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The Japanese Respiratory Society (JRS) scoring system is a useful tool for the rapid presumptive diagnosis of atypical pneumonia in non-elderly (aged60 years) patients. As SARS-CoV-2 vaccination progresses, COVID-19 in elderly people has markedly reduced. We investigated changes in diagnostic usefulness of the JRS scoring system in COVID-19 pneumonia between the Delta variant group (vaccination period) and non-Delta variant group (before the vaccination period).This study was conducted at five institutions and assessed a total of 1121 patients with COVID-19 pneumonia (298 had the Delta variant). During the vaccination period, the Delta variant has spread and replaced the Alfa variant. We evaluated the vaccination period as the Delta variant group.Among the six parameters of the JRS scoring system, matching rates of two parameters were higher in the Delta variant group than the non-Delta variant group (pre-vaccination period): age60 years (77.5% vs 42.2%, P 0.0001) and no or minor comorbid illness (69.1% vs 57.8%, p = 0.0007). The sensitivity of the diagnosis of atypical pneumonia in patients with COVID-19 pneumonia was significantly higher in the Delta variant group compared with the non-Delta variant group (80.2% vs 58.3%, p 0.0001). When the diagnostic sensitivity was analyzed for different ages, the diagnostic sensitivities for the Delta variant and non-Delta variant groups were 92.6% and 95.5% for non-elderly patients and 39.1% and 32.5% for elderly patients, respectively.Our results demonstrated that the JRS scoring system is a useful tool for distinguishing between COVID-19 pneumonia and bacterial pneumonia in the COVID-19 vaccination period, but not before the vaccination period.

Casirivimab-imdevimab, an antibody cocktail containing two severe acute respiratory syndrome coronavirus 2 neutralizing antibodies, reduces the viral load and the risk of coronavirus disease 2019 (COVID-19)-related hospitalization or death. The objective of this study was to evaluate the clinical efficacy of casirivimab-imdevimab in patients with COVID-19 Delta variant in Japan.This study was conducted at five institutions and assessed a total of 461 patients with COVID-19 who met the inclusion criteria. The treatment group received a dose of casirivimab-imdevimab consisting of a cocktail of two monoclonal antibodies, (casirivimab 600 mg and imdevimab 600 mg intravenously). The control consisted of age- and sex-matched COVID-19 patients (n = 461) who sufficed the inclusion criteria but did not receive casirivimab-imdevimab. The outcome was the requirement of oxygen therapy.In the treatment group, patients received oxygen therapy (n = 30), nasal canula (n = 23), high flow nasal cannula (n = 5), and mechanical ventilation (n = 2). In the control group, patients received oxygen therapy (n = 56), nasal canula (n = 45), high flow nasal cannula (n = 8), and mechanical ventilation (n = 3). The administration of oxygen therapy was significantly lower in the treatment group than the control group (6.5% vs. 12.1%, P = 0.0044). All these patients admitted to our hospitals and received additional therapy and recovered.Our results demonstrate that the casirivimab-imdevimab combination antibody treatment is associated with reduced rates of requiring oxygen therapy among high-risk patients with COVID-19 Delta variant.

Atypical pneumonia is caused by atypical pathogens that are not detectable with Gram stain and cannot be cultured using standard methods. The most common causative organisms of atypical pneumonia are Mycoplasma pneumoniae, Chlamydia pneumoniae, and Legionella species. The therapeutic approach for atypical pneumonias is different than that for typical pneumonia. Typical bacterial pathogens classically respond to β-lactam antimicrobial therapy because they have a cell wall amenable to β-lactam disruption. On the contrary, most atypical pathogens do not have a bacterial cell wall, some are intracellular (e.g., Legionella), and some are paracellular (e.g., M. pneumoniae). To prevent an increase in the number of antimicrobial-resistant strains, the Japanese pneumonia guidelines have proposed a differential diagnosis for typical bacterial pneumonia and atypical pneumonia to select an appropriate antibiotic for the management of mild-to-moderate pneumonia. The guidelines have set up six parameters and criteria based on the clinical symptoms, physical signs, and laboratory data. However, in the elderly individuals and patients with underlying diseases, the differential diagnosis may be difficult or a mixed infection may be latent. Therefore, in these individuals, the administration of a β-lactam drug plus a macrolide or tetracycline, or only fluoroquinolone should be considered from the beginning to cover bacterial and atypical pneumonia.

