bluuebunny/crossref_metadata_2025 huggingface dataset:
Broad ligament ectopic pregnancy with full-term live birth: a rare case report from Syria
Authors: Mohaisen Mais Alreem Basel , Shaban Rema Ahmad , Hammoud Rehab Mohammad Dib , Al Khoubie Nour Samir , Al Ahmad Marwa , Sleiay Bilal
Published: December 2024

Ectopic pregnancy, the implantation of a fertilized zygote outside the uterine cavity, presents with abdominal pain and vaginal bleeding. Diagnosis relies on clinical signs, and treatment involves surgery or methotrexate in selected cases. A 24-year-old woman at 37 weeks of gestation underwent elective cesarean delivery under general anesthesia, revealing an unexpected broad ligament ectopic pregnancy. The live fetus and placenta were successfully delivered without complications. The study reports a rare asymptomatic broad ligament ectopic pregnancy until 37 weeks, diagnosed by laparotomy—treatment involved removing the ovary and placenta and preserving the uterus. A healthy male baby and mother recovered well. This rare ectopic pregnancy, with placental implantation in the broad ligament, resulted in a successful cesarean delivery of a healthy infant and complication-free recovery, highlighting the importance of timely diagnosis and skilled surgical intervention.
Primary inferior vena cava synovial sarcoma treated with caval replacement during cardiopulmonary bypass and ante situm liver perfusion
Authors: Frenkel Max , Guenther Timothy , Hermsen Joshua , Collins Kelly , Mezrich Joshua , Al-Adra David , Xia Yu
Published: December 2024

Primary inferior vena cava (IVC) tumors are rare. Most are leiomyosarcomas. The prognosis is poor with those involving and superior to the hepatic veins faring worse than those isolated within the retrohepatic cava. Tumors with superior extension were historically considered unresectable, though there are mounting reports of multicavity resections. We present an exceedingly rare case of a primary IVC synovial sarcoma treated with caval replacement to the right atrium (without hypothermic circulatory arrest) and hepatic vein reconstruction with autologous pericardium during ante situm liver perfusion. We highlight the value of multidisciplinary consideration for extensive primary caval tumors.
Successful endovascular treatment of post-traumatic subclavian arteriovenous fistula
Authors: Embel Veysel , Ihionkhan Emmanuel , Lu Charles , Marcucci Vincent , Jain Vikalp
Published: December 2024

Subclavian arteriovenous fistulas (AVFs) are rare entities, mostly reported as a result of traumatic and iatrogenic injuries. In the literature, congenital subclavian AVFs are also presented. Diagnosis of traumatic AVF may present challenges given the variable clinical presentation, varying location, and difficulty to locate on imaging. If left untreated, it can lead to high-output heart failure. This underlies the importance of understanding the nature of the disease, timely diagnosis, and treatment in order to prevent increased morbidity and mortality. We report a case of a patient having a traumatic left subclavian AVF formation after clavicle and rib surgery, which was successfully treated with a covered stent.
Life in the deadlands: unearthing reasons for visiting and visitor perceptions of wildlife in London’s Magnificent Seven cemeteries
Authors: Moesch Simon S , Ladds Zosia , Francis Robert A
Published: December 2024

Cemeteries, traditionally reserved for mourning, are also valuable urban green spaces contributing to ecosystem services, wildlife habitats, and human well-being. This study focuses on London’s Magnificent Seven cemeteries, which vary in habitat and usage, from semi-wild nature reserves to active burial sites. In autumn 2023, we conducted non-participatory observations of human activities and wildlife presence, and surveyed visitors (n = 176) regarding their perceptions of birds (crows, magpies, parakeets, robins, owls, blackbirds), mammals (fox, grey squirrel, bats, rats, cats, hedgehogs, rabbits, deer) and activities (e.g. biking, dog walking, picnicking). Our observations showed that visitors primarily engaged in solitary or accompanied walks. Observed animals included crows (Corvus spp.) and pigeons (Columba spp.), as well as grey squirrels (Sciurus carolinensis) and foxes (Vulpes vulpes). Regarding visitor perceptions, wildlife was generally perceived positively, with invasive ring-necked parakeets (Psittacula krameri) as well as non-native grey squirrels occasionally evoking negative perceptions. Activities like grave visiting and solitary walks are widely accepted, while picnicking, biking and sports are less favored, with younger participants and locals generally being more accepting to more lively activities. Urban cemeteries play multifunctional roles beyond mourning, offering green spaces for recreation and wildlife habitats. This study highlights the importance of recognizing cemeteries as critical urban refuges for both people and wildlife, demonstrating that sacred grounds and urban wilderness can coexist to create restorative green spaces in busy cities. The future survival of inner-city cemeteries depends on their rejuvenation and integration into local communities, enabling them to act as nature-based solutions to withstand development pressures.
Lighting the path: how light signaling regulates stomatal movement and plant immunity
Authors: Singh Nidhi , Giri Mrunmay Kumar , Chattopadhyay Debasis
Published: December 2024

