Search

10.13039/501100001809-National Natural Science Foundation of China (Grant Number: 62203016, 61973006, T2121002, U21A2019 and 61933007); Beijing Natural Science Foundation of China (Grant Number: JQ20025); Hainan Province Science and Technology Special Fund of China (Grant Number: ZDYF2022SHFZ105); 10.13039/501100002858-China Postdoctoral Science Foundation (Grant Number: 2021TQ0009); Royal Society of the U.K.; Alexander von Humboldt Foundation of Germany.

In this brief, the state estimation problem is investigated for a class of randomly delayed artificial neural networks (ANNs) subject to probabilistic saturation constraints (PSCs) and non-Gaussian noises under the redundant communication channels. A series of mutually independent Bernoulli distributed white sequences are introduced to govern the random occurrence of the time delays, the saturation constraints, and the transmission channel failures. A comprehensive redundant-channel-based communication mechanism is constructed to attenuate the phenomenon of packet dropouts so as to enhance the quality of data transmission. To compensate for the influence of randomly occurring time delays, the corresponding occurrence probability is exploited in the process of particle generation. In addition, an explicit expression of the likelihood function is established based on the statistical information to account for the impact of PSCs and redundant channels. By virtue of the modified operations of particle propagation and weight update, a particle-filter-based state estimation algorithm is proposed with mild restriction on the system type. Finally, an illustrative example with Monte Carlo simulations is provided to demonstrate the effectiveness of the developed state estimation scheme.

In this paper, the particle filtering problem is investigated for a class of nonlinear/non-Gaussian systems with energy harvesting sensors subject to randomly occurring sensor saturations (ROSSs). The random occurrences of the sensor saturations are characterized by a series of Bernoulli distributed stochastic variables with known probability distributions. The energy harvesting sensor transmits its measurement output to the remote filter only when the current energy level is sufficient, where the transmission probability of the measurement is recursively calculated by using the probability distribution of the sensor energy level. The effects of the ROSSs and the possible measurement losses induced by insufficient energies are fully considered in the design of filtering scheme, and an explicit expression of the likelihood function is derived. Finally, the numerical simulation examples (including a benchmark example for nonlinear filtering and the applications in moving target tracking problem) are provided to demonstrate the feasibility and effectiveness of the proposed particle filtering algorithm.

This paper investigates the particle filtering problem for a class of nonlinear/non-Gaussian systems under the dynamic event-triggered protocol. In order to avert frequent data transmission and reduce the communication overhead, a dynamic event-triggered transmission mechanism is adopted to decide whether the data should be transmitted or not. We first consider a scenario where all sensor nodes selectively transmit their newly obtained measurements to a central node, and a full likelihood function at the central node is derived by fusing the transmitted measurements and the information embodied in the non-triggered measurements. Based on the derived full likelihood function, a centralized auxiliary particle filtering algorithm is proposed to select those particles that are more likely to match the current measurement information. Next, based on the diffusion strategy, a distributed auxiliary particle filtering algorithm is further developed, where the local measurements and the local posteriors (approximated by the Gaussian mixture models) are exchanged among neighboring nodes under the dynamic event-triggered communication strategy. Finally, the effectiveness of the proposed filtering schemes is demonstrated via Monte Carlo simulations in a target tracking problem with received-signal-strength sensors.

The Collagen Type VII Alpha 1 Chain (COL7A1) is associated with a variety of cancers, however, COL7A1 gene expression in human lung squamous cell carcinoma (LUSC) and its prognostic value have not been well studied. In this study, we used bioinformatics database to analyze the relationship between COL7A1 expression and survival in LUSC patients such as Oncomine, GEPIA, UALCAN, and STRING. And we used Kaplan–Meier plotter to analyze the prognosis of high or low expression of COL7A1 in different patients. We found that COL7A1 was significantly overexpressed in patients with LUSC. Additionally, in the survival analysis, COL7A1 expression was significantly associated with worse overall survival (OS), first progression (FP), Post-progression survival (PPS) in LUSC patients. Moreover, COL7A1 is closely associated with known biomarkers and key factors of LUSC. We used functional annotation enrichment analysis to show that genes co-expressed with COL7A1 were enriched in biological process (BP), cellular component (CC), molecular function (MF) and KEGG pathways. Furthermore, Laminin 332 and its association with COL7A1 may lead to the activation of the PI3K signaling pathway, ultimately leading to squamous cell carcinoma (SCC). This has also been mentioned in other people's research. Therefore, our work was designed to demonstrate the potential of COL7A1 as a prognostic biomarker in LUSC.

