Continuum sensitivity and design optimization of superconducting systems under critical current densities with magnetic field dependence

Funder: sungkyunkwan university; doi: http://dx.doi.org/10.13039/501100002647AbstractThis paper presents an approach for deriving the continuum sensitivity of superconducting systems operating at critical current densities and an optimization method based on the continuum sensitivity. In the sensitivity problem, the superconducting systems is represented by a variational state equation, wherein the magnetic permeability depends on the magnetic field, which is transformed from a state equation with a field-dependent source. The design sensitivity is derived using the material derivative concept of continuum mechanics and the adjoint variable method. The adjoint system has a material property represented as a symmetric tensor that contains the sensitivity of the current density with respect to the magnetic field. The design sensitivity is represented in the analytical form of a surface integral on the interface between the superconducting material and its surroundings, which depends on the sensitivity of the current density. The optimization scheme is constructed based on the continuum design sensitivity. In the design optimization, the level set method is used to express the shape variation of the superconducting materials. The numerical example of infinite solenoids demonstrates that the design sensitivity provides an accurate design solution considering the critical current condition. In addition, the design example of a magnetic resonance imaging solenoid shows that the derived design sensitivity has the inherent ability for attaining the compact design by treating the input current of a superconducting system as a critical condition.</jats:p

Genome-wide analysis of ivermectin response by Onchocerca volvulus reveals that genetic drift and soft selective sweeps contribute to loss of drug sensitivity

Treatment of onchocerciasis using mass ivermectin administration has reduced morbidity and transmission throughout Africa and Central/South America. Mass drug administration is likely to exert selection pressure on parasites, and phenotypic and genetic changes in several Onchocerca volvulus populations from Cameroon and Ghana-exposed to more than a decade of regular ivermectin treatment-have raised concern that sub-optimal responses to ivermectin's anti-fecundity effect are becoming more frequent and may spread.Pooled next generation sequencing (Pool-seq) was used to characterise genetic diversity within and between 108 adult female worms differing in ivermectin treatment history and response. Genome-wide analyses revealed genetic variation that significantly differentiated good responder (GR) and sub-optimal responder (SOR) parasites. These variants were not randomly distributed but clustered in ~31 quantitative trait loci (QTLs), with little overlap in putative QTL position and gene content between the two countries. Published candidate ivermectin SOR genes were largely absent in these regions; QTLs differentiating GR and SOR worms were enriched for genes in molecular pathways associated with neurotransmission, development, and stress responses. Finally, single worm genotyping demonstrated that geographic isolation and genetic change over time (in the presence of drug exposure) had a significantly greater role in shaping genetic diversity than the evolution of SOR.This study is one of the first genome-wide association analyses in a parasitic nematode, and provides insight into the genomics of ivermectin response and population structure of O. volvulus. We argue that ivermectin response is a polygenically-determined quantitative trait (QT) whereby identical or related molecular pathways but not necessarily individual genes are likely to determine the extent of ivermectin response in different parasite populations. Furthermore, we propose that genetic drift rather than genetic selection of SOR is the underlying driver of population differentiation, which has significant implications for the emergence and potential spread of SOR within and between these parasite populations

Identification of Novel Avian Influenza Virus Derived CD8+ T-Cell Epitopes

Avian influenza virus (AIV) infection is a continuing threat to both humans and poultry. Influenza virus specific CD8+ T cells are associated with protection against homologous and heterologous influenza strains. In contrast to what has been described for humans and mice, knowledge on epitope-specific CD8+ T cells in chickens is limited. Therefore, we set out to identify AIV-specific CD8+ T-cell epitopes. Epitope predictions based on anchor residues resulted in 33 candidate epitopes. MHC I inbred chickens were infected with a low pathogenic AIV strain and sacrificed at 5, 7, 10 and 14 days post infection (dpi). Lymphocytes isolated from lung, spleen and blood were stimulated ex vivo with AIV-specific pooled or individual peptides and the production of IFNγ was determined by ELIspot. This resulted in the identification of 12 MHC B12-restricted, 3 B4-restricted and 1 B19-restricted AIV- specific CD8+ T-cell epitopes. In conclusion, we have identified novel AIV-derived CD8+ T-cell epitopes for several inbred chicken strains. This knowledge can be used to study the role of CD8+ T cells against AIV infection in a natural host for influenza, and may be important for vaccine development

IL23 and TGF-ß diminish macrophage associated metastasis in pancreatic carcinoma

Abstract The precise role of tumor associated macrophages remains unclear in pancreatic ductal adenocarcinoma (PDAC) while TGF-ß has an unclear role in metastases formation. In order to understand the role of IL23, an interleukin associated with macrophage polarization, we investigated IL23 in the context of TGF-ß expression in PDAC. We hypothesized that IL23 expression is associated with metastatic development and survival in PDAC. We investigated IL23 and TGF-ß protein expression on resected PDAC patient tumor sections who were divided into short-term (30 months) survivors. Panc-1 cells treated with IL23, TGF-ß, macrophages, or combinations thereof, were orthotopically implanted into NSG mice. Patients in the long-term survivor group had higher IL23 protein expression (P = 0.01). IL23 expression was linearly correlated with TGF-ß expression in patients in the short-term survivor group (P = 0.038). Macrophages induce a higher rate of PDAC metastasis in the mouse model (P = 0.02), which is abrogated by IL23 and TGF-ß treatment (P < 0.001). Macrophages serve a critical role in PDAC tumor growth and metastasis. TGF-ß contributes to a less tumorigenic TME through regulation of macrophages. Macrophages increases PDAC primary tumor growth and metastases formation while combined IL23 and TGF-ß pre-treatment diminishes these processes

