bluuebunny/crossref_metadata_2025 huggingface dataset:
Wet cleaning of Ta-based extreme ultraviolet photomasks at room temperature
Authors: Park Jehwan , Choi Woong , Kim Jihyun
Published: February 2024

Owing to the wavelength-dependent limits of the deep ultraviolet exposure process, the semiconductor industry introduced extreme ultraviolet (EUV) lithography operating at a 13.5 nm wavelength. Traditional photomasks employ pellicles for protection; however, EUV-specific pellicles are not widely applicable to commercial processes, requiring the development of a EUV photomask cleaning method. In this study, a wet cleaning method for Ta-based EUV photomasks at room temperature was systematically examined in terms of key parameters, including the pattern step height, surface topography, and particulate count, via atomic force microscopy and x-ray reflectivity. Post sulfuric acid-hydrogen peroxide mixture (SPM) treatment, the photomask exhibited a stable step height, indicating minimal pattern degradation. Additionally, discernible alterations in the surface roughness and a decrease in particle count were observed, further indicating to the effectiveness of SPM-mediated cleaning. Conversely, following standard clean-1 (SC-1) treatment, while the pattern step height remained relatively unchanged, a notable increase in surface irregularities and macroscopic particulates was observed, suggesting a suboptimal cleaning efficiency of the SC-1 solution despite its potential for pattern structure preservation. Our room temperature wet cleaning method efficiently reduces wear-out and successfully eliminates contaminants, potentially prolonging the EUV photomask’s productivity and durability.
Automatic segmentation of hepatocellular carcinoma on dynamic contrast-enhanced MRI based on deep learning
Authors: Luo Xiao , Li Peiwen , Chen Hongyi , Zhou Kun , Piao Sirong , Yang Liqin , Hu Bin , Geng Daoying
Published: February 2024

Objective. Precise hepatocellular carcinoma (HCC) detection is crucial for clinical management. While studies focus on computed tomography-based automatic algorithms, there is a rareness of research on automatic detection based on dynamic contrast enhanced (DCE) magnetic resonance imaging. This study is to develop an automatic detection and segmentation deep learning model for HCC using DCE. Approach: DCE images acquired from 2016 to 2021 were retrospectively collected. Then, 382 patients (301 male; 81 female) with 466 lesions pathologically confirmed were included and divided into an 80% training-validation set and a 20% independent test set. For external validation, 51 patients (42 male; 9 female) in another hospital from 2018 to 2021 were included. The U-net architecture was modified to accommodate multi-phasic DCE input. The model was trained with the training-validation set using five-fold cross-validation, and furtherly evaluated with the independent test set using comprehensive metrics for segmentation and detection performance. The proposed automatic segmentation model consisted of five main steps: phase registration, automatic liver region extraction using a pre-trained model, automatic HCC lesion segmentation using the multi-phasic deep learning model, ensemble of five-fold predictions, and post-processing using connected component analysis to enhance the performance to refine predictions and eliminate false positives. Main results. The proposed model achieved a mean dice similarity coefficient (DSC) of 0.81 ± 0.11, a sensitivity of 94.41 ± 15.50%, a precision of 94.19 ± 17.32%, and 0.14 ± 0.48 false positive lesions per patient in the independent test set. The model detected 88% (80/91) HCC lesions in the condition of DSC > 0.5, and the DSC per tumor was 0.80 ± 0.13. In the external set, the model detected 92% (58/62) lesions with 0.12 ± 0.33 false positives per patient, and the DSC per tumor was 0.75 ± 0.10. Significance. This study developed an automatic detection and segmentation deep learning model for HCC using DCE, which yielded promising post-processed results in accurately identifying and delineating HCC lesions.
Blood flow restriction pressure for narrow cuffs (5 cm) cannot be estimated with precision
Authors: Spitz Robert W , Yamada Yujiro , Wong Vickie , Kataoka Ryo , Hammert William B , Song Jun Seob , Kang Anna , Seffrin Aldo , Loenneke Jeremy P
Published: February 2024

Blood flow restriction pressures are set relative to the lowest pressure needed to occlude blood flow with that specific cuff. Due to pressure limitations of some devices, it is often not possible to occlude blood flow in all subjects and apply a known relative pressure in the lower body with a 5 cm wide cuff. Objective. To use a device capable of generating high pressures (up to 907 mmHg) to create and validate an estimation equation for the 5 cm cuff in the lower body using a 12 cm cuff. Approach. 170 participants had their arterial occlusion pressure (AOP) with a 5 cm and 12 cm cuff and their thigh circumference measured in their right leg. The sample was randomly allocated to a prediction group (66%) and validation group (33%). Thigh circumference and 12 cm AOP were used as predictors. A Bland–Altman plot was constructed to assess agreement between measured and predicted values. Main results. The mean difference (95% confidence interval) between the observed (336.8 mmHg) and the predicted (343.9 mmHg) 5 cm AOP was 7.1 (−11.9, 26.1) mmHg. The 95% limits of agreement were −133.6 to 147.8 mmHg. There was a negative relationship between the difference and the average of predicted and measured 5 cm AOP (B = −0.317, p = 0.000043). Significance. Although this was the first study to quantify AOP over 600 mmHg with a 5 cm cuff, our equation is not valid across all levels of pressure. If possible, larger cuff widths should be employed in the lower body.
Witnessing edge modes in trimerized circuit quantum electrodynamic lattice
Authors: Zhao Xuedong , Xing Yan , Cao Ji , Cui Wen-Xue , Liu Shutian , Wang Hong-Fu
Published: February 2024

