Miracle-dz/UniFAR-FTUs huggingface dataset:
Diffusion is All You Need for Learning on Surfaces

We introduce a new approach to deep learning on 3D surfaces such as meshes or point clouds. Our key insight is that a simple learned diffusion layer can spatially share data in a principled manner, replacing operations like convolution and pooling which are complicated and expensive on surfaces. The only other ingredients in our network are a spatial gradient operation, which uses dot-products of derivatives to encode tangent-invariant filters, and a multi-layer perceptron applied independently at each point. The resulting architecture, which we call DiffusionNet, is remarkably simple, efficient, and scalable. Continuously optimizing for spatial support avoids the need to pick neighborhood sizes or filter widths a priori, or worry about their impact on network size/training time. Furthermore, the principled, geometric nature of these networks makes them agnostic to the underlying representation and insensitive to discretization. In practice, this means significant robustness to mesh sampling, and even the ability to train on a mesh and evaluate on a point cloud. Our experiments demonstrate that these networks achieve state-of-the-art results for a variety of tasks on both meshes and point clouds, including surface classification, segmentation, and non-rigid correspondence.
Millimeter Wave Communications on Overhead Messenger Wire: Deep Reinforcement Learning-Based Predictive Beam Tracking

This paper discusses the feasibility of beam tracking against dynamics in millimeter wave (mmWave) nodes placed on overhead messenger wires. As specific disturbances in on-wire deployments, we consider wind-forced perturbations and disturbances caused by impulsive forces to wires. Our contribution is to answer whether the historical positions/velocities of a mmWave node are useful to track directional beams, given the complicated on-wire dynamics. To this end, we implement deep reinforcement learning (DRL) to learn the relationships between the historical positions/velocities and appropriate beam-steering angles. Our numerical evaluations yielded the following key insights: First, against wind perturbations, an appropriate beam-tracking policy can be learned from the historical positions/velocities of a node. Second, against impulsive forces to the wire, the use of the position/velocity of the node is not necessarily sufficient, owing to the rapid node displacement. To resolve this, we propose taking advantage of the positional interaction on the wire. This is done by leveraging the positions/velocities of several points on the wire as state information in DRL. The results confirmed the avoidance of beam misalignment due to impulsive forces, which was not possible using only the position/velocity of the node.
Effect of Bacillus megaterium-Coated Diets on the Growth, Digestive Enzyme Activity, and Intestinal Microbial Diversity of Songpu Mirror Carp Cyprinus specularis Songpu

The present study was conducted to evaluate the effect of a Bacillus megaterium-coated diet on growth performance, digestive enzymes, and intestinal microbial diversity in Songpu mirror carp (Cyprinus specularis Songpu). The fish were manually fed two diets (a control diet and a B. megaterium-coated diet) three times daily until apparent satiation for 56 days. Compared with the control group, supplementation with the B. megaterium-coated diet enhanced the fish growth and significantly reduced the feed conversion ratio (P < 0.05). The activities of foregut amylase and lipase in the treatment group were significantly higher than those in the control group (P < 0.05). The activities of foregut, midgut, and hindgut proteases in the treatment group were all higher than those in the control group (P > 0.05). The results of sequencing the 16S rDNA genes of the microbiota through high-throughput sequencing showed that the diversity and abundance of the intestinal microflora increased along with Songpu mirror carp growth. The Songpu mirror carp fed a diet coated with B. megaterium displayed increased proportions of intestinal Bacillus and Lactococcus at the genus level, and both were significantly higher than those of the control group (P < 0.05). These results therefore suggest that dietary B. megaterium application can improve the growth and digestive enzyme activity of Songpu mirror carp and enrich the beneficial genus composition of its main intestinal microflora.
Collective Housing of Mice of Different Age Groups before Maturity Affects Mouse Behavior

