bluuebunny/crossref_metadata_2025 huggingface dataset:
Vortex-induced vibration of double cylinders under different tandem spacing
Authors: Min Guangyun
Published: February 2025

To investigate the vortex-induced vibration displacement response, force characteristics, and vibration trajectories of double cylinders under different tandem spacing and reduced velocities, a coupled simulation of computational fluid dynamics and computational structural dynamics was carried out in this present study. Unsteady Reynolds-Averaged Navier–Stokes equations were solved using a coupling algorithm, while the structural vibration equations were solved using the fourth-order Runge–Kutta method. The fourth-order Runge–Kutta algorithm was implemented in Fluent through user-defined function. By comparing with the experimental data, the accuracy of the numerical model was verified. The research results show that in terms of frequency response, the change of tandem spacing leads to the alteration of the lock-in regions of the upstream and downstream cylinders with a certain hysteresis, and the lock-in region of the downstream cylinder is enlarged. The lift coefficient of the downstream cylinder decreases with the increase in tandem spacing. Regarding the vibration trajectories, the trajectory of the upstream cylinder gradually exhibits regularity with the increase in spacing, while the trajectory of the downstream cylinder is diverse due to interference. The frequency and power spectral density curves exhibit complex variations, influenced comprehensively by spacing and reduced velocity. These variations follow distinct trends with changes in reduced velocity under different spacings, offering critical data and a robust theoretical foundation for engineering applications and academic research.
Diagnostics of the spatial profile of atomic oxygen in the flowing afterglow of a microwave plasma as a result of variable gas flow conditions
Authors: Primc Gregor , Spasić Kosta , Zaplotnik Rok , Puač Nevena , Malović Gordana , Mozetič Miran , Petrović Zoran Lj
Published: February 2025

The spatial profile of atomic oxygen in a cylindrical afterglow chamber with a height of 41 cm and an inner diameter of 30 cm was measured. The source of oxygen atoms was a remote microwave plasma operating at a discharge power of about 250 W. The gas flowed through a quartz-glass tube with inner and outer diameters of 3.8 and 6.0 mm, respectively. The exhaust of the quartz tube widened to cones of various geometries. The spatial distribution of atomic oxygen was determined for cones with an outer diameter of up to 40 mm. The tube with the widest cone (Tube 3) provided the largest O-atom density of 6 × 1020 m−3 in the upper part of the afterglow chamber away from the main gas stream in the pressure range from 50–200 Pa, while the tube (Tube 1) with the narrowest cone enabled an O-atom density of up to 2 × 1020 m−3. The differences in measured oxygen density for three tubes at positions ‘up’ and ‘down’ decreased with increasing pressure and were below the detection limit at pressures above 350 Pa. In the case of the ‘middle’ position, Tube 2 with an outer diameter of 19.3 mm exhibited a sharper decrease in oxygen density compared to Tube 1 and Tube 3. The O-atom density in the middle of the afterglow chamber increased with the increase in the percentage of pump valve opening at the lowest probed constant pressure of 40 Pa, but it stayed constant for the opening of the pump valve above 70%. For constant pressures above 100 Pa the O-atom density decreases with the larger pump valve opening. The pressure is kept constant by the corresponding increase in oxygen gas flow while increasing the percentage of the pump valve opening. The spatial profiles are explained by the effects of gas flow and diffusion.
First-principles predictions of ferromagnetism in monolayers of the 2D materials Cr2X4Y (X = S, Se; Y = Ga, Ge, In, Sn)
Authors: Guo Yujing , Zhou Haimei , Peng Yiran , Liu Yong , Wan Wenhui , Ge Yanfeng
Published: February 2025

Research on two-dimensional magnetic materials has gained significant attention in recent years owing to their unique thickness-dependent magnetism, tunable properties, and potential applications in spintronics, quantum computing, and next-generation data storage technologies. This study investigated the intrinsic ferromagnetic (FM) properties of Cr2X4Y (X = S, Se; Y = Ga, Ge, In, Sn) monolayers, with emphasis on their potential application in spintronic devices. Comprehensive stability analyses confirmed the feasibility of synthesizing these materials. Our results predict that all of these materials would exhibit robust ferromagnetism with magnetic moments of ∼4 µ

B
per Cr atom and high Curie temperatures (

T

c

) ranging from 170 K to 691 K, with Cr2S4Ga achieving the highest

T

c

. The FM behavior, attributed to superexchange interactions, remains stable under biaxial strain (−6% to 6%). Based on their electronic structures, half-metallicity is predicted for Cr2X4Y (Y = Ga, In), which enables 100% spin polarization, whereas Cr2X4Y (Y = Ge, Sn) are semiconductors with sizable band gaps. These findings indicate that the Cr2X4Y monolayers are promising candidates for room-temperature spintronic devices with tunable magnetic properties.
The dHvA effect in Sn-doped PbTe topological crystalline insulator
Authors: Miertschin Duncan , Nguyen Thinh , Zhang Shengzhi , Lee Minseong , Krishnamoorthi Sritharan , Kumar Ulaganathan Rajesh , Shankar Raman , Graf David E , Shrestha Keshav
Published: February 2025

We report the synthesis, electrical transport, magnetotransport, and high-field torque magnetometry studies of the topological crystalline insulator Sn
x
Pb

