Modeling the mechanochemical feedback for membrane-protein interactions using a continuum mesh model.

The Helfrich free energy is widely used to model the generation of membrane curvature due to different physical and chemical components. The governing equations resulting from the energy minimization procedure are a system of coupled higher order partial differential equations. Simulations of membrane deformation for obtaining quantitative comparisons against experimental observations require computational schemes that will allow us to solve these equations without restrictions to axisymmetric coordinates. Here, we describe one such tool that we developed in our group based on discrete differential geometry to solve these equations along with examples.

Tropical Logistic Regression Model on Space of Phylogenetic Trees.

Classification of gene trees is an important task both in the analysis of multi-locus phylogenetic data, and assessment of the convergence of Markov Chain Monte Carlo (MCMC) analyses used in Bayesian phylogenetic tree reconstruction. The logistic regression model is one of the most popular classification models in statistical learning, thanks to its computational speed and interpretability. However, it is not appropriate to directly apply the standard logistic regression model to a set of phylogenetic trees, as the space of phylogenetic trees is non-Euclidean and thus contradicts the standard assumptions on covariates. It is well-known in tropical geometry and phylogenetics that the space of phylogenetic trees is a tropical linear space in terms of the max-plus algebra. Therefore, in this paper, we propose an analogue approach of the logistic regression model in the setting of tropical geometry. Our proposed method outperforms classical logistic regression in terms of Area under the ROC Curve in numerical examples, including with data generated by the multi-species coalescent model. Theoretical properties such as statistical consistency have been proved and generalization error rates have been derived. Finally, our classification algorithm is proposed as an MCMC convergence criterion for Mr Bayes. Unlike the convergence metric used by Mr Bayes which is only dependent on tree topologies, our method is sensitive to branch lengths and therefore provides a more robust metric for convergence. In a test case, it is illustrated that the tropical logistic regression can differentiate between two independently run MCMC chains, even when the standard metric cannot.

The study of the influence of the geometry of a lateral electric field resonator on its resonant characteristics.

An experimental study of the dependence of the electrical impedance of a lateral electric field resonator on its thickness and the size of the gap between the electrodes was carried out. The resonator was made of PZT-19 piezoceramics in the form of a rectangular parallelepiped with the shear dimensions of 18 × 20 mm2. Two rectangular electrodes with a gap that varied in the range from 4 to 14 mm were applied on one side of the resonator. For each gap width, the frequency dependences of the real and imaginary parts of the electrical impedance were measured using an impedance analyzer. It has been found that increasing the gap width leads to an increase in the resonant frequency and to an increase in the maximum value of the real part of the impedance. Three series of such experiments were carried out for three values of the resonator thickness: 3.02, 2.38 and 1.9 mm. The resonant characteristics of the resonator were also theoretically analyzed by finite element analysis using two models. One resonator model was based on a two-dimensional finite element method. In this case, the vibration modes that existed due to the finite size of the plate in the direction parallel to the gap between the electrodes were not taken into account. The second model of the resonator used a three-dimensional finite element method, which correctly took into account all vibration modes existing in the resonator. Comparison of theory with experiment has shown that the three-dimensional model provides a better agreement between theoretical and experimental results.

DATA-DRIVEN IMAGING GEOMETRIC RECOVERY OF ULTRAHIGH RESOLUTION ROBOTIC MICRO-CT FOR IN-VIVO AND OTHER APPLICATIONS.

We introduce an ultrahigh-resolution (50µm) robotic micro-CT design for localized imaging of carotid plaques using robotic arms, cutting-edge detector, and machine learning technologies. To combat geometric error-induced artifacts in interior CT scans, we propose a data-driven geometry estimation method that maximizes the consistency between projection data and the reprojection counterparts of a reconstructed volume. Particularly, we use a normalized cross correlation metric to overcome the projection truncation effect. Our approach is validated on a robotic CT scan of a sacrificed mouse and a micro-CT phantom scan, both producing sharper images with finer details than that prior correction.

Exploring Progression and Differences in Facial Asymmetry for Hemifacial Microsomia and Isolated Microtia: Insights from Extensive 3D Analysis.

