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Zanthoxylum armatum and Zanthoxylum bungeanum, known as 'Chinese pepper', are distinguished by their extraordinary complex genomes, phenotypic innovation of adaptive evolution and species-special metabolites. Here, we report reference-grade genomes of Z. armatum and Z. bungeanum. Using high coverage sequence data and comprehensive assembly strategies, we derived 66 pseudochromosomes comprising 33 homologous phased groups of two subgenomes, including autotetraploid Z. armatum. The genomic rearrangements and two whole-genome duplications created large (~4.5 Gb) complex genomes with a high ratio of repetitive sequences (82%) and high chromosome number (2n = 4x = 132). Further analysis of the high-quality genomes shed lights on the genomic basis of involutional reproduction, allomones biosynthesis and adaptive evolution in Chinese pepper, revealing a high consistent relationship between genomic evolution, environmental factors and phenotypic innovation. Our study provides genomic resources and new insights for investigating diversification and phenotypic innovation in Chinese pepper, with broader implications for the protection of plants under severe environmental changes.

Cotton fiber is a unicellular seed trichome, and lint fiber initials per seed as a factor determines fiber yield. However, the mechanisms controlling fiber initiation from ovule epidermis are not understood well enough. Here, with single-cell RNA sequencing (scRNA-seq), a total of 14,535 cells were identified from cotton ovule outer integument of Xu142_LF line at four developmental stages (1.5, 1, 0.5 days before anthesis and the day of anthesis). Three major cell types, fiber, non-fiber epidermis and outer pigment layer were identified and then verified by RNA in situ hybridization. A comparative analysis on scRNA-seq data between Xu142 and its fiberless mutant Xu142 fl further confirmed fiber cluster definition. The developmental trajectory of fiber cell was reconstructed, and fiber cell was identified differentiated at 1 day before anthesis. Gene regulatory networks at four stages revealed the spatiotemporal pattern of core transcription factors, and MYB25-like and HOX3 were demonstrated played key roles as commanders in fiber differentiation and tip-biased diffuse growth, respectively. A model for early development of a single fiber cell was proposed here, which sheds light on further deciphering mechanism of plant trichome and the improvement of cotton fiber yield.

Aiming at the problem that the detection and damage recognition algorithm of insulator aerial images is difficult to be applied to the embedded platform, this paper proposed an improved Tiny-YOLOv4 lightweight target detection network algorithm. This algorithm combined the Self-Attention mechanism and ECA-Net (Efficient Channel Attention Neural Networks), which could greatly reduce the complexity of the original YOLOv4 algorithm, and the model size is 24.9 MB. Under the condition of ensuring the detection accuracy (>91%), the detection speed is as high as 94FPS. It is transplanted to the Jetson Xavier NX embedded platform, and the average detection speed reaches 22FPS, which effectively meets the real-time detection requirements in the power inspection.

Upland cotton (Gossypium hirsutum), an allotetraploid, contains At- and Dt- subgenome and most genes have multiple homologous copies, which pose a huge challenge to investigate genes’ function due to the functional redundancy. Therefore, it is of great significance to establish effective techniques for the functional genomics in cotton. In this study, we tested two novel genome editing vectors and compared them with the CRISPR/Cas9 system (pRGEB32-GhU6.7) developed in our laboratory previously. In the first new vector, the sgRNA transcription unite was constructed into the replicon (LIR-Donor-SIR-Rep-LIR) of the bean yellow dwarf virus (BeYDV) and named as pBeYDV-Cas9-KO and in the second vector, the ubiquitin promoter that drives Cas9 protein was replaced with a constitutive CaMV 35S promoter and defined as pRGEB32-35S. The results from transgenic cotton calli/plants revealed that pBeYDV-Cas9-KO vector showed the highest editing efficiency of GhCLA1 in At and Dt subgenomes edited simultaneously up to 73.3% compared to the 44.6% of pRGEB32-GhU6.7 and 51.2% of pRGEB32-35S. The editing efficiency of GhCLA1 in At and Dt subgenome by pBeYDV-Cas9-KO was 85.7% and 97.2%, respectively, whereas the efficiency by pRGEB32-GhU6.7 and pRGEB32-35S vectors was 67.7%, 86.5%, 84%, and 87.2%, respectively. The editing profile of pBeYDV-Cas9-KO was mainly composed of fragment deletion, accounting for 84.0% and ranging 1–10 bp in length. The main editing sites are located at positions 11–17 upstream of PAM site. The off-target effects were not detected in all potential off-target sites. Taken together, the pBeYDV-Cas9-KO system has high editing efficiency and specificity with wide editing range than the traditional CRISPR/Cas9 system, which provides a powerful tool for cotton functional genomics research and molecular breeding.

