bluuebunny/crossref_metadata_2025_split huggingface dataset:
Exploring current conduction dynamics in multiferroic BiFeO3 thin films prepared via modified chemical solution method
Authors: Wani Waseem Ahmad , Venkataraman Harihara , Ramaswamy Kannan 
Published: October 2024

AbstractThe current study describes current conduction mechanisms in BiFeO3 thin films prepared by using a modified chemical solution-based technique. In particular, in these films, X-ray photoelectron spectroscopy revealed that the defect causing Fe2+ ions reduced by about 18% compared to the solution-based synthesis methods reported before, indicating better film quality. The leakage current density was measured to be 1.7 × 10–6 A/cm2 at an applied voltage of 1.5 V, which is one order of magnitude less than the previously reported work in a similar system. Oxygen annealing was found to be effective in further reducing the current conduction, making these films a suitable choice for device applications. The current–voltage curves exhibited three different behaviours of current conduction mechanisms in these films. In particular, when the applied electric field was increased, a transition from Ohmic conduction to trap-filled space charge limited conduction was observed. The presented investigations demonstrate the importance of deposition methods in determining the suitability of thin films for device applications.
18-Years of single-centre DNA testing in over 7000 index cases with inherited retinal dystrophies and optic neuropathies
Authors: Kiel Christina , Biasella Fabiola , Stöhr Heidi , Rating Philipp , Spital Georg , Kellner Ulrich , Hufendiek Karsten , Huchzermeyer Cord , Jaegle Herbert , Ruether Klaus , Weber Bernhard H. F. 
Published: October 2024

AbstractInherited retinal dystrophies (IRDs) and inherited optic neuropathies (IONs) are characterized by distinct genetic causes and molecular mechanisms that can lead to varying degrees of visual impairment. The discovery of pathogenic variants in numerous genes associated with these conditions has deepened our understanding of the molecular pathways that influence both vision and disease manifestation and may ultimately lead to novel therapeutic approaches. Over the past 18 years, our DNA diagnostics unit has been performing genetic testing on patients suspected of having IRD or ION, using state-of-the-art mutation detection technologies that are continuously updated. This report presents a retrospective analysis of genetic data from 6237 IRD and 780 ION patients. Out of these, 3054 IRD patients (49.0%) and 211 ION patients (27.1%) received a definitive molecular diagnosis, with disease-causing variants identified in 139 different genes. The genes most implicated in disease pathologies are ABCA4, accounting for 23.8% of all IRD/ION index cases, followed by BEST1 (7.8%), USH2A (6.2%), PRPH2 (5.7%), RPGR (5.6%), RS1 (5.5%), OPA1 (4.3%), and RHO (3.1%). Our study has compiled the most extensive dataset in combined IRD/ION diagnostics to date and offers valuable insights into the frequencies of mutant alleles and the efficiency of mutation detection in various inherited retinal conditions.
Successful non-invasive imaging of the coronary artery IMT in pediatric patients with Kawasaki disease using high-resolution echocardiography
Authors: Gerling Stephan , Dalla-Pozza Robert , Michel Holger , Jakob André , Melter Michael , Dechant Markus Johannes 
Published: October 2024

