bluuebunny/crossref_metadata_2025 huggingface dataset:
Fully 3D implementation of the end-to-end deep image prior-based PET image reconstruction using block iterative algorithm
Authors: Hashimoto Fumio , Onishi Yuya , Ote Kibo , Tashima Hideaki , Yamaya Taiga
Published: July 2023

Objective. Deep image prior (DIP) has recently attracted attention owing to its unsupervised positron emission tomography (PET) image reconstruction method, which does not require any prior training dataset. In this paper, we present the first attempt to implement an end-to-end DIP-based fully 3D PET image reconstruction method that incorporates a forward-projection model into a loss function. Approach. A practical implementation of a fully 3D PET image reconstruction could not be performed at present because of a graphics processing unit memory limitation. Consequently, we modify the DIP optimization to a block iteration and sequential learning of an ordered sequence of block sinograms. Furthermore, the relative difference penalty (RDP) term is added to the loss function to enhance the quantitative accuracy of the PET image. Main results. We evaluated our proposed method using Monte Carlo simulation with [18F]FDG PET data of a human brain and a preclinical study on monkey-brain [18F]FDG PET data. The proposed method was compared with the maximum-likelihood expectation maximization (EM), maximum a posteriori EM with RDP, and hybrid DIP-based PET reconstruction methods. The simulation results showed that, compared with other algorithms, the proposed method improved the PET image quality by reducing statistical noise and better preserved the contrast of brain structures and inserted tumors. In the preclinical experiment, finer structures and better contrast recovery were obtained with the proposed method. Significance. The results indicated that the proposed method could produce high-quality images without a prior training dataset. Thus, the proposed method could be a key enabling technology for the straightforward and practical implementation of end-to-end DIP-based fully 3D PET image reconstruction.
Agreement between left and right middle cerebral artery blood velocity responses to incremental and constant work-rate exercise in healthy males and females
Authors: Weston Max E , Barker Alan R , Tomlinson Owen W , Coombes Jeff S , Bailey Tom G , Bond Bert
Published: July 2023

Objective. To quantify the agreement between left and right middle cerebral artery blood velocity (MCAv) responses to incremental and constant work-rate exercise in adults. Approach Seventeen healthy adults (23.8 ± 2.4 years, 9 females) completed a ramp incremental test to exhaustion on a cycle ergometer, three 6-minute transitions at a moderate-intensity, and three at a heavy-intensity, all on separate days. Bilateral MCAv was measured throughout using transcranial Doppler ultrasonography, with left and right MCAv data analysed separately. Data were analysed at baseline, gas exchange threshold, respiratory compensation point and exhaustion during ramp incremental exercise. MCAv responses to constant work-rate exercise were analysed using a mono-exponential model, to determine time- and amplitude-based kinetic response parameters. Main Results Left and right MCAv responses to incremental and constant work-rate exercise were significantly, strongly and positively correlated (r ≥ 0.61, P < 0.01). Coefficient of variation (left versus right) ranged from 7.3%–20.7%, 6.4%–26.2% and 5.9%–22.5% for ramp, moderate and heavy-intensity exercise, respectively. The relative change in MCAv from baseline was higher in the right compared to left MCAv during ramp, moderate and heavy-intensity exercise (all P < 0.05), but the effect sizes were small (d ≤ 0.4). Small mean left–right differences were present during ramp incremental exercise at all time-points (<6 cm s−1; <4%), and for all kinetic parameters during moderate and heavy-intensity exercise (<3 cm s−1, <3%, <4 s). Significance These findings demonstrate similarities between left and right MCAv responses to incremental and constant-work rate exercise in adults on a group-level, but also highlight individual variation in the agreement between left and right MCAv exercise responses.
Stochastic equations and cities
Authors: Barthelemy Marc
Published: July 2023

Stochastic equations constitute a major ingredient in many branches of science, from physics to biology and engineering. Not surprisingly, they appear in many quantitative studies of complex systems. In particular, this type of equation is useful for understanding the dynamics of urban population. Empirically, the population of cities follows a seemingly universal law—called Zipf’s law—which was discovered about a century ago and states that when sorted in decreasing order, the population of a city varies as the inverse of its rank. Recent data however showed that this law is only approximate and in some cases not even verified. In addition, the ranks of cities follow a turbulent dynamics: some cities rise while other fall and disappear. Both these aspects—Zipf’s law (and deviations around it), and the turbulent dynamics of ranks—need to be explained by the same theoretical framework and it is natural to look for the equation that governs the evolution of urban populations. We will review here the main theoretical attempts based on stochastic equations to describe these empirical facts. We start with the simple Gibrat model that introduces random growth rates, and we will then discuss the Gabaix model that adds friction for allowing the existence of a stationary distribution. Concerning the dynamics of ranks, we will discuss a phenomenological stochastic equation that describes rank variations in many systems—including cities—and displays a noise-induced transition. We then illustrate the importance of exchanges between the constituents of the system with the diffusion with noise equation. We will explicit this in the case of cities where a stochastic equation for populations can be derived from first principles and confirms the crucial importance of inter-urban migrations shocks for explaining the statistics and the dynamics of the population of cities.
The influence of porosity on the superconducting properties of Y–Ba–Cu–O single grains
Authors: Baumann Josef , Shi Yunhua , Dennis Anthony R , Durrell John H , Cardwell David A
Published: July 2023

