Accurate Template Research Articles

Constructing three-dimension digital rock with porosity information constraint: A double-network-cycled style-based deep-learning approach

Understanding reservoir properties from geophysical responses necessitates the construction of accurate petrophysical templates based on adequate petrophysical data. However, engineering coring is often limited by complex subsurface conditions and high costs. Artificial intelligence (AI) techniques offer an efficient and economical way to synthesize digital samples. Nevertheless, traditional deep learning approaches may suffer from mode collapse, particularly when generating samples with complex structures from a limited number of training samples. To address this challenge, we propose novel Generative Adversarial Networks (GANs) to controllably generate 3D digital rock samples according to porosity distribution. By employing a style-transfer generator, multi-scale information of 3D digital rock is integrated into the generation process, effectively reducing the risk of mode collapse. Embedding the generator into a double-network-cycled framework further enhances the controllability of conditional information in the generated samples. Our analysis shows that the minimum error between the generated samples and the desired samples in terms of porosity is only 0.07%. A clear contrast is observed in morphological parameters, and differences in pore structure lead to significant variations in mechanical and hydraulic properties between original samples and synthetic samples with similar porosity. This indicates that the property contrast is likely caused by differences in pore structures rather than porosity. These findings will assist in future studies on the effect of pore structure on petrophysical properties and improve the utility of rock physics templates in geophysical inversion.

Measuring scalar charge with compact binaries: High accuracy modeling with self-force

Using the self-force approach, we present the premier first-post-adiabatic accuracy formalism for modeling compact binaries in theories with a massless scalar field nonminimally coupled to gravity. We limit the binary secondary to being a non-spinning compact body with no scalar dipole (we will address the spinning and scalar dipole cases in an upcoming paper). By producing an ansatz for the scalar charged point particle action, we derive first- and second-order perturbative field equations and equations of motion for the secondary compact object. Under our assumptions, implementing this formalism will produce sufficiently accurate waveform templates for precision measurements of the scalar charge of the secondary with LISA data on extreme-mass-ratio inspirals. Our formalism is consistent with almost general scalar-tensor theories of gravity. Implementing our formalism builds on self-force models in general relativity; we show the incorporation into the two-timescale formalism is straightforward. Excitingly, implementation poses no significantly more challenging barriers than computing first-post-adiabatic waveforms in general relativity. Published by the American Physical Society 2024

Optimized SMRT-UMI protocol produces highly accurate sequence datasets from diverse populations-Application to HIV-1 quasispecies.

Pathogen diversity resulting in quasispecies can enable persistence and adaptation to host defenses and therapies. However, accurate quasispecies characterization can be impeded by errors introduced during sample handling and sequencing, which can require extensive optimizations to overcome. We present complete laboratory and bioinformatics workflows to overcome many of these hurdles. The Pacific Biosciences single molecule real-time platform was used to sequence polymerase-chain reaction (PCR) amplicons derived from cDNA templates tagged with unique molecular identifiers (SMRT-UMI). Optimized laboratory protocols were developed through extensive testing of different sample preparation conditions to minimize between-template recombination during PCR. The use of UMI allowed accurate template quantitation as well as removal of point mutations introduced during PCR and sequencing to produce a highly accurate consensus sequence from each template. Production of highly accurate sequences from the large datasets produced from SMRT-UMI sequencing is facilitated by a novel bioinformatic pipeline, Probabilistic Offspring Resolver for Primer IDs (PORPIDpipeline). PORPIDpipeline automatically filters and parses circular consensus reads by sample, identifies and discards reads with UMIs likely created from PCR and sequencing errors, generates consensus sequences, checks for contamination within the dataset, and removes any sequence with evidence of PCR recombination, heteroduplex formation, or early cycle PCR errors. The optimized SMRT-UMI sequencing and PORPIDpipeline methods presented here represent a highly adaptable and established starting point for accurate sequencing of diverse pathogens. These methods are illustrated through characterization of human immunodeficiency virus quasispecies in a virus transmitter-recipient pair of individuals.