BACKGROUND: Aiming to measure and compare asymmetry of facial hard and soft tissues in patients with HFM and isolated microtia, examining how it evolves. METHODS: This cross-sectional study assessed facial asymmetry in male East Asian patients aged 5-12 diagnosed with unilateral hemifacial microsomia (Pruzansky-Kaban types I and IIA) or isolated microtia. Using 3D imaging of computed tomography scans, it measured root-mean-square (RMS) values for surface deviations across facial regions. Statistical analyses explored differences between conditions and the relationship of age with facial asymmetry. RESULTS: A total of 120 patients were categorized into four groups by condition (HFM or isolated microtia) and age (5-7 and 8-12 years). Patients with HFM exhibited the greatest asymmetry in the lower cheek, while those with isolated microtia showed primarily upper face asymmetry. Significant differences, except in the forehead and nasal soft tissue, were noted between the groups across age categories. Notable distinctions in hard tissue were found between age groups in the nasal and mid-cheek areas for patients with HFM (median RMS (mm) 0.9 vs. 1.1, P = 0.02; 1.5 vs. 1.7, P = 0.03) and in the nasal and upper lip areas for patients with isolated microtia (median RMS (mm) 0.8 vs. 0.9, P = 0.002; 0.8 vs. 1.0, P = 0.002). Besides these areas for HFM, no significant age-asymmetry correlation was detected. CONCLUSIONS: Significant differences in facial asymmetry were observed between HFM and isolated microtia, with the asymmetry in specific area evolving over time. LEVEL OF EVIDENCE IV: This journal requires that authors assign a level of evidence to each article. For a full description of these Evidence-Based Medicine ratings, please refer to the Table of Contents or the online Instructions to Authors www.springer.com/00266 .

Exploring advanced 2D acquisitions in breast tomosynthesis: T-shaped and Pentagon geometries.

In this study, we investigate the performance of advanced 2D acquisition geometries - Pentagon and T-shaped - in digital breast tomosynthesis (DBT) and compare them against the conventional 1D geometry. Unlike the conventional approach, our proposed 2D geometries also incorporate anterior projections away from the chest wall. Implemented on the Next-Generation Tomosynthesis (NGT) prototype developed by X-ray Physics Lab (XPL), UPenn, we utilized various phantoms to compare three geometries: a Defrise slab phantom with alternating plastic slabs to study low-frequency modulation; a Checkerboard breast phantom (a 2D adaptation of the Defrise phantom design) to study the ability to reconstruct the fine features of the checkerboard squares; and the 360° Star-pattern phantom to assess aliasing and compute the Fourier-spectral distortion (FSD) metric that assesses spectral leakage and the contrast transfer function. We find that both Pentagon and T-shaped scans provide greater modulation amplitude of the Defrise phantom slabs and better resolve the squares of the Checkerboard phantom against the conventional scan. Notably, the Pentagon geometry exhibited a significant reduction in aliasing of spatial frequencies oriented in the right-left (RL) medio-lateral direction, which was corroborated by a near complete elimination of spectral leakage in the FSD plot. Conversely T-shaped scan redistributes the aliasing between both posteroanterior (PA) and RL directions thus maintaining non-inferiority against the conventional scan which is predominantly affected by PA aliasing. The results of this study underscore the potential of incorporating advanced 2D geometries in DBT systems, offering marked improvements in imaging performance over the conventional 1D approach.

Fast Low-Sidelobe Pattern Synthesis Using the Symmetry of Array Geometry.

Array pattern synthesis with low sidelobe levels is widely used in practice. An effective way to incorporate sensor patterns in the design procedure is to use numerical optimization methods. However, the dimension of the optimization variables is very high for large-scale arrays, leading to high computational complexity. Fortunately, sensor arrays used in practice usually have symmetric structures that can be utilized to accelerate the optimization algorithms. This paper studies a fast pattern synthesis method by using the symmetry of array geometry. In this method, the problem of amplitude weighting is formulated as a second-order cone programming (SOCP) problem, in which the dynamic range of the weighting coefficients can also be taken into account. Then, by utilizing the symmetric property of array geometry, the dimension of the optimization problem as well as the number of constraints can be reduced significantly. As a consequence, the computational efficiency is greatly improved. Numerical experiments show that, for a uniform rectangular array (URA) with 1024 sensors, the computational efficiency is improved by a factor of 158, while for a uniform hexagonal array (UHA) with 1261 sensors, the improvement factor is 284.