The trapped field in Y–Ba–Cu–O (YBCO) bulk single grain superconductors correlates directly with the critical current density J
c, which, in turn, is dependent on the microstructure of the bulk material. It has been shown recently and indirectly that porosity influences J
c of these technologically important materials, in addition to the presence of well-researched Y2BaCuO5 (Y-211) particles in the bulk sample. In this work, we report the direct impact of porosity on the critical current density of a single grain YBCO bulk superconductor using 3D x-ray computer tomography scans and superconducting quantum interference device measurements. It is concluded that porosity has a considerably more substantial impact on the measured critical current density than Y-211 on the micrometre scale with, predictably, a decrease in porosity leading to an increase in J
c. J
c is directly proportional to the trapped field, so any method that can reduce porosity, therefore, improves J
c, and, subsequently, the trapped field of these technologically important bulk superconductors.
CMB signature of non-thermal Dark Matter produced from self-interacting dark sector
Authors: Ghosh Dilip Kumar , Ghosh Purusottam , Jeesun Sk
Published: July 2023

The basic idea of this work is to achieve the observed relic density of a non-thermal dark matter(DM) and its connection with Cosmic Microwave Background (CMB) via
additional relativistic degrees of freedom which are simultaneously generated during
the period T
BBN to TCMB
from a long-lived dark sector particle.
To realize this phenomena we minimally extend the type-I seesaw scenario with a Dirac
fermion singlet(χ) and a complex scalar singlet (φ) which transform
non-trivially under an unbroken symmetry Z̶
3. χ being the lightest
particle in the dark sector acts as a stable dark matter candidate while the next to
lightest state φ operates like a long lived dark scalar particle. The initial
density of φ can be thermally produced through either self-interacting number
changing processes (3φ ⟶ 2φ) within dark sector or the standard
annihilation to SM particles (2φ ⟶ 2  SM).
The late time (after neutrino decoupling) non-thermal decay of φ can produce
dark matter in association with active neutrinos. The presence of extra
relativistic neutrino degrees of freedom at the time of CMB can have a
significant impact on ΔNeff. Thus the precise measurement of
ΔNeff by current PLANCK 2018 collaboration and future experiments
like SPT-3G and CMB-S4 can indirectly probe this non-thermal dark matter scenario
which is otherwise completely secluded due to its tiny coupling with the standard
model.
Regularized Maximum Likelihood Image Synthesis and Validation for ALMA Continuum Observations of Protoplanetary Disks
Authors: Zawadzki Brianna , Czekala Ian , Loomis Ryan A. , Quinn Tyler , Grzybowski Hannah , Frazier Robert C. , Jennings Jeff , Nizam Kadri M. , Jian Yina
Published: July 2023

Regularized Maximum Likelihood (RML) techniques are a class of image synthesis methods that achieve better angular resolution and image fidelity than traditional methods like CLEAN for sub-mm interferometric observations. To identify best practices for RML imaging, we used the GPU-accelerated open source Python package MPoL, a machine learning-based RML approach, to explore the influence of common RML regularizers (maximum entropy, sparsity, total variation, and total squared variation) on images reconstructed from real and synthetic Atacama Large millimeter/submillimeter Array (ALMA) continuum observations of protoplanetary disks. We tested two different cross-validation (CV) procedures to characterize their performance and determine optimal prior strengths, and found that CV over a coarse grid of regularization strengths easily identifies a range of models with comparably strong predictive power. To evaluate the performance of RML techniques against a ground truth image, we used MPoL on a synthetic protoplanetary disk data set and found that RML methods successfully resolve structures at fine spatial scales present in the original simulation. We used ALMA DSHARP observations of the protoplanetary disk around HD 143006 to compare the performance of MPoL and CLEAN, finding that RML imaging improved the spatial resolution of the image by up to a factor of 3 without sacrificing sensitivity. We provide general recommendations for building an RML workflow for image synthesis of ALMA protoplanetary disk observations, including effective use of CV. Using these techniques to improve the imaging resolution of protoplanetary disk observations will enable new science, including the detection of protoplanets embedded in disks.
Unveiling localized electronic properties of ReS2 thin layers at nanoscale using Kelvin force probe microscopy combined with tip-enhanced Raman spectroscopy
Authors: Luo 罗 Yu 宇 , Su 苏 Weitao 伟涛 , Zhang 张 Juanjuan 娟娟 , Chen 陈 Fei 飞 , Wu 武 Ke 可 , Zeng 曾 Yijie 宜杰 , Lu 卢 Hongwei 红伟
Published: July 2023

Electronic properties of two-dimensional (2D) materials can be strongly modulated by localized strain. The typical spatial resolution of conventional Kelvin probe force microscopy (KPFM) is usually limited in a few hundreds of nanometers, and it is difficult to characterize localized electronic properties of 2D materials at nanoscales. Herein, tip-enhanced Raman spectroscopy (TERS) is proposed to combine with KPFM to break this restriction. TERS scan is conducted on ReS2 bubbles deposited on a rough Au thin film to obtain strain distribution by using the Raman peak shift. The localized contact potential difference (CPD) is inversely calculated with a higher spatial resolution by using strain measured by TERS and CPD-strain working curve obtained using conventional KPFM and atomic force microscopy. This method enhances the spatial resolution of CPD measurements and can be potentially used to characterize localized electronic properties of 2D materials.
Global simulation of plasma series resonance effect in radio frequency capacitively coupled Ar/O2 plasma
Authors: Bai 白 Xue 雪 , Xu 徐 Hai-Wen 海文 , Tian 田 Chong-Biao 崇彪 , Dong 董 Wan 婉 , Song 宋 Yuan-Hong 远红 , Wang 王 You-Nian 友年
Published: July 2023

