Quantification of airway structures by persistent homology.

We propose two types of novel morphological metrics for quantifying the geometry of tubular structures on computed tomography (CT) images. We apply our metrics to identify irregularities in the airway of patients with chronic obstructive pulmonary disease (COPD) and demonstrate that they provide complementary information to the conventional metrics used to assess COPD, such as the tissue density distribution in lung parenchyma and the wall area ratio of the segmented airway. The three-dimensional shape of the airway and its abstraction as a rooted tree with the root at the trachea carina are automatically extracted from a lung CT volume, and the two metrics are computed based on a mathematical tool called persistent homology; treeH0 quantifies the distribution of branch lengths to assess the complexity of the tree-like structure and radialH0 quantifies the irregularities in the luminal radius along the airway. We show our metrics are associated with clinical outcomes.

Insight into Scattering Mechanisms and Transport Properties of AgCuS for Flexible Thermoelectric Applications.

The development of flexible thermoelectric devices requires materials possessing ductility and high thermoelectric performance at room temperature. However, only a few existing materials meet both criteria. In this study, the ductile properties, electronic structure, and transport properties of the low-temperature phase α-AgCuS were elucidated using first-principles calculations combined with Boltzmann transport theory. With a layered zigzag structure similar to the well-known ductile semiconductor Ag2S, AgCuS is determined to have good metal-like ductility. Through consideration of various intrinsic scattering mechanisms, we found that electron-polar optical phonon interactions have the most significant impact on the transport behavior of AgCuS. The predominance of this type of interaction is also disclosed by the covalent-ionic bonding nature of the Ag-S and Cu-S bonds. Therefore, weakening this interaction via doping or alloying could optimize the thermoelectric performance of the system. At room temperature, a maximum dimensionless figure of merit ZT of up to 0.592 could be achieved under a tuning of hole concentration to 2 × 1019 cm-3, suggesting that α-AgCuS could be a promising p-type candidate for flexible thermoelectric applications.

Changes in oral pathology teaching methods during the COVID-19 pandemic and the impact on student performance (oral pathology teaching changes during the COVID-19 pandemic).

Abstract Background/purpose: Coronavirus disease 2019 (COVID-19) has influenced the dental education in Osaka Dental University. The purpose of this study was to summarize the impact of COVID-19 on student performance and the current more appropriate teaching methods by comparing the changes in various oral pathology exam results before and after COVID-19. Materials and methods: The experimental and control groups consisted of second year students in the department of dentistry at our university for the years 2019 (136 people) and 2020 (125 people). The impact of different teaching methods on student performance was compared by calculating the mean scores and percentage of failures on various exams and whether or not class credits were earned between the two years. A t test was used to determine statistical significance. Results: The mean scores on the mini-tests were lower in 2020 than in 2019, while the average score of the intermediate exam and the number of students receiving class credits were higher. The mean scores on the practical and unit exams were not statistically significant between the years, but the failure rate on both exams was higher in 2019 than in 2020. Conclusion: COVID-19 had impacts on student performance. A comparison of the mean scores on the exams revealed that the use of microscopy, oral questions, and online animations contributed to improved performance on different exams. Therefore, to promote students' understanding and retention of memorized knowledge of oral pathology, the use of microscopes will be resumed whenever possible, as well as continuation with oral questions and online animations.

Analyzing the Effect of Diverse Gaze and Head Direction on Facial Expression Recognition With Photo-Reflective Sensors Embedded in a Head-Mounted Display.