The Characteristics of Long-Wave Irregularities in High-Speed Railway Vertical Curves and Method for Mitigation.

Track geometry measurements (TGMs) are a critical methodology for assessing the quality of track regularities and, thus, are essential for ensuring the safety and comfort of high-speed railway (HSR) operations. TGMs also serve as foundational datasets for engineering departments to devise daily maintenance and repair strategies. During routine maintenance, S-shaped long-wave irregularities (SLIs) were found to be present in the vertical direction from track geometry cars (TGCs) at the beginning and end of a vertical curve (VC). In this paper, we conduct a comprehensive analysis and comparison of the characteristics of these SLIs and design a long-wave filter for simulating inertial measurement systems (IMSs). This simulation experiment conclusively demonstrates that SLIs are not attributed to track geometric deformation from the design reference. Instead, imperfections in the longitudinal profile's design are what cause abrupt changes in the vehicle's acceleration, resulting in the measurement output of SLIs. Expanding upon this foundation, an additional investigation concerning the quantitative relationship between SLIs and longitudinal profiles is pursued. Finally, a method that involves the addition of a third-degree parabolic transition curve (TDPTC) or a full-wave sinusoidal transition curve (FSTC) is proposed for a smooth transition between the slope and the circular curve, designed to eliminate the abrupt changes in vertical acceleration and to mitigate SLIs. The correctness and effectiveness of this method are validated through filtering simulation experiments. These experiments indicate that the proposed method not only eliminates abrupt changes in vertical acceleration, but also significantly mitigates SLIs.

Computational analysis of electrode structure and configuration for efficient and localized neural stimulation.

Neuromodulation technique using electric stimulation is widely applied in neural prosthesis, therapy, and neuroscience research. Various stimulation techniques have been developed to enhance stimulation efficiency and to precisely target the specific area of the brain which involves optimizing the geometry and the configuration of the electrode, stimulation pulse type and shapes, and electrode materials. Although the effects of electrode shape, size, and configuration on the performance of neural stimulation have individually been characterized, to date, there is no integrative investigation of how this factor affects neural stimulation. In this study, we computationally modeled the various types of electrodes with varying shapes, sizes, and configurations and simulated the electric field to calculate the activation function. The electrode geometry is then integratively assessed in terms of stimulation efficiency and stimulation focality. We found that stimulation efficiency is enhanced by making the electrode sharper and smaller. A center-to-vertex distance exceeding 100 µm shows enhanced stimulation efficiency in the bipolar configuration. Additionally, the separation distance of less than 1 mm between the reference and stimulation electrodes exhibits higher stimulation efficiency compared to the monopolar configuration. The region of neurons to be stimulated can also be modified. We found that sharper electrodes can locally activate the neuron. In most cases, except for the rectangular electrode shape with a center-to-vertex distance smaller than 100 µm, the bipolar electrode configuration can locally stimulate neurons as opposed to the monopolar configuration. These findings shed light on the optimal selection of neural electrodes depending on the target applications.

Triaceto-nitrile-(1,4,7-trimethyl-1,4,7-tri-aza-cyclonona-ne)cobalt(II) bis-(tetra-phenyl-borate).

The title cobalt(II) complex, [Co(C2H3N)3(C9H21N3)](C24H20B)2 or [(tacn)Co(NCMe)3][BPh4]2, has been characterized by single-crystal X-ray diffraction. It incorporates the well-known macrocyclic tacn (1,4,7-trimethyl-1,4,7-tri-aza-cyclo-nona-ne) ligand, which is coordinated facially to the metal center. The complex crystallizes in space group P21/c with Z = 4. The divalent cobalt ion exhibits a six-coordinate octa-hedral geometry by one tacn and three aceto-nitrile ligands. Two non-coordinating tetra-phenyl-borate (BPh4 -) anions are also present.

