PDB-Struct: A Comprehensive Benchmark for Structure-based Protein Design

Structure-based protein design has attracted increasing interest, with numerous methods being introduced in recent years. However, a universally accepted method for evaluation has not been established, since the wet-lab validation can be overly time-consuming for the development of new algorithms, and the $\textit{in silico}$ validation with recovery and perplexity metrics is efficient but may not precisely reflect true foldability. To address this gap, we introduce two novel metrics: refoldability-based metric, which leverages high-accuracy protein structure prediction models as a proxy for wet lab experiments, and stability-based metric, which assesses whether models can assign high likelihoods to experimentally stable proteins. We curate datasets from high-quality CATH protein data, high-throughput $\textit{de novo}$ designed proteins, and mega-scale experimental mutagenesis experiments, and in doing so, present the $\textbf{PDB-Struct}$ benchmark that evaluates both recent and previously uncompared protein design methods. Experimental results indicate that ByProt, ProteinMPNN, and ESM-IF perform exceptionally well on our benchmark, while ESM-Design and AF-Design fall short on the refoldability metric. We also show that while some methods exhibit high sequence recovery, they do not perform as well on our new benchmark. Our proposed benchmark paves the way for a fair and comprehensive evaluation of protein design methods in the future. Code is available at https://github.com/WANG-CR/PDB-Struct.Comment: 13 page

VoxelFormer: Bird's-Eye-View Feature Generation based on Dual-view Attention for Multi-view 3D Object Detection

In recent years, transformer-based detectors have demonstrated remarkable performance in 2D visual perception tasks. However, their performance in multi-view 3D object detection remains inferior to the state-of-the-art (SOTA) of convolutional neural network based detectors. In this work, we investigate this issue from the perspective of bird's-eye-view (BEV) feature generation. Specifically, we examine the BEV feature generation method employed by the transformer-based SOTA, BEVFormer, and identify its two limitations: (i) it only generates attention weights from BEV, which precludes the use of lidar points for supervision, and (ii) it aggregates camera view features to the BEV through deformable sampling, which only selects a small subset of features and fails to exploit all information. To overcome these limitations, we propose a novel BEV feature generation method, dual-view attention, which generates attention weights from both the BEV and camera view. This method encodes all camera features into the BEV feature. By combining dual-view attention with the BEVFormer architecture, we build a new detector named VoxelFormer. Extensive experiments are conducted on the nuScenes benchmark to verify the superiority of dual-view attention and VoxelForer. We observe that even only adopting 3 encoders and 1 historical frame during training, VoxelFormer still outperforms BEVFormer significantly. When trained in the same setting, VoxelFormer can surpass BEVFormer by 4.9% NDS point. Code is available at: https://github.com/Lizhuoling/VoxelFormer-public.git

Synthesis of Icariin-Zinc and its Protective Effect on Exercise Fatigue and Reproductive System Related Glands in Male Rats

Background: Icariin, a traditional Chinese medicine, plays a protective role in the treatment of exercise fatigue. Zinc, a trace element, plays an important role in the reproductive system. Therefore, we aimed to synthesize an Icariin-Zinc complex (by chemical means) and verify its protective effect on exercise fatigue and the reproductive system using animal experiments.Methods: The icariin-zinc complex was prepared by the reaction of icariin carbonyl and zinc ions (molar ratio 1:3). The molecular formula and structural formula of the complex were identified and tested. Fifty-six rats selected by swimming training were randomly divided into six groups: static control, exercise control, icariin, gluconate zinc (G-Zn group), icariin glucose zinc and icariin-zinc exercise ( low, high dose/L-E group, H-E group) groups. These groups respectively received the following doses: 1 ml/100 g, daily gavage with NS (for the first two groups), 45 mg/kg icariin, 110 mg/kg Gluconate Zinc, Icariin glucose zinc (45 mg/kg Icariin and 110 mg/kg Gluconate Zinc), 60 mg/kg icariin zinc and 180 mg/kg icariin zinc. After 3 weeks of gavage, we conducted 6 weeks of exhaustive swimming training. Test indices such as exhaustive swimming time of rats and body weight were evaluated after the last training exercise. The seminal vesicles, testes, and prostate gland were weighed, and their indices were calculated. The levels of testosterone (in the plasma) and glycogen (in the liver and muscle homogenates) were also evaluated using ELISA.Results: Compared with the static control group, the exhaustive swimming time of the rats in each group was prolonged. Compared with the other groups, the exhaustive swimming time of the L-E and H-E groups was significantly longer (p < 0.01); the Icariin-Zinc complex significantly increased the exhaustive swimming time of the rats. Compared with the static control group, the plasma testosterone content of the L-E and H-E groups increased significantly (p < 0.05). Compared with the exercise control group and G-Zn group, the plasma testosterone content of the H-E group also increased significantly (p < 0.01). The Icariin-Zinc complex significantly increased the serum levels of testosterone in rats. Compared with the control group, the muscle glycogen reserves of each group decreased, indicating that the muscle glycogen reserves of the rats decreased after swimming. Compared with other groups, the Icariin-Zinc complex can reduce the level of glycogen in the muscles, indicating that it can increase the utilization efficiency of glycogen in muscles. Compared with the static control and exercise control groups, the testicular weight of rats in the administration groups increased slightly. The Icariin-Zinc complex increased the testicular weight, indicating that the function of the reproductive system was improved to some extent.Conclusion: Icariin-Zinc can significantly prolong the exhaustive swimming time, improve exercise ability, and increase the plasma testosterone level (which is beneficial for improving the reproductive ability of male rats). Moreover, the beneficial effect of Icariin-Zinc on the glycogen content, testis index, and other reproductive system glands is dose-dependent

