Learning Harmonic Molecular Representations on Riemannian Manifold

Molecular representation learning plays a crucial role in AI-assisted drug discovery research. Encoding 3D molecular structures through Euclidean neural networks has become the prevailing method in the geometric deep learning community. However, the equivariance constraints and message passing in Euclidean space may limit the network expressive power. In this work, we propose a Harmonic Molecular Representation learning (HMR) framework, which represents a molecule using the Laplace-Beltrami eigenfunctions of its molecular surface. HMR offers a multi-resolution representation of molecular geometric and chemical features on 2D Riemannian manifold. We also introduce a harmonic message passing method to realize efficient spectral message passing over the surface manifold for better molecular encoding. Our proposed method shows comparable predictive power to current models in small molecule property prediction, and outperforms the state-of-the-art deep learning models for ligand-binding protein pocket classification and the rigid protein docking challenge, demonstrating its versatility in molecular representation learning.Comment: 25 pages including Appendi

Multimodal critical-scenarios search method for test of autonomous vehicles

Purpose – The purpose of this paper is to search for the critical-scenarios of autonomous vehicles (AVs) quickly and comprehensively, which is essential for verification and validation (V&V). Design/methodology/approach – The author adopted the index F1 to quantitative critical-scenarios' coverage of the search space and proposed the improved particle swarm optimization (IPSO) to enhance exploration ability for higher coverage. Compared with the particle swarm optimization (PSO), there were three improvements. In the initial phase, the Latin hypercube sampling method was introduced for a uniform distribution of particles. In the iteration phase, the neighborhood operator was adapted to explore more modals with the particles divided into groups. In the convergence phase, the convergence judgment and restart strategy were used to explore the search space by avoiding local convergence. Compared with the Monte Carlo method (MC) and PSO, experiments on the artificial function and critical-scenarios search were carried out to verify the efficiency and the application effect of the method. Findings – Results show that IPSO can search for multimodal critical-scenarios comprehensively, with a stricter threshold and fewer samples in the experiment on critical-scenario search, the coverage of IPSO is 14% higher than PSO and 40% higher than MC. Originality/value – The critical-scenarios' coverage of the search space is firstly quantified by the index F1, and the proposed method has higher search efficiency and coverage for the critical-scenarios search of AVs, which shows application potential for V&V

TrafficMOT: A Challenging Dataset for Multi-Object Tracking in Complex Traffic Scenarios

Multi-object tracking in traffic videos is a crucial research area, offering immense potential for enhancing traffic monitoring accuracy and promoting road safety measures through the utilisation of advanced machine learning algorithms. However, existing datasets for multi-object tracking in traffic videos often feature limited instances or focus on single classes, which cannot well simulate the challenges encountered in complex traffic scenarios. To address this gap, we introduce TrafficMOT, an extensive dataset designed to encompass diverse traffic situations with complex scenarios. To validate the complexity and challenges presented by TrafficMOT, we conducted comprehensive empirical studies using three different settings: fully-supervised, semi-supervised, and a recent powerful zero-shot foundation model Tracking Anything Model (TAM). The experimental results highlight the inherent complexity of this dataset, emphasising its value in driving advancements in the field of traffic monitoring and multi-object tracking.Comment: 17 pages, 7 figure

Realization of high-dynamic-range broadband magnetic-field sensing with ensemble nitrogen-vacancy centers in diamond

We present a new magnetometry method integrating an ensemble of nitrogen-vacancy (NV) centers in a single-crystal diamond with an extended dynamic range for monitoring the fast changing magnetic-field. The NV-center spin resonance frequency is tracked using a closed-loop frequency locked technique with fast frequency hopping to achieve a 10 kHz measurement bandwidth, thus, allowing for the detection of fast changing magnetic signals up to 0.723 T/s.This technique exhibits an extended dynamic range subjected to the working bandwidth of the microwave source. This extended dynamic range can reach up to 4.3 mT, which is 86 times broader than the intrinsic dynamic range. The essential components for NV spin control and signal processing such as signal generation, microwave frequency control, data processing and readout are integrated in a board-level system. With this platform, we demonstrate broadband magnetometry with an optimized sensitivity of 4.2 nT-Hz-1/2. This magnetometry method has the potential to be implemented in a multichannel frequency locked vector magnetometer suitable for a wide range of practical applications such as magnetocardiography and high-precision current sensors.Comment: 18 pages, 9 figure