Radio frequency capacitively coupled plasmas (RF CCPs) play a pivotal role in various applications in etching and deposition processes on a microscopic scale in semiconductor manufacturing. In the discharge process, the plasma series resonance (PSR) effect is easily observed in electrically asymmetric and geometrically asymmetric discharges, which could largely influence the power absorption, ionization rate, etc. In this work, the PSR effect arising from geometrically and electrically asymmetric discharge in argon–oxygen mixture gas is mainly investigated by using a plasma equivalent circuit model coupled with a global model. At relatively low pressures, as Ar content (α) increases, the inductance of the bulk is weakened, which leads to a more obvious PSR phenomenon and a higher resonance frequency (ω
psr). When the Ar content is fixed, varying the pressure and gap distance could also have different effects on the PSR effect. With the increase of the pressure, the PSR frequency shifts towards the higher order, but in the case of much higher pressure, the PSR oscillation would be strongly damped by frequent electron–neutral collisions. With the increase of the gap distance, the PSR frequency becomes lower. In addition, electrically asymmetric waveforms applied to a geometrically asymmetric chamber may weaken or enhance the asymmetry of the discharge and regulate the PSR effect. In this work, the Ar/O2 electronegative mixture gas is introduced in a capacitive discharge to study the PSR effect under geometric asymmetry effect and electrical asymmetry effect, which can provide necessary guidance in laboratory research and current applications.
Efficient ion acceleration driven by a Laguerre–Gaussian laser in near-critical-density plasma
Authors: Gao 高 Jia-Xiang 嘉祥 , Liu 刘 Meng 梦 , Wang 王 Wei-Min 伟民
Published: July 2023

Laser-driven ion accelerators have the advantages of compact size, high density, and short bunch duration over conventional accelerators. Nevertheless, it is still challenging to generate ion beams with quasi-monoenergetic peak and low divergence in experiments with the current ultrahigh intensity laser and thin target technologies. Here we propose a scheme that a Laguerre–Gaussian laser irradiates a near-critical-density (NCD) plasma to generate a quasi-monoenergetic and low-divergence proton beam. The Laguerre–Gaussian laser pulse in an NCD plasma excites a moving longitudinal electrostatic field with a large amplitude, and it maintains the inward bowl-shape for dozens of laser durations. This special distribution of the longitudinal electrostatic field can simultaneously accelerate and converge the protons. Our particle-in-cell (PIC) simulation shows that the efficient proton acceleration can be realized with the Laguerre–Gaussian laser intensity ranging from 3.9 × 1021 W⋅cm−2–1.6 × 1022 W⋅cm−2 available in the near future, e.g., a quasi-monoenergetic proton beam with peak energy ∼ 115 MeV and divergence angles less than 5° can be generated by a 5.3 × 1021 W⋅cm−2 pulse. This work could provide a reference for the high-quality ion beam generation with PWclass laser systems available recently.
Integrated RMP-based ELM-crash-control process for plasma performance enhancement during ELM crash suppression in KSTAR
Authors: Kim Minwoo , Shin G. , Lee J. , Ko W.H. , Han H. , Hahn S.-H. , Kim S.K. , Yang S.M. , Shousha R. , Kim H.S. , Juhn J.-W. , Park G.Y. , Kolemen E.
Published: July 2023

The integrated Resonant Magnetic Perturbation (RMP)-based Edge-Localized Mode (ELM)-crash-control process aims to enhance the plasma performance during the RMP-driven ELM crash suppression, where the RMP induces an unwanted confinement degradation. In this study, the normalized beta (

β

N

) is introduced as a metric for plasma performance. The integrated process incorporates the latest achievements in the RMP technique to enhance

β

N

efficiently. The integrated process triggers the n = 1 Edge-localized RMP (ERMP) at the L–H transition timing using the real-time Machine Learning (ML) classifier. The pre-emptive RMP onset can reduce the required external heating power for achieving the same

β

N

by over 10% compared to the conventional onset. During the RMP phase, the adaptive feedback RMP ELM controller, demonstrating its performance in previous experiments, plays a crucial role in maximizing

β

N

during the suppression phase and sustaining the

β

N

-enhanced suppression state by optimizing the RMP strength. The integrated process achieves

β

N

up to ∼2.65 during the suppression phase, which is ∼10% higher than the previous KSTAR record but ∼6% lower than the target of the K-DEMO first phase (

β

N

= 2.8), and maintains the suppression phase above the lower limit of target

β

N

(= 2.4) for ∼4 s (∼60

τ

E

). In addition to

β

N

enhancement, the integrated process demonstrates quicker restoration of the suppression phase and recovery of

β

N

compared to the adaptive control with the n = 1 Conventional RMP (CRMP). The post-analysis of the experiment shows the localized effect of the ERMP spectrum in radial and the close relationship between the evolution of

β

N

and the electron temperature.
Global gyrokinetic simulations of the impact of magnetic island on ion temperature gradient driven turbulence
Authors: Li Jingchun , Xu J.Q. , Qu Y.R. , Lin Z. , Dong J.Q. , Peng X.D. , Li J.Q.
Published: July 2023

The effect of island width on the multi-scale interactions between magnetic island (MI) and ion temperature gradient (ITG) turbulence has been investigated based on the global gyrokinetic approach. It is found that the coupling between the island and turbulence is enhanced when the MI width (w) becomes larger. A vortex flow that is highly sensitive to the width of the MI can be triggered, ultimately resulting in a potent

