bluuebunny/crossref_metadata_2025 huggingface dataset:
Deep learning for head and neck semi-supervised semantic segmentation
Authors: Luan Shunyao , Ding Yi , Shao Jiakang , Zou Bing , Yu Xiao , Qin Nannan , Zhu Benpeng , Wei Wei , Xue Xudong
Published: February 2024

Objective. Radiation therapy (RT) represents a prevalent therapeutic modality for head and neck (H&N) cancer. A crucial phase in RT planning involves the precise delineation of organs-at-risks (OARs), employing computed tomography (CT) scans. Nevertheless, the manual delineation of OARs is a labor-intensive process, necessitating individual scrutiny of each CT image slice, not to mention that a standard CT scan comprises hundreds of such slices. Furthermore, there is a significant domain shift between different institutions’ H&N data, which makes traditional semi-supervised learning strategies susceptible to confirmation bias. Therefore, effectively using unlabeled datasets to support annotated datasets for model training has become a critical issue for preventing domain shift and confirmation bias. Approach. In this work, we proposed an innovative cross-domain orthogon-based-perspective consistency (CD-OPC) strategy within a two-branch collaborative training framework, which compels the two sub-networks to acquire valuable features from unrelated perspectives. More specifically, a novel generative pretext task cross-domain prediction (CDP) was designed for learning inherent properties of CT images. Then this prior knowledge was utilized to promote the independent learning of distinct features by the two sub-networks from identical inputs, thereby enhancing the perceptual capabilities of the sub-networks through orthogon-based pseudo-labeling knowledge transfer. Main results. Our CD-OPC model was trained on H&N datasets from nine different institutions, and validated on the four local intuitions’ H&N datasets. Among all datasets CD-OPC achieved more advanced performance than other semi-supervised semantic segmentation algorithms. Significance. The CD-OPC method successfully mitigates domain shift and prevents network collapse. In addition, it enhances the network’s perceptual abilities, and generates more reliable predictions, thereby further addressing the confirmation bias issue.
Towards liquid EPR dosimetry using nitroxides in aqueous solution
Authors: Höfel Sebastian , Zwicker Felix , Fix Michael K , Drescher Malte
Published: February 2024

Objective. Water-equivalent dosimeters are desirable for dosimetry in radiotherapy. The present work investigates basic characteristics of novel aqueous detector materials and presents a signal loss approach for electron paramagnetic resonance (EPR) dosimetry. Approach. The proposed principle is based on the radiation dose dependent annihilation of EPR active nitroxides (NO·) in aqueous solutions. Stable nitroxide radicals (3-Maleimido-2,2,5,5-tetramethyl-1-pyrrolidinyloxy (MmP), 3-Carbamoyl-2,2,5,5-tetramethyl-1-pyrrolidinyloxy (CmP)) in aqueous solutions containing dimethyl sulfoxide (DMSO) as an additive were filled in glass capillaries for irradiation and EPR readout. Radiation doses ranging from 1 to 64 Gy were applied with a clinical 6 MV flattening filter free photon beam. EPR readout was then performed with a X-band benchtop spectrometer. The dose response, temporal stability and reproducibility of the samples’ EPR signal amplitudes as well as the influence of the nitroxide concentration between 10 and 160 μM on the absolute signal loss were investigated using MmP. CmP was used to examine the dependence of the dose response on DMSO concentration between 0 and 10 vol%. An indirect effect model was fitted to the experimental data assuming irradiation induced radical reactions as the underlying mechanism. Main results. For an initial MmP concentration of 20 μM, absolute EPR signal loss is linear up to a dose of 16 Gy with a yield G(-NO·) of approximately 0.4 μmol J−1. Within five weeks upon sample irradiation to doses between 0 and 32 Gy relative EPR signal fluctuations were on average (126 readouts) below 1% (1σ). For c(MmP) ≥ 20 μM, absolute signal loss is only weakly dependent on c(MmP), whereas it increases strongly with increasing c(DMSO) in the range 0–5 vol%. An indirect effect model is applicable to describe the reaction mechanism resulting in the observed dose response curve. Significance. Liquids consisting of nitroxides in aqueous solution and small amounts of DMSO (2 vol%) show promising basic characteristics for application as water-equivalent EPR dosimeter materials in radiotherapy. The EPR signal loss is based on an indirect effect mediated by diffusing radicals originating from the radiolysis of the water/DMSO mixture.
A novel predict method for muscular invasion of bladder cancer based on 3D mp-MRI feature fusion
Authors: Yu Jie , Cai Lingkai , Chen Chunxiao , Zou Yuan , Xiao Yueyue , Fu Xue , Wang Liang , Yang Xiao , Liu Peikun , Lu Qiang , Sun Xueying , Shao Qiang
Published: February 2024