Generation of Continuously Variable-mode Orbital Angular Momentum Beams

Orbital angular momentum (OAM) beam emitters with compact structure and high performance are highly desirable for wireless communication and radar technology. Here, we propose a compact emitter that only consists of a ring resonator and a feed line. Continuously-variable-mode OAM beams are generated by adjusting the wavelength and transmission path. The basic design principle and specific evaluation index are discussed. Both the simulated and experimental results demonstrate that the proposed emitter obtains the capacity of generating variable-modes. This approach opens a way for designing novel OAM beam emitter with desired properties

Paeonol Ameliorates Glucose and Lipid Metabolism in Experimental Diabetes by Activating Akt

Our previous study proved that paeonol (Pae) could lower blood glucose levels of diabetic mice. There are also a few reports of its potential use for diabetes treatment. However, the role of Pae in regulating glucose and lipid metabolism in diabetes remains largely unknown. Considering the critical role of serine/threonine kinase B (Akt) in glucose and lipid metabolism, we explored whether Pae could improve glucose and lipid metabolism disorders via Akt. Here, we found that Pae attenuated fasting blood glucose, glycosylated serum protein, serum cholesterol and triglyceride (TG), hepatic glycogen, cholesterol and TG in diabetic mice. Moreover, Pae enhanced glucokinase (GCK) and low-density lipoprotein receptor (LDLR) protein expressions, and increased the phosphorylation of Akt. In insulin-resistant HepG2 cells, Pae increased glucose uptake and decreased lipid accumulation. What’s more, Pae elevated LDLR and GCK expressions as well as Akt phosphorylation, which was consistent with the in vivo results. Knockdown and inhibition experiments of Akt revealed that Pae regulated LDLR and GCK expressions through activation of Akt. Finally, molecular docking assay indicated the steady hydrogen bond was formed between Pae and Akt2. Experiments above suggested that Pae ameliorated glucose and lipid metabolism disorders and the underlying mechanism was closely related to the activation of Akt

PCNA dependent cellular activities tolerate dramatic perturbations in PCNA client interactions

Proliferating cell nuclear antigen (PCNA) is an essential cofactor for DNA replication and repair, recruiting multiple proteins to their sites of action. We examined the effects of the PCNA(S228I) mutation that causes PCNA-associated DNA repair disorder (PARD). Cells from individuals affected by PARD are sensitive to the PCNA inhibitors T3 and T2AA, showing that the S228I mutation has consequences for undamaged cells. Analysis of the binding between PCNA and PCNA-interacting proteins (PIPs) shows that the S228I change dramatically impairs the majority of these interactions, including that of Cdt1, DNMT1, PolD3(p66) and PolD4(p12). In contrast p21 largely retains the ability to bind PCNA(S228I). This property is conferred by the p21 PIP box sequence itself, which is both necessary and sufficient for PCNA(S228I) binding. Ubiquitination of PCNA is unaffected by the S228I change, which indirectly alters the structure of the inter-domain connecting loop. Despite the dramatic in vitro effects of the PARD mutation on PIP-degron binding, there are only minor alterations to the stability of p21 and Cdt1 in cells from affected individuals. Overall our data suggests that reduced affinity of PCNA(S228I) for specific clients causes subtle cellular defects in undamaged cells which likely contribute to the etiology of PARD

Two new species and new records of Otocepheidae (Acari, Oribatida) from Yunnan, Southwest China

This work includes taxonomic data on four species of oribatid mites of the family Otocepheidae from Yunnan, China. Two new species of the genera Basiceramerus and Eurostocepheus are described, respectively. Basiceramerus ovatus sp. nov. differs from B. bangladeshensis Corpuz-Raros & Gruèzo, 2008 by the wavy marginalis passing the base of the adanal setae, prodorsal condyles well separated from median ones, a ventral ridge present, and the anal plate foveolate; it differs from B. igorotus Corpuz-Raros & Gruèzo, 2011 from Vietnam by the wavy marginalis passing the base of the adanal setae, a connected tutorium and lamelliform expansion, a ventral ridge present, a smooth genital plate, and seta an2 located close to the median margin of the anal opening; it differs from B. igorotus from the Philippines by the lamellar setae inserted behind the tip of the lamella, separated prodorsal condyles, lyrifissure im posterior to gla, genital plate smooth, anal plate foveolate, and the wavy marginalis passing the base of the adanal setae. Eurostocepheus (Eurostocepheus) sinutus sp. nov. differs from other known species of this genus by having a ventral groove between the genital aperture and the ventral ridge, eight pairs of notogastral setae, and distinctly shorter and thinner notogastral setae p1, p2, p3, h3. Eurostocepheus (Eurostocepheus) aquilinus Aoki, 1965 and E. (E.) mahunkai Mondal & Kundu, 1999 are reported for the first time from China