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"Jin, Xing"
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VaBTFER: An Effective Variant Binary Transformer for Facial Expression Recognition
Existing Transformer-based models have achieved impressive success in facial expression recognition (FER) by modeling the long-range relationships among facial muscle movements. However, the size of pure Transformer-based models tends to be in the million-parameter level, which poses a challenge for deploying these models. Moreover, the lack of inductive bias in Transformer usually leads to the difficulty of training from scratch on limited FER datasets. To address these problems, we propose an effective and lightweight variant Transformer for FER called VaTFER. In VaTFER, we firstly construct action unit (AU) tokens by utilizing action unit-based regions and their histogram of oriented gradient (HOG) features. Then, we present a novel spatial-channel feature relevance Transformer (SCFRT) module, which incorporates multilayer channel reduction self-attention (MLCRSA) and a dynamic learnable information extraction (DLIE) mechanism. MLCRSA is utilized to model long-range dependencies among all tokens and decrease the number of parameters. DLIE’s goal is to alleviate the lack of inductive bias and improve the learning ability of the model. Furthermore, we use an excitation module to replace the vanilla multilayer perception (MLP) for accurate prediction. To further reduce computing and memory resources, we introduce a binary quantization mechanism, formulating a novel lightweight Transformer model called variant binary Transformer for FER (VaBTFER). We conduct extensive experiments on several commonly used facial expression datasets, and the results attest to the effectiveness of our methods.
Journal Article
IPCARF: improving lncRNA-disease association prediction using incremental principal component analysis feature selection and a random forest classifier
Background
Identifying lncRNA-disease associations not only helps to better comprehend the underlying mechanisms of various human diseases at the lncRNA level but also speeds up the identification of potential biomarkers for disease diagnoses, treatments, prognoses, and drug response predictions. However, as the amount of archived biological data continues to grow, it has become increasingly difficult to detect potential human lncRNA-disease associations from these enormous biological datasets using traditional biological experimental methods. Consequently, developing new and effective computational methods to predict potential human lncRNA diseases is essential.
Results
Using a combination of incremental principal component analysis (IPCA) and random forest (RF) algorithms and by integrating multiple similarity matrices, we propose a new algorithm (IPCARF) based on integrated machine learning technology for predicting lncRNA-disease associations. First, we used two different models to compute a semantic similarity matrix of diseases from a directed acyclic graph of diseases. Second, a characteristic vector for each lncRNA-disease pair is obtained by integrating disease similarity, lncRNA similarity, and Gaussian nuclear similarity. Then, the best feature subspace is obtained by applying IPCA to decrease the dimension of the original feature set. Finally, we train an RF model to predict potential lncRNA-disease associations. The experimental results show that the IPCARF algorithm effectively improves the AUC metric when predicting potential lncRNA-disease associations. Before the parameter optimization procedure, the AUC value predicted by the IPCARF algorithm under 10-fold cross-validation reached 0.8529; after selecting the optimal parameters using the grid search algorithm, the predicted AUC of the IPCARF algorithm reached 0.8611.
Conclusions
We compared IPCARF with the existing LRLSLDA, LRLSLDA-LNCSIM, TPGLDA, NPCMF, and ncPred prediction methods, which have shown excellent performance in predicting lncRNA-disease associations. The compared results of 10-fold cross-validation procedures show that the predictions of the IPCARF method are better than those of the other compared methods.
Journal Article
Ameliorative Effects of Peptides Derived from Oyster (Crassostrea gigas) on Immunomodulatory Function and Gut Microbiota Structure in Cyclophosphamide-Treated Mice
The intestinal flora is recognized as a significant contributor to the immune system. In this research, the protective effects of oyster peptides on immune regulation and intestinal microbiota were investigated in mice treated with cyclophosphamide. The results showed that oyster peptides restored the indexes of thymus, spleen and liver, stimulated cytokines secretion and promoted the relative mRNA levels of Th1/Th2 cytokines (IL-2, IFN-γ, IL-4 and IL-10). The mRNA levels of Occludin, Claudin-1, ZO-1, and Mucin-2 were up-regulated, and the NF-κB signaling pathway was also activated after oyster peptides administration. Furthermore, oyster peptides treatment reduced the proportion of Firmicutes/Bacteroidetes, increased the relative abundance of Alistipes, Lactobacillus, Rikenell and the content of short-chain fatty acids, and reversed the composition of intestinal microflora similar to that of normal mice. In conclusion, oyster peptides effectively ameliorated cyclophosphamide-induced intestinal damage and modified gut microbiota structure in mice, and might be utilized as a beneficial ingredient in functional foods for immune regulation.
