Elucidation of subfamily segregation and intramolecular coevolution of the olfactomedin-like proteins by comprehensive phylogenetic analysis and gene expression pattern assessment

AbstractThe categorization of genes by structural distinctions relevant to biological characteristics is very important for understanding of gene functions and predicting functional implications of uncharacterized genes. It was absolutely necessary to deploy an effective and efficient strategy to deal with the complexity of the large olfactomedin-like (OLF) gene family sharing sequence similarity but playing diversified roles in many important biological processes, as the simple highest-hit homology analysis gave incomprehensive results and led to inappropriate annotation for some uncharacterized OLF members. In light of evolutionary information that may facilitate the classification of the OLF family and proper association of novel OLF genes with characterized homologs, we performed phylogenetic analysis on all 116 OLF proteins currently available, including two novel members cloned by our group. The OLF family segregated into seven subfamilies and members with similar domain compositions or functional properties all fell into relevant subfamilies. Furthermore, our Northern blot analysis and previous studies revealed that the typical human OLF members in each subfamily exhibited tissue-specific expression patterns, which in turn supported the segregation of the OLF subfamilies with functional divergence. Interestingly, the phylogenetic tree topology for the OLF domains alone was almost identical with that of the full-length tree representing the unique phylogenetic feature of full-length OLF proteins and their particular domain compositions. Moreover, each of the major functional domains of OLF proteins kept the same phylogenetic feature in defining similar topology of the tree. It indicates that the OLF domain and the various domains in flanking non-OLF regions have coevolved and are likely to be functionally interdependent. Expanded by a plausible gene duplication and domain couplings scenario, the OLF family comprises seven evolutionarily and functionally distinct subfamilies, in which each member shares similar structural and functional characteristics including the composition of coevolved and interdependent domains. The phylogenetically classified and preliminarily assessed subfamily framework may greatly facilitate the studying on the OLF proteins. Furthermore, it also demonstrated a feasible and reliable strategy to categorize novel genes and predict the functional implications of uncharacterized proteins based on the comprehensive phylogenetic classification of the subfamilies and their relevance to preliminary functional characteristics

Extensions of Lévy-Khintchine Formula and Beurling-Deny Formula in Semi-Dirichlet Forms Setting

The Lévy-Khintchine formula or, more generally, Courrège’s theorem characterizes the infinitesimal generator of a Lévy process or a Feller process on Rd. For more general Markov processes, the formula that comes closest to such a characterization is the Beurling-Deny formula for symmetric Dirichlet forms. In this paper, we extend these celebrated structure results to include a general right process on a metrizable Lusin space, which is supposed to be associated with a semi-Dirichlet form. We start with decomposing a regular semi-Dirichlet form into the diffusion, jumping and killing parts. Then, we develop a local compactification and an integral representation for quasi-regular semi-Dirichlet forms. Finally, we extend the formulae of Lévy-Khintchine and Beurling-Deny in semi-Dirichlet forms setting through introducing a quasi-compatible metric

Formulae of Beurling-Deny and Lejan For Non-Symmetric Dirichlet Forms

By the classical Beurling-Deny formula, any regular symmetric Dirichlet form is decomposed into the diffusion, jumping and killing parts. Further, the diffusion part is characterized by LeJan’s formula. In this paper, both the Beurling-Deny formula and LeJan’s formula are extended to regular non-symmetric Dirichlet forms. In addition, a counterexample is presented to show the gap in the Beurling-Deny formula for non-symmetric Dirichlet forms in the existing literatures

Multiperson Detection and Vital-Sign Sensing Empowered by Space-Time-Coding RISs

Passive human sensing using wireless signals has attracted increasing attention due to its superiorities of non-contact and robustness in various lighting conditions. However, when multiple human individuals are present, their reflected signals could be intertwined in the time, frequency and spatial domains, making it challenging to separate them. To address this issue, this paper proposes a novel system for multiperson detection and monitoring of vital signs (i.e., respiration and heartbeat) with the assistance of space-time-coding (STC) reconfigurable intelligent metasurfaces (RISs). Specifically, the proposed system scans the area of interest (AoI) for human detection by using the harmonic beams generated by the STC RIS. Simultaneously, frequencyorthogonal beams are assigned to each detected person for accurate estimation of their respiration rate (RR) and heartbeat rate (HR). Furthermore, to efficiently extract the respiration signal and the much weaker heartbeat signal, we propose an improved variational mode decomposition (VMD) algorithm to accurately decompose the complex reflected signals into a smaller number of intrinsic mode functions (IMFs). We build a prototype to validate the proposed multiperson detection and vital-sign monitoring system. Experimental results demonstrate that the proposed system can simultaneously monitor the vital signs of up to four persons. The errors of RR and HR estimation using the improved VMD algorithm are below 1 RPM (respiration per minute) and 5 BPM (beats per minute), respectively. Further analysis reveals that the flexible beam controlling mechanism empowered by the STC RIS can reduce the noise reflected from other irrelative objects on the physical layer, and improve the signal-to-noise ratio of echoes from the human chest

