DeepBAM: a high-accuracy single-molecule CpG methylation detection tool for Oxford nanopore sequencing.

Recent nanopore sequencing system (R10.4) has enhanced base calling accuracy and is being increasingly utilized for detecting CpG methylation state. However, the robustness and universality of the methylation calling model in officially supplied Dorado remains poorly tested. In this study, we obtained heterogeneous datasets from human and plant sources to carry out comprehensive evaluations, which showed that Dorado performed significantly different across datasets. We therefore developed deep neural networks and implemented several optimizations in training a new model called DeepBAM. DeepBAM achieved superior and more stable performances compared with Dorado, including higher area under the ROC curves (98.47% on average and up to 7.36% improvement) and F1 scores (94.97% on average and up to 16.24% improvement) across the datasets. DeepBAM-based whole genome methylation frequencies have achieved >0.95 correlations with BS-seq on four of five datasets, outperforming Dorado in all instances. It enables unraveling allele-specific methylation patterns, including regions of transposable elements. The enhanced performance of DeepBAM paves the way for broader applications of nanopore sequencing in CpG methylation studies.

High-accuracy protein model quality assessment using attention graph neural networks.

Great improvement has been brought to protein tertiary structure prediction through deep learning. It is important but very challenging to accurately rank and score decoy structures predicted by different models. CASP14 results show that existing quality assessment (QA) approaches lag behind the development of protein structure prediction methods, where almost all existing QA models degrade in accuracy when the target is a decoy of high quality. How to give an accurate assessment to high-accuracy decoys is particularly useful with the available of accurate structure prediction methods. Here we propose a fast and effective single-model QA method, QATEN, which can evaluate decoys only by their topological characteristics and atomic types. Our model uses graph neural networks and attention mechanisms to evaluate global and amino acid level scores, and uses specific loss functions to constrain the network to focus more on high-precision decoys and protein domains. On the CASP14 evaluation decoys, QATEN performs better than other QA models under all correlation coefficients when targeting average LDDT. QATEN shows promising performance when considering only high-accuracy decoys. Compared to the embedded evaluation modules of predicted ${C}_{\alpha^{-}} RMSD$ (pRMSD) in RosettaFold and predicted LDDT (pLDDT) in AlphaFold2, QATEN is complementary and capable of achieving better evaluation on some decoy structures generated by AlphaFold2 and RosettaFold. These results suggest that the new QATEN approach can be used as a reliable independent assessment algorithm for high-accuracy protein structure decoys.

Correcting correlation quality of portable X-ray fluorescence to better map heavy metal contamination by spatial co-kriging interpolation.

High-precision mapping based on portable X-ray fluorescence (PXRF) data is currently being studied extensively; however, owing to poor correlation with soil metal concentration, the original PXRF data directly used for co-kriging interpolation (CKI) cannot accurately map contaminated sites with heterogeneous concentrations. Therefore, this study selected a landfill-contaminated site for research, explored the best correlation mode between PXRF variants and actual heavy metal concentration, analyzed the impact of improving the correlation model on the CKI of the spatial distribution of heavy metals, and explored the most appropriate CKI mode and point density. The results showed the following: (1) After nonlinear transformation, the correlation model between PXRF and the actual concentration was significantly improved, and the correlation coefficients of five heavy metals increased from 0.214-0.232 to 0.936-0.986. (2) The introduction of corrected PXRF data significantly improves the accuracy of CKI. Compared with the original PXRF co-kriging interpolation (OP-CKI), the ME of the corrected PXRF co-kriging interpolation (CP-CKI) for Zn, Pb, and Cu decreased by 78.2 %, 45.5 %, and 65.3 %, respectively. In terms of the spatial distribution of heavy metal pollutant concentrations, CP-CKI effectively improved the influence of local anomalous high-value points on the interpolation accuracy. (3) When the sample density measured by inductively coupled plasma mass spectrometry (ICP-MS) was less than 4 boreholes/hm2, CKI accuracy decreased significantly, indicating that the sample density should not be less than a certain threshold during CKI. (4) When the sample density measured by PXRF exceeded 7 boreholes/hm2, the mean error and root mean square error of CKI continued to decrease, suggesting that the introduction of enough sample density measured by PXRF can effectively improve the accuracy of CKI.

