELEVANCE STATEMENT: Observers competent in lower limb muscle segmentation are critical to application of quantitative muscle MRI biomarkers in neuromuscular diseases. This study has established competency benchmarks for future human observers or automated segmentation methods. KEY POINTS: • Observers competent in muscle segmentation are critical for quantitative muscle MRI biomarkers. • A training programme for muscle segmentation was undertaken by eight new observers. • We established competency benchmarks for future human observers or automated segmentation methods.

Head-to-Head Comparison: P-POSSUM and ACS-NSQIP® in Predicting Perioperative Risk in Robotic Surgery for Gynaecological Cancers.

Purpose: In this retrospective pilot study, we aim to evaluate the accuracy and reliability of the P-POSSUM and ACS-NSQIP surgical risk calculators in predicting postoperative complications in gynaecological-oncological (GO) robotic surgery (RS). Methods: Retrospective data collection undertaken through a dedicated GO database and patient notes at a tertiary referral cancer centre. Following data lock with the actual post-op event/complication, the risk calculators were used to measure predictive scores for each patient. Baseline analysis of 153 patients, based on statistician advice, was undertaken to evaluate P-POSSUM and ACS-NSQIP validity and relevance in GO patients undergoing RS performed. Results: P-POSSUM reports on mortality and morbidity only; ACS-NSQIP reports some individual complications as well. ACS-NSQIP risk prediction was most accurate for venous thromboembolism (VTE) (area under the curve (AUC)-0.793) and pneumonia (AUC-0.657) and it showed 90% accuracy in prediction of five major complications (Brier score 0.01). Morbidity was much better predicted by ACS-NSQIP than by P-POSSUM (AUC-0.608 vs. AUC-0.551) with the same result in mortality prediction (Brier score 0.0000). Moreover, a statistically significant overestimation of morbidity has been shown by the P-POSSUM calculator (p = 0.018). Conclusions: Despite the limitations of this pilot study, the ACS-NSQIP risk calculator appears to be a better predictor of major complications and mortality, making it suitable for use by GO surgeons as an informed consent tool. Larger data collection and analyses are ongoing to validate this further.

Evolution of STAT2 resistance to flavivirus NS5 occurred multiple times despite genetic constraints.

Zika and dengue virus nonstructural protein 5 antagonism of STAT2, a critical interferon signaling transcription factor, to suppress the host interferon response is required for viremia and pathogenesis in a vertebrate host. This affects viral species tropism, as mouse STAT2 resistance renders only immunocompromised or humanized STAT2 mice infectable. Here, we explore how STAT2 evolution impacts antagonism. By measuring the susceptibility of 38 diverse STAT2 proteins, we demonstrate that resistance arose numerous times in mammalian evolution. In four species, resistance requires distinct sets of multiple amino acid changes that often individually disrupt STAT2 signaling. This reflects an evolutionary ridge where progressive resistance is balanced by the need to maintain STAT2 function. Furthermore, resistance may come with a fitness cost, as resistance that arose early in lemur evolution was subsequently lost in some lemur lineages. These findings underscore that while it is possible to evolve resistance to antagonism, complex evolutionary trajectories are required to avoid detrimental host fitness consequences.

First Results of the Laser-Interferometric Detector for Axions (LIDA).

We present the operating principle and the first observing run of a novel kind of direct detector for axions and axionlike particles in the galactic halo. Sensitive to the polarisation rotation of linearly polarised laser light induced by an axion field, our experiment is the first detector of its kind collecting scientific data. We discuss our peak sensitivity of 1.51×10^{-10} GeV^{-1} (95% confidence level) to the axion-photon coupling strength in the axion mass range of 1.97-2.01 neV which is, for instance, motivated by supersymmetric grand-unified theories. We also report on effects that arise in our high-finesse in-vacuum cavity at an unprecedented optical continuous-wave intensity of 4.7 MW/cm^{2}. Our detector already belongs to the most sensitive direct searches within its measurement band, and our results pave the way towards surpassing the current sensitivity limits even of astrophysical observations in the mass range from 10^{-8} down to 10^{-16} eV via quantum-enhanced laser interferometry, especially with the potential of scaling our detector up to kilometer length.

Reductions of Arenes using a Magnesium-Dinitrogen Complex.