As one of the facial expression recognition techniques for Head-Mounted Display (HMD) users, embedded photo-reflective sensors have been used. In this paper, we investigate how gaze and face directions affect facial expression recognition using the embedded photo-reflective sensors. First, we collected a dataset of five facial expressions (Neutral, Happy, Angry, Sad, Surprised) while looking in diverse directions by moving 1) the eyes and 2) the head. Using the dataset, we analyzed the effect of gaze and face directions by constructing facial expression classifiers in five ways and evaluating the classification accuracy of each classifier. The results revealed that the single classifier that learned the data for all gaze points achieved the highest classification performance. Then, we investigated which facial part was affected by the gaze and face direction. The results showed that the gaze directions affected the upper facial parts, while the face directions affected the lower facial parts. In addition, by removing the bias of facial expression reproducibility, we investigated the pure effect of gaze and face directions in three conditions. The results showed that, in terms of gaze direction, building classifiers for each direction significantly improved the classification accuracy. However, in terms of face directions, there were slight differences between the classifier conditions. Our experimental results implied that multiple classifiers corresponding to multiple gaze and face directions improved facial expression recognition accuracy, but collecting the data of the vertical movement of gaze and face is a practical solution to improving facial expression recognition accuracy.

Identification of a Proline-Kinked Amphipathic α-Helix Downstream from the Methyltransferase Domain of a Potexvirus Replicase and Its Role in Virus Replication and Perinuclear Complex Formation.

Characterized positive-strand RNA viruses replicate in association with intracellular membranes. Regarding viruses in the genus Potexvirus, the mechanism by which their RNA-dependent RNA polymerase (replicase) associates with membranes is understudied. Here, by membrane flotation analyses of the replicase of Plantago asiatica mosaic potexvirus (PlAMV), we identified a region in the methyltransferase (MET) domain as a membrane association determinant. An amphipathic α-helix was predicted downstream from the core region of the MET domain, and hydrophobic amino acid residues were conserved in the helical sequences in replicases of other potexviruses. Nuclear magnetic resonance (NMR) analysis confirmed the amphipathic α-helical configuration and unveiled a kink caused by a highly conserved proline residue in the α-helix. Substitution of this proline residue and other hydrophobic and charged residues in the amphipathic α-helix abolished PlAMV replication. Ectopic expression of a green fluorescent protein (GFP) fusion with the entire MET domain resulted in the formation of a large perinuclear complex, where virus replicase and RNA colocated during virus infection. Except for the proline substitution, the amino acid substitutions in the α-helix that abolished virus replication also prevented the formation of the large perinuclear complex by the respective GFP-MET fusion. Small intracellular punctate structures were observed for all GFP-MET fusions, and in vitro high-molecular-weight complexes were formed by both replication-competent and -incompetent viral replicons and thus were not sufficient for replication competence. We discuss the roles of the potexvirus-specific, proline-kinked amphipathic helical structure in virus replication and intracellular large complex and punctate structure formation. IMPORTANCE RNA viruses characteristically associate with intracellular membranes during replication. Although virus replicases are assumed to possess membrane-targeting properties, their membrane association domains generally remain unidentified or poorly characterized. Here, we identified a proline-kinked amphipathic α-helix structure downstream from the methyltransferase core domain of PlAMV replicase as a membrane association determinant. This helical sequence, which includes the proline residue, was conserved among potexviruses and related viruses in the order Tymovirales. Substitution of the proline residue, but not the other residues necessary for replication, allowed formation of a large perinuclear complex within cells resembling those formed by PlAMV replicase and RNA during virus replication. Our results demonstrate the role of the amphipathic α-helix in PlAMV replicase in a perinuclear complex formation and virus replication and that perinuclear complex formation by the replicase alone will not necessarily indicate successful virus replication.

Mycobacterial lymphadenitis without granuloma formation in a patient with anti-interferon-gamma antibodies.

A previously healthy 49-year-old Japanese woman presented with cervical lymph node swelling and tenderness. Lymph node biopsy revealed reactive lymphadenitis without granulomas. No malignant cells were found, and no acid-fast positive bacilli were identified by Ziehl-Neelsen staining. She was treated unsuccessfully with various antibiotics, and it was very challenging to reach a diagnosis. 18F-Fluorodeoxyglucose (18F-FDG) uptake in bones was evaluated using positron emission tomography-computed tomography (PET-CT), and disseminated mycobacterial infection was suspected. The interferon-gamma (IFN-γ) release assays QuantiFERON (QFT) and T-SPOT were used to diagnose tuberculosis infection. On testing, a difference in mitogen response was found between these assays. The response was low for QFT but adequate for T-SPOT, suggesting the presence of anti-IFN-γ antibodies. This difference depended on whether the patient's plasma (including anti-IFN-γ antibodies) was used within the assay system. Mycobacterium abscessus was isolated from lymph node cultures, and plasma anti-IFN-γ antibodies were confirmed. The patient was diagnosed with disseminated M. abscessus infection with underlying adult-onset immunodeficiency caused by anti-IFN-γ antibodies. Granulomas are a pathological hallmark of mycobacterial infection, but may not fully form in immunodeficient patients. Clinicians should be aware of the possibility of mycobacterial infection without granuloma formation due to anti-IFN-γ antibodies.

