Noise Decomposition Principle in a Coherent Feed-Forward Transcriptional Regulatory Loop

Coherent feed-forward loops exist extensively in realistic biological regulatory systems, and are common signaling motifs. Here, we study the characteristics and the propagation mechanism of the output noise in a coherent feed-forward transcriptional regulatory loop that can be divided into a main road and branch. Using the linear noise approximation, we derive analytical formulae for the total noise of the full loop, the noise of the branch, and the noise of the main road, which are verified by the Gillespie algorithm. Importantly, we find that (i) compared with the branch motif or the main road motif, the full motif can effectively attenuate the output noise level; (ii) there is a transition point of system state such that the noise of the main road is dominated when the underlying system is below this point, whereas the noise of the branch is dominated when the system is beyond the point. The entire analysis reveals the mechanism of how the noise is generated and propagated in a simple yet representative signaling module

Penaeid shrimp genome provides insights into benthic adaptation and frequent molting

Crustacea, the subphylum of Arthropoda which dominates the aquatic environment, is of major importance in ecology and fisheries. Here we report the genome sequence of the Pacific white shrimp Litopenaeus vannamei, covering similar to 1.66 Gb (scaffold N50 605.56 Kb) with 25,596 protein-coding genes and a high proportion of simple sequence repeats (>23.93%). The expansion of genes related to vision and locomotion is probably central to its benthic adaptation. Frequent molting of the shrimp may be explained by an intensified ecdysone signal pathway through gene expansion and positive selection. As an important aquaculture organism, L. vannamei has been subjected to high selection pressure during the past 30 years of breeding, and this has had a considerable impact on its genome. Decoding the L. vannamei genome not only provides an insight into the genetic underpinnings of specific biological processes, but also provides valuable information for enhancing crustacean aquaculture

Condensed Representation Learning for Interactive Driving Styles Recognition

Automated vehicle (AV) validation faces the "billions of miles" challenge, requiring high-fidelity simulations to replicate diverse interactive driving behaviors for safety. Traditional methods oversimplify by using uniform behavioral models, ignoring the diversity of human driving styles, which are deeply influenced by individual psychological traits. This research introduces a condensed framework for representing interactive driving styles, by incorporating these psychological dimensions, balancing completeness and complexity. Key features include: i) individual style recognition via attention mechanisms and hierarchical contrastive learning, capturing subtle cognitive-based interaction patterns that reflect underlying differences in driver psychology (e.g., risk tolerance, decision-making heuristics); ii) scenario-independent style compression, filtering external factors to extract intrinsic driver intentions; iii) dimensionality-aware refinement, mapping complex behaviors to low-dimensional psychological axes for efficient computation. Tests on the NGSIM dataset reduced testing complexity by decoupling styles from scenarios. Compared to traditional methods, style distinctiveness improves by 28% (entropy-based), with 85% edge-case behavior coverage. This framework supports scalable AV testing by integrating diverse, psychologically-informed driving styles without combinatorial complexity

Genome-Wide Identification and Expression Profiles of Myosin Genes in the Pacific White Shrimp, Litopenaeus vannamei

As the main structural protein of muscle fiber, myosin is essential for multiple cellular processes or functions, especially for muscle composition and development. Although the shrimp possess a well-developed muscular system, the knowledge about the myosin family in shrimp is far from understood. In this study, we performed comprehensive analysis on the myosin genes in the genome of the Pacific white shrimp, Litopenaeus vannamei. A total of 29 myosin genes were identified, which were classified into 14 subfamilies. Among them, Myo2 subfamily was significantly expanded in the penaeid shrimp genome. Most of the Myo2 subfamily genes were primarily expressed in abdominal muscle, which suggested that Myo2 subfamily genes might be responsible for the well-developed muscular system of the penaeid shrimp. In situ hybridization detection showed that the slow-type muscle myosin gene was mainly localized in pleopod muscle and superficial ventral muscle of the shrimp. This study provides valuable insights into the evolutionary and functional characterization of myosin genes in shrimps, which provides clues for us to understand the well-developed muscular system of shrimp

Experimental and Field Investigations on the Impact-Resistance Mechanical Properties of Negative Poisson’s Ratio Bolt/Cable

AbstractDynamic impact tests of negative Poisson’s ratio (NPR) and rebar bolts under different impact wavelengths were carried out using a self-developed NPR bolt tensile impact test system. Additionally, a field anti-impact test using blasting was performed to simulate rockburst, and the field anti-impact characteristics of the NPR and conventional cable were compared and analysed. The experimental test results revealed that the peak impact force of the NPR and rebar bolts was inversely proportional to the wavelength. The NPR bolt underwent only constant resistance structural deformation, and the rod body did not break. The rebar bolt body fractured and necked. Under the same impact wavelength, the impact force and elongation of the two bolt types were proportional to the impact velocity. Compared with the greater peak impact force of the rebar bolt, the NPR bolt output structure deformation reduced the peak impact force. At the same impact velocity, as the wavelength increased, the impact force of the NPR bolt decreased rapidly, and the number of peaks also decreased. The impact force peak value of the rebar bolt was high, the impact force-time curve had multipeak characteristics, and no apparent rapid attenuation occurred. The field test results indicated that the NPR cable could produce slip deformation under the action of an explosion impact force to absorb the impact energy and that it had special mechanical properties to maintain a constant resistance. Under the same equivalent blasting impact energy, the conventional cable test section collapsed completely. The NPR cable test section was stable overall, verifying that the NPR cable had better impact-resistance mechanical properties than conventional cable. The research results provide a reliable basis for the effectiveness of NPR bolts/cables in preventing rockbursts

