The application of state‐of‐the‐art deep‐learning approaches to the protein modeling problem has expanded the “high‐accuracy” category in CASP14 to encompass all targets. Building on the metrics used ...for high‐accuracy assessment in previous CASPs, we evaluated the performance of all groups that submitted models for at least 10 targets across all difficulty classes, and judged the usefulness of those produced by AlphaFold2 (AF2) as molecular replacement search models with AMPLE. Driven by the qualitative diversity of the targets submitted to CASP, we also introduce DipDiff as a new measure for the improvement in backbone geometry provided by a model versus available templates. Although a large leap in high‐accuracy is seen due to AF2, the second‐best method in CASP14 out‐performed the best in CASP13, illustrating the role of community‐based benchmarking in the development and evolution of the protein structure prediction field.
•Explained the basic principles of structured light technologies.•Surveyed the major high-speed 3D shape measurement techniques based on structured light methods.•Demonstrated comparing experimental ...and representative data for some popular methods.
High-speed 3D shape measurement (or imaging) has seen tremendous growths over the past decades, especially the past few years due to the improved speed of computing devices and reduced costs of hardware components. 3D shape measurement technologies have started penetrating more into our daily lives than ever before with the recent release of iPhone X that has an built-in 3D sensor for Face ID, along with prior commercial success of inexpensive commercial sensors (e.g., Microsoft Kinect). This paper overviews the primary state-of-the-art 3D shape measurement techniques based on structured light methods, especially those that could achieve high measurement speed and accuracy. The fundamental principles behind those technologies will be elucidated, experimental results will be presented to demonstrate capabilities and/or limitations for those popular techniques, and finally present our perspectives on those remaining challenges to be conquered to make advanced 3D shape measurement techniques ubiquitous.
In just one year, Spaceopal and its partners developed the Galileo HAS Performance Characterization User Algorithm for the EU Agency for the Space Programme (EUSPA). The Galileo HAS User Terminal ...(HAUT) hosts the Galileo HAS Performance Characterization User Algorithm. The Galileo HAS User Terminal is a portable, configurable and autonomous device powered by a triple-frequency Galileo and GPS receiver and calculates a single- (Galileo) or multi-constellation (Galileo + GPS) Galileo HAS and Open Service (OS) positioning, velocity and time (PVT) solution. The User Terminal can be configured to retrieve Galileo HAS corrections either from Galileo Signal-in-Space (SIS) over E6-B or Internet Data Distribution (IDD) over NTRIP in an RTCM3 format and works in different frequency combinations that can be configured by the user. The User Terminal is a robust device (IP64) with multiple communication and logging capabilities. The Galileo HAS Initial Service was declared on 24 January by the European Commission, and provides free-of-charge, high-accuracy Precise Point Positioning (PPP) corrections (orbits, clocks) and code biases for Galileo and GPS to achieve real-time improved user positioning performance. The Galileo HAS Service Definition Document (SDD) and the HAS SIS Interface Control Document (HAS SIS ICD) are freely available to users on the web portal of the European GNSS Service Centre and HAS Internet Data Distribution Interface Control Documents (HAS IDD ICD) are available after registration. Using the Galileo HAS User Terminal, this article presents the results of Galileo HAS User Terminal’s performance, configuring the User Algorithm to assume static dynamics. It is to be noted that this configuration provides a significant performance benefit with respect to a configuration compatible with kinematic operation. Preliminary results indicate the Galileo HAS User Terminal achieves excellent accuracy.
•Multi-vision system is powerful, but unavoidable errors emerge in global calibration.•Global calibration error can be corrected by registration of the common parts.•The features of the targets are ...more adaptive than those of the standard objects.•The corrected models reach higher accuracy than that without correction.•The mean absolute error is 1.06 mm, and the mean relative error is 0.52% respectively.