Stomata, the small pores on the surfaces of plant leaves and stems, are crucial for gas exchange and also play a role in defense against pathogens. Stomatal movement is influenced not only by surrounding light conditions but also by the presence of foliar pathogens. Certain light wavelengths such as blue or high irradiance red light cause stomatal opening, making it easier for bacteria to enter through opened stomata and causing disease progression in plants. Illumination with blue or intense red light autophosphorylates phototropin, a blue light photoreceptor protein kinase, that in turn activates a signaling cascade to open the stomata. Undoubtedly stomatal defense is a fascinating aspect of plant immunology, especially in plant–foliar pathogen interactions. During these interactions, stomata fundamentally serve as entry points for intrusive pathogens and initiate the plant defense signaling cascade. This review highlights how light-activated photoreceptors such as cryptochromes (CRYs), phytochromes (phys), and UV-receptors (UVRs) influence stomatal movement and defense signaling after foliar pathogen intrusion. It also explores the link between stomatal defense, light signaling, and plant immunity, which is vital for safeguarding crops against pathogens.
Unravelling the impact of domestication on competitive ability in durum wheat: a phenotypic plasticity perspective
Authors: Lemoine Taïna , Violle Cyrille , Gonzalez Eric Antoine , Gaubert Mathis , Rocher Aline , Fréville Hélène , Fort Florian
Published: December 2024

The need to address the impact of domestication on plant traits is frequently highlighted in modern agriculture. It is often argued that domesticated plants have lost competitive ability due to reduced phenotypic plasticity. This study investigates whether domestication has affected competitive ability, functional trait values, and plasticity in durum wheat across 39 genotypes representing four key stages of domestication, from wild progenitors to modern elite varieties. Plants were grown in pots, both alone and in competition with the same neighbouring genotype. Biomass, and above- and belowground traits were measured at the end of the vegetative stage. Our results showed that the three domesticated groups lost less biomass in response to competition compared with their wild progenitors. All genotypes developed thinner leaves and thicker roots when grown with a neighbour. While wild progenitors exhibited the highest plasticity, this did not translate to a greater competitive ability. These findings challenge the theoretical expectation that domesticated plants are less suited for competition. Instead, they suggest that domesticated plants perform well in competitive environments and question the need to reintroduce wild traits to improve competitive ability.
Catalytically inactive subgroup VIII receptor-like cytoplasmic kinases regulate the immune-triggered oxidative burst in Arabidopsis thaliana
Authors: Gonçalves Dias Márcia , Dharmasena Thakshila , Gonzalez-Ferrer Carmen , Maika Jan Eric , Miguel Virginia Natali , Dou Ruoqi , Rodriguez Gallo Maria Camila , Bredow Melissa , Siegel Kristen Rose , Uhrig R Glen , Simon Rüdiger , Monaghan Jacqueline
Published: December 2024

Protein kinases are key components of multiple cell signaling pathways. Several receptor-like cytoplasmic kinases (RLCKs) have demonstrated roles in immune and developmental signaling across various plant species, making them of interest in the study of phosphorylation-based signal relay. Here, we present our investigation of a subgroup of RLCKs in Arabidopsis thaliana. Specifically, we focus on subgroup VIII RLCKs: MAZ and its paralog CARK6, as well as CARK7 and its paralog CARK9. We found that both MAZ and CARK7 associate with the calcium-dependent protein kinase CPK28 in planta, and furthermore that CPK28 phosphorylates both MAZ and CARK7 on multiple residues in areas that are known to be critical for protein kinase activation. Genetic analysis suggests redundant roles for MAZ and CARK6 as negative regulators of the immune-triggered oxidative burst. We find evidence that supports homo- and hetero-dimerization between CARK7 and MAZ, which may be a general feature of this subgroup. Multiple biochemical experiments suggest that neither MAZ nor CARK7 demonstrate catalytic protein kinase activity in vitro. Interestingly, we find that a mutant variant of MAZ incapable of protein kinase activity can complement maz-1 mutants, suggesting noncatalytic roles of MAZ in planta. Overall, our study identifies subgroup VIII RLCKs as new players in Arabidopsis immune signaling and highlights the importance of noncatalytic functions of protein kinases.
The importance of hemolysis detection among neonates for interpretation of potassium results
Authors: Wu Alan H B
Published: December 2024

Specimen hemolysis is a frequent finding when blood is collected from neonates. This produces artificially high results for some analytes, such as potassium. Testing samples for electrolytes using point-of-care (POC) blood gas analyzers is convenient and facile. However, unlike testing that is conducted on serum or plasma from a central laboratory, detection of hemolysis using POC analyzers cannot currently be achieved. As described in these cases, the presence of hemolysis can produce ambiguities and delays in the diagnosis and management of neonates.
Immersive Virtual Reality Versus Mannequin-based Simulation Training for Trauma Resuscitation: A Randomized Controlled Noninferiority Trial
Authors: Lange Marta , Bērziņš Ardis , Whitfill Travis , Kravčuks Jevgēnijs , Skotele Dana , Lice Elina , Stepens Ainars
Published: December 2024

Introduction

Despite its high potential, the effect of immersive virtual reality simulation (VRS) in trauma resuscitation training has not been studied. The aim of this study was to test the hypothesis that VRS is non-inferior to mannequin-based simulation (MBS) in trauma resuscitation training.

Methods

In a single-center, randomized controlled noninferiority trial, we compared individual training with an immersive virtual reality Trauma Simulator to live MBS training in a facilitated group. The primary outcome was the Trauma Score (ranging from 55 to 177) during the MBS assessment. The secondary outcomes were the Trauma Score VRS assessment, System Usability Scale (SUS) (ranging from 0 to 100), and Simulation Sickness Questionnaire (SSQ) (ranging from 0 to 235.62).

Results

A total of 38 participants were enrolled in the study. The mean Trauma Score in MBS assessment was 163.2 (SD 7.9) for the control group and 163.1 (SD 13.8) for the intervention group; the difference of means 0.1 (95% confidence interval: −7.3, 7.5; P = .977). The mean Trauma Score in VRS assessment was 134.2 (SD 24.4) for control group and 158.4 (SD 17.6) for intervention group; the difference of means 24.2 (95% confidence interval: 10.1, 38.3; P = .001). The mean SUS of Trauma Simulator was 74.4 (SD 10.5). The median SSQ Total Severity score was 3.7 (IQR 0-18.7).