Objective. To assist urologist and radiologist in the preoperative diagnosis of non-muscle-invasive bladder cancer (NMIBC) and muscle-invasive bladder cancer (MIBC), we proposed a combination models strategy (CMS) utilizing multiparametric magnetic resonance imaging. Approach. The CMS includes three components: image registration, image segmentation, and multisequence feature fusion. To ensure spatial structure consistency of T2-weighted imaging (T2WI), diffusion-weighted imaging (DWI), and dynamic contrast-enhanced imaging (DCE), a registration network based on patch sampling normalized mutual information was proposed to register DWI and DCE to T2WI. Moreover, to remove redundant information around the bladder, we employed a segmentation network to obtain the bladder and tumor regions from T2WI. Using the coordinate mapping from T2WI, we extracted these regions from DWI and DCE and integrated them into a three-branch dual-channel input. Finally, to fully fuse low-level and high-level features of T2WI, DWI, and DCE, we proposed a distributed multilayer fusion model for preoperative MIBC prediction with five-fold cross-validation. Main results. The study included 436 patients, of which 404 were for the internal cohort and 32 for external cohort. The MIBC was confirmed by pathological examination. In the internal cohort, the area under the curve, accuracy, sensitivity, and specificity achieved by our method were 0.928, 0.869, 0.753, and 0.929, respectively. For the urologist and radiologist, Vesical Imaging-Reporting and Data System score >3 was employed to determine MIBC. The urologist demonstrated an accuracy, sensitivity, and specificity of 0.842, 0.737, and 0.895, respectively, while the radiologist achieved 0.871, 0.803, and 0.906, respectively. In the external cohort, the accuracy of our method was 0.831, which was higher than that of the urologist (0.781) and the radiologist (0.813). Significance. Our proposed method achieved better diagnostic performance than urologist and was comparable to senior radiologist. These results indicate that CMS can effectively assist junior urologists and radiologists in diagnosing preoperative MIBC.
Improving the structural performance of low-temperature sputtered AlN on silicon substrate
Authors: Luo Yuchi , Yuan Ye , Liang Zhiwen , Cai Tianren , Yin Hengyi , Zhao Yichen , Zhang Hongmeng , Cao Jiakang , Wan Wenting , Ji Yanda , Yang Anli , Wang Qi , Hao Mingming
Published: February 2024

Preparing high-quality AlN films at low temperatures is always highly demanded in plenty of application-fields, despite the high temperature is always necessary to enable the AlN crystallization. Therefore, improving the structural properties at low temperature is still challenging in the field. In the present work, a metal organic chemical vapor deposition (MOCVD) grown AlN nucleation layer is employed to improve the crystallinity and morphology of sputtered AlN on 6-inch Si (111) substrate at temperatures even as low as 100 °C where it is not principally possible to achieve crystallization of sputtered AlN. When compared with the as-sputtered AlN prepared even at 650 °C, it is found that the full width at half maximum of AlN (002) x-ray rocking curves is intensively decreased to 0.96° from 1.61°, and such a reduction indicates that the screw dislocation density is decreased from 7.31 × 1010 down to 2.14 × 1010 cm−2. In addition to the crystallinity, the morphology is also obviously improved that the root-mean-square roughness is reduced from 4.99 nm down to 0.83 nm in a scanned area of 3 × 3 μm2 through introducing AlN nucleation. Therefore, such a combination highlights the contribution of AlN nucleation grown by MOCVD in improving the structural properties of low-temperature sputtered AlN layer which is compatible with the manufacturing of Si integrated circuits.
River valley-inspired, high-sensitivity, and rapid-response capacitive three-dimensional force tactile sensor based on U-shaped groove structure
Authors: Xu Decheng , Hong Weiqiang , Hu Bing , Zhang Tianxu , Chen Dongliang , Yan Zihao , Yao Xiaomeng , Zhang Xinyi , Zhao Yunong , Sun Taoran , Zhang Chuanzhao , Pan Mingqi , Ruan Xiaoyun , Yan Ruishen , Wang Junyi , Guo Xiaohui
Published: February 2024

High-performance three-dimensional force (3D-force) tactile sensors with the capability of distinguishing normal and tangential forces in sync play a vital role in emerging wearable devices and smart electronics. And there is an urgent need for 3D-force tactile sensors with fast response and high flexibility. Herein, we design a capacitive 3D-force tactile sensors inspired by the U-shaped river valley surface morphology, which has satisfactory performance in terms of rapid response/recovery time (∼36 ms/∼ 36 ms), low hysteresis (4.2%), and high sensitivity (0.487 N−1). A theoretical model of general value for congener sensors is also proposed, obtaining a higher sensitivity through optimizing parameters. To verify the application potential of our device in actual scenarios, the robustness testing and gripping gamepad application were carried out. And it can recognize different motions in humans. Furthermore, principal component analysis is also conducted to demonstrate the distinct classification of different motions. Therefore, our work is eligible for the applications in wearable electronics, human–machine interaction, and soft intelligent robots.
Buckling-driven piezoelectric defect-induced energy localization and harvesting using a Rubik’s cube-inspired phononic crystal structure
Authors: Cao Dong-Xing , Li Sha-Sha , Guo Xiang-Ying , Chen Xu-Min , Lai Siu-Kai
Published: February 2024

