Codon usage patterns of LT-Ag genes in polyomaviruses from different host species

Background Polyomaviruses (PyVs) have a wide range of hosts, from humans to fish, and their effects on hosts vary. The differences in the infection characteristics of PyV with respect to the host are assumed to be influenced by the biochemical function of the LT-Ag protein, which is related to the cytopathic effect and tumorigenesis mechanism via interaction with the host protein. Methods We carried out a comparative analysis of codon usage patterns of large T-antigens (LT-Ags) of PyVs isolated from various host species and their functional domains and sequence motifs. Parity rule 2 (PR2) and neutrality analysis were applied to evaluate the effects of mutation and selection pressure on codon usage bias. To investigate evolutionary relationships among PyVs, we carried out a phylogenetic analysis, and a correspondence analysis of relative synonymous codon usage (RSCU) values was performed. Results Nucleotide composition analysis using LT-Ag gene sequences showed that the GC and GC3 values of avian PyVs were higher than those of mammalian PyVs. The effective number of codon (ENC) analysis showed host-specific ENC distribution characteristics in both the LT-Ag gene and the coding sequences of its domain regions. In the avian and fish PyVs, the codon diversity was significant, whereas the mammalian PyVs tended to exhibit conservative and host-specific evolution of codon usage bias. The results of our PR2 and neutrality analysis revealed mutation bias or highly variable GC contents by showing a narrow GC12 distribution and wide GC3 distribution in all sequences. Furthermore, the calculated RSCU values revealed differences in the codon usage preference of the LT-AG gene according to the host group. A similar tendency was observed in the two functional domains used in the analysis. Conclusions Our study showed that specific domains or sequence motifs of various PyV LT-Ags have evolved so that each virus protein interacts with host cell targets. They have also adapted to thrive in specific host species and cell types. Functional domains of LT-Ag, which are known to interact with host proteins involved in cell proliferation and gene expression regulation, may provide important information, as they are significantly related to the host specificity of PyVs.This work was supported by a grant from the National Research Foundation of Korea funded by the Korea government (MSIP) (No. 2016R1C1B2015511) and the Ministry of Education (No. 2017R1D1A1B03033413)

A Localized Forwarding Scheme for the Shared-Prefix Model-Based Vehicular Mobility Management Over IEEE WAVE IPv6 Networks

IETF IP Wireless Access in Vehicular Environments Working Group proposes a shared-prefix model, where multiple RSUs share a common prefix. In the same prefix domain, a WAVE wireless interface does not need to reconfigure its IPv6 address even if its serving RSU is changed. We had proposed a vehicular mobility management scheme for a shared prefix model over IEEE WAVE IPv6 networks. However, when two vehicles communicate with each other, the data path between two vehicles can be sub-optimal. In the scheme, all incoming packets having a specific prefix are forwarded by a Link Border Router, which manages the prefix, to the serving RSU of the destination vehicle. It causes the triangular data path. To eliminate this triangular data path, we propose a localized forwarding scheme for the vehicular mobility management scheme. This scheme allows that two vehicles within direct communication distance can communicate directly or serving RSUs of two vehicles can communicate directly for intra-vehicular traffic within the WAVE network. It eliminates the triangular data path between two vehicles within the WAVE network. It also reduces the workload of Link Border Routers, which are the hotspot of the vehicular mobility management scheme

Analysis of protein determinants of host-specific infection properties of polyomaviruses using machine learning

Background The large tumor antigen (LT-Ag) and major capsid protein VP1 are known to play important roles in determining the host-specific infection properties of polyomaviruses (PyVs). Objective The objective of this study was to investigate the physicochemical properties of amino acids of LT-Ag and VP1 that have important effects on host specificity, as well as classification techniques used to predict PyV hosts. Methods We collected and used reference sequences of 86 viral species for analysis. Based on the clustering pattern of the reconstructed phylogenetic tree, the dataset was divided into three groups: mammalian, avian, and fish. We then used random forest (RF), naive Bayes (NB), and k-nearest neighbors (kNN) algorithms for host classification. Results Among the three algorithms, classification accuracy using kNN was highest in both LT-Ag (ACC = 98.83) and VP1 (ACC = 96.51). The amino acid physicochemical property most strongly correlated with host classification was charge, followed by solvent accessibility, polarity, and hydrophobicity in LT-Ag. However, in VP1, amino acid composition showed the highest correlation with host classification, followed by charge, normalized van der Waals volume, and solvent accessibility. Conclusions The results of the present study suggest the possibility of determining or predicting the host range and infection properties of PyVs at the molecular level by identifying the host species of active and emerging PyVs that exhibit different infection properties among diverse host species. Structural and biochemical differences of LT-Ag and VP1 proteins in host species that reflect these amino acid properties can be considered primary factors that determine the host specificity of PyV.N