Conclusions

This study showed that VRS led to noninferior effects on trauma resuscitation skills to MBS. Trauma Simulator had good usability, was well received by the participants, and had minimal adverse effects.
Quantifying the Volume of Residual Air in Commercial Intravenous Fluids and Assessing the Stability of Airless Intravenous Fluid Containers
Authors: Babcock Lyle , Brawley Hayley , van Nispen Christiaan , Rall Jason , Jaramillo Jasmine , Rubal Michael , Nowadly Craig
Published: December 2024

Introduction

Commercial off-the-shelf (COTS) intravenous fluid (IVF) containers contain residual air, introducing the risk of venous air embolism (VAE). Venous air embolism occurs when air displaces blood flow in vasculature. The danger from residual air is often negligible in terrestrial settings, where gravitational forces generate buoyancy, pushing residual air to the top of the IVF container. However, in microgravity there is no buoyancy to separate liquid and gas layers. We performed experiments to quantify the amount of air in COTS IVF containers (Experiment 1) and identify the variables that affect the stability of sterilely produced airless containers (Experiment 2).

Materials and Methods

Experiment 1: Residual air was quantified across varying volumes (100, 250, 500, and 1,000 mL), container design, and manufacturer (B. Braun, Baxter, ICU Medical, and Grifols) of 0.9% NaCl COTS IVFs. Each container was assessed for absolute volumes of air, as well as air:fluid ratios normalized to 1,000 mL. Experiment 2: 1,000 mL IVF containers from 3 manufacturers were filled with either (1) 100% saline or (2) 95% saline and 5% air by volume. Containers were stored for 168 days at 25°C or 40 °C. The containers were optically imaged to quantify the accumulation of air within each IVF container.

Results

Experiment 1: There was a trend toward larger container sizes and greater absolute volumes of residual air (R2 = 0.964). However, the smallest air:volume ratio occurred in the Baxter 500 mL VIAFLO Container (18.9 ± 3.8 mL air; 2.3% air by volume), whereas the largest ratio occurred in the B. Braun 250 mL EXCEL Container (55.0 ± 9.3 mL; 22.0% air by volume). Experiment 2: By day 168, 6 experimental containers had ruptured and 100% of the surviving containers (30/36) had an increase in air as compared to baseline. Containers placed at 40 °C had a larger increase in air (27.7 ± 6.6 mL) compared to containers stored at 25 °C (7.5 ± 4.1 mL; P < .0001).

Conclusions

Residual air has a wide variety of volumes in COTS IVFs. The average amount of residual air is high enough to contribute to clinically significant VAEs, although unlikely to be fatal. If airless IVF containers are produced for exploration missions, a progressive increase in the amount of residual air should be expected. Extremes of temperatures and humidity will increase the reaccumulation of residual air and decrease the shelf-life of airless IVFs.
Identification of the cell-surface lectin domain-containing protein expressed in the adhesive colony morphology of Trichosporon asahii
Authors: Ichikawa Tomoe , Ishibashi Yoshio
Published: December 2024

Trichosporon asahii is a yeast pathogen that causes a deep-seated infection. In fungal infections, molecules involved in adhesion to host tissues or catheters are one of the pathogenic factors. A single strain of T. asahii produces various colony morphologies, including highly adhesive colony types, but the molecules involved in the adhesiveness have not been identified. This study compared proteins in cell-surface extracts from weakly and highly adherent colony types and identified a protein abundantly expressed in highly adherent cells, which was named T. asahii R-type lectin domain-containing protein (TAL). TAL was a predicted 48 kDa protein with a carbohydrate-binding region, but a band was detected at ∼250 kDa in sodium dodecyl sulfate-polyacrylamide gel electrophoresis, suggesting that it was highly glycosylated. When TAL was overexpressed in mammalian cells and deglycosylated, the protein size decreased, confirming that it was glycosylated. In weakly adherent colony-type cells, the bands detected by anti-TAL antiserum were barely noted. The absence of bands indicates that the protein expression was low and does not suggest that the degree of glycosylation was different. These results suggested that multiple colony types derived from a single strain have different pathogenic properties.
Dark energy survey year 3 results: cosmology from galaxy clustering and galaxy–galaxy lensing in harmonic space
Authors: Faga L , Andrade-Oliveira F , Camacho H , Rosenfeld R , Lima M , Doux C , Fang X , Prat J , Porredon A , Aguena M , Alarcon A , Allam S , Alves O , Amon A , Avila S , Bacon D , Bechtol K , Becker M R , Bernstein G M , Blazek J , Bocquet S , Brooks D , Buckley-Geer E , Campos A , Rosell A Carnero , Kind M Carrasco , Carretero J , Castander F J , Cawthon R , Chang C , Chen R , Choi A , Cordero J , Crocce M , da Costa L N , Pereira M E S , DeRose J , Diehl H T , Dodelson S , Drlica-Wagner A , Elvin-Poole J , Everett S , Ferrero I , Ferté A , Flaugher B , Fosalba P , Frieman J , García-Bellido J , Gatti M , Gaztanaga E , Giannini G , Gruen D , Gruendl R A , Gutierrez G , Harrison I , Hinton S R , Hollowood D L , Honscheid K , Huterer D , James D J , Jarvis M , Jeltema T , Kuehn K , Lahav O , Lee S , Lidman C , MacCrann N , Marshall J L , McCullough J , Mena-Fernández J , Miquel R , Myles J , Navarro-Alsina A , Palmese A , Pandey S , Paterno M , Pieres A , Malagón A A Plazas , Raveri M , Rodriguez-Monroy M , Rollins R P , Ross A J , Rykoff E S , Samuroff S , Sánchez C , Sanchez E , Cid D Sanchez , Schubnell M , Secco L F , Sevilla-Noarbe I , Sheldon E , Shin T , Smith M , Soares-Santos M , Suchyta E , Swanson M E C , Tarle G , Thomas D , Troxel M A , Tucker B E , Tutusaus I , Weaverdyck N , Wiseman P , Yanny B , Yin B ,   DES Collaboration
Published: December 2024

