bluuebunny/crossref_metadata_2025 huggingface dataset:
The reliability and validity of superb microvascular imaging as a potential disease activity marker in rheumatoid arthritis
Authors: Kurtulus Ozturk Esin , Ozturk Saffet , Kelesoglu Dincer Ayse Bahar
Published: November 2024

Rheumatoid arthritis (RA) is a systemic autoimmune disease of unknown etiology that causes progressive and destructive inflammation in the joints. Superb microvascular imaging (SMI) is a new ultrasound technique that allows visualization of slow blood flow in synovitis. This study aimed to report on the clinical value and utility of the SMI technique and its grading for monitoring RA by determining the correlation with clinical disease activity scores (DAS 28) and power Doppler ultrasound (PDUS).

All RA patients with clinically apparent synovitis were assessed using DAS 28. Synovitis was investigated with PDUS and SMI and each joint was graded semi-quantitatively. All assessments were carried out at baseline and repeated at least at the 4-month follow-up. Correlations between scores were investigated using Spearman’s correlation.

60 RA patients with 552 affected joints were recruited. Clinical and sonographic scores were significantly improved at follow-up (p<0.001). SMI showed significantly more joint count and flow signal scores than clinical examination and PDUS. Moderate correlations were found between the SMI score and clinical scores (p<0.001, 0.586 for SMI score vs. DAS 28-CRP, p=0.001, 0.432 for SMI vs. DAS 28-ESR). There were also stronger correlations between the SMI score and PDUS score at both baseline and follow-up (p<0.001, r = 0.817, 0.842 respectively).

SMI provides greater utility and ability to detect synovial vascularity and to monitor disease activity than PDUS. A new activity scoring system based on SMI and clinical objective findings is required to improve reliability and validity.
Hypoxia-Preconditioned Human Umbilical Cord Mesenchymal Stem Cells Transplantation Ameliorates Inflammation and Bone Regeneration in Peri-Implantitis Rat Model
Authors: Kuntjoro Mefina , Hendrijantini Nike , Prasetyo Eric Priyo , Agustono Bambang , Hong Guang
Published: November 2024

Objective The failure of dental implant treatments is predominantly attributed to peri-implantitis, which entails chronic inflammation within the peri-implant tissue, ultimately leading to tissue degradation. Addressing this condition, human umbilical cord mesenchymal stem cell (hUCMSC) transplantation serves as a regenerative therapy; however, concerns regarding the viability and efficacy of transplanted cells in inflamed regions persist. Hypoxic preconditioning of hUCMSCs has emerged as a potential strategy for augmenting their regenerative and immunomodulatory capacities. This study aimed to evaluate the expression of inflammatory (tumor necrosis factor [TNF]-α) and bone regenerative biomarkers (nuclear factor of activated T-cell [NFATc1], osteocalcin, collagen type I alpha 1 [COL1α1]) within peri-implantitis models subsequent to the transplantation of hypoxia-preconditioned hUCMSCs.

Materials and Methods Peri-implantitis models were established through the insertion of implants into the femur bone of 42 Wistar strain Rattus norvegicus, followed by intrasocket injection of lipopolysaccharide. The experimental animals were categorized into three groups (control, normoxia, and hypoxia) and underwent observation on days 14 and 28. The expression levels of TNF-α, NFATc1, COL1α1, and osteocalcin were evaluated using immunohistochemical staining, and the resulting data were subjected to one-way analysis of variance analysis (p < 0.05).

Results Transplantation of hypoxia-preconditioned hUCMSCs significantly ameliorated inflammation and osteoclastogenesis, as evidenced by significant reductions in TNF-α and NFATc1 expression compared with the control group. Furthermore, hypoxic preconditioning of hUCMSCs demonstrated a significant elevation in the expression of osteocalcin and COL1α1 relative to the control group.

Conclusion The transplantation of hypoxia-preconditioned hUCMSCs exhibited a capacity to ameliorate inflammation and enhance bone regenerative processes in peri-implantitis rat models.
Histone H3K9 Methylation Is Differentially Modified in Odontogenic Cyst and Tumors
Authors: Phattarataratip Ekarat , Lam-ubol Aroonwan
Published: November 2024

Objectives Histone modification in odontogenic lesions is mostly unexplored. Trimethylation of histone H3 at lysine residue 9 (H3K9Me3) has been studied in various pathologic conditions and showed biological significance promising for future therapeutic application. This study aimed to investigate the level and clinical relevance of the H3K9Me3 histone modification in odontogenic cysts and tumors.

Materials and Methods A total of 105 cases of odontogenic lesions, comprising 30 odontogenic keratocysts (OKCs), 30 adenomatoid odontogenic tumors (AOTs), 30 ameloblastomas, and 15 dental follicles, were included in the study. The paraffin-embedded tissues were immunohistochemically stained for H3K9Me3. Both the intensity and the distribution of staining were evaluated and calculated as H-score. The correlation between the H3K9Me3 expression and the clinical characteristics of each lesion was evaluated.

Statistical Analysis The Kruskal–Wallis test followed by Bonferroni's correction was performed to assess the differences in H-score among groups. In addition, Pearson's chi-squared test or Mann–Whitney U test was used to analyze potential factors that could affect protein expression.