1
−
x

Te (x = 0, 0.2, and 0.4). This material undergoes a topological phase transition from trivial to non-trivial at a critical doping of

x

c

= 0.35. The resistivity increases with applied magnetic field, displaying positive magnetoresistance (MR), which reaches up to 4500% at 14 T for PbTe. However, we did not observe Shubnikov–de Haas oscillations in the MR data. To observe quantum oscillations and explore the Fermi surface topology of this material, we conducted torque magnetometry experiments on samples both below (x = 0.2) and above (x = 0.4) the critical doping

x

c

= 0.35 with applied magnetic fields up to 35 T. The torque signal from both samples revealed clear de Haas–van Alphen (dHvA) oscillations above 15 T. These oscillations exhibited single dominant frequencies of 90 T for x = 0.2 and 51 T for x = 0.4, providing insights into the Fermi surface properties. Angular and temperature-dependent analyses of the dHvA oscillations were performed using Lifshitz–Kosevich theory to extract key physical parameters of the Fermi surface. Berry phase analysis based on Landau level fan diagrams revealed non-zero values for both x = 0.2 and x = 0.4, indicating non-trivial topological features. This study provides detailed insights into the quantum oscillations and Fermi surface properties of Sn-doped PbTe/Se compounds, contributing to a deeper understanding of topological crystalline materials and their broader implications for topological physics.
Morphology measurement of cylindrical lens based on the phase deflection method
Authors: Chen Yulong , Zhong Jianfeng , Feng Bin , Guo Haoyang , Tu Zengren , Zhong Jianhua , Zhong Shuncong
Published: February 2025

When using transmission methods to measure the morphology of cylindrical lenses, the refraction of light at the front and rear surfaces of cylindrical lenses often makes it difficult to determine the light path. To address this challenge, this paper proposes a phase deflection method based on transmission to measure the surface morphology of cylindrical lenses. This method involves calculating the displacement of points with the same phase before and after the cylindrical lens is placed in the light path, and then deriving the corresponding thickness of the cylindrical lens at these points from the displacement. The feasibility of this method has been verified through simulations. Experimental measurements of the cylindrical lens morphology were compared with the optical coherence tomography system, yielding a standard error of 5.4 μm and a root mean square error of 6.2 μm, demonstrating the effectiveness of the proposed method. Compared to existing methods, this approach significantly reduces the impact of refraction caused by the rear surface of the cylindrical lens after light transmission. Additionally, it eliminates the need for a camera lens, thereby removing the cumbersome step of camera calibration. Furthermore, interference fringes can be made very dense, enabling precise measurement of small lenses.
Plasma rotation and thermonuclear neutron emission estimates in JET deuterium tritium plasmas from neutron spectroscopy
Authors: Hägg Linus , Eriksson Jacob , Conroy Sean , Ericsson Göran , Kirov Krassimir , Andersson Sundén Erik ,   JET contributors
Published: February 2025

Data from the magnetic proton recoil spectrometer (MPRu) high-resolution neutron spectrometer has been used to estimate two fusion plasma quantities, the plasma rotation and the thermonuclear neutron emission. This paper presents a framework for this method and the current results for a selection of plasma discharges from the JET DTE3 campaign. Data collection during DTE3 was preceded by a hardware upgrade in the form of new digitizers, and an update to the data reduction software. The method involves simulations with the TRANSP code, the DRESS code, and a detector response function. The plasma rotation and thermonuclear neutron emission are estimated through a fit of the simulated detector response to the MPRu measurement data. This exploratory analysis studied a selection of DTE3 discharges with high neutron rates. It was found that the rotation was typically in the range

1.5
×

10
5

 to 

2.5
×

10
5

 

rad s−1 and that neutrons from thermonuclear reactions constitute about 10%–30% of the total neutron emission. For the studied discharges, the neutron emissivity is strongly weighted to the plasma core. Due to the MPRu line of sight passing through the plasma core twice, the plasma rotation and the thermonuclear neutron emission are estimated in the core. This method has the potential to provide complementary data points to other diagnostics.
Reduced order hysteretic magnetization model for composite superconductors
Authors: Dular Julien , Verweij Arjan , Wozniak Mariusz
Published: February 2025

In this paper, we propose the Reduced Order Hysteretic Magnetization (ROHM) model to describe the magnetization and instantaneous power loss of composite superconductors subject to time-varying magnetic fields. Once the parameters of the ROHM model are fixed based on reference simulations, it allows to directly compute the macroscopic response of composite superconductors without the need to solve the detailed current density distribution. It can then be used as part of a homogenization method in large-scale superconducting models to significantly reduce the computational effort compared to detailed simulations. In this contribution, we focus on the case of a strand with twisted superconducting filaments subject to a time-varying transverse magnetic field. We propose two variations of the ROHM model: (i) a rate-independent model that reproduces hysteresis in the filaments, and (ii) a rate-dependent model that generalizes the first level by also reproducing dynamic effects due to coupling and eddy currents. We then describe the implementation and inclusion of the ROHM model in a finite element framework, discuss how to deduce the model parameters, and finally demonstrate the capabilities of the approach in terms of accuracy and efficiency over a wide range of excitation frequencies and amplitudes.
Investigation on the lubrication performance of micro-groove bearings considering journal misalignment and manufacturing errors
Authors: Li Peng , Wang Zengquan , Zhang Yan , Li Yaozong , Zhang Hao
Published: February 2025

