GenoMycAnalyzer: a web-based tool for species and drug resistance prediction for Mycobacterium genomes.

BACKGROUND: Drug-resistant tuberculosis (TB) is a major threat to global public health. Whole-genome sequencing (WGS) is a useful tool for species identification and drug resistance prediction, and many clinical laboratories are transitioning to WGS as a routine diagnostic tool. However, user-friendly and high-confidence automated bioinformatics tools are needed to rapidly identify M. tuberculosis complex (MTBC) and non-tuberculous mycobacteria (NTM), detect drug resistance, and further guide treatment options. RESULTS: We developed GenoMycAnalyzer, a web-based software that integrates functions for identifying MTBC and NTM species, lineage and spoligotype prediction, variant calling, annotation, drug-resistance determination, and data visualization. The accuracy of GenoMycAnalyzer for genotypic drug susceptibility testing (gDST) was evaluated using 5,473 MTBC isolates that underwent phenotypic DST (pDST). The GenoMycAnalyzer database was built to predict the gDST for 15 antituberculosis drugs using the World Health Organization mutational catalogue. Compared to pDST, the sensitivity of drug susceptibilities by the GenoMycAnalyzer for first-line drugs ranged from 95.9% for rifampicin (95% CI 94.8-96.7%) to 79.6% for pyrazinamide (95% CI 76.9-82.2%), whereas those for second-line drugs ranged from 98.2% for levofloxacin (95% CI 90.1-100.0%) to 74.9% for capreomycin (95% CI 69.3-80.0%). Notably, the integration of large deletions of the four resistance-conferring genes increased gDST sensitivity. The specificity of drug susceptibilities by the GenoMycAnalyzer ranged from 98.7% for amikacin (95% CI 97.8-99.3%) to 79.5% for ethionamide (95% CI 76.4-82.3%). The incorporated Kraken2 software identified 1,284 mycobacterial species with an accuracy of 98.8%. GenoMycAnalyzer also perfectly predicted lineages for 1,935 MTBC and spoligotypes for 54 MTBC. CONCLUSIONS: GenoMycAnalyzer offers both web-based and graphical user interfaces, which can help biologists with limited access to high-performance computing systems or limited bioinformatics skills. By streamlining the interpretation of WGS data, the GenoMycAnalyzer has the potential to significantly impact TB management and contribute to global efforts to combat this infectious disease. GenoMycAnalyzer is available at http://www.mycochase.org .

Evaluation of the BioFire® FilmArray® Pneumonia Panel with Conventional Bacterial Culture in Conjunction with Leukocyte Esterase Test.

We evaluated the performance of the BioFire® FilmArray® Pneumonia panel (PN-panel) in detecting bacterial pathogens by comparing it to cultures and to the usefulness of the leukocyte esterase (LE) urine strip test. Between January and June 2022, a total of 67 sputum specimens were obtained from community-acquired pneumonia patients. The PN-panel and LE test were performed simultaneously with conventional cultures. The pathogen detection rates of the PN-panel and culture were 40/67 (59.7%) and 25/67 (37.3%), respectively. The concordance rate between the PN-panel and culture was high (76.9%) when the bacterial burden was high (107 copies/mL), but it was low (8.6%) when it was 104-6 copies/mL, irrespective of the sputum quality. According to the LE positivity, the overall culture positive rate and PN-panel positive rate were significantly higher among the LE-positive specimens (23/45, 31/45) than among the LE-negative specimens (2/21, 8/21). Moreover, the difference in concordance rate between the PN-panel test and culture was significant according to the LE positivity, but not the Gram stain grading. In conclusion, the PN-panel showed high concordance when the bacterial burden was high (107 copies/mL) and ancillary use of LE test will be helpful in interpreting the PN-panel results, especially when the copy number of bacterial pathogens is low.

Low-temperature solution-processed SnO2 electron transport layer modified by oxygen plasma for planar perovskite solar cells.