RTK+OSNMA Positioning for Road Applications: An Experimental Performance Analysis in Finland.

We compare the performance of dual-band (GPS L1/L2 and Galileo E1/E5a) real-time kinematic (RTK) positioning in an open sky and urban scenarios in southern Finland using two different authentication schemes: one using only satellites authenticated by Galileo's open service navigation message authentication (OSNMA) service (which at the moment of our tests led to using only authenticated Galileo satellites) and the other with no authentication. The results show the actual trade-off between accuracy and availability vs. authenticity associated with using only OSNMA-authenticated satellites, while the authentication of only Galileo satellites is possible (e.g., a drop of RTK positioning availability from 96.67 to 86.01% in our open sky and from 73.55 to 18.65% in our urban scenarios, respectively), and an upper bound of the potential performance that could be reached in similar experimental conditions had the authentication of GPS satellites been supported (e.g., an overall 14 cm and 10.20 m 95% horizontal accuracy in our open sky and urban scenarios, with below 30, 20 and 10 cm during 97.39, 96.03 and 92.43% of the time in the open sky and 49.12, 45.96 and 39.63% in the urban scenarios, respectively).

A Self-Temperature Compensation Barometer Based on All-Quartz Resonant Pressure Sensor.

This paper reports a self-temperature compensation barometer based on a quartz resonant pressure sensor. A novel sensor chip that contains a double-ended tuning fork (DETF) resonator and a single-ended tuning fork (SETF) resonator is designed and fabricated. The two resonators are designed on the same diaphragm. The DETF resonator works as a pressure sensor. To reduce the influence of the temperature drift, the SETF resonator works as a temperature compensation sensor, which senses the instantaneous temperature of the DETF resonator. The temperature compensation method based on polynomial fitting is studied. The experimental results show that the accuracy is 0.019% F.S. in a pressure range of 200~1200 hPa over a temperature range of -20 °C~+60 °C. The absolute errors of the barometer are within ±23 Pa. To verify its actual performance, a drone flight test was conducted. The test results are consistent with the actual flight trajectory.

Thermal Deformation Measurement of the Surface Shape of a Satellite Antenna Using High-Accuracy Close-Range Photogrammetry.

To determine both the size of a satellite antenna and the thermal deformation of its surface shape, a novel high-accuracy close-range photogrammetric technique is used in this study. The method is also applied to assess the performance of the antenna in orbit. The measurement principle and solution method of close-range photogrammetry were thoroughly investigated, and a detailed measurement test scheme was developed. A thermal deformation measurement of the surface shape of a satellite antenna was then carried out. The results show that the measurement error using close-range photogrammetry was smaller than 0.04 mm, which meets the accuracy requirement. Thanks to the high accuracy, it was discovered that both the surface shape and the rib precision of the satellite antenna deteriorate with decreasing temperature. The accuracy of the surface shape and ribs was lowest when the temperature node was -60 °C. The maximum root mean square errors (RMSEs) reached 0.878 mm and 0.761 mm, respectively. This indicates that the surface shape deformation error of the antenna caused by high and low temperatures is relatively high. However, the requirement for the technical design index (RMSE ≤ 1 mm for the surface shape accuracy of the antenna) is still met. Furthermore, for temperature differences of 40 °C and 80 °C, the measured RMSEs for the surface shape deformation were 0.216 mm and 0.411 mm, respectively. Overall, the technical design indicators (RMSE ≤ 0.3 mm and RMSE ≤ 0.5 mm, respectively) for the surface shape deformation of the antennas are met.

High-Precision Visual Servoing for the Neutron Diffractometer STRESS-SPEC at MLZ.

With neutron diffraction, the local stress and texture of metallic components can be analyzed non-destructively. For both, highly accurate positioning of the sample is essential, requiring the measurement at the same sample location from different directions. Current sample-positioning systems in neutron diffraction instruments combine XYZ tables and Eulerian cradles to enable the accurate six-degree-of-freedom (6DoF) handling of samples. However, these systems are not flexible enough. The choice of the rotation center and their range of motion are limited. Industrial six-axis robots have the necessary flexibility, but they lack the required absolute accuracy. This paper proposes a visual servoing system consisting of an industrial six-axis robot enhanced with a high-precision multi-camera tracking system. Its goal is to achieve an absolute positioning accuracy of better than 50µm. A digital twin integrates various data sources from the instrument and the sample in order to enable a fully automatic measurement procedure. This system is also highly relevant for other kinds of processes that require the accurate and flexible handling of objects and tools, e.g., robotic surgery or industrial printing on 3D surfaces.