Results The reduced enamel epithelium of the dental follicle showed uniformly strong H3K9Me3 expression. All odontogenic cysts and tumors examined demonstrated a significantly reduced H3K9Me3 level compared with dental follicles. The AOT showed the lowest H3K9Me3 level, followed by OKC and ameloblastoma. Its immunoreactivity was mainly localized in the basal and parabasal cells of OKC and the whorled/duct-like structures of AOT. Ameloblastoma exhibited marked variation in the H3K9Me3 level among cases. Notably, the upregulated H3K9Me3 was related to multilocularity of OKC and ameloblastoma.

Conclusions Histone H3K9 methylation is differentially expressed in odontogenic cysts and tumors. This epigenetic modification may contribute to the pathogenesis and aggressive behavior of odontogenic lesions.
Effect of Cross-sectional Designs on Torsional Resistance of Endodontic Nickel–Titanium Files: A Finite Element Study
Authors: Nanthaprathip Natchaphon , Morakul Sarita , Hiran-us Sirawut , Singhatanadgid Pairod
Published: November 2024

Objectives This study aimed to assess the influence of two key design parameters on the torsional resistance of endodontic rotary files: the ratio of the equivalent radius (re
) to the polar moment of inertia (J), or re
/J ratio, and the percentage of the inner core area. Understanding these factors can guide the development of files with improved performance during root canal procedures.

Materials and Methods Finite element analysis was employed to simulate the behavior of rotary files under torsional loading conditions. This method allowed for the investigation of maximum shear stress across various cross-sections (D4–D16) of the files. The relationship between the re
/J ratio and the maximum shear stress was also evaluated. To assess the impact of cross-sectional design modifications on stress distribution, the study analyzed files with progressively changing configurations.

Results Regions situated outside the inner core circle experienced lower shear stress compared with a circular shaft. Furthermore, a strong linear correlation was observed between the maximum shear stress experienced by the file, the applied torque during operation, and the re
/J ratio. Significantly, the study established a connection between the percentage of the inner core area and the torsional resistance of the file. Files with a larger inner core area exhibited a lower coefficient (C) within a newly derived torsional formula. This lower C value directly translated to a reduction in the maximum shear stress experienced by the file. In essence, files with a higher percentage of inner core area demonstrated enhanced torsional resistance, allowing them to withstand higher torsional loads encountered during root canal procedures.

Conclusion This study identified the re
/J ratio and the percentage of inner core area as the most critical design factors influencing the torsional resistance of rotary files. Files with a lower re
/J ratio and a larger inner core area experienced lower shear stress, resulting in enhanced torsional resistance and potentially reducing the risk of torsional fracture during use. These findings offer valuable insights for both clinicians selecting rotary files and manufacturers designing future iterations, ultimately contributing to improved safety and efficacy during root canal treatments.
The Effect of CLA Supplementation and High-Intensity Interval Training on Plasma Neuregulin 4, Interleukin 6, and TNF-α in Obese Men
Authors: Abbassi-Daloii Asieh , Barari Alireza , Bolboli Niloufar , Saeidi Ayoub , Zahabi Ghadir , García-Ramos Amador , Ilic Vladimir , Nedeljkovic Aleksandar
Published: November 2024

Background Despite extensive research, the effects of conjugated linoleic acid (CLA) supplementation in treating obesity are still unclear and equivocal. Adipokines play an important regulatory role in the activation of adipose tissue function. The purpose of the present research is to investigate the efficacy of CLA supplementation during high-intensity interval training (HIIT) on plasma neuregulin 4 (NRG-4), interleukin 6 (IL-6), and tumor necrosis factor α (TNF-α) in obese men.

Methodology Forty-four nonactive, obese males (age = 26.29 ± 0.97 y, body mass index [BMI] = 32.29 ± 1.27 kg/m2) participated in this research. Participants were randomly divided into four groups: control, without training or CLA supplementation; supplement, CLA supplementation without training; exercise, HIIT without CLA supplementation; supplement + exercise, HIIT with CLA supplementation. HIIT was performed for 12 weeks, three sessions per week, with a training intensity ranging from 60 to 75% of the VO2 max on a treadmill. Subjects in the CLA supplement groups consumed two 1-g CLA capsules daily in two meals with breakfast and dinner. The amount of plasma NRG-4, IL-6, and TNF-α was measured using an ELISA (enzyme-linked immunosorbent assay) kit. Various variables were collected at two time points (pretest and posttest).

Results The study found that both the HIIT and HIIT + CLA groups showed greater improvements in weight and BMI compared with the other groups. Notably, posttest levels of NRG-4 were significantly higher in the CLA, HIIT, and HIIT + CLA groups compared with the control group (p < 0.001). Additionally, following the intervention period, IL-6 levels in the HIIT + CLA group and TNF-α levels in the HIIT and HIIT + CLA groups were significantly lower than in the control group (p < 0.001).

