True Angles Research Articles

RNA-TorsionBERT: leveraging language models for RNA 3D torsion angles prediction.

Predicting the 3D structure of RNA is an ongoing challenge that has yet to be completely addressed despite continuous advancements. RNA 3D structures rely on distances between residues and base interactions but also backbone torsional angles. Knowing the torsional angles for each residue could help reconstruct its global folding, which is what we tackle in this work. This paper presents a novel approach for directly predicting RNA torsional angles from raw sequence data. Our method draws inspiration from the successful application of language models in various domains and adapts them to RNA. We have developed a language-based model, RNA-TorsionBERT, incorporating better sequential interactions for predicting RNA torsional and pseudo-torsional angles from the sequence only. Through extensive benchmarking, we demonstrate that our method improves the prediction of torsional angles compared to state-of-the-art methods. In addition, by using our predictive model, we have inferred a torsion angle-dependent scoring function, called TB-MCQ, that replaces the true reference angles by our model prediction. We show that it accurately evaluates the quality of near-native predicted structures, in terms of RNA backbone torsion angle values. Our work demonstrates promising results, suggesting the potential utility of language models in advancing RNA 3D structure prediction. Source code is freely available on the EvryRNA platform: https://evryrna.ibisc.univ-evry.fr/evryrna/RNA-TorsionBERT. Supplementary data are available from the website.

Mg Exosphere of Mercury Observed by PHEBUS Onboard BepiColombo During Its Second and Third Swing‐Bys

AbstractMercury's exosphere is an important target for understanding the dynamics of coupled systems in space environments, tenuous planetary atmospheres, and planetary surfaces. Magnesium (Mg) is especially crucial for establishing methods for estimating the surface chemical composition distribution through observations of the exosphere because its distribution in the exosphere and on the surface is strongly correlated. However, owing to its low radiance, the Hermean Mg exosphere has only been detected by the Mercury Atmospheric and Surface Composition Spectrometer (MASCS) onboard the Mercury Surface, Space Environment, Geochemistry, and Ranging (MESSENGER) spacecraft. Thus, we have few observation data for areas other than low latitude regions in addition to few detection cases of short‐term or sporadic fluctuations, resulting in a poor understanding of ejection and transportation mechanisms of the Mg exosphere. In this study, we analyzed the distribution of the Hermean Mg exosphere by the Probing of Hermean Exosphere by Ultraviolet Spectroscopy (PHEBUS) onboard the Mercury Planetary Orbiter of the BepiColombo mission during its second and third Mercury swing‐bys (MSBs). First, we constructed a calibration method including background subtraction and calibration using stellar observations. Mg light curves at two true anomaly angles were obtained, which were in agreement with the Chamberlain model and a three‐dimensional numerical calculation. Comparing the Mg and calcium (Ca) radiances obtained by PHEBUS during the MSBs, the exospheric Mg atoms have a lower energy than the exospheric Ca atoms. This is consistent with the lower energy necessary for producing the Mg atoms produced by molecular photodissociation than for Ca atoms.

Analysis of failure properties of red sandstone with structural plane subjected to true triaxial stress paths

In order to study the mechanical behavior and failure characteristics of rock mass with the structural plane in complex deep stress environment, the QKX-YB200 true triaxial rockburst test system, acoustic emission, and digital video recorder were adopted to conduct true triaxial loading and unloading indoor tests on the red sandstone cube specimens. The results show that: (1) Under true triaxial loading conditions, all specimens propagate in the form of anti-wing crack, and the dip angle of the structural plane is linearly related to the average value of the anti-wing crack propagation angle; under true triaxial unloading conditions, the specimens with structural plane dip angles of 30°, 45°, and 60° propagate in the form of wing crack, while those with a 90° angle propagate anti-wing cracks, and the closure of structural plane is related to the the crack type at the tips of structural plane. (2) The unstable failure stages in the stress–strain curve under true triaxial unloading are longer and exhibit more pronounced fluctuations; the peak strength of the specimens under the conditions of true triaxial loading and unloading decrease first and then increase with the increase of the dip angle, reaching the lowest at 45°. (3) During the true triaxial unloading tests, the rockburst degree of the intact rock specimens is more violent than that of the specimens with a structural plane. Additionally, the dip angle of the structural plane influences the severity of rockbursts under the same stress path. (4) The crack propagation mechanism and the closure degree of structural planes under different true triaxial stress paths and dip angles are discussed. It is observed that the crack initiation mode around the structural plane tips and the crack mode near free surface are closely related to the stress environment in different areas of the specimens. (5) Based on the indoor test results and previous experimental data, the differences in peak strength characteristics between open structural planes and closed structural planes are preliminarily analyzed and compared.

