DCT-Net: An effective method to diagnose retinal tears from B-scan ultrasound images.

Retinal tears (RTs) are usually detected by B-scan ultrasound images, particularly for individuals with complex eye conditions. However, traditional manual techniques for reading ultrasound images have the potential to overlook or inaccurately diagnose conditions. Thus, the development of rapid and accurate approaches for the diagnosis of an RT is highly important and urgent. The present study introduces a novel hybrid deep-learning model called DCT-Net to enable the automatic and precise diagnosis of RTs. The implemented model utilizes a vision transformer as the backbone and feature extractor. Additionally, in order to accommodate the edge characteristics of the lesion areas, a novel module called the residual deformable convolution has been incorporated. Furthermore, normalization is employed to mitigate the issue of overfitting and, a Softmax layer has been included to achieve the final classification following the acquisition of the global and local representations. The study was conducted by using both our proprietary dataset and a publicly available dataset. In addition, interpretability of the trained model was assessed by generating attention maps using the attention rollout approach. On the private dataset, the model demonstrated a high level of performance, with an accuracy of 97.78%, precision of 97.34%, recall rate of 97.13%, and an F1 score of 0.9682. On the other hand, the model developed by using the public funds image dataset demonstrated an accuracy of 83.82%, a sensitivity of 82.69% and a specificity of 82.40%. The findings, therefore present a novel framework for the diagnosis of RTs that is characterized by a high degree of efficiency, accuracy and interpretability. Accordingly, the technology exhibits considerable promise and has the potential to serve as a reliable tool for ophthalmologists.

ICP4-Associated Activation of Rap1b Facilitates Herpes Simplex Virus Type I (HSV-1) Infection in Human Corneal Epithelial Cells.

The strong contribution of RAS-related protein 1b (Rap1b) to cytoskeleton remodeling determines intracellular and extracellular physiological activities, including the successful infection of viruses in permissive cells, but its role in the HSV-1 life cycle is still unclear. Here, we demonstrated that the HSV-1 immediate early (IE) gene ICP4 inhibits protein kinase A (PKA) phosphorylation to induce Rap1b-activation-mediated viral infection. Rap1b activation and membrane enrichment begin at the early stage of HSV-1 infection and remain active during the proliferation period of the virus. Treating the cells with Rap1b small interfering RNA (siRNA) showed a dose-dependent decrease in viral infection levels, but no dose-dependent increase was observed after Rap1b overexpression. Further investigation indicated that the suppression of Rap1b activation derives from phosphorylated PKA and Rap1b mutants with partial or complete prenylation instead of phosphorylation, which promoted viral infection in a dose-dependent manner. Furthermore, the PKA agonist Forskolin disturbed Rap1b activation in a dose-dependent manner, accompanied by a decreasing trend in viral infection. Moreover, the HSV-1 IE gene ICP4 induced PKA dephosphorylation, leading to continuous Rap1b activation, followed by cytoskeleton rearrangement induced by cell division control protein 42 (CDC42) and Ras-related C3 botulinum toxin substrate 1 (RAC1). These further stimulated membrane-triggered physiological processes favoring virus infection. Altogether, we show the significance of Rap1b during HSV-1 infection and uncover the viral infection mechanism determined by the posttranslational regulation of the viral ICP4 gene and Rap1b host protein.

Elucidating the potential effects of point mutations on FGFR3 inhibitor resistance via combined molecular dynamics simulation and community network analysis.

FGFR3 kinase mutations are associated with a variety of malignancies, but FGFR3 mutant inhibitors have rarely been studied. Furthermore, the mechanism of pan-FGFR inhibitors resistance caused by kinase domain mutations is still unclear. In this study, we try to explain the mechanism of drug resistance to FGFR3 mutation through global analysis and local analysis based on molecular dynamics simulation, binding free energy analysis, umbrella sampling and community network analysis. The results showed that FGFR3 mutations caused a decrease in the affinity between drugs and FGFR3 kinase, which was consistent with the reported experimental results. Possible mechanisms are that mutations affect drug-protein affinity by altering the environment of residues near the hinge region where the protein binds to the drug, or by affecting the A-loop and interfering with the allosteric communication networks. In conclusion, we systematically elucidated the underlying mechanism of pan-FGFR inhibitor resistance caused by FGFR3 mutation based on molecular dynamics simulation strategy, which provided theoretical guidance for the development of FGFR3 mutant kinase inhibitors.

Enhanced dehydrogenation properties of MgH2by the synergetic effects of transition metal carbides and graphene.

