bluuebunny/crossref_metadata_2025 huggingface dataset:
Histone variant H3.5 in testicular cell differentiation and its interactions with histone chaperones
Authors: Weil Patrick Philipp , Pembaur Anton , Wirth Beatrice , Oetjen Eda , Büsscher Hannes , Zirngibl Klemens , Czarnetzki Malte , Braun Stella , Cremers Jann-Frederik , Gödde Daniel , Degener Stephan , Postberg Jan
Published: December 2024

Testicular cell differentiation is a highly regulated process, essential for male reproductive health. The histone variant H3.5 is apparently a critical player in this intricate orchestra of cell types, but its regulation and function remains poorly understood. To elucidate its role, we fractionized testicular cells using c-Kit/CD117 as a separation marker and analyzed H3.5 expression. Further, we investigated the regulation of H3.5 expression using public data repositories. We explored DNA methylation patterns in specific regions of the H3-5 gene and assessed H3-5 copy number gain in seminoma specimens. Additionally, we examined the testicular localization of H3.5 and its histone chaperone interactions to understand its regulation at the protein level. We used qRT-PCR, MeDIP, and qPCR to study H3.5 expression and DNA methylation in various cell types. H3-5 copy number gain was analyzed using qPCR. Protein interactions were investigated through fluorescence-2-hybrid assays in baby hamster kidney cells. H3.5 is primarily enriched in spermatocytes. DNA methylation of a CpG island overlapping the H3-5 promoter appeared to be involved in the tissue-specific regulation of H3.5 expression. Elevated H3.5 expression was observed in seminoma specimens, suggesting a potential link to testicular tumors. H3-5 copy number gain was associated with elevated H3.5 expression in seminoma specimens. Furthermore, we identified physical interactions between H3.5 and histone chaperones Asf1a and Asf1b, HIRA, CAF p150 and DAXX, shedding light on the protein-level regulation of H3.5. These findings provide valuable insights into the molecular mechanisms governing testicular cell differentiation and the potential role of H3.5 in testicular pathologies.
Geometric deep learning improves generalizability of MHC-bound peptide predictions
Authors: Marzella Dario F. , Crocioni Giulia , Radusinović Tadija , Lepikhov Daniil , Severin Heleen , Bodor Dani L. , Rademaker Daniel T. , Lin ChiaYu , Georgievska Sonja , Renaud Nicolas , Kessler Amy L. , Lopez-Tarifa Pablo , Buschow Sonja I. , Bekkers Erik , Xue Li C.
Published: December 2024

The interaction between peptides and major histocompatibility complex (MHC) molecules is pivotal in autoimmunity, pathogen recognition and tumor immunity. Recent advances in cancer immunotherapies demand for more accurate computational prediction of MHC-bound peptides. We address the generalizability challenge of MHC-bound peptide predictions, revealing limitations in current sequence-based approaches. Our structure-based methods leveraging geometric deep learning (GDL) demonstrate promising improvement in generalizability across unseen MHC alleles. Further, we tackle data efficiency by introducing a self-supervised learning approach on structures (3D-SSL). Without being exposed to any binding affinity data, our 3D-SSL outperforms sequence-based methods trained on ~90 times more data points. Finally, we demonstrate the resilience of structure-based GDL methods to biases in binding data on an Hepatitis B virus vaccine immunopeptidomics case study. This proof-of-concept study highlights structure-based methods’ potential to enhance generalizability and data efficiency, with possible implications for data-intensive fields like T-cell receptor specificity predictions.
Proteomic and metabolomic analyses of the human adult myocardium reveal ventricle-specific regulation in end-stage cardiomyopathies
Authors: Hunter Benjamin , Li Mengbo , Parker Benjamin L. , Koay Yen Chin , Harney Dylan J. , Pearson Evangeline , Cao Jacob , Chen Gavin T. , Guneratne Oneka , Smyth Gordon K. , Larance Mark , O’Sullivan John F. , Lal Sean
Published: December 2024

The left and right ventricles of the human heart are functionally and developmentally distinct such that genetic or acquired insults can cause dysfunction in one or both ventricles resulting in heart failure. To better understand ventricle-specific molecular changes influencing heart failure development, we first performed unbiased quantitative mass spectrometry on pre-mortem non-diseased human myocardium to compare the metabolome and proteome between the normal left and right ventricles. Constituents of gluconeogenesis, glycolysis, lipogenesis, lipolysis, fatty acid catabolism, the citrate cycle and oxidative phosphorylation were down-regulated in the left ventricle, while glycogenesis, pyruvate and ketone metabolism were up-regulated. Inter-ventricular significance of these metabolic pathways was then found to be diminished within end-stage dilated cardiomyopathy and ischaemic cardiomyopathy, while heart failure-associated pathways were increased in the left ventricle relative to the right within ischaemic cardiomyopathy, such as fluid sheer-stress, increased glutamine-glutamate ratio, and down-regulation of contractile proteins, indicating a left ventricular pathological bias.
Structural insights into the enzymatic breakdown of azomycin-derived antibiotics by 2-nitroimdazole hydrolase (NnhA)
Authors: Ahmed F. Hafna , Liu Jian-Wei , Royan Santana , Warden Andrew C. , Esquirol Lygie , Pandey Gunjan , Newman Janet , Scott Colin , Peat Thomas S.
Published: December 2024

