Haplotype-resolved de novo assembly is the ultimate solution to the study of sequence variations in a genome. However, existing algorithms either collapse heterozygous alleles into one consensus copy ...or fail to cleanly separate the haplotypes to produce high-quality phased assemblies. Here we describe hifiasm, a de novo assembler that takes advantage of long high-fidelity sequence reads to faithfully represent the haplotype information in a phased assembly graph. Unlike other graph-based assemblers that only aim to maintain the contiguity of one haplotype, hifiasm strives to preserve the contiguity of all haplotypes. This feature enables the development of a graph trio binning algorithm that greatly advances over standard trio binning. On three human and five nonhuman datasets, including California redwood with a ~30-Gb hexaploid genome, we show that hifiasm frequently delivers better assemblies than existing tools and consistently outperforms others on haplotype-resolved assembly.
Urban public space nourishes social relations, at the same time, the evolution and development of public space are also influenced by social relations. As an important factor affecting the ...development of public space, the interest relation of citizens presents the characteristics of conflict or cooperation in the occupation of public spaces and finally presents itself in the space form. Based on the point, this paper attempts to explain the evolution and development of urban public space from the perspective of stakeholders, and on this basis investigates the generation mechanism of spontaneous order in the development of urban public space. To meet the research aims, this paper first clarified the inherent meaning that space reflects and shapes social relations, and then selected a certain urban area of Jinan in northern China for the case study. Through the data collected from Google earth history images, interviews, and published reports, the evolution of the major public spaces in this case from 2003 to 2020 was objectively presented. On this basis, the author analysed the social relations, appeals, and actions of various stakeholder groups (such as local people and non-local traders) in different periods in this case, as well as the staged outcomes of their effects on the public space. Finally, a game model of stakeholders was established. The results indicated that the development of a city is a process that mitigates the conflict between social and public space resources. In the occupation of public space resources, the relationship between the stakeholders is dynamic: when the cost is high and the return is low, the stakeholders show a trend of "conflict"; when costs are low and returns are high, the tendency to "conflict" diminishes.; When costs and benefits reach some kind of equilibrium, "cooperation" tends to rise and gradually leads to spontaneous order. Although this spontaneous order has its limitations due to the limited rationality of its participants, it still can play a positive role in the development of urban public space. In the concluding section, the paper proposes an optimization strategy of interest integration and coordination for urban space development, which may be of reference value for architects and government management to actively guide this spontaneous order in urban planning and urban governance.
Haplotype-resolved or phased genome assembly provides a complete picture of genomes and their complex genetic variations. However, current algorithms for phased assembly either do not generate ...chromosome-scale phasing or require pedigree information, which limits their application. We present a method named diploid assembly (DipAsm) that uses long, accurate reads and long-range conformation data for single individuals to generate a chromosome-scale phased assembly within 1 day. Applied to four public human genomes, PGP1, HG002, NA12878 and HG00733, DipAsm produced haplotype-resolved assemblies with minimum contig length needed to cover 50% of the known genome (NG50) up to 25 Mb and phased ~99.5% of heterozygous sites at 98-99% accuracy, outperforming other approaches in terms of both contiguity and phasing completeness. We demonstrate the importance of chromosome-scale phased assemblies for the discovery of structural variants (SVs), including thousands of new transposon insertions, and of highly polymorphic and medically important regions such as the human leukocyte antigen (HLA) and killer cell immunoglobulin-like receptor (KIR) regions. DipAsm will facilitate high-quality precision medicine and studies of individual haplotype variation and population diversity.
As sequencing depth of chromatin studies continually grows deeper for sensitive profiling of regulatory elements or chromatin spatial structures, aligning and preprocessing of these sequencing data ...have become the bottleneck for analysis. Here we present Chromap, an ultrafast method for aligning and preprocessing high throughput chromatin profiles. Chromap is comparable to BWA-MEM and Bowtie2 in alignment accuracy and is over 10 times faster than traditional workflows on bulk ChIP-seq/Hi-C profiles and than 10x Genomics' CellRanger v2.0.0 pipeline on single-cell ATAC-seq profiles.