Background Although population housing is recommended by many animal management and ethical guidelines, the effect of collective housing of mice of different age groups on mouse behavior has not been clarified. Since the development of the central nervous system continues to occur before sexual maturation, the stress of social ranking formation among male individuals in mixed housing conditions can affect postmaturation behavior. To assess these effects, sexually immature mice of different ages were housed in the same cage and a series of behavioral tests were performed after maturation. Results The findings for three groups of mice—junior mice housed with older mice, senior mice housed with younger mice, and mice housed with other mice of the same age—were compared. Junior mice showed higher body weight and activity as well as lower grip strength and anxiety-like behaviors than other mice. In contrast, senior mice showed lower body temperature and increased aggression, antinociceptive effect, and home-cage activity in the dark period in comparison with other mice. Conclusions Thus, combined housing of immature mice of different age groups affects mouse behavior after maturation. Appropriate prematuration housing conditions are crucial to eliminate the uncontrollable bias caused by age-related social stratification.
Radix Scutellariae Ameliorates Stress-Induced Depressive-Like Behaviors via Protecting Neurons through the TGFβ3-Smad2/3-Nedd9 Signaling Pathway

Chronic stress can impair hippocampal neurogenesis, increase neuronal apoptosis, and cause depressive-like behaviors. Our previous studies found that Radix Scutellariae (RS) can rescue the stress-induced neuronal injury, but the mechanism is not clear. Here, we continued to investigate the underlying antidepressant mechanisms of the RS extract. A 7-week chronic unpredictable mild stress (CUMS) procedure was used to establish a murine depression model. 0.75 g/kg or 1.5 g/kg RS was administered daily to the mice during the last 4 weeks. Depressive-like behaviors were evaluated by the sucrose preference test (SPT), forced swimming test (FST), open field test (OFT), and tail suspension test (TST). The neuroprotective effect of RS was evaluated with the expression of hippocampal neuron-related markers and apoptosis-associated proteins by Nissl staining, immunohistochemistry, and western blot. Transforming growth factor-β3 (TGFβ3) pathway-related proteins were detected by western blot. Results showed that RS could ameliorate depressive-like behaviors, increase the expression of the antiapoptotic protein B-cell lymphoma 2 (BCL-2), reduce the expression of the proapoptotic protein BCL-2-associated X (BAX), and increase the number of doublecortin- (DCX-), microtubule-associated protein 2- (MAP2-), and neuronal nucleus- (NeuN-) positive cells in the hippocampus. Moreover, RS could reverse the CUMS-induced decrease of TGFβ3 protein, promote the phosphorylation of SMAD2/3, and increase the expression of downstream NEDD9 protein. These results suggest that RS could exert antidepressant effects via protecting neurons. And the molecular mechanism might be related to the regulation of the TGFβ3-SMAD2/3-NEDD9 pathway.
Network Pharmacology-Based Strategy to Investigate Pharmacological Mechanisms of Qiaoshao Formula for Treatment of Premature Ejaculation

Background Qiaoshao (QS) formula, a traditional Chinese medicine (TCM) comprising seven herbs, has been clinically proven to have a favorable treatment effect on premature ejaculation (PE). However, its underlying pharmacological mechanisms in the treatment of PE need to be further clarified. Methods In the present study, a network pharmacology-based strategy was adopted. The active compounds of QS formula were obtained from the Chinese medicine database, and the potential targets of these compounds were collected from the DrugBank database to construct compound-compound targets network. PE-related targets were identified from human disease databases and used to construct the protein-protein interaction (PPI) networks. Compound-disease target PPI network was constructed by merging the PPI network of disease-targets and compound-targets. Cluster and enrichment analyses were performed on the PPI network of disease targets and compound-disease targets. The influence of QS formula on serum 5-HT, NO, oxytocin, and thyroid hormones of PE patients was verified. Results Four primary pharmacological networks of QS formula were constructed, including the compound-compound targets network, PPI network of PE-related targets and compound-disease targets, and the QS-PE mechanism network. The module and pathway enrichment analyses revealed that the QS formula had the potential to affect varieties of biological process and pathways, such as nitric oxide biosynthetic process, oxytocin, thyroid hormone, TNF, PI3K-Akt, and the HIF-1 signaling pathway, that play an important role in the pathogenesis of PE. Meanwhile, the QS formula has been clinically confirmed to regulate the serum level of 5-HT, NO, oxytocin, and TT in PE patients. Conclusion This study preliminarily discovered the potential targets and pathways of QS formula in the treatment of PE, which laid a good foundation for further experimental research.
Screening of T Cell-Related Long Noncoding RNA-MicroRNA-mRNA Regulatory Networks in Non-Small-Cell Lung Cancer