Reliability and accuracy of intraoperative fluoroscopy assessment of acetabular cup anteversion in supine direct anterior approach total hip arthroplasty

Poor implantation positioning of hip prostheses is considered the primary factor affecting postoperative joint wear. Cup anteversion in direct anterior approach (DAA) total hip arthroplasty (THA) is often excessive. Intraoperative fluoroscopy (IF) are effective for improving implant placement accuracy. This study aimed to analyze IF’s reliability and accuracy in assessing intraoperative anteversion. Sixty-two consecutive hips underwent primary THA utilizing DAA alongside IF for cup placement. Intraoperative anteversion was measured using IF images, while postoperative CT and standard anteroposterior (AP) radiographs were used to calculate true anteversion component angles. Differences and correlations between intraoperative and true anteversions were analyzed, and intraclass correlation coefficients (ICC) determined the inter- and intra-observer reliabilities. Excellent intra- and inter-observer reliabilities were observed for all radiographic and CT methods (ICC > 0.9). Strong correlations (PCC > 0.6) existed between anteversion measured on IF image and postoperative CT and AP pelvic measurements. Intraoperative anteversion measured on IF images (16.8 ± 3.2°) was smaller than anteversion measured postoperatively on AP X-rays (21.3 ± 4.7°, P < 0.001) and CT (22.0 ± 4.9°, P < 0.001), with average differences of 4.5°and 5.3°, respectively. Under several influencing factors, the accuracy of IF in assessing cup anteversion in DAA-THA may be limited. However, this still requires large-sample experiments for verification.

The effect of and correction for through-slice dephasing on 2D gradient-echo double angle mapping.

To show that variations through slice and slice profile effects are two major confounders affecting 2D dual angle maps using gradient-echo signals and thus need to be corrected to obtain accurate maps. The 2D gradient-echo transverse complex signal was Bloch-simulated and integrated across the slice dimension including nonlinear variations in inhomogeneities through slice. A nonlinear least squares fit was used to find the factor corresponding to the best match between the two gradient-echo signals experimental ratio and the Bloch-simulated ratio. The correction was validated in phantom and in vivo at 3T. For our RF excitation pulse, the error in the factor scales by approximately 3.8% for every 10 Hz/cm variation in along the slice direction. Higher accuracy phantom maps were obtained after applying the proposed correction; the root mean square error relative to the gold standard decreased from 6.4% to 2.6%. In vivo whole-liver maps using the corrected map registered a significant decrease in gradient through slice. inhomogeneities varying through slice were seen to have an impact on the accuracy of 2D double angle maps using gradient-echo sequences. Consideration of this confounder is crucial for research relying on accurate knowledge of the true excitation flip angles, as is the case of mapping using a spoiled gradient recalled echo sequence.

Quasi-bound states in the continuum in a metal nanograting metasurface for a high figure-of-merit refractive index sensor.

In this work, we investigate the bound states in the continuum (BICs) in a gold nanograting metal-insulator-metal metasurface structure at oblique angles of incidence. The nanograting metasurface consists of a gold nanograting patterned on a silicon dioxide dielectric film deposited on a thick gold film supported by a substrate. With rigorous full-wave finite difference time domain simulations, two bound states in the continuum are revealed upon transverse magnetic wave angular incidence. One BIC is formed by the interference between the surface plasmon polariton mode of the gold nanograting and the FP cavity mode. Another BIC mode is formed by the interference between the metal-dielectric hybrid structure guided mode resonance mode and the FP cavity mode. While true BIC modes cannot be observed, quasi-BIC modes are investigated at angles of incidence slightly off from the corresponding true BIC angles. It is shown that quasi-BIC modes can suppress radiation loss, resulting in narrow resonance spectral linewidths and high quality-factors. The quasi-BIC mode associated with the surface plasmon polariton mode is investigated for refractive index sensing. As a result, a high sensitivity refractive index sensor with a large figure-of-merit of 364 has been obtained.