Periodontitis is an infectious oral disease, which leads to the destruction of periodontal tissues and tooth loss. Although the treatment of periodontitis has improved recently, the effective ...treatment of periodontitis and the periodontitis-affected periodontal tissues is still a challenge. Therefore, it is urgent to explore new therapeutic strategies for periodontitis. Natural products show anti-microbial, anti-inflammatory, anti-oxidant and bone protective effects to periodontitis and most of these natural products are safe and cost-effective. Among these, the plant-derived exosome-like nanoparticles (PELNs), a type of natural nanocarriers repleted with lipids, proteins, RNAs, and other active molecules, show the ability to enter mammalian cells and regulate cellular activities. Reports from the literature indicate the great potential of PELNs in the regulation of immune functions, inflammation, microbiome, and tissue regeneration. Moreover, PELNs can also be used as drug carriers to enhance drug stability and cellular uptake
in vivo
. Since regulation of immune function, inflammation, microbiome, and tissue regeneration are the key phenomena usually targeted during periodontitis treatment, the PELNs hold the promising potential for periodontitis treatment. This review summarizes the recent advances in PELNs-related research that are related to the treatment of periodontitis and regeneration of periodontitis-destructed tissues and the underlying mechanisms. We also discuss the existing challenges and prospects of the application of PELNs-based therapeutic approaches for periodontitis treatment.
This study proposes a novel fault detection (FD) filter design approach for switched systems with unstable modes and intermittent measurement; the FD filter design approach considers asynchronous ...switching and ensures finite‐time stability (FTS). First, a model of switched systems with undesirable communication and unstable modes is established. The FD filter is developed using the observer technique, and the conditions of FTS and H∞ performance for the above systems are proposed and verified. The multiple discontinuous Lyapunov function (MDLF) method and the mode‐dependent average dwell time (DT) method are used to obtain the switching strategy, which includes fast and slow switching to address the stability of unstable and stable modes, respectively. Compared with conventional approaches, the proposed method can realize less conservative stability conditions and a more flexible design framework, providing an efficient approach for improving system performance. Finally, based on the determined FTS criteria and H∞ performance, the FD filter for switched systems is presented. Simulation results are provided to verify the effectiveness of the proposed method.
As the next-generation sequencing (NGS) technologies producing hundreds of millions of reads every day, a tremendous computational challenge is to map NGS reads to a given reference genome ...efficiently. However, existing methods of all-mappers, which aim at finding all mapping locations of each read, are very time consuming. The majority of existing all-mappers consist of 2 main parts, filtration and verification. This work significantly reduces verification time, which is the dominant part of the running time.
An efficient all-mapper, BitMapper, is developed based on a new vectorized bit-vector algorithm, which simultaneously calculates the edit distance of one read to multiple locations in a given reference genome. Experimental results on both simulated and real data sets show that BitMapper is from several times to an order of magnitude faster than the current state-of-the-art all-mappers, while achieving higher sensitivity, i.e., better quality solutions.
We present BitMapper, which is designed to return all mapping locations of raw reads containing indels as well as mismatches. BitMapper is implemented in C under a GPL license. Binaries are freely available at http://home.ustc.edu.cn/%7Echhy.
In this study, a novel nonfragile deep reinforcement learning (DRL) method was proposed to realize the finite-time control of switched unmanned flight vehicles. Control accuracy, robustness, and ...intelligence were enhanced in the proposed control scheme by combining conventional robust control and DRL characteristics. In the proposed control strategy, the tracking controller consists of a dynamics-based controller and a learning-based controller. The conventional robust control approach for the nominal system was used for realizing a dynamics-based baseline tracking controller. The learning-based controller based on DRL was developed to compensate model uncertainties and enhance transient control accuracy. The multiple Lyapunov function approach and mode-dependent average dwell time approach were combined to analyze the finite-time stability of flight vehicles with asynchronous switching. The linear matrix inequalities technique was used to determine the solutions of dynamics-based controllers. Online optimization was formulated as a Markov decision process. The adaptive deep deterministic policy gradient algorithm was adopted to improve efficiency and convergence. In this algorithm, the actor-critic structure was used and adaptive hyperparameters were introduced. Unlike the conventional DRL algorithm, nonfragile control theory and adaptive reward function were used in the proposed algorithm to achieve excellent stability and training efficiency. We demonstrated the effectiveness of the presented algorithm through comparative simulations.
To overcome the limitations of the conventional artificial potential field (APF) method, which is commonly used for unmanned aerial vehicle (UAV) formation obstacle avoidance control. A novel UAV ...formation obstacle avoidance control method based on a light transmission model (LTM) and an improved APF method is proposed. First, inspired by the flight of bird flocks, we combine the LTM with an APF function to present an improved APF model which can help UAV find feasible free space to maneuver. From this, UAV can overcome the drawbacks of non-reachable and local minima under the action of LTM. Then, the obstacle avoidance strategy based on the fixed-wing UAV motion model is proposed, and the obstacle avoidance control algorithm for UAV formation is designed. Finally, simulation results show the effectiveness and superiority of the proposed method, which can result in a dramatic improvement in the performance of UAV formation to obstacle avoidance under the complex and non-deterministic environment.
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