Multi-camera schemes can effectively increase the perception range of vision systems compared to single-camera schemes and are common in many optical applications. Unavoidable errors emerge in the global multi-camera calibration process, however, such as manufacturing error of the optical devices and computational error from marker detection algorithms, which drive down the accuracy of the camera system correlation. This paper discusses the causes of global calibration errors in detail. A four-camera vision system was built to obtain the visual information of targets including static objects and a dynamic concrete-filled steel tubular (CFST) specimen. Local calibration and global calibration were applied successively to realize multi-camera correlation, followed by filtering and stitching operations to acquire filtered global point clouds. A point cloud correction algorithm is designed accordingly to optimize the stitched point cloud structures and further improve the accuracy of the reconstructed surfaces. Based on the density features of the targets themselves (rather than standard calibration markers), the proposed point cloud correction algorithm is effective for various targets and adaptive under dynamic conditions. The point clouds and corresponding reconstructed models are shown to be more accurate after the proposed enhancement process. The point cloud correction algorithm also has strong adaptability to different static targets with complex surfaces and performs well under uncertain geometric changes and vibration. The results presented here provide both theoretical and practical support for advancements in multi-vision applications such as optical measurement, real-time target tracking, quality monitoring, and surface data acquisition.
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.
New auxiliary basis sets for use with the correlation consistent cc‐pV(n + d)Z orbital basis in density fitting Hartree–Fock calculations have been developed and demonstrate significantly improved performance for total molecular and reaction energies. Recommendations for their use in the Hartree–Fock component of an explicitly correlated calculation are also made.
The 3D-QSAR model is one of the most effective techniques for predicting the peptide bioactivity based on their structure properties. The accuracy of model prediction is highly dependent on the ...bio-activity of the peptides in its dataset. However, the same peptide used for constructing the database was reported to have obviously different activities in different published articles, which may significantly decrease the prediction accuracy. Based on this, we chose ACE inhibitory (ACE-I) dipeptides that can be absorbed directly into the human small intestine as research object. Ten dipeptides were randomly selected from the literatures for molecular docking with ACE and synthesized to test their activity. Ultimately, a linear equation was developed between bio-activities and docking scores, which was used to revalidate the reliable ACE-I activities of all reported dipeptides for constructing a credible dataset of 3D-QSAR model. The prediction accuracy was significantly enhanced and the model we established had a high Q2 = 0.840 and R2 = 0.998. Furthermore, dipeptide CW was predicted and tested in vitro to achieve the highest ACE-I activity (IC50 = 0.16 μM), and the inhibition mechanism was also investigated. This study introduced a new method for predicting bio-activity with high precision using the 3D-QSAR model.
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•A liner equation was built to revalidate the reliable ACE-I activity of the reported dipeptides.•Q2 and R2 of CoMSIA were both higher than most of other QSAR model.•CW was predicted and tested in vitro to have the highest ACE-I activity among dipeptides.•The inhibition constant Ki of CW was similar to the commercially antihypertensive drug fosinopril.•Hydrophobicity at C-terminal could significantly improve the ACE-I activity of dipeptide.
High-accuracy (HA) positioning services allow users to achieve sub-decimeter-level positioning accuracy. Although these kinds of services are not new, the market is showing great interest in ...exploiting them for new applications within the mass-market domain. This growing interest is causing a change in the paradigm of HA services, moving from niche sectors to applications targeting billions of users. Considering this framework, the Galileo High Accuracy Service (HAS) provides an open-access service based on the provision of high-accuracy corrections transmitted through the Galileo E6-B signal (E6, data component). The data retrieved by the end-user, which includes orbit, clock, and bias corrections, is reconstructed to allow the computation of Precise Point Positioning (PPP) solutions. This paper is focused on the description and results of GMV’s HAS Positioning Engine (HAS-PE) software library which, implements a PPP solution using the HAS corrections transmitted through Galileo Signal-in-Space. A high-level overview of the integration of the HAS in the Positioning Engine software is presented together with user performance assessments based on static and kinematic tests executed to process real data from GNSS receivers in real time. The static tests are performed using the GMV Global station network, which consists of geodetic grade receivers tracking the signal in open-sky locations around the globe. The kinematic tests are performed with a setup consisting of a mass-market receiver and a high-end receiver for obtaining the E6 pages. The PPP solutions are configured to process both Galileo and GPS corrections transmitted through the Galileo satellites. The assessment performed includes the computation of a set of performance indicators aimed at the analysis of high-accuracy positioning performances. The results of this assessment show that a PPP user taking advantage of this Galileo HAS initial service may easily achieve decimeter-level accuracy on the horizontal and vertical components.