The antibiotic 2-nitroimidazole (2NI) or azomycin, used for treating drug-resistant tuberculosis and imaging tumor hypoxia, requires activation by bacterial nitroreductases for its antibiotic and cytotoxic effect. Mycobacterium sp. JS330 produces 2-nitroimidazole nitrohydrolase (NnhA) that circumvents 2NI activation, conferring 2NI resistance by hydrolysing it to nitrite and imidazol-2-one (IM2O) instead. This study elucidates NnhA’s structure, catalytic mechanism, and evolutionary background within the guanidino-group modifying enzyme (GME) superfamily, aided by a more soluble protein variant engineered through directed evolution. Despite low sequence similarity and limited occurrence in a few soil-dwelling mycobacteria and Actinomycetota, NnhA maintains the α/β propeller fold characteristic of GME superfamily enzymes and forms an unusual hexameric ring structure formed by a trimer of domain-swapped dimers. The similarity of its active site to arginine deiminases (ADIs) and human dimethylarginine dimethylaminohydrolases (DDAHs), along with molecular dynamics simulations, suggests NnhA’s catalytic mechanism resembles the hydrolysis reactions of these related enzymes.
Flexibility of intrinsic neural timescales during distinct behavioral states
Authors: Çatal Yasir , Keskin Kaan , Wolman Angelika , Klar Philipp , Smith David , Northoff Georg
Published: December 2024

Recent neuroimaging studies demonstrate a heterogeneity of timescales prevalent in the brain’s ongoing spontaneous activity, labeled intrinsic neural timescales (INT). At the same time, neural timescales also reflect stimulus- or task-related activity. The relationship of the INT during the brain’s spontaneous activity with their involvement in task states including behavior remains unclear. To address this question, we combined calcium imaging data of spontaneously behaving mice and human electroencephalography (EEG) during rest and task states with computational modeling. We obtained four primary findings: (i) the distinct behavioral states can be accurately predicted from INT, (ii) INT become longer during behavioral states compared to rest, (iii) INT change from rest to task is correlated negatively with the variability of INT during rest, (iv) neural mass modeling shows a key role of recurrent connections in mediating the rest-task change of INT. Extending current findings, our results show the dynamic nature of the brain’s INT in reflecting continuous behavior through their flexible rest-task modulation possibly mediated by recurrent connections.
Enhanced Weyl semimetal signature in Co3Sn2S2 Kagome ferromagnet by chlorine doping
Authors: He Bin , Yao Mengyu , Pan Yu , Arpino Kathryn E. , Chen Dong , Serrano-Sanchez Federico M. , Ju Sailong , Shi Ming , Sun Yan , Felser Claudia
Published: December 2024

Weyl fermions are chiral massless fermions with exotic properties. In the first established magnetic Weyl semimetal, Co3Sn2S2, a giant anomalous Hall effect has been observed, while its Fermi energy remaining 60 meV from the Weyl points. Shifting the Fermi energy closer to the Weyl points may assist in the identification of Weyl Fermion related transport signatures. Here we show that effective chlorine doping has resulted in a shift of the Fermi energy by 15 meV towards the Weyl points, which is confirmed by a combination of the systematic angular-resolved photoemission spectroscopy measurements and density function theory calculations. A five-fold reduction in resistivity is observed in the ferromagnetic phase, accompanied by a pronounced magnetoresistance of over 150%. The anomalous Hall conductivity shows a peak of 1680 Scm−1 at 40 K, which is 30% higher than the undoped sample due to a stronger Weyl point contribution. This work demonstrates the essential role of doping in Co3Sn2S2 for an enhanced Weyl semimetal signature.
Cu-MOF-based targeted nanomedicine utilizing biorthogonally catalyzed chemotherapy and chemodynamic therapy with spatiotemporal orchestration to treat hepatocellular carcinoma
Authors: Wan Xiuyan , Zhang Yu , Zhang Huiwen , Pan Wei , Qiao Xincheng , Li Na , Tang Bo
Published: December 2024

A targeted nanomedicine based on a Cu-MOF was developed to treat hepatocellular carcinoma utilizing biorthogonally catalyzed chemotherapy and chemodynamic therapy, which significantly suppresses tumor growth with minimum toxicity.
Correction: Elucidation of the mechanism of the esterification of boric acid with aliphatic diols: a computational study to help set the record straight
Authors: Bacchiocchi Corrado , Petroselli Manuel
Published: December 2024

Correction for ‘Elucidation of the mechanism of the esterification of boric acid with aliphatic diols: a computational study to help set the record straight’ by Corrado Bacchiocchi et al., Chem. Commun., 2024, 60, 13239–13242, https://doi.org/10.1039/d4cc02999b.
Catalysis under electric-/magnetic-/electromagnetic-field coupling
Authors: Hu Canyu , Dong Yueyue , Shi Qianqi , Long Ran , Xiong Yujie
Published: December 2024

This review outlines recent advances in field-regulated catalysis and reveals the key role of dipole manipulation by electric/magnetic/electromagnetic fields.
CO2 and asymmetry: reviewing the advances in enantioselective catalytic strategies
Authors: Ghosh Debashis , Dabas Shilpa , Kalose Sushma A. , Gotgi Nandini M. , Subramanian Saravanan
Published: December 2024

This review systematically discusses the last two-decade advances in asymmetric CO2 fixation including chemical, electrochemical and photochemical pathways.
The investigation of early metabolic level perturbation of northern quahog (Mercenaria mercenaria) in response to brevetoxin
Authors: Wang Bo , McKenna Nicole , Pollak Julie , Mayonu Moses , Jiang Lin
Published: December 2024

