High spectral efficiency modulation scheme based on joint interaction of orthogonal compressed chirp division multiplexing and power superimposed code.

In this paper, we propose a high spectral efficiency modulation scheme based on joint interaction of orthogonal compressed chirp division multiplexing (OCCDM) and power superimposed code (PSC) under the intensity modulation and direct detection (IM/DD) system. OCCDM is a novel orthogonal chirp division multiplexing technology featuring spectral compression through the implementation of processing similar to a discrete Fourier transform, enhancing the spectral efficiency (SE) through bandwidth savings without loss of orthogonality of each chirp. Meanwhile, PSC technology enables multiple code words being transmitted superimposed on the same chirp. This technique involves allocating varying power levels to different users, thereby distinguishing them, increasing the transmission's net bit rate and substantially boosting the SE. The transmission has been performed experimentally using a 2 km 7-core fiber span. The impact of the above-mentioned technologies on the bit error rate (BER) performance is assessed in the power, frequency, and joint domain. The BER and enhancements in the SE can be balanced when the spectral bandwidth compression factor (α) and power distribution ratio are equal to 0.9 and 4, respectively. The observed outcome leads to the transmission's SE increase to more than double the baseline value, at 2.22 times. Based on the above analysis, we believe this structure is expected to become a potential for developing next-generation PON.

Physical layer security scheme for key concealment and distribution based on carrier scrambling.

The purpose of this study is to present a physical layer security scheme for key concealment and distribution based on carrier scrambling. The three-dimensional (3D) Lorenz system is used to generate independent chaotic sequences that encrypt the information with bit, constellation and subcarrier. In order to realize the flexible distribution of the key and ensure its security, the key information is loaded into a specific subcarrier. While key subcarrier and the ciphertext subcarrier are scrambled simultaneously. The encrypted key position information is processed and transmitted in conjunction with the training sequence (TS) to facilitate demodulation by the legitimate receiver. The processed TS can accommodate up to 10 key position information, thereby demonstrating the scheme's exceptional scalability. Experimental results show that the proposed scheme can safely transmit 131.80 Gb/s Orthogonal frequency division multiplexing (OFDM) signals across 2 km 7-core fiber. Meanwhile, the scheme enables simultaneous flexible distribution and concealment of the key, thereby offering a promising solution for physical layer security.

High-security space division multiplexing optical transmission scheme based on constellation grid selective twisting.

In this paper, we propose a high-security space division multiplexing optical transmission scheme based on constellation grid selective twisting, which adopts the Rossler chaos model for encrypting PDM-16QAM signals, being applied to a multicore, few-mode multiplexing system. The bitstream of the program is passed through XOR function before performing constellation grid selective twisting and rotation of the constellation map to improve the security of the system. The proposed system is verified experimentally by using 80-wave and 4-mode multiplexing in one of the 19-core 4-mode fibers. Based on the proposed encryption method, a net transmission rate of 34.13 Tbit/s, a transmission distance of 6000 km, and a capacity distance product of 204.8 Pb/s × km is achieved under encrypted PDM-QPSK modulation. Likewise, a net transmission rate of 68.27 Tbit/s, a transmission distance of 1000 km, and a capacity distance product of 68.27 Pb/s × km is achieved based on encrypted PDM-16QAM modulation. It is experimentally verified that the sensitivity of the initial value in Rossler's chaotic model is in the range of 10-16∼10-17. Meanwhile, the proposed encryption scheme achieves a large key space of 10101, which is compatible with the high-capacity distance product multicore and few-mode multiplexing system. It is a promising candidate for the next-generation highly-secured high-capacity transmission system.

The reference genome and transcriptome of the limestone langur, Trachypithecus leucocephalus, reveal expansion of genes related to alkali tolerance.

