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Sophora moorcroftiana, a Leguminosae shrub species that is restricted to the arid and semi-arid regions of the Qinghai-Tibet Plateau, is an ecologically important foundation species and exhibits substantial drought tolerance in the Plateau. There are no functional genomics resources in public databases for understanding the molecular mechanism underlying the drought tolerance of S. moorcroftiana. Therefore, we performed a large-scale transcriptome sequencing of this species under drought stress using the Illumina sequencing technology. A total of 62,348,602 clean reads were obtained. The assembly of the clean reads resulted in 146,943 transcripts, including 66,026 unigenes. In the assembled sequences, 1534 transcription factors were identified and classified into 23 different common families, and 9040 SSR loci, from di- to hexa-nucleotides, whose repeat number is greater than five, were presented. In addition, we performed a gene expression profiling analysis upon dehydration treatment. The results indicated significant differences in the gene expression profiles among the control, mild stress and severe stress. In total, 4687, 5648 and 5735 genes were identified from the comparison of mild versus control, severe versus control and severe versus mild stress, respectively. Based on the differentially expressed genes, a Gene Ontology annotation analysis indicated many dehydration-relevant categories, including 'response to water 'stimulus' and 'response to water deprivation'. Meanwhile, the Kyoto Encyclopedia of Genes and Genomes pathway analysis uncovered some important pathways, such as 'metabolic pathways' and 'plant hormone signal transduction'. In addition, the expression patterns of 25 putative genes that are involved in drought tolerance resulting from quantitative real-time PCR were consistent with their transcript abundance changes as identified by RNA-seq. The globally sequenced genes covered a considerable proportion of the S. moorcroftiana transcriptome, and the expression results may be useful to further extend the knowledge on the drought tolerance of this plant species that survives under Plateau conditions.

We present two fast algorithms for finding the solution of the nonsingular lower Hessenberg quasi-Toeplitz linear system stem from Markov chain. And we confirm the complexity of these two algorithms is both O based on the fact that a lower Hessenberg quasi-Toeplitz matrix can be written as the sum of a Toeplitz matrix and a rank-one matrix, such that the fast solver involves O operators for solving the Toeplitz linear system can be adopted. Finally, numerical results prove the superiority and accuracy of our algorithms by comparing the values of residual and CPU time with existing algorithms.

The energy cost minimization for mission-critical internet-of-things (IoT) in mobile edge computing (MEC) system is investigated in this work. Therein, short data packets are transmitted between the IoT devices and the access points (APs) to reduce transmission latency and prolong the battery life of the IoT devices. The effects of short-packet transmission on the radio resource allocation is explicitly revealed. We mathematically formulate the energy cost minimization problem as a mixed-integer non-linear programming (MINLP) problem, which is difficult to solve in an optimal way. More specifically, the difficulty is essentially derived from the coupling of the binary offloading variables and the resource management among all the IoT devices. For analytical tractability, we decouple the mixed-integer and non-convex optimization problem into two sub-problems, namely, the task offloading decision-making and the resource optimization problems, respectively. It is proved that the resource allocation problem for IoT devices under the fixed offloading strategy is convex. On this basis, an iterative algorithm is designed, whose performance is comparable to the best solution for exhaustive search, and aims to jointly optimize the offloading strategy and resource allocation. Simulation results verify the convergence performance and energy-saving function of the designed joint optimization algorithm. Compared with the extensive baselines under comprehensive parameter settings, the algorithm has better energy-saving effects.

Cache‐enabled device‐to‐device (D2D) network has been deemed as an effective technique to offload the data traffic. However, the gain of the caching schemes is closely related to the homogeneity among users' preference distribution. To tackle this issue, recommendation is a promising proactive approach. It increases the request probability of recommended contents, reshaping users' contents demand patterns, and improving caching performance. Moreover, considering the heterogeneous network settings, i.e. content retrieval costs vary, the routing design becomes a non‐negligible factor on caching performance optimization. On these grounds, the average system cost of D2D‐enabled wireless caching networks with multiple BSs is first described. Then the routing strategies are designed together with caching and recommendation policies by minimizing the average cost of these networks. The optimization problem is proven as NP‐hard. To facilitate the analysis, the original problem is decoupled into two sub‐problems and solve them respectively. Afterwards, all the variables are optimized in an alternating manner until the convergence is achieved. The proposed algorithm's convergence performance and benefits over benchmark strategies in terms of total cost and cache hit ratio are supported by Monte‐Carlo simulation results. In this paper, the cost minimization problem was investigated for D2D‐aware wireless caching networks via jointly optimizing caching, recommendation and routing strategy with the limited cache space per cache unit and the requirements of recommendation quantity and quality per user.