Conclusion CLA supplementation, in conjunction with HIIT, emerges as a highly effective approach and more benefits on the amount of adipokines secreted from fat tissue in obese people than either of them separately.
Influence of Body Mass Index on Health-Related Physical Fitness in School-Going Children of North and South Mangaluru
Authors: Shetty Nischitha U. , Chippala Purusotham
Published: November 2024

Background Being underweight, overweight, or obese has a negative impact on health outcomes in adulthood. Focusing on body mass index (BMI) since childhood may improve the quality of life and well-being of an individual in future.

Objective The aim of this study was to find the correlation of low, normal, and high BMI with health-related physical fitness components of the FITNESSGRAM test battery in school-going children of North and South Mangaluru.

Materials and Methods The study analyzed 166 respondents aged 5 to 10 years from seven Dakshina Kannada Zilla Panchayat schools in Mangaluru city. The children were divided into three groups (low, normal, and high BMI) based on their World Health Organization (WHO) growth chart standards, and they were assessed for health-related physical fitness using the FITNESSGRAM test battery.

Results There was a strong positive correlation of normal, low, and high BMI with FITNESSGRAM tests such as skinfold measurements of triceps (r = 0.903, 0.889, and 0.913). and calf (r = 0.881, 0.889, and 0.900), curl-up (r = 0.787, 0.776, and 0.881), and 90-degree pushup (r = 0.816, 0.769, and 0.858). The progressive aerobic cardiovascular endurance run (PACER) had a weak positive correlation with normal BMI (r = 0.122), moderate positive with low BMI (r = 0.301), and moderate negative with high BMI (r = −0.584), while the trunk lift test had a moderate positive correlation with normal, low, and high BMI (r = 0.618, 0.640, and 0.641).

Conclusion The study concludes that there is a positive correlation between BMI and health-related physical fitness components of FITNESSGRAM in school-going children of North and South Mangaluru.
A tale of two cities: regulating lobbying through public and private instruments in Brussels and Washington D.C
Authors: Năstase Andreea
Published: November 2024

This article explores the relationship between public (i.e. government-led) and private (i.e. industry-led) forms of lobby regulation, by inquiring over the conditions that render a mix between these two regulatory forms more likely. Drawing on the governance of professions scholarship, it presents a theoretically informed comparison between two jurisdictions—the US (federal level) and the EU (supranational level)—where the public regulation of lobbying is built on different models, namely a command-and-control model based on legally binding rules in the US and a cooperative model based on incentives and rewards in the EU. Findings show that, although formal public–private regulatory mixes are not present in either jurisdiction, the EU regulators have hewn closer to this arrangement by coopting lobbyists’ professional associations as semi-permanent but unofficial governance ‘allies’. This outcome is due to an amalgam of factors, chief among which is the severity of political scandals involving lobbyists, which affects policymakers’ reputational incentives for framing the public regulation of lobbying as a punitive or cooperative intervention. Methodologically, the article uses a combination of documentary analysis and expert interviews with lobby practitioners and public regulators on both sides of the Atlantic.
A study of cognitive factor sequences and relations to creativity quality levels
Authors: Yin Yuan , Childs Peter R. N.
Published: November 2024

Cognitive factors such as association, memory, and combination have been verified to be related to the creative design process. However, limited research has considered the effects of cognitive factors and their interaction on creative processes in practical creative design processes. This study aimed to detect the interactive effects of cognitive factors on creative processes in a practical creative design process. In particular, how the sequence of cognitive factors affects creativity quality levels of the creative solutions was investigated. Seventy-one participants were recruited to undertake a design task using the think-aloud method. The results of this study are as follows. (i) The sequences of cognitive factors can contribute to different creativity quality levels of solutions. The sequence of semantic memory, common association, remote association, episodic memory, remote combination, idea expression, and idea evaluation is more likely to lead to a higher creativity quality level of solutions. (ii) The repetition of the same cognitive factor in a creative design process, especially semantic memory, does not necessarily contribute to a high-creativity-quality-level solution. (iii) Creativity quality levels of solutions are related to how many cognitive factors categories are involved in the creative design process. The more cognitive factors included, the higher the creativity quality of the solutions will be.
Doubling photon-processing power for MKID readout
Authors: Patrick Chris
Published: November 2024

Scalable platform based on Radio-Frequency System-on-Chip technology can read out twice as many Microwave Kinetic Inductance Detectors as previous systems.
Element-specific ultrafast lattice dynamics in FePt nanoparticles
Authors: Turenne Diego , Vaskivskyi Igor , Sokolowski-Tinten Klaus , Wang Xijie J. , Reid Alexander H. , Shen Xiaozhe , Lin Ming-Fu , Park Suji , Weathersby Stephen , Kozina Michael , Hoffmann Matthias C. , Wang Jian , Sebesta Jakub , Takahashi Yukiko K. , Grånäs Oscar , Oppeneer Peter M. , Dürr Hermann A.
Published: November 2024