Wireless sensor networks that enable advanced internet of things (IoT) applications have experienced significant development. However, low-power electronics are limited by battery lifetime. Energy harvesting presents a solution for self-powered technologies. Vibration-based energy harvesting technology is one of the effective approaches to convert ambient mechanical energy into electrical energy. Various dynamic oscillating systems have been proposed to investigate the effectiveness of energizing low-power electronic sensor devices for supporting various IoT applications across engineering disciplines. Phononic crystal structures have been implemented in vibrational energy harvesters due to their unique bandgap and wave propagation properties. This work proposes a Rubik’s cube-inspired defective-state locally resonant three-dimensional (3D) phononic crystal with a 5 × 5 × 5 perfect supercell that contains 3D piezoelectric energy harvesting units. The advantage of defect-induced energy localization is utilized to harness vibrational energy. The 3D piezoelectric energy harvesting units are constructed by the buckling-driven assembling principle. Adapting to the low-frequency and broadband characteristics of ambient vibration sources, soft silicone gel is used to encapsulate the buckled 3D piezoelectric units, which are embedded in the 3D cubic phononic crystal to assemble an entire system. The energy harvesting performance of various defective layouts and their defect modes is discussed. The results demonstrate that the harvester functions well under multidirectional, multimodal, and low-frequency conditions. The proposed methodology also offers a new perspective on vibrational energy harvesters for defective phononic crystals with superior working performance.
Hamiltonian switching control of noisy bipartite qubit systems
Authors: Yang Zhibo , Kosut Robert L , Birgitta Whaley K
Published: February 2024

We develop a Hamiltonian switching ansatz for bipartite control that is inspired by the quantum approximate optimization algorithm, to mitigate environmental noise on qubits. We demonstrate the control for a central spin coupled to bath spins via isotropic Heisenberg interactions, and then make physical applications to the protection of quantum gates performed on superconducting transmon qubits coupling to environmental two-level-systems (TLSs) through dipole-dipole interactions, as well as on such qubits coupled to both TLSs and a Lindblad bath. The control field is classical and acts only on the system qubits. We use reinforcement learning with policy gradient to optimize the Hamiltonian switching control protocols, using a fidelity objective for specific target quantum gates. We use this approach to demonstrate effective suppression of both coherent and dissipative noise, with numerical studies achieving target gate implementations with fidelities over 0.9999 (four nines) in the majority of our test cases and showing improvement beyond this to values of 0.999 999 999 (nine nines) upon a subsequent optimization by GRadient Ascent Pulse Engineering (GRAPE). We analyze how the control depth, total evolution time, number of environmental TLS, and choice of optimization method affect the fidelity achieved by the optimal protocols and reveal some critical behaviors of bipartite control of quantum gates.
Influence of gravitational tilt on the thermocapillary convection in a non-axisymmetric liquid bridge
Authors: Yang Shuo , Zhang Yupeng , Cui Jie , Qin Daocheng , Wang Yuhang , Ge Pushi , Luo Jintao , Guan Duojiao , Zheng Yunyi
Published: February 2024

Fluid slosh caused by residual acceleration in microgravity is a common problem encountered in space engineering. To solve this problem, the ground-based experiment research on the influence of gravity jitter and gravitational tilt on the thermocapillary convection (TCC) transition behaviour of non-axisymmetric liquid bridge has become an important issue in microgravity fluid management. Based on a mesoscale liquid bridge experimental platform which can realize gravitational tilt, the effect of gravitational tilt on TCC by using a high-speed camera equipped with a near-focus lens and a self-developed interface image recognition package. The results show that the spatio-temporal evolution of TCC by the influence of gravitational tilt is still divided into steady and oscillatory flow. In the stable TCC, the vortex core distortion of cellular flow caused by the imbalance left and right interface curvature invites cellular flow close to the free surface, and it shrinks to the intermediate height. As gravitational tilt increases, the transverse/longitudinal velocity peaks are significantly reduced, peak velocity has been reduced by 26%–27%. Meanwhile, the longitudinal velocity gradient at the free interface increases significantly. Therefore, gravitational tilt plays an important role in improving the surface flow velocity. In the oscillatory TCC, the position of vortex core is closer to the free interface at the hot/cold corner as the periodic mutual occupation of the left and right cellular flows. The TCC is obviously inhibited due to the gravitational tilt. The critical temperature difference is increased by 25% and the onset of temperature oscillation at the hot corner is delayed by 20% compared with conventional gravity condition.
WARP: The Data Reduction Pipeline for the WINERED Spectrograph
Authors: Hamano Satoshi , Ikeda Yuji , Otsubo Shogo , Katoh Haruki , Fukue Kei , Matsunaga Noriyuki , Taniguchi Daisuke , Kawakita Hideyo , Takenaka Keiichi , Kondo Sohei , Sameshima Hiroaki
Published: February 2024

We present a data reduction pipeline written in Python for data obtained with the near-infrared cross-dispersed echelle spectrograph, WINERED, which yields a 0.91–1.35 μm spectrum with the resolving power of