In this paper, we propose a low-rank matrix approximation algorithm for solving the Toeplitz matrix completion (TMC) problem. The approximation matrix was obtained by the mean projection operator on the set of feasible Toeplitz matrices for every iteration step. Thus, the sequence of the feasible Toeplitz matrices generated by iteration is of Toeplitz structure throughout the process, which reduces the computational time of the singular value decomposition (SVD) and approximates well the solution. On the theoretical side, we provide a convergence analysis to show that the matrix sequences of iterates converge. On the practical side, we report the numerical results to show that the new algorithm is more effective than the other algorithms for the TMC problem.

Background/Aims: Long non-coding RNAs (lncRNAs) act as competing endogenous RNAs (ceRNAs) to compete for microRNAs (miRNAs) in cancer metastasis. Head and neck squamous cell carcinoma (HNSCC) is one of the most common human cancers and rare biomarkers could predict the clinical prognosis of this disease and its therapeutic effect. Methods: Weighted gene co-expression network analysis (WGCNA) was performed to identify differentially expressed mRNAs (DEmRNAs) that might be key genes. GO enrichment and protein–protein interaction (PPI) analyses were performed to identify the principal functions of the DEmRNAs. An lncRNA-miRNA-mRNA network was constructed to understand the regulatory mechanisms in HNSCC. The prognostic signatures of mRNAs, miRNAs, and lncRNAs were determined by Gene Expression Profiling Interactive Analysis (GEPIA) and using Kaplan–Meier survival curves for patients with lung squamous cell carcinoma. Results: We identified 2,023 DEmRNAs, 1,048 differentially expressed lncRNAs (DElncRNAs), and 82 differentially expressed miRNAs (DEmiRNAs). We found that eight DEmRNAs, 53 DElncRNAs, and 16 DEmiRNAs interacted in the ceRNA network. Three ceRNAs (HCG22, LINC00460 and STC2) were significantly correlated with survival. STC2 transcript levels were significantly higher in tumour tissues than in normal tissues, and the STC2 expression was slightly upregulated at different stages of HNSCC. Conclusion: LINC00460, HCG22 and STC2 exhibited aberrant levels of expression and may participate in the pathogenesis of HNSCC.

Heterophylly, or leaf morphological changes along plant shoot axes, is an important indicator of plant eco-adaptation to heterogeneous microenvironments. Despite extensive studies on the genetic control of leaf shape, the genetic architecture of heterophylly remains elusive. To identify genes related to heterophylly and their associations with plant saline tolerance, we conducted a leaf shape mapping experiment using leaves from a natural population of Populus euphratica . We included 106 genotypes grown under salt stress and salt-free (control) conditions using clonal seedling replicates. We developed a shape tracking method to monitor and analyze the leaf shape using principal component (PC) analysis. PC1 explained 42.18% of the shape variation, indicating that shape variation is mainly determined by the leaf length. Using leaf length along shoot axes as a dynamic trait, we implemented a functional mapping-assisted genome-wide association study (GWAS) for heterophylly. We identified 171 and 134 significant quantitative trait loci (QTLs) in control and stressed plants, respectively, which were annotated as candidate genes for stress resistance, auxin, shape, and disease resistance. Functions of the stress resistance genes ABSCISIC ACIS-INSENSITIVE 5-like ( ABI5 ), WRKY72 , and MAPK3 were found to be related to many tolerance responses. The detection of AUXIN RESPONSE FACTOR17-LIKE ( ARF17 ) suggests a balance between auxin-regulated leaf growth and stress resistance within the genome, which led to the development of heterophylly via evolution. Differentially expressed genes between control and stressed plants included several factors with similar functions affecting stress-mediated heterophylly, such as the stress-related genes ABC transporter C family member 2 ( ABCC2 ) and ABC transporter F family member ( ABCF ), and the stomata-regulating and reactive oxygen species (ROS) signaling gene RESPIRATORY BURST OXIDASE HOMOLOG ( RBOH ). A comparison of the genetic architecture of control and salt-stressed plants revealed a potential link between heterophylly and saline tolerance in P. euphratica , which will provide new avenues for research on saline resistance-related genetic mechanisms.