Correction: Intrinsic defect formation and the effect of transition metal doping on transport properties in a ductile thermoelectric material α-Ag2S: a first-principles study.

Correction for 'Intrinsic defect formation and the effect of transition metal doping on transport properties in a ductile thermoelectric material α-Ag2S: a first-principles study' by Ho Ngoc Nam et al., Phys. Chem. Chem. Phys., 2021, DOI: .

Intrinsic defect formation and the effect of transition metal doping on transport properties in a ductile thermoelectric material α-Ag2S: a first-principles study.

In this paper, the electronic structure and transport properties of a ductile thermoelectric material α-Ag2S are examined using first-principles calculations combined with the Boltzmann transport equation within a constant relaxation-time approximation. The use of the exchange-correlation functional SCAN + rVV10 successfully describes the geometric and electronic structure of α-Ag2S with a direct bandgap value of 0.99 eV, which is consistent with the previous experimental observations. Based on the calculations of the formation energy of typical intrinsic defects, it is found that intrinsic defect formation greatly affects the conductivity of the system where silver vacancy and interstitial silver act as p-type and n-type defects, respectively. Large Seebeck coefficients at room-temperature, of around -760 µV K-1 for n-type and 1400 µV K-1 for p-type, are realized. It is also suggested that the doping of fully filled d-block elements such as Cu and Au not only maintained the Seebeck coefficients at high values but also improved electrical conductivity by more than 1.4 times, leading to the improvement of the power factor by up to 40% compared to the non-doped sample at low carrier concentration.

Comparison of drug-susceptibility patterns and gene sequences associated with clarithromycin and azithromycin resistance in Mycobacterium abscessus complex isolates and evaluation of the accumulation of intrinsic macrolide resistance.

Introduction. Mycobacterium abscessus complex (MABC) is an infectious agent associated with macrolide resistance and treatment failure.Hypothesis/Gap Statement. Despite drug-susceptibility testing for MABC isolates including clarithromycin (CAM), long-term treatment with azithromycin (AZM) for MABC disease is recommended.Aim. We compared phenotypic and genotypic resistance to AZM and CAM in clinical isolates and evaluated the accumulation of intrinsic macrolide resistance (AIM) and morphological changes by macrolides exposure.Methodology. Forty-nine isolates were characterized regarding erm(41) sequevars. Sequencing data were compared to the nucleotide sequence of rrl and whiB7. The AIM MIC was performed in three reference strains and 15 isolates were randomized [each set of five isolates with M. abscessus subsp. abscessus (MAA) T28, MAA C28 and subsp. massiliense (MAM)].Results. The 49 isolates were distributed as 24 MAA T28, 5 MAA C28 and 20 MAM. The MIC50 values to CAM at day 3 in MAA T28, C28 and MAM were 1, 0.12 and 0.12 µg ml-1, while those at day 14 were 32, 0.5 and 0.12 µg ml-1, respectively. The AZM-MIC50 values at day 3 of the above isolates were 4, 0.25 and 0.5 µg ml-1, while those at day 14 were >64, 0.5 and 0.5 µg ml-1, respectively. Neither mutations in rrl of MAA T28 with acquired resistance nor deletions in whiB7 of MAA T28 without inducible resistance were observed . For AIM MIC, MAA T28 showed that the time-to-detection of AZM resistance was significantly faster over that of CAM (P<0.05). Morphological changes were not determined in all isolates.Conclusion. Our findings did not support the suggestion for the preferential use of AZM for, at least, MAA T28 disease due to the high-level MIC value and the increased AIM. The long duration of AZM-based treatment eventually may favour the emergence of isolates with a high-level of intrinsic resistance.