Learning accurate template matching with differentiable coarse-to-fine correspondence refinement

Template matching is a fundamental task in computer vision and has been studied for decades. It plays an essential role in manufacturing industry for estimating the poses of different parts, facilitating downstream tasks such as robotic grasping. Existing methods fail when the template and source images have different modalities, cluttered backgrounds, or weak textures. They also rarely consider geometric transformations via homographies, which commonly exist even for planar industrial parts. To tackle the challenges, we propose an accurate template matching method based on differentiable coarse-to-fine correspondence refinement. We use an edge-aware module to overcome the domain gap between the mask template and the grayscale image, allowing robust matching. An initial warp is estimated using coarse correspondences based on novel structure-aware information provided by transformers. This initial alignment is passed to a refinement network using references and aligned images to obtain sub-pixel level correspondences which are used to give the final geometric transformation. Extensive evaluation shows that our method to be significantly better than state-of-the-art methods and baselines, providing good generalization ability and visually plausible results even on unseen real data.

Reanalysis of a μ opioid receptor crystal structure reveals a covalent adduct with BU72

BackgroundThe first crystal structure of the active μ opioid receptor (μOR) exhibited several unexplained features. The ligand BU72 exhibited many extreme deviations from ideal geometry, along with unexplained electron density. I previously showed that inverting the benzylic configuration resolved these problems, establishing revised stereochemistry of BU72 and its analog BU74. However, another problem remains unresolved: additional unexplained electron density contacts both BU72 and a histidine residue in the N-terminus, revealing the presence of an as-yet unidentified atom.ResultsThese short contacts and uninterrupted density are inconsistent with non-covalent interactions. Therefore, BU72 and μOR form a covalent adduct, rather than representing two separate entities as in the original model. A subsequently proposed magnesium complex is inconsistent with multiple lines of evidence. However, oxygen fits the unexplained density well. While the structure I propose is tentative, similar adducts have been reported previously in the presence of reactive oxygen species. Moreover, known sources of reactive oxygen species were present: HEPES buffer, nickel ions, and a sequence motif that forms redox-active nickel complexes. This motif contacts the unexplained density. The adduct exhibits severe strain, and the tethered N-terminus forms contacts with adjacent residues. These forces, along with the nanobody used as a G protein substitute, would be expected to influence the receptor conformation. Consistent with this, the intracellular end of the structure differs markedly from subsequent structures of active μOR bound to Gi protein.ConclusionsLater Gi-bound structures are likely to be more accurate templates for ligand docking and modelling of active G protein-bound μOR. The possibility of reactions like this should be considered in the choice of protein truncation sites and purification conditions, and in the interpretation of excess or unexplained density.

Binary neutron star merger simulations with neutrino transport and turbulent viscosity: impact of different schemes and grid resolution

ABSTRACT We present a systematic numerical relativity study of the impact of different physics input and grid resolution in binary neutron star mergers. We compare simulations employing a neutrino leakage scheme, leakage plus M0 scheme, the M1 transport scheme, and pure hydrodynamics. Additionally, we examine the effect of a sub-grid scheme for turbulent viscosity. We find that the overall dynamics and thermodynamics of the remnant core are robust, implying that the maximum remnant density could be inferred from gravitational wave observations. Black hole collapse instead depends significantly on viscosity and grid resolution. Differently from recent work, we identify possible signatures of neutrino effects in the gravitational waves only at the highest resolutions considered; new high-resolution simulations will be thus required to build accurate gravitational wave templates to observe these effects. Different neutrino transport schemes impact significantly mass, geometry, and composition of the remnant’s disc and ejecta; M1 simulations show systematically larger proton fractions, reaching maximum values larger than 0.4. r-process nucleosynthesis yields reflect the different ejecta compositions; they are in agreement and reproduce residual solar abundances only if M0 or M1 neutrino transport schemes are adopted. We compute kilonova light curves using spherically-symmetric radiation-hydrodynamics evolutions up to 15 d post-merger, finding that they are mostly sensitive to the ejecta mass and electron fraction; accounting for multiple ejecta components appears necessary for reliable light curve predictions. We conclude that advanced neutrino schemes and resolutions higher than current standards are essential for robust long-term evolutions and detailed astrophysical predictions.