E
×
B

shear flow and a consequent reduction in turbulent transport. The shearing rate induced by the vortex flow is minimum at the O-point while it is maximum at both of the two reconnection points of the island, i.e. the X-points, regardless of the island width. There exists a nonmonotonic relationship between zonal flow (ZF) amplitude and island width, showing that the ZF is partially suppressed by medium-sized MIs whereas enhanced in the case of large island. A larger MI can tremendously damage the ITG mode structure, resulting in higher turbulent transport at the X-point whereas a lower one at the O-point, respectively. Such phenomenon will be less distinct at very small island widths below w/a ∼ 8% ≈ 12

ρ
i

(a is the minor radius and

ρ
i

the ion gyroradius), where it shows that turbulence near the X-point is hardly affected although it is still suppressed inside the island. Furthermore, the influence of different island sizes on turbulence transport level is also discussed.
Comparison of a novel machine learning approach with dynamical downscaling for Australian precipitation
Authors: Nishant Nidhi , Hobeichi Sanaa , Sherwood Steven , Abramowitz Gab , Shao Yawen , Bishop Craig , Pitman Andy
Published: July 2023

Dynamical downscaling (DD), and machine learning (ML) based techniques have been widely applied to downscale global climate models and reanalyses to a finer spatiotemporal scale, but the relative performance of these two methods remains unclear. We implement an ML regression approach using a multi-layer perceptron (MLP) with a novel loss function to downscale coarse-resolution precipitation from the Bureau of Meteorology Atmospheric high-resolution Regional Reanalysis for Australia from grids of 12–48 km to 5 km, using the Australia Gridded Climate Data observations as the target. A separate MLP is developed for each coarse grid to predict the fine grid values within it, by combining coarse-scale time-varying meteorological variables with fine-scale static surface properties as predictors. The resulting predictions (on out-of-sample test periods) are more accurate than DD in capturing the rainfall climatology, as well as the frequency distribution and spatiotemporal variability of daily precipitation, reducing biases in daily extremes by 15%–85% with 12 km prediction fields. When prediction fields are coarsened, the skill of the MLP decreases—at 24 km relative bias increases by ∼10%, and at 48 km it increases by another ∼4%—but skill remains comparable to or, for some metrics, much better than DD. These results show that ML-based downscaling benefits from higher-resolution driving data but can still improve on DD (and at far less computational cost) when downscaling from a global climate model grid of ∼50 km.
Shared mobility and lifestyles as mechanisms to reduce environmental impacts from passenger transportation
Authors: Arbeláez Vélez Ana María , Ivanova Diana , Stadler Konstantin
Published: July 2023

Despite the deployment of low- or zero-emission technologies, achieving emissions reductions in the passenger transportation sector remains challenging. Demand-side mechanisms can be instrumental in reducing environmental impacts of transportation and reconfiguring transportation systems in a way that shifts users away from private car ownership. In this article we look at the Netherlands, Sweden, and the United States to quantify the environmental benefits from such shifts in passenger transportation, considering socio-technological drivers of transportation including well-being, digitalization, shared mobility, and electrification. We establish pathways for each of these countries considering their context. We frame these pathways using the avoid-shift-improve framework which shapes the scenarios that we quantify in our analysis. We use a travel demand model as an input to calculate carbon, energy, and air pollution footprints. We quantify direct emissions considering the characteristics of the private fleet and indirect using multiregional input-output analysis. The results show that target thresholds can be reached under the proposed supply and demand initiatives. For the United States, these actions are more dramatic than for the Netherlands and Sweden due to that country’s stronger car dependence. A deep social transformation is needed to make these scenarios possible and enable a shift towards public, active and shared transportation in urban areas.
Screening for volatile biomarkers of colorectal cancer by analyzing breath and fecal samples using thermal desorption combined with GC-MS (TD-GC-MS)
Authors: Śmiełowska Monika , Ligor Tomasz , Kupczyk Wojciech , Szeliga Jacek , Jackowski Marek , Buszewski Bogusław
Published: July 2023

Breath and fecal VOCs, among others, represent a new and encouraging clinical practice for the differential diagnosis of CRC. The purpose of our research was to identify VOCs present in exhaled air and feces of 20 HVs and 15 CRC patients. For collection of gas phase released from feces, emission microchambers were applied. Sorption tubes were used to enrich analytes for both breath and fecal samples. TD technique combined with GC-MS was used at the separation and identification step. The combination of statistical methods was used to evaluate the ability of VOCs to classify control group and CRC patients. Heptanoic acid, acetone, 2,6,10-trimethyldodecane, n-hexane, skatole, and dimethyl trisulfide are observed in elevated amounts in the patients group. The performance of diagnostic models on the tested data set was above 90%. This study is the first attempt to document the using of TD-GC-MS to analyze both breath and fecal samples to search for volatile biomarkers of CRC. A full evaluation of the results described herein requires further studies involving a larger number of samples. Moreover, it is particularly important to understand the metabolic pathways of substances postulated as tumor biomarkers.
Establishing a cell-based screening workflow for determining the efficiency of CYP2C9 metabolism: moving towards the use of breath volatiles in personalised medicine
Authors: Lochmann Franziska , Nikolajevic Aleksandar , Stock Valentina , Kammerer Sarah , Fernández-Quintero Monica L , Loeffler Johannes R , Liedl Klaus R , Troppmair Jakob , Mayhew Chris A , Ruzsanyi Veronika
Published: July 2023