Virtual Screening of Bioassay Data

Background: There are three main problems associated with the virtual screening of bioassay data. The first is access to freely-available curated data, the second is the number of false positives that occur in the physical primary screening process, and finally the data is highly-imbalanced with a low ratio of Active compounds to Inactive compounds. This paper first discusses these three problems and then a selection of Weka cost-sensitive classifiers (Naive Bayes, SVM, C4.5 and Random Forest) are applied to a variety of bioassay datasets. Results: Pharmaceutical bioassay data is not readily available to the academic community. The data held at PubChem is not curated and there is a lack of detailed cross-referencing between Primary and Confirmatory screening assays. With regard to the number of false positives that occur in the primary screening process, the analysis carried out has been shallow due to the lack of crossreferencing mentioned above. In six cases found, the average percentage of false positives from the High-Throughput Primary screen is quite high at 64%. For the cost-sensitive classification, Weka's implementations of the Support Vector Machine and C4.5 decision tree learner have performed relatively well. It was also found, that the setting of the Weka cost matrix is dependent on the base classifier used and not solely on the ratio of class imbalance. Conclusions: Understandably, pharmaceutical data is hard to obtain. However, it would be beneficial to both the pharmaceutical industry and to academics for curated primary screening and corresponding confirmatory data to be provided. Two benefits could be gained by employing virtual screening techniques to bioassay data. First, by reducing the search space of compounds to be screened and secondly, by analysing the false positives that occur in the primary screening process, the technology may be improved. The number of false positives arising from primary screening leads to the issue of whether this type of data should be used for virtual screening. Care when using Weka's cost-sensitive classifiers is needed - across the board misclassification costs based on class ratios should not be used when comparing differing classifiers for the same dataset

A novel repeat sequence-based PCR (rep-PCR) using specific repeat sequences of Mycobacterium intracellulare as a DNA fingerprinting

Repetitive sequence-based PCR (rep-PCR) is a potential epidemiological technique that can provide high-throughput genotype fingerprints of heterogeneous Mycobacterium strains rapidly. Previously published rep-PCR primers, which are based on nucleotide sequences of Gram-negative bacteria may have low specificity for mycobacteria. Moreover, it was difficult to ensure the continuity of the study after the commercial rep-PCR kit was discontinued. Here, we designed a novel rep-PCR for Mycobacterium intracellulare, a major cause of nontuberculous mycobacterial pulmonary disease with frequent recurrence. We screened the 7,645 repeat sequences for 200 fragments from the genome of M. intracellulare ATCC 13950 in silico, finally generating five primers with more than 90% identity for a total of 226 loci in the genome. The five primers could make different band patterns depending on the genome of three different M. intracellulare strains using an in silico test. The novel rep-PCR with the five primers was conducted using 34 bacterial samples of 7 species containing 25 M. intracellulare clinical isolates, compared with previous published rep-PCRs. This shows distinguished patterns depending on species and blotting assay for 6 species implied the sequence specificity of the five primers. The Designed rep-PCR had a 95–98% of similarity value in the reproducibility test and showed 7 groups of fingerprints in M. intracellulare strains. Designed rep-PCR had a correlation value of 0.814 with VNTR, reference epidemiological method. This study provides a promising genotype fingerprinting method for tracing the recurrence of heterogeneous M. intracellulare

A Putative Transcription Factor MYT1 Is Required for Female Fertility in the Ascomycete Gibberella zeae

Gibberella zeae is an important pathogen of major cereal crops. The fungus produces ascospores that forcibly discharge from mature fruiting bodies, which serve as the primary inocula for disease epidemics. In this study, we characterized an insertional mutant Z39P105 with a defect in sexual development and identified a gene encoding a putative transcription factor designated as MYT1. This gene contains a Myb DNA-binding domain and is conserved in the subphylum Pezizomycotina of Ascomycota. The MYT1 protein fused with green fluorescence protein localized in nuclei, which supports its role as a transcriptional regulator. The MYT1 deletion mutant showed similar phenotypes to the wild-type strain in vegetative growth, conidia production and germination, virulence, and mycotoxin production, but had defect in female fertility. A mutant overexpressing MYT1 showed earlier germination, faster mycelia growth, and reduced mycotoxin production compared to the wild-type strain, suggesting that improper MYT1 expression affects the expression of genes involved in the cell cycle and secondary metabolite production. This study is the first to characterize a transcription factor containing a Myb DNA-binding domain that is specific to sexual development in G. zeae