Designing and Testing an IoT Low-Cost PPP-RTK Augmented GNSS Location Device.

Nowadays, the availability of affordable multi-constellation multi-frequency receivers has broadened access to accurate positioning. The abundance of satellite signals coupled with the implementation of ground- and satellite-based correction services has unlocked the potential for achieving real-time centimetre-level positioning with low-cost instrumentation. Most of the current and future applications cannot exploit well-consolidated satellite positioning techniques such as Network Real Time Kinematic (RTK) and Precise Point Positioning (PPP); the former is inapplicable for large user bases due to the necessity of a two-way communication link between the user and the NRTK service provider, while the latter necessitates long convergence times that are not in keeping with kinematic application. In this context, the hybrid PPP-RTK technique has emerged as a potential solution to meet the demand for real-time, low-cost, accurate, and precise positioning. This paper presents an Internet of Things (IoT) GNSS device developed with low-cost hardware; it leverages a commercial PPP-RTK correction service which delivers corrections via IP. The main target is to obtain both horizontal and vertical decimetre-level accuracies in urban kinematic tests, along with other requisites such as solution availability and the provision of connection ports for interfacing an IoT network. A vehicle-borne kinematic test has been conducted to evaluate the device performance. The results show that (i) the IoT device can deliver horizontal and vertical positioning solutions at decimetre-level accuracy with the targeted solution availability, and (ii) the provided IoT ports are feasible for gathering the position solutions over an internet connection.

Correlation consistent auxiliary basis sets in density fitting Hartree-Fock: The atoms sodium through argon revisited.

We present a series of auxiliary basis sets, for the elements Na to Ar, for use in density-fitted Hartree-Fock calculations with the correlation consistent cc-pV(n + d)Z orbital basis sets. Benchmarking on total molecular energies, reaction energies and the spectroscopic constants of the SO molecule demonstrate that the new sets address the deficiencies of using existing auxiliary sets in combination with these orbital basis sets. We also report auxiliary basis sets for Na and Mg matched to cc-pVnZ, along with recommendations for pairing auxiliary basis sets to the cc-pVnZ-F12 basis sets for Hartree-Fock calculations.

A magnetically controlled chemical-mechanical polishing (MC-CMP) approach for fabricating channel-cut silicon crystal optics for the High Energy Photon Source.

Crystal monochromators are indispensable optical components for the majority of beamlines at synchrotron radiation facilities. Channel-cut monochromators are sometimes chosen to filter monochromatic X-ray beams by virtue of their ultrahigh angular stability. Nevertheless, high-accuracy polishing on the inner diffracting surfaces remains challenging, thus hampering their performance in preserving the coherence or wavefront of the photon beam. Herein, a magnetically controlled chemical-mechanical polishing (MC-CMP) approach has been successfully developed for fine polishing of the inner surfaces of channel-cut crystals. This MC-CMP process relieves the constraints of narrow working space dictated by small offset requirements and achieves near-perfect polishing on the surface of the crystals. Using this method, a high-quality surface with roughness of 0.614 nm (root mean square, r.m.s.) is obtained in a channel-cut crystal with 7 mm gap designed for beamlines at the High Energy Photon Source, a fourth-generation synchrotron radiation source under construction. On-line X-ray topography and rocking-curve measurements indicate that the stress residual layer on the crystal surface was removed. Firstly, the measured rocking-curve width is in good agreement with the theoretical value. Secondly, the peak reflectivity is very close to theoretical values. Thirdly, topographic images of the optics after polishing were uniform without any speckle or scratches. Only a nearly 2.5 nm-thick SiO2 layer was observed on the perfect crystalline matrix from high-resolution transmission electron microscopy photographs, indicating that the structure of the bulk material is defect- and dislocation-free. Future development of MC-CMP is promising for fabricating wavefront-preserving and ultra-stable channel-cut monochromators, which are crucial to exploit the merits of fourth-generation synchrotron radiation sources or hard X-ray free-electron lasers.

Learning curve across 2000 thoracolumbar pedicle screw placements using O-arm navigation: technical difficulties and their solutions.