We present the joint tomographic analysis of galaxy-galaxy lensing and galaxy clustering in harmonic space (HS), using galaxy catalogues from the first three years of observations by the Dark Energy Survey (DES Y3). We utilize the redMaGiC and MagLim catalogues as lens galaxies and the metacalibration catalogue as source galaxies. The measurements of angular power spectra are performed using the pseudo-$C_\ell$ method, and our theoretical modelling follows the fiducial analyses performed by DES Y3 in configuration space, accounting for galaxy bias, intrinsic alignments, magnification bias, shear magnification bias and photometric redshift uncertainties. We explore different approaches for scale cuts based on non-linear galaxy bias and baryonic effects contamination. Our fiducial covariance matrix is computed analytically, accounting for mask geometry in the Gaussian term, and including non-Gaussian contributions and super-sample covariance terms. To validate our HS pipelines and covariance matrix, we used a suite of 1800 log-normal simulations. We also perform a series of stress tests to gauge the robustness of our HS analysis. In the $\Lambda$CDM model, the clustering amplitude $S_8 =\sigma _8(\Omega _m/0.3)^{0.5}$ is constrained to $S_8 = 0.704\pm 0.029$ and $S_8 = 0.753\pm 0.024$ (68 per cent C.L.) for the redMaGiC and MagLim catalogues, respectively. For the wCDM, the dark energy equation of state is constrained to $w = -1.28 \pm 0.29$ and $w = -1.26^{+0.34}_{-0.27}$, for redMaGiC and MagLim catalogues, respectively. These results are compatible with the corresponding DES Y3 results in configuration space and pave the way for HS analyses using the DES Y6 data.
Kinetic field theory applied to planetesimal formation I: freely streaming dust particles
Authors: Shi Jiahan , Bartelmann Matthias , Klahr Hubert , Dullemond Cornelis P
Published: December 2024

Planet formation in the Solar system was started when the first planetesimals were formed from the gravitational collapse of pebble clouds. Numerical simulations of this process, especially in the framework of streaming instability, produce various power laws for the initial mass function for planetesimals. While recent advances have shed light on turbulence and its role in particle clustering, a comprehensive theoretical framework linking turbulence characteristics to particle cluster properties and planetesimal mass function remains incomplete. Recently, a kinetic field theory (KFT) for ensembles of point-like classical particles in or out of equilibrium has been applied to cosmic structure formation. This theory encodes the dynamics of a classical particle ensemble by a generating functional specified by the initial probability distribution of particles in phase space and their equations of motion. Here, we apply KFT to planetesimal formation. A model for the initial probability distribution of dust particles in phase space is obtained from a quasi-initial state for a three-dimensional streaming-instability simulation that is a particle distribution with velocities for gas and particles from the Nakagawa relations. The equations of motion are chosen for the simplest case of freely streaming particles. We calculate the non-linearly evolved density power spectrum of dust particles and find that it develops a universal $k^{-3}$ tail at small scales, suggesting scale-invariant structure formation below a characteristic and time-dependent length-scale. Thus, the KFT analysis indicates that the initial state for streaming instability simulations does not impose a constraint on structure evolution during planetesimal formation.
ATOMS: ALMA three-millimeter observations of massive star-forming regions – XIX. The origin of SiO emission
Authors: Liu Rong , Liu Tie , Jiménez-Serra Izaskun , Li Jin-Zeng , Martín-Pintado Jesús , Liu Xunchuan , Lee Chang Won , Sanhueza Patricio , Chibueze James O , Rivilla Víctor M , Juvela Mika , Colzi Laura , Bronfman Leonardo , Liu Hong-Li , Sanz-Novo Miguel , López-Gallifa Álvaro , Li Shanghuo , Megías Andrés , San Andrés David , Garay Guido , Hwang Jihye , Zhou Jianwen , Xu Fengwei , Martínez-Henares Antonio , Saha Anindya , Nazeer Hafiz
Published: December 2024

The production of silicon monoxide (SiO) can be considered as a fingerprint of shock interaction. In this work, we use high-sensitivity observations of the SiO (2–1) and H$^{13}$CO$^{+}$ (1–0) emission to investigate the broad and narrow SiO emission towards 146 massive star-forming regions in the ATOMS (ALMA Three-millimeter Observations of Massive Star-forming regions) survey. We detected SiO emission in 136 regions and distinguished broad and narrow components across the extension of 118 sources (including 58 UC H ii regions) with an average angular resolution of 2.5 arcsec. The derived SiO luminosity ($L_{\rm SiO}$) across the whole sample shows that the majority of $L_{\rm SiO}$ (above 66 per cent) can be attributed to broad SiO, indicating its association with strong outflows. The comparison of the ALMA SiO images with the filamentary skeletons identified from H$^{13}$CO$^{+}$ and in the infrared data (at 4.5, 8, and 24 μm), further confirms that most SiO emission originates from outflows. However, note that for nine sources in our sample, the observed SiO emission may be generated by expanding UC H ii regions. There is a moderate positive correlation between the bolometric luminosity ($L_{\rm bol}$) and $L_{\rm SiO}$ for both components (narrow and broad). The UC H ii sources show a weaker positive correlation between $L_{\rm bol}$ and $L_{\rm SiO}$ and higher $L_{\rm SiO}$ compared to the sources without UC H ii regions. These results imply that the SiO emission from UC H ii sources might be affected by UV-photochemistry induced by UC H ii regions.
Deciphering the origins and growth of supermassive black holes
Authors: Aggarwal Yash
Published: December 2024