BACKGROUND: Trachypithecus leucocephalus, the white-headed langur, is a critically endangered primate that is endemic to the karst mountains in the southern Guangxi province of China. Studying the genomic and transcriptomic mechanisms underlying its local adaptation could help explain its persistence within a highly specialized ecological niche. RESULTS: In this study, we used PacBio sequencing and optical assembly and Hi-C analysis to create a high-quality de novo assembly of the T. leucocephalus genome. Annotation and functional enrichment revealed many genes involved in metabolism, transport, and homeostasis, and almost all of the positively selected genes were related to mineral ion binding. The transcriptomes of 12 tissues from three T. leucocephalus individuals showed that the great majority of genes involved in mineral absorption and calcium signaling were expressed, and their gene families were significantly expanded. For example, FTH1 primarily functions in iron storage and had 20 expanded copies. CONCLUSIONS: These results increase our understanding of the evolution of alkali tolerance and other traits necessary for the persistence of T. leucocephalus within an ecologically unique limestone karst environment.

PcircRNA_finder: a software for circRNA prediction in plants.

MOTIVATION: Recent studies reveal an important role of non-coding circular RNA (circRNA) in the control of cellular processes. Because of differences in the organization of plant and mammal genomes, the sensitivity and accuracy of circRNA prediction programs using algorithms developed for animals and humans perform poorly for plants. RESULTS: A circRNA prediction software for plants (termed PcircRNA_finder) was developed that is more sensitive in detecting circRNAs than other frequently used programs (such as find_circ and CIRCexplorer), Based on analysis of simulated and real rRNA-/RNAase R RNA-Seq data from Arabidopsis thaliana and rice PcircRNA_finder provides a more comprehensive sensitive, precise prediction method for plants circRNAs. AVAILABILITY AND IMPLEMENTATION: http://ibi.zju.edu.cn/bioinplant/tools/manual.htm CONTACT: fanlj@zju.edu.cnSupplementary information: Supplementary data are available at Bioinformatics online.

Full-length sequence assembly reveals circular RNAs with diverse non-GT/AG splicing signals in rice.

Circular RNAs (circRNAs) have been identified in diverse eukaryotic species and are characterized by RNA backsplicing events. Current available methods for circRNA identification are able to determine the start and end locations of circRNAs in the genome but not their full-length sequences. In this study, we developed a method to assemble the full-length sequences of circRNAs using the backsplicing RNA-Seq reads and their corresponding paired-end reads. By applying the method to an rRNA-depleted/RNase R-treated RNA-Seq dataset, we for the first time identified full-length sequences of nearly 3,000 circRNAs in rice. We further showed that alternative circularization of circRNA is a common feature in rice and, surprisingly, found that the junction sites of a large number of rice circRNAs are flanked by diverse non-GT/AG splicing signals while most human exonic circRNAs are flanked by canonical GT/AG splicing signals. Our study provides a method for genome-wide identification of full-length circRNAs and expands our understanding of splicing signals of circRNAs.

An in vitro porcine model evaluating a novel stent retriever for thrombectomy of the common carotid artery.

OBJECTIVES: This study aimed to test the safety and efficiency of a novel stent retriever, RECO, in a swine model. BACKGROUND: The stent retrievers show great benefit for patients with acute ischemic stroke. METHODS: The framework of the stent was optimized. The proximal stent was closed; mechanical connection replaced the electrolysis connection and the push wire located on the longitudinal axis. After tests in vitro, the safety and thrombectomy efficiency of RECO device were evaluated by angiography and histological analysis in a swine model with placement of experimental soft or hard thrombi. RESULTS: No device-related thrombi were observed on the perioperative term or 1 month later. The endothelial cells were intact and the smooth muscle cells did not migrate or proliferate. Device-related vasospasm was detected in 9% vessels undergoing the procedure and was alleviated after delivery of a dose of nitroglycerin. The RECO device demonstrated a high recanalization rate in the target vessels with a mean of 1.3 runs. No residual thrombi were observed under the DSA or microscope. CONCLUSIONS: Our data indicated that RECO device was a novel, safe and effective stent based clot retriever. A phase IIa clinical trial, RESTORE, is undergoing (NCT01983644).

Elevated circulating CD19+CD24hiCD38hi B cells display pro-inflammatory phenotype in idiopathic membranous nephropathy.