INTRODUCTION: Instrumentation using the intraoperative O-arm navigation technique appears safer than its predecessor techniques. However, only a handful of surgeons often used navigation during spinal surgeries. Too many operative glitches and unreliable navigation accuracy were the important reasons cited even by experienced surgeons for not using spinal navigation. We have studied the accuracy of pedicle screw placement during the learning curve and beyond it. We have also discussed in detail the intricacies of the technique and solutions to the difficulties encountered using spinal navigation. MATERIALS AND METHODS: A total of 2000 thoracolumbar pedicle screws have been placed in the 324 spine surgeries meeting the inclusion and exclusion criteria included in this retrospective study. We have divided 2000 pedicle screw placements into consecutive groups of 200 each. We have compared these groups for the accuracy of screw placement with the surgeon's experience. RESULTS: The accuracy of pedicle screw placement using the "in-versus-out" grading system in group 1 was 85.5% which significantly increased in group 2 to 93.5% (p-value: 0.0099), and thereafter, there was a nonsignificant increase in subsequent groups with the graph achieving the shape of a plateau. CONCLUSION: Surgeons should learn the correct principles of the technique of O-arm navigation to prevent the loss of accuracy and place pedicle screws with high accuracy. There is a learning curve of around 30-35 surgeries or 200 pedicle screw placements to acclimatize with the technique of O-arm navigation and learn its principles.

Application of "Galileo High Accuracy Service" on Single-Point Positioning.

Employment of precise positioning techniques will enable low-cost receivers for a variety of applications. The complexity of techniques such as Precise Point Positioning (PPP), or differential techniques that require the use of external sources of corrections, could be a disadvantage for users. On the other hand, a simple technique such as Single-Point Positioning (SPP) alone does not provide high-level accuracy. Nevertheless, the entry Galileo High-Accuracy Service (HAS), even if developed to be applied on PPP, could offer a positive impact on SPP. The objective of this study is the analysis of the effects of HAS on SPP, which are evaluated for Galileo and GPS, in single- and double-constellation mode. Results are encouraging, especially on the vertical channel, where some centimetric improvements are obtained.

Smart Temperature Sensor Design and High-Density Water Temperature Monitoring in Estuarine and Coastal Areas.

Acquiring in situ water temperature data is an indispensable and important component for analyzing thermal dynamics in estuarine and coastal areas. However, the long-term and high-density monitoring of water temperature is costly and technically challenging. In this paper, we present the design, calibration, and application of the smart temperature sensor TS-V1, a low-power yet low-cost temperature sensor for monitoring the spatial-temporal variations of surface water temperatures and air temperatures in estuarine and coastal areas. The temperature output of the TS-V1 sensor was calibrated against the Fluke-1551A sensor developed in the United States and the CTD-Diver sensor developed in the Netherlands. The results show that the accuracy of the TS-V1 sensor is 0.08 °C, while sensitivity tests suggest that the TS-V1 sensor (comprising a titanium alloy shell with a thermal conductivity of 7.6 W/(m °C)) is approximately 0.31~0.54 s/°C slower than the CTD-Diver sensor (zirconia shell with thermal conductivity of 3 W/(m °C)) in measuring water temperatures but 6.92~10.12 s/°C faster than the CTD-Diver sensor in measuring air temperatures. In addition, the price of the proposed TS-V1 sensor is only approximately 1 and 0.3 times as much as the established commercial sensors, respectively. The TS-V1 sensor was used to collect surface water temperature and air temperature in the western part of the Pearl River Estuary from July 2022 to September 2022. These data wells captured water and air temperature changes, frequency distributions, and temperature characteristics. Our sensor is, thus, particularly useful for the study of thermal dynamics in estuarine and coastal areas.

High-Accuracy Three-Dimensional Deformation Measurement System Based on Fringe Projection and Speckle Correlation.

Fringe projection profilometry (FPP) and digital image correlation (DIC) are widely applied in three-dimensional (3D) measurements. The combination of DIC and FPP can effectively overcome their respective shortcomings. However, the speckle on the surface of an object seriously affects the quality and modulation of fringe images captured by cameras, which will lead to non-negligible errors in the measurement results. In this paper, we propose a fringe image extraction method based on deep learning technology, which transforms speckle-embedded fringe images into speckle-free fringe images. The principle of the proposed method, 3D coordinate calculation, and deformation measurements are introduced. Compared with the traditional 3D-DIC method, the experimental results show that this method is effective and precise.