Modeling transient resonances in extreme-mass-ratio inspirals

Extreme-mass-ratio inspirals are one of the most exciting and promising target sources for space-based interferometers (such as LISA, TianQin). The observation of their emitted gravitational waves will offer stringent tests on general theory of relativity, and provide a wealth of information about the dense environment in galactic centers. To unlock such potential, it is necessary to correctly characterize EMRI signals. However, resonances are a phenomena that occurs in EMRI systems and can impact parameter inference, and therefore the science outcome, if not properly modeled. Here, we explore how to model resonances and develop an efficient implementation. Our previous work has demonstrated that tidal resonances induced by the tidal field of a nearby astrophysical object alters the orbital evolution, leading to a significant dephasing across observable parameter space. Here, we extensively explore a more generic model for the tidal perturber with additional resonance combinations, to study the dependence of resonance strength on the intrinsic orbital and tidal parameters. To analyze the resonant signals, accurate templates that correctly incorporate the effects of the tidal field are required. The evolution through resonances is obtained using a step function, whose amplitude is calculated using an analytic interpolation of the resonance jumps. We benchmark this procedure by comparing our approximate method to a numerical evolution. We find that there is no significant error caused by this simplified prescription, as far as the astronomically reasonable range in the parameter space is concerned. Further, we use Fisher matrices to study both the measurement precision of parameters and the systematic bias due to inaccurate modeling. Modeling of self-force resonances can also be carried out using the implementation presented in this study, which will be crucial for EMRI waveform modeling.

Saliency Detection via Fusing Color Contrast and Hash Fingerprint

Saliency detection is a technique for automatically extracting regions of interest from the background and has been widely used in the computer vision field. This study proposes a simple and effective saliency detection method combining color contrast and hash fingerprint. In our solution, the input image is segmented into nonoverlapping superpixels, so as to perform the saliency detection at the region level to reduce computational complexity. A background optimization selection is used to construct an accurate background template. Based on this, a saliency map that highlights the whole salient region is obtained by estimating color contrast. Besides, another saliency map that enhances the salient region while restraining the background is also generated through hash fingerprint matching. Ultimately, the final saliency map can be obtained by fusing the two saliency maps. Comparing the performance with other methods, the proposed algorithm works better even in the presence of complex background or very large salient regions.

Quantification of synthetic errors during chemical synthesis of DNA and its suppression by non-canonical nucleosides

Substitutions, insertions, and deletions derived from synthetic oligonucleotides are the hurdles for the synthesis of long DNA such as genomes. We quantified these synthetic errors by next-generation sequencing and revealed that the quality of the enzymatically amplified final combined product depends on the conditions of the preceding solid phase chemical synthesis, which generates the initial pre-amplified fragments. Among all possible substitutions, the G-to-A substitution was the most prominently observed substitution followed by G-to-T, C-to-T, T-to-C, and A-to-G substitutions. The observed error rate for G-to-A substitution was influenced by capping conditions, suggesting that the capping step played a major role in the generation of G-to-A substitution. Because substitutions observed in long DNA were derived from the generation of non-canonical nucleosides during chemical synthesis, non-canonical nucleosides resistant to side reactions could be used as error-proof nucleosides. As an example of such error-proof nucleosides, we evaluated 7-deaza-2´-deoxyguanosine and 8-aza-7-deaza-2´-deoxyguanosine and showed 50-fold decrease in the error rate of G-to-A substitution when phenoxyacetic anhydride was used as capping reagents. This result is the first example that improves the quality of synthesized sequences by using non-canonical nucleosides as error-proof nucleosides. Our results would contribute to the development of highly accurate template DNA synthesis technologies.

Recent progress in the structural study of ion channels as insecticide targets

Ion channels, many expressed in insect neural and muscular systems, have drawn huge attention as primary targets of insecticides. With the recent technical breakthroughs in structural biology, especially in cryo-electron microscopy (cryo-EM), many new high-resolution structures of ion channel targets, apo or in complex with insecticides, have been solved, shedding light on the molecular mechanism of action of the insecticides and resistance mutations. These structures also provide accurate templates for structure-based insecticide screening and rational design. This review summarizes the recent progress in the structural studies of 5 ion channel families: the ryanodine receptor (RyR), the nicotinic acetylcholine receptor (nAChR), the voltage-gated sodium channel (VGSC), the transient receptor potential (TRP) channel, and the ligand-gated chloride channel (LGCC). We address the selectivity of the channel-targeting insecticides by examining the conservation of key coordinating residues revealed by the structures. The possible resistance mechanisms are proposed based on the locations of the identified resistance mutations on the 3D structures of the target channels and their impacts on the binding of insecticides. Finally, we discuss how to develop "green" insecticides with a novel mode of action based on these high-resolution structures to overcome the resistance.