Resumption/efficacy and safety of an azithromycin-containing regimen against Mycobacterium avium complex lung disease in patients who experienced adverse effects with a clarithromycin-containing regimen.

BACKGROUND: Antibiotic therapy, including clarithromycin (CLR), has been widely used for the management of Mycobacterium avium complex (MAC) lung disease in clinical settings. When patients develop adverse events (AEs) during CLR-based treatment, the treatment regimen is modified or chemotherapy itself is discontinued. The need for alternative macrolide treatment strategies is emphasized due to the high rate of AEs possibly caused by CLR. Thus, the current study aimed to examine the efficacy and safety of azithromycin (AZM) in patients with MAC lung disease whose treatment was switched from CLR to AZM. METHODS: We performed a retrospective study of patients with MAC lung disease. The inclusion criteria were as follows: (1) patients who experienced AEs during treatment with antibiotics, including CLR, between December 2012 and November 2017, and (2) those who had antimicrobial therapy that was switched from CLR to AZM. The efficacy and safety of AZM during the clinical course of the disease after switching the regimen from CLR to AZM were investigated. RESULTS: Antibiotic therapy was switched in 31 patients who presented with AEs including drug-induced fever, rash, dysgeusia, liver dysfunction, and neutropenia during treatment with CLR-containing regimens. After switching to AZM, the median duration of treatment was 1286 (364-4615) days. During follow-up, 13 patients had a negative conversion of sputum culture. CONCLUSIONS: AZM may be safe and effective for patients with MAC lung disease who have difficulty tolerating CLR. In patients who experienced AEs possibly caused by CLR, switching from CLR to AZM might be an appropriate strategy.

Risk factors for hemoptysis in Mycobacterium avium complex lung disease.

BACKGROUND: Hemoptysis is a frequent and sometimes fatal complication of non-tuberculous mycobacterial (NTM) lung disease. The risk factors for hemoptysis are not well understood. In the current study, potential risk factors for hemoptysis were investigated in patients with Mycobacterium avium complex (MAC) lung disease, which is the most common NTM in Japan. METHODS: Medical records from the Kinki-Chuo Chest Medical Center were reviewed. Consecutive patients with MAC lung disease diagnosed in 2014 and followed up for more than 1 year in the hospital were included in the study. Hemoptysis was confirmed between 2014 and 2016. The characteristics of patients with hemoptysis and non-hemoptysis at the time of the initial diagnosis of MAC lung disease were obtained from the medical records, and the two groups were compared. The radiological findings assessed included nodules, infiltration shadows, cavities, and bronchiectasis. Each was classified and scored individually in six lung fields, and these data were used to generate radiological scores. RESULTS: The study included 82 patients with MAC lung disease, 18 with hemoptysis and 64 without. Higher total radiological severity score at the time of the initial diagnosis of MAC was associated with an increased risk of hemoptysis. Among the radiological scores, infiltration and cavities were marginally associated with the risk of hemoptysis. CONCLUSIONS: The radiological severity score at the time of initial diagnosis of MAC lung disease was associated with hemoptysis.

Two New Cases of Pulmonary Infection by Mycobacterium shigaense, Japan.

We report 2 case-patients in Japan with Mycobacterium shigaense pulmonary infections. One patient was given aggressive treatment and the other conservative treatment, according to distinctive radiologic evidence. A close phylogenetic relationship based on whole-genome sequencing was found between strain from the conservatively treated patient and a reference strain of cutaneous origin.

Model Construction and a Possibility of Cupratelike Pairing in a New d

Effective models are constructed for a newly discovered superconductor (Nd,Sr)NiO_{2}, which has been considered as a possible nickelate analog of the cuprates. Estimation of the effective interaction, which turns out to require a multiorbital model that takes account of all the orbitals involved on the Fermi surface, shows that the effective interactions are significantly larger than in the cuprates. A fluctuation exchange study suggests occurrence of d_{x^{2}-y^{2}}-wave superconductivity, where the transition temperature should be lowered from the cuprates due to the larger interaction.