SnO2 has attracted significant attention as an electron transport layer (ETL) because of its wide optical bandgap, electron mobility, and transparency. However, the annealing temperature of 180 °C-200 °C, as reported by several studies, for the fabrication of SnO2 ETL limits its application for flexible devices. Herein, we demonstrated that the low-temperature deposition of SnO2 ETL and further surface modification with oxygen plasma enhances its efficiency from 2.3% to 15.30%. Oxygen plasma treatment improves the wettability of the low-temperature processed SnO2 ETL that results in a larger perovskite grain size. Hence, oxygen plasma treatment effectively improves the efficiency of perovskite solar cells at a low temperature and is compatible with flexible applications.

Compact SnO2/Mesoporous TiO2 Bilayer Electron Transport Layer for Perovskite Solar Cells Fabricated at Low Process Temperature.

Charge transport layers have been found to be crucial for high-performance perovskite solar cells (PSCs). SnO2 has been extensively investigated as an alternative material for the traditional TiO2 electron transport layer (ETL). The challenges facing the successful application of SnO2 ETLs are degradation during the high-temperature process and voltage loss due to the lower conduction band. To achieve highly efficient PSCs using a SnO2 ETL, low-temperature-processed mesoporous TiO2 (LT m-TiO2) was combined with compact SnO2 to construct a bilayer ETL. The use of LT m-TiO2 can prevent the degradation of SnO2 as well as enlarge the interfacial contacts between the light-absorbing layer and the ETL. SnO2/TiO2 bilayer-based PSCs showed much higher power conversion efficiency than single SnO2 ETL-based PSCs.

Characterization of Silver Nanowire-Based Transparent Electrodes Obtained Using Different Drying Methods.

Metal-based transparent top electrodes allow electronic devices to achieve transparency, thereby expanding their application range. Silver nanowire (AgNW)-based transparent electrodes can function as transparent top electrodes, owing to their excellent conductivity and transmittance. However, they require a high-temperature drying process, which damages the bottom functional layers. Here, we fabricated two types of AgNW-based electrodes using the following three drying methods: thermal, room-temperature, and vacuum. Thereafter, we investigated the variation in their morphological, electrical, and optical characteristics as a function of the drying method and duration. When the AgNW-exposed electrode was dried at room temperature, it exhibited a high surface roughness and low conductivity, owing to the slow solvent evaporation. However, under vacuum, it exhibited a similar electrical conductivity to that achieved by thermal drying because of the decreased solvent boiling point and fast solvent evaporation. Conversely, the AgNW-embedded electrodes exhibited similar roughness values and electrical conductivities regardless of the drying method applied. This was because the polymer shrinkage during the AgNW embedding process generated capillary force and improved the interconnectivity between the nanowires. The AgNW-based electrodes exhibited similar optical properties regardless of the drying method and electrode type. This study reveals that vacuum drying can afford transparent top electrodes without damaging functional layers.

Enhanced Polymerization and Surface Hardness of Colloidal Siloxane Films via Electron Beam Irradiation.

Electron beam (EB) curing is a foldable hard coating process and has attracted significant research attention in the field of flexible electronic devices. In this study, we report a method for enhancing material surface hardness with low-energy EB curing in a short time. The low-energy EB improved the coating hardness of films by inducing cross-linking polymerization of the silicon-containing monomer. The hardness of the cured coating layer was measured as 3 H using a pencil hardness tester, and the transparency of the coating was higher than 90%. Owing to a series of cross-linking reactions between Si-O-C and Si-OH groups under EB curing and the formation of Si-Si bonds, the cured layer exhibited remarkable durability in the 100000-flexible cycle test. Additionally, the natural oxidation of the C-O groups on the surface of the coating formed carboxyl groups that improved the hydrophilic properties of the coating layer. To the best of our knowledge, this is the first study to propose that the hardness of polyethylene terephthalate films can be improved using low-energy EBs to rapidly cure silicon-containing coatings. Our results provide a novel and commercially viable approach for improving the hardness of touch screens and foldable displays.

Characterization of optical manipulation using microlens arrays depending on the materials and sizes in organic photovoltaics.