A Composite-Type MEMS Pirani Gauge for Wide Range and High Accuracy.

To achieve a wide range and high accuracy detection of the vacuum level, for example, in an encapsulated vacuum microcavity, a composite-type MEMS Pirani gauge has been designed and fabricated. The Pirani gauge consists of two gauges of different sizes connected in series, with one gauge having a larger heat-sensitive area and a larger air gap for extending the lower measurable limit of pressure (i.e., the high vacuum end) and the other gauge having a smaller heat-sensitive area and a smaller air gap for extending the upper measurable limit. The high-resistivity titanium metal was chosen as the thermistor; SiNx was chosen as the dielectric layer, considering the factors relevant to simulation and manufacturing. By simulation using COMSOL Multiphysics and NI Multisim, a range of measurement of 2 × 10-2 to 2 × 105 Pa and a sensitivity of 52.4 mV/lgPa were obtained in an N2 environment. The performance of the fabricated Pirani gauge was evaluated by using an in-house made vacuum test system. In the test, the actual points of measurement range from 6.6 × 10-2 to 1.12 × 105 Pa, and the highest sensitivity is up to 457.6 mV/lgPa. The experimental results are better in the range of measurement, sensitivity, and accuracy than the simulation results. The Pirani gauge proposed in this study is simple in structure, easy to manufacture, and suitable for integration with other MEMS devices in a microcavity to monitor the vacuum level therein.

Low-Cost GNSS and PPP-RTK: Investigating the Capabilities of the u-blox ZED-F9P Module.

GNSS has become ubiquitous in high-precision applications, although the cost of high-end GNSS receivers remains a major obstacle for many applications. Recent advances in GNSS receiver technology have led to the development of low-cost GNSS receivers, making high-precision positioning available to a wider range of users. One such technique for achieving high-precision positioning is Precise Point Positioning-Real Time Kinematic (PPP-RTK). It is a GNSS processing technique that combines the PPP and RTK approaches to provide high-precision positioning in real time without the need for a base station. In this work, we aim to assess the performance of the low-cost u-blox ZED-F9P GNSS module in PPP-RTK mode using the low-cost u-blox ANN-MB antenna. The experiment was designed to investigate both the time it takes the receiver to resolve the phase ambiguity and to determine the positioning accuracies achievable. Results showed that the u-blox ZED-F9P GNSS module could achieve centimeter-level positioning accuracy in about 60 s in PPP-RTK mode. These results make the PPP-RTK technique a good candidate to fulfill the demand for mass-market accurate and robust navigation since uses satellite-based corrections to provide accurate positioning information without the need for a local base station or network. Furthermore, due to its rapid acquisition capabilities and accurate data georeferencing, the technique has the potential to serve as a valuable method to improve the accuracy of the three-S techniques (GIS, remote sensing, and GPS/GNSS).

Accurate Nonlinearity and Temperature Compensation Method for Piezoresistive Pressure Sensors Based on Data Generation.

Piezoresistive pressure sensors exhibit inherent nonlinearity and sensitivity to ambient temperature, requiring multidimensional compensation to achieve accurate measurements. However, recent studies on software compensation mainly focused on developing advanced and intricate algorithms while neglecting the importance of calibration data and the limitation of computing resources. This paper aims to present a novel compensation method which generates more data by learning the calibration process of pressure sensors and uses a larger dataset instead of more complex models to improve the compensation effect. This method is performed by the proposed aquila optimizer optimized mixed polynomial kernel extreme learning machine (AO-MPKELM) algorithm. We conducted a detailed calibration experiment to assess the quality of the generated data and evaluate the performance of the proposed method through ablation analysis. The results demonstrate a high level of consistency between the generated and real data, with a maximum voltage deviation of only 0.71 millivolts. When using a bilinear interpolation algorithm for compensation, extra generated data can help reduce measurement errors by 78.95%, ultimately achieving 0.03% full-scale (FS) accuracy. These findings prove the proposed method is valid for high-accuracy measurements and has superior engineering applicability.

On methodology and application of smoothed particle hydrodynamics in fluid, solid and biomechanics.