Mercury's Exosphere as Seen by BepiColombo/PHEBUS Visible Channels During the First Two Flybys

AbstractBepiColombo, the ESA/JAXA joint mission performed its first flyby of Mercury on 1 October 2021 and its second on 23 June 2022. PHEBUS observed the exosphere of Mercury during these flybys notably with its visible channels c404 (centered on the potassium emission line at 404 nm) and c422 (centered on the calcium emission line at 422 nm). The c422 signal shows not only an enhancement of calcium (Ca) near the dawn region but also a very extensive Ca exosphere on the morning side beyond 10,000 km. The e‐folding distance deduced from our Ca profiles (2,500–2,800 km) is in agreement with the value reported by MESSENGER at similar true anomaly angles. We use a Chamberlain model to determine the temperature and density at the exobase. Using the morning side low‐altitude data, we derived a high temperature at the exobase (&gt;50,000 K), in agreement with the MESSENGER results. We also report a day/night asymmetry in the Ca exosphere that could indicate that the source of Ca is predominantly on the dayside or be the consequence of a shift of the main source of Ca away from the dawn region. The c404 channel detected additional species at low altitudes on the morning side during both flybys. Comparison with previous studies is inconclusive and further analysis will be necessary to identify the species. Nevertheless, we can note that the e‐folding distance deduced from our profile is relatively small (135 km) and that the Chamberlain model applied to our profiles seems to indicate a temperature at the exobase &lt;3,000 K.

A method for measuring the angle between left atrial and left ventricular long axes using 3D echocardiography.

Left ventricle (LV) optimized views are routinely used for left atrial (LA) volume and strain measurements on 2D echocardiography. This might be a source of the error because of the variation of the angle between the left atrial and left ventricle long axes (LA-LV angle), leading to foreshortening of the LA. We investigated two novel parameters: the angle between the left atrial and left ventricle long axes (LA-LV angle) and its deviation from the 4-chamber plane. To accurately measure the angles in 3D space, these measurements were performed using 3D echocardiography. We developed a method for the measurement based on marking anatomic points of reference in the 3D echocardiogram and measuring the angles between these points. We used three types of phantoms made of wood and agar-agar to investigate the repeatability and reproducibility of these measurements and performed measurements on human subjects. The ultrasound measurements were in excellent agreement with the true angles of the phantoms: LA-LV angle bias was .5 degrees (95% CI -1.8 to +2.7) in the wooden phantoms and 1.2 degrees (-.7 to +3.1) in the agar-agar phantoms, while the angle deviation from the 4-chamber plane was -.9 degrees (-4.3 to +4.1) in the wooden phantoms and .0 degrees (-3.3 to +3.3) in the agar-agar phantoms. The measurements demonstrated good repeatability and reproducibility (Pearson correlation coefficients ranging from .91 to .99). The measurements from human hearts showed good repeatability (Pearson correlation was .81 for repeated LA-LV angle measurements and .97 for repeated measurements of the deviation from the 4-chamber plane). The measurement of the LA-LV angle is a feasible tool to investigate one eventual error of 2D echocardiography.

Simultaneous Estimation of Hand Configurations and Finger Joint Angles Using Forearm Ultrasound