In this contribution, we present "Birch-type", and other reductions of simple arenes by the potassium salt of an anionic magnesium dinitrogen complex, [{K(TCHPNON)Mg}2(µ-N2)] (TCHPNON=4,5-bis(2,4,6-tricyclohexylanilido)-2,7-diethyl-9,9-dimethyl-xanthene), which acts as a masked dimagnesium(I) diradical in these reactions. This reagent is non-hazardous, easy-to-handle, and in some cases provides access to 1,4-cyclohexadiene reduction products under relatively mild reaction conditions. This system works effectively to reduce benzene, naphthalene and anthracene through magnesium-bound "Birch-type" reduction intermediates. Cyclohexadiene products can be subsequently released from the magnesium centres by protonolysis with methanol. In contrast, the reduction of substituted arenes is less selective and involves competing reaction pathways. For toluene and 1,3,5-triphenylbenzene, the structural authentication of "Birch-type" reduction intermediates is conclusive, although the formation of corresponding 1,4-cyclohexadiene derivatives was low yielding. Reduction of anisole did not yield an isolable "Birch-type" intermediate, but instead gave a C-O activation product. Treating triphenylphosphine with [{K(TCHPNON)Mg}2(µ-N2)] resulted in the extrusion of both biphenyl and dinitrogen to afford a magnesium(II) phosphanide [{K(TCHPNON)Mg(µ-PPh2)}2]. Reduction of fluorobenzene proceeded via C-F activation of the arene, and isolation of the magnesium(II) fluoride [{K(TCHPNON)Mg(µ-F)}2]. Finally, the two-electron reduction of 1,3,5,7-cyclooctatetraene (COT) with [{K(TCHPNON)Mg}2(µ-N2)] yielded a complex, [{K(TCHPNON)Mg}2(µ-COT)], incorporating the aromatic dianion (COT2-).

Low oxidation state and hydrido group 2 complexes: synthesis and applications in the activation of gaseous substrates.

Numerous industrial processes utilise gaseous chemical feedstocks to produce useful chemical products. Atmospheric and other small molecule gases, including anthropogenic waste products (e.g. carbon dioxide), can be viewed as sustainable building blocks to access value-added chemical commodities and materials. While transition metal complexes have been well documented in the reduction and transformation of these substrates, molecular complexes of the terrestrially abundant alkaline earth metals have also demonstrated promise with remarkable reactivity reported towards an array of industrially relevant gases over the past two decades. This review covers low oxidation state and hydrido group 2 complexes and their role in the reduction and transformation of a selection of important gaseous substrates towards value-added chemical products.

Enforcing Metal-Arene Interactions in Bulky p-Terphenyl Bis(anilide) Complexes of Group 2 Metals (Be-Ba): Potential Precursors for Low-Oxidation-State Alkaline Earth Metal Systems.

An extremely bulky p-terphenyl bis(aniline), p-C6H4{C6H4[N(H)TCHP]-2}2 (TCHP = 2,4,6-tricyclohexylphenyl) TCHPTerphH2, has been developed. Deprotonation of a less bulky analogue, DipTerphH2 (Dip = 2,6-diisopropylphenyl), with BePh2 affords the bimetallic system, [(BePh)2(µ-DipTerph)] 1. Treating either TCHPTerphH2 or DipTerphH2 with Mg{CH2(SiMe3)}2 gives the monomeric bis(anilide) complexes [Mg(ArTerph)] (Ar = Dip 2, TCHP 3) which display rare examples of η6-arene coordination to the metal center. Treating 2 with THF leads to partial dissociation of the Mg···arene interaction and formation of [Mg(DipTerph)(THF)] 4. Reactions of the bis(aniline)s with the group 2 metal amides [M{N(SiMe3)2}2] afford dimeric, structurally analogous compounds [{M(ArTerph)}2] (Ar = Dip, M = Ca 5, Sr 6, Ba 7; Ar = TCHP, M = Ca 8, Sr 9, Ba 10) which display intermolecular M···arene interactions in the solid state. Computational studies have shown that the intramolecular M···Î·6-arene interactions in models of the ether-free metal bis(anilide) compounds are largely electrostatic in nature. Reductions of these compounds with alkali metals led to mixtures of unidentified products.

Synthesis and Reactivity of Discrete Europium(II) Hydride Complexes.

The bulky ß-diketiminate ligand frameworks [BDIDCHP]- and [BDIDipp/Ar]- (BDI=[HC{C(Me)2N-Dipp/Ar}2]- (Dipp=2,6-diisopropylphenyl (Dipp); Ar=2,6-dicyclohexylphyenyl (DCHP) or 2,4,6-tricyclohexylphyenyl (TCHP)) have been developed for the kinetic stabilisation of the first europium (II) hydride complexes, [(BDIDCHP)Eu(µ-H)]2, [(BDIDipp/DCHP)Eu(µ-H)]2 and [(BDIDipp/TCHP)Eu(µ-H)]2, respectively. These complexes represent the first step beyond the current lanthanide(II) hydrides that are all based on ytterbium. Tuning the steric profile of ß-diketiminate ligands from a symmetrical to unsymmetrical disposition, enhanced solubility and stability in the solution-state. This provides the first opportunity to study the structure and bonding of these novel Eu(II) hydride complexes crystallographically, spectroscopically and computationally, with their preliminary reactivity investigated.