The use of volatile biomarkers in exhaled breath as predictors to individual drug response would advance the field of personalised medicine by providing direct information on enzyme activity. This would result in enormous benefits, both for patients and for the healthcare sector. Non-invasive breath tests would also gain a high acceptance by patients. Towards this goal, differences in metabolism resulting from extensive polymorphisms in a major group of drug-metabolizing enzymes, the cytochrome P450 (CYP) family, need to be determined and quantified. CYP2C9 is responsible for metabolising many crucial drugs (e.g., diclofenac) and food ingredients (e.g., limonene). In this paper, we provide a proof-of-concept study that illustrates the in vitro bioconversion of diclofenac in recombinant HEK293T cells overexpressing CYP2C9 to 4ʹ-hydroxydiclofenac. This in vitro approach is a necessary and important first step in the development of breath tests to determine and monitor metabolic processes in the human body. By focusing on the metabolic conversion of diclofenac, we have been able to establish a workflow using a cell-based system for CYP2C9 activity. Furthermore, we illustrate how the bioconversion of diclofenac is limited in the presence of limonene, which is another CYP2C9 metabolising substrate. We show that increasing limonene levels continuously reduce the production of 4ʹ-hydroxydiclofenac. Michaelis-Menten kinetics were performed for the diclofenac 4ʹ-hydroxylation with and without limonene, giving a kinetic constant of the reaction, K
M, of 103 µM and 94.1 µM, respectively, and a maximum reaction rate, V
max, of 46.8 pmol min−1 106 cells−1 and 56.0 pmol min−1 106 cells−1 with and without the inhibitor, respectively, suggesting a non-competitive or mixed inhibition type. The half-maximal inhibitory concentration value (IC50) for the inhibition of the formation of 4ʹ-hydroxydiclofenace by limonene is determined to be 1413 µM.
Laser-guided programmable construction of cell-laden hydrogel microstructures for in vitro drug evaluation
Authors: Dong Jianpei , Zhou Jianhua , Tang Hao , Chen Baiqi , Huang Lu
Published: July 2023

Cell-laden hydrogel microstructures have been used in broad applications in tissue engineering, translational medicine, and cell-based assays for pharmaceutical research. However, the construction of cell-laden hydrogel microstructures in vitro remains challenging. The technologies permitting generation of multicellular structures with different cellular compositions and spatial distributions are needed. Herein, we propose a laser-guided programmable hydrogel-microstructures-construction platform, allowing controllable and heterogeneous assembly of multiple cellular spheroids into spatially organized multicellular structures with good bioactivity. And the cell-laden hydrogel microstructures could be further leveraged for in vitro drug evaluation. We demonstrate that cells within hydrogels exhibit significantly higher half-maximal inhibitory concentration values against doxorubicin compared with traditional 2D plate culture. Moreover, we reveal the differences in drug responses between heterogeneous and homogeneous cell-laden hydrogel microstructures, providing valuable insight into in vitro drug evaluation.
Synthesis of partially coherent Bessel-mode vortex-beams with radial coherence
Authors: Olvera-Santamaría M Á , Ostrovsky A S
Published: July 2023

Partially coherent Bessel-mode vortex-beams with radial coherence are introduced. The generated beams are fully coherent at pair of points along the same radial coordinate. The field is completely incoherent for pairs of points belonging to different angular positions. By using the coherent-mode structure of propagation invariant fields, the analytical expression of the propagated cross-spectral density, representing fields with radial coherence, is derived. It is shown that beams of this type can be generated in a Fourier transforming optical system. An important feature of the synthesized beams is their ability of being invariant under propagation. The behaviour of the degree of coherence is analysed in terms of the eigenvalues of the modal structure. A numerical ensemble of realizations, at both planes of the considered system, was generated. From this ensemble, the spectral intensity of the proposed beams was obtained. The numerical results show a well-defined principal thin ring of maximum intensity followed by secondary concentric rings, in complete agreement with theoretical predictions. We believe that presented scheme can trigger new research routes in the synthesis of fields with structured coherence.
Effects of quenching temperature on threshold, driving voltage and morphology of reverse mode liquid crystal gel films
Authors: Chen Yi-Xuan , Hsu Jy-Shan
Published: July 2023

This study demonstrated that the electro-optical properties and morphology of reverse mode liquid crystal (LC) gel films are strongly influenced by the quenching temperature (TQ) during the manufacturing processes. Composite films were self-assembled using LC and gelator molecules by using different TQ values (70, 80, 90, 100, 110 and 120 °C) and a cold brine (−15 °C). As TQ increased, the morphology of the gel in the polarised light microscope images are changed from neatly arranged fibre-like patterns to random disordered networks. Furthermore, the threshold and driving voltages of the films decreased. For further investigating the gelation processes, Steady cooling rates of 3, 10 and 30 °C min−1 were adopted during the manufacturing process of the LC films. The corresponding morphologies of the films were carefully inspected and compared with those of the quenched films.
Dynamic & norm-based weights to normalize imbalance in back-propagated gradients of physics-informed neural networks
Authors: Deguchi Shota , Asai Mitsuteru
Published: July 2023