AbstractKawasaki Disease (KD) is a multisystemic vasculitis of medium- and small-sized arteries. Abnormal intimal thickening may develop in the involved arterial area after regression of coronary artery aneurysm (CAA). Intimal dysfunction may induce local stenosis or arteriosclerosis in the future. In this case–control study, we investigated 29 consecutive KD patients [20 male, median current age, 7.9 years; median follow-up duration, 5.7 years] and a group of 29 healthy matched controls (CON) [19 male, median current age, 10.8 years]. They were assesed and compared for CAA, LVFS, GCS, GLS, coronary artery (CA) Z scores, carotid intima-media thickness (IMT) and coronary artery IMT by high-resolution transthoracic echocardiography (hrTTE). Coronary artery IMT (caIMT) was significantly higher in patients with a maximal CA Z score > 2.5 in acute KD than in CON: KD caIMT: 0.62 mm [IQR, 0.57–0.72 mm] vs. 0.53 mm [0.51–0.60 mm], p = 0.043. CAAs were found in 15 (51.7%) patients with acute KD. The maximal median LCA Z score in acute KD was 2.57z [IQR, 1.93—3.2z] and in follow-up −0.39z [IQR, −1.25 to −0.36z]. There was no significant difference in carotid IMT between KD patients and CON. Signs of CA intima-media thickening were detected by hrTTE in patients with a maximal CA Z score > 2.5 in acute KD. These data indicate that these patients may be at risk for cardiovascular sequale even in the absence of permanent CA luminal abnormalities. Therefore long-term follow-up of this group of KD patients may be required.
Double exchange interaction in Mn-based topological kagome ferrimagnet
Authors: Wang Jiameng , Ernst Arthur , Antonov Victor N. , Jiang Qi , Qian Haoji , Wang Deyang , Cao Jiefeng , Zhu Fangyuan , Qiao Shan , Ye Mao 
Published: October 2024

AbstractRecently discovered Mn-based kagome materials, such as RMn6Sn6 (R = rare-earth element), exhibit the coexistence of topological electronic states and long-range magnetic order, offering a platform for studying quantum phenomena. However, understanding the electronic and magnetic properties of these materials remains incomplete. Here, we investigate the electronic structure and magnetic properties of GdMn6Sn6 using x-ray magnetic circular dichroism, photoemission spectroscopy, and theoretical calculations. We observe localized electronic states from spin frustration in the Mn-based kagome lattice and induced magnetic moments in the nonmagnetic element Sn experimentally, which originate from the Sn-$$p$$
p
and Mn-$$d$$
d
orbital hybridization. Our calculations also reveal ferromagnetic coupling within the kagome Mn-Mn layer, driven by double exchange interaction. This work provides insights into the mechanisms of magnetic interaction and magnetic tuning in the exploration of topological quantum materials.
Social threat avoidance depends on action-outcome predictability
Authors: Sequestro Matteo , Serfaty Jade , Grèzes Julie , Mennella Rocco 
Published: October 2024

AbstractAvoiding threatening individuals is pivotal for adaptation to our social environment. Yet, it remains unclear whether social threat avoidance is subtended by goal-directed processes, in addition to stimulus-response associations. To test this, we manipulated outcome predictability during spontaneous approach/avoidance decisions from avatars displaying angry facial expressions. Across three virtual reality experiments, we showed that participants avoided more often when they could predict the outcome of their actions, indicating goal-directed processes. However, above-chance avoidance rate when facing unpredictable outcomes suggested that stimulus-response associations also played a role. We identified two latent classes of participants: the “goal-directed class” showed above-chance avoidance only in the predictable condition, while the “stimulus-response class” showed no credible difference between conditions but had a higher overall avoidance rate. The goal-directed class exhibited greater cardiac deceleration in the predictable condition, associated with better value integration in decision-making. Computationally, this class had an increased drift-rate in the predictable condition, reflecting increased value estimation of threat avoidance. In contrast, the stimulus-response class showed higher responsiveness to threat, indicated by increased drift-rate for avoidance and increased muscular activity at response time. These results support the central role of goal-directed processes in social threat avoidance and reveal its physiological and computational correlates.
Normal‐mode planar meander‐line antenna array with bidirectional broadside radiation pattern
Authors: Liu Meicheng , Jin Peiqi , Hou Yuefeng 
Published: October 2024

AbstractIn this letter, a normal‐mode planar bidirectional broadside antenna array with the merits of high gain, broadband, low aerodynamic drag, and high assembly robustness is proposed. First, the bidirectional antenna array is implemented based on a novel design strategy. The expected radiation field generated by currents along the same direction is superimposed while the unexpected radiation field is offset due to the out‐of‐phase currents, achieving a normal‐mode high‐gain bidirectional pattern. Then, the bidirectional antenna array is designed with two metallic meander lines, featuring low aerodynamic drag and cost‐efficiency. Moreover, a simple feed structure using an impedance transformer parallel strip line is adopted for a wide bandwidth. Besides, the bidirectional antenna array exhibits a stable impedance when the array scale increases. The stable impedance is also observed when the antenna array is bent to different angles, ensuring ease of installation and high assembly robustness. To validate the design strategy, a prototype with an aperture length of 5.8λ at 2.4 GHz is fabricated. The proposed antenna array is designed to operate from 2.2 to 2.6 GHz, with a maximum gain of 13 dBi around the center of frequency, which can be a promising candidate in long and narrow communication scenarios.
Computational hermeneutics of emotion: a comparative study of emotional landscapes in the Dostoevsky’s novel “Crime and Punishment”
Authors: Picca Davide , Schnyder Antonin , Romele Alberto 
Published: October 2024

