How enlightened self-interest guided global vaccine sharing benefits all: a modelling study

Background: Despite the consensus that vaccines play an important role in combating the global spread of infectious diseases, vaccine inequity is still rampant with deep-seated mentality of self-priority. This study aims to evaluate the existence and possible outcomes of a more equitable global vaccine distribution and explore a concrete incentive mechanism that promotes vaccine equity. Methods: We design a metapopulation epidemiological model that simultaneously considers global vaccine distribution and human mobility, which is then calibrated by the number of infections and real-world vaccination records during COVID-19 pandemic from March 2020 to July 2021. We explore the possibility of the enlightened self-interest incentive mechanism, i.e., improving one's own epidemic outcomes by sharing vaccines with other countries, by evaluating the number of infections and deaths under various vaccine sharing strategies using the proposed model. To understand how these strategies affect the national interests, we distinguish the imported and local cases for further cost-benefit analyses that rationalize the enlightened self-interest incentive mechanism behind vaccine sharing. ...Comment: Accepted by Journal of Global Healt

Comprehensive Analysis of Codon Usage Patterns in Chinese Porcine Circoviruses Based on Their Major Protein-Coding Sequences

Porcine circoviruses (PCVs) are distributed in swine herds worldwide and represent a threat to the health of domestic pigs and the profits of the swine industry. Currently, four PCV species, including PCV-1, PCV-2, PCV-3 and PCV-4, have been identified in China. Considering the ubiquitous characteristic of PCVs, the new emerged PCV-4 and the large scale of swine breeding in China, an overall analysis on codon usage bias for Chinese PCV sequences was performed by using the major proteins coding sequences (ORF1 and ORF2) to better understand the relationship of these viruses with their host. The data from genome nucleotide frequency composition and relative synonymous codon usage (RSCU) analysis revealed an overrepresentation of AT pair and the existence of a certain codon usage bias in all PCVs. However, the values of an effective number of codons (ENC) revealed that the bias was of low magnitude. Principal component analysis, ENC-plot, parity rule two analysis and correlation analysis suggested that natural selection and mutation pressure were both involved in the shaping of the codon usage patterns of PCVs. However, a neutrality plot revealed a stronger effect of natural selection than mutation pressure on codon usage patterns. Good host adaptation was also shown by the codon adaptation index analysis for all these viruses. Interestingly, obtained data suggest that PCV-4 might be more adapted to its host compared to other PCVs. The present study obtained insights into the codon usage pattern of PCVs based on ORF1 and ORF2, which further helps the understanding the molecular evolution of these swine viruses.info:eu-repo/semantics/publishedVersio

Asiantuntijoiden yhdistelmä kuvien luokitteluun

Mixture of Experts (MoE) is a machine learning tool that utilizes multiple expert models to solve machine learning tasks. By combining perspectives of individual experts using a product of their output, the overall system can produce comprehensive decisions. The hope is that by doing this, the individual experts can focus on modeling different aspects of the data. In this thesis, we study MoEs in the context of deep learning and image classification using empirical comparisons. The different datasets, gating and expert networks, numbers of experts and objective functions for the gate are controlled in the experiments, and the performance (classification accuracy) and the behavior (how the gate distributes the data over the experts) are obtained as the results. Based on the result that the experimented mixtures of networks are performing mostly on par with the single network baseline, we conclude that either the mixture of experts is not suitable to be learned for the image classification tasks or it requires some different engineering in the architecture and/or optimization algorithm selection

Comprehensive Analysis of Codon Usage Patterns in Chinese Porcine Circoviruses Based on Their Major Protein-Coding Sequences

Porcine circoviruses (PCVs) are distributed in swine herds worldwide and represent a threat to the health of domestic pigs and the profits of the swine industry. Currently, four PCV species, including PCV-1, PCV-2, PCV-3 and PCV-4, have been identified in China. Considering the ubiquitous characteristic of PCVs, the new emerged PCV-4 and the large scale of swine breeding in China, an overall analysis on codon usage bias for Chinese PCV sequences was performed by using the major proteins coding sequences (ORF1 and ORF2) to better understand the relationship of these viruses with their host. The data from genome nucleotide frequency composition and relative synonymous codon usage (RSCU) analysis revealed an overrepresentation of AT pair and the existence of a certain codon usage bias in all PCVs. However, the values of an effective number of codons (ENC) revealed that the bias was of low magnitude. Principal component analysis, ENC-plot, parity rule two analysis and correlation analysis suggested that natural selection and mutation pressure were both involved in the shaping of the codon usage patterns of PCVs. However, a neutrality plot revealed a stronger effect of natural selection than mutation pressure on codon usage patterns. Good host adaptation was also shown by the codon adaptation index analysis for all these viruses. Interestingly, obtained data suggest that PCV-4 might be more adapted to its host compared to other PCVs. The present study obtained insights into the codon usage pattern of PCVs based on ORF1 and ORF2, which further helps the understanding the molecular evolution of these swine viruses.info:eu-repo/semantics/publishedVersio