The paper aims to examine the influence of journal misalignment and manufacturing errors on the lubrication performance of micro-groove bearings. Based on the film thickness equation considering the coupling factors of the surface profile and the mass conservation Reynolds equation, a lubrication model of journal bearings is developed. According to the numerical model, the lubrication performance of bearing considering different surface profile factors is systematically investigated, including journal misalignment with different degrees and angles, circumferential waviness with different amplitudes and numbers, axial errors with three radians of concavity, convexity and taper, and surface micro-groove with different distributions and shapes. Meanwhile, an experimental measurement is performed to verify the effectiveness and feasibility of the numerical model. The results indicate that journal misalignment and manufacturing errors play a critical role in the bearing performance, and the analysis for micro-groove bearings considering the coupling factors of the surface profile is closer to the actual engineering. Additionally, the parameters of the micro-groove greatly affect friction reduction effect. By comparing surface micro-grooves with different distributions and shapes, it can be found that the straight-groove with suitable parameters can increase the bearing capacity and reduce the friction coefficient. Research results have great guidance significance for the optimum design of the surface micro-texture, especially for the further study of the lubrication performance of micro-groove bearings with the coupling factors of the surface profile.
Study of aerodynamic noise from UAV rotor in hover and forward flight
Authors: Wang Qigan , Liu Jishan , Wu Han , Dong Yu , Zhang Zhijun
Published: February 2025

This study employed the Delayed Detached Eddy Simulation (DDES) turbulence model and the Ffowcs Williams-Hawkings (FW-H) acoustic analogy method to investigate the flow field and acoustic characteristics of a 1045 Unmanned Aerial Vehicle (UAV) rotor in both hover and forward flight, considering both dipole noise and overall noise. Results showed that lift fluctuations during forward flight were significantly higher, and the tip vortex dissipation rate was much greater than in hover. A comparison of noise spectra and directivity between hover and forward flight revealed that the noise intensity of the rotor in forward flight was notably higher. Hover rotor noise was dominated by low-frequency noise below 100 Hz, while forward flight rotor noise concentrated near the blade passage frequency (BPF) fundamental. Analysis of the spectral relationship between dipole noise and overall noise indicated that dipole noise was the primary noise source in forward flight. Further investigation of the forward flight rotor under different rotor speeds and shaft angles suggested that reducing rotor speed, could effectively reduce noise, whereas adjusting shaft angle had limited impact on noise reduction. This research provides theoretical insights for noise assessment and reduction in rotorcraft UAV design.
Label-free full-thickness imaging of porcine vagus nerve fascicular anatomy by polarization-sensitive optical coherence tomography
Authors: Yoon Yong-Chul , Saytashev Ilyas , Chen Rex Chin-Hao , Settell Megan , Guastaldi Fernando , Hammer Daniel X , Ludwig Kip A , Vakoc Benjamin J
Published: February 2025

Objective. Improving the efficacy of vagus nerve (VN) stimulation therapy requires a detailed understanding of the anatomical and functional organization of nerve fiber bundles and their fascicles. Various ex-vivo imaging platforms have been optimized for this purpose. However, all existing tools with micrometer resolution require labeling to enhance the fascicle contrast, and this labeling is resource-intensive and time-consuming. Polarization-sensitive optical coherence tomography (PS-OCT) was previously used to perform high-speed, label-free small animal (rat) sciatic nerve imaging but has not been applied for imaging the full-thickness large animal VNs (>1 mm diameter thick) due to tissue-limited imaging depth. We developed a PS-OCT platform that circumvents this problem and demonstrate high-speed label-free imaging of full-depth, multiple centimeters-long mammalian VNs for the first time. Approach. We employed a custom-built PS-OCT system with a dual-surface scanning microscope to capture opposite sides of the sample in a single frame. A tailored post-processing algorithm maximized fascicle contrast and merged the two surfaces together. Multi-centimeter-long porcine VNs were imaged. Main Results. Our approach reconstructed fascicle information throughout the full-thickness of the VN when compressed to a 650 μm thickness. Moreover, we cross-validated PS-OCT measurements of fascicular organization and retardance to assess myelination against pair histology from the same specimens, showing Spearman’s rank correlation coefficient value of 0.69 (p-value < 0.001). Significance. We demonstrated a label-free optical imaging method for large-volume VN imaging. The time to image a 6.8 cm nerve was 680 s with 0.1 mm s−1 longitudinal sample translation speed, which is more than two orders of magnitude faster than existing modalities that require labeling. With this gain in speed and the possibility of label-free quantification of a fascicle’s myelination level, important studies on inter-sample variability in fascicle organization become feasible.
Evaluation of tungsten influx rate using line emissions from W5+ ions in EAST tokamak
Authors: Zhang Fengling , Mitnik Darío , Zhang Ling , Bao Runjia , Zhang Wenmin , Morita Shigeru , Cheng Yunxin , Hu Ailan , Zhou Chengxi , Chen Jihui , Ding Xiaobin , Jie Yinxian , Liu Haiqing
Published: February 2025

The S/XB ratios (ionization events per emitted photon) allow one to relate spectroscopic emissivity measurements to the impurity influx from a localized source. In this work, we determine the tungsten influx by examining two dominant extreme ultraviolet line emissions at 382.13 Å and 394.07 Å, corresponding to the