AbstractThis study employs computational hermeneutics to explore emotional representations in Fyodor Dostoevsky’sCrime and Punishment. Using advanced Natural Language Processing (NLP) techniques, including sentiment analysis powered by the BERT model and other tools, we examine the emotional and existential aspects embedded in the narrative. Our approach combines computational tools with traditional hermeneutic methods to deconstruct the emotional journey of the protagonist, Rodion Raskolnikov. We quantitatively analyze his emotional evolution before and after the pivotal crime, mapping his psychological transition from detachment to engagement. The study focuses on four key emotional dimensions: Attitude, Introspection, Sensitivity, and Temper. By transforming qualitative textual data into a quantitative framework, we provide a novel illustration of Raskolnikov’s psychological progression from a state of depersonalization to full emotional contact. This computational analysis is contextualized within a broader philosophical interpretation, drawing on concepts such as Stoicapatheiaand HeideggerianSorge. Our research serves a dual purpose: it enhances our understanding of Dostoevsky’s work while demonstrating the potential of computational methods in literary analysis. By bridging digital humanities and traditional literary criticism, this study contributes to the growing field of digital hermeneutics and opens new avenues for interdisciplinary research in literature, philosophy, and computational linguistics.
Envelope Inversion with Source encoding for Ultrasound Computed Tomography
Authors: Zhang Nuomin , Zhou Naixin , Yuan Yu , Shen Yi , Zhao Yue 
Published: October 2024

Abstract
Ultrasound computed tomography (USCT) is a noninvasive and non-ionizing imaging technique for soft tissue and limb bones. Full waveform inversion (FWI) has received increased interest due to its high resolution. The difficulties in FWI are twofold: high computational burden and poor convergence. To address these issues, an envelope inversion with source coding (EI-SE) algorithm is proposed in this paper. The envelope-based objective function measures the matching degree between the predicted and measured envelopes. It can provide the low-frequency components of the signal that are not available to FWI. Therefore, the EI can provide an accurate solution even when the initial model is far from the ground truth and low-frequency data are missing. The simulations are conducted to demonstrate the validity of the proposed algorithm. The root mean squared error (RMSE) of the proposed algorithm is much smaller than that of conventional FWI. The results show that EI-SE is effective in avoiding cycle skipping.
Comparison between experimental and numerical results for piezoelectric signals generated in water-saturated cancellous bone by ultrasound irradiation
Authors: Hosokawa A 
Published: October 2024

Abstract
The bone formation is considered to be accompanied by the piezoelectric effects in bone. Therefore, the piezoelectric effect under ultrasound irradiation should be elucidated to realize the effective healing. Then, the piezoelectric properties in cancellous bone have been attempted to clarify by complementing experiments and simulations with each other. In this paper, the piezoelectric signals generated in water-saturated cancellous bone by ultrasound irradiation were experimentally and numerically observed, and the effect of the trabecular orientation was investigated. The experimental observation was performed by the piezoelectric cell (PE-cell), which corresponds to an ultrasound receiver using the cancellous bone specimen as a piezoelectric element. The numerical observation was performed by the piezoelectric finite-difference time-domain (PE-FDTD) method, which is an elastic FDTD method with piezoelectric constitutive equations. In both the experimental and simulated results, the piezoelectric signal amplitude increased with the mean intercept lengths (MILs) of the trabecular elements and the pore spaces or the strength of the trabecular orientation. From the fact that the ultrasound propagation in water-saturated cancellous bone can depend on the trabecular orientation, it was considered that the ultrasound properties could be largely associated with the piezoelectric properties.
Investigation on the fatigue properties of adhesives for acoustic transducers in deep logging wells
Authors: Wei Qian , Liu Bin , Cong Jiansheng 
Published: October 2024

