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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.

The cyp11 includes cyp11a and cyp11b in most mammals and teleosts, encoded cholesterol side chain lyase and 11β-hydroxylase, respectively. It is essential in steroid hormone synthesis. However, studies on the regulation of cyp11 are limited, especially in teleosts. In this study, the molecular characterization and function of cyp11a and cyp11b of black rockfish was investigated. Both of them showed high homology with other teleost counterparts by phylogenetic analysis. The expression of cyp11a and cyp11b exhibited a clear sexually dimorphic pattern, with a higher expression level in testis than that of in ovaries. During the different developmental stages (40 dpf, 80 dpf, 190 dpf, 360 dpf, 720 dpf), the expression of cyp11a was earlier than cyp11b. In situ hybridization results showed that cyp11a and cyp11b were mainly expressed in oogonia and oocytes of the ovary. They were located in spermatogonia and interstitial compartment in the 1.5-year-old gonads, and spermatocytesgonia and the peritubular myoid cell of the testis in the 2.5-year-old gonads. To explore the distinct roles of cyp11a and cyp11b in gonads, oestrogen and androgens were used to stimulate the primary testicular and ovarian cells. The expressions of cyp11a and cyp11b were tested under different dose of 17α-methyltestosterone (17α-MT) and 17β-estradiol (E2). The results showed cyp11a was significantly increased at 10-6 mol ml-1 of 17α-MT and 10-8 mol ml-1 of E2 in ovary and 10-10 mol ml-1 of 17α-MT and E2 in testis, while cyp11b was significantly decreased after 17α-MT and E2 treatment. These results indicated that cyp11a and cyp11b were likely to have different functions, and also implied they might play an important roles in the differentiation of gonads and the synthesis of steroids in black rockfish.

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.

This paper investigates the remote state estimation issue for the jump Markov nonlinear systems (JMNLSs) with the stochastic event-triggered transmission strategy. For the purpose of saving the scarce network resources, the stochastic event-triggered communication is employed to cut down the number of measurement transmission. The interacting multiple model (IMM) scheme is incorporated due to its strength in alleviating computational burden encountered in the multiple model state estimation problem. In addition, the estimated measurement is utilized to update the mode probability in IMM-based filter when the current measurement is not available to the remote estimators. The proposed algorithm is applied in a two-dimensional maneuvering target tracking problem and the simulation results are presented, which validates the usefulness of the developed 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.

In this paper, the weighted average consensus-based unscented Kalman filtering combined with event-triggered communication mechanism is developed. Each sensor node chooses to transmit its latest measurement update to the corresponding remote estimator based on its own event-triggering condition. A sufficient condition is derived to guarantee that the estimation error is bounded in mean square. Finally, an illustrative example is presented to demonstrate the feasibility and effectiveness of the proposed algorithm.

In this paper, a distributed extended Kalman filtering algorithm is developed for a class of discrete-time nonlinear systems subject to stochastic disturbances and randomly occurring deception attacks. In order to utilize the limited communication and computation resources efficiently, the event-triggered communication scheme is introduced such that data transmission is executed only when the predefined condition is violated. Furthermore, a set of independent Bernoulli random variables with known statistical properties is defined to characterize the phenomenon of randomly occurring deception attacks. An upper bound for the estimation error covariance considering the event-triggered meachanism and linearization errors is derived via the variance-constrained approach. The filter gain for each node can be calculated recursively by solving two Raccati-like difference equations to minimize such an upper bound, which is suitable for online application. Finally, an illustrative example is presented to verify the feasibility and effectiveness of the proposed algorithm.