4

f

14

5
f
→
4

f

14

5
d

radiative transitions of the W5+ ion. The ground configuration of W5+ consists of the ground level and a metastable level, with the latter having a higher population than the ground state. Therefore, a simple approach assuming that the transitions are independent, i.e. only populated by a unique level source, requires correction. To address this, we have developed a fully collisional-radiative modeling in which 430 levels contribute to the ionization. We have utilized three advanced computational codes – hullac (Hebrew University—Lawrence Livermore Atomic Code, AS (AutoStructure), and FAC (Flexible Atomic Code) – for the atomic structure calculations. These codes provide the necessary information such as wavelengths, collisional and radiative transition rate coefficients. The fac code was also used to calculate the direct electron-impact ionization under the distorted-wave approximation. We also included contributions to total ionization from excitation-autoionization processes up to n = 15 manifolds from the distorted-wave calculations. Subsequently, we used these results to ascertain the tungsten impurity influx in a dedicated discharge of the EAST tokamak, which operates with full tungsten divertors. In our findings, we observed that for the density range relevant to the edge region of a tokamak plasma, the S/XB ratios are almost independent of electron density but exhibit significant variation with electron temperature.
Public understanding of climate change in malaysia: results of a national survey
Authors: Azhari Azliyana , Richardson Lucy M , Pandya-Wood Raksha , Lester Libby
Published: February 2025

The Malaysia National Survey of Climate Change Concern and Behaviour is the first of its kind to provide insights into the Malaysian public’s understanding of climate change. This is crucial for Malaysia, a country experiencing weather disruptions and climate-induced disasters. This nationally representative survey (n = 1063) assessed climate change awareness, literacy levels, policy support, motivations for change, individual actions and media preferences. It also deployed an audience segmentation tool to support the design of targeted communications about both the impacts and risks of climate change and the roll out of climate solutions. The research finds that the Malaysian public has a high level of alarm or concern over climate change (81%). 40–56% of respondents understand the commonly used terminologies (e.g., greenhouse gas, low carbon technology, mitigation and renewable energy). It also finds that Malaysians have adopted greener choices (65–79%) in a range of energy, consumer and waste-related behaviours to address climate change. Results also show that ‘easier’ behaviours are more commonly adopted, such as reducing electricity use, while measures that cost money or time such as installing solar panels and using public transport are less likely to be adopted. Our findings show that Malaysians are worried about climate change, but effective communication strategies are required to help the shift to ‘harder’ change. Such strategies will be crucial for better disaster and health responses and policy support for the transition to a net zero future.
H-bonded liquid crystals: effect of ZnO nanoparticles on the enhancement in electrical conductivity
Authors: Sonali M K , Pisharody Gayathri R , Kulkarni Suresh D , Bhagavath Poornima
Published: February 2025

Integrating nanoparticles (NPs) with liquid crystals has emerged as a contemporary research domain in soft matter. The interplay between the two can substantially transform their properties and dynamics. The study conducted the experiments using nanocomposites of hydrogen-bonded supramolecular calamitic liquid crystals doped with ZnO NPs. It is found that the concentration of ZnO and the carbon chain length of the host compounds played a significant role in determining the mesophase transition and crystallization temperatures. The study aimed to investigate the effect of NPs on the electrical properties of liquid crystal nanocomposites, using varying weight percentages (0.5wt%, 2wt%, and 5wt%). Zinc oxide NPs with a particle size of 118 nm is synthesized using a simple starting material. Hydrogen-bonded liquid crystals (HBLCs) viz., P8:FBA and P18:FBA with chain lengths of 8 and 18 carbons, obtained from acid moieties and Schiff bases acted as a host. The nanocomposites exhibited enhanced conductivity with the increase in the dopant concentration while the conductivity decreased as the chain length increased from 8 to 18. It is believed that an increased concentration of NPs increases conductivity through the ion hopping pathway. Adding ZnO NPs to the host HBLC reduces the activation energy and enhances conductivity, making it suitable as functional materials.
Marginal abatement costs for greenhouse gas emissions in the United States using an energy systems approach
Authors: Blackhurst Michael , Venkatesh Aranya , Sinha Aditya , Jordan Katherine , Muller Nicholas Z , Wade Cameron , Johnson Jeremiah X , Jaramillo Paulina
Published: February 2025

Deep decarbonization requires fundamental changes in meeting energy service demands, with some efforts increasing overall costs. Examining abatement measures in isolation, however, fails to capture their interactive effects within the energy system. Here we show the abatement costs of decarbonization in the United States using an energy system optimization model to capture technological interactions, multi-decadal path dependence, and endogenous end-use technology selection. Energy-system-wide net-zero CO2-eq emissions are achieved in 2050 at a cost under $400 per tonne CO2-eq, led by emissions reductions in power generation, end-use electrification of ground transportation, space heating, and some industrial applications. Differences in mitigation costs and CO2 geological storage potential lead to regional heterogeneities in mitigation rates and residual emissions. The marginal abatement cost curves show that additional decarbonization comes at higher incremental costs, this cost penalty decreases over time, and substantially greater abatement occurs in future time periods at the same abatement cost.
An evidence-driven classification of non-filtering ingredients for topical photoprotection
Authors: Brown Anthony , Passeron Thierry , Granger Corinne , Gilaberte Yolanda , Trullas Carles , Piquero-Casals Jaime , Leone Giovanni , Schalka Sergio , Lim Henry W , Krutmann Jean
Published: February 2025

This article provides an evidence-driven classification of non-filtering photoprotective ingredients that modulate skin's biological response to sunlight.
Risk factors for PrEP and ART medication adherence challenges in cis-gender South African men who have sex with men in Johannesburg and Pretoria
Authors: Pienaar Jacqueline , Tsope Lindiwe , Mabena Mapaseka , Komane Pontsho , Sibanyoni Maria , Ramashala Boitumelo , Wahome Elizabeth , Denousse Charlene , Gakunu Ankiza , van der Elst Elise M , Giovenco Danielle , Operario Don , Sanders Eduard J
Published: February 2025

Background

Mental health challenges are common among men who have sex with men (MSM) in South Africa and may impact medication adherence.