Light–matter interaction at the nanoscale in magnetic alloys and heterostructures is a topic of intense research in view of potential applications in high-density magnetic recording. While the element-specific dynamics of electron spins is directly accessible to resonant x-ray pulses with femtosecond time structure, the possible element-specific atomic motion remains largely unexplored. We use ultrafast electron diffraction (UED) to probe the temporal evolution of lattice Bragg peaks of FePt nanoparticles embedded in a carbon matrix following excitation by an optical femtosecond laser pulse. The diffraction interference between Fe and Pt sublattices enables us to demonstrate that the Fe mean square vibration amplitudes are significantly larger that those of Pt as expected from their different atomic mass. Both are found to increase as energy is transferred from the laser-excited electrons to the lattice. Contrary to this intuitive behavior, we observe a laser-induced lattice expansion that is larger for Pt than for Fe atoms during the first picosecond after laser excitation. This effect points to the strain-wave driven lattice expansion with the longitudinal acoustic Pt motion dominating that of Fe.
Existence of ground state sign-changing solutions for a class of quasilinear scalar field equations originating from nonlinear optics
Authors: Zhang Xingyong , Yu Xiaoli
Published: November 2024

This paper is mainly concerned with the existence of ground state sign-changing solutions for a class of second order quasilinear elliptic equations in bounded domains, which derived from nonlinear optics models. Combining a non-Nehari manifold method due to Tang and Cheng [J. Differ. Equations 261, 2384–2402 (2016)] and a quantitative deformation lemma with Miranda theorem, we obtain that the problem has at least one ground state solution and one ground state sign-changing solution with two precise nodal domains and we present the concrete lower bounds of ground state solution and ground state energy. We also obtain that any weak solution of the problem has C1,σ-regularity for some σ ∈ (0, 1). With the help of Maximum Principle, we reach the conclusion that the energy of the ground state sign-changing solutions is strictly larger than twice that of the ground state solutions.
Solar convective velocities: Updated helioseismic constraints
Authors: Birch A. C. , Proxauf B. , Duvall T. L. , Gizon L. , Hanasoge S. , Hindman B. W. , Sreenivasan K. R.
Published: November 2024

Modeling heat transport by convection is one of the most challenging aspects of solar and stellar physics. The literature currently provides apparently inconsistent observational estimates of the strength of large-scale convective flows in the upper layers of the solar convection zone. In addition, the large-scale convective flows predicted from numerical simulations are substantially stronger than some of the observational inferences in the literature. The current work aims to provide a consistent presentation of some of the main results in the literature both from observations and simulations. To achieve this aim, we carry out an analysis of published estimates of the strength of solar convection at different spatial scales. In particular, we employ a consistent set of conventions to compute the kinetic energy density in the east-west flows. This establishes a clear baseline for future work. The main conclusion is that there are inconsistencies between different observational results and also differences between observations and simulations. This conclusion is important as it demonstrates a need to determine the sources of the inconsistencies between different observational inferences and also to determine the missing ingredients in simulations of solar subsurface convection.
Insights into local wall erosion characteristics and prevention measures for cyclone separators
Authors: Guo Ming , Xia Gaoju , Guo Penghui , Manickam Sivakumar , Yoon Joon Yong , Sun Xun
Published: November 2024

Cyclone separators are separation devices that use the principle of inertia to remove particulate matter from flue gases. The present study mainly focuses on wall erosion in cyclone separators and associated research. The main locations of erosion in gas–solid cyclone separators, including the entrance impact section, cyclone roof corner, vortex finder outer surface, spiral-type erosion strip, and lower cone section, are examined in detail. The main factors influencing wall erosion are discussed, including inlet flow velocity, solid particle properties and loading, geometrical structure, and manufacturing quality. Finally, several practically preventive measures against wall erosion are presented, including adjustment of operating conditions, the use of erosion-resistant materials, optimization of geometrical structures, and the addition of auxiliary devices, all of which are essential for ensuring operational efficiency, equipment reliability, safety, and environmental protection in various industrial applications. This paper aims to provide a basis for further research into erosion in cyclone separators as well as guidance for engineers involved in their industrial applications.
Transport coefficient sensitivities in a semi-analytic model for magnetized liner inertial fusion
Authors: Lawrence Y. , Davies J. R. , McBride R. D. , Sefkow A. B.
Published: November 2024

Performance of magnetized liner inertial fusion (MagLIF) experiments is highly dependent on transport processes including magnetized heat flows and magnetic flux losses. Magnetohydrodynamic simulations used to model these experiments require a choice of model for the transport coefficients, which are the constants of proportionality relating driving terms, such as temperature gradients and currents, to the associated heat and magnetic field transport. The coefficients have been the subject of repeated recalculation using various methods throughout the years. Using a semi-analytic MagLIF model [McBride and Slutz, Phys. Plasmas 22, 052708 (2015)], we compare models for the transport coefficients provided by Braginskii [Reviews of Plasma Physics, edited by M. A. Leontovich (Consultants Bureau, New York, 1965), Vol. 1, p. 205], Epperlein and Haines [Phys. Fluids 29, 1029 (1986)], Ji and Held [Phys. Plasmas 20, 042114 (2013)], Davies et al. [Phys. Plasmas 28, 012305 (2021)], and Sadler et al. [Phys. Rev. Lett. 126, 075001 (2021)]. The choice of model modifies magnetic-flux losses caused by the Nernst thermoelectric effect and thermal conduction losses. We present simulated results from parameter scans conducted in order to compare the effects of the different models on parameters of interest in MagLIF. In some regions of parameter space, discrepancies of up to 38% are found in integrated quantities like the fusion yield. These results may serve as a guide for experimental validation of the various models, particularly as laser preheat energies and initial axial field strengths are increased on MagLIF experiments.
An investigation of escape and scaling properties of a billiard system
Authors: Rolim Sales Matheus , Borin Daniel , da Costa Diogo Ricardo , Szezech José Danilo , Leonel Edson Denis
Published: November 2024