Transition metal carbides show remarkable catalysis for MgH2, and the addition of carbon materials can attach excellent cycling stability. In this paper, Mg-doped with transition metal carbides (TiC) and graphene (G) composite (denoted as Mg-TiC-G) is designed to assess the influence of TiC and graphene on the hydrogen storage performance of MgH2. The as-prepared Mg-TiC-G samples showed favorable dehydrogenation kinetics compared to the pristine Mg system. After adding TiC and graphene, the dehydrogenation activation energy of MgH2decreases from 128.4 to 111.2 kJ mol-1. The peak desorption temperature of MgH2doped with TiC and graphene is 326.5 °C, which is 26.3 °C lower than the pure Mg. The improved dehydrogenation performance of Mg-TiC-G composites is attributed to synergistic effects between catalysis and confinement.

Fine mapping of the antigenic epitopes of the Gc protein of Guertu virus.

Guertu virus (GTV), a newly discovered member of the genus Banyangvirus in the family Phenuiviridae, poses a potential health threat to humans and animals. The viral glycoprotein (GP) binds to host cell receptors to induce a neutralizing immune response in the host. Therefore, identification of the B-cell epitopes (BCEs) in the immunodominant region of the GTV Gc protein is important for the elucidation of the virus-host cell interactions and the development of GTV epitope assays and vaccines. In this study, an improved overlapping biosynthetic peptide method and rabbit anti-GTV Gc polyclonal antibodies were used for fine mapping of the minimal motifs of linear BCEs of the GTV Gc protein. Thirteen BCE motifs were identified from eleven positive 16mer-peptides, namely EGc1 (19KVCATTGRA27), EGc2 (58KKINLKCKK66), EGc3 (68SSYYVPDA75), EGc4 (75ARSRCTSVRR84), EGc5 (79CTSVRRCRWA88), EGc6 (90DCQSGCPS97), EGc7 (96PSHFTSNS103), EGc8 (115AGLGFSG121), EGc9 (148ENPHGVI154), EGc10 (179KVFHPMS185), EGc11 (230QAGMGVVG237), EGc12 (303RSHDSQGKIS312), and EGc13 (430DIPRFV435). Of these, 7 could be recognized by GTV IgG-positive sheep sera. Three-dimensional structural analysis revealed that all 13 BCEs were present on the surface of the Gc protein. Sequence alignment of the 13 BCEs against homologous proteins from 10 closely related strains of severe fever with thrombocytopenia syndrome virus from different geographical regions revealed that the amino acid sequences of EGc4, EGc5, EGc8, EGc11, and EGc12 were highly conserved, with 100% similarity. The remaining 8 epitopes (EGc1, EGc2, EGc3, EGc6, EGc7, EGc9, EGc10, and EGc13) showed high sequence similarity in the range of 71.43%-87.50%. These 13 BCEs of the GTV Gc protein provide a molecular foundation for future studies of the immunological properties of GTV glycoproteins and the development of GTV multi-epitope assays and vaccines.

Echinococcus multilocularis infection induces UBE2N suppression via exosomal emu-miR-4989.

Echinococcus multilocularis metacestodes mainly reside in liver in humans and animals, and cause serious damages. UBE2N was herein shown to be downregulated in response to the infection. UBE2N was further shown to be predominantly expressed in the hepatocytes, which was also significantly downregulated during the infection. UBE2N was a target of emu-miR-4989, which was loaded into the exosomes secreted by parasites. These emu-miR-4989-encapsulating exosomes were internalized by hepatocytes, and induced a significant decrease of relative luciferase activity in the cells transfected with the construct containing a wild type of UBE2N 3'-UTR compared to the control (p < 0.05). These results demonstrate that emu-miR-4989 is involved in the UBE2N inhibition in the hepatocytes during E. multilocularis through exosomes.

Comparative Proteomic Analysis of Different Parts of Taenia Hydatigena.

Taenia hydatigena, a globally distributed parasite, is a canine tapeworm and causes huge economic losses in the food industry. Using LC-MS/MS, the proteomes of T. hydatigena cyst scolex, designated as CS, and the cyst without the scolex, designated as CWS, were profiled and a total of 764 different proteins were identified, 664 of which were identified in CS, 412 identified in CWS, and 312 in both. Comparative analysis revealed that CS had more abundant proteins associated with growth and development, while CWS had more abundant proteins constituting a scaffolding and protective extracellular matrix. Consistent with the sequencing data, the abundance of the five selected proteins was validated to be higher in CWS than CS by Western blotting. The current data will provide a clue for further pinpointing a role of these proteins in the biology of T. hydatigena.