We propose a scheme to investigate and witness edge modes of general one-dimensional photonic trimers in a circuit quantum electrodynamic lattice. These in-gap edge modes are strictly and analytically solved and the criteria for their emergence are indicated respectively. Moreover, the energy spectrum of the system shows two different regimes characterized by a discrepancy in the number of edge modes. Specifically, while there are always a couple of edge modes only present at one single boundary in both the regimes, one of the regimes also shows another pair of edge modes localized on the opposite boundary. Furthermore, these edge modes are witnessed with the aid of continuous-time quantum walks and average photon number measurements. Our scheme provides a comprehensive method for studying the edge modes of matter.
Dynamical evolution of exciton-polariton Bose–Einstein condensate under coupled interaction
Authors: Wang Ying , Liu Xiaoning , Ren Yuan , Liu Zhengliang , Wu Hao , Xiong Zhenyu
Published: February 2024

We studied the exciton-polariton Bose–Einstein condensation (BEC) under light field manipulation by considering the coupled interaction of the system between exciton-polariton and light. Based on the coupled Gross–Pitaevskii equation (GPE) model and with modified variational method, we analytically derived the solutions of the excitonic system under the polar angle direction perturbation and system rotation. We identified that for different rotational angular velocities and different coupled strengths, the system evolves from a meta-stable oscillation state to monotonically decaying state, with potential for the study of quantum vortex identification for such kind of coupled systems. Our theoretical results can be used to guide the study of the evolution mode of the exciton-polariton system involving coupled interaction.
Progress in efficient doping of Al-rich AlGaN
Authors: Wang Jiaming , Xu Fujun , Zhang Lisheng , Lang Jing , Fang Xuzhou , Zhang Ziyao , Guo Xueqi , Ji Chen , Ji Chengzhi , Tan Fuyun , Yang Xuelin , Kang Xiangning , Qin Zhixin , Tang Ning , Wang Xinqiang , Ge Weikun , Shen Bo
Published: February 2024

The development of semiconductors is always accompanied by the progress in controllable doping techniques. Taking AlGaN-based ultraviolet (UV) emitters as an example, despite a peak wall-plug efficiency of 15.3% at the wavelength of 275 nm, there is still a huge gap in comparison with GaN-based visible light-emitting diodes (LEDs), mainly attributed to the inefficient doping of AlGaN with increase of the Al composition. First, p-doping of Al-rich AlGaN is a long-standing challenge and the low hole concentration seriously restricts the carrier injection efficiency. Although p-GaN cladding layers are widely adopted as a compromise, the high injection barrier of holes as well as the inevitable loss of light extraction cannot be neglected. While in terms of n-doping the main issue is the degradation of the electrical property when the Al composition exceeds 80%, resulting in a low electrical efficiency in sub-250 nm UV-LEDs. This review summarizes the recent advances and outlines the major challenges in the efficient doping of Al-rich AlGaN, meanwhile the corresponding approaches pursued to overcome the doping issues are discussed in detail.
Research progress of alkaline earth metal iron-based oxides as anodes for lithium-ion batteries
Authors: Ye Mingyuan , Hao Xiaorui , Zeng Jinfeng , Li Lin , Wang Pengfei , Zhang Chenglin , Liu Li , Shi Fanian , Wu Yuhan
Published: February 2024

Anode materials are an essential part of lithium-ion batteries (LIBs), which determine the performance and safety of LIBs. Currently, graphite, as the anode material of commercial LIBs, is limited by its low theoretical capacity of 372 mA·h·g−1, thus hindering further development toward high-capacity and large-scale applications. Alkaline earth metal iron-based oxides are considered a promising candidate to replace graphite because of their low preparation cost, good thermal stability, superior stability, and high electrochemical performance. Nonetheless, many issues and challenges remain to be addressed. Herein, we systematically summarize the research progress of alkaline earth metal iron-based oxides as LIB anodes. Meanwhile, the material and structural properties, synthesis methods, electrochemical reaction mechanisms, and improvement strategies are introduced. Finally, existing challenges and future research directions are discussed to accelerate their practical application in commercial LIBs.
Enhanced thermal emission from metal-free, fully epitaxial structures with epsilon-near-zero InAs layers
Authors: Stašys Karolis , Geižutis Andrejus , Devenson Jan
Published: February 2024

We introduce a novel method to create mid-infrared (MIR) thermal emitters using fully epitaxial, metal-free structures. Through the strategic use of epsilon-near-zero (ENZ) thin films in InAs layers, we achieve a narrow-band, wide-angle, and p-polarized thermal emission spectra. This approach, employing molecular beam epitaxy, circumvents the complexities associated with current layered structures and yields temperature-resistant emission wavelengths. Our findings contribute a promising route towards simpler, more efficient MIR optoelectronic devices.
Controllable thermal rectification design for buildings based on phase change composites
Authors: Ding Hengbin , Li Xiaoshi , Li Tianhang , Zhao Xiaoyong , Tian He
Published: February 2024

Phase-change material (PCM) is widely used in thermal management due to their unique thermal behavior. However, related research in thermal rectifier is mainly focused on exploring the principles at the fundamental device level, which results in a gap to real applications. Here, we propose a controllable thermal rectification design towards building applications through the direct adhesion of composite thermal rectification material (TRM) based on PCM and reduced graphene oxide (rGO) aerogel to ordinary concrete walls (CWs). The design is evaluated in detail by combining experiments and finite element analysis. It is found that, TRM can regulate the temperature difference on both sides of the TRM/CWs system by thermal rectification. The difference in two directions reaches to 13.8 K at the heat flow of 80 W/m2. In addition, the larger the change of thermal conductivity before and after phase change of TRM is, the more effective it is for regulating temperature difference in two directions. The stated technology has a wide range of applications for the thermal energy control in buildings with specific temperature requirements.
Two-step growth of β-Ga2O3 on c-plane sapphire using MOCVD for solar-blind photodetector
Authors: Ma Peipei , Zheng Jun , Liu Xiangquan , Liu Zhi , Zuo Yuhua , Cheng Buwen
Published: February 2024

