A comparison of phenotypic and WGS drug susceptibility testing in Mycobacterium tuberculosis isolates from the Republic of Korea

BACKGROUND: WGS has significant potential to help tackle the major public health problem of TB. The Republic of Korea has the third highest rates of TB of all Organisation for Economic Cooperation and Development countries but there has been very limited use of WGS in TB to date. OBJECTIVES: A retrospective comparison of Mycobacterium tuberculosis (MTB) clinical isolates from 2015 to 2017 from two centres in the Republic of Korea using WGS to compare phenotypic drug susceptibility testing (pDST) and WGS drug susceptibility predictions (WGS-DSP). METHODS: Fifty-seven MTB isolates had DNA extracted and were sequenced using the Illumina HiSeq platform. The WGS analysis was performed using bwa mem, bcftools and IQ-Tree; resistance markers were identified using TB profiler. Phenotypic susceptibilities were carried out at the Supranational TB reference laboratory (Korean Institute of Tuberculosis). RESULTS: For first-line antituberculous drugs concordance for rifampicin, isoniazid, pyrazinamide and ethambutol was 98.25%, 92.98%, 87.72% and 85.96%, respectively. The sensitivity of WGS-DSP compared with pDST for rifampicin, isoniazid, pyrazinamide and ethambutol was 97.30%, 92.11%, 78.95% and 95.65%, respectively. The specificity for these first-line antituberculous drugs was 100%, 94.74%, 92.11% and 79.41%, respectively. The sensitivity and specificity for second-line drugs ranged from 66.67% to 100%, and from 82.98% to 100%, respectively. CONCLUSIONS: This study confirms the potential role for WGS in drug susceptibility prediction, which would reduce turnaround times. However, further larger studies are needed to ensure current databases of drug resistance mutations are reflective of the TB present in the Republic of Korea

Enhanced Immunogenicity of Engineered HER2 Antigens Potentiates Antitumor Immune Responses

For cancer vaccines, the selection of optimal tumor-associated antigens (TAAs) that can maximize the immunogenicity of the vaccine without causing unwanted adverse effects is challenging. In this study, we developed two engineered Human epidermal growth factor receptor 2 (HER2) antigens, K965 and K1117, and compared their immunogenicity to a previously reported truncated HER2 antigen, K684, within a B cell and monocyte-based vaccine (BVAC). We found that BVAC-K965 and BVAC-K1117 induced comparable antigen-specific antibody responses and antigen-specific T cell responses to BVAC-K684. Interestingly, BVAC-K1117 induced more potent antitumor activity than the other vaccines in murine CT26-HER2 tumor models. In addition, BVAC-K1117 showed enhanced antitumor effects against truncated p95HER2-expressing CT26 tumors compared to BVAC-K965 and BVAC-K684 based on the survival analysis by inducing T cell responses against intracellular domain (ICD) epitopes. The increased ICD epitope-specific T cell responses induced by BVAC-K1117 compared to BVAC-K965 and BVAC-K684 were recapitulated in human leukocyte antigen (HLA)-untyped human PBMCs and HLA-A*0201 PBMCs. Furthermore, we also observed synergistic antitumor effects between BVAC-K1117 and anti-PD-L1 antibody treatment against CT26-HER2 tumors. Collectively, our findings demonstrate that inclusion of a sufficient number of ICD epitopes of HER2 in cellular vaccines can improve the antitumor activity of the vaccine and provide a way to optimize the efficacy of anticancer cellular vaccines targeting HER2.Y

Evaluation of Positive and Negative Methods for Isolation of Circulating Tumor Cells by Lateral Magnetophoresis

We developed an epithelial cell adhesion molecule (EpCAM)-based positive method and CD45/CD66b-based negative method for isolating circulating tumor cells (CTCs) by lateral magnetophoresis. The CTC recovery rate, white blood cell depletion rate, and purity of CTCs isolated using the positive and negative methods were analyzed using blood samples spiked with cancer cells with different expression levels of EpCAM. The aim was to assess the strengths and weaknesses of the positive and negative isolation methods for CTC-based diagnostics, prognostics, and therapeutics for cancer. The EpCAM-based positive method yielded CTCs of high purity, while the CD45/CD66b-based negative method yielded a large number of CTCs. In conclusion, the positive method shows promise for detecting somatic oncogenic mutations and the negative method shows promise for discovery of cellular and transcriptomic biomarkers of cancer