Background: Plasma cell-free DNA (cfDNA) has low sensitivity to detect locoregional molecular residual disease (MRD) immediately after surgery for limited-stage head and neck cancer. To enhance locoregional MRD sensitivity, we utilize a novel biofluid proximal to the primary tumor: the serosanguinous fluid collected by surgical drains inserted into the wound bed following regional lymph node dissection. We demonstrate that cancer-associated cfDNA in the surgical drain fluid (SDF) is a sensitive biomarker of locoregional MRD detection, risk stratification, and prognostication. Methods: We extracted DNA from 168 SDFs, 48 paired plasmas, and 44 tumor specimens collected 24 hours after surgery from 90 patients: 74 HPV (+) oropharyngeal cancers (OPC), 8 HPV (-) oral cancers, 2 thyroid cancers, and 6 benign neck pathologies. SDFs were also collected at 0, 6, 12, and 24 hours after surgery from 11 HPV (+) patients. We applied TaqMan qPCR to our specimens to quantify cell-free HPV (cf-HPV), a proxy for cancer-associated cfDNA in HPV (+) malignancies. We then measured the association between cf-HPV and extranodal extension (ENE), AJCC 8 staging, and established clinical and pathological risk criteria from 4 HPV (+) OPC clinical trials. We validated our findings using HPV next-generation sequencing. We also compared the predictive value of high-risk pathology with cf-HPV MRD for HPV (+) OPC recurrences. Lastly, we developed a second assay for cell-free BRAF V600E (cf-V600E) in thyroid cancer SDF. Results: Serially collected SDF revealed cf-HPV decreased continuously from 0 to 24 hours postoperative, and that the 24-hour timepoint stratified detectable versus undetectable persistent residual disease. At 24 hours, SDF was significantly more enriched with cf-HPV compared to plasma (P < 0.0001). In a subset of 9 patients, HPV genotype and detection in SDF were 100% concordant between NGS and PCR. Strikingly, SDF cf-HPV was 11-fold higher in pN2 patients versus pN1/N0 (P = 0.02) and 15-fold higher in cases with ENE (P = 0.003), suggesting SDF reflects aggressive nodal pathology and captures locoregional MRD. When we classified our patients according to established clinical and pathological risk criteria, we found significantly higher SDF cf-HPV among high-risk patients (AUC = 0.77). Crucially, in HPV (+) patients treated with surgery alone, SDF MRD detected 100% of locoregional recurrences, while plasma MRD and high-risk pathology detected 0%. Lastly, as proof of concept, we demonstrated SDF cf-V600E detection in the context of high-risk thyroid cancer. Conclusions: Surgical drain fluid cancer-associated cfDNA is a novel minimally invasive biomarker. Our SDF assay was strongly associated with high-risk criteria and detected locoregional relapse with 100% sensitivity compared to 0% in plasma. Our data suggest that SDF liquid biopsy is ultra-sensitive and has the potential to inform postoperative molecular-based risk stratification. Citation Format: Noah Earland, Ricardo J. Ramirez, Sophie P. Gerndt, Peter K. Harris, Andrew I. Hearn, Matthew Inkman, Jeffrey J. Szymanski, Nick Semenkovich, Benjamin M. Wahle, Zhongping Xu, Kevin Chen, Jin Zhang, Jose P. Zevallos, Aadel A. Chaudhuri. Sensitive detection of locoregional MRD after head and neck cancer surgery [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2023; Part 1 (Regular and Invited Abstracts); 2023 Apr 14-19; Orlando, FL. Philadelphia (PA): AACR; Cancer Res 2023;83(7_Suppl):Abstract nr 3359.

Transposable element (TE) amplification has been recognized as a driving force mediating genome size expansion and evolution, but the consequences for shaping 3D genomic architecture remains largely unknown in plants. Here, we report reference-grade genome assemblies for three species of cotton ranging 3-fold in genome size, namely Gossypium rotundifolium (K2), G. arboreum (A2), and G. raimondii (D5), using Oxford Nanopore Technologies. Comparative genome analyses document the details of lineage-specific TE amplification contributing to the large genome size differences (K2, 2.44 Gb; A2, 1.62 Gb; D5, 750.19 Mb) and indicate relatively conserved gene content and synteny relationships among genomes. We found that approximately 17% of syntenic genes exhibit chromatin status change between active (“A”) and inactive (“B”) compartments, and TE amplification was associated with the increase of the proportion of A compartment in gene regions (∼7,000 genes) in K2 and A2 relative to D5. Only 42% of topologically associating domain (TAD) boundaries were conserved among the three genomes. Our data implicate recent amplification of TEs following the formation of lineage-specific TAD boundaries. This study sheds light on the role of transposon-mediated genome expansion in the evolution of higher-order chromatin structure in plants.

Background Base editors (BEs) display diverse applications in a variety of plant species such as Arabidopsis, rice, wheat, maize, soybean, and cotton, where they have been used to mediate precise base pair conversions without the collateral generation of undesirable double-stranded breaks (DSB). Studies of single-nucleotide polymorphisms (SNPs) underpinning plant traits are still challenging, particularly in polyploidy species where such SNPs are present in multiple copies, and simultaneous modification of all alleles would be required for functional analysis. Allotetraploid cotton has a number of homoeologous gene pairs located in the A and D sub-genomes with considerable SNPs, and it is desirable to develop adenine base editors (ABEs) for efficient and precise A-to-G single-base editing without DSB in such complex genome. Results We established various ABE vectors based on different engineered adenosine deaminase (TadA) proteins fused to Cas9 variants (dCas9, nCas9), enabling efficient A to G editing up to 64% efficiency on-target sites of the allotetraploid cotton genome. Comprehensive analysis showed that GhABE7.10n exhibited the highest editing efficiency, with the main editing sites specifically located at the position A5 (counting the PAM as positions 21–23). Furthermore, DNA and RNA off-target analysis of cotton plants edited with GhABE7.10n and GhABE7.10d by whole genome and whole-transcriptome sequencing revealed no DNA off-target mutations, while very low-level RNA off-target mutations were detected. A new base editor, namely GhABE7.10dCpf1 (7.10TadA + dCpf1), that recognizes a T-rich PAM, was developed for the first time. Targeted A-to-G substitutions generated a single amino acid change in the cotton phosphatidyl ethanolamine-binding protein (GhPEBP), leading to a compact cotton plant architecture, an ideotype for mechanized harvesting of modern cotton production. Conclusions Our data illustrate the robustness of adenine base editing in plant species with complex genomes, which provides efficient and precise toolkit for cotton functional genomics and precise molecular breeding.