NMR metabolomics was applied to M. mercenaria exposed to a series of sublethal doses of Brevetoxins for the targeted metabolic pathway and early marker discovery.
Ball-milling and piezoelectric materials enabled radical trifluoromethylation of enamides and acrylamides
Authors: Solomin Vitalii , Liard Matthias , Jubault Philippe , Castanheiro Thomas
Published: December 2024

A sustainable solid-state direct radical C(sp2)–H trifluoromethylation of enamide derivatives was developed by merging ball-milling with a stoichiometric amount of piezoelectric materials. Acrylamide were suitable substrates in this transformation.
Numerical evaluation of bi-facial ZnO/MoTe2 photovoltaic solar cells with N-doped Cu2O as the BSF layer for enhancing VOCvia device simulation
Authors: Rajib Arifuzzaman , Chandra Saha Tapos , Rahman Md. Mustafizur , Sarker Hridoy , Dhali Ruddro , Hossain Sumon Md. Sabbir , Rahman Atowar
Published: December 2024

Molybdenum telluride (MoTe2) shows great promise as a solar absorber material for photovoltaic (PV) cells owing to its wide absorption range, adjustable bandgap, and lack of dangling bonds at the surface.
Straight-chain thiols as chemical kinetic transporters accelerate Li2S 3D nucleation
Authors: Han Wenchang , Hou Jiyue , Zhang Bao , Wang Yongqi , Yang Chunman , Ai Wengxiang , Wang Qian , Zhang Enfeng , Dong Peng , Zhang Yiyong , Zhang Yingjie , Zhang Yannan
Published: December 2024

1,8-OT is proposed as a chemical power transmitter to accelerate polysulfide conversion and control Li2S 3D nucleation through chemical catalysis. Ultimately, electrode passivation was suppressed and excellent cycling stability was achieved in LSBs.
Exploring the influence of anionic lipids in the host cell membrane on viral fusion
Authors: Birtles Daniel , Lee Jinwoo
Published: December 2024

Membrane fusion is an essential component of the viral lifecycle that allows the delivery of the genetic information of the virus into the host cell. Specialized viral glycoproteins exist on the surface of mature virions where they facilitate fusion through significant conformational changes, ultimately bringing opposing membranes into proximity until they eventually coalesce. This process can be positively influenced by a number of specific cellular factors such as pH, enzymatic cleavage, divalent ions, and the composition of the host cell membrane. In this review, we have summarized how anionic lipids have come to be involved in viral fusion and how the endosomal resident anionic lipid BMP has become increasingly implicated as an important cofactor for those viruses that fuse via the endocytic pathway.
UV processing of icy pebbles in the outer parts of VSI-turbulent disks
Authors: Flores-Rivera Lizxandra , Lambrechts Michiel , Gavino Sacha , Lorek Sebastian , Flock Mario , Johansen Anders , Mignone Andrea
Published: December 2024

Icy dust particles emerge in star-forming clouds and are subsequently incorporated in protoplanetary disks, where they coagulate into larger pebbles up to millimeter in size. In the disk midplane, ices are shielded from UV radiation, but moderate levels of disk turbulence can lift small particles to the disk surface, where they can be altered, or destroyed. Nevertheless, studies of comets and meteorites generally find that ices at least partly retain their interstellar medium (ISM) composition before being accreted onto these minor bodies. We modeled this process through hydrodynamical simulations with vertical shear instability (VSI) driven turbulence in the outer protoplanetary disk. We used the PLUTO code in a 2.5 D global accretion setup and included Lagrangian dust particles of 0.1 and 1 mm sizes. In a post-processing step, we used the RADMC3D code to generate the local UV radiation field to assess the level of ice processing of pebbles. We find that a small fraction (∼17%) of 100 µm size particles are frequently lifted up to Z/R = 0.2, which can result in the loss of their pristine composition as their residence time in this layer allow effective CO and water photodissociation. The larger 1 mm size particles remain UV-shielded in the disk midplane throughout the dynamical evolution of the disk. Our results indicate that the assembly of icy bodies via the accretion of drifting millimeter-sized icy pebbles can explain the presence of pristine ice from the ISM, even in VSI-turbulent disks. Nevertheless, particles ≤100 µm experience efficient UV processing and may mix with unaltered icy pebbles, resulting in a less ISM-like composition in the midplane.
Inelastic H + H3+ collision rates and their impact on the determination of the excitation temperature of H3+
Authors: Félix-González Daniel , del Mazo-Sevillano Pablo , Aguado Alfredo , Roncero Octavio , Le Bourlot Jacques , Roueff Evelyne , Le Petit Franck , Bron Emeric
Published: December 2024

Context. In diffuse interstellar clouds, the excitation temperature derived from the lowest levels of H3+ is systematically lower than that derived from H2. The differences may be attributed to the lack of state-specific formation and destruction rates of H3+, which are needed to thermalize the two species.

Aims. In this work, we aim to investigate the possible influence of rotational excitation collisions of H3+ with atomic hydrogen on its excitation temperature.

Methods. We used a time-independent close-coupling method to calculate the state-to-state rate coefficients, incorporating a very accurate and full-dimensional potential energy surface recently developed for H4+. We take a symmetric top approach to describe a frozen H3+ as an equilateral triangle.