We present a well-tested, theoretically supported empirical relation that helps decipher the origins, growth, and properties of supermassive black holes (SMBHs). Based on theoretical considerations and analysis of mass (MBH) versus age (t) distribution of high-redshift (>5.6) SMBHs, we get MBH = Ms exp [14.6(t – 100)/t(Myr)], which gives the SMBH's seed mass Ms, and its derivative gives the instantaneous mass-accretion rate. It yields seeds of ∼20–420 M☉ (solar masses) for the recently discovered SMBHs GNz11, CEERS_1019, and UHZ1, and ∼3 × 104 M☉ for the largest (1.24 × 1010 M☉) high-z SMBH. It is applied to 132446 SMBHs at z < 2.4. The resultant seeds are classified based on size and likely formation mechanism: ∼54 per cent are classified as light (<350 M☉) deemed to be Pop III remnants; ∼40 per cent as intermediate (350–2 × 103 M☉) and ∼6 per cent as heavier seeds (2 × 103–3 × 104 M☉), both of which formed possibly by mergers of Pop III remnants. The direct collapse black hole (DCBH) mechanism is not required but not excluded. Furthermore, the results show the following. The mass-accretion rate increases exponentially from the seed's inception (z ∼ 30), reaches a broad plateau at z ∼ 8.5–6 coincident with the epoch of reionization, and decreases monotonically thereafter. Sub-Eddington accretion is the norm, except during the first ∼150 Myr SMBHs either experienced super-Eddington accretion or the radiative efficiency was much < 0.1. The largest seed can potentially grow via luminous accretion to (6.6 ± 2.2) × 1010 M☉, consistent with a theoretical limit of ∼5 × 1010 M☉. The Eddington ratio decreases and radiative efficiency increases as z decreases, consistent with recent findings.
A spectrophotometric analysis and dust properties of classical nova V5584 Sgr
Authors: Bisht Mohit Singh , Raj A , Walter F M , Bisht D , Shaw Gargi , Belwal K , Biswas S
Published: December 2024

In this work, optical observations of the nova V5584 Sgr are presented. These observations cover different phases including pre-maximum, early decline, and nebular. The spectra are dominated by hydrogen Balmer, Fe ii, and O i lines with P-Cygni profiles in the early phase, which are subsequently observed in complete emission. The presence of numerous Fe ii lines and low ejecta velocity aligns with the Fe ii type nova classification. From optical and NIR colours, it is clear that this nova manifests dust formation in the ejecta. The dust temperature and mass were estimated from a spectral energy distribution (SED) fit to the JHK band magnitudes and the Wide field Infrared Survey Explorer data. Light-curve analysis shows t$_2$ and t$_3$ values of $\sim$ 26 and $\sim$ 48 d, classifying the nova as moderately fast. The physical and chemical properties during early decline and later phases were evaluated using the photoionization code CLOUDY. The best-fitting model parameters from two epochs of multiwavelength spectra are compatible with a hot white dwarf source with a roughly constant luminosity of $\sim$(2.08 $\pm$ 0.10) $\times$ 10$^{36}$ erg s$^{-1}$. We find an ejected mass of $\sim$(1.59 $\pm$ 0.04) $\times$ 10$^{-4}$ M$_{\odot }$. Abundance analysis indicates that the ejecta is significantly enriched relative to solar values, with O/H = 30.2, C/H = 10.8, He/H = 1.8, Mg/H = 1.68, Na/H = 1.55, and N/H = 45.5 in the early decline phase, and O/H = 4.5, Ne/H = 1.5, and N/H = 24.5 in the nebular phase.
Modelling biases from constant stellar mass-to-light ratio assumption in galaxy dynamics and strong lensing
Authors: Liang Yan , Xu Dandan , Sluse Dominique , Sonnenfeld Alessandro , Shu Yiping
Published: December 2024

A constant stellar mass-to-light ratio $M_\star /L$ has been widely used in studies of galaxy dynamics and strong lensing, which aim at disentangling the mass distributions of dark matter and baryons. However, systematic biases arising from constant $M_\star /L$ assumption have not been fully quantified. In this work, we take massive early-type galaxies from the TNG100 simulation to investigate possible systematic biases in the inferences due to a constant $M_\star /L$ assumption. We construct two-component matter density models, where one component describes the dark matter, the other for the stars, which is made to follow the light profile by assuming a constant $M_\star /L$. We fit the two-component model directly to the total matter density distributions of simulated galaxies to eliminate systematics coming from other model assumptions. We find that galaxies generally have more centrally concentrated stellar mass profile than their light distribution. Given the light profiles adopted (i.e. single- and double-Sérsic profiles), the assumption of a constant $M_\star /L$ would artificially break the model degeneracy between baryons and dark matter for non-constant$M_\star /L$ systems. For such systems, without knowing the true $M_{\star }/L$ but assuming a constant ratio, the two-component modelling procedure tend to generally overestimate $M_{\star }/L$ by $30{\small --}50~{{\ \rm per\ cent}}$, and underestimate the central dark matter fraction $f_{\rm DM}$ by $\sim 20~{{\ \rm per\ cent}}$ on average.
Evolutionary growth of molecular clouds as traced by their infrared bright fraction
Authors: Watkins E J , Peretto N , Rigby A J , Smith R J , Kreckel K , Fuller G A
Published: December 2024