Roughage quality determines the production performance of post-weaned Hu sheep via altering ruminal fermentation, morphology, microbiota, and the global methylome landscape of the rumen wall

Roughage quality is a crucial factor influencing the growth performance and feeding cost of ruminants; however, a systematic investigation of the mechanisms underlying this is still lacking. In this study, we examined the growth performance, meat quality, ruminal fermentation parameters, rumen microbiome, and tissue methylomes of post-weaned Hu sheep fed low- or high-quality forage-based diets. Our results showed that sheep in the alfalfa hay (AG) and peanut vine (PG) groups exhibited better growth performance, slaughter performance, and meat quality than sheep in the wheat straw group (WG). The sheep in the AG possessed relatively higher contents of serum immunoglobins (IgA, IgG, and IgM) and lower contents of serum inflammation factors (TNF-α, IL-1β, IL-6, and IL-8) than those in the WG and the PG did. In addition, the levels of blood T lymphocytes (CD4+ and CD8+) and the CD4-to-CD8 ratio were significantly higher in the AG sheep than in the WG sheep and PG sheep. The concentration of ruminal NH3-N was highest in WG sheep, whereas the concentrations of individual and total short-chain fatty acids (SCFAs) were highest in the PG sheep. The length, width, and surface area of ruminal papillae were markedly different among the three groups, with the sheep in the PG being the most morphologically developed. The main ruminal microbes at the genus level include Prevotella 1, Rikenellaceae RC9 gut group, norank f F082, Ruminococcus 1, and Ruminococcus 2. The relative abundances of certain species are positively or negatively associated with fermentation parameters and growth index. For example, the fibrolytic bacteria Ruminococcaceae UGG-001 showed positive relationships with the concentration of SCFAs, except propionate. In addition, the relative abundances of fibrolytic bacteria (e.g., Ruminoccus 1) showed a negative relationship with starch-degrading bacteria (e.g., Prevotellaceae). The genome-wide DNA methylation analysis revealed that rumen tissues in the PG sheep and WG sheep occupied different global DNA methylomes. The genes with differentially methylated promoters were involved in known pathways (e.g., the FoxO signaling pathway) and the Gene Ontology (GO) terms (e.g., anatomical structure morphogenesis) pertaining to rumen development. Two candidate genes (ACADL and ENSOARG00020014533) with hyper- and hypo-methylated promoters were screened as potential regulators of rumen development. In conclusion, roughage quality determines sheep growth performance via directly influencing rumen fermentation and microbiome composition, and indirectly affecting rumen development at the epigenetic level

Wnt Signaling Pathway Linked to Intestinal Regeneration via Evolutionary Patterns and Gene Expression in the Sea Cucumber Apostichopus japonicus

Many echinoderms are regenerative species that exhibit exceptional regenerative capacity, and sea cucumber is a representative organism that could regenerate the whole intestine after evisceration. There are many signaling pathways participate in the regeneration process, but it is not clear which is essential for the intestinal regeneration. In this study, we performed genome-wide comprehensive analyses on these regeneration-related signaling pathways, and found the Wnt signaling pathway was one of the most conservative pathways among regenerative species. Additionally, among these signaling pathways, we found that the Wnt signaling pathway was the only one under positive selection in regenerative echinoderms, and the only one enriched by differentially expressed genes during the intestinal regeneration. Thus, it suggests both coding sequence and gene expression of the Wnt signaling pathway have been shaped by natural selection to provide the genetic architecture for intestinal regeneration. Wnt7, Fz7, and Dvl are the three positively selected genes and also happen to be three upstream genes in the Wnt signaling pathway. They are all significantly upregulated at the early stages of regeneration, which may contribute significantly to the early activation of Wnt signaling and the initiation of intestinal regeneration. Expression knockdown of Wnt7 and Dvl by RNA interference significantly inhibit intestinal extension, implying that they are essential for intestinal regeneration. As an important regeneration-related gene, the downstream gene c-Myc is also conserved and highly expressed during the whole regeneration stages, which may make the Wnt/c-Myc signaling to be an important way to promote intestinal regeneration. Therefore, it is reasonable to conclude that the Wnt signaling pathway is the chosen one to play an important role in intestinal regeneration of sea cucumbers, or even in the regeneration of other echinoderms