Journal Article
Binding of a C-type lectin’s coiled-coil domain to the Domeless receptor directly activates the JAK/STAT pathway in the shrimp immune response to bacterial infection
C-type lectins (CTLs) are characterized by the presence of a C-type carbohydrate recognition domain (CTLD) that by recognizing microbial glycans, is responsible for their roles as pattern recognition receptors in the immune response to bacterial infection. In addition to the CTLD, however, some CTLs display additional domains that can carry out effector functions, such as the collagenous domain of the mannose-binding lectin. While in vertebrates, the mechanisms involved in these effector functions have been characterized in considerable detail, in invertebrates they remain poorly understood. In this study, we identified in the kuruma shrimp (Marsupenaeus japonicus) a structurally novel CTL (MjCC-CL) that in addition to the canonical CTLD, contains a coiled-coil domain (CCD) responsible for the effector functions that are key to the shrimp's antibacterial response mediated by antimicrobial peptides (AMPs). By the use of in vitro and in vivo experimental approaches we elucidated the mechanism by which the recognition of bacterial glycans by the CTLD of MjCC-CL leads to activation of the JAK/STAT pathway via interaction of the CCD with the surface receptor Domeless, and upregulation of AMP expression. Thus, our study of the shrimp MjCC-CL revealed a striking functional difference with vertebrates, in which the JAK/STAT pathway is indirectly activated by cell death and stress signals through cytokines or growth factors. Instead, by cross-linking microbial pathogens with the cell surface receptor Domeless, a lectin directly activates the JAK/STAT pathway, which plays a central role in the shrimp antibacterial immune responses by upregulating expression of selected AMPs.
Journal Article
Corticostriatal control of defense behavior in mice induced by auditory looming cues
Animals exhibit innate defense behaviors in response to approaching threats cued by the dynamics of sensory inputs of various modalities. The underlying neural circuits have been mostly studied in the visual system, but remain unclear for other modalities. Here, by utilizing sounds with increasing (vs. decreasing) loudness to mimic looming (vs. receding) objects, we find that looming sounds elicit stereotypical sequential defensive reactions: freezing followed by flight. Both behaviors require the activity of auditory cortex, in particular the sustained type of responses, but are differentially mediated by corticostriatal projections primarily innervating D2 neurons in the tail of the striatum and corticocollicular projections to the superior colliculus, respectively. The behavioral transition from freezing to flight can be attributed to the differential temporal dynamics of the striatal and collicular neurons in their responses to looming sound stimuli. Our results reveal an essential role of the striatum in the innate defense control.
Innate defense behaviours in animals in response to approaching threats are mostly studied in response to visual stimuli. Here, the authors show that looming sounds elicit stereotypical sequential defensive reactions that require the auditory cortex, superior colliculus and the striatum.
Journal Article
Simulation of a ground-mounted prism in ABL flow using LES: on overview of error metrics and distribution
The accuracy of wind loading predictions using Large Eddy Simulation (LES) is usually influenced by numerous model parameters, which can influence the obtained results. The validation of numerical simulations with traditional Wind Tunnel Test (WTT) is still an important task, necessary to increase our
a priori
knowledge of possible inaccuracies and set up mitigation strategies. In this study, LES is used to simulate the wind fields around an isolated model high-rise building, under seven wind attack angles and validated with WTT results. The influence of various settings and parameters on the model performance is studied. For the angle of attack showing higher inaccuracy, different mesh refinement strategies and turbulence models are tested. Results indicate that LES can accurately predict the mean and local maxima of the pressure coefficients for both perpendicular and skew wind attack angles, as well as reproduce global forces and their envelopes with very good accuracy. Conversely, pronounced errors are found in the prediction of the pressure coefficient standard deviation and the local minima. The highest deviations between LES and WTT are found close to the leading edge in correspondence of flow separations which are observed in WTT and not in LES for skew flows. The addition of boundary layer cells and the use of different subgrid models have very limited effectiveness in modifying the obtained results for the analysed case.