R

max

≡
λ

/

Δ
λ
=
28,000

or 70,000 depending on the observing mode. The pipeline was developed to efficiently extract the spectrum from the raw data with high quality. It comprises two modes: the calibration and the science mode. The calibration mode automatically produces the flat-fielding image, bad pixel map, echellogram distortion map and the dispersion solution from the set of the calibration data. Using calibration images and parameters, the science data of astronomical objects can be reduced automatically using the science mode. The science mode is also used for the real-time quick look at the data during observations. An example of the spectra reduced with WARP is presented. The effect of the highly inclined slit image on the spectral resolution is discussed.
A new quasilinear model for turbulent momentum transport in tokamaks with flow shear and plasma shaping
Authors: Sun Haomin , Ball Justin , Brunner Stephan , Volčokas Arnas
Published: February 2024

In tokamak experiments, sufficiently strong E × B flow shear reduces turbulent transport, thereby improving the prospects for fusion power plants. It is therefore of great importance to efficiently explore parameter space to find where strong plasma flow can be achieved. To this end, we propose a new, physically motivated quasi-linear model for estimating momentum transport from turbulence in the presence of toroidal flow shear and plasma shaping. The method gives good estimates of momentum transport for up–down asymmetric geometries as well as low magnetic shear and tight aspect ratio. The results are benchmarked with high-fidelity nonlinear GENE simulations, demonstrating that it provides a fast and accurate estimate of momentum transport.
Biofabrication of biomimetic undulating microtopography at the dermal-epidermal junction and its effects on the growth and differentiation of epidermal cells
Authors: Gao Chuang , Lu Chunxiang , Liu Huazhen , Zhang Yi , Qiao Hao , Jin Aoxiang , Dai Qiqi , Liu Yuanyuan
Published: February 2024

The undulating microtopography located at the junction of the dermis and epidermis of the native skin is called rete ridges (RRs), which plays an important role in enhancing keratinocyte function, improving skin structure and stability, and providing three-dimensional (3D) microenvironment for skin cells. Despite some progress in recent years, most currently designed and manufactured tissue-engineered skin models still cannot replicate the RRs, resulting in a lack of biological signals in the manufactured skin models. In this study, a composite manufacturing method including electrospinning, 3D printing, and functional coating was developed to produce the epidermal models with RRs. Polycaprolactone (PCL) nanofibers were firstly electrospun to mimic the extracellular matrix environment and be responsible for cell attachment. PCL microfibers were then printed onto top of the PCL nanofibers layer by 3D printing to quickly prepare undulating microtopography and finally the entire structures were dip-coated with gelatin hydrogel to form a functional coating layer. The morphology, chemical composition, and structural properties of the fabricated models were studied. The results proved that the multi-process composite fabricated models were suitable for skin tissue engineering. Live and dead staining, cell counting kit-8 (CCK-8) as well as histology (haematoxylin and eosin (HE) methodology) and immunofluorescence (primary and secondary antibodies combination assay) were used to investigate the viability, metabolic activity, and differentiation of skin cells for in vitro culturing. In vitro results showed that each model had high cell viability, good proliferation, and the expression of differentiation marker. It was worth noting that the sizes of the RRs affected the cell growth status of the epidermal models. In addition, the unique undulation characteristics of the epidermal-dermal junction can be reproduced in the developed epidermal models. Overall, these in vitro human epidermal models can provide valuable reference for skin transplantation, screening and safety evaluation of drugs and cosmetics.
Roles of chain stretch and concentration gradients in capillary thinning of polymer solutions
Authors: Chase Dylan , Cromer Michael
Published: February 2024

Polymers inhibit the breakup of a liquid filament thinning under surface tension. The coupling of elasticity, capillarity and inertia leads to the well-known beads-on-a-string (BOAS) formation. Additionally, under different conditions, smaller satellite drops can form along the liquid bridge between the main beads. The development of BOAS and satellite drops is controlled by the rheology of the polymer solution. In this study, we consider the roles played by finite extensibility and anisotropic drag on the formation of satellite beads. In particular, we show that the more stretching a polymer chain can undergo, satellite beads are suppressed. The latter stages of capillary thinning has been shown to result in a phase separation resulting in what is referred to as a blistering pattern. We thus also conduct simulations of an inhomogeneous dilute polymer model that considers the competing effects of diffusion and stress gradients. We show that polymer is pulled axially towards the region connecting string and bead. This simple model does not predict a phase separation, but does reveal that pinchoff could be inhibited by the buildup of polymer concentration.
Initiation of motion for an isolated finite size particle in a rotating tank flow
Authors: Rastello Marie , Marié Jean-Louis , Karan Venayagamoorthy S
Published: February 2024

The initiation of motion of an isolated finite size particle within a rotating fluid in a tank is investigated experimentally. The study leverages on the absence of slip velocity to explore the impact rotation has on the initiation of the motion of a particle. Results show that the motion, when it occurs, is purely radial. It is initiated when the centrifugal force acting on the particle overcomes the friction force exerted on it by the tank bottom. A model of friction force that reproduces the experimental data quite well is proposed. It is based on the classical Coulomb’s friction law and pressure considerations. Denoting rc
as the radial position of a particle when its motion starts, the critical radius

r

∗
c

=

r
c

/

d

essentially depends on the density ratio γ, the Froude number

F

r

ω

=

ω
2

d

/

g

but also the ratio of the tank radius to the particle size:

α
=
R

/

d

.

