The transcriptomic landscape of canonical activation of NLRP3 inflammasome from bone marrow-derived macrophages.

The NLRP3 inflammasome has gained significant attention due to its participation in diverse cellular processes. Nevertheless, the detailed framework of the canonical NLRP3 inflammasome assembly still remains unrevealed. This study aims to elucidate the transcriptomic landscape of the various stages involved in the canonical activation of the NLRP3 inflammasome in BMDMs by integrating RNA-seq, bioinformatics, and molecular dynamics analyses. The model for the canonical activation of the NLRP3 inflammasome was confirmed through morphological observations, functional assessments (ELISA and LDH), and protein detection (western blot). Subsequently, cells were subjected to RNA sequencing following three groups: control, priming (LPS 500 ng/ml, 4 h), and activation (LPS 500 ng/ml, 4 h; ATP 5 mM, 1 h). A total of 9116 differentially expressed genes (DEGs) were identified, which exerted regulatory effects on various pathways, including cell metabolism, ion fluxes, post-translational modifications, and organelles. Subsequently, six hub genes (Sirt3, Stat3, Syk, Trpm2, Tspo, and Txnip) were identified via integrating literature review and database screening. Finally, the three-dimensional structures of these six hub proteins were obtained using the MD-optimized RoseTTAFold and Gromacs simulations (at least 200 ns). In summary, our research offers novel insights into the transcriptomic-level understanding of the assembly of the canonical NLRP3 inflammasome.

ZFP57 dictates allelic expression switch of target imprinted genes.

ZFP57 is a master regulator of genomic imprinting. It has both maternal and zygotic functions that are partially redundant in maintaining DNA methylation at some imprinting control regions (ICRs). In this study, we found that DNA methylation was lost at most known ICRs in Zfp57 mutant embryos. Furthermore, loss of ZFP57 caused loss of parent-of-origin-dependent monoallelic expression of the target imprinted genes. The allelic expression switch occurred in the ZFP57 target imprinted genes upon loss of differential DNA methylation at the ICRs in Zfp57 mutant embryos. Specifically, upon loss of ZFP57, the alleles of the imprinted genes located on the same chromosome with the originally methylated ICR switched their expression to mimic their counterparts on the other chromosome with unmethylated ICR. Consistent with our previous study, ZFP57 could regulate the NOTCH signaling pathway in mouse embryos by impacting allelic expression of a few regulators in the NOTCH pathway. In addition, the imprinted Dlk1 gene that has been implicated in the NOTCH pathway was significantly down-regulated in Zfp57 mutant embryos. Our allelic expression switch models apply to the examined target imprinted genes controlled by either maternally or paternally methylated ICRs. Our results support the view that ZFP57 controls imprinted expression of its target imprinted genes primarily through maintaining differential DNA methylation at the ICRs.

Pedestrian Pose Recognition Based on Frequency-Modulated Continuous-Wave Radar with Meta-Learning.

With the continuous advancement of autonomous driving and monitoring technologies, there is increasing attention on non-intrusive target monitoring and recognition. This paper proposes an ArcFace SE-attention model-agnostic meta-learning approach (AS-MAML) by integrating attention mechanisms into residual networks for pedestrian gait recognition using frequency-modulated continuous-wave (FMCW) millimeter-wave radar through meta-learning. We enhance the feature extraction capability of the base network using channel attention mechanisms and integrate the additive angular margin loss function (ArcFace loss) into the inner loop of MAML to constrain inner loop optimization and improve radar discrimination. Then, this network is used to classify small-sample micro-Doppler images obtained from millimeter-wave radar as the data source for pose recognition. Experimental tests were conducted on pose estimation and image classification tasks. The results demonstrate significant detection and recognition performance, with an accuracy of 94.5%, accompanied by a 95% confidence interval. Additionally, on the open-source dataset DIAT-µRadHAR, which is specially processed to increase classification difficulty, the network achieves a classification accuracy of 85.9%.

Choroidal blood perfusion could predict the sensitivity of myopia formation in Guinea pigs.