With the advancement in computing and robotics, it is necessary to develop fluent and intuitive methods for interacting with digital systems, augmented/virtual reality (AR/VR) interfaces, and physical robotic systems. Hand motion recognition is widely used to enable these interactions. Hand configuration classification and metacarpophalangeal (MCP) joint angle detection is important for a comprehensive reconstruction of hand motion. Surface electromyography (sEMG) and other technologies have been used for the detection of hand motions. Forearm ultrasound images provide a musculoskeletal visualization that can be used to understand hand motion. Recent work has shown that these ultrasound images can be classified using machine learning to estimate discrete hand configurations. Estimating both hand configuration and MCP joint angles based on forearm ultrasound has not been addressed in the literature. In this paper, we propose a convolutional neural network (CNN) based deep learning pipeline for predicting the MCP joint angles. The results for the hand configuration classification were compared by using different machine learning algorithms. Support vector classifier with different kernels, multi-layer perceptron, and the proposed CNN have been used to classify the ultrasound images into 11 hand configurations based on activities of daily living. Forearm ultrasound images were acquired from 6 subjects instructed to move their hands according to predefined hand configurations. Motion capture data was acquired to get the finger angles corresponding to the hand movements at different speeds (0.5 Hz, 1 Hz, & 2 Hz) for the index, middle, ring, and pinky fingers. Average classification accuracy of 82.7 ± 9.7% for the proposed CNN and over 80% for SVC for different kernels was observed on a subset of the dataset. An average RMSE of <inline-formula xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink"> <tex-math notation="LaTeX">$7.35^{\circ }\pm 1.3$ </tex-math></inline-formula> ° was obtained between the predicted and the true MCP joint angles. A low latency (6.25 - 9.1 Hz) pipeline has been proposed for estimating both MCP joint angles and hand configuration aimed at real-time control of human-machine interfaces.

Machine learning approaches demonstrate that protein structures carry information about their genetic coding

Synonymous codons translate into the same amino acid. Although the identity of synonymous codons is often considered inconsequential to the final protein structure, there is mounting evidence for an association between the two. Our study examined this association using regression and classification models, finding that codon sequences predict protein backbone dihedral angles with a lower error than amino acid sequences, and that models trained with true dihedral angles have better classification of synonymous codons given structural information than models trained with random dihedral angles. Using this classification approach, we investigated local codon–codon dependencies and tested whether synonymous codon identity can be predicted more accurately from codon context than amino acid context alone, and most specifically which codon context position carries the most predictive power.

Comparison of Mars rotation angle models

AbstractWe compare published solutions for the rotation angle W(t) which describes the location of the prime meridian of Mars with respect to the ICRF equator in IAU recommendations. If the model for W includes a very long period term, we transform it into a quadratic polynomial with updated epoch value and rate, resulting in a difference in the mean epoch value up to 200 km. The mean and true epoch rotation angles are about 800 mas (13 m) apart in J2000 and should not be confused with each other in order to accurately locate the prime meridian. We identify two groups of radio-science solutions for W, which can be distinguished by the prime meridian location they used as a priori that differ from each other by about 100 m at J2000.

A new method for assessing powder flowability based on physical properties and cohesiveness of particles using a small quantity of samples

Characterising powder flowability can be a challenge if only a small quantity of samples is available, e.g. pharmaceutical formulations. The paper focuses on a new method for assessing powder flowability based on physical properties and cohesiveness of particles using a few grams of powders. The technique applies Bond number to represent powder cohesiveness, which detects particle adhesion at median particle size using a mechanical surface energy tester developed at the Wolfson Centre. To establish the method, correlations between the Bond numbers and the flow functions of several powders measured on a shear cell tester have been explored empirically. With the correlations, a prediction model has been developed not only for powder flow functions but also for other flow properties such as compressibility, internal friction angles and true friction angles. This investigation has been undertaken using a wide range of materials from free-flowing to very cohesive for the method establishment and a group of different types of materials for a blind validation of the method. The methodology shows promising results for powder flowability prediction and other flow properties such as compressibility and internal friction angles. The validation results show a good agreement against the results measured using a shear cell tester.

Influence of Kite Characteristics on Propulsive Power Applied to Ship Auxiliary Propulsion

A Design of Experiment method was applied combined with a performance prediction program to assess the influence of four design parameters on the propulsive capacity of kites used as auxiliary propulsion for merchant vessels. Those parameters are the lift coefficient, the lift to drag ratio or drag angle, the maximal load bearable by the kite and the ratio of the tether length on the square root of the kite area. These parameters are independent from the kite area and, therefore, they could be used with various kite ranges and types. The maximum wing load parameter is the one that shows the most influence on the propulsive force. Over 50% of the gains obtained through this study are directly attributable to it. Then the ratio of the tether length on the square root of the kite area comes as the second greatest influence factor for true wind angles above 70°. While the drag angle is more influential for the narrower angles. In fact, the most substantial gains are made upwind.