In the present study, the PLC characteristic parameters and DSA mechanism of Al-(2.86~9.41) Mg alloy sheets were investigated during tensile testing at room temperature with a tensile rate of 1 × 10−3 s−1. On the basis of the solution Mg concentrations in the α-Al matrix, the initial vacancy concentration, the second-phase particle configuration and the recrystallized grain configuration are almost the same by quenching treatment. The results show that the type of room-temperature tensile stress–strain curves of quenched Al-(2.86~9.41) Mg alloy sheets varied according to the Mg content. The type of stress–strain curve of the Al-2.86 Mg alloy sheet was B + C, while the type of stress–strain curve of the Al-(4.23~9.41) Mg alloy sheets was C. When the quenched Al-(2.86~9.41) Mg alloy sheets were stretched at room temperature, the strain cycle of the rectangular waves corresponding to the high stress flow ΔεTmax and stress drop amplitude Δσ on the zigzag stress–strain curve of alloy sheets increased with increasing the Mg content. Moreover, the strain cycle of ΔεTmax and Δσ on the stress–strain curve of alloy sheets increased gradually with increasing tensile deformation. The yield stress of quenched Al-(2.86~9.41) Mg alloy sheets increased gradually with increasing the Mg content. Moreover, the critical strain corresponding to yield stress εσ and the critical strain corresponding to the occurrence of the PLC shearing band εc of alloy sheets both increased with increasing the Mg content. However, the difference in flow strain value Δεc−σ between εc and εσ of alloy sheets decreased gradually with increasing the Mg content.

ZrC/ZrSi composite fibers were directly electro-synthesized from inexpensive and abundantly available ZrSiO4/C precursors in molten CaCl2–NaCl at 850 °C. Electrolysis was conducted at a constant voltage of 2.8 V using a graphite anode and a cathode composed of ZrSiO4/carbon mixture. The reaction mechanism of electro-synthesis process was systematically investigated by examination of partially and fully reduced samples. Results show that as-synthesized nanofiber is composed of ZrSi single crystal core and ZrC outer coating. The mechanism of composite fiber formation is a complex reaction pathway involving decomposition, electro-deoxidation and in situ carbonization. The electrochemical route in molten salt is a new promising method for simple fabrication of Zr-based composite fibers.

Fibroblast growth factors (FGFs) are short polypeptides that play essential roles in various cellular biological processes, including cell migration, proliferation, and differentiation, as well as tissue regeneration, immune response, and organogenesis. However, studies focusing on the characterization and function of FGF genes in teleost fishes are still limited. In this study, we identified and characterized expression patterns of 24 FGF genes in various tissues of embryonic and adult specimens of the black rockfish (Sebates schlegelii). Nine FGF genes were found to play essential roles in myoblast differentiation, as well as muscle development and recovery in juvelines of S. schlegelii. Moreover, sex-biased expression pattern of multiple FGF genes was recorded in the species’ gonads during its development. Among them, expression of the FGF1 gene was recorded in interstitial and sertoli cells of testes, promoting germ-cell proliferation and differentiation. In sum, the obtained results enabled systematic and functional characterization of FGF genes in S. schlegelii, laying a foundation for further studies on FGF genes in other large teleost fishes.