Journal Article
FOXO regulates the expression of antimicrobial peptides and promotes phagocytosis of hemocytes in shrimp antibacterial immunity
Invertebrates rely on innate immunity, including humoral and cellular immunity, to resist pathogenic infection. Previous studies showed that forkhead box transcription factor O (FOXO) participates in mucosal immune responses of mammals and the gut humoral immune regulation of invertebrates. However, whether FOXO is involved in systemic and cellular immunity regulation in invertebrates remains unknown. In the present study, we identified a FOXO from shrimp (
Marsupenaeus japonicus)
and found that it was expressed at relatively basal levels in normal shrimp, but was upregulated significantly in shrimp challenged by
Vibrio anguillarum
. FOXO played a critical role in maintaining hemolymph and intestinal microbiota homeostasis by promoting the expression of
Relish
, the transcription factor of the immune deficiency (IMD) pathway for expression of antimicrobial peptides (AMPs) in shrimp. We also found that pathogen infection activated FOXO and induced its nuclear translocation by reducing serine/threonine kinase AKT activity. In the nucleus, activated FOXO directly regulated the expression of its target
Amp
and
Relish
genes against bacterial infection. Furthermore, FOXO was identified as being involved in cellular immunity by promoting the phagocytosis of hemocytes through upregulating the expression of the phagocytotic receptor scavenger receptor C (
Src
), and two small GTPases,
Rab5
and
Rab7
, which are related to phagosome trafficking to the lysosome in the cytoplasm. Taken together, our results indicated that FOXO exerts its effects on homeostasis of hemolymph and the enteric microbiota by activating the IMD pathway in normal shrimp, and directly or indirectly promoting AMP expression and enhancing phagocytosis of hemocytes against pathogens in bacteria-infected shrimp. This study revealed the different functions of FOXO in the mucosal (local) and systemic antibacterial immunity of invertebrates.
Journal Article
Plastomes of eight Ligusticum species: characterization, genome evolution, and phylogenetic relationships
Background
The genus
Ligusticum
consists of approximately 60 species distributed in the Northern Hemisphere. It is one of the most taxonomically difficult taxa within Apiaceae, largely due to the varied morphological characteristics. To investigate the plastome evolution and phylogenetic relationships of
Ligusticum
, we determined the complete plastome sequences of eight
Ligusticum
species using a de novo assembly approach.
Results
Through a comprehensive comparative analysis, we found that the eight plastomes were similar in terms of repeat sequence, SSR, codon usage, and RNA editing site. However, compared with the other seven species,
L. delavayi
exhibited striking differences in genome size, gene number, IR/SC borders, and sequence identity. Most of the genes remained under the purifying selection, whereas four genes showed relaxed selection, namely
ccsA
,
rpoA
,
ycf1
, and
ycf2
. Non-monophyly of
Ligusticum
species was inferred from the plastomes and internal transcribed spacer (ITS) sequences phylogenetic analyses.
Conclusion
The plastome tree and ITS tree produced incongruent tree topologies, which may be attributed to the hybridization and incomplete lineage sorting. Our study highlighted the advantage of plastome with mass informative sites in resolving phylogenetic relationships. Moreover, combined with the previous studies, we considered that the current taxonomy system of
Ligusticum
needs to be improved and revised. In summary, our study provides new insights into the plastome evolution, phylogeny, and taxonomy of
Ligusticum
species.
Journal Article
Mechanics of biofilms formed of bacteria with fimbriae appendages
Gram-negative bacteria, as well as some Gram-positive bacteria, possess hair-like appendages known as fimbriae, which play an important role in adhesion of the bacteria to surfaces or to other bacteria. Unlike the sex pili or flagellum, the fimbriae are quite numerous, with of order 1000 fimbriae appendages per bacterial cell. In this paper, a recently developed hybrid model for bacterial biofilms is used to examine the role of fimbriae tension force on the mechanics of bacterial biofilms. Each bacterial cell is represented in this model by a spherocylindrical particle, which interact with each other through collision, adhesion, lubrication force, and fimbrial force. The bacterial cells absorb water and nutrients and produce extracellular polymeric substance (EPS). The flow of water and EPS, and nutrient diffusion within these substances, is computed using a continuum model that accounts for important effects such as osmotic pressure gradient, drag force on the bacterial cells, and viscous shear. The fimbrial force is modeled using an outer spherocylinder capsule around each cell, which can transmit tensile forces to neighboring cells with which the fimbriae capsule collides. We find that the biofilm structure during the growth process is dominated by a balance between outward drag force on the cells due to the EPS flow away from the bacterial colony and the inward tensile fimbrial force acting on chains of cells connected by adhesive fimbriae appendages. The fimbrial force also introduces a large rotational motion of the cells and disrupts cell alignment caused by viscous torque imposed by the EPS flow. The current paper characterizes the competing effects of EPS drag and fimbrial force using a series of computations with different values of the ratio of EPS to bacterial cell production rate and different numbers of fimbriae per cell.
Journal Article