Sap-sucking insects cause severe damage to cotton production. Long non-coding RNAs (lncRNAs) play vital regulatory roles in various development processes and stress response, however, the function of lncRNAs during sap-sucking insect infection in cotton is largely unknown. In this study, the transcriptome profiles between resistant (HR) and susceptible (ZS) cotton cultivars under whitefly infestation at different time points (0, 4, 12, 24, and 48 h) were compared. A total of 6,651 lncRNAs transcript and 606 differentially expressed lncRNAs were identified from the RNA-seq data. A co-expression network indicated that lncA07 and lncD09 were potential hub genes that play a regulatory role in cotton defense against aphid infestation. Furthermore, CRISPR/Cas9 knock-out mutant of lncD09 and lncA07 showed a decrease of jasmonic acid (JA) content, which potentially lead to increased susceptibility toward insect infestation. Differentially expressed genes between wild type and lncRNA knock-out plants are enriched in modulating development and resistance to stimulus. Additionally, some candidate genes such as Ghir_A01G022270, Ghir_D04G014430, and Ghir_A01G022270 are involved in the regulation of the JA-mediated signaling pathway. This result provides a novel insight of the lncRNA role in the cotton defense system against pests.

BackgroundMillennia of directional human selection has reshaped the genomic architecture of cultivated cotton relative to wild counterparts, but we have limited understanding of the selective retention and fractionation of genomic components.ResultsWe construct a comprehensive genomic variome based on 1961 cottons and identify 456 Mb and 357 Mb of sequence with domestication and improvement selection signals and 162 loci, 84 of which are novel, including 47 loci associated with 16 agronomic traits. Using pan-genome analyses, we identify 32,569 and 8851 non-reference genes lost fromGossypium hirsutumandGossypium barbadensereference genomes respectively, of which 38.2% (39,278) and 14.2% (11,359) of genes exhibit presence/absence variation (PAV). We document the landscape of PAV selection accompanied by asymmetric gene gain and loss and identify 124 PAVs linked to favorable fiber quality and yield loci.ConclusionsThis variation repertoire points to genomic divergence during cotton domestication and improvement, which informs the characterization of favorable gene alleles for improved breeding practice using a pan-genome-based approach.

Cotton (Gossypium hirsutum) is an allotetraploid species and a typical thermophilic crop that can survive and grow well under temperatures up to 45°C. CRISPR/LbCpf1 (LbCas12a) is a temperature‐sensitive system for plant genome editing (Malzahn et al., 2019) and has been successfully applied in species such as rice, soybean, tobacco, maize and cotton (Lee et al., 2019; Li et al., 2018; Tang et al., 2017; Xu et al., 2019). However, the temperature sensitivity of LbCpf1 has not been tested in cotton yet, a high temperature‐resistant crop. In order to improve LbCpf1 efficiency and determine the optimum temperature for cotton genome editing, we investigated the effects of different temperatures on LbCpf1 activity and genome editing efficiency. Moreover, we created nontransgenic and glandless cotton plants with seeds free of gossypol, representing a valuable germplasm resource for cotton breeding.

Summary The base‐editing technique using CRISPR/nCas9 (Cas9 nickase) or dCas9 (deactivated Cas9) fused with cytidine deaminase is a powerful tool to create point mutations. In this study, a novel G. hirsutum‐Base Editor 3 (GhBE3) base‐editing system has been developed to create single‐base mutations in the allotetraploid genome of cotton (Gossypium hirsutum). A cytidine deaminase sequence (APOBEC) fused with nCas9 and uracil glycosylase inhibitor (UGI) was inserted into our CRISPR/Cas9 plasmid (pRGEB32‐GhU6.7). Three target sites were chosen for two target genes, GhCLA and GhPEBP, to test the efficiency and accuracy of GhBE3. The editing efficiency ranged from 26.67 to 57.78% at the three target sites. Targeted deep sequencing revealed that the C→T substitution efficiency within an ‘editing window’, approximately six‐nucleotide windows of −17 to −12 bp from the PAM sequence, was up to 18.63% of the total sequences. The 27 most likely off‐target sites predicted by CRISPR‐P and Cas‐OFFinder tools were analysed by targeted deep sequencing, and it was found that rare C→T substitutions (average

We have demonstrated that Prussian green (PG) film can be directly grown on fluorine-doped tin oxides (FTO) glass by a facile, template-free and one-step hydrothermal process, and a reaction mechanism for the formation of PG film under the hydrothermal conditions is also proposed. The as-grown PG film exhibits a much better cycling stability than PG film prepared by electrochemical method. The electrochromic device based on the as-grown PG film shows reversible and multi-stage color changes among green, blue and colorless states. Large optical modulations of 58% and 42% between colorless and both blue and green state, respectively, fast switching times of 1.1 and 2.4 s and a high coloration efficiency of 79.1 cm2 C−1 are also achieved for the PG device, making it promising candidates for applications in high-performance smart windows and displays.