F

r

ω

is based on the particle diameter d, the shear velocity

Δ
U
=
ω
d

with ω the rotation rate and g the acceleration due to gravity. The agreement of the model with the experimental data is obtained for the same friction coefficient λ = 0.019 whatever the particles. The value is not far from the value 0.05 generally expected for lubricated smooth plastic/plastic friction coefficients. The model also shows that for a given tank radius a critical rotation speed exists below which, no initiation of motion can be expected.
Site-controlled preparation of metallic microstructures via mechanical scratch-induced selective electrodeposition
Authors: Zhu Jie , Gan Yinkai , Cui Licong , Liu Renxing , Tan Rui , Jiang Yanlin , Qian Linmao , Yu Bingjun
Published: February 2024

Controlled preparation of metallic microstructures attracts wide interest in sensor and electronic fields. However, limited by fabrication technology, it faces challenges in achieving template-free and orientational formation of metallic microstructures. Herein, a site-controlled strategy via scratch-induced selective electrodeposition was proposed to prepare high-quality metallic structures on silicon (Si) surface with the assistance of scanning probe lithography (SPL). The effects of scratching and depositing conditions were systematically investigated for optimizing the preparation process. Selective electrodeposition mechanisms were addressed through topographic and conductive detections. It was found that single-cycle scratch created under higher loads was beneficial for preparing compact and continuous Cu structures. Further analysis indicated that higher normal loads in scratching can facilitate obtaining more conductive sites, promoting orientated migration of metal ions during the reaction, while the increase of reciprocating cycles can cause more amorphous layers and hinder electron transport. Moreover, post-annealing treatment can lead to the growth of Cu grain sizes, which contributes to the crystallinity. Notably, the proposed method is demonstrated with the preparation of Cu coils, which is sensitive to alternating magnetic field. These findings shed new light on the site-controlled preparation of high-quality metallic microstructures and the applications.
Superconductivity and electron self-energy in tungsten-sulfur-hydride monolayer
Authors: Seeyangnok J , Ul Hassan M M , Pinsook U , Ackland G J
Published: February 2024

Hydrogen-rich structures have recently gained attention as a candidate for room-temperature superconductors. Hydrogen has high phonon frequencies and can be an ideal component for superconductors if it also exhibits strong electron–phonon coupling. In bulk materials, this has been achieved only under very high pressure. Two-dimensional hydrogen-decorated materials can also be expected to become superconductors. Recently, it was shown that a Janus MoSH monolayer can be synthesized (Lu et al 2017 Nat. Nanotechnol.
12 744–9), and a theoretical investigation of this MoSH monolayer claimed that T
c = 28.58 K at atmospheric pressure (Liu et al 2022 Phys. Rev. B 105 245420). In this work, we propose that tungsten sulfur hydride (WSH) is also a superconducting Janus monolayer. The

T

c

is carefully calculated with very high resolution via the Eliashberg spectral function and the electron self-energy. We find that WSH is a conventional BCS superconductor with T
c = 12.2 K at ambient pressure. For practical applications, sensitive dependence on substrate is inferred. We also reported the electron self-energy of WSH, which can be compared directly with future measurements from angle-resolved photoelectron spectroscopy.
New twisted van der Waals fabrication method based on strongly adhesive polymer
Authors: Park Giung , Son Suhan , Kim Jongchan , Chang Yunyeong , Zhang Kaixuan , Kim Miyoung , Lee Jieun , Park Je-Geun
Published: February 2024

Observations of emergent quantum phases in twisted bilayer graphene prompted a flurry of activities in van der Waals (vdW) materials beyond graphene. Most current twisted experiments use a so-called tear-and-stack method using a polymer called polypropylene carbonate (PPC). However, despite the clear advantage of the current PPC tear-and-stack method, there are also technical limitations, mainly a limited number of vdW materials that can be studied using this PPC-based method. This technical bottleneck has been preventing further development of the exciting field beyond a few available vdW samples. To overcome this challenge and facilitate future expansion, we developed a new tear-and-stack method using a strongly adhesive polycaprolactone. With similar angular accuracy, our technology allows fabrication without a capping layer, facilitating surface analysis and ensuring inherently clean interfaces and low operating temperatures. More importantly, it can be applied to many other vdW materials that have remained inaccessible with the PPC-based method. We present our results on twist homostructures made with a wide choice of vdW materials—from two well-studied vdW materials (graphene and MoS2) to the first-ever demonstrations of other vdW materials (NbSe2, NiPS3, and Fe3GeTe2). Therefore, our new technique will help expand moiré physics beyond few selected vdW materials and open up more exciting developments.
Dipolar interactions enhanced by two-dimensional dielectric screening in few-layer van der Waals structures
Authors: Hou Yuhang , Yu Hongyi
Published: February 2024