In this work, a two-step metal organic chemical vapor deposition (MOCVD) method was applied for growing β-Ga2O3 film on c-plane sapphire. Optimized buffer layer growth temperature (T
B) was found at 700 °C and the β-Ga2O3 film with full width at half maximum (FWHM) of 0.66° was achieved. A metal−semiconductor−metal (MSM) solar-blind photodetector (PD) was fabricated based on the β-Ga2O3 film. Ultrahigh responsivity of 1422 A/W @ 254 nm and photo-to-dark current ratio (PDCR) of 106 at 10 V bias were obtained. The detectivity of 2.5 × 1015 Jones proved that the photodetector has outstanding performance in detecting weak signals. Moreover, the photodetector exhibited superior wavelength selectivity with rejection ratio (R
250 nm/R
400 nm) of 105. These results indicate that the two-step method is a promising approach for preparation of high-quality β-Ga2O3 films for high-performance solar-blind photodetectors.
Cryogenic RPWELL: a novel charge-readout element for dual-phase argon TPCs
Authors: Tesi A. , Leardini S. , Moleri L. , Morales M. , Gonzalez-Diaz D. , Jash A. , Breskin A. , Bressler S.
Published: February 2024

The first operation of a cryogenic Resistive Plate WELL
(RPWELL) detector in the saturated vapor of liquid argon is
reported. The RPWELL detector was composed of a Thick Gas Electron
Multiplier (THGEM) electrode coupled to a metallic anode via
Fe2O3/YSZ ceramics (Fe2O3 in weight equal to 75%),
with tunable bulk resistivity in the range
109–1012 Ω·cm. The detector was operated at
liquid argon temperature in saturated argon vapor (90 K, 1.2 bar)
and characterized in terms of its effective charge gain and
stability against discharges. Maximum stable gain of G≈17
was obtained, without discharges. In addition, preliminary results
from novel 3D-printed thermoplastic plates doped with carbon
nanotubes are presented.
Electromechanical enhancement of live jellyfish for ocean exploration
Authors: Anuszczyk Simon R , Dabiri John O
Published: February 2024

The vast majority of the ocean’s volume remains unexplored, in part because of limitations on the vertical range and measurement duration of existing robotic platforms. In light of the accelerating rate of climate change impacts on the physics and biogeochemistry of the ocean, the need for new tools that can measure more of the ocean on faster timescales is becoming pressing. Robotic platforms inspired or enabled by aquatic organisms have the potential to augment conventional technologies for ocean exploration. Recent work demonstrated the feasibility of directly stimulating the muscle tissue of live jellyfish via implanted microelectronics. We present a biohybrid robotic jellyfish that leverages this external electrical swimming control, while also using a 3D printed passive mechanical attachment to streamline the jellyfish shape, increase swimming performance, and significantly enhance payload capacity. A six-meter-tall, 13 600 l saltwater facility was constructed to enable testing of the vertical swimming capabilities of the biohybrid robotic jellyfish over distances exceeding 35 body diameters. We found that the combination of external swimming control and the addition of the mechanical forebody resulted in an increase in swimming speeds to 4.5 times natural jellyfish locomotion. Moreover, the biohybrid jellyfish were capable of carrying a payload volume up to 105% of the jellyfish body volume. The added payload decreased the intracycle acceleration of the biohybrid robots relative to natural jellyfish, which could also facilitate more precise measurements by onboard sensors that depend on consistent platform motion. While many robotic exploration tools are limited by cost, energy expenditure, and varying oceanic environmental conditions, this platform is inexpensive, highly efficient, and benefits from the widespread natural habitats of jellyfish. The demonstrated performance of these biohybrid robots suggests an opportunity to expand the set of robotic tools for comprehensive monitoring of the changing ocean.
Quantifying vehicle restriction related PM2.5 reduction using field observations in an isolated urban basin
Authors: Guo Yumin , Tian Pengfei , Li Mengqi , Yu Zeren , Song Xin , Shi Jinsen , Chang Yi , Zhang Lei
Published: February 2024

Vehicle (related particulate matter) emissions, including primary vehicle (related particulate matter) emissions, secondary nitrate, and road dust, have become an important source of fine particulate matter (PM2.5) in many cities across the world. The relationship between vehicle emissions and PM2.5 during vehicle restrictions has not yet been revealed using field observational data. To address this issue, a three-month field campaign on physical and chemical characteristics of PM2.5 at hourly resolution was conducted in Lanzhou, an urban basin with a semi-arid climate. The Lanzhou municipal government implemented more strict vehicle restriction measure during the latter part of field campaign period. The concentration of nitrogen oxides (NO
x
) and PM2.5 decreased by 15.6% and 10.6%, respectively during the strict vehicle restriction period. The daily traffic fluxes decreased by 11.8% due to the vehicle restriction measure. The vehicle emission reduction led to a decrease of 2.43 μg·m−3 in PM2.5, including the decrease of primary vehicle emissions, secondary nitrate, and road dust. The contribution of vehicle emissions to PM2.5 decreased by 9.0% based on the results derived from a positive matrix factorization model. The sources other than vehicle emissions increased by 0.2 μg·m−3. Combining all evidence from the observations, the reduction of vehicle emissions is almost equal to the observed reduction in PM2.5. A further extrapolation that 9.0% reduction in vehicle emissions led to the observed reduction in PM2.5 (2.32 μg·m−3). This study clearly quantifies the vehicle restriction related PM2.5 reduction using field observations. The results provide scientific support for the implementation of effective vehicle emission reduction measures.
Local-scale heterogeneity of soil thermal dynamics and controlling factors in a discontinuous permafrost region
Authors: Wang Chen , Shirley Ian , Wielandt Stijn , Lamb John , Uhlemann Sebastian , Breen Amy , Busey Robert C , Bolton W Robert , Hubbard Susan , Dafflon Baptiste
Published: February 2024