Clinical applications and prospects of 3D printing guide templates in orthopaedics.

BackgroundWith increasing requirements for medical effects, and huge differences among individuals, traditional surgical instruments are difficult to meet the patients' growing medical demands. 3D printing is increasingly mature, which connects to medical services critically as well. The patient specific surgical guide plate provides the condition for precision medicine in orthopaedics.MethodsIn this paper, a systematic review of the orthopedic guide template is presented, where the history of 3D-printing-guided technology, the process of guides, and basic clinical applications of orthopedic guide templates are described. Finally, the limitations of the template and possible future directions are discussed.ResultsThe technology of 3D printing surgical templates is increasingly mature, standard, and intelligent. With the help of guide templates, the surgeon can easily determine the direction and depth of the screw path, and choose the angle and range of osteotomy, increasing the precision, safety, and reliability of the procedure in various types of surgeries. It simplifies the difficult surgical steps and accelerates the growth of young and mid-career physicians. But some problems such as cost, materials, and equipment limit its development.ConclusionsIn different fields of orthopedics, the use of guide templates can significantly improve surgical accuracy, shorten the surgical time, and reduce intraoperative bleeding and radiation. With the development of 3D printing, the guide template will be standardized and simplified from design to production and use. 3D printing guides will be further sublimated in the application of orthopedics and better serve the patients.The translational potential of this paperPrecision, intelligence, and individuation are the future development direction of orthopedics. It is more and more popular as the price of printers falls and materials are developed. In addition, the technology of meta-universe, digital twin, and artificial intelligence have made revolutionary effects on template guides. We aim to summarize recent developments and applications of 3D printing guide templates for engineers and surgeons to develop more accurate and efficient templates.

A new and Homogeneous metallicity scale for Galactic classical Cepheids

Context. Classical Cepheids are the most popular distance indicators and tracers of young stellar populations. The key advantage is that they are bright and they can be easily identified in Local Group and Local Volume galaxies. Their evolutionary and pulsation properties depend on their chemical abundances. Aims. The main aim of this investigation is to perform a new and accurate abundance analysis of 20 calibrating Galactic Cepheids. We used high spectral resolution (R ~ 40 000–115 000) and high S/N spectra (~400), covering the entire pulsation cycle. Methods. We focused our attention on plausible systematics that would affect the estimate of atmospheric parameters and elemental abundances along the pulsation cycle. We cleaned the line list by using atomic transition parameters based on laboratory measurements and by removing lines that are either blended or that display abundance variations along the pulsation cycle. Results. The spectroscopic approach we developed brings forward small dispersions in the variation of the atmospheric parameters (σ(Teff) ~ 50 K, σ(log g) ~ 0.2 dex, and σ(ξ) ~ 0.2 kms−1) as well as in the abundance of both iron (≲0.05 dex) and α elements (≲0.10 dex) over the entire pulsation cycle. We also provide new and accurate effective temperature templates by splitting the calibrating Cepheids into four different period bins, ranging from short to long periods. For each period bin, we performed an analytical fit with Fourier series providing θ = 5040/Teff as a function of the pulsation phase. Conclusions. The current findings are a good viaticum for tracing the chemical enrichment of the Galactic thin disk by using classical Cepheids as a fundamental stepping stone for further investigations into the more metal-poor regime that is typical of Magellanic Cepheids.

Crystal structure of the PX domain of Vps17p from Saccharomyces cerevisiae.