Background Lung cancer (LC) has the highest mortality rate among all the other types of cancer in the world. T cells are known to be the key factor in inducing the immune response during LC. Objective In this study, we aimed to screen and analyze RNAs associated with CD8(+) T cells and activated memory CD4(+) T cells in lung adenocarcinomas, a subtype of non-small-cell lung cancer (NSCLC-LUAD). Methods Gene expression RNA-seq data and clinical data of NSCLC-LUAD were downloaded from the XENA database. The data were divided into low scores and high scores based on the Stromal and Immune scores. Then, all the genes were screened for identifying those specifically associated with CD8(+) T cells and activated memory CD4(+) T cells. The screened genes were used for the construction of the protein-protein interaction (PPI) network and for Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway enrichment analysis along with prognosis analysis. Based on the results of the prognostic analysis, the prognostic-related genes were used to analyze long noncoding (lnc)RNA-micro(mi)RNA-mRNA networks and to predict small chemical molecules. Results According to the Immune and Stromal scores, a total of 885 upregulated and 29 downregulated RNAs were identified. A total of 90 differentially expressed genes (DEGs) were found to be related to CD8(+) T immune cells, and 48 DEGs were related to activated memory CD4(+) T cells. GPR174 and CD226 suggested a favorable prognosis. For CD8(+) and activated memory CD4(+) T cells, 112 and 113 PPI edges were obtained, respectively. GPR174 was found to be regulated by hsa-miR-19b-5p and hsa-miR-19b-2-5p, and both of these two miRNAs were regulated by lncRNA PCED1B-AS1. CD226 was regulated by hsa-miR-379-5p, which was in turn regulated by lncRNA RP11-81H14.2. Conclusion Our findings provide a deeper understanding of the T cell-related ceRNA regulatory mechanism in NSCLC-LUAD pathogenesis.
The tetraspanin Cd63 is required for eye morphogenesis in Xenopus

illustrates significance of the effect. C Unilateral loss of cd63 in the eye field lineage revealed altered expression pattern of otx2 in neurula and later tailbud stages. At neurulation, otx2 showed no reduction in intensity but indicated alterations of the targeted eye vesicle (black arrowhead). Sections revealed defects in medial forebrain closure and lateral optic vesicle formation. In tailbud stages, loss of cd63 resulted in partial reduction of eye tissues (black arrowhead) compared to matching controls. Both effects were reduced by co-injection of cd63 mRNA (white arrowheads). D cd63 TBMO injection did not block TNC migration or dct expression in eyes or melanophores of unilateral morphants. Sections revealed massively impaired formation of eye tissue (black arrowhead) compared to WT eyes of controls. Asterisks mark the injected side. a, anterior; co, control; d, dorsal; p, posterior; TBMO, translation blocking Morpholino oligomer; TNC, trunk neural crest; st., stage; v, ventral; wt, wild type.
Repurposing Napabucasin as an Antimicrobial Agent against Oral Streptococcal Biofilms

Objectives Disruption of microbial biofilms is an effective way to control dental caries. Drug resistance and side effects of the existing antimicrobials necessitate the development of novel antibacterial agents. The current study was aimed at investigating the antibacterial activities of the repurposed natural compound napabucasin against oral streptococci. Methods The minimum inhibitory concentration, minimum bactericidal concentration, minimum biofilm inhibition concentration, and minimum biofilm reduction concentration of Streptococcus mutans, Streptococcus gordonii, and Streptococcus sanguinis were examined by a microdilution method. Cytotoxicity of napabucasin against human oral keratinocytes, human gingival epithelia, and macrophage RAW264.7 was evaluated by CCK8 assays. The dead/live bacterium and exopolysaccharide in the napabucasin-treated multispecies biofilms were evaluated by confocal laser scanning microscopy. Microbial composition within the napabucasin-treated biofilms was further visualized by fluorescent in situ hybridization and qPCR. And the cariogenicity of napabucasin-treated biofilms was evaluated by transverse microradiography. Results Napabucasin exhibited good antimicrobial activity against oral streptococcal planktonic cultures and biofilms but with lessened cytotoxicity as compared to chlorhexidine. Napabucasin reduced the cariogenic S. mutans and increased the proportion of the commensal S. gordonii in the multispecies biofilms. More importantly, napabucasin significantly reduced the demineralization capability of biofilms on tooth enamels. Conclusion Napabucasin shows lessened cytotoxicity and comparable antimicrobial effects to chlorhexidine. Repurposing napabucasin may represent a promising adjuvant for the management of dental caries.
Cycloaddition of oestrogen-like molecules on fullerene: theoretical approach