Steric control of Mg-Mg bond formation vs. N2 activation in the reduction of bulky magnesium diamide complexes.

Reduction of the magnesium(II) diamide [Mg(TripNON)] (TripNON = 4,5-bis(2,4,6-triisopropylanilido)-2,7-diethyl-9,9-dimethyl-xanthene) with 5% w/w K/KI leads to a good yield of a dianionic dimagnesium(I) species, as its potassium salt, [{K(TripNON)Mg}2]. An X-ray crystallographic analysis shows the molecule to contain a very long Mg-Mg bond (3.137(2) Å). The formation of [{K(TripNON)Mg}2] contrasts with a previously reported reduction of a magnesium(II) complex incorporating a bulkier diamide ligand, which instead afforded a magnesium-dinitrogen complex. In the current study, [{K(TripNON)Mg}2] has been shown to be a viable reagent for the reductive activation of CO, H2 and N2O.

Pinacol Cross-Coupling Promoted by an Aluminyl Anion.

A simple sequential addition protocol for the reductive coupling of ketones and aldehydes by a potassium aluminyl grants access to unsymmetrical pinacolate derivatives. Isolation of an aluminium ketyl complex presents evidence for the accessibility of radical species. Product release from the aluminium centre was achieved using an iodosilane, forming the disilylated 1,2-diol and a neutral aluminium iodide, thereby demonstrating the steps required to generate a closed synthetic cycle for pinacol (cross) coupling at an aluminyl anion.

Sequence capture identifies fastidious chytrid fungi directly from host tissue.

The chytrid fungus Batrachochytrium dendrobatidis (Bd) was discovered in 1998 as the cause of chytridiomycosis, an emerging infectious disease causing mass declines in amphibian populations worldwide. The rapid population declines of the 1970s-1990s were likely caused by the spread of a highly virulent lineage belonging to the Bd-GPL clade that was introduced to naïve susceptible populations. Multiple genetically distinct and regional lineages of Bd have since been isolated and sequenced, greatly expanding the known biological diversity within this fungal pathogen. To date, most Bd research has been restricted to the limited number of samples that could be isolated using culturing techniques, potentially causing a selection bias for strains that can grow on media and missing other unculturable or fastidious strains that are also present on amphibians. We thus attempted to characterize potentially non-culturable genetic lineages of Bd from distinct amphibian taxa using sequence capture technology on DNA extracted from host tissue and swabs. We focused our efforts on host taxa from two different regions that likely harbored distinct Bd clades: (1) wild-caught leopard frogs (Rana) from North America, and (2) a Japanese Giant Salamander (Andrias japonicus) at the Smithsonian Institution's National Zoological Park that exhibited signs of disease and tested positive for Bd using qPCR, but multiple attempts failed to isolate and culture the strain for physiological and genetic characterization. We successfully enriched for and sequenced thousands of fungal genes from both host clades, and Bd load was positively associated with number of recovered Bd sequences. Phylogenetic reconstruction placed all the Rana-derived strains in the Bd-GPL clade. In contrast, the A. japonicus strain fell within the Bd-Asia3 clade, expanding the range of this clade and generating additional genomic data to confirm its placement. The retrieved ITS locus matched public barcoding data from wild A. japonicus and Bd infections found on other amphibians in India and China, suggesting that this uncultured clade is widespread across Asia. Our study underscores the importance of recognizing and characterizing the hidden diversity of fastidious strains in order to reconstruct the spatiotemporal and evolutionary history of Bd. The success of the sequence capture approach highlights the utility of directly sequencing pathogen DNA from host tissue to characterize cryptic diversity that is missed by culture-reliant approaches.

Roles of epidermal growth factor receptor, claudin-1 and occludin in multi-step entry of hepatitis C virus into polarized hepatoma spheroids.

The multi-step process of hepatitis C virus (HCV) entry is facilitated by various host factors, including epidermal growth factor receptor (EGFR) and the tight junction proteins claudin-1 (CLDN1) and occludin (OCLN), which are thought to function at later stages of the HCV entry process. Using single particle imaging of HCV infection of polarized hepatoma spheroids, we observed that EGFR performs multiple functions in HCV entry, both phosphorylation-dependent and -independent. We previously observed, and in this study confirmed, that EGFR is not required for HCV migration to the tight junction. EGFR is required for the recruitment of clathrin to HCV in a phosphorylation-independent manner. EGFR phosphorylation is required for virion internalization at a stage following the recruitment of clathrin. HCV entry activates the RAF-MEK-ERK signaling pathway downstream of EGFR phosphorylation. This signaling pathway regulates the sorting and maturation of internalized HCV into APPL1- and EEA1-associated early endosomes, which form the site of virion uncoating. The tight junction proteins, CLDN1 and OCLN, function at two distinct stages of HCV entry. Despite its appreciated function as a "late receptor" in HCV entry, CLDN1 is required for efficient HCV virion accumulation at the tight junction. Huh-7.5 cells lacking CLDN1 accumulate HCV virions primarily at the initial basolateral surface. OCLN is required for the late stages of virion internalization. This study produced further insight into the unusually complex HCV endocytic process.