Physics-Informed Neural Networks (PINNs) have been a promising machine learning model for evaluating various physical problems. Despite their success in solving many types of partial differential equations (PDEs), some problems have been found to be difficult to learn, implying that the baseline PINNs is biased towards learning the governing PDEs while relatively neglecting given initial or boundary conditions. In this work, we propose Dynamically Normalized Physics-Informed Neural Networks (DN-PINNs), a method to train PINNs while evenly distributing multiple back-propagated gradient components. DN-PINNs determine the relative weights assigned to initial or boundary condition losses based on gradient norms, and the weights are updated dynamically during training. Through several numerical experiments, we demonstrate that DN-PINNs effectively avoids the imbalance in multiple gradients and improves the inference accuracy while keeping the additional computational cost within a reasonable range. Furthermore, we compare DN-PINNs with other PINNs variants and empirically show that DN-PINNs is competitive with or outperforms them. In addition, since DN-PINN uses exponential decay to update the relative weight, the weights obtained are biased toward the initial values. We study this initialization bias and show that a simple bias correction technique can alleviate this problem.
Cartan actions of higher rank abelian groups and their classification
Authors: Spatzier Ralf , Vinhage Kurt
Published: July 2023

We study

R

k

×

Z

ℓ

\mathbb {R}^k \times \mathbb {Z}^\ell

actions on arbitrary compact manifolds with a projectively dense set of Anosov elements and 1-dimensional coarse Lyapunov foliations. Such actions are called totally Cartan actions. We completely classify such actions as built from low-dimensional Anosov flows and diffeomorphisms and affine actions, verifying the Katok-Spatzier conjecture for this class. This is achieved by introducing a new tool, the action of a dynamically defined topological group describing paths in coarse Lyapunov foliations, and understanding its generators and relations. We obtain applications to the Zimmer program.
Evidence that tissue recoil in the early Drosophila embryo is a passive not active process
Authors: Goldner Amanda Nicole , Fessehaye Salena M. , Rodriguez Nataly , Mapes Kelly Ann , Osterfield Miriam , Doubrovinski Konstantin
Published: July 2023

Techniques to examine the contribution of specific proteins to tissue mechanical properties are extremely limited. Here, Goldner et al. develop two complementary techniques for rapid protein depletion combined with mechanical measurements and show that myosin activity is dispensable for tissue elasticity.
A new layer of regulation of chromosomal passenger complex (CPC) translocation in budding yeast
Authors: Sherwin Delaney , Gutierrez-Morton Emily , Bokros Michael , Haluska Cory , Wang Yanchang
Published: July 2023

Kinetochore-localized chromosomal passenger complex (CPC) is essential for chromosome bipolar attachment, but it moves to the spindle during anaphase. The reversal of CDK-dependent phosphorylation Sli15, a CPC subunit, has been shown to promote CPC translocation. Here, we found that reversal of Ipl1-dependent Sli15 phosphorylation by Fin1-PP1 also causes CPC translocation, thereby revealing a new layer of regulation for CPC translocation.
ATP yield of plant respiration: potential, actual and unknown
Authors: Amthor J S
Published: July 2023

Background and Aims

The ATP yield of plant respiration (ATP/hexose unit respired) quantitatively links active heterotrophic processes with substrate consumption. Despite its importance, plant respiratory ATP yield is uncertain. The aim here was to integrate current knowledge of cellular mechanisms with inferences required to fill knowledge gaps to generate a contemporary estimate of respiratory ATP yield and identify important unknowns.

Method

A numerical balance sheet model combining respiratory carbon metabolism and electron transport pathways with uses of the resulting transmembrane electrochemical proton gradient was created and parameterized for healthy, non-photosynthesizing plant cells catabolizing sucrose or starch to produce cytosolic ATP.

Key Results

Mechanistically, the number of c subunits in the mitochondrial ATP synthase Fo sector c-ring, which is unquantified in plants, affects ATP yield. A value of 10 was (justifiably) used in the model, in which case respiration of sucrose potentially yields about 27.5 ATP/hexose (0.5 ATP/hexose more from starch). Actual ATP yield often will be smaller than its potential due to bypasses of energy-conserving reactions in the respiratory chain, even in unstressed plants. Notably, all else being optimal, if 25 % of respiratory O2 uptake is via the alternative oxidase – a typically observed fraction – ATP yield falls 15 % below its potential.

Conclusions

Plant respiratory ATP yield is smaller than often assumed (certainly less than older textbook values of 36–38 ATP/hexose) leading to underestimation of active-process substrate requirements. This hinders understanding of ecological/evolutionary trade-offs between competing active processes and assessments of crop growth gains possible through bioengineering of processes that consume ATP. Determining the plant mitochondrial ATP synthase c-ring size, the degree of any minimally required (useful) bypasses of energy-conserving reactions in the respiratory chain, and the magnitude of any ‘leaks’ in the inner mitochondrial membrane are key research needs.
Heterologous expression of α-1,3-glucanase Agn1p from Schizosaccharomyces pombe, and efficient production of nigero-oligosaccharides by enzymatic hydrolysis from solubilized α-1,3;1,6-glucan
Authors: Horaguchi Yui , Takahashi Masaki , Takamatsu Keigo , Konno Hiroyuki , Makabe Koki , Yano Shigekazu
Published: July 2023