Estimation of Virus Host Range using Receptor Sequence

Although attempts have been made to dealing with emerging and re-emerging viruses causing infectious diseases for decades, there are still limitations in prediction of the risk of infection or transmission of diverse viral pathogens. In this study, we evaluated the risk of cross-species infection of the virus through evolutionary distance matrix and phylogenetic analysis using receptor sequences. We defined the DI (distance index) to the maximum value of the evolutionary distance for infected hosts, and the host range was estimated using the DI for all taxa on the phylogenetic tree. The reconstructed trees showed that taxa with values less than or equal to DI are primarily assessed as potential hosts by clustering into the host range with regard to the receptor similarity. Interestingly, the distribution of distance values for each tree showed that the host range is more clearly classified in the receptor-based trees than in the mt-based trees, although the classification patterns were highly similar. In conclusion, we have found that the similarity of the receptor proteins, which was measured by evolutionary distance and phylogenetic relationship, can be used as a useful parameter to predict the virus host range, and may be more appropriate than using mitochondrial genomes.N

Characterization of Codon Usage Patterns and Evolutionary Relationships in Partitiviruses

This study investigated the overall sequence characteristics and codon usage patterns of Partitiviridae viruses and applied them to viruses that are part of the family Partitiviridae but are unassigned to a genus. In addition, phylogenetic analysis was performed to investigate the evolutionary relationships of viruses belonging to Partitiviridae in relation to their fungal hosts. The sequence data of the CDS region were downloaded from GenBank, including that of the conserved RdRP, capsid protein. The results showed that Botryotinia fuckeliana partitivirus 1, Beauveria bassiana partitivirus 1, Beauveria bassiana partitivirus 2, Penicillium marneffei partitivirus-1, and Aspergillus fumigatus partitivirus 2 had evolutionary relationships with Gammapartitivirus. Among them, Aspergillus fumigatus partitivirus 2 and Penicillium marneffei partitivirus-1 preferred U-ended codons similar to Gammapartitivirus in terms of codon usage patterns. In addition, Botryosphaeria dothidea virus 1 showed a different pattern from the viruses belonging to Partitiviridae in all the analysis results. This virus showed a strong bias towards the C-ended codons and the lowest ENC value among the analyzed viruses, forming a separate cluster in the phylogenetic tree. These results may help to understand the genetic diversity and evolutionary relationships of the members and tentative members of the family Partitiviridae.N

Lightweight End-to-End Stress Recognition using Binarized CNN-LSTM Models

In this paper, we propose a novel end-to-end stress recognition model by combining binarized convolutional neural network (CNN) and long short-term memory (LSTM) models. Based on the previous CNN-LSTM model using electrocardiogram (ECG) and respiration (RESP) signals, we newly apply the bandit-based hyperparameter optimization to find more accurate solutions. Analyzing the computational costs of the accuracy-aware model, we also introduce advanced memory-reduction techniques with downscaling and binarization for realizing the cost-efficient stress recognition solution. As a result, compared to the state-of-the-art methods, the proposed model reduces the memory size, the inference latency, and the energy consumption by 93 %, 39 %, and 42 %, respectively, while even increasing the recognition accuracy up to 87%.2

Microstructure and Mechanical Properties of P21-STS316L Functionally Graded Material Manufactured by Direct Energy Deposition 3D Print

Functionally graded materials (FGMs) have a characteristic whereby the composition and structure are gradually changed according to the location, and the mechanical properties or chemical properties are gradually changed accordingly. In this study, using a multi-hopper direct energy deposition 3D printer, an FGM material whose composition changes gradually from P21 ferritic steel to stainless steel 316L austenitic steel was fabricated. From optical microscope, scanning electron microscope, and X-ray diffraction analysis, columnar, cell, and point type solidified micro-structure and precipitations were observed depending on the deposited compositions. Electron probe microanalysis and electron backscatter diffraction analysis confirmed the component segregation, ferrite austenite volume fraction and phase distribution behavior according to compositions. In the FGM specimen test, the ultimate tensile strength of STS316L, which was the most fragile, was measured, and the toughness was measured for the notch area, which did not represent the FGM characteristics. Hardness showed changes according to FGM position and was suitable for FGM analysis. The maximum hardness was measured in the FGM duplex area, which was caused by grain refinement, precipitate strengthening, and solid solution strengthening. In nuclear power plant welds high strength can cause adverse effects on stress corrosion cracking, and caution is needed in applying FGM