We investigate some statistical properties of escaping particles in a billiard system whose boundary is described by two control parameters with a hole on its boundary. Initially, we analyze the survival probability for different hole positions and sizes. We notice that the survival probability follows an exponential decay with a characteristic power-law tail when the hole is positioned partially or entirely over large stability islands in phase space. We find that the survival probability exhibits scaling invariance with respect to the hole size. In contrast, the survival probability for holes placed in predominantly chaotic regions deviates from the exponential decay. We introduce two holes simultaneously and investigate the complexity of the escape basins for different hole sizes and control parameters by means of the basin entropy and the basin boundary entropy. We find a non-trivial relation between these entropies and the system’s parameters and show that the basin entropy exhibits scaling invariance for a specific control parameter interval.
MKIDGen3: Energy-resolving, single-photon-counting microwave kinetic inductance detector readout on a radio frequency system-on-chip
Authors: Smith Jennifer Pearl , Bailey John I. , Cuda Aled , Zobrist Nicholas , Mazin Benjamin A.
Published: November 2024

Microwave Kinetic Inductance Detectors (MKIDs) are superconducting detectors capable of single-photon counting with energy resolution across the ultraviolet, optical, and infrared (UVOIR) spectrum with microsecond timing precision. MKIDs are also multiplexable, providing a feasible way to create large-format, cryogenic arrays for sensitive imaging applications in biology, astronomy, and quantum information. Building large, cryogenic MKID arrays requires processing highly multiplexed, wideband readout signals in real time; this task has previously required large, heavy, and power-intensive custom electronics. In this work, we present the third-generation UVOIR MKID readout system (Gen3), which is capable of reading out twice as many detectors with an order of magnitude lower power, weight, volume, and cost-per-pixel as compared to the previous system. Gen3 leverages the Xilinx RFSoC4x2 platform to read out 2048, 1 MHz MKID channels per board. The system takes a modern approach to FPGA design using Vitis High-Level Synthesis to specify signal processing blocks in C/C++, Vivado ML intelligent design runs to inform implementation strategy and close timing, and Python productivity for Zynq to simplify interacting with and programming the FPGA using Python. This design suite and tool flow allows general users to contribute to and maintain the design and positions Gen3 to rapidly migrate to future platforms as they become available. In this work, we describe the system requirements, design, and implementation. We also provide performance characterization details and show that the system achieves detector-limited resolving power in the case of few readout tones and minimal degradation with all 2048 tones. Planned upgrades and future work are also discussed. The Gen3 MKID readout system is fully open-source and is expected to facilitate future array scaling to megapixel-sized formats and increase the feasibility of deploying UVOIR MKIDs in space.
Statistical mechanics of crystal nuclei of hard spheres
Authors: de Jager Marjolein , Vega Carlos , Montero de Hijes Pablo , Smallenburg Frank , Filion Laura
Published: November 2024

In the study of crystal nucleation via computer simulations, hard spheres are arguably the most extensively explored model system. Nonetheless, even in this simple model system, the complex thermodynamics of crystal nuclei can sometimes give rise to counterintuitive results, such as the recent observation that the pressure inside a critical nucleus is lower than that of the surrounding fluid, seemingly clashing with the strictly positive Young–Laplace pressure we would expect in liquid droplets. Here, we re-derive many of the founding equations associated with crystal nucleation and use the hard-sphere model to demonstrate how they give rise to this negative pressure difference. We exploit the fact that, in the canonical ensemble, a nucleus can be in a (meta)stable equilibrium with the fluid and measure the surface stress for both flat and curved interfaces. Additionally, we explain the effect of defects on the chemical potential inside the crystal nucleus. Finally, we present a simple, fitted thermodynamic model to capture the properties of the nucleus, including the work required to form critical nuclei.
High cell throughput, programmable fixation reveals the RNA and protein co-regulation with spatially resolved NFκB pseudo-signaling
Authors: Zhang Nicholas , Wang Mingshuang , Nambiar Dhruv , Iyer Samyukta , Kadakia Priyam , Luo Qianqi , Pang Sicheng , Qu Aaron , Bharadwaj Nivik Sanjay , Qiu Peng , Coskun Ahmet F.
Published: November 2024