The glycoside hydrolase family 71 α-1,3-glucanase (Agn1p) of Schizosaccharomyces pombe was expressed in Escherichia coli Rosetta-gami B (DE3). Agn1p (0.5 nmol/mL) hydrolyzed insoluble α-1,3-glucan (1%), and about 3.3 mm reducing sugars were released after 1440 min of reaction. The analysis of reaction products by high-performance liquid chromatography revealed that pentasaccharides accumulated in the reaction mixture as the main products, along with a small amount of mono-, di-, tri-, tetra-, and hexasaccharides. Soluble glucan was prepared from insoluble α-1,3;1,6-glucan by alkaline and sonication treatment to improve the hydrolytic efficiency. As a result, this solubilized α-1,3;1,6-glucan maintained a solubilized state for at least 6 h. Agn1p (0.5 nmol/mL) hydrolyzed the solubilized α-1,3;1,6-glucan (1%), and about 8.2 mm reducing sugars were released after 240 min of reaction. Moreover, Agn1p released about 12.3 mm reducing sugars from 2% of the solubilized α-1,3;1,6-glucan.
Rapid genome functional annotation pipeline anchored to the house sparrow (Passer domesticus, Linnaeus 1758) genome reannotation
Authors: Magallanes-Alba Melisa Eliana , Baricalla Agustín , Rego Natalia , Brun Antonio , Karasov William H , Caviedes-Vidal Enrique
Published: July 2023

The house sparrow (Passer domesticus) is a valuable avian model for studying evolutionary genetics, development, neurobiology, physiology, behavior, and ecology, both in laboratory and field-based settings. The current annotation of the P. domesticus genome available at the Ensembl Rapid Release site is primarily focused on gene set building and lacks functional information. In this study, we present the first comprehensive functional reannotation of the P. domesticus genome using intestinal Illumina RNA sequencing (RNA-Seq) libraries. Our revised annotation provides an expanded view of the genome, encompassing 38592 transcripts compared to the current 23574 transcripts in Ensembl. We also predicted 14717 protein-coding genes, achieving 96.4% completeness for Passeriformes lineage BUSCOs. A substantial improvement in this reannotation is the accurate delineation of untranslated region (UTR) sequences. We identified 82.7% and 93.8% of the transcripts containing 5′- and 3′-UTRs, respectively. These UTR annotations are crucial for understanding post-transcriptional regulatory processes. Our findings underscore the advantages of incorporating additional specific RNA-Seq data into genome annotation, particularly when leveraging fast and efficient data processing capabilities. This functional reannotation enhances our understanding of the P. domesticus genome, providing valuable resources for future investigations in various research fields.
Has the time come to assess small-molecule/biologic drug combinations for the management of moderate-to-severe hidradenitis suppurativa?
Authors: Maronese Carlo Alberto , Ingram John R , Marzano Angelo V
Published: July 2023

As the landscape for hidradenitis suppurativa (HS) medical treatment is rapidly expanding, seemingly taking the same steps that marked the evolution of psoriasis management, upcoming agents still do not appear to offer complete disease control. Better control of severe cases of HS refractory to biologic monotherapy may require investigation of pathogenesis-driven, combination regimens sooner rather than later.
Major adverse cardiovascular events in patients with atopic dermatitis treated with oral Janus kinase inhibitors: a systematic review and meta-analysis
Authors: Ertus Cécile , Scailteux Lucie-Marie , Lescoat Alain , Berthe Pauline , Auffret Vincent , Dupuy Alain , Oger Emmanuel , Droitcourt Catherine
Published: July 2023

Background

On the basis of safety data for patients with inflammatory rheumatism or inflammatory bowel disease, treatment with Janus kinase (JAK) inhibitors (JAKi) has been linked to the occurrence of major adverse cardiovascular events (MACE). However, these inflammatory diseases are proatherogenic; in contrast, patients with atopic dermatitis (AD) do not usually have a high cardiovascular (CV) comorbidity burden.

Objectives

To perform a systematic review and meta-analysis of MACE in patients with AD treated with JAKi.

Methods

We systematically searched PubMed, Embase, Cochrane Library and Google Scholar from their inception to 2 September 2022. Cohort studies, randomized controlled trials and pooled safety analyses providing CV safety data on patients taking JAKi for AD were selected. We included patients aged ≥ 12 years. We built a ‘controlled-period’ cohort (n = 9309; 6000 exposed to JAKi and 3309 exposed to comparators) and an ‘all-JAKi’ cohort (n = 9118 patients exposed to a JAKi in any of the included studies). The primary outcome was a composite of acute coronary syndrome (ACS), ischaemic stroke and CV death. The broader secondary MACE outcome encompassed ACS, stroke (whether ischaemic or haemorrhagic), transient ischaemic attack and CV death. The frequency of primary and secondary MACE was assessed in both cohorts. A fixed-effects meta-analysis using the Peto method was used to calculate the odds ratio (OR) for MACE in the ‘controlled-period’ cohort. Evaluation of the risk of bias was done using the Cochrane risk-of-bias tool (version 2). Certainty of evidence was assessed using the Grading of Recommendations Assessment, Development and Evaluation (GRADE) approach.

Results

Eight per cent of the records identified initially met the selection criteria, corresponding to 23 records included in the ‘all-JAKi’ cohort. Patients had been exposed to baricitinib, upadacitinib, abrocitinib, ivarmacitinib, placebo or dupilumab. Four primary events (three with JAKi and one with placebo) and five secondary events (four with JAKi and one with placebo) occurred among 9309 patients in the ‘controlled-period’ cohort (MACE frequency 0.04% and 0.05%, respectively). Eight primary events and 13 secondary events occurred among 9118 patients in the ‘all-JAKi’ cohort (MACE frequency 0.08% and 0.14%, respectively). The OR for primary MACE in patients with AD treated with JAKi vs. placebo or dupilumab was 1.35 (95% confidence interval 0.15–12.21; I  2 = 12%, very low certainty of evidence).