e18050 Background: Human papillomavirus (HPV) is the primary driver of oropharyngeal squamous cell carcinoma (OPC) in the US. Previous studies have investigated the role of plasma and saliva-based cell-free HPV DNA in OPC, yet the pathophysiological impact of exosomes in HPV+ OPC remains unknown. Exosomes are nanometer-sized membrane vesicles of endocytic origin carrying DNA, RNA and proteins, and have been shown to exist in blood, plasma, and in urine. We hypothesize that serosanguinous fluid drained from the postoperative bed, which we call “surgical drain fluid” (SDF) also contains exosomes. We further hypothesize that exosomes derived from SDF in HPV+ OPC patients contain HPV DNA that can be directly transmitted into HPV-negative cells. Methods: Twenty-six 5-mL SDF samples were collected following surgical neck dissections directly from the surgical drain; 21 from HPV+ and 5 from HPV- OPC patients. Exosomes were isolated from SDF using the Qiagen exoEasy kit. Exosome structure was characterized by transmission electron microscopy (TEM) and nanoparticle tracking analysis (NTA). Western blotting (WB) targeted known exosomal surface markers. Exosomes were pretreated with DNase (New England Biolabs) to cleave the surface DNA, then exosomal DNA was extracted using a cell-free DNA isolation kit (Sigma). TaqMan real-time PCR was employed to detect HPV16 copy numbers. Lastly, exosomes isolated from 3 HPV+ patients’ SDF and 1 HPV- patient’s SDF were incubated with HPV- cell lines, SCC22A and SCC25, in order to query exosome-mediated HPV transmission. Results: TEM identified exosomes as round/oval-shaped vesicles measuring between 70 and 150 nm. NTA enumerated an average of 1.5 x 1011 particles per mL of SDF. WB further confirmed exosomal identity with strong CD63, CD9, and TSG101 signal detected. Among SDF exosomes from HPV+ OPC, 81% (n = 17) had detectable HPV16 DNA by real-time PCR, while all HPV- SDF exosomes (n = 5) showed undetectable HPV16. Paired comparison of HPV16 levels within exosomes to total HPV16 in SDF revealed an average of 90% of HPV16 in SDF was contained within exosomes. In an in vitro assay, SCC22A and SCC25 cells treated with HPV16 + exosomes became real-time PCR-positive for HPV16, while cells treated with HPV16- exosomes remained HPV16 negative. Conclusions: This study demonstrates that SDF, a novel post-surgical biofluid analyte, is enriched for HPV-containing exosomes in HPV+ OPC patients. We also found that exosomes from HPV+ OPC patients can transmit HPV to HPV-negative cells, suggesting a novel mode of virus-mediated spread of disease.

Additional file 2. Figures S1-S30.

Additional file 3. Supplementary Notes.

Additional file 4. Review history.

Plant bugs (Miridae species) have become major agricultural pests that cause increasing and severe economic damage. Plant-mediated RNA interference (RNAi) is emerging as an eco-friendly, efficient, and reliable strategy for pest management. In this study, we isolated and characterized a lethal gene of Apolygus lucorum and named it Apolygus lucorum LIM (AlLIM), which produced A. lucorum mortality rates ranging from 38% to 81%. Downregulation of the AlLIM gene expression in A. lucorum by injection of a double-stranded RNA (dsRNA) led to muscle structural disorganization that resulted in metamorphosis deficiency and increased mortality. Then we constructed a plant expression vector that enabled transgenic cotton to highly and stably express dsRNA of AlLIM (dsAlLIM) by Agrobacterium-mediated genetic transformation. In the field bioassay, dsAlLIM transgenic cotton was protected from A. lucorum damage with high efficiency, with almost no detectable yield loss. Therefore, our study successfully provides a promising genetically modified strategy to overpower A. lucorum attack.

At present, there are many kinds of electricity theft and the corresponding approaches to combat this are insufficient. Manual approaches result in a heavy staff workload and are inefficient. In this paper, the data from an electricity information acquisition system is collected and mined using Python. Based on an understanding of the business and an analysis of the information value (IV) measure, important characteristic indexes are selected and an improved decision tree algorithm is used to construct a model of power theft by users. This method effectively narrows the range of users suspected of power theft, improving the pertinence of audit, and providing strong support for reducing the financial losses of power supply enterprises and ensuring the safety of power grid operation.

Statistics show that power theft is one of the main reasons for the dramatic increase in power grid line loss. In this paper, a genetic algorithm is used to optimize a neural network and establish a power theft prediction model. With the grey prediction model, the predicted values of variables are obtained and then applied to the prediction model of a GA-BP neural network to obtain relatively accurate predictions from limited samples, reducing the absolute error. Through the two levels of prediction and analysis, the model is demonstrated to have good universality in predicting power theft behavior, and is a practical and effective method for power companies to carry out power theft analysis.