Models for Generating and Processing of Signals of the Panoramic Sensor of Aerodynamic Angle and True Airspeed

The importance of information about the true airspeed and aerodynamic angles of aircraft and replenishment of arsenal of their measuring means with only electronic design scheme, low weight and cost, providing a panoramic measurement of the gliding angle is noted. It is shown that traditional measuring means of true airspeed of AP, which implement the aerodynamic and vane measuring methods of parameters of incoming air flow, using receivers and sensors distributed over the fuselage, have a complex design, significant weight and cost, and limited ranges of measuring aerodynamic angles, which limits their use on small-sized aircraft plane. The integrated sensor of aerodynamic angle and true airspeed, which implements a vortex method for measuring the parameters of incoming air flow, is considered. A single fixed flow receiver simplifies the design, and the time-frequency primary informative signals reduce the errors of instrumentation channel. The limited range of measurement of the gliding angle limits the use of the sensor on small AP. The integrated sensor of aerodynamic angle and true airspeed, which implements the ion-mark method for measuring the parameters of incoming air flow, is considered. The sensor provides a panoramic measurement of aerodynamic angle using receivers distributed in the measurement plane. But the multichannel measuring circuit significantly complicates the design, increases the weight and cost of the sensor, which limits its use on small-sized aircraft plane. The functional scheme of the original panoramic purely electronic sensor of the aerodynamic angle and true airspeed with one fixed receiver of the incoming air flow and ultrasonic instrumentation channels is revealed. Analytical models of the formation, processing and determination of the aerodynamic angle and true airspeed using frequency, time-pulse and phase informative signals are obtained. The analysis of the variants of used informative signals determines the prospects of using of the panoramic sensor with frequency informative signals on small-sized aircraft plane, in which there are no methodological errors from the influence of the ambient temperature when changing the flight altitude.

An Improved Procedure for Strongly Coupled Prediction of Sailing Yacht Performance

Abstract In this paper, an improved procedure for strongly coupled prediction of sailing yacht performance is developed. The procedure uses 3D RANS CFD to compute the hydrodynamic forces. When coupled to a rigid body motion solver and a sail force model, along with a rudder control algorithm, this allows sailing yacht performance to be predicted within CFD software. The procedure provides improved convergence when compared to a previously published method. The grid motion scheme, partially using overset grid techniques, means that correct alignment between the free surface and the background grid is ensured even at large heel angles. The capabilities are demonstrated with performance predictions for the SYRF 14 m yacht, at one true wind speed, over a range of true wind angles, with up- and downwind sailsets. The results are compared to predictions from the ORC-VPP for a yacht with similar main particulars.

A new method for estimating three-dimensional movement of the patella using a surface mapping method and computed tomography

IntroductionA previous study reported a method called the 2D-3D registration technique to examine three-dimensional movement of the patella. However, that method requires a biplane fluoroscopy system. In the present study, the aim was to establish a new method (CT-based surface mapping method) to estimate three-dimensional positions and angles of the patella with a motion capture system and CT. MethodsIn Study 1, the most appropriate parameters for the CT-based surface mapping method (i.e., target edge length, threshold of thickness of the soft tissue, and minimum distance between markers) were explored and determined. In Study 2, three-dimensional movement (i.e., positions and angles) of the patella using the CT-based surface mapping method and the most appropriate parameters were determined, and they were compared with the true positions and angles obtained by CT. ResultsThe results of Study 1 showed that the most appropriate conditions were as follows: (1) target edge length, 3 mm; (2) threshold of thickness of the soft tissue, 0–20 mm; and (3) minimum distance between markers, 10 mm. The results of Study 2 showed that the errors of the positions and angles were less than approximately 10 mm and 10° at most, respectively (both supine and sitting positions). ConclusionThe CT-based surface mapping method may be useful for a future study to clarify differences in three-dimensional movements of the patella between patients with patellar tendinitis and healthy subjects.