Various physical structures have improved light-harvesting and power-conversion efficiency in organic photovoltaic devices, and optical simulations have supported the improvement of device characteristics. Herein, we experimentally investigated how microlens arrays manipulate light propagation in microlens films and material stacks for organic photovoltaics to understand the influence of the constituent materials and sizes of the microlens. As materials to fabricate a microlens array, poly(dimethylsiloxane) and Norland Optical Adhesive 63 were adopted. The poly(dimethylsiloxane) microlens array exhibited higher total transmittance and higher diffuse transmittance, further enhancing the effective optical path and light extinction in material stacks for organic photovoltaics. This resulted in more current generation in an organic photovoltaic device with a poly(dimethylsiloxane) microlens array than in a Norland Optical Adhesive 63 microlens array. The sizes of the microlenses were controlled from 0.5 to 10 µm. The optical characteristics of microlens array films and material stacks with microlenses generally increased with size of the microlens, leading to a 10.6% and 16.0% improvement in the light extinction and power-conversion efficiency, respectively. In addition, electron and current generation in material stacks for organic photovoltaics were calculated from light extinction. The theoretical current generation matched well with experimental values derived from organic photovoltaic devices. Thus, the optical characterization of physical structures helps to predict how much more current can be generated in organic photovoltaic cells with a certain physical structure; it can also be used for screening the physical structures of organic photovoltaic cells.

Effect of Low-Pressure Plasma Treatment Parameters on Wrinkle Features.

Wrinkles attract significant attention due to their ability to enhance the mechanical and optical characteristics of various optoelectronic devices. We report the effect of the plasma gas type, power, flow rate, and treatment time on the wrinkle features. When an optical adhesive was treated using a low-pressure plasma of oxygen, argon, and nitrogen, the oxygen and argon plasma generated wrinkles with the lowest and highest wavelengths, respectively. The increase in the power of the nitrogen and oxygen plasma increased the wavelengths and heights of the wrinkles; however, the increase in the power of the argon plasma increased the wavelengths and decreased the heights of the wrinkles. Argon molecules are heavier and smaller than nitrogen and oxygen molecules that have similar weights and sizes; moreover, the argon plasma comprises positive ions while the oxygen and nitrogen plasma comprise negative ions. This resulted in differences in the wrinkle features. It was concluded that a combination of different plasma gases could achieve exclusive control over either the wavelength or the height and allow a thorough analysis of the correlation between the wrinkle features and the characteristics of the electronic devices.

Enhancement of Antibacterial Performance of Silver Nanowire Transparent Film by Post-Heat Treatment.

Silver nanomaterials (AgNMs) have been applied as antibacterial agents to combat bacterial infections that can cause disease and death. The antibacterial activity of AgNMs can be improved by increasing the specific surface area, so significant efforts have been devoted to developing various bottom-up synthesis methods to control the size and shape of the particles. Herein, we report on a facile heat-treatment method that can improve the antibacterial activity of transparent silver nanowire (AgNW) films in a size-controllable, top-down manner. AgNW films were fabricated via spin-coating and were then heated at different temperatures (230 and 280 °C) for 30 min. The morphology and the degree of oxidation of the as-fabricated AgNW film were remarkably sensitive to the heat-treatment temperature, while the transparency was insensitive. As the heat-treatment temperature increased, the AgNWs spontaneously broke into more discrete wires and droplets, and oxidation proceeded faster. The increase in the heat-treatment temperature further increased the antibacterial activity of the AgNW film, and the heat treatment at 280 °C improved the antibacterial activity from 31.7% to 94.7% for Staphylococcus aureus, and from 57.0% to 98.7% for Escherichia coli. Following commonly accepted antibacterial mechanisms of AgNMs, we present a correlation between the antibacterial activity and surface observations of the AgNW film.

Surface Engineering of Low-Temperature Processed Mesoporous TiO2 via Oxygen Plasma for Flexible Perovskite Solar Cells.

A major problem in the application of mesoporous TiO2 as an electron transport layer for flexible perovskite solar cells is that a high-temperature sintering process is required to remove organic additives from the TiO2 layer. A facile oxygen plasma process is herein demonstrated to fabricate mesoporous-structured perovskite solar cells with significant photovoltaic performance at low temperatures. When the low-temperature processed TiO2 layer is modified via oxygen plasma, the organic additives in the TiO2 layer that hinder the charge transport process are successfully decomposed. The oxygen plasma treatment improves the wettability and infiltration of the perovskite layer and also passivates the oxygen vacancy related traps in TiO2. Hence, the oxygen plasma treatment evidently enhances charge extraction and transport, thereby improving photovoltaic performance and decreasing hysteresis.