RNA translation to protein is paramount to creating life, yet RNA and protein correlations vary widely across tissues, cells, and species. To investigate these perplexing results, we utilize a time-series fixation method that combines static stimulation and a programmable formaldehyde perfusion to map pseudo-Signaling with Omics signatures (pSigOmics) of single-cell data from hundreds of thousands of cells. Using the widely studied nuclear factor kappa B (NFκB) mammalian signaling pathway in mouse fibroblasts, we discovered a novel asynchronous pseudotime regulation (APR) between RNA and protein levels in the quintessential NFκB p65 protein using single molecule spatial imaging. Prototypical NFκB dynamics are successfully confirmed by the rise and fall of NFκB response as well as A20 negative inhibitor activity by 90 min. The observed p65 translational APR is evident in both statically sampled timepoints and dynamic response gradients from programmable formaldehyde fixation, which successfully creates continuous response measurements. Finally, we implement a graph neural network model capable of predicting APR cell subpopulations from GAPDH RNA spatial expression, which is strongly correlated with p65 RNA signatures. Successful decision tree classifiers on Potential of Heat-diffusion for Affinity-based Trajectory Embedding embeddings of our data, which illustrate partitions of APR cell subpopulations in latent space, further confirm the APR patterns. Together, our data suggest an RNA-protein regulatory framework in which translation adapts to signaling events and illuminates how immune signaling is timed across various cell subpopulations.
A single-particle energy-conserving dissipative particle dynamics approach for simulating thermophoresis of nanoparticles in polymer networks
Authors: Lu Yu , Li Zhen , Song Jun , Hu Guo-Hui
Published: November 2024

The transport of nanoparticles in polymer networks has critical implications in biology and medicine, especially through thermophoresis in response to temperature gradients. This study presents a single-particle energy-conserving dissipative particle dynamics (seDPD) method by integrating a single-particle model into the energy-conserving DPD model to simulate the mesoscopic thermophoretic behavior of nanoparticles in polymer matrices. We first validate the newly developed seDPD model through comparisons with analytical solutions for nanoparticle viscosity, thermal diffusivity, and hydrodynamic drag and then demonstrate the effectiveness of the seDPD model in capturing thermophoretic forces induced by temperature gradients. The results show that nanoparticles driven by the Soret forces exhibit unique transport characteristics, such as drift velocity and diffusivity, leading to a significant acceleration of nanoparticle diffusion in the polymer network, which has been known as the giant acceleration of diffusion. Quantifying how nanoparticles move in flexible polymer networks sheds light on the interaction dynamics of nanoparticles within polymer networks, providing insight into nanoparticle behavior in complex environments that could be leveraged in various applications from drug delivery to material design.
Extrinsic fluctuations in the p53 cycle
Authors: Hernández-García Manuel Eduardo , Gómez-Schiavon Mariana , Velázquez-Castro Jorge
Published: November 2024

Fluctuations are inherent to biological systems, arising from the stochastic nature of molecular interactions, and influence various aspects of system behavior, stability, and robustness. These fluctuations can be categorized as intrinsic, stemming from the system’s inherent structure and dynamics, and extrinsic, arising from external factors, such as temperature variations. Understanding the interplay between these fluctuations is crucial for obtaining a comprehensive understanding of biological phenomena. However, studying these effects poses significant computational challenges. In this study, we used an underexplored methodology to analyze the effect of extrinsic fluctuations in stochastic systems using ordinary differential equations instead of solving the master equation with stochastic parameters. By incorporating temperature fluctuations into reaction rates, we explored the impact of extrinsic factors on system dynamics. We constructed a master equation and calculated the equations for the dynamics of the first two moments, offering computational efficiency compared with directly solving the chemical master equation. We applied this approach to analyze a biological oscillator, focusing on the p53 model and its response to temperature-induced extrinsic fluctuations. Our findings underscore the impact of extrinsic fluctuations on the nature of oscillations in biological systems, with alterations in oscillatory behavior depending on the characteristics of extrinsic fluctuations. We observed an increased oscillation amplitude and frequency of the p53 concentration cycle. This study provides valuable insights into the effects of extrinsic fluctuations on biological oscillations and highlights the importance of considering them in more complex systems to prevent unwanted scenarios related to health issues.
Tilted columnar metal film as transducer of transverse coherent acoustic phonons in picosecond acoustics
Authors: Chargui A. , Martin N. , Ferro G. , Devos A.
Published: November 2024

Picosecond acoustics has been widely used to study thin film elasticity, hypersound attenuation, and adhesion of thin films to substrates. A major limitation of the technique is its restriction to only longitudinal waves. Although work has been reported on the ultrafast generation and detection of transverse waves, a general method compatible with thin films deposited on silicon is still missing. In this work, we show that by depositing a tilted columnar metal film and using an optical detection sensitive to light polarization, it is possible to excite and detect optically both types of bulk acoustic waves in thin films. The protocol is first established on metalized glass substrates, then applied to a range of transparent films deposited on silicon (silica, AlN, AlScN, and SiC). In each case, Brillouin oscillations are detected at two frequencies, one being the longitudinal mode, the other the transverse. The film thickness and two sound velocities are measured in each thin film. Transverse coherent phonons as high as 116 GHz are observed in the SiC thin film.
Effects of boundary conditions on the transmitral pressure gradient for numerical simulation of flow in a left heart model
Authors: Wu Fan , Feng Shuyi , He Xinyi , Wang Hongping , Kong Pengxu , Wei Peijian , Pan Xiangbin , Wang Shizhao
Published: November 2024