Results. We derive rotational excitation collision rate coefficients of H3+ with atomic hydrogen in a temperature range corresponding to diffuse interstellar conditions up to (J, K, ±) = (7, 6, +) and (J, K, ±) = (6, 4, +) for its ortho and para forms. This allows us to obtain a consistent set of collisional excitation rate coefficients and to improve on a previous study that included speculations regarding these contributions.

Conclusions. The new state-specific inelastic H3+ + H rate coefficients yield differences of up to 20% in the excitation temperature, and their impact increases with decreasing molecular fraction. We also confirm the impact of chemical state-to-state destruction reactions on the excitation balance of H3+, and that reactive H + H3+ collisions are also needed to account for possible further ortho to para transitions.
Evaluation of irritable bowel syndrome in patients with systemic
sclerosis based on Rome IV criteria
Authors: Tuncel Elif Tugba , Sahinoglu Irem , Uslu Sadettin
Published: December 2024

Objectives The gastrointestinal system is the second most frequently
affected organ system in patients with systemic sclerosis (SSc). Patients with
SSc experience gastrointestinal dysmotility due to pathophysiological changes,
including alterations in intestinal microbiota, inflammation, fibrosis, vascular
ischaemia, and muscle atrophy. The aim of this study was to determine the
prevalence of functional gastrointestinal disorders in patients with SSc.

Material and Methods This study included 66 patients with SSc. Demographic
data, including age, gender, and clinical findings, were recorded. The Rome IV
criteria were used to assess gastrointestinal complaints.

Results A total of 66 (F=61, M=5) patients (limited cutaneous SSc
(lcSSc=31), diffuse cutaneous SSc (dcSSc=35)) were included in this study. In
lcSSs patients, the prevalence of functional dyspepsia, irritable bowel syndrome
(IBS), constipation, and diarrhoea was 29.0%, 12.9%, 6.5% and 3.2%,
respectively, whereas in dcSSc, the prevalence of these disorders was 37.1%,
8.6%, 8.6%, and 0.0%, respectively. There was no statistically significant
difference regarding the presence of functional gastrointestinal disorders
between lcSSc and dcSSc patients. When patients with SSc were compared based on
functional gastrointestinal disorders, no significant differences were observed
between the groups in terms of mean age, disease duration, smoking, lung
involvement, and presence of body mass index≥25.

Conclusion Alterations in gut microbiota and inflammatory changes have
been proposed as contributing factors in IBS. Chronic inflammatory diseases,
such as SSc, may therefore predispose individuals to its development. In our
study, IBS was found in 10.7% of the SSc patients. To identify patients at high
risk of IBS, further studies are required.
Utility of Urine Dipstick Testing in Pediatric Appendicitis: Assessing its Role in Identifying Complicated Cases and Retrocecal Appendicitis
Authors: Biehl Clara Månsson , Elliver Matilda , Gudjonsdottir Johanna , Salö Martin
Published: December 2024

Background Diagnosing appendicitis in children remains a challenge, and the role of urine dipstick is controversial. This study aimed to evaluate the association between abnormal urine dipstick results and appendicitis, particularly appendicitis severity and appendix position.

Methods A prospective cohort study was conducted from 2017 to 2021 at a tertiary hospital in Sweden. Children aged ≤ 15 years with suspected appendicitis were included. Logistic regression was used to assess associations between abnormal urine dipstick results and sex, age, peritonitis, body temperature, C-reactive protein, complicated appendicitis, and appendix position.

Results A total of 311 children with suspected appendicitis were included, with 193 (62%) diagnosed with appendicitis. Among these, 80 (41%) had complicated appendicitis. There was no difference in appendicitis rate between children with positive and normal urine dipstick results. Among children with appendicitis, 119 (62%) had positive urine dipstick results: 49% ketones, 29% erythrocytes, 23% protein, 19% leukocytes, and 2% nitrite. Multivariable analysis revealed that female sex (adjusted odds ratio: 2.41 [95% confidence interval, CI: 1.21–4.80], p = 0.013), retrocecal appendicitis (aOR: 2.39 [95% CI: 1.18–4.84], p = 0.015), and complicated appendicitis (aOR: 2.27 [1.01–5.13], p = 0.015) were significantly associated with abnormal urine dipstick results. Sensitivity and specificity of positive urine dipstick for complicated appendicitis was 56% (95% CI: 45–67%) and 64% (95% CI: 54–73%), respectively, with an area under the curve of 0.62 (95% CI: 0.54–0.70). Limitations in this study include potential unmeasured confounders such as hydration status and urinary tract infections.

Conclusion Abnormal urine dipstick results are common in children with appendicitis. Urine dipstick might help identify cases of complicated and retrocecal appendicitis.
Long-Chain Polysaturated Fatty Acid in Atrial Fibrillation-Associated Stroke: Lipidomic-GWAS Study
Authors: Jung Youngae , Kim Beomsu , Kim Chi Kyung , Won Hong Hee , Suhyun Chae , Oh Kyung-Mi , Shin Min-Jeong , Hwang Geum-Sook , Seo Woo-Keun
Published: December 2024