Methods

We determined the prevalence and risk factors of medication adherence challenges among 160 pre-exposure prophylaxis (PrEP)- and 40 antiretroviral therapy (ART)-taking MSM registered at two key population clinics in Johannesburg and Pretoria in 2023. We used modified Poisson regression to estimate associations between participant characteristics and medication adherence challenges (missed dosage on ≥1 d in the last month).

Results

A total of 106 (53.5%) participants (57.6% on PrEP, 37.5% on ART; p=0.02) had medication adherence challenges and 61 (30.5%) participants (31.2% on PrEP, 27.5% on ART; p=0.23) met criteria for moderate to severe symptoms of depression (score ≥10 on the 9-item Patient Health Questionnaire). In multivariable analysis, predictors included PrEP use (adjusted prevalence ratio [aPR]=1.81 [95% confidence interval {CI} 1.21 to 2.73), clinic in Pretoria (aPR 1.43 [95% CI 1.08 to 1.89]), transactional sex (aPR 1.81 [95% CI 1.34 to 2.44]), moderate to severe depression (aPR 1.50 [95% CI 1.19 to 1.89]) and use of social media (aPR 1.45 [95% CI 1.05 to 2.00]).

Conclusions

Depression is common and may be an important risk factor for poor medication adherence among MSM in South Africa. Future research should leverage a longitudinal study design to inform potential interventions.
CORONATINE INSENSITIVE 1-mediated repression of immunity-related genes in Arabidopsis roots is overcome upon infection with Verticillium longisporum
Authors: Ulrich Louisa , Schmitz Johanna , Thurow Corinna , Gatz Christiane
Published: February 2025

Verticillium longisporum is a soil-borne fungal pathogen causing vascular disease predominantly in Brassicaceae. We have reported previously that the receptor of the plant defense hormone jasmonoyl-isoleucine (JA-Ile), CORONATINE INSENSITIVE 1 (COI1), is required in roots for efficient proliferation of the fungus in the shoot implicating a mobile root-borne signal that influences the outcome of the disease in shoots. This susceptibility-promoting COI1 function is independent from JA-Ile. To explore the underlying mechanism we compared the root transcriptome of coi1 with the transcriptomes of the susceptible JA-Ile-deficient allene oxide synthase (aos) mutant and susceptible wild-type (WT) plants. The biggest difference between the transcriptomes of coi1 versus WT and aos was due to 316 immunity-related genes that were constitutively higher expressed in coi1 as compared to the susceptible genotypes. Interfering with the expression of a subgroup of these genes partially suppressed the coi1-mediated tolerance phenotype. We therefore hypothesize that secreted defense compounds encoded by genes constitutively expressed in coi1 are transported to the shoot with the transpiration stream where they accumulate to interfere with fungal growth. We furthermore report that 149 of the 316 COI1-repressed genes are induced in WT and aos upon infection reaching similar levels as in mock-treated coi1. These were not further induced in coi1 upon infection. Thus, the repressive effect of COI1 is either lifted or overridden upon infection with V. longisporum.
Radio signatures of a massive black hole in GHZ9 at z ∼ 10
Authors: Latif Muhammad A , Whalen Daniel J
Published: February 2025

Synergies between the JWST and the Chandra X-ray observatory have advanced the observational frontier by detecting a handful of active galactic nuclei beyond $z \sim$ 10. In particular, the recent discovery of a candidate $\rm 8 \times 10^7$$\mathrm{M}_{\odot }$ black hole (BH) in the galaxy GHZ9 at $z =$ 10.4 favours massive seed formation channels for these objects. Motivated by prospects for their detection in radio by recent studies, we estimate radio fluxes for GHZ9 and explore the possibility of their detection with the Square Kilometer Array (SKA) and next-generation Very Large Array (ngVLA). We find that ngVLA should be able to detect radio emission from GHZ9 for integration times as short as 1 h, while SKA will require integration times of up to 100 h. We also find that radio emission from the BH can be distinguished from that due to H ii regions and supernovae in its host galaxy. The detection of a few hundred nJy radio signal at frequencies $>\!\! 2$ GHz will be a smoking gun for the presence of a BH in GHZ9.
Snapshots of ID Week 2024
Authors: Samoriski Colin , Passarelli Patrick , Sudnik Paulina , Anlage Troy , Sportiello Michael , Stephen Tyler , Louie Ted
Published: February 2025

This is a summary of several presentations from ID Week 2024, selected for their clinical relevance.
Community-acquired methicillin-resistant Staphylococcus aureus: is it still a significant pathogen for skin and soft tissue infections? A 30-year overview
Authors: Burillo Almudena , Bouza Emilio
Published: February 2025

Purpose of review

The prevalence of community-acquired methicillin-resistant Staphylococcus aureus (CA-MRSA) in skin and soft tissue infections (SSTI) has significantly changed in recent decades. We conducted a literature review to determine whether this microorganism, which became increasingly common as a cause of SSTI in the 2000s, still plays a significant role in these infections today.