Transposable element (TE) amplification has been recognized as a driving force mediating genome size expansion and evolution, but the effect on shaping of 3D genomic architecture remains largely unknown in plants. Here, we report three reference-grade cotton genome assemblies of Gossypium rotundifolium (K2), G. arboreum (A2) and G. raimondii (D5) using Oxford Nanopore sequencing technology. Comparative genome analyses document the details of lineage-specific TE amplification contributing to three-fold change of genome size (K2, 2.44 Gb; A2, 1.62 Gb; D5, 750.19 Mb), and indicate a relatively conserved gene content and synteny relationship among genomes. We found that approximately 17% of syntenic genes exhibit chromatin status switching of A/B compartment, and active TE amplification increases the proportion of A compartment in gene regions in K2 and A2 relative to D5. We also found that only 42% of topologically associating domain (TAD) boundaries were conserved by comparing three genomes, and abundant TE amplification was linked to the organization of lineage-specific TADs. This study sheds light on the regulatory role of transposon-mediated genome expansion in the evolution of higher-order chromatin structure in plants.

Double carbon-power index is an important index to measure regional carbon dioxide emission, regional economic development and carbon emission reduction implementation.It can determine whether carbon dioxide has reached a peak in a region or industry, so that the government can take targeted measures to guide enterprises to reduce carbon dioxide.Through build wuxi double carbon power index system, based on the Delphi method to carry out the comprehensive evaluation, explore their short-term carbon emissions to peak, the path of the development of long-term carbon neutral, assist the government in a timely manner to master carbon, carbon reduction status, so as to promote comprehensive ground application carbon reduction measures, for zero carbon high quality under the restriction of power in wuxi city development.

Background Wintersweet (Chimonanthus praecox), an important ornamental plant, has evolved unique fragrant aroma and winter-flowering properties, which are critical for its successful sexual reproduction. However, the molecular mechanisms underlying these traits are largely unknown in this species. In addition, wintersweet is also a typical representative species of the magnoliids, where the phylogenetic position of which relative to eudicots and monocots has not been conclusively resolved. Results Here, we present a chromosome-level wintersweet genome assembly with a total size of 695.36 Mb and a draft genome assembly of Calycanthus chinensis. Phylogenetic analyses of 17 representative angiosperm genomes suggest that Magnoliids and eudicots are sister to monocots. Whole-genome duplication signatures reveal two major duplication events in the evolutionary history of the wintersweet genome, with an ancient one shared by Laurales, and a more recent one shared by the Calycantaceae. Whole-genome duplication and tandem duplication events have significant impacts on copy numbers of genes related to terpene and benzenoid/phenylpropanoid (the main floral scent volatiles) biosynthesis, which may contribute to the characteristic aroma formation. An integrative analysis combining cytology with genomic and transcriptomic data reveals biological characteristics of wintersweet, such as floral transition in spring, floral organ specification, low temperature-mediated floral bud break, early blooming in winter, and strong cold tolerance. Conclusions These findings provide insights into the evolutionary history of wintersweet and the relationships among the Magnoliids, monocots, and eudicots; the molecular basis underlying floral scent biosynthesis; and winter flowering, and highlight the utility of multi-omics data in deciphering important ornamental traits in wintersweet.

Summary The CRISPR/Cas9 and Cas12a (Cpf1) tools have been used on a large scale for genome editing. A new effector with a single nuclease domain, a relatively small size, low‐frequency off‐target effects and cleavage capability under high temperature has been recently established and designated CRISPR/Cas12b (C2c1). Cas12b has also shown temperature inducibility in mammalian systems. Therefore, this system is potentially valuable for editing the genomes of plant species, such as cotton, that are resistant to high temperatures. Using this new system, mutants of upland cotton were successfully generated following Agrobacterium‐mediated genetic transformation under a range of temperatures. Transformants (explants infected by Agrobacterium) exposed to 45 °C for 4 days showed the highest editing efficiency. No off‐target mutation was detected by whole‐genome sequencing. Genome edits by AacCas12b in T0 generation were faithfully passed to the T1 generation. Taken together, CRISPR/Cas12b is therefore an efficient and precise tool for genome editing in cotton plants.

Additional file 4. Review history.

Urban rail transit has become the main mode to ease traffic congestion. Researches on the dynamic variation regularity of passenger flow distribution and passenger flow volume of urban rail transit hub platform have important implication in hub capacity design, operation organization and risk prevention. Simulation designs are built with Java and Anylogic, which contain simulation system functional framework, implementation path, simulation processes and simulation models. By case study, the performance comparison between two simulation methods indicates that simulation designs are scientific and accordant with the reality scene.

Aiming at the complex environment for passenger flow distribution and considering the related research achievements in URTH, based on the theory and method of complex network, topology structure attribute, the measurement indexes sets and the reliability analysis method are developed; simulation method for network reliability-oriented is built; further, the typical URTH is selected for case study. In conclusion, the theory and method of the modeling and simulation of URTH are established.

Additional file 3: Supplementary Note 1. Estimation of Genome Size and Chromosome Number Assessment; Identification of Orthologs of Flowering Time Genes; Identification of MADS-box Genes; Genes Expression Analysis. Supplementary Note 2. Headspace Collection and GC–MS Analyses of Floral Volatiles; Changes of volatile compounds during flower development; Phylogenetic and Structural Analysis of TPS Family; Subcellular Location of the fused CpTPS4/9/42-fused green Fluorescent Protein; Construction of CpTPS4 Overexpressed Tobacco Plants, Analysis of Transcription of Factors; Analysis of the genes involved in terpene and benzenoid biosynthesis transport. Supplementary Note 3. Tandem duplication analysis; The order of speciation and WGD event in Liriodendron and wintersweet lineage.