Background and Purpose This study aimed to explore the relationship between lipidomic domains, particularly free fatty acids (FFAs), and the presence of AF in patients with acute stroke, and to identify mechanisms of AF-associated stroke through genetic studies.
Methods A total of 483 patients of stroke in patients without AF (n = 391) and with AF (n = 92) were selected from a prospectively collected stroke registry. Lipidomic profiling was conducted and the lipid components associated with AF were explored using fold-change analyses and clustering. Genotyping was conducted through trait comparison. Colocalization was also performed.
Results Among the lipidomic domains, the free fatty acid (FFA) class was positively associated with AF. Long-chain fatty acids with 14-24 carbons and unsaturated FFAs distinguished AF. Clustering analysis based on FFAs revealed differences in AF proportion across groups. GWAS identified two loci associated with clustered groups of FFA metabolites: near MIR548F3 associated with FFA 20:1, FFA 20:2, FFA 22:5, and FFA 22:6; and near RPL37A associated with FFA 22:5 and FFA 22:6. These loci were associated with increased fibrinogen levels. In the GWAS for the FFA metabolite-quantitative trial locus analysis, loci near rs28456 and rs3770088, and FFA 20:4-QTLs were co-localized with the eQTLs of FADS2, a gene involved in the peroxisome proliferative-activated receptor gamma-related signaling pathway, in the whole blood, left ventricle, and atrial appendage tissue.
Conclusion Elevated FFA levels, especially those of long-chain unsaturated FFAs, are strongly associated with AF-associated stroke. This relationship is regulated by the peroxisome proliferator-activated receptor gamma-related signaling pathway.
Effect of the interaction with the substrate on the superfluidity of a helium film
Authors: Pikhitsa P. V.
Published: December 2024

It is shown that, in a superfluid helium film, the rotons are crowded near the substrate and the normal surface density has an elevated value.
Superconductivity in Y2Mo3Si4
Authors: Aliev F. G. , Gorelenko Yu. K. , Moshchalkov V. V. , Skolozdra R. V.
Published: December 2024

The temperature dependence of the electrical resistivity ρ(T) is studied in the compound Y2Mo3Si4 over the temperature range 0.05 < T < 300 °K. A transition to the superconducting state with critical temperature Tc = 1.1 °K is found. The critical field curve Hc2Tc) is measured, revealing that Y2Mo3Si4 is a type II superconductor with Hc2(0) = 4.8 kOe.
Initial data for first-order causal viscous conformal fluids in general relativity
Authors: Disconzi Marcelo , Isenberg James , Maxwell David
Published: December 2024

We solve the Einstein constraint equations for a first-order causal viscous relativistic hydrodynamic theory in the case of a conformal fluid. For such a theory, a direct application of the conformal method does not lead to a decoupling of the equations, even for constant-mean curvature initial data. We combine the conformal method applied to a background perfect fluid theory with a perturbative argument in order to obtain the result.
Laser-stimulated photodetachment of electrons from the negatively charged dielectric substrates
Authors: Ussenov Y. , Shneider M. N. , Yatom S. , Raitses Y.
Published: December 2024

The photon-stimulated emission of bulk electrons has been extensively studied for various types of materials, while the photodetachment of surplus surface electrons has not been fully explored. The photodetachment barrier energy is commonly defined by the surface electron affinity of material, which is typically less than the work function and more pronounced for non-conducting substrates and in environments with a continuous flux of electrons to the surface, such as in gas discharge plasmas. Herein, it is experimentally shown that the photodetachment yield of surplus electrons created by plasma-induced charging of non-conductive surfaces of dielectric materials depends on the initial surface charge density and do not correlate with the tabulated affinity values of these materials under gas discharge charging conditions. This result obtained using laser-stimulated photodetachment for fused silica, boron nitride, and alumina, is critically important for the understanding of charging and discharging dynamics, secondary electron emission, and photo emission effects affecting plasma–wall interactions relevant to surface and capacitively coupled discharges, dusty plasmas, electrostatic probe diagnostics, and applications for plasma processing of materials, plasma propulsion, and gas breakdown.
Theoretical study of acoustic field caused by single bubble behavior
Authors: Meng Mao , Li Xiao-Bin , Zhang Hong-Na , Li Feng-Chen
Published: December 2024

Boiling noise is a mode of energy release accompanying bubble dynamics, and its noise characteristic is a potential recognition mode of bubble behavior. In this paper, the angular spectrum method is used to calculate the transient sound field and analyze the noise characteristics induced by single bubble deformation and the classical nucleation growth process theoretically. The relationship between the induced noise intensity and the vibration parameters of the bubble surface is obtained quantitatively. It is shown that bubble volume oscillations and deformation are the main sources of noise, while bubble nucleation-induced noise has limited contribution to noise, and the high-frequency information contained in the bubble surface motion plays a key role in the noise intensity. In addition, in order to analyze the noise characteristics induced by boiling bubbles, a boiling correction is introduced based on the Kirkwood–Bethe (K-B) equation.
Experimental investigation on the cavity sealing transformation of elliptical cylinders during water entry
Authors: Wang Anhua , Liu Xiaohan , Zhou Biaojun , Li Haoyong , Yao Weiguang , Dai Qi , Zhao Zijie
Published: December 2024