Additional file 1 of Phylogenetically evolutionary analysis provides insights into the genetic diversity and adaptive evolution of porcine deltacoronavirus

Supplementary Material 1: Table S1. Sequence information in this stud

Impairment of the antibody-dependent phagocytic function of PMNs through regulation of the FcγRs expression after porcine reproductive and respiratory syndrome virus infection.

Porcine reproductive and respiratory syndrome (PRRS) is identified as one of the most important etiological agents in multifactorial respiratory disease of swine and can predispose pigs to secondary infections by other pathogens, usually bacteria. To understand the mechanism for an increased susceptibility to secondary bacterial infections, we investigated the antibody-dependent phagocytosis behaviour and killing ability of PMNs after infection by PRRSV strains BJ-4 or HN07-1. PMN's antibody-dependent phagocytosis and their ability to kill E.coli were both noticeably decreased following PRRSV infection, in particular with the highly pathogenic strain HN07-1. As the change in this function of the PMNs may reflect a variation in the expression of FcγRs, the expression profiles of the activating and the inhibitory FcγRs were examined. We found that RNA expression of the inhibitory receptor FcγRIIB was up-regulated post-infection, and this was greater after infection with the more virulent PRRSV strain HN07-1. The activating receptor FcγRIIIA RNA expression was on the other hand inhibited to the same extent by both PRRSV strains. Neutralizing antibody titers post-infection by PRRSV strains BJ-4 or HN07-1 were also detected. All of the pigs in infection groups showed viraemia by the end of the study (56 DPI). These observations may help to understand the mechanism of increased susceptibility to secondary bacterial infections following PRRSV infection

Efficient purification of cell culture-derived classical swine fever virus by ultrafiltration and size-exclusion chromatography

Large-scale production of cell culture-based classical swine fever virus (CSFV) vaccine is hampered by the adverse reactions caused by contaminants from host cell and culture medium. Hence, we have developed an efficient method for purifying CSFV from cell-culture medium. Pure viral particles were obtained with two steps of tangential-flow filtration (TFF) and size-exclusion chromatography (SEC), and were compared with particles from ultracentrifugation by transmission electron microscopy (TEM), infectivity and recovery test, and real time fluorescent quantitative PCR (FQ-PCR). TFF concentrated the virus particles effectively with a retention rate of 98.5%, and 86.2% of viral particles were obtained from the ultrafiltration retentate through a Sepharose 4 F F column on a biological liquid chromatography system. CSFV purified by TFF-SEC or ultracentrifugation were both biologically active from 1.0×10-4.25 TCID50·mL-1 to 3.0×10-6.25 TCID50·mL-1, but the combination of TFF and SEC produced more pure virus particles than by ultracentrifugation alone. In addition, pure CSFV particles with the expected diameter of 40—60 nm were roughly spherical without any visible contamination. Mice immunized with CSFV purified by TFF-SEC produced higher antibody levels compared with immunization with ultracentrifugation-purified CSFV (P<0.05). The purification procedures in this study are reliable technically and feasible for purification of large volumes of viruses

The viability of IgG-opsonized<i>E.coli</i> after incubation with PMN following PRRSV inoculation.

<p>IgG-opsonized <i>E.coli</i> were incubated with PMN at 4°C for 30 min. Cells were split over two aliquots and subsequently incubated for 30 min at either 4 or 37°C. Bacterial killing was determined from the difference between the numbers of viable bacteria initially attached to PMN (cells incubated at 4°C) and after bacterial phagocytosis (cells incubated at 37°C). The percentage of bacteria killed by PMN was calculated as follows: the percentage of killing = 100 × (1-N37/N4) Results are shown as mean ± SE (n = 5)*, p<0.05. **, p<0.01.</p