Additional file 2: Fig. S1. Evaluation of Chimonanthus praecox genome by k-mer analysis and cell flow cytometry. Fig. S2. Hi-C map of the wintersweet genome showing genome-wide all-by-all interactions. Fig. S3. Chromosome biology of Chimonanthus praecox (a) and Calycanthus chinensis. Fig. S4. Annotation of the wintersweet-specific and expanded genes. Fig. S5. An uneven TE distribution across wintersweet genome and TE distribution in genic regions. Fig. S6. LTR insertion time estimation. Fig. S7. Phylogenetic analysis of wintersweet LTR retrotransposons. Fig. S8. Concatenated- and ASTRAL-based phylogenetic trees. Fig. S9. The phylogenetic tree based on 38 chloroplast genes from 26 species. Fig. S10. A phylogenetic tree of 29 plant species based on 2420 concatenated genes trees using RAxML. Fig. S11. Types of gene duplication in the wintersweet genome. Fig. S12. Duplications of genomic paralogous genes in wintersweet. Fig. S13. Distribution of synonymous substitution levels (Ks) of syntenic orthologous (solid curves) and paralogous genes (dashed curves). Fig. S14. Topologies of gene trees depicting the two possible scenarios of speciation among wintersweet and Liriodendron. Fig. S15. A modified pipeline of ancestral genome reconstruction. Fig. S16. Phylogenetic analysis of FT-like and SVP-like and the analysis of bud break and cell division (CpCDs) related genes and genes involved in phytohormone-related pathways. Fig. S17. Gas chromatogram of glycosidic floral volatiles from the flowers of wintersweet. Fig. S18. Changes of the major floral volatiles during flower development in wintersweet. Fig. S19. Subcellular location of CpTPS proteins. Fig. S20. Cluster and STEM analysis of differentially expressed TFs during flower development. Fig. S21. Promoter cis-element analysis of 52 CpTPSs. Fig. S22. Analysis of benzenoid carboxyl methyltransferases (BCMTs) and cell division (CpCDs) related genes. Fig. S23. Gene structure and classification of putative CpTPSs. Fig. S24. Annotation of the Tandem duplicated genes.

Black pepper (Piper nigrum), dubbed the ‘King of Spices’ and ‘Black Gold’, is one of the most widely used spices. Here, we present its reference genome assembly by integrating PacBio, 10x Chromium, BioNano DLS optical mapping, and Hi-C mapping technologies. The 761.2 Mb sequences (45 scaffolds with an N50 of 29.8 Mb) are assembled into 26 pseudochromosomes. A phylogenomic analysis of representative plant genomes places magnoliids as sister to the monocots-eudicots clade and indicates that black pepper has diverged from the shared Laurales-Magnoliales lineage approximately 180 million years ago. Comparative genomic analyses reveal specific gene expansions in the glycosyltransferase, cytochrome P450, shikimate hydroxycinnamoyl transferase, lysine decarboxylase, and acyltransferase gene families. Comparative transcriptomic analyses disclose berry-specific upregulated expression in representative genes in each of these gene families. These data provide an evolutionary perspective and shed light on the metabolic processes relevant to the molecular basis of species-specific piperine biosynthesis., Black pepper (Piper nigrum) belongs to the long-isolated lineage of basal angiosperm and its fruit has been used for food spice and phytomedicines for thousands of years. Here, the authors assemble the reference genome of this species and analyze gene families associated with piperine biosynthesis.

We have demonstrated that nanostructured Prussian blue (PB) film can be directly grown on fluorine-doped tin oxide (FTO)-coated glass substrate by using a facile and template-free hydrothermal technique. The as-grown film with a lot of nanochannels is well adhesive to substrate. An electrochromic device fabricated using the as-grown PB film shows a fast coloration/bleaching response of 2.4/1.0 s and a high coloration efficiency of 87.4 cm 2 C −1 , which shows a promising application in high-performance electrochromic smart windows.

Thermal groundwater is relatively abundant in the deep-seated bedrock underlying the Beijing plain area. The main geothermal reservoir is composed of dolomites of the Wumishan Group of the Meso&ndash, Neoproterozic Jixian System. The thermal groundwater has been developed and utilized since the 1970s and significant declines in groundwater levels were observed. A 3D unsteady flow model of an anisotropic karst-fissure aquifer based on the equivalent continuum is used to describe the flow of thermal groundwater and heat transport. The heat transportation is described by the governing equation including convection and dispersion. The simulation of this paper aims to solve such problems as uneven distribution and thinness of the aquifer, insufficient initial monitoring data, and poor knowledge of the properties of the horizontal boundary. They are solved by considering vertical stratification of the aquifer with equal thickness, replacing initial water level data by surface elevation, and choosing natural boundary far away from the exploitation areas. Through a trial&ndash, error procedure, the simulated and measured groundwater level and temperature in the simulation period are well fitted. Three exploitation schemes are proposed to predict the spatial and temporal changes in groundwater level and temperature of the thermal groundwater in the study area. The prediction results show that the reinjection can effectively slow the decline in the thermal groundwater levels. Except for the Dongnanchengqu, Xiaotangshan, and Liangxiang subgeothermal fields, the other six subgeothermal fields have the potential for further development of thermal groundwater.