Organic chemistry lecture course and exercises based on true scale models

Abstract 3D models of chemical structures are an important tool for chemistry lectures and exercises. Usually, simplified models based on standard bond length and angles are used. These models allow for a visualized discussion of (stereo)chemical aspects, but they do not represent the true spatial conditions. 3D-printing technologies facilitate the production of scale models. Several protocols describe the process from X-ray structures, calculated geometries or virtual molecules to printable files. In contrast, only a few examples describe the integration of scaled models in lecture courses. True bond angles and scaled bond lengths allow for a detailed discussion of the geometry and parameters derived therefrom, for example double bond character, aromaticity and many more. Here, we report a complete organic chemistry/stereochemistry lecture course and exercise based on a set of 37 scale models made from poly(lactic acid) as sustainable material. All models have been derived from X-ray structures and quantum chemical calculations. Consequently, the models reflect the true structure as close as possible. A fixed scaling factor of 1 : 1.8·108 has been applied to all models. Hands-on measuring of bond angles and bond length leads to an interactive course. The course has been evaluated with a very positive feedback.

A Novel Fuzzy-Adaptive Extended Kalman Filter for Real-Time Attitude Estimation of Mobile Robots.

This paper proposes a novel fuzzy-adaptive extended Kalman filter (FAEKF) for the real-time attitude estimation of agile mobile platforms equipped with magnetic, angular rate, and gravity (MARG) sensor arrays. The filter structure employs both a quaternion-based EKF and an adaptive extension, in which novel measurement methods are used to calculate the magnitudes of system vibrations, external accelerations, and magnetic distortions. These magnitudes, as external disturbances, are incorporated into a sophisticated fuzzy inference machine, which executes fuzzy IF-THEN rules-based adaption laws to consistently modify the noise covariance matrices of the filter, thereby providing accurate and robust attitude results. A six-degrees of freedom (6 DOF) test bench is designed for filter performance evaluation, which executes various dynamic behaviors and enables measurement of the true attitude angles (ground truth) along with the raw MARG sensor data. The tuning of filter parameters is performed with numerical optimization based on the collected measurements from the test environment. A comprehensive analysis highlights that the proposed adaptive strategy significantly improves the attitude estimation quality. Moreover, the filter structure successfully rejects the effects of both slow and fast external perturbations. The FAEKF can be applied to any mobile system in which attitude estimation is necessary for localization and external disturbances greatly influence the filter accuracy.

Direction of Groove Detection for Wear Image of Four‐Ball Friction Test Based on Gray Difference of Inclination Angle

In order to avoid subjective estimation of the direction of groove by using a tester in the four‐ball friction test, an automatic wear angle detection method based on gray difference of inclination angle is proposed in this paper. First, the gray difference between the pixel and its W × 2W neighborhood pixels is acquired, in which each neighborhood pixel corresponds to an inclination angle. Second, a row’s grayscale difference of inclination angle is calculated, which is the sum of grayscale difference of all pixels in the same row with the same inclination angle. Third, the inclination angle corresponding to the minimum row’s grayscale difference is defined as the approach angles. Finally, the first t approaching angles with the highest frequency determine the wear angles. Compared with true angles determined manually, the simulation results of 200 samples show that the average absolute error is 2.1238° and the average running time is 1.3 s per frame. The influence of the algorithm parameters on detection precision is also analyzed.

Sparse linear array in the estimation of AoA and AoD with high resolution and low complexity

AbstractHigh resolution with low complexity angle of arrival and departure estimation in real‐time radar and wireless communication has been a topic of intensive research. In this paper, two novel algorithms are proposed, namely, minimum redundancy and minimum redundancy–reduced correlation algorithms, for finding the angles of arrival and departure with high resolution and low complexity. The first of the two proposed algorithms is meant for the reduction in the active number of antennas (minimum redundancy) without generating virtual angles. The second involves a reduction in subspace leakage to enable improvement of the peak power of the estimated true angles. The authors have assumed the users as coherent and the channel following Saleh‐Valenzuela model. This has been done for the validation of the performance of the proposed algorithms. Numerical simulations demonstrate the out performance of the existing sparse array subspace‐based methods in the estimation of angles by the proposed methods.