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Applying an integrated mode of labeling theory, this study conducted an empirical analysis of 427 probationers from 48 judicial offices in China. The results found that, after controlling for age, gender, educational background, marital status, and social support, perceived discrimination is positively correlated with social alienation; shame plays a partial positive mediating role in the relationship between perceived discrimination and social alienation. Additionally, Zhongyong thinking can moderate the direct effect of perceived discrimination on social alienation and the mediating effect of shame in a negative way. The results further empirically validated an integrated model of labeling theory.

Opium poppy (Papaver somniferum), which produces benzylisoquinoline alkaloids (BIAs), is an important medicinal plant. However, due to the 70.9% repetitive content and the whole-genome duplication event of the opium poppy genome, it is difficult to generate accurate and comprehensive gene annotations. To overcome this problem, we used the PacBio single-molecule long-read isoform sequencing (IsoSeq) technology to improve opium poppy genome annotation and identify genome-wide alternative splicing (AS). In total, we identified 410 699 full-length isoforms, correcting 1007 misannotated genes and identifying 10 473 unannotated genes. Notably, the annotations of two BIA metabolism genes, CYP80B1 (PS0533980.1) and BBE (PS1014490.1), were corrected, and a novel copy of CYP80B1 was discovered. In addition, we found current opium poppy genome annotation was biased on GC content and exon number, leading to missing of some younger genes. Furthermore, 474 169 novel splicing junctions were identified, revealing splicing sites characteristics difference of genes originating from different phylostratums. Based on the splicing junctions identified by the full-length transcripts, we discovered the tissue- and development-specific AS modes. More specifically, we found the percentage of retained introns (RIs) in the petal and stamen decreased, correlating with the lower GC content of the transcriptome. Also, there was a decrease in the percentage of splicing (PSI) at RI sites after cotyledon growth. The development-related pathways were also enriched among the genes of the RI sites, indicating the post-transcriptional mechanism during the seedling development of opium poppy. Our data provide abundant transcriptome insights into the AS of the opium poppy.

As the state-of-the-art sequencing technologies and computational methods enable investigation of challenging regions in the human genome, an update variant benchmark is demanded. Herein, we sequenced a Chinese Quartet, consisting of two monozygotic twin daughters and their biological parents, with multiple advanced sequencing platforms, including Illumina, BGI, PacBio, and Oxford Nanopore Technology. We phased the long reads of the monozygotic twin daughters into paternal and maternal haplotypes using the parent-child genetic map. For each haplotype, we utilized advanced long reads to generate haplotype-resolved assemblies (HRAs) with high accuracy, completeness, and continuity. Based on the ingenious quartet samples, novel computational methods, high-quality sequencing reads, and HRAs, we established a comprehensive variant benchmark, including 3,883,283 SNVs, 859,256 Indels, 9,678 large deletions, 15,324 large insertions, 40 inversions, and 31 complex structural variants shared between the monozygotic twin daughters. In particular, the preciously excluded regions, such as repeat regions and the human leukocyte antigen (HLA) region, were systematically examined. Finally, we illustrated how the sequencing depth correlated with the de novo assembly and variant detection, from which we learned that 30 × HiFi is a balance between performance and cost. In summary, this study provides high-quality haplotype-resolved assemblies and a variant benchmark for two Chinese monozygotic twin samples. The benchmark expanded the regions of the previous report and adapted to the evolving sequencing technologies and computational methods.