The water-entry cavity sealing of elliptical cylinders is systematically investigated with experimental methods, which features the inconsistent lengths of major and minor axes. By comparing with the cylinder entering water, the effects of aspect ratio and Froude number on the cavity sealing are analyzed to reveal the mechanism of sealing mode transformation among deep, transition, and surface seals. In the deep seal mode, the water-entry cavity of cylinders pinches off at a singularity, but the minor-axis cavity of elliptical cylinders shows an oval hole when the cavity in the major axis pinches off. During the water entry of elliptical cylinders, the water hardly splashes in the major axis but mostly splashes in the minor axis. Thus, the minor-axis cavity is larger than the major-axis cavity in the surface seal. Especially, when the splash crown seals to the tail plane, the transition seal mode occurs with surface and deep seals successively appearing. The shedding cavity in the deep seal of cylinders is penetrated by a central water column, while the shedding cavity of elliptical cylinders merges with the downward jet and splits into two separate halves. As the aspect ratio increases, the minor-axis splash crown obtains more kinetic energy and gradually expands outwards. Consequently, the deep seal happens later with a larger pinch-off depth, but the surface seal occurs faster with a smaller cavity volume. Therefore, the sealing mode transformation sequentially undergoes surface, transition, and deep seals, which is contrary to the mode transformation with the increment of Froude number.
Fluid–structure interaction of panel under swept shock wave/boundary layer interaction
Authors: Ye Kun , Chen Shubao , Li Guoliang , Xie Pengze , Qu Feng , Ye Zhengyin
Published: December 2024

Swept shock wave/boundary layer interaction (SSBLI) is a typical flow phenomenon in hypersonic vehicles. Under the influence of lightweight structural design, the stiffness of the panel will be significantly reduced, which can easily lead to fluid–structure interaction (FSI) issues. Based on an in-house FSI program, the dynamical characteristics of the flexible panel and the influence of the FSI on flow characteristics was investigated by varying the area of a plate immersed in the separation zone induced by SSBLI. The results show that as the immersion area increases, the dominant mode of the panel changes from low-order to high-order, and the pressure and displacement response transition from limit cycle oscillation to multi-frequency irregular oscillation. The evolution of pressure pulsations at the line of surface-flow coalescence and the line of surface-flow divergence in the flow field is consistent with that of the panel. Furthermore, the degree of destruction of the quasi-conical characteristics increases with the increase in the immersed area. Moreover, as the displacement of the panel increases, the “depression” of the separation shock wave becomes more pronounced, and the expansion wave gradually strengthens and moves farther away from the sharp fin. This study provides an important reference for the refined design of aircraft under complex hypersonic flows.
The effect of single rough element on fracture nonlinear seepage behavior by lattice Boltzmann method
Authors: Dai Changlin , Ma Haichun , Qian Jiazhong , Luo Qiankun , Ma Lei
Published: December 2024

Fracture seepage is a critical issue in both engineering and scientific research, yet the role of rough fracture surfaces in driving nonlinear behavior remains poorly understood. This study uses the lattice Boltzmann method to numerically simulate the effects of semicircular rough elements of varying sizes on the flow field, starting from a simplified scenario to explore the nonlinear evolution of rough fractures. The results reveal that rough elements alter both velocity and pressure profiles, with increased velocity above the rough elements and a corresponding pressure drop. Recirculation zones are also formed, growing larger as the rough element radius increases. A relationship was established to describe the interaction between rough elements and fluid, linking the drag coefficient to relative roughness and Reynolds number. Pressure distribution analysis around the rough elements shows that they experience forces primarily in the direction of fluid flow within the channel. By examining non-Darcy flow behavior, a nonlinear seepage model based on the Forchheimer equation was developed for individual rough elements. The findings demonstrate that rough elements are the key factor driving nonlinear seepage changes [Re∈100,160]. The complex morphology of the fracture surface leads to variations in velocity and pressure, formation of recirculation zones, and the emergence of nonlinear behavior.
Bending elasticity of the reversible freely jointed chain
Authors: Yi Minsu , Lee Dongju , Benetatos Panayotis
Published: December 2024

The freely jointed chain model with reversible hinges (rFJC) is the simplest theoretical model, which captures reversible transitions of the local bending stiffness along the polymer chain backbone (e.g., helix-coil-type of local conformational changes or changes due to the binding/unbinding of ligands). In this work, we analyze the bending fluctuations and the bending response of a grafted rFJC in the Gibbs (fixed-force) ensemble. We obtain a recursion relation for the partition function of the grafted rFJC under a bending force, which allows, in principle, an exact-numerical calculation of the behavior of an rFJC of arbitrary size. In contrast to stretching, we show that under sufficiently stiff conditions, the differential bending compliance and the mean fraction of closed hinges are non-monotonic functions of the force. We also obtain the persistence length Lp of the rFJC and the moments ⟨R2⟩ (mean-square end-to-end distance) and ⟨z2⟩ (mean-square transverse deflection) for the discrete chain and take the continuum limit. The tangent vector auto-correlation decays exponentially, as in the wormlike chain model (WLC). Remarkably, the expression of ⟨R2⟩ as a function of the contour length L becomes the same as that in the WLC. In the thermodynamic limit, we have calculated the exact bending response analytically. As expected, for L ≫ Lp, the boundary conditions do not matter, and the bending becomes equivalent to stretching. In contrast, for Lp ≫ L, we have shown the non-monotonicity of the bending response (the compliance and mean fraction of closed hinges).
High interest for long-acting injectable PrEP among men who have sex with men at most risk for HIV in San Francisco, 2021
Authors: Hernandez Christopher J. , Turner Caitlin M. , Trujillo Dillon , Tate Moranda , Quintana Jerry , Baguso Glenda , McNaughton Katherine C. , Arayasirikul Sean , McFarland Willi , Wilson Erin C.
Published: December 2024