In permafrost regions, the strong spatial and temporal variability in soil temperature cannot be explained by the weather forcing only. Understanding the local heterogeneity of soil thermal dynamics and their controls is essential to understand how permafrost systems respond to climate change and to develop process-based models or remote sensing products for predicting soil temperature. In this study, we analyzed soil temperature dynamics and their controls in a discontinuous permafrost region on the Seward Peninsula, Alaska. We acquired one-year temperature time series at multiple depths (at 5 or 10 cm intervals up to 85 cm depth) at 45 discrete locations across a 2.3 km2 watershed. We observed a larger spatial variability in winter temperatures than that in summer temperatures at all depths, with the former controlling most of the spatial variability in mean annual temperatures. We also observed a strong correlation between mean annual ground temperature at a depth of 85 cm and mean annual or winter season ground surface temperature across the 45 locations. We demonstrate that soils classified as cold, intermediate, or warm using hierarchical clustering of full-year temperature data closely match their co-located vegetation (graminoid tundra, dwarf shrub tundra, and tall shrub tundra, respectively). We show that the spatial heterogeneity in soil temperature is primarily driven by spatial heterogeneity in snow cover, which induces variable winter insulation and soil thermal diffusivity. These effects further extend to the subsequent summer by causing variable latent heat exchanges. Finally, we discuss the challenges of predicting soil temperatures from snow depth and vegetation height alone by considering the complexity observed in the field data and reproduced in a model sensitivity analysis.
Vacuum energy of scalar fields on spherical shells with general matching conditions
Authors: Fucci Guglielmo , Romaniega César
Published: February 2024

In this work we analyze the spectral zeta function for massless scalar fields propagating in a D-dimensional flat space under the influence of a shell potential. The static nature of the potential, and the spherical symmetry, allows us to focus on the spatial part of the field which satisfies a one-dimensional Schrodinger equation endowed with a point potential. The shell potential is defined in terms of the two-interval self-adjoint extensions of the one-dimensional Schrodinger equation that describes the radial part of the scalar field. After performing the necessary analytic continuation, we utilize the spectral zeta function of the system to compute the vacuum energy of the field.
Non-commutative gauge symmetry from strong homotopy algebras
Authors: Kupriyanov Vladislav , Oliveira Fernando , Sharapov Alexey , Vassilevich Dmitri
Published: February 2024

We explicitly construct an L

∞

algebra that defines U

⋆

(
1
)

gauge transformations on a space with an arbitrary noncommutative and even nonassociative star product. Matter fields are naturally incorporated in this scheme as L

∞

modules. Some possibilities for including P

∞

algebras are also discussed.
Estimation of river discharge using Monte Carlo simulations and a 1D hydraulic model based on the artificial multi-segmented rating curves at the confluence of two rivers
Authors: Kang Hansol , Kim Yeonsu , An Hyunuk , Byun Jisun , Noh Joonwoo
Published: February 2024

During extreme floods caused by climate change, reliable flow discharge data are essential for successful reservoir operation to mitigate downstream flood damage. Generally, the flow discharge is computed using the rating curve (RC) established from the relationship between the flow rate and water stage level. Determining the parameters of rating curves is subject to uncertainties related to the difficulties and limitations of flow monitoring in covering a wide range of flow variations. Especially at river confluences, the uncertainties are pronounced when floods occur owing to several factors such as roughness change, backwaters, and levee overflow. The Seomjin River Basin in Korea suffered from flood inundation that occurred at the tributary confluence during an extreme flood in 2020. To identify a reliable flow rate of the main stream and tributary, this study proposes an indirect flow assessment scheme using a 1D hydrodynamic simulation model to find the best simulated water level in an iterative manner based on Monte Carlo (MC) simulations. With a large amount of discharge data generated from random-number combinations, it is possible to obtain the best results automatically by specifying the reliability limitation considering the uncertainty of the predetermined RC parameters associated with the roughness coefficient. Nash Sutcliffe Efficiency (NSE) was incorporated to evaluate the reproduced water level to meet the threshold specified for NSE ≥ 0.75. The simulated flowrates computed from the revised RC and roughness coefficients revealed an error range of 8%–36.6% compared with the design flood. The approach proposed in this study is applicable for determining the valid parameters necessary to create a revised RC at an existing water level gauge station, where the uncertainties of the RC are pronounced, particularly in the vicinity of the channel confluence.
Comprehensive analysis on the thermal comfort of various greening forms: a study in hot-humid areas
Authors: Lin Chang , Wu Zhuotong , Li Hui , Huang Jun , Huang Quanle
Published: February 2024