We theoretically examined how the dielectric screening of two-dimensional (2D) layered materials affects the dipolar interaction between interlayer excitons (IXs) in few-layer van der Waals structures. Our analysis indicates that the dipolar interaction is largely enhanced by 2D dielectric screening at an inter-exciton separation of several nanometers or larger. The underlying mechanism can be attributed to the induced-charge densities in layered materials, which give rise to induced-dipole densities at large distances with directions parallel to that of the IX. The interaction between quadrupolar excitons in trilayer structures are found to be enhanced even larger, with a magnitude one to two orders stronger than that without 2D dielectric screening. The strengths of these dipolar and quadrupolar interactions can be further tuned by engineering the dielectric environment.
Radioactive source localization employing resistive electrode array (REA) detector
Authors: Hoegele Wolfgang , Zhang Victoria , Grace Vasquez Elena , Gineitaite Indre , Sajo Erno , Brivio Davide , Zygmanski Piotr
Published: February 2024

Objective. In this feasibility study, we explore an application of a Resistive Electrode Array (REA) for localization of a radioactive point source. The inverse problem posed by multichannel REA detection is studied from mathematical perspective and involves the questions of the minimal configuration of the conductive leads that can achieve this goal. The basic configuration consists of a circularly shaped REA with four opposite electrical lead–pairs at its perimeter. Approach. A robust mathematical reconstruction method for a 3D radioactive source relative to the REA is presented. The characteristic empirical Green’s function for the detector response of the REA is determined by numerically solving Laplace equations with appropriate boundary conditions. Based on this model, Monte Carlo simulations of the inverse problem with Gaussian noise are performed and the overall accuracy of the localization is investigated. Main results. The results show a 3D error distribution of localization which is uniform in the (x, y)–plane of the REA and strongly correlated in the orthogonal z–axis. The overall accuracy decreases with higher distance of the source to the detector which is intuitive due to approximate flux dependence following the inverse square law. Further, a saturation in accuracy regarding the number of electrical leads and a linear dependence of the reconstruction error on the measurement noise level are observed. Significance. A broad range of REA detector configurations and their characteristics are investigated by this study for radioactive source localization allowing diverse practical applications with detector diameters ranging from millimeters to meters.
Mathematical diversity of parts for a continuous distribution
Authors: Rajaram R , Ritchey N , Castellani B
Published: February 2024

The current paper is part of a series exploring how to link diversity measures (e.g., Gini-Simpson index, Shannon entropy, Hill numbers) to a distribution’s original shape and to compare parts of a distribution, in terms of diversity, with the whole. This linkage is crucial to understanding the exact relationship between the density of an original probability distribution, denoted by p(x), and the diversity D in non-uniform distributions, both within parts of a distribution and the whole. Empirically, our results are an important advance since we can compare various parts of a distribution, noting that systems found in contemporary data often have unequal distributions that possess multiple diversity types and have unknown and changing frequencies at different scales (e.g. income, economic complexity ratings, rankings, etc.). To date, we have proven our results for discrete distributions. Our focus here is continuous distributions. In both instances, we do so by linking case-based entropy, a diversity approach we developed, to a probability distribution’s shape for continuous distributions. This allows us to demonstrate that the original probability distribution g
1, the case-based entropy curve g
2, and the slope of diversity g
3 (c
(a,x) versus the

c

(
a
,
x
)

*
ln

A

(
a
,
x
)

curve) are one-to-one (or injective). Put simply, a change in the probability distribution, g
1, leads to variations in the curves for g
2 and g
3. Consequently, any alteration in the permutation of the initial probability distribution, which results in a different form, will distinctly define the graphs g
2 and g3
. By demonstrating the injective property of our method for continuous distributions, we introduce a unique technique to gauge the level of uniformity as indicated by D/c. Furthermore, we present a distinct method to calculate D/c for different forms of the original continuous distribution, enabling comparison of various distributions and their components.
Energy system changes in the agricultural sector: testing a value-congruent communication approach to foster positive attitudes
Authors: Olvermann Madita , Kauffeld Simone
Published: February 2024

Multiple sectors, including agriculture, are subject to decarbonization and wide-ranging system changes. With a growing distance between agriculture and the public, communicating changes and fostering public acceptance as crucial factors for the success of these changes has become challenging. Therefore, understanding public attitudes towards emerging system changes in unfamiliar sectors helps identify appropriate communication strategies and provides information about possible responses from different stakeholders. To address the scarcity of studies on system changes in agriculture and their acceptability, a multidimensional evaluation of attitudes was undertaken using a factorial survey to test the utility of value-congruent information for enhancing positive attitudes. Electrical field cultivation (EFC) served as a case example for one potential energy system change in agriculture. The data were collected via an open scientific survey panel in Germany (N = 300) using a written vignette in the form of a newspaper article; different benefit foci and hypotheses were tested using path analysis. Although the different benefit foci did not reveal significant differences, problem awareness and knowledge were found to predict positive attitudes toward EFC. For once, results highlight the need to foster overall problem awareness for fossil fuels to garner public support for various pathways. Additionally, results underscore the perceived lack of personal affectedness by transition pathways as a barrier to responding to communication strategies, specifically in unfamiliar sectors such as agriculture. The study outlines the need for stakeholders to design communication strategies under consideration of fostering personal affectedness and overall problem understanding.
Surface enhanced infrared absorption mechanism and modification of the plasmonic response
Authors: Colleu Tanguy , Fekete Adam , Gonze Xavier , Cloots Alexandre , Liégeois Vincent , Rignanese Gian-Marco , Henrard Luc
Published: February 2024