Fine mapping epitope on Glycoprotein-Gn from Severe Fever with Thrombocytopenia Syndrome Virus.

Severe Fever with Thrombocytopenia Syndrome Virus (SFTSV) was recently identified as a tick-borne pathogen that threat to human health. Since 2010, many countries including China, South Korea, and Japan have reported Human SFTS caused by SFTSV infection. The glycoprotein encoded by the SFTSV M gene is the major antigenic component on the viral surface, and responsible for the viral entry, which makes it an important viral antigen and a clinical diagnostic target. The present study aimed to map linear B cell epitopes (BCEs) on the N-terminal glycoprotein (Gn) from SFTSV strain WCH/97/HN/China/2011 using the modified biosynthetic peptide method. Five fine epitopes (E1, 196FSQSEFPD203; E2, 232GHSHKII238; E3, 256VCYKEGTGPC265; E4, 285FCKVAG290, and E5, 316SYGGM320) were identified using the rabbit antisera. Western blot analysis showed that all the five epitopes interacted with the positive serum of sheep that had been naturally infected with SFTSV. Three-dimensional structural modeling analysis showed that all identified BCEs were located on the surface of the SFTSV-Gn and contained flexible loops. The sequence alignment revealed high conservation of the identified BCEs among 13 SFTSV strains from different lineage. These mapped epitopes will escalate the understanding of the epitope distribution and pathogenic mechanism of SFTSV, and could provide a basis for the development of a SFTSV multi-epitope detection antigen.

microRNA-21: a key modulator in oncogenic viral infections.

Oncogenic viruses are associated with approximately 15% of human cancers. In viral infections, microRNAs play an important role in host-pathogen interactions. miR-21 is a highly conserved non-coding RNA that not only regulates the development of oncogenic viral diseases, but also responds to the regulation of intracellular signal pathways. Oncogenic viruses, including HBV, HCV, HPV, and EBV, co-evolve with their hosts and cause persistent infections. The upregulation of host miR-21 manipulates key cellular pathways to evade host immune responses and then promote viral replication. Thus, a better understanding of the role of miR-21 in viral infections may help us to develop effective genetically-engineered oncolytic virus-based therapies against cancer.

Comparative analysis of different extracellular vesicles secreted by Echinococcus granulosus protoscoleces.

Extracellular vesicles (EVs) are heterogeneous populations of different membrane-wrapped vesicles in size and encapsulated cargo and have recently emerged as a crucial carrier with the functions in intercellular communication, being involved in host-parasite interactions. However, Echinococcus granulosus EVs are not fully described. To separate EVs with a different size, the culture supernatant of E. granulosus protoscoleces (PSCs) was sequentially centrifuged at 2,000g, 10,000g and 110,000g, and the resulting precipitates were accordingly named as 2K, 10K and 110K EVs, respectively. The size and morphology of three different EVs were identified using ZETASIZER NANO and transmission electron microscopy (TEM), respectively. Then mass spectrometry was applied to define protein cargo of EVs and EV internalization was assessed using fluorescent microscopy and flow cytometry. The results showed that 2K EVs mainly ranged from 450 to 950 nm in diameter, 10K EVs ranged from 220 to 390 nm and 110K EVs from 60 to 150 nm. A total of 901 EV proteins were identified, 328 of which were commonly found in the three types of EVs. GO analysis revealed that these proteins were mainly involved in binding (44%) and catalytic activity (44%). Three types of EVs were different in biomarkers (Enolase and 14-3-3) and in reactivity with anti-echinococcosis positive serum. Moreover, 110K EVs were more easily internalized by hepatic cells than 10K EVs as well as 2K EVs (p < 0.0001). These results reveal the physical and biological discrepancy among 2K, 10K and 110K EVs, suggesting a distinct role in host-parasite interactions.

miRNA-seq of Echinococcus multilocularis Extracellular Vesicles and Immunomodulatory Effects of miR-4989.

Alveolar echinococcosis caused by Echinococcus multilocularis is an important zoonotic disease. In the infected mice, emu-miR-4989-3p is present in sera, but its role remains unknown. Using high-throughput sequencing and qPCR, emu-miR-4989-3p was herein confirmed to be encapsulated into E. multilocularis extracellular vesicles. In the transfected macrophages, emu-miR-4989-3p was demonstrated to significantly inhibit NO production compared to the control (p < 0.05). Moreover, transfection of emu-miR-4989-3p also gave rise to the increased expression of TNF-α (p < 0.01). Furthermore, emu-miR-4989-3p induced the dysregulation of several key components in the LPS/TLR4 signaling pathway compared with the control, especially TLR4 and NF-κB that both were upregulated. Conversely, the NO production and the expression of TNF-α, TLR4 and NF-κB tended to be increased and decreased in the mimics-transfected cells upon emu-miR-4989-3p low expression, respectively. These results suggest that emu-miR-4989-3p is one of 'virulence' factors encapsulated into the extracellular vesicles, potentially playing a role in the pathogenesis of E. multilocularis.