Background Men who have sex with men (MSM) represent a disproportionate total of incident HIV cases. Oral pre-exposure prophylaxis (PrEP) has contributed to significant declines in total HIV incidence. Barriers to PrEP include individual and structural factors that can prevent PrEP adherence and persistence. Long-acting injectable PrEP (LA-IP) can be leveraged to address high incident rates of HIV. Methods This study was a secondary analysis of the National HIV Behavioral Surveillance (NHBS) survey. We measured interest in LA-IP and associated factors among MSM in San Francisco from June 2021 to December 2021. Results Of the 505 MSM who were recruited, 409 reported not living with HIV. Interest in LA-IP among MSM in San Francisco was high (78.0%). Interest was associated with the use of on-demand PrEP (adjusted prevalence ratio [aPR] 3.68, 95% confidence interval [CI] 1.24–10.9), having two or more sexual partners (aPR 3.65, 95% CI 1.89–7.03), and having condomless insertive anal intercourse (aPR 2.15, 95% CI 1.19–3.87). LA-IP was inversely associated with having a high school education or lower (aPR 0.23, 95% CI 0.08–0.70) and being aged 50 years or more (aPR 0.32, 95% CI 0.19–0.56). Strikingly, we found that five of the six participants who were found to have incident HIV infections in this study were interested in LA-IP. Further, they had used oral PrEP in the past 30 days with suboptimal adherence. Conclusions These findings suggest that a population with elevated risk for HIV and barriers to daily oral PrEP adherence may find LA-IP a preferable alternative to daily oral PrEP in meeting their HIV prevention needs.
Mechanism of proton release during water oxidation in Photosystem II
Authors: Allgöwer Friederike , Pöverlein Maximilian C. , Rutherford A. William , Kaila Ville R. I.
Published: December 2024

Photosystem II (PSII) catalyzes light-driven water oxidation that releases dioxygen into our atmosphere and provides the electrons needed for the synthesis of biomass. The catalysis occurs in the oxygen-evolving oxo-manganese-calcium (Mn
4
O
5
Ca) cluster that drives the oxidation and deprotonation of substrate water molecules leading to the O
2
formation. However, despite recent advances, the mechanism of these reactions remains unclear and much debated. Here, we show that the light-driven Tyr161
D1
(Y
z
) oxidation adjacent to the Mn
4
O
5
Ca cluster, decreases the barrier for proton transfer from the putative substrate water molecule (W3/W
x
) to Glu310
D2
, accessible to the luminal bulk. By combining hybrid quantum/classical (QM/MM) free energy calculations with atomistic molecular dynamics simulations, we probe the energetics of the proton transfer along the Cl1 pathway. We demonstrate that the proton transfer occurs via water molecules and a cluster of conserved carboxylates, driven by redox-triggered electric fields directed along the pathway. Glu65
D1
establishes a local molecular gate that controls the proton transfer to the luminal bulk, while Glu312
D2
acts as a local proton storage site. The identified gating region could be important in preventing backflow of protons to the Mn
4
O
5
Ca cluster. The structural changes, derived here based on the dark-state PSII structure, strongly support recent time-resolved X-ray free electron laser data of the S
3
→ S
4
transition (Bhowmick
et al
. Nature
617
, 2023) and reveal the mechanistic basis underlying deprotonation of the substrate water molecules. Our findings provide insight into the water oxidation mechanism of PSII and show how the interplay between redox-triggered electric fields, ion-pairs, and hydration effects control proton transport reactions.
Chiral π domain walls composed of twin half-integer surface disclinations in ferroelectric nematic liquid crystals
Authors: Yi Shengzhu , Hong Zening , Ma Zhongjie , Zhou Chao , Jiang Miao , Huang Xiang , Huang Mingjun , Aya Satoshi , Zhang Rui , Wei Qi-Huo
Published: December 2024

Ferroelectric nematic liquid crystals are polar fluids characterized by microscopic orientational ordering and macroscopic spontaneous polarizations. Within these fluids, domain walls that separate regions of different polarizations are ubiquitous. We demonstrate that the π walls in films of the polar fluids consist of twin half-integer surface disclinations spaced horizontally, enclosing a subdomain where the polarization exhibits left- or right-handed π twists across the film. The degenerate geometric arrangements of the twin disclinations generate kinks and antikinks, parting subdomains of opposite chirality, like the spin-up and spin-down in Ising chains. The hierarchical structures dictate that field-driven polar switching undergo two-step annihilations of the surface disclinations. These findings provide an insight for both comprehending other walls in the polar fluids and domain engineering crucial for advancing their nonlinear and optoelectronic applications.
New series expansion for the periapsis shift
Authors: Katsumata Akihito , Harada Tomohiro , Ogasawara Kota , Iizuka Hayami
Published: December 2024

We propose a prescription for a new series expansion of the periapsis shift. The prescription formulates the periapsis shift in various spacetimes analytically without using special functions and provides simple and highly accurate approximate formulae. We derive new series representations for the periapsis shift in the Kerr and the Chazy–Curzon spacetimes by using the prescription, where the expansion parameter is defined as the eccentricity divided by the non-dimensional quantity that vanishes in the limit of the innermost stable circular orbit (ISCO). That is to say, the expansion parameter characterizes both the eccentricity of the orbit and its proximity to the ISCO. The smaller the eccentricity, the higher the accuracy of the formulae that are obtained by truncating the new series representations up to a finite number of terms. If the eccentricity is sufficiently small, the truncated new representations have higher accuracy than the post-Newtonian (PN) expansion formulae even in strong gravitational fields where the convergence of the PN expansion formula is not guaranteed. On the other hand, even if the orbit is highly eccentric, the truncated new representations have comparable or higher accuracy than the PN expansion formulae if the semi-major axis is sufficiently large. An exact formula for the periapsis shift of the quasi-circular orbit in the Chazy–Curzon spacetime is also obtained as a special case of the new series representation.
Learning physics while monitoring vibrations of the Earth—investigating seismic phenomena by using a Raspberry Pi
Authors: Foesel A , Hinz D
Published: December 2024