Enhancement of Antibacterial Properties of a Silver Nanowire Film via Electron Beam Irradiation.

Infectious diseases and the deaths caused due to contact with germ-contaminated surfaces are severe problems worldwide. Antibacterial materials based on silver nanowires (AgNWs) have a structural advantage when addressing this issue; this is because agglomeration is minimized when nanowires are fabricated into a film. Therefore, employing AgNWs for antimicrobial applications has garnered continuous interest, and increased research for further improvements has been observed. In this study, a AgNW film was fabricated onto glass by spin-coating and then subjected to surface irradiation up to a dose of 1200 kGy, using a low-energy electron beam (e-beam). This "e-beam" irradiation changed the surface morphology and chemical composition; consequently, this improved the performance of the film. The generation of a silver oxide (Ag2O and AgO) outer layer was identified over the AgNWs by X-ray photoelectron spectroscopy (XPS). The antibacterial test corresponding to a contact time of 1 h revealed that the e-beam irradiation increased the antibacterial activity in the log reduction from 1.2 to 1.4 for Staphylococcus aureus and from 1.5 to 3.7 for Escherichia coli. Based on the experimental results and the known antibacterial mechanisms of silver (Ag) nanospecies, we discuss the method by which the antibacterial performance of the AgNW film was improved via the e-beam irradiation. This work provides a simple and swift method to functionally enhance the AgNW antibacterial film via e-beam irradiation.

Facile Interfacial Engineering of Mesoporous TiO2 for Low-Temperature Processed Perovskite Solar Cells.

The mesoporous TiO2 nanoparticle-based scaffold structure is the best electron transport layer (ETL) for perovskite solar cells (PSCs) and is still used in most PSCs with optimal photovoltaic characteristics. However, the high sintering temperature of TiO2 nanoparticles required to remove binders from the TiO2 paste limits PSC application to flexible electronics. In this study, a simple interface modification process involving ethanol rinsing is developed to enhance the photovoltaic characteristics of low-temperature processed PSCs. This easy and fast technique could enable remarkable performance by PSCs by significantly increasing the fill factor and current density, leading to a power conversion efficiency more than four times that of untreated solar cells.

Effect of Ultraviolet-Ozone Treatment on the Properties and Antibacterial Activity of Zinc Oxide Sol-Gel Film.

To combat infectious diseases, zinc oxide (ZnO) has been identified as an effective antibacterial agent; however, its performance can be adversely affected by harsh application environments. The ozone impact on ZnO antibacterial film needs to be evaluated prior to its application in an ozone disinfection system. In this study, ZnO films synthesized via sol-gel/spin-coating were subjected to ultraviolet-ozone (UVO) treatment for different periods. Surface investigations using scanning electron microscopy, ultraviolet-visible spectroscopy, and X-ray photoelectron spectroscopy revealed that the treatment-induced film changes. With longer UVO treatment, the surface porosity of the film gradually increased from 5% to 30%, causing the transmittance reduction and absorbance increase in visible-light range. Phase transformation of Zn(OH)2 to ZnO occurred during the first 10 min of UVO treatment, followed by oxygen uptake as a consequence of the reaction with reactive oxygen species generated during UVO treatment. However, despite these surface changes, the satisfactory antibacterial activity of the synthesized ZnO film against Staphylococcus aureus and Escherichia coli was sustained even after 120 min of UVO treatment. This indicates that the UVO-induced surface changes do not have a significant effect on the antibacterial performance and that the ZnO sol-gel film possesses good functional durability in ozone environments.

Enhancing Thermal Oxidation Stability of Silver Nanowire Transparent Electrodes by Using a Cesium Carbonate-Incorporated Overcoating Layer.