In this study, we explored the predictive role of choroidal blood perfusion (ChBP) and choroidal thickness (ChT) on the development of myopia in guinea pigs. Optical Coherence Tomography Angiography (OCTA) was used to assess the baseline choroidal blood perfusion (ChBP) and choroidal thickness (ChT) in 4-week-old guinea pigs. Refraction and axial length (AL) were measured at baseline. Myopia was induced for one week using form-deprivation (FD) or negative lenses followed by measurements of refraction, axial length and choroidal parameters (ChT and ChBP). The correlations were evaluated between the baseline choroidal values and the magnitude of myopia induced, along with the magnitude of changes in ChT and ChBP after myopia induction. There was a significant correlation between the baseline choroidal parameters and ocular refraction. Myopia induction led to choroidal thinning and less ChBP as well as longer eyes. On the other hand, following exposure to the same non-obstructed visual induction period, the myopic shift was less, and it was associated with thicker choroids and more ChBP at baseline. One week of myopia induction also resulted in thinner choroids and less ChBP, and these declines also correlated with their baseline values. In conclusion, the present study shows that the changes in the baseline choroidal ChT and ChBP parameters are proportional to the magnitude of myopia development and axial elongation in guinea pigs. These significant correlations between baseline ChBP and ChT and myopia development suggest that they may be a viable predictor of this process in guinea pigs.

Paenibacillus sedimenti sp. nov., isolated from freshwater wetland sediment.

A Gram-stain-positive, motile, rod-shaped, facultatively anaerobic bacterium, designated strain WST5T, isolated from sediment was characterized using a polyphasic approach. Phylogenetic analysis based on 16S rRNA gene sequences indicated that strain WST5T was most closely related to Paenibacillus aestuarii CJ25T (96.8 % similarity). The genome size of the WST5T was 6.5 Mb, contained 4500 predicted protein-coding genes, and had a DNA G+C content of 46.6%. The values of whole-genome average nucleotide identity analysis and digital DNA-DNA hybridization between strain WST5T and its closely related type strains were less than 76 and 25.6 %, respectively. The predominant cellular fatty acids (>10 %) were anteiso-C15 : 0 and C16 : 1 ω5c and the main menaquinone was MK-7. The major polar lipids were identified as diphospholidylglycerol, phosphatidylethanolamine, phosphatidylglycerol and two unknown aminophospholipids. Based on the results of phenotypic, genotypic, chemotaxonomic and phylogenetic analyses, strain WST5T is considered to represent a novel species of the genus Paenibacillus, for which the name Paenibacillus sedimentum sp. nov. is proposed. The type strain is WST5T (=NBRC 115194 T=CGMCC 1.18706T).

A Novel Optimized iBeacon Localization Algorithm Modeling.

The conventional methods for indoor localization rely on technologies such as RADAR, ultrasonic, laser range localization, beacon technology, and others. Developers in the industry have started utilizing these localization techniques in iBeacon systems that use Bluetooth sensors to measure the object's location. The iBeacon-based system is appealing due to its low cost, ease of setup, signaling, and maintenance; however, with current technology, it is challenging to achieve high accuracy in indoor object localization or tracking. Furthermore, iBeacons' accuracy is unsatisfactory, and they are vulnerable to other radio signal interference and environmental noise. In order to address those challenges, our study focuses on the development of error modeling algorithms for signal calibration, uncertainty reduction, and interfered noise elimination. The new error modeling is developed on the Curve Fitted Kalman Filter (CFKF) algorithms. The reliability, accuracy, and feasibility of the CFKF algorithms are tested in the experiments. The results significantly show the improvement of the accuracy and precision with this novel approach for iBeacon localization.

Comparative genome analysis of 12 Shigella sonnei strains: virulence, resistance, and their interactions.