The [2+2] cycloaddition reaction between a double bond from a fullerene and an oestrogen or similar organic derivative has been studied in the scheme of the ab initio atom-centred density matrix propagation molecular dynamics model. The reaction was simulated considering vacuum, a little polar medium (butyric acid) and a strong polar medium (water). The results are completely different with the change of environments; some leading to an unidentified broken species without identification, whereas others produced a defined organic complex. The reaction stages have been analysed here and possible applications for medicine are achieved.
Exosomal miR-22-3p Derived from Chronic Rhinosinusitis with Nasal Polyps Regulates Vascular Permeability by Targeting VE-Cadherin

Background The abnormal vascular permeability is associated with the formation of chronic rhinosinusitis with nasal polyps (CRSwNP). Previously, our study demonstrated that the nasal lavage fluid- (NLF-) derived exosomes from CRSwNP can promote the vascular permeability of human umbilical vein endothelial cells (HUVECs). miR-22-3p, a specific differentiated miRNA, is reported to regulate microvessels in some diseases. This study is purposed to explore the impact of exosomal miR-22-3p derived from CRSwNP on vascular permeability and identify the underlying targets. Methods Exosomes were extracted from NLF of 26 CRSwNP patients and 10 control patients. Quantitative real-time PCR (qRT- PCR) was applied to evaluate the relative level of exosomal miR-22-3p. The impact of exosomal miR-22-3p on HUVECs was assessed by permeability assays in vitro. The potential molecular targets of miR-22-3p were investigated by applying such technologies as dual-luciferase reporter assay and western blot. Results miR-22-3p was upregulated in NLF-derived exosomes from CRSwNP. Exosomal miR-22-3p derived from CRSwNP enhanced the tubule permeability of HUVECs. Vascular endothelial- (VE-) cadherin (CDH5) was identified as a direct target of miR-22-3p. miR-22-3p regulated the vascular permeability by targeting VE-cadherin in HUVECs. Conclusions Exosomal miR-22-3p derived from NLF of CRSwNP plays an important role in regulating vascular permeability by targeting VE-cadherin.
Cerebellar and vestibular nuclear synapses in the inferior olive have distinct release kinetics and neurotransmitters

The inferior olive (IO) is composed of electrically-coupled neurons that make climbing fiber synapses onto Purkinje cells. Neurons in different IO subnuclei are inhibited by synapses with wide ranging release kinetics. Inhibition can be exclusively synchronous, asynchronous, or a mixture of both. Whether the same boutons, neurons or sources provide these kinetically distinct types of inhibition was not known. We find that in mice the deep cerebellar nuclei (DCN) and vestibular nuclei (VN) are two major sources of inhibition to the IO that are specialized to provide inhibitory input with distinct kinetics. DCN to IO synapses lack fast synaptotagmin isoforms, release neurotransmitter asynchronously, and are exclusively GABAergic. VN to IO synapses contain fast synaptotagmin isoforms, release neurotransmitter synchronously, and are mediated by combined GABAergic and glycinergic transmission. These findings indicate that VN and DCN inhibitory inputs to the IO are suited to control different aspects of IO activity.
Aluminium foil as a potential substrate for ATR-FTIR, transflection FTIR or Raman spectrochemical analysis of biological specimens