CD19+CD24hiCD38hi regulatory B cells exert immunosuppressive functions by producing IL-10, but their role in idiopathic membranous nephropathy (IMN) remains elusive. Here, we investigated the frequency and functional changes of circulating CD19+CD24hiCD38hi B cells and evaluated the correlation of CD19+CD24hiCD38hi B cells with clinical features and T helper cell subsets in IMN patients. Compared with healthy controls (HCs), IMN patients showed an increased frequency of CD19+CD24hiCD38hi B cells, but a significant reduction in the percentage of CD19+CD24hiCD38hi B cells was observed 4 weeks after cyclophosphamide treatment. The frequency of CD19+CD24hiCD38hi B cells was positively correlated with the levels of 24h urinary protein, but negatively correlated with serum total protein and serum albumin, respectively. CD19+CD24hiCD38hi B cells in IMN patients displayed a skewed pro-inflammatory cytokine profile with a higher level of IL-6 and IL-12, but a lower concentration of IL-10 than their healthy counterparts. Accompanied by upregulation of Th2 and Th17 cells in IMN patients, the percentage of CD19+CD24hiCD38hi B cell subset was positively associated with Th17 cell frequency. In conclusion, CD19+CD24hiCD38hi B cells were expanded but functionally impaired in IMN patients. Their altered pro-inflammatory cytokine profile may contribute to the pathogenesis of IMN.

The Physalis floridana genome provides insights into the biochemical and morphological evolution of Physalis fruits.

The fruits of Physalis (Solanaceae) have a unique structure, a lantern-like fruiting calyx known as inflated calyx syndrome (ICS) or the Chinese lantern, and are rich in steroid-related compounds. However, the genetic variations underlying the origin of these characteristic traits and diversity in Physalis remain largely unknown. Here, we present a high-quality chromosome-level reference genome assembly of Physalis floridana (~1.40 Gb in size) with a contig N50 of ~4.87 Mb. Through evolutionary genomics and experimental approaches, we found that the loss of the SEP-like MADS-box gene MBP21 subclade is likely a key mutation that, together with the previously revealed mutation affecting floral MPF2 expression, might have contributed to the origination of ICS in Physaleae, suggesting that the origination of a morphological novelty may have resulted from an evolutionary scenario in which one mutation compensated for another deleterious mutation. Moreover, the significant expansion of squalene epoxidase genes is potentially associated with the natural variation of steroid-related compounds in Physalis fruits. The results reveal the importance of gene gains (duplication) and/or subsequent losses as genetic bases of the evolution of distinct fruit traits, and the data serve as a valuable resource for the evolutionary genetics and breeding of solanaceous crops.

Effects of annealing atmosphere on the performance of Cu(InGa)Se2 films sputtered from quaternary targets.

Quaternary sputtering without additional selenization is a low-cost alternative method for the preparation of Cu(InGa)Se2 (CIGS) thin film for photovoltaics. However, without selenization, the device efficiency is much lower than that with selenization. To comprehensively examine this problem, we compared the morphologies, depth profiles, compositions, electrical properties and recombination mechanism of the absorbers fabricated with and without additional selenization. The results revealed that the amount of surface Se on CIGS films annealed in a Se-free atmosphere is less than that on CIGS films annealed in a Se-containing atmosphere. Additionally, the lower amount of surface Se reduced the carrier concentration, enhanced the resistivity of the CIGS film and allowed CIGS/CdS interface recombination to be the dominant recombination mechanism of CIGS device. The increase of interface recombination reduced the efficiency of the device annealed in a Se-free atmosphere.

A high-quality reference genome of wild Cannabis sativa.

Cannabis sativa is a well-known plant species that has great economic and ecological significance. An incomplete genome of cloned C. sativa was obtained by using SOAPdenovo software in 2011. To further explore the utilization of this plant resource, we generated an updated draft genome sequence for wild-type varieties of C. sativa in China using PacBio single-molecule sequencing and Hi-C technology. Our assembled genome is approximately 808 Mb, with scaffold and contig N50 sizes of 83.00 Mb and 513.57 kb, respectively. Repetitive elements account for 74.75% of the genome. A total of 38,828 protein-coding genes were annotated, 98.20% of which were functionally annotated. We provide the first comprehensive de novo genome of wild-type varieties of C. sativa distributed in Tibet, China. Due to long-term growth in the wild environment, these varieties exhibit higher heterozygosity and contain more genetic information. This genetic resource is of great value for future investigations of cannabinoid metabolic pathways and will aid in promoting the commercial production of C. sativa and the effective utilization of cannabinoids. The assembled genome is also a valuable resource for intensively and effectively investigating the C. sativa genome further in the future.