Surface enhanced infrared absorption (SEIRA) is an experimental method where trace amount of a compound can be detected with high sensibility. This high detection sensibility is the result of the interaction of the molecules with a localized plasmon, usually from a metallic nanoparticle. In this study we numerically investigate by discrete dipole approximation the origin of the Fano-like response of the system, including the induced transparency when the plasmon resonance and the molecular vibrational mode coincide. The detailed analysis of the localization of the absorption shows that the modification of the absorption cross-section when the molecule is present comes from a change of the plasmonic resonance, not from the direct molecular response which is negligible. This sheds a new light on the SEIRA mechanism. In particular, it demonstrates that the sensibility is associated with the influence of the molecule on the plasmon resonance rather than with the local field enhancement itself.
NanoCon: contrastive learning-based deep hybrid network for nanopore methylation detection
Authors: Yin Chenglin , Wang Ruheng , Qiao Jianbo , Shi Hua , Duan Hongliang , Jiang Xinbo , Teng Saisai , Wei Leyi
Published: February 2024

Motivation

5-Methylcytosine (5mC), a fundamental element of DNA methylation in eukaryotes, plays a vital role in gene expression regulation, embryonic development, and other biological processes. Although several computational methods have been proposed for detecting the base modifications in DNA like 5mC sites from Nanopore sequencing data, they face challenges including sensitivity to noise, and ignoring the imbalanced distribution of methylation sites in real-world scenarios.

Results

Here, we develop NanoCon, a deep hybrid network coupled with contrastive learning strategy to detect 5mC methylation sites from Nanopore reads. In particular, we adopted a contrastive learning module to alleviate the issues caused by imbalanced data distribution in nanopore sequencing, offering a more accurate and robust detection of 5mC sites. Evaluation results demonstrate that NanoCon outperforms existing methods, highlighting its potential as a valuable tool in genomic sequencing and methylation prediction. In addition, we also verified the effectiveness of our representation learning ability on two datasets by visualizing the dimension reduction of the features of methylation and nonmethylation sites from our NanoCon. Furthermore, cross-species and cross-5mC methylation motifs experiments indicated the robustness and the ability to perform transfer learning of our model. We hope this work can contribute to the community by providing a powerful and reliable solution for 5mC site detection in genomic studies.

Availability and implementation

The project code is available at https://github.com/Challis-yin/NanoCon.
Detection of α-papillomaviruses in extragenital cutaneous squamous cell carcinomas
Authors: Weiss Morgane , Ferré Valentine M , Deschamps Lydia , Evrard Diane , Gonthier Clémentine , Charpentier Charlotte , Brunet-Possenti Florence
Published: February 2024

Previous studies have demonstrated that human papillomaviruses (HPVs) of the beta genus can contribute to the onset of cutaneous carcinomas in organ transplant recipients. In contrast, there are limited data related to the oncogenicity of alpha (α)-HPVs in the skin. Herein, we explore the characteristics of three cutaneous squamous cell carcinomas presenting α-HPV infection occurring in patients with HIV, in order to determine the role of α-HPV in these skin cancers.
Multivariate lesion symptom mapping for predicting trajectories of recovery from aphasia
Authors: Levy Deborah F , Entrup Jillian L , Schneck Sarah M , Onuscheck Caitlin F , Rahman Maysaa , Kasdan Anna , Casilio Marianne , Willey Emma , Davis L Taylor , de Riesthal Michael , Kirshner Howard S , Wilson Stephen M
Published: February 2024

Individuals with post-stroke aphasia tend to recover their language to some extent; however, it remains challenging to reliably predict the nature and extent of recovery that will occur in the long term. The aim of this study was to quantitatively predict language outcomes in the first year of recovery from aphasia across multiple domains of language and at multiple timepoints post-stroke. We recruited 217 patients with aphasia following acute left hemisphere ischaemic or haemorrhagic stroke and evaluated their speech and language function using the Quick Aphasia Battery acutely and then acquired longitudinal follow-up data at up to three timepoints post-stroke: 1 month (n = 102), 3 months (n = 98) and 1 year (n = 74). We used support vector regression to predict language outcomes at each timepoint using acute clinical imaging data, demographic variables and initial aphasia severity as input. We found that ∼60% of the variance in long-term (1 year) aphasia severity could be predicted using these models, with detailed information about lesion location importantly contributing to these predictions. Predictions at the 1- and 3-month timepoints were somewhat less accurate based on lesion location alone, but reached comparable accuracy to predictions at the 1-year timepoint when initial aphasia severity was included in the models. Specific subdomains of language besides overall severity were predicted with varying but often similar degrees of accuracy. Our findings demonstrate the feasibility of using support vector regression models with leave-one-out cross-validation to make personalized predictions about long-term recovery from aphasia and provide a valuable neuroanatomical baseline upon which to build future models incorporating information beyond neuroanatomical and demographic predictors.
Diffusion weighted magnetic resonance spectroscopy revealed neuronal specific microstructural alterations in Alzheimer’s disease
Authors: Spotorno Nicola , Najac Chloé , Strandberg Olof , Stomrud Erik , van Westen Danielle , Nilsson Markus , Ronen Itamar , Hansson Oskar
Published: February 2024