The substantial cost of substrates is an enormous obstacle in the successful translation of biospectroscopy (IR or Raman) into routine clinical/laboratory practice (screening or diagnosis). As a cheap and versatile substrate, we compared the performance of readily available aluminium (Al) foil with low-E, Au-coated and glass slides for cytological and histological specimen analysis by attenuated total reflection Fourier-transform infrared (ATR-FTIR), transflection FTIR or Raman spectroscopy. The low and almost featureless background signal of Al foil enables the acquisition of IR or Raman spectra without substrate interference or sacrificing important fingerprint biochemical information of the specimen, even for very thin samples with thicknesses down to 2 μm. Al foil is shown to perform as well as, if not better than, low-E or Au-coated slide, irrespective of its relatively rough surface. Although transmission FTIR is not possible on Al foil, this work demonstrates Al foil is an inexpensive, readily available and versatile substrate suitable for ATR-FTIR, transflection FTIR or Raman spectrochemical measurements of diverse biological specimens. The features of Al foil demonstrated here could promote a transition towards accessible substrates that can be readily implemented in either research or clinical settings.
Inflammatory-Related Clinical and Metabolic Outcomes in COVID-19 Patients

Background Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-COV-2) infection elicits inflammatory manifestations that relate with a “cytokine storm. ” Objective The aim of this research was to assess the role of circulating interleukin 6 (IL-6) levels and other inflammatory markers in patients with coronavirus disease 2019 (COVID-19) on metabolic functions and accompanying clinical complications. Patients and Methods. A total of 165 patients diagnosed with COVID-19 pneumonia were examined for medical features and inflammatory markers such as blood IL-6, CRP, ferritin, LDH, neutrophil/lymphocyte index (NLI), D-Dimer, and Red Cell Distribution Width (RDW). Regression analyses concerning electronically collected medical data were adjusted by appropriate factors and confounding variables. Results. Plasma IL-6 determinations evidenced a consistent association with hospital stay days, Intensive Care Unit (ICU) admission, and mortality rates. Similar trends were found for other proinflammatory variables, where ferritin and NLI showed a remarkable value as surrogates. Hyperglycaemia and the Charlson Comorbidity Index Score were positively associated with the inflammatory response induced by the SARS-COV-2 infection. An unhealthy lifestyle such as smoking and alcoholic drinks consumption as well as excessive body adiposity influenced inflammatory-related outcomes in the screened patients. Conclusion IL-6 together with other inflammatory biomarkers accompanied poor clinical and metabolic outcomes in COVID-19-infected patients. IL-6 may result in a suitable proxy to individually categorise patients in order to manage this infectious pandemic.
Development of an Autophagy Score Signature for Predicting Overall Survival in Papillary Renal Cell Carcinoma

Background Autophagy is considered to be closely associated with cancer, functioning as either an anticancer or procancer mechanism depending on the cancer stage. However, the prognostic value of autophagy on papillary renal cell carcinoma (pRCC) remains unclear. In this study, our purpose was to determine the autophagy-related mRNA signature to predict the overall survival of patients with pRCC. Materials and Methods A total of 284 patients with pathologic confirmed pRCC in The Cancer Genome Atlas (TCGA) dataset were recruited and included. We choose patients who have smoked less than 15 years but staging 3 or 4 (including nontobacco exposure) vs. more than 15 years but staging 1 or 2. Fourteen differentially expressed mRNAs were found with fold change > 2 and P value < 0.001 through limma package after making a pair between nontobacco exposure or less than 15 years and tobacco exposure more than 15 years by matchIt package. Results Six mRNAs were identified to be significantly associated with overall survival. Then, using a risk score based on the signature of these six mRNAs, we divided the patients into low-risk and high-risk groups with significantly different OS. Further multivariate Cox regression analyses revealed that the 6-mRNA signature was independent of age, TNM stage, and tumor type. In the present study, a novel 6-mRNA signature that is useful in survival prediction in pRCC patients was developed. If validated, this mRNA signature might assist in selecting high-risk subpopulation that needs more aggressive therapeutic intervention. The risk score involved in several cancer-related pathways was identified using gene set enrichment analysis. Conclusion We initially generated a six autophagy-related genes' signature, which correlates with AJCC N stage, tumor type, and pathological stage and independently predicts OS.