Shigellosis is a highly infectious disease that is mainly transmitted via fecal-oral contact of the bacteria Shigella. Four species have been identified in Shigella genus, among which Shigella flexneri is used to be the most prevalent species globally and commonly isolated from developing countries. However, it is being replaced by Shigella sonnei that is currently the main causative agent for dysentery pandemic in many emerging industrialized countries such as Asia and the Middle East. For a better understanding of S. sonnei virulence and antibiotic resistance, we sequenced 12 clinical S. sonnei strains with varied antibiotic-resistance profiles collected from four cities in Jiangsu Province, China. Phylogenomic analysis clustered antibiotic-sensitive and resistant S. sonnei into two distinct groups while pan-genome analysis reveals the presence and absence of unique genes in each group. Screening of 31 classes of virulence factors found out that type 2 secretion system is doubled in resistant strains. Further principle component analysis based on the interactions between virulence and resistance indicated that abundant virulence factors are associated with higher levels of antibiotic resistance. The result present here is based on statistical analysis of a small sample size and serves basically as a guidance for further experimental and theoretical studies.

Pseudomonas pratensis sp. nov., Isolated from Grassland Soil from Inner Mongolia, China.

A novel bacterial strain, designated MHJ-10JT, was isolated from a soil sample obtained from a grassland in Inner Mongolia, China. MHJ-10JT strain could grow at 4-37 °C (optimum: 30 °C) and pH 4-9 (optimum: pH 6), as well as in the presence of 0-6% NaCl (optimum: 1%). Cells of strain MHJ-10JT are Gram-negative, rod-shaped, and motile. Phylogenetic analysis based on 16S rRNA gene sequences indicated that strain MHJ-10JT was most closely related to Pseudomonas lutea OK2T (98.5% 16S rRNA gene sequence similarity). The values of the average nucleotide identities (ANI) and digital DNA-DNA hybridization (dDDH) between strain MHJ-10JT and its related species were all below 80.5% and 24.4%, respectively, which are significantly lower than the thresholds of 95% for ANI and 70% for DDH for species delineation. The genomic G + C content of the MHJ-10JT strain is 64.8 mol%. Based on the phenotypic, genotypic, chemotaxonomic, and phylogenetic analyses, strain MHJ-10JT can be assigned to the genus Pseudomonas. In this study, we propose that strain MHJ-10JT be classified as a novel species belonging to the genus Pseudomonas with the species name Pseudomonas pratensis sp. nov. The type strain of the proposed novel species is MHJ-10JT (= KCTC 82206T = CGMCC 17322T).

The Effects of Random Porosities in Resonant Frequencies of Graphene Based on the Monte Carlo Stochastic Finite Element Model.

With the distinguished properties in electronics, thermal conductivity, optical transparence and mechanics, graphene has a powerful potential in nanosensors, nano-resonators, supercapacitors, batteries, etc. The resonant frequency of graphene is an important factor in its application and working environment. However, the random dispersed porosities in graphene evidently change the lattice structure and destroy the integrity and geometrical periodicity. This paper focuses on the effects of random porosities in resonant frequencies of graphene. Monte Carlo simulation is applied to propagate the porosities in the finite element model of pristine graphene. The statistical results and probability density distribution of porous graphene with atomic vacancy defects are computed based on the Monte Carlo finite element model. The results of porous graphene with atomic vacancy defects are compared and discussed with the results of graphene with bond vacancy defects. The enhancement effects of atomic vacancy defects are confirmed in porous graphene. The influences of atomic vacancy defects on displacement and rotation vector sums of porous graphene are more concentrated in local places.

A Kriging Surrogate Model for Uncertainty Analysis of Graphene Based on a Finite Element Method.

Due to the inevitable presence of random defects, unpredictable grain boundaries in macroscopic samples, stress concentration at clamping points, and unknown load distribution in the investigation of graphene sheets, uncertainties are crucial and challenging issues that require more exploration. The application of the Kriging surrogate model in vibration analysis of graphene sheets is proposed in this study. The Latin hypercube sampling method effectively propagates the uncertainties in geometrical and material properties of the finite element model. The accuracy and convergence of the Kriging surrogate model are confirmed by a comparison with the reported references. The uncertainty analysis for both Zigzag and Armchair graphene sheets are compared and discussed.