Liming effects on dissolved and colloid-associated transport of cadmium in soil under intermittent simulated rainfall.

Liming has been regarded as an effective measure to reduce the bioavailability and mobility of cadmium (Cd) in soil. However, its effect on Cd transport in colloid-associated form remains unclear. In this study, relative importance of dissolved and colloid-associated transport of Cd was explored in columns packed with moist soil aggregates (diameter <2 mm) under intermittent simulated rainfall of distilled water or 5 mmol L-1 CaCl2 solution. The Cd2+/Ca2+ exchange selectivity coefficient determined in column experiments displayed gradual decreases with decreasing ionic strength. It is proposed that the exchange selectivity coefficient determined by repeated batch extraction can be used to predict Cd discharge in dissolved form in column effluent. Colloid-associated Cd was the main Cd form in the first flushing effluent sample upon resuming infiltration of distilled water. Otherwise, Cd was transported mainly in dissolved form, accounting for 81-93 % and 54-72 % of total Cd discharge for unlimed soils and limed soils, respectively. Liming remarkably reduced dissolved Cd concentration but only slightly enhanced colloidal Cd transport. Cd was enriched on colloids, and the enrichment factor was enhanced by liming. Colloidal Cd transport through preferential pathways (e.g., macropores, shrinkage cracks, tile drains) should be paid due attention.

Serum immunoglobulin a antibodies to glycopeptidolipid core antigen for Mycobacteroides abscessus complex lung disease.

Background: Mycobacteroides abscessus complex (MABC) exhibits smooth morphotypes, expressing glycopeptidolipid (GPL), and rough morphotypes, expressing diminished GPL, on the MABC cell wall. Few reports have focused on the relationship between anti-GPL-core immunoglobulin A (IgA) antibody and colony morphology in MABC lung disease. Methods: This study aimed to test GPL core antigen in patients with MABC lung disease to investigate the relationship between coinfection/contamination in other nontuberculous mycobacteria species and colony morphology variant in MABC isolates. Patients with MABC lung disease and contamination diagnosed between 2012 and 2017 at our hospital were enrolled retrospectively. Results: Of the assessed patients, 43 patients with MABC lung disease and 13 with MABC contamination were included. There was a significant difference in anti-GPL-core IgA antibody levels between them (P = 0.02). Forty-three patients with MABC lung disease were divided into two groups as positive and negative antibodies groups. A significant increase in the positive anti-GPL-core IgA antibody was observed in coexistence with both Mycobacterium avium complex (MAC) (P = 0.02) and the isolate of the smooth variant (P = 0.03) in MABC. Conclusions: Anti-GPL-core IgA antibodies in patients with MABC are greatly influenced by MAC coexistence, and colony morphology variant of the MABC isolate.

Bacterial population kinetics in heteroresistant Mycobacterium tuberculosis harbouring rare resistance-conferring mutations in gyrA and rpoB imply an epistatic interaction of mutations in a pre-XDR-TB patient.

OBJECTIVES: Bacterial population kinetics of strains harbouring drug resistance-conferring mutations within a patient often show cryptic resistance in clinical practice. We report a case that showed emergence and dominance of Mycobacterium tuberculosis with uncommon rpoB and gyrA mutations, followed by an rpoC compensatory mutation, during treatment. METHODS: A pre-XDR-TB patient showed heteroresistance to rifampicin and levofloxacin during treatment as a result of intermittent self-cessation. WGS was applied to investigate intra-host strain composition using five pairs of isolates from sputum samples. RESULTS: The subclone in this study possessed rare mutations conferring resistance to rifampicin (rpoB V170F) and levofloxacin (gyrA S91P) and it rapidly outcompeted other subclones during treatment that included levofloxacin but not rifampicin (<7 days). The high-probability compensatory mutation rpoC V483A also emerged and became dominant subsequent to the rpoB V170F mutation. CONCLUSIONS: To the best of our knowledge, this is the first case showing the emergence of such a rare variant that dominated the population within a patient during treatment of TB.