Firewall ruleset visualization analysis tool based on segmentation

Although most companies operate a firewall to protect their information assets, they have difficulties in identifying the control conditions of firewalls. This study proposes an analysis tool to visualize segment-based firewall rules to facilitate verification of the current control conditions. The proposed visualization tool analyzes the current control conditions of packets automatically, thereby eliminating the need for manual inspection as before, and displays the conditions with a visualization model to allow them to be easily verified. This enables managers to perform fast and accurate verification to assess whether packets are allowed or denied. This present study involved implementing the proposed visualization tool, and simulations were conducted to verify that the proposed approach was achievable. The present study also included conducting interviews with firewall experts whose feedback was positive. A video of the proposed visualization tool can be found on the following web site: https://youtu.be/q4HMnBvXbk

Bin2Vec: A Better Wafer Bin Map Coloring Scheme for Comprehensible Visualization and Effective Bad Wafer Classification

A wafer bin map (WBM), which is the result of an electrical die-sorting test, provides information on which bins failed what tests, and plays an important role in finding defective wafer patterns in semiconductor manufacturing. Current wafer inspection based on WBM has two problems: good/bad WBM classification is performed by engineers and the bin code coloring scheme does not reflect the relationship between bin codes. To solve these problems, we propose a neural network-based bin coloring method called Bin2Vec to make similar bin codes are represented by similar colors. We also build a convolutional neural network-based WBM classification model to reduce the variations in the decisions made by engineers with different expertise by learning the company-wide historical WBM classification results. Based on a real dataset with a total of 27,701 WBMs, our WBM classification model significantly outperformed benchmarked machine learning models. In addition, the visualization results of the proposed Bin2Vec method makes it easier to discover meaningful WBM patterns compared with the random RGB coloring scheme. We expect the proposed framework to improve both efficiencies by automating the bad wafer classification process and effectiveness by assigning similar bin codes and their corresponding colors on the WBM

Investigation of thermal degradation with extrusion-based dispensing modules for 3D bioprinting technology

Recently, numerous three-dimensional (3D) bioprinting systems have been introduced for the artificial regeneration of tissues. Among them, the extrusion-based dispensing module is the most widely used because of the processability it gives various biomaterials. The module uses high forces and temperature to dispense materials through a micro-nozzle. Generally, the harsh conditions induce thermal degradation of the material in the dispensing procedure. The thermal degradation affects the properties of the materials, and the change of the properties should be carefully controlled, because it severely affects the regeneration of tissues. Therefore, in this research, the relationship between the dispensing module and the thermal degradation of material was investigated. Extrusion-based dispensing modules can be divided into the syringe type (ST) and filament type (FT) based on working principles. We prepared a poly lactic-co-glycolic acid (PLGA) scaffold with the two methods at various time points. Then, the characteristics of the printed scaffolds were assessed by measuring molecular weight (M-w), glass transition temperature (T-g), in vitro degradation, compressive modulus, and cytocompatibility. The results showed that the PLGA scaffold with the FT dispensing module maintained its properties regardless of printing time points. In contrast, severe thermal degradation was observed in the scaffold group prepared by the ST dispensing module. Consequentially, it was obvious that the FT dispensing module was more suitable for producing scaffolds without severe thermal degradation.clos

Roles of NKT cells in cancer immunotherapy

Cancer immunotherapy has emerged as an effective therapeutic strategy to treat cancer. Among diverse immune populations, invariant natural killer T (iNKT) cells have shown potent antitumor activity by linking innate and adaptive immune systems. Upon activation by lipid antigens on CD1d molecules, iNKT cells rapidly produce various cytokines and trigger antitumor immunity directly or indirectly by activating other antitumor immune cells. Administration of a representative iNKT cell ligand alpha-galactosylceramide (-GalCer) or -GalCer-pulsed APCs effectively stimulates iNKT cells and thereby induces antitumor effects. In this review, we will introduce the biology and importance of NKT cells in antitumor immunity. Previous studies have demonstrated that iNKT cells not only activate various immune cells but also reinvigorate exhausted immune cells in the tumor microenvironment. Furthermore, we will summarize the major clinical trials utilizing iNKT-based immunotherapies.N