Despite their excellent electrical and optical properties, Ag nanowires (NWs) suffer from oxidation when exposed to air for several days. In this study, we synthesized a Cs carbonate-incorporated overcoating layer by spin-coating and ultraviolet curing to prevent the thermal oxidation of Ag NWs. Cs incorporation increased the decomposition temperature of the overcoating layer, thus enhancing its thermal resistance. The effects of the Cs carbonate-incorporated overcoating layer on the optoelectrical properties and stability of Ag NWs were investigated in detail. The Ag NW electrode reinforced with the Cs carbonate-incorporated overcoating layer exhibited excellent thermal oxidation stability after exposure to air for 55 days at 85 °C and a relative humidity of 85%. The novel overcoating layer synthesized in this study is a promising passivation layer for Ag NWs against thermal oxidation under ambient conditions. This overcoating layer can be applied in large-area optoelectronic devices based on Ag NW electrodes.

Spray Deposition of Ag Nanowire⁻Graphene Oxide Hybrid Electrodes for Flexible Polymer⁻Dispersed Liquid Crystal Displays.

We investigated the effect of different spray-coating parameters on the electro-optical properties of Ag nanowires (NWs). Highly transparent and conductive Ag NW⁻graphene oxide (GO) hybrid electrodes were fabricated by using the spray-coating technique. The Ag NW percolation network was modified with GO and this led to a reduced sheet resistance of the Ag NW⁻GO electrode as the result of a decrease in the inter-nanowire contact resistance. Although electrical conductivity and optical transmittance of the Ag NW electrodes have a trade-off relationship, Ag NW⁻GO hybrid electrodes exhibited significantly improved sheet resistance and slightly decreased transmittance compared to Ag NW electrodes. Ag NW⁻GO hybrid electrodes were integrated into smart windows based on polymer-dispersed liquid crystals (PDLCs) for the first time. Experimental results showed that the electro-optical properties of the PDLCs based on Ag NW⁻GO electrodes were superior when compared to those of PDLCs based on only Ag NW electrodes. This study revealed that the hybrid Ag NW⁻GO electrode is a promising material for manufacturing the large-area flexible indium tin oxide (ITO)-free PDLCs.

Hybrid Ag nanowire transparent conductive electrodes with randomly oriented and grid-patterned Ag nanowire networks.

To improve the electrical properties of silver nanowire (Ag NW) transparent conductive electrodes (TCEs), the density of Ag NW networks should be increased, to increase the number of percolation paths. However, because of the inverse relationship between optical transmittance and electrical resistivity, the optical properties of Ag NW TCEs deteriorate with increasing density of the Ag NW network. In this study, a hybrid Ag NW electrode composed of randomly oriented and grid-patterned Ag NW networks is demonstrated. The hybrid Ag NW electrodes exhibit significantly improved sheet resistances and slightly decreased transmittances compared to randomly oriented Ag NW networks. Hybrid Ag NW TCEs show excellent mechanical flexibilities and durabilities in bending tests with a 5 mm radius of curvature. Moreover, flexible transparent film heaters (TFHs) based on the hybrid Ag NW electrodes show elevated maximum temperatures relative to TFHs based on randomly oriented Ag NW electrodes, when operated at the same input voltages.

Cross-buckled structures for stretchable and compressible thin film silicon solar cells.

Increasing interests in stretchable electronic devices have resulted in vigorous research activities, most of which are focused on structural configurations. Diverse structural configurations are available for stretchability, including stiff-island, serpentine, and buckled structures. With easily deformable shapes and simple fabrication processes, buckled structures have the potential to realize stretchability. However, conventional buckled structures exhibit stretchability only in a single-axis direction. In the present study, a new type of cross-buckled structure, which can overcome the limitations of conventional buckled structures is developed. The stretchable thin film solar cells with the cross-buckled structure showed stable mechanical and electrical characteristics under both stretching and compressing conditions. The cross-buckled structure for stretchable electronic devices is expected to broaden the fields of wearable electronics, stretchable displays, and biocompatible applications.

Ultrasmooth, extremely deformable and shape recoverable Ag nanowire embedded transparent electrode.