Cotton, a natural fiber producing crop of huge importance, is often prone to attack of Verticillium dahliae. Papain-like cysteine proteases (PLCPs) constitute a large family in plants and were proposed to involve in plant defense against pathogen attack in a number of studies. However, there is no detailed characterization of PLCP genes in cotton against infection of V. dahliae. In this study, we carried out a genome-wide analysis in cotton and identified seventy-eight PLCPs, which were divided into nine subfamilies based on their evolution phylogeny: RD21 (responsive to desiccation 21), CEP (cysteine endopeptidase), XCP (xylem cysteine peptidase), XBCP3 (xylem bark cysteine peptidase 3), THI, SAG12 (senescence-associated gene 12), RD19 (responsive to desiccation 19), ALP (aleurain-like protease) and CTB (cathepsin B-like). Genes in each subfamily exhibit a similar structure and motif composition. The expression patterns of these genes in different organs were examined, and subfamily RD21 was the most abundant in these families. Expression profiles under abiotic stress showed that thirty-five PLCP genes were induced by multiple stresses. Further transcriptome analysis showed that sixteen PLCP genes were up-regulated in response to V. dahliae in cotton. Among those, GhRD21-7 showed a higher transcription level than most other PLCP genes. Additionally, over-expression of GhRD21-7 led to enhanced resistance and RNAi lines were more susceptible to V. dahliae in cotton. Our results provide valuable information for future functional genomic studies of PLCP gene family in cotton.

Cotton, a natural fiber producing crop of huge importance, is often prone to attack of Verticillium dahliae. Papain-like cysteine proteases (PLCPs) constitute a large family in plants and were proposed to involve in plant defense against pathogen attack in a number of studies. However, there is no detailed characterization of PLCP genes in cotton against infection of V. dahliae. In this study, we carried out a genome-wide analysis in cotton and identified seventy-eight PLCPs, which were divided into nine subfamilies based on their evolution phylogeny: RD21 (responsive to desiccation 21), CEP (cysteine endopeptidase), XCP (xylem cysteine peptidase), XBCP3 (xylem bark cysteine peptidase 3), THI, SAG12 (senescence-associated gene 12), RD19 (responsive to desiccation 19), ALP (aleurain-like protease) and CTB (cathepsin B-like). Genes in each subfamily exhibit a similar structure and motif composition. The expression patterns of these genes in different organs were examined, and subfamily RD21 was the most abundant in these families. Expression profiles under abiotic stress showed that thirty-five PLCP genes were induced by multiple stresses. Further transcriptome analysis showed that sixteen PLCP genes were up-regulated in response to V. dahliae in cotton. Among those, GhRD21-7 showed a higher transcription level than most other PLCP genes. Additionally, over-expression of GhRD21-7 led to enhanced resistance and RNAi lines were more susceptible to V. dahliae in cotton. Our results provide valuable information for future functional genomic studies of PLCP gene family in cotton.

The traditional data mining algorithm focuses too much on a single dimension of data time or space, ignoring the association between time and space, which leads to a large amount of computation and low processing efficiency of the mining algorithm and makes it difficult to guarantee the final data mining effect. In response to the above problems, a hierarchical mining algorithm based on association rules for high-dimensional spatio-temporal big data is proposed. Based on the traditional association rules, after establishing the association rules of spatio-temporal data, the data to be mined are cleaned for redundancy. After selecting the local linear embedding algorithm to reduce the dimensionality of the data, a hierarchical mining strategy is developed to realize high-dimensional spatio-temporal big data mining by searching frequent predicates to form a spatio-temporal transaction database. The simulation experiment results verify that the algorithm has high complexity and can effectively reduce the processing volume, which can improve the processing efficiency by at least 56.26% compared with other algorithms.

Harvesting full spectrum sunlight for direct absorption solar collectors (DASCs) has attracted extensive attention and a number of potential nanofluids have been reported. In the current work, oxygen-deficient TiO2 (TiO2-x) improves the defects of conventional TiO2, making it fascinating optical absorption in the full solar spectrum. In the current work, oxygen-deficient TiO2 is obtained by NaBH4-reduction. The lower the reduction temperature is, the poorer the full solar absorption possesses. 600 °C is an appropriate reducing temperature from the results of XRD and UV–Vis–NIR. TiO2-x is stably dispersed in two oil system (heat transfer oil and silicone oil), leading to good medium-temperature solar thermal conversion. Au nanoparticles can further enhance the full solar absorption of oxygen-deficient TiO2. The highest temperature can be arrived at 91 °C for 100 ppm 5% Au/TiO2-x, 26.6 °C higher than base silicone oil. The excellent full solar absorption properties of TiO2-x and Au/TiO2-x in oil nanofluids bring new paradigms for working fluids in DASCs with medium temperatures.

Plants have developed sophisticated systems to cope with herbivore challenge, including morphological barriers and secondary metabolites to reduce damage. In this study, 550 Gossypium genotypes were evaluated for whitefly (Bemisia tabaci) resistance in five experiments including two in the field and three in the greenhouse, with 23 resistant and 19 susceptible genotypes selected. Whitefly-resistance index determination showed that a leaf having a high density of hairs had resistance to whitfly egg/nymph production. Longer leaf hairs were also important for resistance. This study revealed that okra shaped leaves reduced adult whitefly oviposition preference, while glabrous leaves and high hair density helped not only in the reduction of the adults but also decreased oviposition preference. Gossypol was also observed to be involved in the reduction of adult whitefly development and/or survival.