Tagging Functional Polymorphism in 3' Untranslated Region of Methylene Tetrahydrofolate Reductase and Risk of Ischemic Stroke.

BACKGROUND/AIMS: The association between genetic polymorphisms in the exon or untranslated region of the methylenetetrahydrofolate reductase gene (MTHFR) and the risk of human ischemic stroke (IS) has been well-documented. In this study, we focused on a polymorphism previously screened by high-throughput analysis and on its potential function in patients with IS Methods: This hospital-based case-control study was conducted in 400 patients and 400 healthy volunteers. Genotyping was conducted using TaqMan probes. Potential interactions were predicted by multiple bioinformatics analysis. Relative expression levels of MTHFR were detected confirmed by dual-luciferase assay. RESULTS: The MTHFR polymorphism rs142884651 was significantly associated with a decreased risk of IS compared with the wild-type GA genotype (P = 0.02) and AA genotype (P = 0.001). According to bioinformatics analysis and luciferase assay, this polymorphism could attenuate the binding of let-7f and miR-196a (P = 0.021 and 0.019, respectively) leading to the accumulation of MTHFR and degradation of serum homocysteine, and resulting in a better IS outcome. CONCLUSION: This study demonstrated that the MTHFR rs142884651 polymorphism is associated with a decreased risk of IS and may act as a biomarker of short-term outcome in patients with IS.

IDH1 Associated with Neuronal Apoptosis in Adult Rats Brain Following Intracerebral Hemorrhage.

Isocitrate dehydrogenase 1 (IDH1), one member of the IDH family can convert isocitrate to α-ketoglutarate (α-KG) via oxidative decarboxylation. IDH1 and IDH2 mutations have been identified in multiple tumor types and the mutations confer neomorphic activity in the mutant protein, resulting in the conversion of α-KG to the oncometabolite, D-2-hydroxyglutarate (2-HG). The subsequent accumulation of 2-HG results in epigenetic dysregulation via inhibition of α-KG-dependent histone and DNA demethylase. And the glutamate levels are reduced in IDH mutant cells compared to wild-type. We have known that diffuse gliomas contain a high frequency of mutations in the IDH1 gene. However, the expression of IDH1 and its roles in Intracranial hemorrhage (ICH) remain largely unknown. We observed increased expression of IDH1 in neurons after intracerebral hemorrhage. Up-regulation of IDH1 was found to be accompanied by the increased expression of active caspase-3 and pro-apoptotic Bcl-2-associated X protein and decreased expression of anti-apoptotic protein B cell lymphoma-2 in vivo and vitro studies. So we hypothesized that IDH1 was involved in the regulation of neuronal apoptosis. The present research for the first time detected the expression and variation of IDH1 surrounding the hematoma, and all data proved the involvement of IDH1 in neuronal apoptosis following ICH.

Radially Aligned Electrospun Fibers with Continuous Gradient of SDF1α for the Guidance of Neural Stem Cells.

Repair of spinal cord injury will require enhanced recruitment of endogenous neural stem cells (NSCs) from the central canal region to the lesion site to reestablish neural connectivity. The strategy toward this goal is to provide directional cues, e.g., alignment topography and biological gradients from the rostral and caudal ends toward the center. This study demonstrates a facile method for fabrication of continuous gradients of stromal-cell-derived factor-1α (SDF1α) embedded in the radially aligned electrospun collagen/poly (ε-caprolactone) mats. Gradients can be readily produced in a controllable and reproducible fashion by adjusting the collection time and collector size during electrospinning. To get a long-term gradient, the SDF1α is fused with a unique peptide of collagen-binding domain (CBD), which can bind to collagen specifically. Aligned CBD-SDF1α gradients show stable, sustained, and gradual release during 7 d. Further, the effect of aligned CBD-SDF1α gradients on the guidance of NSCs is investigated. It is found that the CBD-SDF1α gradient scaffolds direct and enhance NSC migration from the periphery to the center along the aligned electrospun fibers. Taken together, the tubular conduits based on radially aligned electrospun fibers with continuous SDF1α gradient show great potential for guiding nerve regeneration.