Recent findings

Over the past 30 years, there has been a pattern of increase and then decrease in these infections. The highest frequency was observed in the United States, to the extent that guidelines recommended empirical antibiotic treatment for this pathogen in SSTI. Clone USA300 is the primary causative agent in the United States. In Europe, SSTI are much less common than in the United States, and the presence of this clone has been significantly lower. A decrease in the frequency of SSTI and CA-MRSA has been observed in developed countries. However, the spread of specific clones in Latin America, Asia and Africa highlights the need for rigorous global surveillance.

In recent years, the prevalence of CA-MRSA SSTI has decreased in developed countries. However, globalisation, immigration and intercontinental travel have favoured the spread of some clones with epidemic potential. It remains to be seen whether the current lower frequency will be maintained or whether these clones will give rise to a new wave.
High-quality PacBio draft genome sequences of 17 free-living Bradyrhizobium and four related Nitrobacteraceae strains isolated from arid soils in the Santa Catalina Mountains of Southern Arizona
Authors: Kridler Melanie R. , Howe Amanda , Legins Jimaree A. , Guerrero Christina , Bartelme Ryan P. , Taylor Bridget , Carini Paul
Published: February 2025

Non-symbiotic Bradyrhizobium are among the most abundant and ubiquitous microbes in bulk soils globally. Despite this, most available genomic resources for Bradyrhizobium are derived from plant-associated strains. We present high-quality draft genomes for 17 Bradyrhizobium and four Nitrobacteraceae cultures isolated from bulk semiarid soils in Arizona, USA. The genome sizes range from 5.99 to 10.4 Mbp. Phylogenomic analysis of the 21 genomes indicates they fall into four clades. Two of the clades are nested within the Bradyrhizobium genus. The other two clades were associated with Nitrobacteraceae outgroups basal to Bradyrhizobium. All genomes lack genes coding for molybdenum or vanadium nitrogenases, and nod genes that code for proteins involved in nodulation, suggesting these isolates are free-living, non-symbiotic and do not fix dinitrogen gas. These genomes offer new resources for investigating free-living Bradyrhizobium lineages.
DNA G-quadruplex Profiling Reveals Functional and Mechanistic Role of G-quadruplexes in Skeletal Muscle Stem Cells
Authors: Chen Xiaona , Yang Feng , Zhang Suyang , Guo Xiaofan , Zhao Jieyu , Qiao Yulong , He Liangqiang , Li Yang , Zhou Qin , Ong Michael Tim Yun , Kwok Chun Kit , Sun Hao , Wang Huating
Published: February 2025

DNA G-quadruplexes (G4s) are non-canonical secondary structures formed in guanine-rich DNA sequences and play important roles in modulating biological processes through a variety of gene regulatory mechanisms. Emerging G4 profiling permits global mapping of endogenous G4 formation. Here in this study, we map the G4 landscapes in adult skeletal muscle stem cells (MuSCs) which are essential for injury induced muscle regeneration. Throughout the myogenic lineage progression of MuSCs from quiescent to activated and further differentiated cells, we uncover dynamic endogenous G4 formation with a pronounced G4 induction when MuSCs become activated and proliferating. We further demonstrate that the G4 induction promotes MuSC activation thus the regeneration process. Mechanistically, we found that promoter associated G4s regulate gene transcription through facilitating chromatin looping. Furthermore, we found that G4 sites are enriched for transcription factor (TF) binding events in activated MuSCs; MAX binds to G4 structures to synergistically facilitate chromatin looping and gene transcription thus promoting MuSC activation and regeneration. The above uncovered global regulatory functions/mechanisms are further dissected on the paradigm ofCcne1promoter, demonstratingCcne1is a bona fide G4/MAX regulatory target in activated MuSCs. Altogether, our findings for the first time demonstrate the prevalent and dynamic formation of G4s in adult MuSCs and the mechanistic role of G4s in modulating gene expression and MuSC activation/proliferation.
ABCF Protein-Mediated Resistance Shapes Bacterial Responses to antibiotics Based on their Type and Concentration
Authors: Koběrská Markéta , Veselá Ludmila , Novotná Michaela , Mahor Durga , Mazumdar Aninda , Pinďáková Nikola , Petravicius Pamela Omena , Pokorná Julie , Kameník Zdeněk , Balíková Novotná Gabriela
Published: February 2025

ABCF ATPases are increasingly recognized as translation factors that rescue stalled ribosomes, whether they encounter challenging mRNA templates or antibiotic-induced stalling. The latter defines ARE ABCF proteins, known for their role in antibiotic resistance. However, in this study, we reveal a broader role of ARE ABCFs in antibiotic-responsive regulation. Using genetic, OMICs, and biochemical approaches we showed that ARE ABCF proteins TiaA and Are5sc inStreptomyces coelicoloruse their resistance functions to modulate specialized metabolism and proteosynthesis in response to lincosamide, streptogramin A, and pleuromutilin (LSAP) antibiotics. Although under LSAP exposure, either Are5sc or TiaA is essential for activating the biosynthesis of the redox-active antimicrobial actinorhodin, these proteins exhibit distinct functions at the proteome level, defined by their resistance profiles and temporally regulated expression. Are5sc facilitates early adaptive responses by modulating the WblC regulon across a broad range of LSAP concentrations, while TiaA is induced later, specifically at higher concentrations, where it suppresses antibiotic stress responses, particularly against pleuromutilins. TiaA function thus reflects the ecological context of LSAP antibiotics as pleuromutilins are produced by fungi, whereas lincosamides/streptogramins originate from actinomycetes. Our findings demonstrate that ARE ABCF proteins, through their resistance function, act as global regulators of translation, mirroring the roles of non-ARE ABCF proteins like EttA. This highlights their broader ecological and physiological significance, extending beyond their established role in antibiotic resistance.