Teleost fish are the most diverse group of vertebrates and provide opportunities to study the evolution of sex determination (SD) systems. Using genomic and functional analyses, we identified a male-specific duplication of anti-Müllerian hormone (amh) gene as the male master sex-determining (MSD) gene in Sebastes schlegelii. By resequencing 10 males and 10 females, we characterized a 5 kb-long fragment in HiC_Scaffold_12 as a male-specific region, which contained an amh gene (named amhy). We then demonstrated that amhy is a duplication of autosomal amh that was later translocated to the ancestral Y chromosome. amha and amhy shared high-nucleotide identity with the most significant difference being two insertions in intron 4 of amhy. Furthermore, amhy overexpression triggered female-to-male sex reversal in S. schlegelii, displaying its fundamental role in driving testis differentiation. We developed a PCR assay which successfully identified sexes in two species of northwest Pacific rockfish related to S. schlegelii. However, the PCR assay failed to distinguish the sexes in a separate clade of northeast Pacific rockfish. Our study provides new examples of amh as the MSD in fish and sheds light on the convergent evolution of amh duplication as the driving force of sex determination in different fish taxa.

Black rockfish (Sebastes schlegelii) is a teleost species where eggs are fertilized internally and retained in the maternal reproductive system, where they undergo development until live birth (termed viviparity). In the present study, we report a chromosome-level black rockfish genome assembly. High-throughput transcriptome analysis (RNA-seq and ATAC-seq), coupled with in situ hybridization (ISH) and immunofluorescence, identify several candidate genes for maternal preparation, sperm storage and release, and hatching. We propose that zona pellucida (ZP) genes retain sperm at the oocyte envelope, while genes in two distinct astacin metalloproteinase subfamilies serve to release sperm from the ZP and free the embryo from chorion at pre-hatching stage. Finally, we present a model of black rockfish reproduction, and propose that the rockfish ovarian wall has a similar function to uterus of mammals. Taken together, these genomic data reveal unprecedented insights into the evolution of an unusual teleost life history strategy, and provide a sound foundation for studying viviparity in non-mammalian vertebrates and an invaluable resource for rockfish ecology and evolution research.

Myosins are important eukaryotic motor proteins that bind actin and utilize the energy of ATP hydrolysis to perform a broad range of functions such as muscle contraction, cell migration, cytokinesis, and intracellular trafficking. However, the characterization and function of myosin is poorly studied in teleost fish. In this study, we identified 60 myosin family genes in a marine teleost, black rockfish (Sebastes schlegelii), and further characterized their expression patterns. myosin showed divergent expression patterns in adult tissues, indicating they are involved in different types and compositions of muscle fibers. Among 12 subfamilies, S. schlegelii myo2 subfamily was significantly expanded, which was driven by tandem duplication events. The up-regulation of five representative genes of myo2 in the skeletal muscle during fast-growth stages of juvenile and adult S. schlegelii revealed their active role in skeletal muscle fiber synthesis. Moreover, the expression regulation of myosin during the process of myoblast differentiation in vitro suggested that they contribute to skeletal muscle growth by involvement of both myoblast proliferation and differentiation. Taken together, our work characterized myosin genes systemically and demonstrated their diverse functions in a marine teleost species. This lays foundation for the further studies of muscle growth regulation and molecular mechanisms of indeterminate skeletal muscle growth of large teleost fishes.

Myosins are important eukaryotic motor proteins that bind actin and utilize the energy of ATP hydrolysis to perform a broad range of functions such as muscle contraction, cell migration, cytokinesis, and intracellular trafficking. However, the characterization and function of myosin is poorly studied in teleost fish. In this study, we identified 60 myosin family genes in a marine teleost, black rockfish (Sebastes schlegelii), and further characterized their expression patterns. myosin showed divergent expression patterns in adult tissues, indicating they are involved in different types and compositions of muscle fibers. Among 12 subfamilies, S. schlegelii myo2 subfamily was significantly expanded, which was driven by tandem duplication events. The up-regulation of five representative genes of myo2 in the skeletal muscle during fast-growth stages of juvenile and adult S. schlegelii revealed their active role in skeletal muscle fiber synthesis. Moreover, the expression regulation of myosin during the process of myoblast differentiation in vitro suggested that they contribute to skeletal muscle growth by involvement of both myoblast proliferation and differentiation. Taken together, our work characterized myosin genes systemically and demonstrated their diverse functions in a marine teleost species. This lays foundation for the further studies of muscle growth regulation and molecular mechanisms of indeterminate skeletal muscle growth of large teleost fishes.