As the state-of-the-art sequencing technologies and computational methods enable investigation of challenging regions in the human genome, an update variant benchmark is demanded. Herein, we sequenced a Chinese Quartet, consisting of two monozygotic twin daughters and their biological parents, with multiple advanced sequencing platforms, including Illumina, BGI, PacBio, and Oxford Nanopore Technology. We phased the long reads of the monozygotic twin daughters into paternal and maternal haplotypes using the parent-child genetic map. For each haplotype, we utilized advanced long reads to generate haplotype-resolved assemblies (HRAs) with high accuracy, completeness, and continuity. Based on the ingenious quartet samples, novel computational methods, high-quality sequencing reads, and HRAs, we established a comprehensive variant benchmark, including 3,883,283 SNVs, 859,256 Indels, 9,678 large deletions, 15,324 large insertions, 40 inversions, and 31 complex structural variants shared between the monozygotic twin daughters. In particular, the preciously excluded regions, such as repeat regions and the human leukocyte antigen (HLA) region, were systematically examined. Finally, we illustrated how the sequencing depth correlated with thede novoassembly and variant detection, from which we learned that 30 × HiFi is a balance between performance and cost. In summary, this study provides high-quality haplotype-resolved assemblies and a variant benchmark for two Chinese monozygotic twin samples. The benchmark expanded the regions of the previous report and adapted to the evolving sequencing technologies and computational methods.

Background: Various forms of model have been applied to predict the trend of the epidemic since the outbreak of COVID-19 at the hardest-hit city of Wuhan. Methods: In this study, we designed a dynamic graph model, not for precisely predicting the number of infected cases, but for a glance of the dynamics under a public epidemic emergency situation and of different contributing factors. Findings: We demonstrated the impact of asymptomatic transmission in this outbreak and showed the effectiveness of city lockdown to halt virus spread within a city. We further illustrated that sudden emergence of a large number of cases could overwhelm the city medical system, and external medical aids are critical to not only containing the further spread of the virus but also reducing fatality. Interpretation: Our model simulation showed that highly populated modern cities are particularly vulnerable and lessons learned in China could facilitate other countries to plan the proactive and decisive actions. We shall pay close attention to the asymptomatic transmission being suggested by rapidly accumulating evidence as dramatic changes in quarantine protocol are required to contain SARS-CoV-2 from spreading globally. Funding Statement: This study was supported by the National Science Foundation of China (grand NO. 61702406 31671372, 31701739, and 8191101420), the National Key R&D Program of China (grand NO. 2018YFC0910400, 2017YFC0907500), the National Science and Technology Major Project of China (grand NO. 2018ZX10302205), the “World-Class Universities and the Characteristic Development Guidance Funds for the Central Universities”, Thousand Talents Plan Professorship for Young Scholars (3111500001), Xi'an Jiaotong University Young Talent Support Program and Xi’an Jiaotong University Basic Research and Profession Grant (xtr022019003). Declaration of Interests: None.

For millions of years, plants evolve plenty of structurally diverse secondary metabolites (SM) to support their sessile lifestyles through continuous biochemical pathway innovation. While new genes commonly drive the evolution of plant SM pathway, how a full biosynthetic pathway evolves remains poorly understood. The evolution of pathway involves recruiting new genes along the reaction cascade forwardly, backwardly, or in a patchwork manner. With three chromosome-scale Papaver genome assemblies, we here reveal whole-genome duplications (WGDs) apparently accelerate chromosomal rearrangements with a nonrandom distribution towards SM optimization. A burst of structural variants involving fusions, translocations and duplications within 7.7 million years have assembled nine genes into the benzylisoquinoline alkaloids gene cluster, following a punctuated patchwork model. Biosynthetic gene copies and their total expression matter to morphinan production. Our results demonstrate how new genes have been recruited from a WGD-induced repertoire of unregulated enzymes with promiscuous reactivities to innovate efficient metabolic pathways with spatiotemporal constraint., Papaver species P. setigerum, P. rhoeas, and P. somniferum accumulates different levels of morphine and noscapine. Here, the authors report the improved genome assembly of P. somniferum and de novo assembly of the other two species, and reveal the evolution of the benzylisoquinoline alkaloids biosynthetic pathway.