New-onset movement disorder in the immediate postpartum period.

This case report describes a woman who developed involuntary, uncoordinated movements of her face and limbs following a spontaneous vaginal delivery, complicated by postpartum haemorrhage. Using systematic assessment with multidisciplinary team input, a differential diagnosis was proposed and relevant investigations were undertaken. Atypical eclamptic or generalised seizures were excluded clinically and neuroimaging ruled out an intracranial vascular event such as stroke or venous sinus thrombosis. Local anaesthetic systemic toxicity was managed empirically with intravenous lipid emulsion and intravenous fluids. A diagnosis of drug-induced dyskinesia was made, most likely secondary to ondansetron, with which dystonias and myoclonus have been described. This woman's symptoms were transient and resolved within 2 hours.This case presented a complex differential diagnosis, highlighting the paucity of guidance available. We propose a diagnostic algorithm to aid in the identification of acute involuntary movements in pregnancy and the puerperium.

The effect of single mutations in Zika virus envelope on escape from broadly neutralizing antibodies.

IMPORTANCE: The wide endemic range of mosquito-vectored flaviviruses-such as Zika virus and dengue virus serotypes 1-4-places hundreds of millions of people at risk of infection every year. Despite this, there are no widely available vaccines, and treatment of severe cases is limited to supportive care. An avenue toward development of more widely applicable vaccines and targeted therapies is the characterization of monoclonal antibodies that broadly neutralize all these viruses. Here, we measure how single amino acid mutations in viral envelope protein affect neutralizing antibodies with both broad and narrow specificities. We find that broadly neutralizing antibodies with potential as vaccine prototypes or biological therapeutics are quantifiably more difficult to escape than narrow, virus-specific neutralizing antibodies.

Machine Learning-Accelerated Discovery of A2BC2 Ternary Electrides with Diverse Anionic Electron Densities.

This study combines machine learning (ML) and high-throughput calculations to uncover new ternary electrides in the A2BC2 family of compounds with the P4/mbm space group. Starting from a library of 214 known A2BC2 phases, density functional theory calculations were used to compute the maximum value of the electron localization function, indicating that 42 are potential electrides. A model was then trained on this data set and used to predict the electride behavior of 14,437 hypothetical compounds generated by structural prototyping. Then, the stability and electride features of the 1254 electride candidates predicted by the model were carefully checked by high-throughput calculations. Through this tiered approach, 41 stable and 104 metastable new A2BC2 electrides were predicted. Interestingly, all three kinds of electrides, i.e., electron-deficient, electron-neutral, and electron-rich electrides, are present in the set of predicted compounds. Three of the most promising new electrides (two electron-rich, Nd2ScSi2 and La2YbGe2, and one electron-deficient Y2LiSi2) were then successfully synthesized and characterized experimentally. Furthermore, the synthesized electrides were found to exhibit high catalytic activities for NH3 synthesis under mild conditions when Ru-loaded. The electron-deficient Y2LiSi2, in particular, was seen to exhibit a good balance of catalytic activity and chemical stability, suggesting its future application in catalysis.

Titania Mixed with Silica: A Low Thermal-Noise Coating Material for Gravitational-Wave Detectors.

Coating thermal noise is one of the dominant noise sources in current gravitational wave detectors and ultimately limits their ability to observe weaker or more distant astronomical sources. This Letter presents investigations of TiO_{2} mixed with SiO_{2} (TiO_{2}:SiO_{2}) as a coating material. We find that, after heat treatment for 100 h at 850 °C, thermal noise of a highly reflective coating comprising of TiO_{2}:SiO_{2} and SiO_{2} reduces to 76% of the current levels in the Advanced LIGO and Advanced Virgo detectors-with potential for reaching 45%, if we assume the mechanical loss of state-of-the-art SiO_{2} layers. Furthermore, those coatings show low optical absorption of <1 ppm and optical scattering of ≲5 ppm. Notably, we still observe excellent optical and thermal noise performance following crystallization in the coatings. These results show the potential to meet the parameters required for the next upgrades of the Advanced LIGO and Advanced Virgo detectors.