An evolutionary‐based definition and classification of target evaluation units (EUs) is presented for the 14th round of the critical assessment of structure prediction (CASP14). CASP14 targets ...included 84 experimental models submitted by various structural groups (designated T1024–T1101). Targets were split into EUs based on the domain organization of available templates and performance of server groups. Several targets required splitting (19 out of 25 multidomain targets) due in part to observed conformation changes. All in all, 96 CASP14 EUs were defined and assigned to tertiary structure assessment categories (Topology‐based FM or High Accuracy‐based TBM‐easy and TBM‐hard) considering their evolutionary relationship to existing ECOD fold space: 24 family level, 50 distant homologs (H‐group), 12 analogs (X‐group), and 10 new folds. Principal component analysis and heatmap visualization of sequence and structure similarity to known templates as well as performance of servers highlighted trends in CASP14 target difficulty. The assigned evolutionary levels (i.e., H‐groups) and assessment classes (i.e., FM) displayed overlapping clusters of EUs. Many viral targets diverged considerably from their template homologs and thus were more difficult for prediction than other homology‐related targets. On the other hand, some targets did not have sequence‐identifiable templates, but were predicted better than expected due to relatively simple arrangements of secondary structural elements. An apparent improvement in overall server performance in CASP14 further complicated traditional classification, which ultimately assigned EUs into high‐accuracy modeling (27 TBM‐easy and 31 TBM‐hard), topology (23 FM), or both (15 FM/TBM).
In the article, we prove that the double inequalityπ2J(r′)−51π−160160r16<E(r)<π2J(r′)−5π3×231r16holds for all r ∈ (0, 1), where E(r)=∫0π/21−r2sin2(t)dt is the complete elliptic integral of the second ...kind, r′=(1−r2)1/2 andJ(r)=51r2+20rr+50r+20r+5116(5r+2r+5).
We proposed a single-color fluorogenic DNA decoding sequencing method designed to improve sequencing accuracy, increase read length and throughput, as well as decrease scanning time. This method ...involves the incorporation of a mixture of four types of 3’-O-modified nucleotide reversible terminators into each reaction. Among them, two nucleotides are labeled with the same fluorophore, while the remaining two are unlabeled. Only one nucleotide can be extended in each reaction, and an encoding that partially defines base composition can be obtained. Through cyclic interrogation of a template twice with different nucleotide combinations, two sets of encodings are sequentially obtained, enabling the determination of the sequence. We demonstrate the feasibility of this method using established sequencing chemistry, achieving a cycle efficiency of approximately 99.5 %. Notably, this strategy exhibits remarkable efficacy in the detection and correction of sequencing errors, achieving a theoretical error rate of 0.00016 % at a sequencing depth of ×2, which is lower than Sanger sequencing. This method is theoretically compatible with the existing sequencing-by-synthesis (SBS) platforms, and the instrument is simpler, which may facilitate further reductions in sequencing costs, thereby broadening its applications in biology and medicine. Moreover, we demonstrate the capability to detect known mutation sites using information from only a single sequencing run. We validate this approach by accurately identifying a mutation site in the human mitochondrial DNA.
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•We proposed a single-color fluorogenic DNA decoding sequencing, with conservative theoretical error rate as 0.00016 %.•This strategy is effective for correcting errors, and it greatly improves the sequencing accuracy.•This strategy can be utilized as an alternative to conventional sequencing systems.•This approach provides a powerful NGS tool to identify rare mutations.
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