Large scale wind consumption capability is influenced by generation mix, load characteristics, transmission network deliverability and even wind power characteristics. This paper performed chronological simulation with consideration of secure unit commitment constraints to study wind power consumption of a test system in North China. Case study indicates that the most challenging time period of wind power consumption is winter night especially during the Spring Festival when the load is very low and generation output cannot be decreased to meet heating needs.

Background Bronchiolitis obliterans syndrome (BOS), chronic lung allograft rejection, remains an impediment for the function of the transplanted organ. In this study, we defined the role of the microRNA (miRNA) miR-144 in fibroproliferation leading to BOS. Methods Biopsy specimens were obtained from 20 lung transplant recipients with BOS( + ) and 19 without BOS( – ). Expression of miR-144 and its target, transforming growth factor-β (TGF-β)–induced factor homeobox 1(TGIF1), were analyzed by real-time polymerase chain reaction and Western blot. Overexpression of miR-144 and luciferase reporter genes were performed to elucidate miRNA-target interactions. The function of miR-144 was evaluated by transfecting fibroblasts and determining the response to TGF-β by analyzing Sma- and Mad-related family (Smads), fibroblast growth factor, TGF-β, and vascular endothelial growth factor. Smooth muscle actin-α–positive stress fibers and F-actin filaments in lung fibroblasts were analyzed by immunofluorescence. Results Analysis of miR-144 in the biopsy specimens demonstrated 4.1 ± 0.8-fold increases in BOS + compared with BOS – patients, with a significant reduction in TGIF1 (3.6 ± 1.2-fold), a corepressor of Smads. In vitro transfection confirmed that over-expression of miR-144 results in a reduction in TGIF1 and an increase in SMAD2, SMAD4, fibroblast growth factor-6, TGF-β, and vascular endothelial growth factor. Increasing miR-144 by transfecting, increased smooth muscle actin-α and fibronectin, and knockdown of miR-144 diminished fibrogenesis in MRC-5 fibroblasts. Conclusions miR-144 is a critical regulator of the TGF-β signaling cascade and is over-expressed in lungs with BOS. Therefore, miR-144 is a potential target toward preventing fibrosis leading to BOS after lung transplant.

The paper is aimed at solving the problems of inconsistency, inaccuracy and non-real time of customer profile in the electric power marketing information system, and proposes the new methods of improving the customer profile in electric power marketing based on the big data analysis of customer's addresses. The core idea of the methods is that by the introduction of other industry data resources, the electricity address provided by electric power marketing information system and the customer address provided by other resources are analyzed with the big data technologies to achieve precise matching of these addresses. The address matching is followed by three steps: Chinese word segmentation with Hidden Markov Model algorithm, sentence similarity calculation based on the semantic and word order, and finally geographical coordinates matching for cross validation. Based on the matching results, the procedures of updating customer profile are processed respectively according to customer contact changes or changes in customer property rights, to achieve the consistency, accuracy and real-time data of customer profile. By implementing the automatic and intelligent operations of perfecting customer profile, the strong information support is provided for the marketing departments to enhance the “Internet+” electric power marketing services.

Al films and TiO2 films were separately coated on AZ31 magnesium alloy substrates by means of magnetron sputtering method. The surface properties of the samples were explored and compared. Scanning electron microscope (SEM) observed the compact structure characteristics of as-deposited Al films and TiO2 films. After heat treatment under 200oC for half an hour the films kept the compact structure characteristics and there didn’t exist structural defects on the surface of the films. Nano-indentation measurement results display that the micro-hardness of as-deposited Al film and TiO2 film reaches about 1.90 Gpa and 1.51 Gpa, separately. Al film is a bit harder than TiO2 film. Finally, the corrosion experiments in simulated body fluid initially indicate the different corrosion properties for Al film and TiO2 film. Al film presents more effective anti-corrosion properties than TiO2 film.

Cottonseed oil is recognized as an important oil in food industry for its unique characters: low flavor reversion and the high level of antioxidants (VitaminE) as well as unsaturated fatty acid. However, the cottonseed oil content of cultivated cotton (Gossypium hirsutum) is only around 20%. In this study, we modified the accumulation of oils by the down-regulation of phosphoenolpyruvate carboxylase 1 (GhPEPC1) via RNA interference in transgenic cotton plants. The qRT-PCR and enzyme activity assay revealed that the transcription and expression of GhPEPC1 was dramatically down-regulated in transgenic lines. Consequently, the cottonseed oil content in several transgenic lines showed a significant (P GhPEPC1 in the regulation of seed oil content, we quantified the expression of the carbon metabolism related genes of transgenic GhPEPC1 RNAi lines by transcriptome analysis. This analysis revealed the decrease of GhPEPC1 expression led to the increase expression of triacylglycerol biosynthesis-related genes, which eventually contributed to the lipid biosynthesis in cotton. This result provides a valuable information for cottonseed oil biosynthesis pathway and shows the potential of creating high cottonseed oil germplasm by RNAi strategy for cotton breeding.