IMPORTANCE

Bacteria adapt to diverse stimuli mainly through transcriptional changes that regulate adaptive protein factors. Here, we show that responses to protein synthesis-inhibiting antibiotics are fine-tuned by antibiotic resistance ABCF proteins at the translational level, enabling bacteria to differentiate between antibiotic classes and concentrations for a tailored response. Additionally, we have demonstrated that these proteins can specialize in conferring high-level resistance to specific antibiotics. Given their prevalence in pathogenic bacteria, ARE ABCF proteins may play a crucial role in resistance development, particularly against new antibiotics targeting the ribosomal catalytic center, presenting a significant challenge for antimicrobial therapy.
Diagnostic Testing Accuracy of Sucrose-stimulated Salivary pH for Screening Early Childhood Caries Diagnosis and Severity: An Observational Study
Authors: Okuji David , Tian Victoria , Odusanwo Olutayo , Twi-Yeboah Alberta
Published: February 2025

Purpose

The purpose of this study was to determine the diagnostic testing accuracy of child and maternal sucrose-stimulated salivary pH as screening tools for early childhood caries diagnosis and severity.

Methods

From a sample population of 642 mother-child dyads, with child-subjects under age six years old, child and maternal sucrose-stimulated saliva specimens were collected to measure salivary pH thirty minutes after consumption of sucrose by mouth. Immediately after the pH measurement and oral clinical examination, the pediatric dentist provider determined for child-subjects their diagnoses for early childhood caries and severity, respectively guided by the gold-standard classifications promulgated by the American Academy of Pediatric Dentistry and International Caries Detection and Assessment System. Salivary pH of 6.0 was statistically calculated as the screening cut-off point. Statistical analyses calculated values for true positive, false positive, true negative, false negative, and the diagnostic testing accuracy metrics for prevalence, specificity, sensitivity, diagnostic odds ratio, positive and negative predictive values, positive and negative likelihood ratios, and Youden’s Index. Regression models were utilized to determine the respective odds ratio associations between child and maternal sucrose-stimulated salivary pH versus the diagnosis and severity of early childhood caries.

Results

For early childhood caries diagnosis, child sucrose-stimulated salivary pH yielded diagnostic test accuracy metrics of 47.7 percent prevalence, 72.42 percent specificity, 59.47 percent sensitivity, 66.30 percent positive predictive value, and 66.20 percent negative predictive value, and diagnostic odds ratio 3.85. The results for maternal sucrose-stimulated salivary pH for caries severity were similar in value. Maternal sucrose-stimulated salivary pH displayed lower overall DTA metrics compared to child sucrose-stimulated salivary pH, but both child and maternal sucrose-stimulated salivary pH had higher specificity than sensitivity and displayed moderate levels of positive and negative predictive values. Child sucrose-stimulated salivary pH less than 6.0 had 3.89 times higher odds for ECC diagnosis and 3.56 times higher odds of moderate-extensive caries severity than child sucrose-stimulated salivary pH greater than 6.0. Maternal sucrose-stimulated salivary pH less than 6.0 had 1.60 times higher odds of moderate-extensive caries severity than maternal sucrose-stimulated salivary pH greater than 6.0.

Conclusion

Child and maternal sucrose-stimulated salivary pH screening tests are useful as a screening tool to identify children at high-risk for early childhood caries.
Crusty-Pinky: A Novel Polyextremotolerant Fungus and itsMethylobacteriumSymbionts Could be an Essential Symbiosis for the Biological Soil Crust Consortium
Authors: Carr Erin C , Saha Rajib , Harris Steven D , Riekhof Wayne R
Published: February 2025

JF2 08-2F Crusty is a novel melanized polyextremotolerant fungus isolated from a biological soil crust, which we believe harborsMethylobacteriumspp. endosymbionts, called Pinky. Crusty is capable of utilizing many sources of carbon and nitrogen and is resistant to multiple metals and UV-C due to its melanized cell wall. We were unable to recover a Pinky-free culture of Crusty via usage of antibiotics. However, when exposed to antibiotics that kill or stop the growth of the Pinky, growth of Crusty is significantly stunted, implying that actively growing Pinky symbionts are needed for Crusty’s optimal growth. The Crusty-Pinky symbiosis also seems to be able to perform active metabolism in carbonless and nitrogenless medium, which we believe is due to Pinky’s ability to perform aerobic anoxygenic photosynthesis. Finally, Pinky was identified as being capable of growth stimulation of the algaeChlorella sorokiniana, indicating that Pinky likely produces cytokinins or auxins whichMethylobacteriumare known for. Features of this symbiosis provide us insight into the ecological roles of these microbes within the biological soil crust.
Spatial transcriptomics uncovers hybrid, pro-inflammatory and pro-fibrotic cellular niches in pulmonary granuloma of patients with chronic sarcoidosis
Authors: Christian Leonard , Yilmaz Hande , Ruwisch Jannik , Giercke Leon , Seeliger Benjamin , Kamp Jan C. , Bayraktar Sirvan , Ewen Raphael , Graalmann Theresa , Fuge Jan , Greer Mark , Ius Fabio , Welte Tobias , Hohlfeld Jens M. , Hoeper Marius M. , Gottlieb Jens , Kaminski Naftali , Prasse Antje , Jonigk Danny , Li Yang , Falk Christine , Neubert Lavinia , Schupp Jonas C.
Published: February 2025

Background

Sarcoidosis is a disease of unknown etiology characterized by the formation of immune cell accumulation (granuloma) in the lung and other tissues. Chronic sarcoidosis may lead to pulmonary fibrosis.