The potential impact of greening on improving thermal environments is widely recognized. However, few studies have comprehensively evaluated the influence of different forms of greening, such as various tree crown widths, green facades, green roofs, and their combinations, on both outdoor and indoor environments. In this study, we conducted an extensive investigation within a residential precinct at Guangzhou University by combining on-site measurements and numerical simulations with the ENVI-met model. Physiologically Equivalent Temperature (PET) and Temperature Humidity Index (THI) were used to assess outdoor thermal comfort. The results indicated that planting trees had a greater impact on improving the outdoor thermal environment than green facades and green roofs, and this effect increased with the crown width of the trees, with a maximum potential reduction of 4.8 °C (0.2 °C) in PET (THI). Green facades can bring a change of up to 101.9 W m−2 in sensible heat flux, resulting in a reduction of up to 1.8 °C in indoor Ta (air temperature). Conversely, green roofs composed of grass exhibit minimal effects in both outdoor and indoor environments. Finally, we provide recommendations for the construction and renovation of projects in residential areas, with a focus on hot-humid areas.
Seeking borophene on Ni3Al(111): an experimental characterization of boron segregation and oxidation
Authors: Grisan Qiu Y Y , Biasin P , Mantegazza P , Baronio S , Heinrich M , Muntwiler M K , Vesselli E
Published: February 2024

Synthesis of a stable, well ordered honeycomb borophene (hB) phase has been achieved to date by exploiting Al(111) as a growth substrate, which provides the necessary charge doping to compensate the high hexagonal-holes density. However, B/Al(111) is governed by a strong B–Al interaction so to yield the actual formation of an AlB2 hB phase. Dilution of aluminum by alloying could then in principle weaken the boron-support bonding. By means of a combined spectroscopy and microscopy experimental approach, we find instead that the growth of boron layers on the Ni3Al(111) alloy termination is driven by B dissolution into the bulk and surface segregation mechanisms. While no long-range ordered boron-induced phase is observed, locally ordered superstructural units with triangular appearance are stabilized by substrate pinning, following the chemical p(2 × 2) surface order. Oxidation involves both boron and aluminum, inducing surface segregation of B, while nickel remains in its metallic form.
Numerical analysis of functionally graded piezoelectric bionic fishtail based on Hermite element-free method
Authors: Ma Xiao , Zhou Bo , Li Changhe , Zhang Yanbin , Yang Min , Li Benkai , Liu Mingzheng , Cui Xin
Published: February 2024

Piezoelectric bionic fishtails have good flexibility, response speed, anti-interference ability, and have great application prospects in ocean exploration. However, the inherent drawbacks of the mechanical properties of traditional homogeneous piezoelectric materials significantly affect the propulsion performance and reliability of the piezoelectric bionic fishtails. To fill this gap, this paper develops a functionally graded piezoelectric bionic fishtail (FGPBF) by imitating the tail characteristics of groupers. The geometric structure and working principle of the FGPBF are introduced in detail. Based on the first-order shear deformation theory and Hermite element-free method, an element-free model for the FGPBF is established. The effects of gradient factor, substrate material, substrate thickness and electrical load on the propulsion performance of the FGPBF are addressed. The results show that the current results are in good agreement with the finite element results. The deformation of the FGPBF is negatively correlated with the thickness and stiffness of the substrate and linearly positively correlated with the electrical load. As the gradient factor increases, the deflection of the FGPBF first increases and then decreases. When the gradient factor is 2, the potential is 200 V, the dimensionless aluminum substrate thickness is 1, the propulsion performance of the FGPBF is improved by 28% compared to the homogeneous piezoelectric bionic fishtail.
Dynamic correlations: exact and approximate methods for mutual information
Authors: Demirtaş Kemal , Erman Burak , Haliloğlu Türkan
Published: February 2024

Motivation

Proteins are dynamic entities that undergo conformational changes critical for their functions. Understanding the communication pathways and information transfer within proteins is crucial for elucidating allosteric interactions in their mechanisms. This study utilizes mutual information (MI) analysis to probe dynamic allostery. Using two cases, Ubiquitin and PLpro, we have evaluated the accuracy and limitations of different approximations including the exact anisotropic and isotropic models, multivariate Gaussian model, isotropic Gaussian model, and the Gaussian Network Model (GNM) in revealing allosteric interactions.

Results

Our findings emphasize the required trajectory length for capturing accurate mutual information profiles. Long molecular dynamics trajectories, 1 ms for Ubiquitin and 100 µs for PLpro are used as benchmarks, assuming they represent the ground truth. Trajectory lengths of approximately 5 µs for Ubiquitin and 1 µs for PLpro marked the onset of convergence, while the multivariate Gaussian model accurately captured mutual information with trajectories of 5 ns for Ubiquitin and 350 ns for PLpro. However, the isotropic Gaussian model is less successful in representing the anisotropic nature of protein dynamics, particularly in the case of PLpro, highlighting its limitations. The GNM, however, provides reasonable approximations of long-range information exchange as a minimalist network model based on a single crystal structure. Overall, the optimum trajectory lengths for effective Gaussian approximations of long-time dynamic behavior depend on the inherent dynamics within the protein's topology. The GNM, by showcasing dynamics across relatively diverse time scales, can be used either as a standalone method or to gauge the adequacy of MD simulation lengths.