Conclusions

Our review highlights rare cases of MACE among JAKi users for AD. JAKi may have little-to-no effect on the occurrence of MACE in patients with AD vs. comparators, but the evidence is uncertain. Real-life long-term population-level safety studies are needed.
Living with neurofibromatosis
Authors: Murphy Lisa , Andrawis Madonna , Beatty Paula , Costa Blasco Marta , Doyle Claire , McFeely Orla , O’Mahony Sarah , Wolinska Anna , Connolly Maureen
Published: July 2023

Neurofibromatosis type 1 is a genetic disorder that has a number of cutaneous manifestations. Although these lesions typically do not require any form of intervention, it is important for clinicians to be sensitive to the impact that this condition can have on patients’ quality of life regardless. This viewpoint highlights the difficulties encountered by our patient as a result of this condition.
Antibiotic Consumption During the Coronavirus Disease 2019 Pandemic and Emergence of Carbapenemase-Producing Klebsiella pneumoniae Lineages Among Inpatients in a Chilean Hospital: A Time-Series Study and Phylogenomic Analysis
Authors: Allel Kasim , Peters Anne , Conejeros José , Martínez José R W , Spencer-Sandino Maria , Riquelme-Neira Roberto , Rivas Lina , Rojas Pamela , Orellana Chea Cristian , García Patricia , Araos Rafael , McGovern Olivia , Patel Twisha S , Arias Cesar A , Lessa Fernanda C , Undurraga Eduardo A , Munita José M
Published: July 2023

Background

The impact of coronavirus disease 2019 (COVID-19) on antimicrobial use (AU) and resistance has not been well evaluated in South America. These data are critical to inform national policies and clinical care.

Methods

At a tertiary hospital in Santiago, Chile, between 2018 and 2022, subdivided into pre- (3/2018–2/2020) and post–COVID-19 onset (3/2020–2/2022), we evaluated intravenous AU and frequency of carbapenem-resistant Enterobacterales (CRE). We grouped monthly AU (defined daily doses [DDD]/1000 patient-days) into broad-spectrum β-lactams, carbapenems, and colistin and used interrupted time-series analysis to compare AU during pre- and post-pandemic onset. We studied the frequency of carbapenemase-producing (CP) CRE and performed whole-genome sequencing analyses of all carbapenem-resistant (CR) Klebsiella pneumoniae (CRKpn) isolates collected during the study period.

Results

Compared with pre-pandemic, AU (DDD/1000 patient-days) significantly increased after the pandemic onset, from 78.1 to 142.5 (P < .001), 50.9 to 110.1 (P < .001), and 4.1 to 13.3 (P < .001) for broad-spectrum β-lactams, carbapenems, and colistin, respectively. The frequency of CP-CRE increased from 12.8% pre–COVID-19 to 51.9% after pandemic onset (P < .001). The most frequent CRE species in both periods was CRKpn (79.5% and 76.5%, respectively). The expansion of CP-CRE harboring blaNDM was particularly noticeable, increasing from 40% (n = 4/10) before to 73.6% (n = 39/53) after pandemic onset (P < .001). Our phylogenomic analyses revealed the emergence of two distinct genomic lineages of CP-CRKpn: ST45, harboring blaNDM, and ST1161, which carried blaKPC.

Conclusions

AU and the frequency of CP-CRE increased after COVID-19 onset. The increase in CP-CRKpn was driven by the emergence of novel genomic lineages. Our observations highlight the need to strengthen infection prevention and control and antimicrobial stewardship efforts.
Prescribing of Outpatient Antibiotics Commonly Used for Respiratory Infections Among Adults Before and During the Coronavirus Disease 2019 Pandemic in Brazil
Authors: Solanky Dipesh , McGovern Olivia L , Edwards Jonathan R , Mahon Garrett , Patel Twisha S , Lessa Fernanda C , Hicks Lauri A , Patel Payal K
Published: July 2023

Background

The coronavirus disease 2019 (COVID-19) pandemic may have impacted outpatient antibiotic prescribing in low- and middle-income countries such as Brazil. However, outpatient antibiotic prescribing in Brazil, particularly at the prescription level, is not well-described.

Methods

We used the IQVIA MIDAS database to characterize changes in prescribing rates of antibiotics commonly prescribed for respiratory infections (azithromycin, amoxicillin-clavulanate, levofloxacin/moxifloxacin, cephalexin, and ceftriaxone) among adults in Brazil overall and stratified by age and sex, comparing prepandemic (January 2019–March 2020) and pandemic periods (April 2020–December 2021) using uni- and multivariate Poisson regression models. The most common prescribing provider specialties for these antibiotics were also identified.

Results

In the pandemic period compared to the prepandemic period, outpatient azithromycin prescribing rates increased across all age–sex groups (incidence rate ratio [IRR] range, 1.474–3.619), with the greatest increase observed in males aged 65–74 years; meanwhile, prescribing rates for amoxicillin-clavulanate and respiratory fluoroquinolones mostly decreased, and changes in cephalosporin prescribing rates varied across age–sex groups (IRR range, 0.134–1.910). For all antibiotics, the interaction of age and sex with the pandemic in multivariable models was an independent predictor of prescribing changes comparing the pandemic versus prepandemic periods. General practitioners and gynecologists accounted for the majority of increases in azithromycin and ceftriaxone prescribing during the pandemic period.

Conclusions

Substantial increases in outpatient prescribing rates for azithromycin and ceftriaxone were observed in Brazil during the pandemic with prescribing rates being disproportionally different by age and sex. General practitioners and gynecologists were the most common prescribers of azithromycin and ceftriaxone during the pandemic, identifying them as potential specialties for antimicrobial stewardship interventions.