Microstructure and Mechanical Properties of P21-STS316L Functionally Graded Material Manufactured by Direct Energy Deposition 3D Print

Functionally graded materials (FGMs) have a characteristic whereby the composition and structure are gradually changed according to the location, and the mechanical properties or chemical properties are gradually changed accordingly. In this study, using a multi-hopper direct energy deposition 3D printer, an FGM material whose composition changes gradually from P21 ferritic steel to stainless steel 316L austenitic steel was fabricated. From optical microscope, scanning electron microscope, and X-ray diffraction analysis, columnar, cell, and point type solidified micro-structure and precipitations were observed depending on the deposited compositions. Electron probe microanalysis and electron backscatter diffraction analysis confirmed the component segregation, ferrite austenite volume fraction and phase distribution behavior according to compositions. In the FGM specimen test, the ultimate tensile strength of STS316L, which was the most fragile, was measured, and the toughness was measured for the notch area, which did not represent the FGM characteristics. Hardness showed changes according to FGM position and was suitable for FGM analysis. The maximum hardness was measured in the FGM duplex area, which was caused by grain refinement, precipitate strengthening, and solid solution strengthening. In nuclear power plant welds high strength can cause adverse effects on stress corrosion cracking, and caution is needed in applying FGM

A retrospective study on 198 mpox cases in South Florida: Clinical characteristics and outcomes with focus on human immunodeficiency virus status

Background Men who have sex with men (MSM) and persons living with human immunodeficiency virus (PLWH) were disproportionately affected by global mpox outbreak in 2022. In this retrospective review, we describe epidemiology and clinical characteristics of mpox infection in South Florida with a focus on human immunodeficiency virus (HIV) status. Methods This was a retrospective observational study of 198 adult patients with confirmed diagnosis of mpox between 01 January 2020, and 10 September 2022, in two large health systems in South Florida. A descriptive analysis was performed to summarize demographic, clinical and laboratory characteristics, and outcomes of the patients. Results Young male patients and PLWH were disproportionately represented among patients with mpox. HIV positive patients were less likely to have adenopathy and myalgia and were more likely to have oral or facial lesions. 22.7% of studied patients were diagnosed with one or more concurrent STI at the time of mpox diagnosis. Conclusions We suggest screening for sexually transmitted infections and HIV for patients diagnosed with mpox. We suggest prompt consultation or referral to infectious disease specialist if needed for the patients who are diagnosed with mpox especially in the severely immunocompromised host

Mechanistic insights into the anti-restenotic effects of HSP27 and HO1 modulated by reconstituted HDL on neointimal hyperplasia

High-density lipoprotein (HDL) therapy has demonstrated beneficial effects in acute stroke and acute myocardial infarction models by reducing infarct size. In this study, we investigated the inhibitory effects of reconstituted HDL (rHDL) on neointimal hyperplasia and elucidated its underlying mechanism using a balloon injury rat model. Our finding revealed a significant 37% reduction in the intima to media ratio in the arteries treated with 80 mg/kg rHDL compared to those subjected to injury alone (p < 0.05), indicating a specific inhibition of neointimal hyperplasia. In vivo analysis further supported the positive effects of rHDL by demonstrating a reduction in smooth muscle cell (SMC) proliferation and an increase in endothelial cell (EC) proliferation. Additionally, rHDL treatment led to decreased infiltration of leukocytes and downregulated the expression of matrix metallopeptidase 9 (MMP9) in the neointimal area. Notably, rHDL administration resulted in decreased expression of VCAM1 and HIF1α, alongside increased expression of heme oxygenase 1 (HO1) and heat shock protein 27 (HSP27). Overexpression of HSP27 and HO1 effectively inhibited SMC proliferation. Moreover, rHDL-mediated suppression of injury-induced HIF1α coincided with upregulation of HSP27. Interestingly, HSP27 and HO1 had varying effects on the expression of chemokine receptors and rHDL did not exert significant effect on chemokine receptor expression in THP1 cells. These findings underscore the distinct roles of HSP27 and HO1 as potential regulatory factors in the progression of restenosis. Collectively, our study demonstrates that rHDL exerts a potent anti-neointimal hyperplasia effect by reducing leukocytes infiltration and SMC proliferation while promoting EC proliferation. © 2023, The Author(s).11Nsciescopu