Understanding how stars form, evolve, and impact molecular clouds is key to understanding why star formation is such an inefficient process globally. In this paper, we use the infrared bright fraction, $f_\text{IRB}$ (the fraction of a given molecular cloud that appears bright against the 8 $\mu$m Milky Way background) as a proxy for time evolution to test how cloud properties change as star formation evolves. We apply this metric to 12 000 high-mass star-forming molecular clouds we identify using the Herschel–Hi-GAL survey between $|\ell |{\lt }70^{\circ }$ on the Milky Way plane. We find clouds are not static while forming stars. Instead, molecular clouds continuously gain mass while star formation progresses. By performing principal component analysis on the cloud properties, we find that they evolve down two paths distinguished by their mass gain. Most clouds (80 per cent) gain four times more mass as a function of $f_\text{IRB}$. The remaining 20 per cent experience an extreme period of growth, growing in mass by a factor of 150 on average and during this period, they initially gain mass fast enough to outpace their star formation. For all clouds, it is only after half their area becomes star forming that mass-loss occurs. We expect stellar feedback and potentially galactic shear is responsible. By analysing cloud positions, we suggest that the rate of mass growth may be linked to the larger galactic environment. Altogether, these results have strong implications on how we assess star-forming ability on cloud scales when assuming molecular cloud masses are fixed in time.
Spectroscopic observations of flares and superflares on AU Mic
Authors: Odert P , Leitzinger M , Greimel R , Kabáth P , Lipták J , Heinzel P , Karjalainen R , Wollmann J , Guenther E W , Skarka M , Srba J , Škoda P , Frýda J , Brahm R , Vanzi L , Janík J
Published: December 2024

The young active flare star AU Mic is the planet host star with the highest flare rate from Transiting Exoplanet Survey Satellite data. Therefore, it represents an ideal target for dedicated ground-based monitoring campaigns with the aim to characterize its numerous flares spectroscopically. We performed such spectroscopic monitoring with the ESO1.52-m telescope of the PLATOSpec consortium. In more than 190 h of observations, we find 24 flares suitable for detailed analysis. We compute their parameters (duration, peak flux, and energy) in eight chromospheric lines (H $\alpha$, H $\beta$, H $\gamma$, H $\delta$, Na i D1&D2, He i D3, He i 6678) and investigate their relationships. Furthermore, we obtained simultaneous photometric observations and low-resolution spectroscopy for part of the spectroscopic runs. We detect one flare in the g$^{\prime }$-band photometry, which is associated with a spectroscopic flare. Additionally, an extreme flare event occurred on 2023-09-16 of which only a time around its possible peak was observed, during which chromospheric line fluxes were raised by up to a factor of three compared to the following night. The estimated energy of this event is around $10^{33}$ erg in H $\alpha$ alone, i.e. a rare chromospheric line superflare.
BUFFALO wild wings: a high-precision free-form lens model of MACSJ0416 with constraints on dark matter from substructure and highly magnified arcs
Authors: Perera Derek , Williams Liliya L R , Liesenborgs Jori , Kelly Patrick L , Taft Sarah H , Li Sung Kei , Jauzac Mathilde , Diego Jose M , Natarajan Priyamvada , Steinhardt Charles L , Faisst Andreas L , Rich R Michael , Limousin Marceau
Published: December 2024

We present new free-form and hybrid mass reconstructions of the galaxy cluster lens MACS J0416.1$-$2403 at $z=0.396$ using the lens inversion method GRALE. The reconstructions use 237 spectroscopically confirmed multiple images from Bergamini et al. (2023) as the main input. Our primary model reconstructs images to a positional accuracy of 0.191 arcsec, thus representing one of the most precise reconstructions of this lens to date. Our models find broad agreement with previous reconstructions, and identify two $\sim 10^{12}\, {\rm M}_{\odot }$ light-unaffiliated substructures. We focus on two highly magnified arcs: Spock and Mothra. Our model features a unique critical curve structure around the Spock arc with 2 crossings. This structure enables sufficient magnification across this arc to potentially explain the large number of transients as microlensing events of supergiant stars. Additionally, we develop a model of the millilens substructure expected to be magnifying Mothra, which may be a binary pair of supergiants with $\mu \sim 6000$. This model accounts for flexibility in the millilens position while preserving the observed flux and minimizing image position displacements along the Mothra arc. We constrain the millilens mass and core radius to $\lesssim 10^6 {\rm M}_{\odot }$ and $\lesssim 17$ pc, respectively, which would render it one of the smallest and most compact substructures constrained by lensing. If the millilens is dominated by wave dark matter, the axion mass is constrained to be $\lesssim 3.0 \times 10^{-21}$ eV. Further monitoring of this lens with JWST will uncover more transients, permitting tighter constraints on the structure surrounding these two arcs.
A first glimpse at the MeerKAT DEEP2 field at S-band
Authors: Ranchod S , Wagenveld J D , Klöckner H -R , Wucknitz O , Deane R P , Sridhar S S , Barr E , Buchner S , Camilo F , Damas-Segovia A , Kasemann C , Kramer M , Legodi L S , Mao S A , Menten K , Rammala I , Rugel M R , Wieching G
Published: December 2024