Abstract
Deep well exploration of oil and gas resources requires acoustic transducers that can withstand temperatures above 200 degrees. It is particularly important to overcome the key technology of high-temperature dipole transmitters. The bonding strength of the dipole transmitters with a tri-laminar structure is studied numerically and experimentally. Transducers were prepared using structural adhesives. The aging and fatigue test is conducted at a high temperature of 200 degrees. The aging lasted for 15 hours and the strong electric field fatigue cycle number reached up to 36000. The conductivity curve remains almost unchanged after the high-temperature test. The work provides an application basis for deep acoustic logging technology.
Theoretical analysis of the dimensionality of ultrasonic attenuation in polycrystalline materials with elongated grains
Authors: Victoria Giraldo Juan Camilo , Tie Bing , Laurent Jérôme , Lhémery Alain , Solas Denis 
Published: October 2024

Abstract
In the present work, the grain scattering-induced attenuation coefficient is obtained for longitudinal bulk waves in untextured cubic polycrystalline materials with elongated grains using proposed 2D and 3D theoretical models. These models are obtained based on previously developed 2D and 3D models for equiaxed grains. Comparison of the 2D and 3D models allows an analysis of the dimensionality of grain scattering-induced attenuation, which involves more complex mechanisms with elongated grains. In the higher stochastic scattering regime, both 3D and 2D longitudinal attenuations are found to be dependent on the grain size parallel to the wave propagation. In the Rayleigh scattering regime the 3D attenuation is volume dependent and in contrast, the 2D longitudinal attenuation is found to be cross-section dependent and is therefore helpful for identifying the 3D grain shape/rotation.
Signal de-noising based on ICEEMDAN for delamination detection by phased array ultrasonic testing
Authors: Zhang PH , Ma SW , Huang KH , Pan YD 
Published: October 2024

Abstract
Aiming at the problem of clutter noise of inter-layer reflections that occurs in multilayer heterogeneous medium such as hybrid fibre composites during ultrasonic inspection, a signal de-noising method based on the improved complete ensemble empirical mode decomposition with adaptive noise (ICEEMDAN) is proposed in this paper. In the method, the cross-correlation coefficient is utilized to identify the intrinsic mode function (IMF) that is related to raw ultrasonic signal. Particularly, the root mean square error (RMSE), as selection criterions, are employed conjunctively to sift the optimal IMF among selected decomposition signals. Hilbert transform is used to extract the envelope of the signal after removing the interlayer reflection noise. Experimental results show that, the proposed method can adaptively decompose the non-stationary ultrasonic signal into several IMFs with different spectrum so as to dealing with clutter noises. For delaminate detection by phased array ultrasonic testing for hybrid fibre composites, structural noises are significantly suppressed in the reconstructed signal that retains the distinct echo characteristics of a delaminated defect.
TLR4 promotes smooth muscle cell-derived foam cells formation by inducing receptor-independent macropinocytosis
Authors: Chen Xue , Kang Yulai , Tang Chunhua , Zhang Lili , Guo Lu 
Published: October 2024

Abstract
Foam cells are primarily formed through scavenger receptors that mediate the uptake of various modified low-density lipoproteins (LDL) into cells. In addition to the receptor-dependent pathway, macropinocytosis is an essential nonreceptor endocytic pathway for vascular smooth muscle cells (VSMCs) to take up lipids. However, the molecular mechanisms underlying this process remain unclear. Primary cultured VSMCs were stimulated with 200 ng/mL lipopolysaccharide (LPS) and 200 µg/mL native LDL (nLDL). We observed a significant increase in Toll-like receptor 4 (TLR4) protein expression and a significant activation of macropinocytosis, which correlated with the highest uptake of nLDL and intracellular lipid deposition in WT VSMCs. However, macropinocytosis was inhibited and lipid accumulation decreased after treatment with macropinocytosis inhibitors and Syk inhibitors in WT VSMCs. Consistently, TLR4 knockout significantly suppressed macropinocytosis and lipid droplets accumulation in VSMCs. Taken together, our findings suggest a critical role of TLR4/Syk signaling in promoting receptor-independent macropinocytosis leading to VSMC-derived foam cells formation.
Urban sensory conditions alter rival interactions and mate choice in urban and forest túngara frogs
Authors: Smit Judith A H , Thijssen Vera , Cronin Andrew D , Ellers Jacintha , Halfwerk Wouter 
Published: October 2024