Skeletal myoblasts are activated satellite cells capable of proliferation and differentiation. Studies on mammalian myoblast differentiation and myogenesis could be carried out in vitro thanks to the availability of mouse myoblast cell line C2C12. Lacking of muscle cell line hinders the studies of teleost fish myogenesis. Here, we established a continuous skeletal muscle cell line from juvenile rockfish (Sebastes schlegelii) muscle using explant method and subcultured more than 50 passages for over 150 days. Stable expression of myoblast-specific marker, MyoD (myoblast determination protein) and the potential of differentiation into multi-nucleated skeletal myotubes upon induction suggested the cell line were predominately composed of myoblasts. Transcriptome analysis revealed a total of 4375 genes differentially expressed at four time points after the switch to differentiation medium, which were mainly involved in proliferation and differentiation of myoblasts. KIF22 (kinesin family member 22) and POLA1 (DNA polymerase alpha 1) were identified as the key genes involved in fish myoblast proliferation whereas MYL3 (myosin light chain 3) and TNNT2 (troponin T2) were determined as the crucial genes responsible for differentiation. In all, the continuous myoblasts cultured in this study provided a cell platform for future studies on marine fish myoblast differentiation and myogenesis. The molecular process of myoblast differentiation revealed in this study will open a window into the understanding of indeterminate muscle growth of large teleost.

Additional file 2: Fig. S2. Tissue expression pattern of genes involved in regulation of vasoconstriction. Heatmap was constructed by comparing 20 tissues. The x‐axis shows sampled tissues, with the prefix F_ for female and M_ for male samples, and the y‐axis shows genes. The color scale shows standardized TPM values normalized by Z-score method. Five genes (Ssc_10023120, Ssc_1004710, Ssc_10011522, Ssc_10023117 and Ssc_10023118) have a bias expression in ovarian wall and genitalia, three of which are Bdkrb2 genes (Ssc_10023117, Ssc_10023118 and Ssc_10023120).

Additional file 5: Fig. S4. Similarity comparison of amino acid sequences of the Bdkrb2 ORF in black rock fish. Ssc_13, Ssc_10023113; Ssc_14, Ssc_10023114; Ssc_15, Ssc_10023115; Ssc_16, Ssc_10023116; Ssc_17, Ssc_10023117; Ssc_18, Ssc_10023118; Ssc_19, Ssc_10023119; Ssc_20, Ssc_10023120. The results are shaded to four levels. Dark shadows indicate very high conservative amino acid residues.

Additional file 7: Fig. S6. Expression pattern of genes involved in regulation of vasoconstriction in the ovary in the reproductive cycle. A) Heatmap was constructed by comparing three kinds of samples at different stage of the reproductive cycle. The x‐axis shows sampled tissues with the prefix C. for connective tissue rich in blood vessels covering the egg membrane and E. for embryos and O. for ovarian wall. Arabic numerals represent different stages. 1, pre-fertilization; 2, 1-cell; 3, 8-cells; 4, 16-cells; 5, gastrula stage; 6, 8-somites stage; 7, tailbud stage; 8, pre-hatching; 9, hatching.

Additional file 1: Fig. S1. Tissue expression pattern of genes involved in angiogenesis. Heatmap was constructed by comparing 20 tissues. The x‐axis shows sampled tissues, with the prefix F_ for female and M_ for male samples, and the y‐axis shows genes. The color scale shows standardized TPM values normalized by Z-score method.

This article is concerned with the secure particle filtering problem for a class of discrete-time nonlinear cyber-physical systems with binary sensors in the presence of non-Gaussian noises and multiple malicious attacks. The multiple attacks launched by the adversaries, which take place in a random manner, include the denial-of-service attacks, the deception attacks, and the flipping attacks. Three sequences of Bernoulli-distributed random variables with known probability distributions are employed to describe the characteristics of the random occurrence of the multiple attacks. The raw or corrupted measurements are transmitted to sensors, whose outputs are binary according to engineering practice. A modified likelihood function is constructed to compensate for the influence of the randomly occurring multiple attacks by introducing the random occurrence probability information into the design process. Subsequently, a secure particle filter is proposed based on the constructed likelihood function. Finally, a moving target tracking application is elaborated to verify the viability of the proposed secure particle filtering algorithm.