We present the first wide-field extragalactic continuum catalogue with the MeerKAT S-band (2.5 GHz), of the radio-selected DEEP2 field. The combined image over the S1 (1.96–2.84 GHz) and S4 (2.62–3.50 GHz) sub-bands has an angular resolution of 6.8 arcsec $\times$ 3.6 arcsec (4.0 arcsec $\times$ 2.4 arcsec) at a robust weighting of $R = 0.3$ ($R=-0.5$) and a sensitivity of 4.7 (7.5) µJy beam$^{-1}$ with an on-source integration time of 70 min and a minimum of 52 of the 64 antennas, for respective observations. We present the differential source counts for this field, as well as a morphological comparison of resolved sources between S-band and archival MeerKAT L-band images. We find consistent source counts with the literature and provide spectral indices fitted over a combined frequency range of 1.8 GHz. These observations provide an important first demonstration of the capabilities of MeerKAT S-band imaging with relatively short integration times, as well as a comparison with existing S-band surveys, highlighting the rich scientific potential with future MeerKAT S-band surveys.
Long-term optical variations in Swift J1858.6–0814: evidence for ablation and comparisons to radio properties
Authors: Rhodes L , Russell D M , Saikia P , Alabarta K , van den Eijnden J , Knight A H , Baglio M C , Lewis F
Published: December 2024

We present optical monitoring of the neutron star low-mass X-ray binary Swift J1858.6–0814 during its 2018–2020 outburst and subsequent quiescence. We find that there was strong optical variability present throughout the entire outburst period covered by our monitoring, while the average flux remained steady. The optical spectral energy distribution is blue on most dates, consistent with emission from an accretion disc, interspersed by occasional red flares, likely due to optically thin synchrotron emission. We find that the fractional rms variability has comparable amplitudes in the radio and optical bands. This implies that the long-term variability is likely to be due to accretion changes, seen at optical wavelengths, that propagate into the jet, seen at radio frequencies. We find that the optical flux varies asymmetrically about the orbital period, peaking at phase $\sim$0.7, with a modulation amplitude that is the same across all optical wavebands, suggesting that reprocessing off of the disc, companion star and ablated material is driving the phase dependence. The evidence of ablation found in X-ray binaries is vital in understanding the long-term evolution of neutron star X-ray binaries and how they evolve into (potentially isolated) millisecond pulsars.
A case of polyarteritis nodosa with severe lower limb ulcer that was treated with prednisolone and tocilizumab
Authors: Okubo Naoto , Oba Yuki , Ikuma Daisuke , Mizuno Hiroki , Yamanouchi Masayuki , Suwabe Tatsuya , Ubara Yoshifumi , Sawa Naoki
Published: December 2024

Polyarteritis nodosa (PAN) is a rare systemic necrotising vasculitis that can lead to the formation of refractory lower limb ulcers requiring amputation. The standard treatment for severe PAN involves combination therapy with steroids and cyclophosphamide; however, some cases prove to be challenging. Recently, case reports have described the use of biological agents for PAN treatment. We present the case of a 61-year-old Japanese man with cutaneous PAN and refractory recurrent lower limb ulcers. In 2017, the patient was admitted to the hospital because of exacerbation of a right lower limb ulcer. Despite combination therapy with corticosteroids, cyclophosphamide, and endovascular therapy, the gangrene in the right lower leg progressed, and amputation was performed. The patient was temporarily stabilised with prednisolone monotherapy. In 2019, new ulcers were observed on the left lower limb. Owing to steroid resistance, subcutaneous tocilizumab (162 mg/week) was initiated. Over a few months, the ulcer healed completely, and left lower limb amputation was avoided. Therefore, tocilizumab could potentially be one of the treatment options for severe cases in the future.
Optimization of ACE-tRNAs function in translation for suppression of nonsense mutations
Authors: Porter Joseph J , Ko Wooree , Sorensen Emily G , Lueck John D
Published: December 2024

Nonsense suppressor transfer RNAs (tRNAs) or AntiCodon-Edited tRNAs (ACE-tRNAs) have long been envisioned as a therapeutic approach to overcome genetic diseases resulting from the introduction of premature termination codons (PTCs). The ACE-tRNA approach for the rescue of PTCs has been hampered by ineffective delivery through available modalities for gene therapy. Here we have screened a series of ACE-tRNA expression cassette sequence libraries containing >1800 members in an effort to optimize ACE-tRNA function and provide a roadmap for optimization in the future. By optimizing PTC suppression efficiency of ACE-tRNAs, we have decreased the amount of ACE-tRNA required by ∼16-fold for the most common cystic fibrosis-causing PTCs.
CRISPR-based dissection of miRNA binding sites using isogenic cell lines is hampered by pervasive noise
Authors: Prajapat Mahendra K , Maria Andrea G , Vidigal Joana A
Published: December 2024

Non-coding regulatory sequences play essential roles in adjusting gene output to cellular needs and are thus critical to animal development and health. Numerous such sequences have been identified in mammalian genomes ranging from transcription factors binding motifs to recognition sites for RNA-binding proteins and non-coding RNAs. The advent of CRISPR has raised the possibility of assigning functionality to individual endogenous regulatory sites by facilitating the generation of isogenic cell lines that differ by a defined set of genetic modifications. Here we investigate the usefulness of this approach to assign function to individual miRNA binding sites. We find that the process of generating isogenic pairs of mammalian cell lines with CRISPR-mediated mutations introduces extensive molecular and phenotypic variability between biological replicates confounding attempts at assigning function to the binding site. Our work highlights an important consideration when employing CRISPR editing to characterize non-coding regulatory sequences in cell lines and calls for the development and adoption of alternative strategies to address this question in the future.
Point mutations in functionally diverse genes are associated with increased natural DNA transformation in multidrug resistant Streptococcus pneumoniae
Authors: Peillard-Fiorente Flora , Pham Nguyen Phuong , Gingras Hélène , Godin Chantal , Feng Jie , Leprohon Philippe , Ouellette Marc
Published: December 2024