Abstract
Sexual communication often takes place in networks with multiple competing signalers being simultaneously assessed by mate choosers. Altered sensory conditions, such as noise and light pollution, can affect communication by altering signal production and perception. While evidence of sensory pollution affecting sexual signaling is widespread, few studies assess impacts on sexual signaling during rival interactions as well as mate choice, let alone whether urban and non-urban populations have diverged in their response. Here, we investigate the effects of urban sensory conditions on sexual communication in urban and forest túngara frogs (Engystomops pustulosus). We recorded dyadic vocal rival interactions and assessed mate choice with and without noise and light pollution in the lab. We show that urban sensory conditions can directly impact the intensity of rival interactions, differences between rivals, and mate choice, though changes were often in opposite directions for frogs of urban and forest origins. Moreover, we demonstrate that urban-induced changes in rival interactions can also indirectly affect how females choose between potential mates. Our study reveals origin-dependent direct and indirect effects of noise and light pollution and suggests local adaptation of sexual communication in urban populations.
arcMS: transformation of multi-dimensional high-resolution mass spectrometry data to columnar format for compact storage and fast access
Authors: Le Roux Julien , Sade Julien 
Published: October 2024

Abstract

Summary
The arcMS R package addresses the challenges posed by proprietary and open-source high-resolution mass spectrometry data formats by providing functions to collect MSE data from the Waters UNIFI software and store it in the efficient Apache Parquet format, facilitating fast, easy access, and compatibility with various programming environments. This solution facilitates the manipulation of complex mass spectrometry data, including ion mobility or other additional dimensions, enabling potential integration into efficient and open-source workflows.

Availability and implementation
arcMS is an open-source R package and is available on GitHub at https://github.com/leesulab/arcMS. The complete documentation, including details on UNIFI configuration and tutorials for data conversion, access to Parquet files, and filtration of data, is available at https://leesulab.github.io/arcMS. An R/Shiny companion application is also provided for visualization of Parquet data and demonstration of data filtering with the Arrow library https://github.com/leesulab/arcms-dataviz.
Addressing the antibody germline bias and its effect on language models for improved antibody design
Authors: Olsen Tobias H , Moal Iain H , Deane Charlotte M 
Published: October 2024

Abstract

Motivation
The versatile binding properties of antibodies have made them an extremely important class of biotherapeutics. However, therapeutic antibody development is a complex, expensive, and time-consuming task, with the final antibody needing to not only have strong and specific binding but also be minimally impacted by developability issues. The success of transformer-based language models in protein sequence space and the availability of vast amounts of antibody sequences, has led to the development of many antibody-specific language models to help guide antibody design. Antibody diversity primarily arises from V(D)J recombination, mutations within the CDRs, and/or from a few nongermline mutations outside the CDRs. Consequently, a significant portion of the variable domain of all natural antibody sequences remains germline. This affects the pre-training of antibody-specific language models, where this facet of the sequence data introduces a prevailing bias toward germline residues. This poses a challenge, as mutations away from the germline are often vital for generating specific and potent binding to a target, meaning that language models need be able to suggest key mutations away from germline.

Results
In this study, we explore the implications of the germline bias, examining its impact on both general-protein and antibody-specific language models. We develop and train a series of new antibody-specific language models optimized for predicting nongermline residues. We then compare our final model, AbLang-2, with current models and show how it suggests a diverse set of valid mutations with high cumulative probability.

Availability and implementation
AbLang-2 is trained on both unpaired and paired data, and is freely available at https://github.com/oxpig/AbLang2.git.