Structural analysis of metalloform-selective inhibition of methionine aminopeptidase

One of the challenges in the development of methionine aminopeptidase (MetAP) inhibitors as antibacterial and anticancer agents is to define the metal ion actually used by MetAP in vivo and to discover MetAP inhibitors that can inhibit the metalloform that is relevant in vivo. Two distinct classes of novel nonpeptidic MetAP inhibitors that are not only potent but also highly selective for either the MnII or CoII form have been identified. Three crystal structures of Escherichia coli MetAP complexed with the metalloform-selective inhibitors 5-(2,5-dichlorophenyl)furan-2-carboxylic acid (2), 5-[2-(trifluoromethyl)phenyl]furan-2-carboxylic acid (3) and N-cyclopentyl-N-(thiazol-2-yl)oxalamide (4) have been solved and analysis of these structures has revealed the structural basis for their metalloform-selective inhibition. The MnII-form selective inhibitors (2) and (3) both use their carboxylate group to coordinate with the two MnII ions at the dinuclear metal site and both adopt a non-coplanar conformation for the two aromatic rings. The unique coordination geometry of these inhibitors may determine their MnII-form selectivity. In contrast, the CoII-form selective inhibitor (4) recruits an unexpected third metal ion, forming a trimetallic enzyme–metal–inhibitor complex. Thus, an important factor in the selectivity of (4) for the CoII form may be a consequence of a greater preference for a softer N,O-donor ligand for the softer CoII

Passive Human Sensing Enhanced by Reconfigurable Intelligent Surface: Opportunities and Challenges

Reconfigurable intelligent surfaces (RISs) have flexible and exceptional performance in manipulating electromagnetic waves and customizing wireless channels. These capabilities enable them to provide a plethora of valuable activity-related information for promoting wireless human sensing. In this article, we present a comprehensive review of passive human sensing using radio frequency signals with the assistance of RISs. Specifically, we first introduce fundamental principles and physical platform of RISs. Subsequently, based on the specific applications, we categorize the state-of-the-art human sensing techniques into three types, including human imaging,localization, and activity recognition. Meanwhile, we would also investigate the benefits that RISs bring to these applications. Furthermore, we explore the application of RISs in human micro-motion sensing, and propose a vital signs monitoring system enhanced by RISs. Experimental results are presented to demonstrate the promising potential of RISs in sensing vital signs for manipulating individuals. Finally, we discuss the technical challenges and opportunities in this field

CADSim: Robust and Scalable in-the-wild 3D Reconstruction for Controllable Sensor Simulation

Realistic simulation is key to enabling safe and scalable development of % self-driving vehicles. A core component is simulating the sensors so that the entire autonomy system can be tested in simulation. Sensor simulation involves modeling traffic participants, such as vehicles, with high quality appearance and articulated geometry, and rendering them in real time. The self-driving industry has typically employed artists to build these assets. However, this is expensive, slow, and may not reflect reality. Instead, reconstructing assets automatically from sensor data collected in the wild would provide a better path to generating a diverse and large set with good real-world coverage. Nevertheless, current reconstruction approaches struggle on in-the-wild sensor data, due to its sparsity and noise. To tackle these issues, we present CADSim, which combines part-aware object-class priors via a small set of CAD models with differentiable rendering to automatically reconstruct vehicle geometry, including articulated wheels, with high-quality appearance. Our experiments show our method recovers more accurate shapes from sparse data compared to existing approaches. Importantly, it also trains and renders efficiently. We demonstrate our reconstructed vehicles in several applications, including accurate testing of autonomy perception systems.Comment: CoRL 2022. Project page: https://waabi.ai/cadsim