DNA transformation is key for phenotypic diversity and adaptation of Streptococcus pneumoniae including in the emergence of multidrug resistance (MDR). Under laboratory conditions, DNA transformation is facilitated by the artificial triggering of competence by the competence stimulating peptide (CSP). In ongoing DNA transformation work, we observed that exogenous CSP was dispensable depending on the combination of strains and culture media. Here, we carried out a chemogenomic screen to select for S. pneumoniae mutants capable of natural transformation in medium that normally would not sustain natural transformation. Our chemogenomic screen relied on chemical mutagenesis followed by selection of mutants with increased DNA transformation capacities. Sequencing the genome of these mutants revealed an abundance and diversity of mutated genes proven experimentally to increase natural transformation. A genome wide association study between MDR and sensitive clinical isolates revealed gene mutations associated with MDR, many of which intersected with those pinpointed by our chemogenomic screens and that were proven to increase natural transformation. S. pneumoniae has adopted DNA transformation as its lifestyle and can select for mutations facilitating DNA transformation.
KRBP72 facilitates ATPase-dependent editing progression through a structural roadblock in mitochondrial A6 mRNA
Authors: Dubey Ashutosh P , Tylec Brianna L , Yi Soon , Tedeschi Frank A , Smith Joseph T , Read Laurie K
Published: December 2024

Uridine insertion/deletion editing of mitochondrial messenger RNAs (mRNAs) in kinetoplastids entails the coordinated action of three complexes. RNA Editing Catalytic Complexes (RECCs) catalyze the enzymatic reactions, while the RNA Editing Substrate Binding Complex (RESC) and RNA Editing Helicase 2 Complex (REH2C) coordinate interactions between RECCs, mRNAs and hundreds of guide RNAs that direct edited sequences. Additionally, numerous auxiliary factors are required for productive editing of specific mRNAs. Here, we elucidate the role of KRBP72, an editing auxiliary factor of the ABC adenosine triphosphatase (ATPase) family that exhibits RNA-binding activity. In procyclic form Trypanosoma brucei, KRBP72 knockdown leads to a pause in editing at the base of a predicted stem loop structure in adenosine triphosphate synthase subunit 6 (A6) mRNA. Enhanced cross-linking and affinity purification revealed KRBP72 binding sites both within and upstream of this stem loop. KRBP72 ATPase activity is essential for its A6 mRNA editing function; however, its RNA-binding activity is dispensable. KRBP72 interacts with most RESC proteins in an RNase-sensitive manner. By contrast, RESC12A associates with KRBP72 in an RNase-insensitive fashion, and RESC12A promotes KRBP72’s interaction with RNA. Hence, KRBP72 ATPase activity facilitates progression of editing through a challenging secondary structure, highlighting this protein's crucial role in A6 mRNA editing.
Structural insights into a DNA polymerase reading the xeno nucleic acid HNA
Authors: Gutfreund Cédric , Betz Karin , Abramov Mikhail , Coosemans Frédérick , Holliger Phillipp , Herdewijn Piet , Marx Andreas
Published: December 2024

Xeno nucleic acids (XNAs) are unnatural analogues of the natural nucleic acids in which the canonical ribose or deoxyribose rings are replaced with alternative sugars, congener structures or even open-ring configurations. The expanding repertoire of XNAs holds significant promise for diverse applications in molecular biology as well as diagnostics and therapeutics. Key advantages of XNAs over natural nucleic acids include their enhanced biostability, superior target affinity and (in some cases) catalytic activity. Natural systems generally lack the mechanisms to transcribe, reverse transcribe or replicate XNAs. This limitation has been overcome through the directed evolution of nucleic acid-modifying enzymes, especially polymerases (pols) and reverse transcriptases (RTs). Despite these advances, the mechanisms by which synthetic RT enzymes read these artificial genetic polymers remain largely unexplored, primarily due to a scarcity of structural information. This study unveils first structural insights into an evolved thermostable DNA pol interacting with the XNA 1,5-anhydrohexitol nucleic acid (HNA), revealing unprecedented HNA nucleotide conformations within a ternary complex with the enzyme. These findings not only deepen our understanding of HNA to DNA reverse transcription but also set the stage for future advancements of this and similar enzymes through deliberate design.
Enzymatic bypass of G-quadruplex structures containing oxidative lesions
Authors: Podbevšek Peter , Plavec Janez
Published: December 2024

The function of many DNA processing enzymes involves sliding along the double helix or individual DNA strands. Stable secondary structures in the form of G-quadruplexes are difficult for such enzymes to bypass. We used a polymerase stop assay to determine which structural features of the human telomeric and the BCL2 promoter G-quadruplexes can stall progression of the Klenow fragment. Primer extension profiles revealed that G-quartets are effective roadblocks for the Klenow fragment, while auxiliary base pairs can be easily bypassed. Furthermore, we utilized 8-oxoguanine to simulate oxidative damage in G-rich regions and determine the effects on enzyme bypass. In rare cases, oxidative lesions reduce the level of G-quadruplex bypass. In general, however, oxidative lesions reduce G-quadruplex stability and facilitate bypassing of such G-rich regions, especially if the lesion persists in unfolding intermediates. Our findings using Klenow fragment can be extrapolated to other G-quadruplex forming sequences and enzymes that utilise a clamp-like structure to slide along DNA and are involved in processes such as gene expression regulation and telomere maintenance.