Availability and implementation

Mutual information codes are available at https://github.com/kemaldemirtas/prc-MI.git.
Membrane inflammasome activation by choriodecidual Ureaplasma parvum infection without intra-amniotic infection in a Non-Human Primate model
Authors: Tripathy Sudeshna , Burd Irina , Kelleher Meredith A
Published: February 2024

Intrauterine infection is a significant cause of neonatal morbidity and mortality. Ureaplasma parvum is a microorganism commonly isolated from cases of preterm birth and preterm premature rupture of membranes (pPROM). However, the mechanisms of early stage ascending reproductive tract infection remain poorly understood. To examine inflammation in fetal (chorioamnionic) membranes we utilized a non-human primate (NHP) model of choriodecidual U. parvum infection. Eight chronically catheterized pregnant rhesus macaques underwent maternal–fetal catheterization surgery at ~105–112 days gestation and choriodecidual inoculation with U. parvum (105 CFU/mL, n =4) or sterile media (controls; n = 4) starting at 115–119 days, repeated at 5-day intervals until C-section at 136–140 days (term=167 days). The average inoculation to delivery interval was 21 days, and Ureaplasma infection of the amniotic fluid (AF) was undetectable in all animals. Choriodecidual Ureaplasma infection resulted in increased fetal membrane expression of MMP-9 and PTGS2, but did not result in preterm labor or increased concentrations of AF pro-inflammatory cytokines. However, membrane expression of inflammasome sensors, NLRP3, NLRC4, AIM2, and NOD2, and adaptor ASC (PYCARD) gene expression were significantly increased. Gene expression of IL-1β, IL-18, IL-18R1  , CASPASE-1, and pro-CASPASE-1 protein increased with Ureaplasma infection. Downstream inflammatory genes MYD88 and NFκB (Nuclear factor kappa-light-chain-enhancer of activated B cells) were also significantly upregulated. These results demonstrate that choriodecidual Ureaplasma infection, can cause activation of inflammasome complexes and pathways associated with pPROM and preterm labor prior to microbes being detectable in the AF.
Ethical considerations for artificial intelligence in dermatology: a scoping review
Authors: Gordon Emily R , Trager Megan H , Kontos Despina , Weng Chunhua , Geskin Larisa J , Dugdale Lydia S , Samie Faramarz H
Published: February 2024

The field of dermatology is experiencing the rapid deployment of artificial intelligence (AI), from mobile applications (apps) for skin cancer detection to large language models like ChatGPT that can answer generalist or specialist questions about skin diagnoses. With these new applications, ethical concerns have emerged. In this scoping review, we aimed to identify the applications of AI to the field of dermatology and to understand their ethical implications. We used a multifaceted search approach, searching PubMed, MEDLINE, Cochrane Library and Google Scholar for primary literature, following the PRISMA Extension for Scoping Reviews guidance. Our advanced query included terms related to dermatology, AI and ethical considerations. Our search yielded 202 papers. After initial screening, 68 studies were included. Thirty-two were related to clinical image analysis and raised ethical concerns for misdiagnosis, data security, privacy violations and replacement of dermatologist jobs. Seventeen discussed limited skin of colour representation in datasets leading to potential misdiagnosis in the general population. Nine articles about teledermatology raised ethical concerns, including the exacerbation of health disparities, lack of standardized regulations, informed consent for AI use and privacy challenges. Seven addressed inaccuracies in the responses of large language models. Seven examined attitudes toward and trust in AI, with most patients requesting supplemental assessment by a physician to ensure reliability and accountability. Benefits of AI integration into clinical practice include increased patient access, improved clinical decision-making, efficiency and many others. However, safeguards must be put in place to ensure the ethical application of AI.
Construction of triptycene molecular rotors with intermeshing arrangement and low rotational barrier
Authors: Furuta Tomoki , Oka Kouki , Tohnai Norimitsu
Published: February 2024

Molecular rotors are one of the building blocks of molecular machines and they are nano-sized with mechanically rotating moieties. Among them, intermeshing triptycenes with a gear-like skeleton allow the construction of a molecular rotor that transmits rotational motion. For triptycenes to mesh with each other without loss of rotation, intermeshing them in parallel and adjusting the distance between their axes to 8.1 Å are required. However, with conventional methods, because of the restrictions on bond lengths and atomic radii, achieving an ideal arrangement in which the triptycenes mesh in parallel at 8.1 Å has been difficult. In this work, we synthesized disulfonic acid containing a triptycene as a rotator and combined it with amines of 2 different steric factors (normal-amylamine [nAmA] and guanidine [Gu]), which allowed us to prepare organic salts with varying arrangements of triptycenes. In the organic salt with the planar amine (Gu), the crystal structure was close to the ideal intermeshing arrangement of the triptycene and the distance between their axes was 7.7 Å. The T1ρ  13C spin-lattice relaxation time using solid-state nuclear magnetic resonance (NMR) demonstrated that triptycene rotates efficiently at 24 kHz at 313 K with a low rotational barrier (10.9 kcal/mol) compared with non-intermeshing structures.
Transcriptomic response of peripheral blood mononuclear cells to secukinumab in epidermolytic ichthyosis
Authors: Hou Ping-Chen , Hong Yi-Kai , Lin Yu-Chen , Yang Min-Chia , Hsu Chung-Ting , McGrath John A , Hsu Chao-Kai
Published: February 2024

Epidermolytic ichthyosis (EI) is a subtype of ichthyosis, characterized by generalized blistering and erythroderma since birth followed by scaling and palmoplantar keratoderma. Several major orphan forms of ichthyosis have been linked to T helper (Th)17 signalling upregulation. Anecdotal reports also described the beneficial role of Th17-targeted agents in ichthyosis. However, the therapeutic efficacy and the transcriptomic changes caused by secukinumab in EI have rarely been discussed. We present a patient treated with secukinumab for 1 year and evaluated the transcriptomic alterations in peripheral blood after treatment, which revealed that interleukin-1 signalling and Toll-like receptor 2 cascade may underpin the inflammatory and hyperkeratotic footprint in EI.
When temporary relief is not worth the cost: a warning on using sunbeds to self-treat acne in teenagers
Authors: Andrawis Madonna , Granahan Aoife , Carty Kieran , O’Mahony Sarah , Keeling Elizabeth , Byrne Berbie , Rafferty Siobhan , Fleming Sarah , Drumm Claire , Tobin Anne-Marie
Published: February 2024