In Alzheimer’s disease, reconfiguration and deterioration of tissue microstructure occur before substantial degeneration become evident. We explored the diffusion properties of both water, a ubiquitous marker measured by diffusion MRI, and N-acetyl-aspartate, a neuronal metabolite probed by diffusion-weighted magnetic resonance spectroscopy, for investigating cortical microstructural changes downstream of Alzheimer’s disease pathology. To this aim, 50 participants from the Swedish BioFINDER-2 study were scanned on both 7 and 3 T MRI systems. We found that in cognitively impaired participants with evidence of both abnormal amyloid-beta (CSF amyloid-beta42/40) and tau accumulation (tau-PET), the N-acetyl-aspartate diffusion rate was significantly lower than in cognitively unimpaired participants (P < 0.05). This supports the hypothesis that intraneuronal tau accumulation hinders diffusion in the neuronal cytosol. Conversely, water diffusivity was higher in cognitively impaired participants (P < 0.001) and was positively associated with the concentration of myo-inositol, a preferentially astrocytic metabolite (P < 0.001), suggesting that water diffusion is sensitive to alterations in the extracellular space and in glia. In conclusion, measuring the diffusion properties of both water and N-acetyl-aspartate provides rich information on the cortical microstructure in Alzheimer’s disease, and can be used to develop new sensitive and specific markers to microstructural changes occurring during the disease course.
ASIC1 promotes migration and invasion of hepatocellular carcinoma via the PRKACA/AP-1 signaling pathway
Authors: Liu Youyi , Wang Boshi , Cheng Yang , Fang Yipeng , Hou Yingjian , Mao Yong , Wu Xiaomin , Jiang Donglin , He Youzhao , Jin Cheng
Published: February 2024

Hepatocellular carcinoma (HCC) exhibits a high mortality rate due to its high invasion and metastatic nature, and the acidic microenvironment plays a pivotal role. Acid-sensing ion channel 1 (ASIC1) is upregulated in HCC tissues and facilitates tumor progression in a pH-dependent manner, while the specific mechanisms therein remain currently unclear. Herein, we aimed to investigate the underlying mechanisms by which ASIC1 contributes to the development of HCC. Using bioinformatics analysis, we found a significant association between ASIC1 expression and malignant transformation of HCC, such as poor prognosis, metastasis and recurrence. Specifically, ASIC1 enhanced the migration and invasion capabilities of Li-7 cells in the in vivo experiment using an HCC lung metastasis mouse model, as well as in the in vitro experiments such as wound healing assay and Transwell assay. Furthermore, our comprehensive gene chip and molecular biology experiments revealed that ASIC1 promoted HCC migration and invasion by activating the PRKACA/AP-1 signaling pathway. Our findings indicate that targeting ASIC1 could have therapeutic potential for inhibiting HCC progression.
Participant Diversity in United States Randomized Controlled Trials of Antibacterials for Staphylococcus aureus Infections, 2000–2021
Authors: Kwon Jiye , Pelletiers William , Galloway Peña Jessica , van Duin David , Ledbetter Leila , Baum Keri , Ruffin Felicia , Knisely Jane M , Bizzell Erica , Fowler Vance G , Chambers Henry F , Pettigrew Melinda M
Published: February 2024

Background

Equitable representation of members from historically marginalized groups is important in clinical trials, which inform standards of care. The goal of this study was to characterize the demographics and proportional subgroup reporting and representation of participants enrolled in randomized controlled trials (RCTs) of antibacterials used to treat Staphylococcus aureus infections.

Methods

We examined randomized controlled registrational and strategy trials published from 2000 to 2021 to determine the sex, race, and ethnicity of participants. Participant to incidence ratios (PIRs) were calculated by dividing the percentage of study participants in each demographic group by the percentage of the disease population in each group. Underrepresentation was defined as a PIR < 0.8.

Results

Of the 87 included studies, 82 (94.2%) reported participant sex, 69 (79.3%) reported participant race, and 20 (23.0%) included ethnicity data. Only 17 (19.5%) studies enrolled American Indian/Alaskan Native participants. Median PIRs indicated that Asian and Black participants were underrepresented in RCTs compared with the incidence of methicillin-resistant S. aureus infections in these subgroups. Underrepresentation of Black participants was associated with a larger study size, international sites, industry sponsorship, and phase 2/3 trials compared with phase 4 trials (P < .05 for each). Black participants had more than 4 times the odds of being underrepresented in phase 2/3 trials compared with phase 4 trials (odds ratio, 4.57; 95% confidence interval: 1.14–18.3).

Conclusions

Standardized reporting methods for race and ethnicity and efforts to increase recruitment of marginalized groups would help ensure equity, rigor, and generalizability in RCTs of antibacterial agents and reduce health inequities.