Pretrained Models for ESM-GearNet

<p>These are model weights of ESM-GearNet pre-trained with Multiview Contrast, Residue Type Prediction, Distance Prediction, Angle Prediction, and Dihedral Prediction. Please refer to the <a href="https://arxiv.org/abs/2303.06275">article</a> for further details.</p&gt

Delving into the Pre-training Paradigm of Monocular 3D Object Detection

The labels of monocular 3D object detection (M3OD) are expensive to obtain. Meanwhile, there usually exists numerous unlabeled data in practical applications, and pre-training is an efficient way of exploiting the knowledge in unlabeled data. However, the pre-training paradigm for M3OD is hardly studied. We aim to bridge this gap in this work. To this end, we first draw two observations: (1) The guideline of devising pre-training tasks is imitating the representation of the target task. (2) Combining depth estimation and 2D object detection is a promising M3OD pre-training baseline. Afterwards, following the guideline, we propose several strategies to further improve this baseline, which mainly include target guided semi-dense depth estimation, keypoint-aware 2D object detection, and class-level loss adjustment. Combining all the developed techniques, the obtained pre-training framework produces pre-trained backbones that improve M3OD performance significantly on both the KITTI-3D and nuScenes benchmarks. For example, by applying a DLA34 backbone to a naive center-based M3OD detector, the moderate ${\rm AP}_{3D}70$ score of Car on the KITTI-3D testing set is boosted by 18.71\% and the NDS score on the nuScenes validation set is improved by 40.41\% relatively

Optimization of immunoturbidimetric assay system enhanced by β2-microglobulin latex

In this study, three-factor and three-level orthogonal experiment was used to optimize the detection system of clinical renal function marker β2-microglobulin latex enhanced immune turbidity, so as to prepare a detection system with a wider linear range, solve the false negative problem in clinical detection of high-concentration samples, and improve the detection accuracy. Based on latex enhanced immunoturbidimetry, automatic biochemical analyzer was used to establish the linear relationship between the β2-microglobulin standard with different concentrations and the absorbance change value of 546 nm, and optimize the antibody source, latex microsphere particle size, activator concentration, sealer concentration and buffer system in the β2-microglobulin detection system. The linear range and accuracy of the optimized detection system were evaluated. After optimization, the optimal detection system was obtained, and its detection linear range was 0.2-30 mg/L, which reached the upper limit of the reference range of β2-microglobulin in normal population by 10 times, and the accuracy was in line with clinical standards, which solved the false negative problem of high-concentration samples in clinical testing, eliminated the repeated dilution process of high-concentration samples, simplified the detection steps, and improved the detection accuracy

Micrometer-Accuracy 2D Displacement Interferometer with Plasmonic Metasurface Resonators

In this Letter, a high-accuracy, two-dimensional displacement sensor is proposed, designed, and demonstrated based on the concept of an extrinsic Fabry–Perot Interferometer. The sensor is composed of two bundled single-mode optic fibers in parallel and two plasmonic metasurface resonators inscribed on a gold substrate via a focused ion beam. The fiber end surface and the metasurface are in parallel with a small cavity between. The cavity change or Z-component displacement is determined from the pattern of interference fringes. The X-component displacement, perpendicular to the Z component, is identified from wavelength-selective metasurface resonators, which possess unique resonant wavelengths due to different nanostructure designs. The sensor was calibrated with six displacements applied through a three-axis precision linear stage. Test results indicated that the proposed interferometer can measure displacements with a maximum error of 5.4 µm or 2.2%

Vibration Control of Semi-Submersible Offshore Wind Turbines Using Inerter-Based Absorbers

Compared with fixed offshore wind turbines, the vibration problem of floating offshore wind turbines is particularly prominent, and further reduction of the vibration of floating offshore wind turbines has become an engineering challenge. In order to solve this problem, a novel vibration suppression device, inerter-based absorber (IBA) is introduced, and the vibration control of semi-submersible offshore wind turbines is studied. A comprehensive optimization method, namely the structure-immittance approach, is utilized to design the IBA in a systematic way. In order to search for the optimum vibration suppression performance, a simplified dynamic model of the semi-submersible offshore wind turbine, and the IBA dynamic equations are established using D’Alembert’s principle. Simultaneous suppression of the vibration response of the floating platform and tower of a semi-submersible offshore wind turbine is realized using the dual IBA control strategy. Furthermore, by implementing the optimum IBA in the OpenFAST software, the vibration suppression benefits of the dual IBA compared with the dual tuned mass damper (TMD) are verified under the coupling effects of wind and waves. The results show that the vibration control performance of the dual IBA control strategy is significantly better than that of the single one, and that of the dual IBA is better than that of the dual TMD. In addition, under the condition of achieving the same suppression performance as the TMD, IBA installed at the nacelle and the platform can respectively decrease the required absorber mass by 23.9% and 32.2%, which can greatly reduce the manufacture cost of the device

β-Catenin signaling in hepatocellular carcinoma.

Deregulated Wnt/β-catenin signaling is one of the main genetic alterations in human hepatocellular carcinoma (HCC). Comprehensive genomic analyses have revealed that gain-of-function mutation of CTNNB1, which encodes β-catenin, and loss-of-function mutation of AXIN1 occur in approximately 35% of human HCC samples. Human HCCs with activation of the Wnt/β-catenin pathway demonstrate unique gene expression patterns and pathological features. Activated Wnt/β-catenin synergizes with multiple signaling cascades to drive HCC formation, and it functions through its downstream effectors. Therefore, strategies targeting Wnt/β-catenin have been pursued as possible therapeutics against HCC. Here, we review the genetic alterations and oncogenic roles of aberrant Wnt/β-catenin signaling during hepatocarcinogenesis. In addition, we discuss the implication of this pathway in HCC diagnosis, classification, and personalized treatment