A Survey on Knee-Oriented Multiobjective Evolutionary Optimization

Yu G, Ma L, Jin Y, Du W, Liu Q, Zhang H. A Survey on Knee-Oriented Multiobjective Evolutionary Optimization. IEEE Transactions on Evolutionary Computation. 2022;26(6):1452-1472.Conventional multiobjective optimization algorithms (MOEAs) with or without preferences are successful in solving multi- and many-objective optimization problems. However, a strong hypothesis underlying their performance is that MOEAs are able to find a representative solution set to cover the entire Pareto-optimal front (PF) and decision makers are able to conveniently and precisely articulate their preference, which is not always easy to fulfill in practice. Accordingly, it is suggested that representative solutions in the naturally interesting regions of the PF rather than the whole PF should be targeted. A large body of research has been proposed to search or identify the knees or knee regions over the past decades. Therefore, this article aims to provide a comprehensive survey of the research on knee-oriented optimization. We start with a discussion of the importance and basic concepts of the knees, followed by a summary of knee-oriented benchmarks and indicators. After that, knee-oriented frameworks and techniques, and real-world applications are presented. Finally, potential challenges are pointed out and a few promising future lines of research are suggested. The survey offers a new perspective to develop MOEAs for solving multi- and many-objective optimization problems

Transcriptional Profiling of Swine Lung Tissue after Experimental Infection with Actinobacillus pleuropneumoniae

Porcine pleuropneumonia is a highly contagious respiratory disease that causes great economic losses worldwide. In this study, we aimed to explore the underlying relationship between infection and injury by investigation of the whole porcine genome expression profiles of swine lung tissues post-inoculated with experimentally Actinobacillus pleuropneumoniae. Expression profiling experiments of the control group and the treatment group were conducted using a commercially available Agilent Porcine Genechip including 43,603 probe sets. Microarray analysis was conducted on profiles of lung from challenged versus non-challenged swine. We found 11,929 transcripts, identified as differentially expressed at the p ≤0.01 level. There were 1188 genes annotated as swine genes in the GenBank Data Base. GO term analysis identified a total of 89 biological process categories, 82 cellular components and 182 molecular functions that were significantly affected, and at least 27 biological process categories that were related to the host immune response. Gene set enrichment analysis identified 13 pathways that were significantly associated with host response. Many proinflammatory-inflammatory cytokines were activated and involved in the regulation of the host defense response at the site of inflammation; while the cytokines involved in regulation of the host immune response were suppressed. All changes of genes and pathways of induced or repressed expression not only led to a decrease in antigenic peptides presented to T lymphocytes by APCs via the MHC and alleviated immune response injury induced by infection, but also stimulated stem cells to produce granulocytes (neutrophils, eosinophils, and basophils) and monocyte, and promote neutrophils and macrophages to phagocytose bacterial and foreign antigen at the site of inflammation. The defense function of swine infection with Actinobacillus pleuropneumoniae was improved, while its immune function was decreased

Effects of antibacterial peptides on rumen fermentation function and rumen microorganisms in goats.

Although many studies have confirmed that antimicrobial peptides (AMPs: PBD-mI and LUC-n) can be used as feed additives, there are few reports of their use in ruminants. The present study aimed to investigate the impact of AMPs on ameliorating rumen fermentation function and rumen microorganisms in goats. Eighteen 4-month-old Chuanzhong black goats were used in a 60-day experiment (6 goats per group). Group I was used as the control and was fed a basal diet, the group II were fed the basal diet supplemented with 2 g of AMPs [per goat/day] and group III were fed the basal diet supplemented 3 g of AMPs [per goat/day], respectively. Rumen fluid samples were collected at 0, 20 and 60 days. Bacterial 16S rRNA genes and ciliate protozoal 18S rRNA genes were amplified by PCR from DNA extracted from rumen samples. The amplicons were sequenced by Illumina MiSeq. Rumen fermentation parameters and digestive enzyme activities were also examined. Our results showed that dietary supplementation with AMPs increased the levels of the bacterial genera Fibrobacter, Anaerovibrio and Succiniclasticum and also increased the ciliates genus Ophryoscolex, but reduced the levels of the bacterial genera Selenomonas, Succinivibrio and Treponema, and the ciliate genera Polyplastron, Entodinium, Enoploplastron and Isotricha. Supplementation with AMPs increased the activities of xylanase, pectinase and lipase in the rumen, and also increased the concentrations of acetic acid, propionic acid and total volatile fatty acids. These changes were associated with improved growth performance in the goats. The results revealed that the goats fed AMPs showed improved rumen microbiota structures, altered ruminal fermentation, and improved efficiency regarding the utilization of feed; thereby indicating that AMPs can improve growth performance. AMPs are therefore suitable as feed additives in juvenile goats

Transcriptional Profiling of Hilar Nodes from Pigs after Experimental Infection with Actinobacillus Pleuropneumoniae

The gram-negative bacterium Actinobacillus pleuropneumoniae (APP) is an inhabitant of the porcine upper respiratory tract and the causative agent of porcine pleuropneumonia (PP). In recent years, knowledge about the proinflammatory cytokine and chemokine gene expression that occurs in lung and lymph node of the APP-infected swine has been advanced. However, systematic gene expression profiles on hilar nodes from pigs after infection with Actinobacillus pleuropneumoniae have not yet been reported. The transcriptional responses were studied in hilar nodes (HN) from swine experimentally infected with APP and the control groupusing Agilent Porcine Genechip, including 43,603 probe sets. 9,517 transcripts were identified as differentially expressed (DE) at the p ≤ 0.01 level by comparing the log2 (normalized signal) of the two groups named treatment group (TG) and controls (CG). Eight hundred and fifteen of these DE transcripts were annotated as pig genes in the GenBank database (DB). Two hundred and seventy-two biological process categories (BP), 75 cellular components and 171 molecular functions were substantially altered in the TG compared to CG. Many BP were involved in host immune responses (i.e., signaling, signal transmission, signal transduction, response to stimulus, oxidation reduction, response to stress, immune system process, signaling pathway, immune response, cell surface receptor linked signaling pathway). Seven DE gene pathways (VEGF signaling pathway, Long-term potentiation, Ribosome, Asthma, Allograft rejection, Type I diabetes mellitus and Cardiac muscle contraction) and statistically significant associations with host responses were affected. Many cytokines (including NRAS, PI3K, MAPK14, CaM, HSP27, protein phosphatase 3, catalytic subunit and alpha isoform), mediating the proliferation and migration of endothelial cells and promoting survival and vascular permeability, were activated in TG, whilst many immunomodulatory cytokines were suppressed. The significant changes in the expression patterns of the genes, GO terms, and pathways, led to a decrease of antigenic peptides with antigen presenting cells presented to T lymphocytes via the major histocompatibility complex, and alleviated immune response induced APP of HN. The immune response ability of HN in the APP-infected pigs was weakened; however, cell proliferation and migration ability was enhanced