Additional file 6: Fig. S5. Expression pattern of genes involved in regulation of angiogenesis in the ovary in the reproductive cycle. A) Heatmap was constructed by comparing three kinds of samples at different stage of the reproductive cycle. The x‐axis shows sampled tissues with the prefix C. for connective tissue rich in blood vessels covering the egg membrane and E. for embryos and O. for ovarian wall. Arabic numerals represent different stages. 1, pre-fertilization; 2, 1-cell; 3, 8-cells; 4, 16-cells; 5, gastrula stage; 6, 8-somites stage; 7, tailbud stage; 8, pre-hatching; 9, hatching.

Additional file 4: Fig. S3. Similarity comparison of nucleotide sequences of the Bdkrb2 ORF in black rock fish. Ssc_13, Ssc_10023113; Ssc_14, Ssc_10023114; Ssc_15, Ssc_10023115; Ssc_16, Ssc_10023116; Ssc_17, Ssc_10023117; Ssc_18, Ssc_10023118; Ssc_19, Ssc_10023119; Ssc_20, Ssc_10023120. The results are shaded to four levels. Dark shadows indicate very high conservative amino acid residues.

Additional file 3: Table S1. Sequence similarity of Bdkrb2 genes in black rockfish.

Additional file 8: Table S2. Sample and data statistics of ovarian RNA-seq.

In this paper, the particle filtering problem is studied for a class of general nonlinear cyber-physical systems with non-Gaussian noises under Round-Robin protocol (RRP) subject to the randomly occurring deception attacks. In order to prevent the data from collisions and alleviate the communication overhead for the shared network with limited resources, the RRP is introduced in the sensor-to-filter channel to schedule the multiple sensors with a predefined transmission order. Under the RRP, only one sensor can be granted the access to the shared channel for measurement transmission at each time instant. A Bernoulli-distributed stochastic variable is utilized to describe the characteristic of random occurrence of deception attacks initiated by the adversaries. A RRP-based particle filtering algorithm is developed by establishing a modified likelihood function, where the statistical property of the randomly occurring deception attacks is exploited and the RRP-induced effect on the filter design is reflected. Finally, an illustrative example regarding the target tracking problem is provided to verify the feasibility and effectiveness of the developed particle filtering scheme.

Background: The quantitative real-time reverse transcription PCR (qRT-PCR) is a widely used technique that relies on the reference gene for gene expression normalization. Selecting a suitable reference gene is a crucial step to obtain an accurate result in qRT-PCR. However, most previous studies of fishes adopted reference genes that were commonly used in mammals without validation. Results: In this study, we utilized 89 transcriptome datasets covering early developmental stages and adult tissues, and carried out transcriptome-wide identification and validation of reference genes in Sebastes schlegelii. Finally, 121 candidate reference genes were identified based on four criteria. Eight candidates (METAP2, BTF3L4, EIF5A1, TCTP, UBC, PAIRB, RAB10, and DLD) and four commonly used reference genes (TUBA, ACTB, GAPDH, RPL17) in mammals were selected for validation via qRT- PCR and four statistical methods (delta-Ct, BestKeeper, geNorm, and NormFinder). The results revealed that the candidate reference genes we recommended are more stable than traditionally used ones. Conclusions: This is the first study to conduct transcriptome-wide identification and validation of reference genes for quantitative RT-PCR in the black rockfish, and lay an important foundation for gene expression analysis in teleost.