The transmitral pressure gradient is a crucial clinical indicator for diagnosing mitral regurgitation and stenosis. Numerical simulation of specific patients can obtain the complete pressure distribution in the left heart system, which is an important approach to evaluate cardiac function. However, the results are sensitive to the boundary conditions used in the numerical simulations. In the present work, we constructed a left heart model and assessed the effects of four typical boundary conditions on the transmitral pressure gradient, which is computed based on the Bernoulli equation and the line probe, respectively. The results show that the transmitral pressure gradient obtained by the line probe is sensitive to the boundary conditions. The sensitivity is closely related to the pressure in the atrium but has negligible effect on the pressure in the ventricle. This study sheds light on evaluating the pressure gradient of patient-specific treatments based on the numerical simulation of a left heart model.
Cooperative lattice theory for CO2 adsorption in diamine-appended metal-organic framework at humid direct air capture conditions
Authors: Marshall Bennett D. , Kortunov Pavel , Peters Aaron , Vroman Hilda
Published: November 2024

The effect of humidity on the cooperative adsorption of CO2 from the air on amine-appended metal–organic frameworks is studied both experimentally and theoretically. Breakthrough experiments show that, at low relative humidities, there is an anomalous induction effect, where the kinetics at short times are slower than kinetics at long times. The induction effect gradually vanishes as relative humidity is increased, corresponding to an increase in CO2 adsorption rate. A new theory is proposed based on the lattice kinetic theory (LKT), which explains these experimental results. LKT can accurately represent the measured data over the full range of humidities by postulating that the presence of adsorbed water shifts the equilibrium clusters from cooperatively bound chains to non-cooperatively bound CO2. A consequence of this transition is that CO2 exhibits step adsorption isotherm in dry air and a standard Langmuir adsorption isotherm in high humidity air.
Learning glass transition temperatures via dimensionality reduction with data from computer simulations: Polymers as the pilot case
Authors: Glova Artem , Karttunen Mikko
Published: November 2024

Machine learning methods provide an advanced means for understanding inherent patterns within large and complex datasets. Here, we employ the principal component analysis (PCA) and the diffusion map (DM) techniques to evaluate the glass transition temperature (Tg) from low-dimensional representations of all-atom molecular dynamic simulations of polylactide (PLA) and poly(3-hydroxybutyrate) (PHB). Four molecular descriptors were considered: radial distribution functions (RDFs), mean square displacements (MSDs), relative square displacements (RSDs), and dihedral angles (DAs). By applying Gaussian Mixture Models (GMMs) to analyze the PCA and DM projections and by quantifying their log-likelihoods as a density-based metric, a distinct separation into two populations corresponding to melt and glass states was revealed. This separation enabled the Tg evaluation from a cooling-induced sharp increase in the overlap between log-likelihood distributions at different temperatures. Tg values derived from the RDF and MSD descriptors using DM closely matched the standard computer simulation-based dilatometric and dynamic Tg values for both PLA and PHB models. This was not the case for PCA. The DM-transformed DA and RSD data resulted in Tg values in agreement with experimental ones. Overall, the fusion of atomistic simulations and DMs complemented with the GMMs presents a promising framework for computing Tg and studying the glass transition in a unified way across various molecular descriptors for glass-forming materials.
Waveflow: Boundary-conditioned normalizing flows applied to fermionic wave functions
Authors: Thiede Luca , Sun Chong , Aspuru-Guzik Alán
Published: November 2024

An efficient and expressive wave function Ansatz is key to scalable solutions for complex many-body electronic structures. While Slater determinants are predominantly used for constructing antisymmetric electronic wave function Ansätze, this construction can result in limited expressiveness when the targeted wave function is highly complex. In this work, we introduce Waveflow, an innovative framework for learning many-body fermionic wave functions using boundary-conditioned normalizing flows. Instead of relying on Slater determinants, Waveflow imposes antisymmetry by defining the fundamental domain of the wave function and applying necessary boundary conditions. A key challenge in using normalizing flows for this purpose is addressing the topological mismatch between the prior and target distributions. We propose using O-spline priors and I-spline bijections to handle this mismatch, which allows for flexibility in the node number of the distribution while automatically maintaining its square-normalization property. We apply Waveflow to a one-dimensional many-electron system, where we variationally minimize the system’s energy using variational quantum Monte Carlo (VQMC). Our experiments demonstrate that Waveflow can effectively resolve topological mismatches and faithfully learn the ground-state wave function.
Collision of cesium atoms on helium nanodroplets: Unraveling mechanisms for surface capture at experimental velocities
Authors: Bonhommeau David A.
Published: November 2024

The collision of cesium atoms on the surface of helium nanodroplets (HNDs) containing 1000 atoms is described by the ZPAD-mPL approach, a zero-point averaged dynamics (ZPAD) method based on a He–He pseudopotential adjusted to better reproduce the total energy of He1000. Four types of collisional patterns were identified depending on the initial projectile speed v0 and impact parameter b. At the lowest speeds (v0 ≲ 250 m s−1), Cs atoms are softly captured by the HND surface, while at the highest ones (v0 ≳ 500–600 m s−1), Cs atoms can travel through the droplet and move away. In between these two extreme cases, Cs atoms can be temporarily submerged in the HND before being expelled to the surface if b = 0 or cross the HND before being captured on its surface. The possibility for Cs capture at experimental velocities and droplet piercings at the highest ones contrasts with time-dependent density functional theory calculations, which predict Cs capture for velocities lower than 75 m s−1, and ring-polymer molecular dynamics (RPMD) or former ZPAD-like methods, which predict soft Cs capture up to 500 m s−1. ZPAD-mPL results are attributed to the liquid but non-superfluid nature of the droplet, which favors energy exchanges with the helium environment, and to low He–He binding energy and HND surface tension, which can stimulate helium ejections, especially at high projectile speeds. Despite the use of a pseudopotential to model He–He interactions, the heliophobicity of Cs atoms is maintained as demonstrated by their ability to remain localized on the HND surface or to be expelled to the HND surface after transient submersion in helium.
Orbits of a system of three point vortices and the associated chaotic mixing
Authors: Dritschel David G. , Dritschel Gregory N. , Scott Richard K.
Published: November 2024