The genetic adaptations of fall armyworm Spodoptera frugiperda facilitated its rapid global dispersal and invasion.

The fall armyworm (Spodoptera frugiperda) is a lepidopteran insect pest that causes huge economic losses. This notorious insect pest has rapidly spread over the world in the past few years. However, the mechanisms of rapid dispersal are not well understood. Here, we report a chromosome-level assembled genome of the fall armyworm, named the ZJ-version, using PacBio and Hi-C technology. The sequenced individual was a female collected from the Zhejiang province of China and had high heterozygosity. The assembled genome size of ZJ-version was 486 Mb, containing 361 contigs with an N50 of 1.13 Mb. Hi-C scaffolding further assembled the genome into 31 chromosomes and a portion of W chromosome, representing 97.4% of all contigs and resulted in a chromosome-level genome with scaffold N50 of 16.3 Mb. The sex chromosomes were identified by genome resequencing of a single male pupa and a single female pupa. About 28% of the genome was annotated as repeat sequences, and 22,623 protein-coding genes were identified. Comparative genomics revealed the expansion of the detoxification-associated gene families, chemoreception-associated gene families, nutrition metabolism and transport system gene families in the fall armyworm. Transcriptomic and phylogenetic analyses focused on these gene families revealed the potential roles of the genes in polyphagia and invasion of fall armyworm. The high-quality of the fall armyworm genome provides an important genomic resource for further explorations of the mechanisms of polyphagia and insecticide resistance, as well as for pest management of fall armyworm.

Chemistry and immunostimulatory activity of a polysaccharide from Undaria pinnatifida.

An immunologically active polysaccharide named as UPP-2 (1035.52 kDa) was isolated from Undaria pinnatifida using traditional water extraction followed by DEAE Sepharose fast flow chromatography. UPP-2 was proven to be a low sulfated polysaccharide with relatively abundant uronic acid (13.08 ±â€¯0.67%). UPP-2 mainly consisted of xylose (64.55%), glucose (23.81%), arabinose (5.90%) and mannose (4.26%), and its main glycosidic linkage types included →2)-α-D-Xylp-(1→, →4)-α-D-Glcp-(1→, α-D-Xylp-(1→ and →2,4)-ß-D-Xylp-(1 → . Results indicated that UPP-2 significantly promoted the proliferation and pinocytic capacity of RAW264.7 cells, and upregulated the mRNA expressions of iNOS, TNF-α, IL-6 and IL-1ß at 100-600 µg/mL with a maximum of 195, 42, 768 and 539 times of those of the negative control, respectively. Moreover, UPP-2 significantly increased the secretions of nitric oxide, TNF-α and IL-6 at 100-600 µg/mL (8.0, 73.1 and 188.7 times compared to those of the negative control, respectively), as well as promoted the production of IL-1ß obviously at 600 µg/mL. Overall, UPP-2 could be served as a potential dietary supplement or functional food based on its immunostimulatory activity.

Genomic variation associated with local adaptation of weedy rice during de-domestication.

De-domestication is a unique evolutionary process by which domesticated crops are converted into 'wild predecessor like' forms. Weedy rice (Oryza sativa f. spontanea) is an excellent model to dissect the molecular processes underlying de-domestication. Here, we analyse the genomes of 155 weedy and 76 locally cultivated rice accessions from four representative regions in China that were sequenced to an average 18.2 × coverage. Phylogenetic and demographic analyses indicate that Chinese weedy rice was de-domesticated independently from cultivated rice and experienced a strong genetic bottleneck. Although evolving from multiple origins, critical genes underlying convergent evolution of different weedy types can be found. Allele frequency analyses suggest that standing variations and new mutations contribute differently to japonica and indica weedy rice. We identify a Mb-scale genomic region present in weedy rice but not cultivated rice genomes that shows evidence of balancing selection, thereby suggesting that there might be more complexity inherent to the process of de-domestication.