The structure determination of the PX (phox homology) domain of the Saccharomyces cerevisiae Vps17p protein presented a challenging case for molecular replacement because it has noncrystallographic symmetry close to a crystallographic axis. The combination of diffraction-quality crystals grown under microgravity on the International Space Station and a highly accurate template structure predicted by AlphaFold2 provided the key to successful crystal structure determination. Although the structure of the Vps17p PX domain is seen in many PX domains, no basic residues are found around the canonical phosphatidylinositol phosphate (PtdIns-P) binding site, suggesting an inability to bind PtdIns-P molecules.

Adiabatic equatorial inspirals of a spinning body into a Kerr black hole

The detection of gravitational waves from Extreme mass Ratio Inspirals (EMRIs) by the future space-based gravitational-wave detectors demands the generation of accurate enough waveform templates. Since the spin of the smaller secondary body cannot be neglected for the detection and parameter estimation of EMRIs, we study its influence on the phase of the gravitational waves from EMRIs with spinning secondary. We focus on generic eccentric equatorial orbits around a Kerr black hole. To model the spinning secondary object, we use the Mathisson-Papapetrou-Dixon equations in the pole-dipole approximation. Furthermore, we linearize in spin the orbital variables and the gravitational-wave fluxes from the respective orbits. We obtain these fluxes by using the Teukolsky formalism in the frequency domain. We derive the evolution equations for the spin induced corrections to the adiabatic evolution of an inspiral. Finally, through their numerical integration we find the gravitational-wave phase shift between an inspiral of a spinning and a non-spinnig body.

Waveforms and fluxes: Towards a self-consistent effective one body waveform model for nonprecessing, coalescing black-hole binaries for third generation detectors

We present a comprehensive comparison between numerical relativity (NR) angular momentum fluxes at infinity and the corresponding quantity entering the radiation reaction in TEOBResumS, an Effective-One-Body (EOB) waveform model for nonprecessing coalescing black hole binaries on quasi-circular orbits. This comparison prompted us to implement two changes in the model: (i) including Next-to-Quasi-Circular corrections in the $\ell=m$, $\ell\leq 5$ multipoles entering the radiation reaction and (ii) consequently updating the NR-informed spin-orbital sector of the model. This yields a new waveform model that presents a higher self-consistency between waveform and dynamics and an improved agreement with NR simulations. We test the model computing the EOB/NR unfaithfulness $\bar{F}_{\rm EOB/NR}$ over all 534 spin-aligned configurations available through the Simulating eXtreme Spacetime catalog, notably using the noise spectral density of Advanced LIGO, Einstein Telescope and Cosmic Explorer, for total mass up to $500M_\odot$. We find that the maximum unfaithfulness $\bar{F}^{\rm max}_{\rm EOB/NR}$ is mostly between $10^{-4}$ and $10^{-3}$, and the performance progressively worsens up to $\sim 5\times 10^{-3}$ as the effective spin of the system is increased. We perform similar analyses on the \SEOB{} model, that delivers $\bar{F}^{\rm max}_{\rm EOB/NR}$ values uniformly distributed versus effective spin and mostly between $10^{-3}$ and $10^{-2}$. We conclude that the improved TEOBResumS model already represents a reliable and robust first step towards the development of highly accurate waveform templates for third generation detectors.

Crystal Structure Analysis and IgE Epitope Mapping of Allergic Predominant Region in Scylla paramamosain Filamin C, Scy p 9.

Filamin C (FLN c) is a novel allergen in shellfish. In this study, FLN c from Scylla paramamosain was divided into three regions for recombinant expression based on the number of domains and amino acids. Using dot blot and basophil activation tests, the allergic predominant region of FLN c was determined to be 336-531 amino acid positions (named FLN c-M). It was confirmed that by X-ray diffraction, the crystal structure of FLN c-M with immunoglobulin-like folding at a resolution of 1.7 Å was obtained. The monomer was a barrel structure composed of 16 β-strands and 2 α-helices. Three conformational epitopes were predicted, six linear epitopes were verified by serological test, and they were positioned on the crystal structure of FLN c-M. For the first time, the crystal structure of the allergic predominant region of FLN c was determined, and it provided an accurate template for the localization of IgE epitopes.

Tumor Microenvironment Responsive Single-Atom Nanozymes for Enhanced Antitumor Therapy.