Fine epitope mapping of glycoprotein Gn in Guertu virus.

Guertu virus (GTV) is a tick-borne phleboviruses (TBPVs) which belongs to the genus Banyangvirus in the family of Phenuiviridae. In vitro and in vivo studies of GTV demonstrated that it was able to infect animal and human cell lines and could cause pathological lesions in mice. Glycoproteins (GP, including Gn and Gc) on the surface of Guertu virus (GTV) could bind to receptors on host cells and induce protective immunity in the host, but knowledge is now lacking on the information of B cell epitopes (BCEs) present on GTV-GP protein. The aim of this study was to identify all BCEs on Gn of the GTV DXM strain using rabbit pAbs against GTV-Gn. Seven fine BCEs and two antigenic peptides (APs) from nine reactive 16mer-peptides were identified, which are EGn1 (2PIICEGLTHS11), EGn2 (135CSQDSGT141), EGn3 (165IP EDVF170), EGn4 (169VFQEL K174), EGn5 (187IDGILFN193), EGn6 (223QTKWIQ228), EGn7 (237CHKDGIGPC245), AP-8 (299GVRVRPKCYGFSRMMA314) and AP-9 (355CASH FCSSAESGKKNT370), of which six of mapped BCEs were recognized by the IgG-positive sheep serum obtained from sheep GTV-infected naturally. Multiple sequence alignments (MSA) based on each mapped BCE motif identified that the most of identified BCEs and APs are highly conserved among 10 SFTSV strains from different countries and lineages that share relatively close evolutionary relationships with GTV. The fine epitope mapping of the GTV-Gn would provide basic data with which to explore the GTV-Gn antigen structure and pathogenic mechanisms, and it could lay the foundation for the design and development of a GTV multi-epitope peptide vaccine and detection antigen.

Fine mapping epitope on glycoprotein Gc from Crimean-Congo hemorrhagic fever virus.

Crimean-Congo hemorrhagic fever (CCHF) is a tick-borne zoonosis, caused by CCHF virus (CCHFV) and which there are no diagnostic or therapeutic strategies. The C-terminus of glycoprotein (Gc) encoded by the CCHFV M gene is responsible for CCHFV binding to cellular receptors and acts as a neutralizing-antibody target. In this study, a modified biosynthetic peptide technique (BSP) was used to identify fine epitopes of Gc from the CCHFV YL04057 strain using rabbit antiserum against CCHFV-Gc. Six B cell epitopes (BCEs) and one antigenic peptide (AP) were identified: E1 (88VEDASES94), E2 (117GDRQVEE123), E3 (241EIVTLH246), AP-4 (281DFQVYHVGNLLRGDKV296), E5a (370GDTP QLDL377), E5b (373PQLDLKAR380), and E6 (443HVRSSD448). Western blotting analysis showed that each epitope interacted with the positive serum of sheep that had been naturally infected with CCHFV, and the results were consistent with that of Dot-ELISA. The multiple sequence alignment (MSA) revealed high conservation of the identified epitopes among ten CCHFV strains from different areas, except for epitopes AP-4 and E6. Furthermore, three-dimensional structural modeling showed that all identified epitopes were located on the surface of the Gc "head" domain. These mapped epitopes of the CCHFV Gc would provide a basis for further increase our understanding CCHFV glycoprotein function and the development of a CCHFV epitope-based diagnostics vaccine and detection antigen.

Comparative analysis of miRNAs in exosomes released by sheeppox virus-infected ovine testicular cells.