Impact of impeller design on anaerobic digestion: Assessment of mixing dynamics, methane yield, microbial communities and digestate dewaterability.

The efficiency of anaerobic digestion (AD) processes is intricately tied to mixing quality. This research investigates the influence of two impeller types, namely a helical ribbon impeller (HRI) and a pitched-blade impeller (PBI), on key aspects of AD. The investigation encompassed mixing dynamics, methane production, microbial communities, and the previously unexplored impact on digestate dewaterability. Results show that agitation with the PBI exhibited stratification, with bottom layer TS values of 3.1% for the PBI and 2.6% for the HRI. Nevertheless, methane yield remained unchanged, averaging 286 LN/kg VSadded. Slower mixing with the HRI achieved more uniform mixing and reduced energy requirements. Additionally, impeller type significantly affected digestate dewaterability, leading to a 3.8% increase in TS of the dewatered sludge when using the PBI. These findings highlight the importance of considering mixing not only for methane production and reduced maintenance but also for achieving optimal digestate dewaterability.

Reference-free calibration method for asynchronous rotation in robotic CT.

BACKGROUND: Geometry calibration for robotic CT system is necessary for obtaining acceptable images under the asynchrony of two manipulators. OBJECTIVE: We aim to evaluate the impact of different types of asynchrony on images and propose a reference-free calibration method based on a simplified geometry model. METHODS: We evaluate the impact of different types of asynchrony on images and propose a novel calibration method focused on asynchronous rotation of robotic CT. The proposed method is initialized with reconstructions under default uncalibrated geometry and uses grid sampling of estimated geometry to determine the direction of optimization. Difference between the re-projections of sampling points and the original projection is used to guide the optimization direction. Images and estimated geometry are optimized alternatively in an iteration, and it stops when the difference of residual projections is close enough, or when the maximum iteration number is reached. RESULTS: In our simulation experiments, proposed method shows better performance, with the PSNR increasing by 2%, and the SSIM increasing by 13.6% after calibration. The experiments reveal fewer artifacts and higher image quality. CONCLUSION: We find that asynchronous rotation has a more significant impact on reconstruction, and the proposed method offers a feasible solution for correcting asynchronous rotation.

High physical activity is associated with greater cortical bone size, better physical function, and with lower risk of incident fractures independently of clinical risk factors in older women from the SUPERB study.

The Physical Activity Scale for the Elderly (PASE) is a validated test to assess physical activity in older people. It has not been investigated if physical activity, according to PASE, is associated with fracture risk independently from the clinical risk factors (CRFs) in FRAX, bone mineral density (BMD), comorbidity, and if such an association is due to differences in physical performance or bone parameters. The purpose of this study was to evaluate if PASE score is associated with bone characteristics, physical function, and independently predicts incident fracture in 3014 75-80-year-old women from the population-based cross-sectional SUPERB study. At baseline participants answered questionnaires, and underwent physical function tests, detailed bone phenotyping with dual x-ray absorptiometry, and high-resolution peripheral quantitative computed tomography. Incident fractures were x-ray verified. Cox regression models were used to assess the association between PASE score and incident fractures, with adjustments for CRFs, FN BMD and Charlson comorbidity index. Women were divided into quartiles according to PASE score. Quartile differences in bone parameters (1.56% for cortical volumetric BMD and 4.08% for cortical area, Q4 vs. Q1, p = 0.007 and p = 0.022, respectively) were smaller than quartile differences in physical performance (27% shorter timed up and go test, 52% longer one leg standing time, Q4 vs. Q1). During 8 years (median, range 0.20-9.9) of follow-up, 1077 women had any fracture, 806 a major osteoporotic fracture (MOF; spine, hip, forearm, humerus), and 236 a hip fracture. Women in Q4 had 30% lower risk of any fracture, 32% lower risk of MOF, and 54% lower risk of hip fracture, compared to women in Q1. These associations remained in fully adjusted models. In conclusion, high physical activity was associated with substantially better physical function and a lower risk of any fracture, MOF and hip fracture, independently of risk factors used in FRAX, FN BMD and comorbidity.