Single-atom nanozymes (SAzymes) with specific response to the unique tumor microenvironment (TME) feature providing 100 % metal atoms utilization for high-efficient enzyme-catalyzed therapy and accurate template for the study of therapeutic mechanisms. In this review, we first introduce the various synthetic strategies of SAzymes, and the TME-responsive SAzymes activities. Next, the TME-responsive enhanced antitumor therapeutic approaches based on the enzymatic activities of SAzymes are summarized, and the corresponding therapy mechanisms are elaborated. Subsequently, a concise but concentrated summary, and the challenges and opportunities for the future design and engineering of SAzyme are outlined. As a new discipline, SAzymes have vast space for development in enhanced antitumor therapy. This timely review provides guidance and constructive suggestions for the future of SAzymes.

Influence of Different Fabrication Techniques on the Accuracy of Radiographic Scan Templates in Cases of Full-Arch Computer-Guided Implant Placement: An In Vitro Study.

To evaluate the influence of using different fabrication techniques, including intraoral scans, CBCT scans of patients' existing dentures, or denture duplicates, on the accuracy of radiographic scan templates. The influence of selecting different segmentation threshold values during reconstruction of CBCT data was also evaluated. A reference model was obtained by scanning five pairs of maxillary and mandibular acrylic complete dentures using a desktop laboratory laser scanner (DWOS 7Series, Dental Wings). Test scans were obtained from intraoral scans of dentures, CBCT scans of dentures and denture duplicates reconstructed at different grayscale segmentation thresholds, and a laboratory scan of denture duplicates. The resultant STL scan files were imported to an open source and cloud storage software (Medit Link) for the accuracy measurements by calculating root mean square estimate (RMSE) between reference and test scans. Collected data were then analyzed. Qualitative analysis was also performed using 3D color maps. The lowest RMSE (352.7) was found with intraoral denture scans. The highest RMSE (1,336.3) was found with the CBCT scans of the denture duplicates at segmentation threshold of -700 grayscale level. Qualitative analysis revealed that the intraoral denture scans exhibited the most homogenous deviation pattern relative to reference lab scans. Within the limitations of this study, the intraoral scans of the patients' existing dentures resulted in the fabrication of the most accurate radiographic scan templates. The improved accuracy of scan templates fabricated using the intraoral scanners can eliminate the possible laboratory errors associated with the conventional technical procedures as well as reduce the inaccuracies resulting from the image processing and segmentation of CBCT data.

Higher-order tail contributions to the energy and angular momentum fluxes in a two-body scattering process

The need for more and more accurate gravitational wave templates requires taking into account all possible contributions to the emission of gravitational radiation from a binary system. Therefore, working within a multipolar-post-Minkowskian framework to describe the gravitational wave field in terms of the source multipole moments, the dominant instantaneous effects should be supplemented by hereditary contributions arising from nonlinear interactions between the multipoles. The latter effects are referred to as tails being described in terms of integrals depending on the past history of the source. We compute higher-order tail (i.e., tail-of-tail and tail-squared) contributions to both energy and angular momentum fluxes and their averaged values along hyperboliclike orbits at the leading post-Newtonian approximation, using harmonic coordinates and working in the Fourier domain. Due to the increasing level of accuracy recently achieved in the determination of the scattering angle in a two-body system by several complementary approaches, the knowledge of these terms will provide useful information to compare results from different formalisms.

Integrating Vision System to a Pick and Place Cartesian Robot

Vision aided pick and place cartesian robot is a combination of machine vision system and robotic system. They communicate with each other simultaneously to perform object sorting. In this project, machine vision algorithm for object sorting to solve the problem in failure sorting due to imperfection of images edges and different types of colours is proposed. The image is acquired by a camera and followed by image calibration. Pre-processing of image is performed through these methods, which are HSI colour space transformation, Gaussian filter for image filtering, Otsu’s method for image binarization, and Canny edge detection. LabVIEW edge-based geometric matching is selected for template matching. After the vision application analysed the image, electrical signal will send to robotic arm for object sorting if the acquired image is matched with template image. The proposed machine vision algorithm has yielded an accurate template matching score from 800 to 1000 under different disturbances and conditions. This machine vision algorithm provides more customizable parameters for each methods yet improves the accuracy of template matching.