Smoothed particle hydrodynamics (SPH), as one of the earliest meshfree methods, has broad prospects in modeling a wide range of problems in engineering and science, including extremely large deformation problems such as explosion and high velocity impact. This paper aims to provide a comprehensive overview on the recent advances of SPH method in the fields of fluid, solid, and biomechanics. First, the theory of SPH is described, and improved algorithms of SPH with high accuracy are summarized, such as the finite particle method (FPM). Techniques used in SPH method for simulating fluid, solid and biomechanics problems are discussed. The δ-SPH method and Godunov SPH (GSPH) based on the Riemann model are described for handling instability issues in fluid dynamics. Next, the interface contact algorithm for fluid-structure interaction is also discussed. The common algorithms for improving the tensile instability and the framework of total Lagrangian SPH are examined for challenging tasks in solid mechanics. In terms of biomechanics, the governing equations and the coupling forces based on SPH method are exemplified. Then, various typical engineering applications and recent advances are elaborated. The application of fluid mainly depicts the interaction between fluid and rigid body as well as elastomer, while some complicated fluid-structure interaction ocean engineering problems are also presented. In the aspect of solid dynamics, galaxy, geotechnical mechanics, explosion and impact, and additive manufacturing are summarized. Furthermore, the recent advancements of SPH method in biomechanics, such as hemodynamically and gut health, are discussed in general. In addition, to overcome the limitations of computational efficiency and computational scale, the multiscale adaptive resolution, the parallel algorithm and the automated mesh generation are addressed. The development of SPH software in China and abroad is also summarized. Finally, the challenging task of SPH method in the future is summarized. In future research work, the establishment of multi-scale coupled SPH model and deep learning technology in solid and biodynamics will be the focus of expanding the engineering applications of SPH methods.

High-Accuracy Height-Independent 3D VLP Based on Received Signal Strength Ratio.

Visible light positioning (VLP) has attracted intensive attention from both academic and industrial communities thanks to its high accuracy, immunity to electromagnetic interference, and low deployment cost. In general, the receiver in a VLP system determines its own position by exploring the received signal strength (RSS) from the transmitter according to a pre-built RSS attenuation model. In such model-based methods, the LED's emission power and the receiver's height are usually required known and constant parameters to obtain reasonable positioning accuracy. However, the LED's emission power is normally time-varying due to the fact that the LED's optical output power is prone to changing with the LED's temperature, and the receiver's height is random in a realistic application scenario. To this end, we propose a height-independent three-dimensional (3D) VLP scheme based on the RSS ratio (RSSR), rather than only using RSS. Unlike existing RSS-based VLP methods, our method is able to independently find the horizontal coordinate, i.e., two-dimensional (2D) position, without a priori height information of the receiver, and also avoids the negative effect caused by fluctuation of the LED's emission power. Moreover, we can further infer the height of the receiver to achieve three-dimensional (3D) positioning by iterating the 2D results back into positioning equations. To quickly verify the proposed scheme, we conduct theoretical analysis with mathematical proof and experimental results with real data, which confirm that the proposed scheme can achieve high position accuracy without known information of the receiver's height and LED's emission power. We also implement a VLP prototype with five LED transmitters, and experimental results show that the proposed scheme can achieve very low average errors of 2.73 cm in 2D and 7.20 cm in 3D.

Utilization of AlphaFold2 to Predict MFS Protein Conformations after Selective Mutation.

The major facilitator superfamily (MFS) is the largest secondary transporter family and is responsible for transporting a broad range of substrates across the biomembrane. These proteins are involved in a series of conformational changes during substrate transport. To decipher the transport mechanism, it is necessary to obtain structures of these different conformations. At present, great progress has been made in predicting protein structure based on coevolutionary information. In this study, AlphaFold2 was used to predict different conformational structures for 69 MFS transporters of E. coli after the selective mutation of residues at the interface between the N- and C-terminal domains. The predicted structures for these mutants had small RMSD values when compared to structures obtained using X-ray crystallography, which indicates that AlphaFold2 predicts the structure of MSF transporters with high accuracy. In addition, different conformations of other transporter family proteins have been successfully predicted based on mutation methods. This study provides a structural basis to study the transporting mechanism of the MFS transporters and a method to probe dynamic conformation changes of transporter family proteins when performing their function.