As a teenager, I struggled with severe cystic acne that caused low self-esteem, social anxiety and embarrassment. Desperate for a quick solution, I started regularly using tanning beds based on claims it could clear my skin. While my acne initially improved, I was unaware of the cumulative damage the UV rays from the tanning bed could have on my skin.
Duke Infective Endocarditis Criteria 3.0 for the Clinician: Defining What Is Possible
Authors: Chambers Henry F , Zhang ShanShan , Evans Scott
Published: February 2024

This commentary summarizes the results and clinical implications of validation studies evaluating the performance of the 2023 Duke-ISCID criteria for infective endocarditis.
Eyes Wide Shut: A Cohort Study Questioning the Role of Fundoscopy in Infective Endocarditis Diagnosis
Authors: Stavropoulou Elisavet , Guery Benoit , Tzimas Georgios , Guex-Crosier Yan , Hoogewoud Florence , Tozzi Piergiorgio , Kirsch Matthias , Monney Pierre , Papadimitriou-Olivgeris Matthaios
Published: February 2024

In this retrospective/prospective study, we assessed the role of fundoscopy in 711 episodes with suspected infective endocarditis (IE); 238 (33%) had IE. Ocular embolic events (retinal emboli or chorioretinitis/endophthalmitis) and Roth spots were found in 37 (5%) and 34 (5%) episodes, respectively, but had no impact on IE diagnosis.
Tobacco Smoke Exposure in Early Childhood and Later Risk of Inflammatory Bowel Disease: A Scandinavian Birth Cohort Study
Authors: Sigvardsson Ida , Ludvigsson Johnny , Andersson Björn , Størdal Ketil , Mårild Karl
Published: February 2024

Objectives

To examine the association between early-life smoking exposure and later risk of inflammatory bowel disease [IBD].

Methods

We followed 115663 participants from the Norwegian Mother, Father and Child [MoBa] and All Babies in Southeast Sweden [ABIS] cohorts from birth [1997–2009] through 2021. IBD was identified through national patient registers. Validated questionnaire data defined maternal smoking during pregnancy, maternal environmental tobacco smoke [ETS] exposure during pregnancy, and child ETS exposure by ages 12 and 36 months. Cox regression was used to estimate adjusted hazard ratios [aHRs] for sex, maternal age, education level, parental IBD, and origin. Cohort-specific estimates were pooled using a random-effects model.

Results

During 1 987 430 person-years of follow-up, 444 participants developed IBD [ABIS, 112; MoBa, 332]. Any vs no maternal smoking during pregnancy yielded a pooled aHR of 1.30 [95% CI = 0.97–1.74] for offspring IBD. Higher level of maternal smoking during pregnancy (compared with no smoking, average ≥6 cigarettes/day: pooled aHR = 1.60 [95% CI = 1.08–2.38]) was associated with offspring IBD, whereas a lower smoking level was not (average 1–5 cigarettes/day: pooled aHR = 1.09 [95% CI = 0.73–1.64]). Child ETS exposure in the first year of life was associated with later IBD (any vs no ETS, pooled aHR = 1.32 [95% CI = 1.03–1.69]). Estimates observed for child ETS exposure by 36 months were similar but not statistically significant.

Conclusions

In this prospective Scandinavian cohort study, children exposed to higher levels of maternal smoking during pregnancy or ETS during the first year of life were at increased risk of later IBD.
Transcatheter aortic valve replacement planning with cardiac computed tomography in quadricuspid aortic valve stenosis: a case series
Authors: Aquino-Bruno Heberto , Muratalla-González Roberto , Garcia-Garcia Juan F , Triano-Doroteo José L , Rivera Kevin Felix , Balcarcel Gerardo Carreon , Navarrete-Osuna Marisol
Published: February 2024

Background

The presence of severe aortic stenosis in quadricuspid aortic valve (QAV) is an extremely rare combination, and it is unknown whether transcatheter aortic valve replacement (TAVR) is a safe option due to the low incidence.

Case summary

We present two patients diagnosed with severe aortic stenosis with QAV morphology type 1 (Nakamura classification). All patients presented to our hospital for evaluation because of worsening functional class, dyspnoea, or syncope. During tomographic planning, the aortic annulus was measured at the level of the deepest sinus for the selection of the number of devices. Due to the presence of four cusps, the smallest cusp was excluded, and three sinuses were virtualized for placement of the pigtail catheter during the procedure. Without complications, a 23 mm Edwards SAPIEN 3 was deployed through the femoral artery in both patients. Control aortography showed no valve leakage or regurgitation.

Discussion

In patients with QAV and aortic stenosis undergoing TAVR, similar to the tricuspid valve, tomographic planning can be used to ensure the success of the procedure. However, unlike the tricuspid valve, where the selection of the device number is based on the measurements of the aortic annulus at the level of the non-coronary sinus, in these QAV cases, we perform the measurements at the level of the deepest aortic sinus (right coronary sinus).
Using natural language processing for automated classification of disease and to identify misclassified ICD codes in cardiac disease
Authors: Falter Maarten , Godderis Dries , Scherrenberg Martijn , Kizilkilic Sevda Ece , Xu Linqi , Mertens Marc , Jansen Jan , Legroux Pascal , Kindermans Hanne , Sinnaeve Peter , Neven Frank , Dendale Paul
Published: February 2024

Aims

ICD codes are used for classification of hospitalizations. The codes are used for administrative, financial, and research purposes. It is known, however, that errors occur. Natural language processing (NLP) offers promising solutions for optimizing the process. To investigate methods for automatic classification of disease in unstructured medical records using NLP and to compare these to conventional ICD coding.