Effective treatment for clarithromycin-resistant Mycobacterium avium complex lung disease.

Clinical management of macrolide-resistant Mycobacterium avium complex (MR-MAC) lung disease is difficult. To date, there only exist a limited number of reports on the treatment of clarithromycin-resistant MAC (CR-MAC) lung disease. This study aimed to evaluate prognostic factors and identify effective treatments in CR-MAC lung disease. We retrospectively collected clinical data of patients newly diagnosed with CR-MAC lung disease at the Kinki-Chuo Chest Medical Center between August 2010 and June 2018. Altogether, 37 patients with CR-MAC lung disease were enrolled. The median age was 69 years; 30, 22, and 21 patients received clarithromycin, ethambutol, and rifampicin, respectively, on their own or in drug combination. The observed sputum culture conversion rate was 29.7% (11/37 patients). In univariate analysis, ethambutol significantly increased the rate of sputum culture conversion (p = 0.027, odds ratio (OR) 10; 95% confidence interval (CI) 1.11-89.77). Multivariate analysis confirmed that ethambutol increased sputum culture conversion rate (p = 0.026; OR 21.8; 95% CI 1.45-329) while the existence of lung cavities decreased it (p = 0.04; OR 0.088; 95% CI 0.009-0.887). The combined use of ethambutol with other drugs may improve sputum culture conversion rate in CR-MAC lung disease.

Soft tissue infection caused by Mycolicibacter kumamotonensis.

Mycolicibacter kumamotonensis (M. kumamotonensis), formerly Mycobacterium kumamotonense, is a nontuberculous mycobacteria species, which was first separated from Mycobacterium terrae complex in 2006. Reports about infections caused by M. kumamotonensis are extremely rare, with most of them being lung infection. Here, we report the case of a 68-year-old man with a hobby of gardening who developed swelling in his right middle finger. He underwent surgical debridement at a previous hospital and was diagnosed with nontuberculous mycobacteria infection based on positive findings of acid-fast staining of pus obtained from the surgical specimen. He was treated with rifampicin, ethambutol, and clarithromycin, but the swelling worsened. Therefore, he was referred to our hospital for further examination and treatment. We performed a second debridement and added isoniazid to the treatment regimen, but the swelling continued to worsen. We then administered levofloxacin, but his condition did not change. Matrix-assisted laser desorption/ionization-time of flight mass spectrometry and DNA sequencing analysis confirmed M. kumamotonensis as the causative bacterium. Since the finger swelling did not improve, the patient underwent a third debridement and amikacin was added to the treatment regimen. Finally, the infection was controlled. He completed amikacin therapy and will continue treatment with the other five antibiotics for a total of 24 months. To the best of our knowledge, this is the first report of a patient with M. kumamotonensis soft tissue infection. We consider this case might provide important insights into the diagnosis and treatment of soft tissue infections caused by M. kumamotonensis.

Antimicrobial susceptibility patterns and MICs among non-photochromogenic rapidly growing Mycobacteroides and Mycolicibacterium species.

Introduction. Non-photochromogenic rapidly growing mycobacteria (NPRGM) that branch distinctly from Mycobacteroides (Myco) and Mycolicibacterium (Mycolici) are increasingly observed clinically and present a complicated treatment challenge; thus, appropriate in vitro susceptibility testing is required.Methodology. We evaluated the MICs of nine antimicrobials used in the treatment of infections of 25 NPRGM type strains. The relation of inducible macrolide resistance with functional erythromycin ribosomal methylase (erm) genes was also investigated.Results. The initial clarithromycin MIC reading at 3 days showed resistance in four of the Mycolici strains. In contrast, the presence of erm genes among Mycolici species differed from previous findings. Both Myco and Mycolici species were highly susceptible to amikacin and linezolid. Myco species were resistant to fluoroquinolones, while Mycolici species were susceptible. Meropenem showed low activity against Myco species, but high activity against Mycolici species.Conclusion. NPRGM clade-specific susceptibility patterns suggest an urgent need to establish distinct breakpoints for Myco and Mycolici species.