We study the general periodic motion of a set of three point vortices in the plane, as well as the potentially chaotic motion of one or more tracer particles. While the motion of three vortices is simple in that it can only be periodic, the actual orbits can be surprisingly complex and varied. This rich behavior arises from the existence of both co-linear and equilateral relative equilibria (steady motion in a rotating frame of reference). Here, we start from a general (unsteady) co-linear array with arbitrary vortex circulations. The subsequent motion may take the vortices close to a distinct co-linear relative equilibrium or to an equilateral one. Both equilibrium states are necessarily unstable, as we demonstrate by a linear stability analysis. We go on to study mixing by examining Poincaré sections and finite-time Lyapunov exponents. Both indicate widespread chaotic motion in general, implying that the motion of three vortices efficiently mixes the nearby surrounding fluid outside of small regions surrounding each vortex.
Study on the effect of morphology of anthracite coal containing through-fracture on CO2 enhanced coalbed methane recovery
Authors: Liu Xinyuan , Zhang Lei , Pan Jiangzhong , Tian Ye , Sun Wenjibin , Tian Shixiang
Published: November 2024

When CO2 is injected into the coal seam, different forms of fractures within the coal have different effective diffusion areas and distribution characteristics for the gas, affecting methane's adsorption-desorption-diffusion and seepage behavior. In this study, based on the control experiments of the intact coal sample, CO2 injection experiments were carried out on three groups of coals containing through-fracture to investigate the influence of fracture morphology on CO2-enhanced coalbed methane recovery behaviors and to discuss and analyze the changes in the volume of the coal samples, the composition of the tailing gas, and the changes in the permeability during the gas injection process. The results show that: the existence of fractures has an inhibitory effect on the volume expansion after gas adsorption of the coal, and the larger the surface area of fractures, the more obvious inhibitory effect, and at the same time, the faster the strain rate; the breakthrough time of CO2 in the fractured coal samples is much shorter than that in the intact samples; the increase in the surface area of the fractures and uniformity of distribution can enhance the concentration of CH4 in the tail gas, and in the pre-injection stage, uniformity of the distribution of the fractures is more important than the surface area of the fractures in increasing the output CH4 concentration; the magnitude of permeability change and the change rate of the coal samples during CO2 injection increased with the increase in the fracture surface area of the coal samples.
Microstructural characterization of DEM-based random packings of monodisperse and polydisperse non-convex particles
Authors: Ma Zhihong , Jia Mingkun , Liu Jiaping , Xu Wenxiang
Published: November 2024

Understanding of hard particles in morphologies and sizes on microstructures of particle random packings is of significance to evaluate physical and mechanical properties of many discrete media, such as granular materials, colloids, porous ceramics, active cells, and concrete. The majority of previous lines of research mainly dedicated microstructure analysis of convex particles, such as spheres, ellipsoids, spherocylinders, cylinders, and convex-polyhedra, whereas little is known about non-convex particles that are more close to practical discrete objects in nature. In this study, the non-convex morphology of a three-dimensional particle is devised by using a mathematical-controllable parameterized method, which contains two construction modes, namely, the uniformly distributed contraction centers and the randomly distributed contraction centers. Accordingly, three shape parameters are conceived to regulate the particle geometrical morphology from a perfect sphere to arbitrary non-convexities. Random packing models of hard non-convex particles with mono-/poly-dispersity in sizes are then established using the discrete element modeling Diverse microstructural indicators are utilized to characterize configurations of non-convex particle random packings. The compactness of non-convex particles in packings is characterized by the random close packing fraction fd and the corresponding average coordination number Z. In addition, four statistical descriptors, encompassing the radial distribution function g(r), two-point probability function S2(i)(r), lineal-path function L(i)(r), and cumulative pore size distribution function F(δ), are exploited to demonstrate the high-order microstructure information of non-convex particle random packings. The results demonstrate that the particle shape and size distribution have significant effects on Z and fd; the construction mode of the randomly distributed contraction centers can yield higher fd than that of the uniformly distributed contraction centers, in which the upper limit of fd approaches to 0.632 for monodisperse sphere packings. Moreover, non-convex particles of sizes following the famous Fuller distribution of the power-law distribution of the exponent q = 2.5, have the highest fd (≈0.761) with respect to other q. In contrast, the particle shapes have an almost negligible effect on the four statistical descriptors, but they are remarkably sensitive to particle packing fraction fp and size distribution. The results can provide sound guidance for custom-design of granular media by tailoring specific microstructures of particles.