Arabidopsis thaliana is an important and long-established model species for plant molecular biology, genetics, epigenetics, and genomics. However, the latest version of reference genome still contains significant number of missing segments. Here, we report a high-quality and almost complete Col-0 genome assembly with two gaps (Col-XJTU) using combination of Oxford Nanopore Technology ultra-long reads, PacBio high-fidelity long reads, and Hi-C data. The total genome assembly size is 133,725,193 bp, introducing 14.6 Mb of novel sequences compared to the TAIR10.1 reference genome. All five chromosomes of Col-XJTU assembly are highly accurate with consensus quality (QV) scores > 60 (ranging from 62 to 68), which are higher than those of TAIR10.1 reference (QV scores ranging from 45 to 52). We have completely resolved chromosome (Chr) 3 and Chr5 in a telomere-to-telomere manner. Chr4 has been completely resolved except the nucleolar organizing regions, which comprise long repetitive DNA fragments. The Chr1 centromere (CEN1), reportedly around 9 Mb in length, is particularly challenging to assemble due to the presence of tens of thousands of CEN180 satellite repeats. Using the cutting-edge sequencing data and novel computational approaches, we assembled about 4 Mb of sequence for CEN1 and a 3.5-Mb-long CEN2. We investigated the structure and epigenetics of centromeres. We detected four clusters of CEN180 monomers, and found that the centromere-specific histone H3-like protein (CENH3) exhibits a strong preference for CEN180 cluster 3. Moreover, we observed hypomethylation patterns in CENH3-enriched regions. We believe that this high-quality genome assembly, Col-XJTU, would serve as a valuable reference to better understand the global pattern of centromeric polymorphisms, as well as genetic and epigenetic features in plants.

Complex structural variants (CSVs) are genomic alterations that have more than two breakpoints and are considered as simultaneous occurrence of simple structural variants. However, detecting the compounded mutational signals of CSVs is challenging through a commonly used model-match strategy. As a result, there has been limited progress for CSV discovery compared with simple structural variants. We systematically analyzed the multi-breakpoint connection feature of CSVs, and proposed Mako, utilizing a bottom-up guided model-free strategy, to detect CSVs from paired-end short-read sequencing. Specifically, we implemented a graph-based pattern growth approach, where the graph depicts potential breakpoint connections and pattern growth enables CSV detection without predefined models. Comprehensive evaluations on both simulated and real datasets revealed that Mako outperformed other algorithms. Notably, validation rates of CSV on real data based on experimental and computational validations as well as manual inspections are around 70%, where the medians of experimental and computational breakpoint shift are 13bp and 26bp, respectively. Moreover, Mako CSV subgraph effectively characterized the breakpoint connections of a CSV event and uncovered a total of 15 CSV types, including two novel types of adjacent segments swap and tandem dispersed duplication. Further analysis of these CSVs also revealed impact of sequence homology in the formation of CSVs. Mako is publicly available at https://github.com/jiadong324/Mako.

Using a survey data of 508 probationers from the judicial bureaus of Jiangsu Province, Guangdong Province, Yunnan Province and Beijing City, this study examines how the general strain variables (i.e. negative coping style) and the action control variables (i.e. emotion regulation strategies) mediate and moderate the relationship between the perceived discrimination and future dangerousness of probationers. The findings suggest that perceived discrimination is positively correlated with future dangerousness, and negative coping style plays a partial positive mediating role in the relationship between perceived discrimination and future dangerousness. Additionally, emotion regulation strategies can moderate the direct effect of perceived discrimination on future dangerousness and the mediating effect of negative coping style in a negative way. The results of this study further enrich the integrated theory of crime labeling, and offer some guidance for the judicial management and correction strategy of probation correction officials.

Field experiments and static chamber-gas chromatography analysis were conducted in 2016-2017 to study the effects of deficit irrigation on CO

In this paper, the crank-connecting rod mechanism of Santana 2000AJR automobile engine is modeled by UG8.0 software with CAD technology, and then the motion simulation module is used to create the motion drive. After pre-processing and post-processing, the motion simulation design of the crank-connecting rod mechanism is completed. In the development of automobile, the motion simulation technology can simulate the motion law of crank-connecting rod mechanism and replace the complicated physical experiments in practice, shorten the calculation cycle and cost, and lay a foundation for optimizing the design of crank-connecting rod mechanism.