Transparent electrodes have been widely used in electronic devices such as solar cells, displays, and touch screens. Highly flexible transparent electrodes are especially desired for the development of next generation flexible electronic devices. Although indium tin oxide (ITO) is the most commonly used material for the fabrication of transparent electrodes, its brittleness and growing cost limit its utility for flexible electronic devices. Therefore, the need for new transparent conductive materials with superior mechanical properties is clear and urgent. Ag nanowire (AgNW) has been attracting increasing attention because of its effective combination of electrical and optical properties. However, it still suffers from several drawbacks, including large surface roughness, instability against oxidation and moisture, and poor adhesion to substrates. These issues need to be addressed before wide spread use of metallic NW as transparent electrodes can be realized. In this study, we demonstrated the fabrication of a flexible transparent electrode with superior mechanical, electrical and optical properties by embedding a AgNW film into a transparent polymer matrix. This technique can produce electrodes with an ultrasmooth and extremely deformable transparent electrode that have sheet resistance and transmittance comparable to those of an ITO electrode.

Loss of Heterozygosities in Five Tumor Suppressor Genes (FHIT Gene, p16, pRb, E-Cadherin and p53) in Thyroid Tumors.

OBJECTIVES: To evaluate the loss of heterozygosities (LOH) of chromosomes 3p14 (FHIT gene), 9p21 (p16), 13q21 (pRb), 6q22 (E-cadherin) and 17p13 (p53) in various thyroid tumors. METHODS: Eighty thyroid tumor cases (20 follicular adenomas, 10 follicular carcinomas, and 50 papillary carcinomas) have been analyzed for the presence of LOH in chromosomes 3p14, 9p21, 13q21, 6q22, and 17p13 allelic loss, using microsatellite markers and DNA obtained from formalin-fixed paraffin-embedded archival tissues. RESULTS: LOH on 3p14 was found in 10.5%, 33.3%, and 30.4% of follicular adenomas, follicular carcinomas, and papillary carcinomas, respectively. LOH on 9p21 was detected in 6%, 44.4%, and 47.8%, respectively. LOH on pRb gene was found in 5.3%, 20.0%, and 35.4%, respectively. LOH on E-cadherin gene was found in 5.3%, 22.2%, and 43.8%, respectively. LOH on 17p13 was detected in 0%, 40%, and 45.8%, respectively. LOH in FHIT gene, p16, pRb, E-cadherin, and p53 genes were more frequently identified in follicular carcinoma and papillary carcinoma than in follicular adenoma. CONCLUSION: LOH results of the five tumor suppressor genes (FHIT gene, p16, pRb, E-cadherin, and p53) showed statistical differences between benign tumor and malignant tumor. Among papillary carcinoma, LOH in p16, E-cadherin and p53 genes well correlated with poorly differentiated grade, and LOH of E-cadherin was associated with lymph node metastasis.

Loss of heterozygosity of tumor suppressor genes (p16, Rb, E-cadherin, p53) in hypopharynx squamous cell carcinoma.

OBJECTIVE: Microsatellite alterations, especially those that cause loss of heterozygosity (LOH), have recently been postulated as a novel mechanism of carcinogenesis and a useful prognostic factor in many kinds of malignant tumors. However, few studies have focused on a specific site, hypopharynx. The aim of this study was to evaluate the relationship between LOH and hypopharyngeal squamous cell carcinoma (HPSCC). STUDY DESIGN: Laboratory-based study. SETTING: Integrated health care system. SUBJECTS AND METHODS: Matched normal and cancerous tissues from 30 patients with HPSCC were examined for LOH in 4 tumor suppressor genes (TSGs) (p16, Rb, E-cadherin, and p53) at loci 9p21, 13q21, 6q22, and 17p13, respectively, using microsatellite markers amplified by polymerase chain reaction. The results for each loci were compared with clinicopathological features. RESULTS: Among the 30 cases, 26 (86.7%) exhibited LOH, with the most common alteration being LOH at p53 (52.6%). Significantly higher rates of LOH detection were seen in Rb, p53, and the LOH-high group (cases where 2 or more loci with LOH were found) in cases of lymph node metastasis. Compared with stage I and II carcinoma, tumors of stages III and IV had significantly higher frequencies of LOH in Rb, p53, and the LOH-high group. However, the presence of LOH was not significantly correlated with survival. CONCLUSION: These results suggest that LOH in TSGs such as Rb and p53 may contribute to the development and progression of HPSCC. The presence of LOH in the primary tumor may also be predictive of lymph node metastasis.