Aim

To unravel cellular niches within pulmonary granuloma of chronic sarcoidosis patients using spatial transcriptomics.

Methods

Spatial transcriptomics using the Visium platform (10x Genomics) was performed on nine granuloma-containing lung explants from sarcoidosis patients. Validation of gene expression was performed through immunohistofluorescence protein staining and RNAin situhybridization.

Results

Spatial gene expression covered 30,587 gene expression spots and 173 granulomas. A CD68+macrophage niche was localized in the center of the granuloma, with a CD3+T and CD20+B cell niche in close proximity, surrounded by a COL3A1+fibroblast niche. In the central granuloma macrophage niche, expression of the pro-fibrotic macrophage genesSPP1,CHIT1andCHI3L1was observed, genes whose expression has recently been described for macrophages in idiopathic pulmonary fibrosis. Additionally, pro-inflammatory macrophage genes were expressed in the central granuloma niche: macrophages appear armed for lysosomal degradation and ready for phagocytosis. Inner granuloma niches showed high responsiveness to interferon gamma (IFN-γ), expressing a multitude of IFN-γ-induced genes. High collagen andCTHRC1expression were observed in granuloma fibroblasts niches, characteristics of pro-fibrotic lung remodeling. Ligand-receptor analysis identified pro-inflammatory and pro-fibrotic interactions between granuloma niches.

Conclusion

Taken together, macrophages in the center of the sarcoidosis granuloma form an armed-and-ready, hybrid pro-inflammatory and pro-fibrotic niche, supporting granuloma persistence through continuous IFN-γ-stimulation and fibrotic remodeling conducted by fibrotic fibroblasts surrounding the granuloma.
Ultra processed food exposure and cognitive outcomes: A systematic review of observational studies.
Authors: Smith Megan , Watson Pippa , Gallacher John , Bauermeister Sarah
Published: February 2025

Background: Ultra processed food (UPF) intake has been associated with multiple negative health outcomes. Research investigating UPF intake and cognitive health outcomes has begun. The aim of this review is to summarise the existing evidence of associations between exposure to UPFs, as defined by the NOVA food classification system, and cognitive health outcomes. Methods: We conducted a systematic search across MEDLINE, PsycINFO, Embase, and APA Psych Articles through OVID, and PubMed for relevant studies up-until October 2024. The Newcastle-Ottawa Scale was used to assess the quality of included studies. A narrative approach was used to summarise and integrate results across studies. Results: Three hundred and eighty-three articles were screened and five met the inclusion criteria. All studies were published between 2022 and 2024. The association between UPF intake and four different cognitive outcomes (dementia risk, cognitive impairment risk, cognitive performance and cognitive change trajectories) were explored across the studies. Three out of the five included studies found a significant negative main effect of consuming UPF on the cognitive outcome of interest. All studies identified adverse consequences of consumption in either a sub-group of the population or a sub-group of UPF type. Conclusions: Deleterious effects of UPF consumption on multiple cognitive health outcomes were identified across all studies. However, the results suggest the relationship may be specific to sub-groups of the population or sub-groups of UPF type. Conclusions should be drawn with caution due to the limited number of studies available examining UPF intake according to NOVA and its association with cognitive outcomes, as well as the variability in cognitive measures assessed and other methodological differences across studies.
Dissecting the RNA binding capacity of the multi-RRM protein Rrm4 essential for endosomal mRNA transport
Authors: Stoffel Nina Kim , Sankaranarayanan Srimeenakshi , Müntjes Kira , Busch Anke , König Julian , Zarnack Kathi , Feldbrügge Michael
Published: February 2025

RNA-binding proteins (RBPs) utilize multiple RNA-binding domains (RBDs) to engage with extensive mRNA networks. Understanding the intricate interplay of modular RBDs is essential for uncovering RBP function. Yet, how individual RBDs shape transcriptome-wide interactions remains poorly understood. Here, we dissect the roles of the three RNA recognition motifs (RRMs) in the endosomal mRNA transporter Rrm4 during polar growth ofUstilago maydis. Using a comparative mutant-based iCLIP2 approach, we disclose an extensive inventory of RRM-specific binding sites. Most binding sites are prominently governed by RRM3, however, they are not critical for function. Conversely, functionally essential binding sites are recognized by a more complex RBD interplay, involving RRM1 and/or RRM2 with partial support from RRM3. By integrating transcriptome-wide RNA binding data with transcriptomics, we pinpoint their function as regulatory RNA elements affecting mRNA abundance, linking endosomal transport to stability. The modular RNA binding of Rrm4 defines distinct RNA regulons controlling mitochondrial activity, polarity factors, and cell wall remodeling – processes critical for polar growth. These findings disclose the intricate binding modes of an RBPin vivo, emphasizing how multiple RBDs differentiate functional binding sites from accessory ones to determine mRNA fate.

Graphical abstract

Figure 1.