As a crucial member of the Forkhead Box family, class O (FoxO) plays an essential role in growth, cell differentiation, metabolism, immunization, and apoptosis. Meanwhile, FoxO3 is the primary regulator and effective inhibitor of primordial follicle activation. In this study, seven foxo genes were identified in black rockfish (Sebastes schlegelii), including two foxo1 genes (foxo1a, foxo1b), two foxo3 genes (foxo3, foxo3l), one foxo4 gene, and two foxo6 genes (foxo6a, foxo6b). foxo3l was derived from teleost-specific whole-genome duplication events. Evaluation of tissue expression pattern revealed that foxo3l displayed sexually dimorphic expression with a high level in the ovary and spatial expression only in the cytoplasm of follicle cells and oocytes. When the ovaries were stimulated by estrogen and gonadotropin, foxo3l expression was remarkably reduced, and the effect of androgen was completely different. We considered that foxo3l lost its ability to inhibit follicular precocity because of mass ovulation by hormone stimulation, resulting in its decreased expression. Such evidence indicated that foxo3l is an important regulator of reproduction-related functions in black rockfish. This study provides new insights into foxo3l genes for further functional research in teleost.

User representation learning is vital to capture diverse user preferences, while it is also challenging as user intents are latent and scattered among complex and different modalities of user-generated data, thus, not directly measurable. Inspired by the concept of user schema in social psychology, we take a new perspective to perform user representation learning by constructing a shared latent space to capture the dependency among different modalities of user-generated data. Both users and topics are embedded to the same space to encode users' social connections and text content, to facilitate joint modeling of different modalities, via a probabilistic generative framework. We evaluated the proposed solution on large collections of Yelp reviews and StackOverflow discussion posts, with their associated network structures. The proposed model outperformed several state-of-the-art topic modeling based user models with better predictive power in unseen documents, and state-of-the-art network embedding based user models with improved link prediction quality in unseen nodes. The learnt user representations are also proved to be useful in content recommendation, e.g., expert finding in StackOverflow.

Background: Black rockfish ( Sebastes schlegelii ) is a viviparous teleost . In the prior study, we reported a chromosome-level black rockfish genome assembly and proposed that the rockfish ovarian wall has a similar function to the uterus of mammals. In the present study, the well-developed vascular system was observed in the ovary wall and the exterior surface of the egg membrane. Adaptation of the ovary vasculature to the rising needs of the embryos occurs through both vasodilation and neovascularization. Bdkrb2 encodes a receptor for bradykinin. The two play a critical role in the control of vasodilatation by regulating NO production. Results: Eight Bdkrb2 genes were identified in the black rockfish genome. These genes are located on chromosome 14, which are arranged in a tandem array, forming a gene cluster spanning 50 kb. Protein structure prediction, phylogenetic analysis, and tissue expression pattern analysis was done to clarify the relationship of the Bdkrb2 genes and a preliminary exploration of function was conducted. The results show that the eight Bdkrb2 genes evolved two kinds of protein structure and three kinds of tissue expression pattern. Furthermore, some have a relatively high expression in ovarian wall, especially in stages of pre-fertilization and pre-hatching. Conclusions: Our study characterizes eight Bdkrb2 genes in the black rockfish, which have a regulatory role in the preparation for fertilization and hatching. This research provides a novel view of viviparity adaption and lays the groundwork for future research into vascular regulation of ovarian in the breeding cycle in black rockfish.

Pax3 and Pax7 are members of the Pax gene family which are essential for embryo and organ development. Both genes have been proved to be markers of muscle satellite cells and play key roles in the process of muscle growth and repair. Here, we identified two Pax3 genes (SsPax3a and SsPax3b) and two Pax7 genes (SsPax7a and SsPax7b) in a marine teleost, black rockfish (Sebastes schlegelii). Our results showed SsPax3 and SsPax7 marked distinct populations of muscle satellite cells, which originated from the multi-cell stage and somite stage, respectively. In addition, we constructed a muscle injury model to explore the function of these four genes during muscle repair. Hematoxylin–eosin (H–E) of injured muscle sections showed new-formed myofibers occurred at 16 days post-injury (dpi). ISH (in situ hybridization) analysis demonstrated that the expression level of SsPax3a and two SsPax7 genes increased gradually during 0–16 dpi and peaked at 16 dpi. Interestingly, SsPax3b showed no significant differences during the injury repair process, indicating that the satellite cells labeled by SsPax3b were not involved in muscle repair. These results imply that the muscle stem cell populations in teleosts are more complicated than in mammals. This lays the foundation for future studies on the molecular mechanism of indeterminant growth and muscle repair of large fish species.