The Physical Activity Scale for the Elderly (PASE) is a test to assess physical activity in older people. The purpose of this study was to evaluate if physical activity, according to PASE, is associated with bone parameters, physical function, and independently predicts future fracture in 3014 75­80-year-old women from the population-based SUPERB study. At baseline participants answered questionnaires, underwent physical function tests and dual x-ray absorptiometry. Subsequent fractures were x-ray verified. Women were divided into quartiles according to PASE score (Q1 least and Q4 most physically active). Women in Q4 had 27% shorter timed up and go test and 52% longer one leg standing time compared with Q1. During 8 years of follow-up, 1077 women had any fracture, 806 a major osteoporotic fracture (MOF; spine, hip, forearm, humerus), and 236 a hip fracture. Women in Q4 had 30% lower risk of any fracture, 32% lower risk of MOF, and 54% lower risk of hip fracture, compared to women in Q1. These associations remained in models considering comorbidity, bone mineral density and clinical risk factors. In conclusion, high physical activity was independently associated with better physical function and a lower risk of any fracture.

Corn leaf disease: insightful diagnosis using VGG16 empowered by explainable AI.

The agricultural sector is pivotal to food security and economic stability worldwide. Corn holds particular significance in the global food industry, especially in developing countries where agriculture is a cornerstone of the economy. However, corn crops are vulnerable to various diseases that can significantly reduce yields. Early detection and precise classification of these diseases are crucial to prevent damage and ensure high crop productivity. This study leverages the VGG16 deep learning (DL) model to classify corn leaves into four categories: healthy, blight, gray spot, and common rust. Despite the efficacy of DL models, they often face challenges related to the explainability of their decision-making processes. To address this, Layer-wise Relevance Propagation (LRP) is employed to enhance the model's transparency by generating intuitive and human-readable heat maps of input images. The proposed VGG16 model, augmented with LRP, outperformed previous state-of-the-art models in classifying corn leaf diseases. Simulation results demonstrated that the model not only achieved high accuracy but also provided interpretable results, highlighting critical regions in the images used for classification. By generating human-readable explanations, this approach ensures greater transparency and reliability in model performance, aiding farmers in improving their crop yields.

A transient radial cortical microtubule array primes cell division in Arabidopsis.

Although the formation of new walls during plant cell division tends to follow maximal tensile stress direction, analyses of individual cells over time reveal a much more variable behavior. The origin of such variability as well as the exact role of interphasic microtubule behavior before cell division have remained mysterious so far. To approach this question, we took advantage of the Arabidopsis stem, where the tensile stress pattern is both highly anisotropic and stable. Although cortical microtubules (CMTs) generally align with maximal tensile stress, we detected a specific time window, ca. 3 h before cell division, where cells form a radial pattern of CMTs. This microtubule array organization preceded preprophase band (PPB) formation, a transient CMT array predicting the position of the future division plane. It was observed under different growth conditions and was not related to cell geometry or polar auxin transport. Interestingly, this cortical radial pattern correlated with the well-documented increase of cytoplasmic microtubule accumulation before cell division. This radial organization was prolonged in cells of the trm678 mutant, where CMTs are unable to form a PPB. Whereas division plane orientation in trm678 is noisier, we found that cell division symmetry was in contrast less variable between daughter cells. We propose that this "radial step" reflects a trade-off in robustness for two essential cell division attributes: symmetry and orientation. This involves a "reset" stage in G2, where an increased cytoplasmic microtubule accumulation transiently disrupts CMT alignment with tissue stress.

Quantum mechanics of particles constrained to spiral curves with application to polyene chains.