Dracocephalum tanguticum Maxim, a Lamiaceae species endemic to the Qinghai-Tibetan Plateau and adjacent regions, is an important ornamental, medicinal and aromatic herb. In this study, a comprehensive transcriptome of 18 libraries from six organs namely, roots, stems, leaves, sepals, flowers and seeds of D. tanguticum were generated. More than 100 Gb of sequence data were obtained and assembled de novo into 187,447 transcripts, including 151,463 unigenes, among which the six organs shared 17.7% (26,841). In addition, all unigenes were assigned to 362 pathways, in which ‘biosynthesis of secondary metabolites’ is the second enriched pathway. Furthermore, rosmarinic acid (RA) is one of the multifunctional phenolic bioactive compounds produced in some Lamiaceae species. The six organs of D. tanguticum were confirmed to produce RA. A total of 22 predicted biosynthetic genes related to RA from the transcriptome were further isolated. Two of these genes were identified as candidates by evaluating the correlation coefficient between the RA contents and the expression of the predicted biosynthetic genes in the six organs. The new sequence information will improve the knowledge of D. tanguticum , as well as provide a reference tool for future studies of biosynthetic genes related to RA in this species.

Introduction. Our previous study suggested that NSC-CM (neural stem cell-conditioned medium) inhibited cell apoptosis in vitro. In addition, many studies have shown that neurotrophic factors and microparticles secreted into a conditioned medium by NSCs had neuroprotective effects. Thus, we hypothesized that NSC-CM had the capacity of protecting against cerebral I/R injury. Methods. Adult male Sprague-Dawley rats receiving middle cerebral artery occlusion surgery as an animal model of cerebral I/R injury were randomly assigned to two groups: the control group and NSC-CM-treated group. 1.5 ml NSC-CM or PBS (phosphate buffer saline) was administrated slowly by tail vein at 3 h, 24 h, and 48 h after ischemia onset. Results. NSC-CM significantly ameliorated neurological defects and reduced cerebral infarct volume, accompanied by preserved mitochondrial ultrastructure. In addition, we also found that NSC-CM significantly inhibited cell apoptosis in the ischemic hemisphere via improving the expression of Bcl-2 (B-cell lymphoma-2). Conclusion. NSC-CM might be an alternative and effective therapeutic intervention for ischemic stroke.

De novo shoot regeneration is one of the important manifestations of cell totipotency in organogenesis, which reflects a survival strategy organism evolved when facing natural selection. Compared with tissue regeneration, and somatic embryogenesis, de novo shoot regeneration denotes a shoot regeneration process directly from detatched or injured tissues of plant. Studies on plant shoot regeneration had identified key genes mediating shoot regeneration. However, knowledge was derived from Arabidopsis; the regeneration capacity is hugely distinct among species. To achieve a comprehensive understanding of the shoot regeneration mechanism from tree species, we select four genetic lines of Populus euphratica from a natural population to be sequenced at transcriptome level. On the basis of the large difference of differentiation capacity, between the highly differentiated (HD) and low differentiated (LD) groups, the analysis of differential expression identified 4920 differentially expressed genes (DEGs), which were revealed in five groups of expression patterns by clustering analysis. Enrichment showed crucial pathways involved in regulation of regeneration difference, including “plant hormone signal transduction”, “cell differentiation”, \"cellular response to auxin stimulus\", and “auxin-activated signaling pathway”. The expression of nine genes reported to be associated with shoot regeneration was validated using quantitative real-time PCR (qRT-PCR). For the specificity of regeneration mechanism with P. euphratica, large amount of DEGs involved in \"plant-pathogen interaction\", ubiquitin-26S proteosome mediated proteolysis pathway, stress-responsive DEGs, and senescence-associated DEGs were summarized to possibly account for the differentiation difference with distinct genotypes of P. euphratica. The result in this study helps screening of key regulators in mediating the shoot differentiation. The transcriptomic characteristic in P. euphratica further enhances our understanding of key processes affecting the regeneration capacity of de novo shoots among distinct species.