Methods and results

Two datasets were used: the open-source Medical Information Mart for Intensive Care (MIMIC)-III dataset (n = 55.177) and a dataset from a hospital in Belgium (n = 12.706). Automated searches using NLP algorithms were performed for the diagnoses ‘atrial fibrillation (AF)’ and ‘heart failure (HF)’. Four methods were used: rule-based search, logistic regression, term frequency-inverse document frequency (TF-IDF), Extreme Gradient Boosting (XGBoost), and Bio-Bidirectional Encoder Representations from Transformers (BioBERT). All algorithms were developed on the MIMIC-III dataset. The best performing algorithm was then deployed on the Belgian dataset. After preprocessing a total of 1438 reports was retained in the Belgian dataset. XGBoost on TF-IDF matrix resulted in an accuracy of 0.94 and 0.92 for AF and HF, respectively. There were 211 mismatches between algorithm and ICD codes. One hundred and three were due to a difference in data availability or differing definitions. In the remaining 108 mismatches, 70% were due to incorrect labelling by the algorithm and 30% were due to erroneous ICD coding (2% of total hospitalizations).

Conclusion

A newly developed NLP algorithm attained a high accuracy for classifying disease in medical records. XGBoost outperformed the deep learning technique BioBERT. NLP algorithms could be used to identify ICD-coding errors and optimize and support the ICD-coding process.
Recombinant Full-length Plasmodium falciparum Circumsporozoite Protein–Based Vaccine Adjuvanted With Glucopyranosyl Lipid A–Liposome Quillaja saponaria 21: Results of Phase 1 Testing With Malaria Challenge
Authors: Friedman-Klabanoff DeAnna J , Berry Andrea A , Travassos Mark A , Shriver Mallory , Cox Catherine , Butts Jessica , Lundeen Jordan S , Strauss Kathleen A , Joshi Sudhaunshu , Shrestha Biraj , Mo Annie X , Nomicos Effie Y H , Deye Gregory A , Regules Jason A , Bergmann-Leitner Elke S , Pasetti Marcela F , Laurens Matthew B
Published: February 2024

Background

Malaria is preventable yet causes >600 000 deaths annually. RTS,S, the first marketed malaria vaccine, has modest efficacy, but improvements are needed for eradication.

Methods

We conducted an open-label, dose escalation phase 1 study of a full-length recombinant circumsporozoite protein vaccine (rCSP) administered with adjuvant glucopyranosyl lipid A–liposome Quillaja saponaria 21 formulation (GLA-LSQ) on days 1, 29, and 85 or 1 and 490 to healthy, malaria-naive adults. The primary end points were safety and reactogenicity. The secondary end points were antibody responses and Plasmodium falciparum parasitemia after homologous controlled human malaria infection.

Results

Participants were enrolled into 4 groups receiving rCSP/GLA-LSQ: 10 µg × 3 (n = 20), 30 µg × 3 (n = 10), 60 µg × 3 (n = 10), or 60 µg × 2 (n = 9); 10 participants received 30 µg rCSP alone × 3, and there were 6 infectivity controls. Participants experienced no serious adverse events. Rates of solicited and unsolicited adverse events were similar among groups. All 26 participants who underwent controlled human malaria infection 28 days after final vaccinations developed malaria. Increasing vaccine doses induced higher immunoglobulin G titers but did not achieve previously established RTS,S benchmarks.

Conclusions

rCSP/GLA-LSQ had favorable safety results. However, tested regimens did not induce protective immunity. Further investigation could assess whether adjuvant or schedule adjustments improve efficacy.

Clinical Trials Registration

NCT03589794
Comparison of prebiotic candidates in ulcerative colitis using an in vitro fermentation model
Authors: Kennedy James M , De Silva Aminda , Walton Gemma E , Poveda Carlos , Gibson Glenn R
Published: February 2024

Aims

This study explored the effect of three different prebiotics, the human milk oligosaccharide 2′-fucosyllactose (2′-FL), an oligofructose-enriched inulin (fructo-oligosaccharide, or FOS), and a galacto-oligosaccaride (GOS) mixture, on the faecal microbiota from patients with ulcerative colitis (UC) using in vitro batch culture fermentation models. Changes in bacterial groups and short-chain fatty acid (SCFA) production were compared.

Methods and results

In vitro pH controlled batch culture fermentation was carried out over 48 h on samples from three healthy controls and three patients with active UC. Four vessels were run, one negative control and one for each of the prebiotic substrates. Bacterial enumeration was carried out using fluorescence in situ hybridization with flow cytometry. SCFA quantification was performed using gas chromatography mass spectrometry. All substrates had a positive effect on the gut microbiota and led to significant increases in total SCFA and propionate concentrations at 48 h. 2′-FL was the only substrate to significantly increase acetate and led to the greatest increase in total SCFA concentration at 48 h. 2′-FL best suppressed Desulfovibrio spp., a pathogen associated with UC.

Conclusions

2′FL, FOS, and GOS all significantly improved the gut microbiota in this in vitro study and also led to increased SCFA.