Automated choroid segmentation based on gradual intensity distance in HD-OCT images.

The choroid is an important structure of the eye and plays a vital role in the pathology of retinal diseases. This paper presents an automated choroid segmentation method for high-definition optical coherence tomography (HD-OCT) images, including Bruch's membrane (BM) segmentation and choroidal-scleral interface (CSI) segmentation. An improved retinal nerve fiber layer (RNFL) complex removal algorithm is presented to segment BM by considering the structure characteristics of retinal layers. By analyzing the characteristics of CSI boundaries, we present a novel algorithm to generate a gradual intensity distance image. Then an improved 2-D graph search method with curve smooth constraints is used to obtain the CSI segmentation. Experimental results with 212 HD-OCT images from 110 eyes in 66 patients demonstrate that the proposed method can achieve high segmentation accuracy. The mean choroid thickness difference and overlap ratio between our proposed method and outlines drawn by experts was 6.72µm and 85.04%, respectively.

A false color fusion strategy for drusen and geographic atrophy visualization in optical coherence tomography images.

PURPOSE: To display drusen and geographic atrophy (GA) in a single projection image from three-dimensional spectral domain optical coherence tomography images based on a novel false color fusion strategy. METHODS: We present a false color fusion strategy to combine drusen and GA projection images. The drusen projection image is generated with a restricted summed-voxel projection (axial sum of the reflectivity values in a spectral domain optical coherence tomography cube, limited to the region where drusen is present). The GA projection image is generated by incorporating two GA characteristics: bright choroid and thin retina pigment epithelium. The false color fusion method was evaluated in 82 three-dimensional optical coherence tomography data sets obtained from 7 patients, for which 2 readers independently identified drusen and GA as the gold standard. The mean drusen and GA overlap ratio was used as the metric to determine accuracy of visualization of the proposed method when compared with the conventional summed-voxel projection, (axial sum of the reflectivity values in the complete spectral domain optical coherence tomography cube) technique and color fundus photographs. RESULTS: Comparative results demonstrate that the false color image is more effective in displaying drusen and GA than summed-voxel projection and CFP. The mean drusen/GA overlap ratios based on the conventional summed-voxel projection method, color fundus photographs, and the false color fusion method were 6.4%/100%, 64.1%/66.7%, and 85.6%/100%, respectively. CONCLUSION: The false color fusion method was more effective for simultaneous visualization of drusen and GA than the conventional summed-voxel projection method and color fundus photographs, and it seems promising as an alternative method for visualizing drusen and GA in the retinal fundus, which commonly occur together and can be confusing to differentiate without methods such as this proposed one.

Epigenetic regulation in adult neural stem cells.

Neural stem cells (NSCs) exhibit self-renewing and multipotential properties. Adult NSCs are located in two neurogenic regions of adult brain: the ventricular-subventricular zone (V-SVZ) of the lateral ventricle and the subgranular zone of the dentate gyrus in the hippocampus. Maintenance and differentiation of adult NSCs are regulated by both intrinsic and extrinsic signals that may be integrated through expression of some key factors in the adult NSCs. A number of transcription factors have been shown to play essential roles in transcriptional regulation of NSC cell fate transitions in the adult brain. Epigenetic regulators have also emerged as key players in regulation of NSCs, neural progenitor cells and their differentiated progeny via epigenetic modifications including DNA methylation, histone modifications, chromatin remodeling and RNA-mediated transcriptional regulation. This minireview is primarily focused on epigenetic regulations of adult NSCs during adult neurogenesis, in conjunction with transcriptional regulation in these processes.

DNA methylation plays important roles in lifestyle transition of Arthrobotrys oligospora.