Exosomes, secreted by various cells, are nanometer-scale vesicles with the functions in intercellular communication. To understand a role of exosomal miRNAs in the sheeppox virus infection, exosomes were isolated from sheeppox virus-infected sheep testicular cells 0 h, 24 h and 72 h post infection. The results of transmission electron microscopy and size distribution showed that all three exosome samples were spherical particles with negatively-stained membrane, ranging from 39 nm to 127 nm in diameter. A total of 106 known and 279 novel miRNAs were identified, and 78 known and 54 novel miRNAs were commonly detected in three exosome samples. Compared with the exosomes by the uninfected controls, a total of 34 known miRNAs were aberrantly expressed in the exosomes from infected cells. In agreement with the sequencing data, the expression of oar-miR-21 and oar-miR-10b was shown to be the highest in exosomes at 24 h after SPPV-infected, and the expression of oar-let-7f was the highest in exosomes at 72 h. Conversely, the expression of oar-let-7b and oar-miR-221 was significantly decreased 24 h and 72 h post infection compared with 0 h. The analysis results also revealed that differentially expressed miRNAs were mostly involved in an immune system process and stimulus response. These results provide rich data to further investigate a role of exosomal miRNAs in SPPV-host interactions.

Exosomes in virus-associated cancer.

Exosomes are phospholipid bilayer membrane-enclosed vesicles in a size from 30 to 150 nm, carrying a variety of active components, such as proteins, mRNA and miRNAs, and are involved in intercellular communication. Exosomes are released by almost all living cells and detected in various biological fluids. Viruses especially oncogenic viruses have been reported to influence the formation of virus-associated cancer through reshaping the tumor microenvironment via exosomes. In this review, a role of exosomes released by oncogenic virus-infected cells in promoting or inhibiting cancer formation is outlined. Moreover, the prospects and challenges of exosome applications in cancer therapies are critically discussed.

Identification of emu-TegP11, an EF-hand domain-containing tegumental protein of Echinococcus multilocularis.

Tegumental proteins (TegPs) are a group of proteins that coat on the surface of worms, mainly being involved in ion uptake and immune evasion. Echinococcus species have many TegPs, but none of them have been characterized and their role remains unclear. The genome-wide analysis revealed that there were at least 14 tegp genes (tegp1 - 14) in Echinococcus species, the majority of which were found to contain an EF-hand domain or a dynein light chain-like domain or both. Despite low identity, all TegP11 proteins from 25 flatworms were conserved in structure. Echinococcus multilocularis TegP11 (emu-TegP11) was verified to be secreted by extracellular vesicles and to be localized in different spatiotemporal patterns in protoscoleces. Moreover, emu-TegP11 was also shown to have weak or no Ca2+-binding capacity. In treated macrophages, emu-TegP11 interfered with the small RNA-induced silencing pathway via inducing ectopic expression of some key component genes. Additionally, emu-TegP11 remarkably promoted NO secretion possibly by upregulation of inos gene expression (p < 0.05). It was further shown that emu-TegP11 acted as a suppressor of inflammation, with il-12B and il-1ß being significantly down-regulated (p < 0.01), and il-10 and il-4 being significantly upregulated (p < 0.05). The study demonstrates a regulatory role of emu-TegP11, likely acting as a immunomodulator to be involved in regulation of host immune system during Echinococcus infection.

MicroRNA Roles in the Nuclear Factor Kappa B Signaling Pathway in Cancer.

Nuclear factor kappa B (NF-κB) is a pluripotent and crucial dimer transcription factor that orchestrates various physiological and pathological processes, especially cell proliferation, inflammation, and cancer development and progression. NF-κB expression is transient and tightly regulated in normal cells, but it is activated in cancer cells. Recently, numerous studies have demonstrated microRNAs (miRNAs) play a vital role in the NF-κB signaling pathway and NF-κB-associated immune responses, radioresistance and drug resistance of cancer, some acting as inhibitors and the others as activators. Although it is still in infancy, targeting NF-κB or the NF-κB signaling pathway by miRNAs is becoming a promising strategy of cancer treatment.

Suppression of nemo-like kinase by miR-71 in Echinococcus multilocularis.

Echinococcus multilocularis metacestodes are a causative pathogen for alveolar echinococcosis in human beings, and have been found to express miRNAs including emu-miR-71. miR-71 is evolutionarily conserved and highly expressed across platyhelminths, but little is known about its role. Here it was shown that emu-miR-71 was differentially expressed in protoscoleces and was unlikely to be expressed in neoblasts. The results of the luciferase assay indicated that emu-miR-71 was able to bind in vitro to the 3'-UTR of emu-nlk, encoding a key regulator of cell division, causing significant downregulation of luciferase activity (p < 0.01) compared to the negative control and the construct with mutations in the binding site. Consistent with the decreased luciferase activity, transfection of emu-miR-71 mimics into protoscoleces notably repressed emu-NLK (p < 0.05). These results demonstrate the suppression of emu-nlk by emu-miR-71, potentially involved in the protoscolex development.