CONTEXT: Due to advances in synthesizing lower-dimensional materials, there is the challenge of finding the wave equation that effectively describes quantum particles moving on 1D and 2D domains. Jensen and Koppe and Da Costa independently introduced a confining potential formalism showing that the effective constrained dynamics is subjected to a scalar geometry-induced potential; for the confinement to a curve, the potential depends on the curve's curvature function. METHOD: To characterize the π electrons in polyenes, we follow two approaches. First, we utilize a weakened Coulomb potential associated with a spiral curve. The solution to the Schrödinger equation with Dirichlet boundary conditions yields Bessel functions, and the spectrum is obtained analytically. We employ the particle-in-a-box model in the second approach, incorporating effective mass corrections. The π - π ∗ transitions of polyenes were calculated in good experimental agreement with both approaches, although with different wave functions.

A Study of Directionality Effects in Three-Beam Coaxial Titanium Wire-Based Laser Metal Deposition.

Coaxial wire-based laser metal deposition is a versatile and efficient additive process that can achieve a high deposition rate in the manufacturing of complex structures. In this paper, a three-beam coaxial wire system is studied, with particular attention given to the effects of the deposition direction and laser beam orientation on the resulting bead geometry symmetry. With the three-beam laser delivery, the laser spot pattern is not always symmetric with respect to the deposition direction. Single titanium beads are deposited in different directions and at varying deposition rates, and the bead profile is quantitatively scored for multiple symmetry measures. Through an analysis of variance, the deposition direction and deposition rate were found to be insignificant with respect to the resulting bead symmetry for the developed measures. The bead symmetry and geometry are important factors in determining if a build is free of critical defects, and in this study, it is shown that the three-beam coaxial wire deposition setup is a directionally independent process.

The hemodynamic and geometric characteristics of carotid artery atherosclerotic plaque formation.

Background: Ischemic stroke, which has a high incidence, disability, and mortality rate, is mainly caused by carotid atherosclerotic plaque. The difference in the geometric structures of the carotid arteries inevitably leads to the variability in the local hemodynamics, which plays a key role in the formation of carotid atherosclerosis. At present, the combined mechanisms of hemodynamic and geometric in the formation of carotid atherosclerotic plaque are not clear. Thus, this study characterized the geometric and hemodynamic characteristics of carotid atherosclerotic plaque formation using four-dimensional (4D) flow magnetic resonance imaging (MRI). Methods: Ultimately, 122 carotid arteries from 61 patients were examined in this study. According to the presence of plaques at the bifurcation of the carotid artery on cervical vascular ultrasound (US), carotid arteries were placed into a plaque group (N=69) and nonplaque group (N=53). The ratio of the maximum internal carotid artery (ICA) inner diameter to the maximum common carotid artery (CCA) inner diameter (ICA-CCA diameter ratio), bifurcation angle, and tortuosity were measured using neck three-dimensional time-of-flight magnetic resonance angiography (3D TOF-MRA). Meanwhile, 4D flow MRI was used to obtain the following hemodynamic parameters of the carotid arteries: volume flow rate, velocity, wall shear stress (WSS), and pressure gradient (PG). Independent sample t-tests were used to compare carotid artery geometry and hemodynamic changes between the plaque group and nonplaque group. Results: The ICA-CCA diameter ratio between the plaque group and the nonplaque group was not significantly different (P=0.124), while there were significant differences in the bifurcation angle (P=0.005) and tortuosity (P=0.032). The bifurcation angle of the plaque group was greater than that of the nonplaque group (60.70°±20.75° vs. 49.32°±22.90°), and the tortuosity was smaller than that of the nonplaque group (1.07±0.04 vs. 1.09±0.05). There were no significant differences between the two groups in terms of volume flow rate (P=0.351) and the maximum value of velocity (velocitymax) (P=0.388), but the axial, circumferential, and 3D WSS values were all significantly different, including their mean values (all P values <0.001) and the maximum value of 3D WSS (P<0.001), with the mean axial, circumferential, 3D WSS values, along with the maximum 3D WSS value, being lower in the plaque group. The two groups also differed significantly in terms of maximum PG value (P=0.030) and mean PG value (P=0.026), with these values being greater in the nonplaque group than in the plaque group. Conclusions: A large bifurcation angle and a low tortuosity of the carotid artery are geometric risk factors for plaque formation in this area. Low WSS and low PG values are associated with carotid atherosclerotic plaque formation.