Trap formation is the key indicator of carnivorous lifestyle transition of nematode-trapping fungi (NTF). Here, the DNA methylation profile was explored during trap induction of Arthrobotrys oligospora, a typical NTF that captures nematodes by developing adhesive networks. Whole-genome bisulfite sequencing identified 871 methylation sites and 1979 differentially methylated regions (DMRs). This first-of-its-kind investigation unveiled the widespread presence of methylation systems in NTF, and suggested potential regulation of ribosomal RNAs through DNA methylation. Functional analysis indicated DNA methylation's involvement in complex gene regulations during trap induction, impacting multiple biological processes like response to stimulus, transporter activity, cell reproduction and molecular function regulator. These findings provide a glimpse into the important roles of DNA methylation in trap induction and offer new insights for understanding the molecular mechanisms driving carnivorous lifestyle transition of NTF.

Advancements in acne detection: application of the CenterNet network in smart dermatology.

Introduction: Acne detection is critical in dermatology, focusing on quality control of acne imagery, precise segmentation, and grading. Traditional research has been limited, typically concentrating on singular aspects of acne detection. Methods: We propose a multi-task acne detection method, employing a CenterNet-based training paradigm to develop an advanced detection system. This system collects acne images via smartphones and features multi-task capabilities for detecting image quality and identifying various acne types. It differentiates between noninflammatory acne, papules, pustules, nodules, and provides detailed delineation for cysts and post-acne scars. Results: The implementation of this multi-task learning-based framework in clinical diagnostics demonstrated an 83% accuracy in lesion categorization, surpassing ResNet18 models by 12%. Furthermore, it achieved a 76% precision in lesion stratification, outperforming dermatologists by 16%. Discussion: Our framework represents a advancement in acne detection, offering a comprehensive tool for classification, localization, counting, and precise segmentation. It not only enhances the accuracy of remote acne lesion identification by doctors but also clarifies grading logic and criteria, facilitating easier grading judgments.

Fabrication of soy protein nanoparticles based on metal-phenolic networks for stabilization of nano-emulsions delivery system.

The use of soy protein isolate (SPI) nanoparticles as a stabilizer in nano-emulsion systems has garnered significant interest. While metal-phenolic networks (MPNs) have been explored for their multifunctional surface modification capabilities, their integration with food protein-based delivery systems remains less explored. In this study, we attempt to develop a novel strategy to encapsulate cinnamaldehyde using MPNs (EGCG-Fe3+) with self-assembling soy protein nanoparticles (SE-Fe NPs) as a stabilizer for nano-emulsions. UV, Raman, and X-ray photoelectron spectroscopy analyses demonstrated that SE-Fe NPs were generated through metal-phenolic coordination and covalent interactions. SE-Fe NPs had a narrower particle size distribution and enhanced radical scavenging (up to 3.35-fold), as well as thermal stability. Furthermore, the smaller droplet size, higher modulus, higher cinnamaldehyde encapsulation efficiency (from 63.5% to 84.2%), and improved bio-accessibility of SE-Fe NPs stabilized nano-emulsions delivery system demonstrated in this study shows promising future applications in the food industry.

Modulatory role of neuropeptide FF system in macrophages.

Neuropeptide FF (NPFF) is an octapeptide that regulates various cellular processes, especially pain perception. Recently, there has been a growing interest in understanding the modulation of NPFF in neuroendocrine inflammation. This review aims to provide a thorough overview of the regulation of NPFF in macrophage-mediated biological processes. We delve into the impact of NPFF on macrophage polarization, self-renewal modulation, and the promotion of mitophagy, facilitating the transition from thermogenic fat to fat-storing adipose tissue. Additionally, we explore the NPFF-dependent regulation of the inflammatory response mediated by macrophages, its impact on the differentiation of macrophages, and its capacity to induce alterations in the transcriptome of macrophages. We also address the potential of NPFF as a therapeutic molecule in the field of neuroendocrine inflammation. Overall, our work offers an understanding of the influence of NPFF on macrophage, facilitating the exploration of its pharmacological significance in future studies.