This article deals with the context of seismology and its relevance to the teaching of physics in a modern and highly motivating way. A modular system called Raspberry Shake RS1D is presented, which is capable of detecting earthquakes as well as everyday vibrations. The Raspberry Shake 1D Vertical Motion Seismograph combines a Raspberry Pi mini-computer, a vertical geophone, a 24-bit digitizer and a near-real-time (miniSEED) data transmission. While the Raspberry Shake is a low cost professional and already well known tool for seismologists, we as physicists ‘simply’ used that computer-based measurement system. We describe how the seismograph works. We present the detection of ground motion from earthquakes as well as from everyday vibrations using selected examples. Thereby, we focus on teaching physics in the context of seismology, presenting didactic ideas for learning about acoustics, for utilizing measurement systems and for applying scientific methods. This article is especially relevant for teaching undergraduate students. Basic facts about earthquakes that are essential for the study of the seismic phenomena discussed in this article are conveyed.
Chemical damping of the motion of a piston: irreversibilities arising from nonequilibrium conditions on the chemical potential
Authors: Corti David S , Uline Mark J
Published: December 2024

We revisit the thermodynamic analysis of an isothermal ideal gas mixture enclosed within a cylinder and separated from the surrounding atmosphere by a movable and frictionless piston. When equilibrium conditions based on the chemical potentials of one or more species in the mixture are not satisfied at all times, which occurs for example for a chemical reaction with finite and non-zero reaction rates in the forward and reverse directions and for mass transfer of one species across a permeable membrane occurring at a finite and non-zero rate, an irreversibility is necessarily introduced into the system with a resulting increase in the entropy of the Universe. Consequently, when the piston is set in motion, it cannot oscillate indefinitely. The piston must again come to rest despite there not being any mechanical dissipative mechanisms, i.e. friction or viscous dissipation, nor a thermal dissipative mechanism, i.e. irreversible heat transfer, operating within the system. Only when the system is reversible, such that the entropy of the Universe remains constant at all times, will the piston oscillate indefinitely. ‘Chemical damping,’ or an irreversibility arising from nonequilibrium conditions on the chemical potential, provides another dissipative mechanism that has not yet been analyzed before.
Slipping characteristics of rolling element bearing considering local defects and cage flexibility
Authors: Chen Wanglong , Yan Changfeng , Kang Jianxiong , Tian Yu , Shi Zhifeng , Wu Lixiao
Published: December 2024

Slipping and local defects are significant causes of abnormal vibration and instability in rolling element bearings (REBs). In particular, the secondary slipping of rolling elements (REs) triggered by local defects on the raceway would exacerbate the vibration and reduce rotational precision of the bearing system. Therefore, to more accurately reveal the characteristics of local slipping and the vibration response mechanisms in defective bearings, a comprehensive 4N
b + 4 degrees of freedom dynamic model of defective REB with flexible cage is proposed. This model based on the consideration of time-varying displacement excitation, cage stiffness and damping, pocket clearance, and isothermal elastohydrodynamic lubrication. Through comparisons the simulation results with both experimental and reference results, the proposed model is verified. The study investigated variations in contact forces between REs and overall raceways in detail, especially the trend of changes within the local defect area as the defect width increases. Furthermore, the effects of flexible cage stiffness, radial load, and speed on bearing slipping behavior are explored, along with the secondary slipping phenomenon triggered by local raceway defects. The results indicate that with increase of flexible cage stiffness and load, the REs slipping speed and cage slipping rate would decrease. Conversely, as rotational speed increases, both slipping speed and cage slipping rate would also increase.
Dexterous grasping of robotic hand posture and force generation through visual–tactile fusion
Authors: An Jing , Jia Qingxuan , Li Tong , Chen Gang , Zhu Xiaojun , Wang Yifan , Yan Yuhang
Published: December 2024

Accurately grasping objects with varying levels of hardness and softness is a challenging task. Current robotic grasping methods rely solely on visual to determine the grasping posture, without considering the grasping force of different objects, which might increase the risk of slippage or damage. For the purpose of realize the improvement and supplementation of visual information from the dimension of force, several robots include tactile sensors installed at fingertips. In this paper, we propose a method that integrates visual and tactile information to accurately determine the 6D posture and force for robot grasping. The main challenges of this research include (1) grasping representation of visual and tactile data from heterogeneous sources, (2) Construction of the implicit link between grasping posture and clutching force , (3) a visual–tactile training dataset. To address these challenges, we first use a grasping quality assessment module to filter the grasping posture and a transformer-depth separation convolution module to predict the grasping force; second, we propose a diffusion model with multi-stage convolution module to generate the optimal grasping. In addition, we created a visual–tactile grasping data representation form that included the grasping quality of grasping postures, and matching tactile data for objects of 8 distinct hardness. Experiments show that our method achieves a 98% success rate and decreases grasping force redundancy by 78% compared to purely visual methods,which significantly improves the accuracy and stability of the robot grasping.