Adoption of CRISPR–Cas systems, such as CRISPR–Cas9 and CRISPR–Cas12a, has revolutionized genome engineering in recent years; however, application of genome editing with CRISPR type I—the most abundant CRISPR system in bacteria—remains less developed. Type I systems, such as type I-E, and I-F, comprise the CRISPR-associated complex for antiviral defense (‘Cascade’: Cas5, Cas6, Cas7, Cas8 and the small subunit) and Cas3, which degrades the target DNA; in contrast, for the sub-type CRISPR–Cas type I-D, which lacks a typical Cas3 nuclease in its CRISPR locus, the mechanism of target DNA degradation remains unknown. Here, we found that Cas10d is a functional nuclease in the type I-D system, performing the role played by Cas3 in other CRISPR–Cas type I systems. The type I-D system can be used for targeted mutagenesis of genomic DNA in human cells, directing both bi-directional long-range deletions and short insertions/deletions. Our findings suggest the CRISPR–Cas type I-D system as a unique effector pathway in CRISPR that can be repurposed for genome engineering in eukaryotic cells.

Nursing and healthcare-associated pneumonia (NHCAP) is associated with decreased physical function. We investigated the functional outcomes at 1 year after hospital discharge in patients with COVID-19 pneumonia. Functional decline rates for calculating the Barthel Index at the time of hospital discharge and at 1 year after hospital discharge were significantly higher in the NHCAP group than the community-acquired pneumonia group (at hospital discharge, 54.0% vs. 31.2%, respectively, p 0.0001; 1 year follow-up, 37.9% vs. 8.6%, respectively, p 0.0001). It is necessary to consider early rehabilitation, and treatment depending on the presence or absence of applicable criteria for NHCAP.

Cough and sputum are common complaints at outpatient visits. In this digest version, we provide a general overview of these two symptoms and discuss the management of acute (up to three weeks) and prolonged/chronic cough (longer than three weeks). Flowcharts are provided, along with a step-by-step explanation of their diagnosis and management. Most cases of acute cough are due to an infection. In chronic respiratory illness, a cough could be a symptom of a respiratory infection such as pulmonary tuberculosis, malignancy such as a pulmonary tumor, asthma, chronic obstructive pulmonary disease, chronic bronchitis, bronchiectasis, drug-induced lung injury, heart failure, nasal sinus disease, sinobronchial syndrome, eosinophilic sinusitis, cough variant asthma (CVA), atopic cough, chronic laryngeal allergy, gastroesophageal reflux (GER), and post-infectious cough. Antibiotics should not be prescribed for over-peak cough but can be considered for atypical infections. The exploration of a single/major cause is recommended for persistent/chronic cough. When sputum is present, a sputum smear/culture (general bacteria, mycobacteria), cytology, cell differentiation, chest computed tomography (CT), and sinus X-ray or CT should be performed. There are two types of rhinosinusitis. Conventional sinusitis and eosinophilic rhinosinusitis present primarily with neutrophilic inflammation and eosinophilic inflammation, respectively. The most common causes of dry cough include CVA, atopic cough/laryngeal allergy (chronic), GER, and post-infectious cough. In the last chapter, future challenges and perspectives are discussed. We hope that the clarification of the pathology of cough hypersensitivity syndrome will lead to further development of "pathology-specific non-specific therapeutic drugs" and provide benefits to patients with chronic refractory cough.

We designed and synthesized a medium-firm drug-candidate library of cryptand-like structures possessing a randomized peptide linker on the bacteriophage T7. From the macrocyclic library with a 10^9 diversity, we obtained a binder toward a cancer-related protein (Hsp90) with an antibody-like strong affinity (K_D = 62 nM) and the binding was driven by the enthalpy. The selected supramolecular ligand inhibited Hsp90 activity by site-specific binding outside of the well-known ATP-binding pocket on the N-terminal domain (NTD).

Yoshihisa Ishiura,1 Masaki Fujimura,2 Noriyuki Ohkura,3 Johsuke Hara,3 Kahori Nakahama,1 Yusuke Sawai,1 Takeshi Tamaki,1 Ryuta Murai,1 Toshiki Shimizu,1 Naoyuki Miyashita,1 Shosaku Nomura1 1First Department of Internal Medicine, Kansai Medical University, Osaka, Japan; 2Respiratory Medicine, National Hospital Organization Nanao Hospital, Nanao, Japan; 3Respiratory Medicine, Kanazawa University Hospital, Kanazawa, JapanCorrespondence: Yoshihisa Ishiura, First Department of Internal Medicine, Kansai Medical University, 10-15 Fumizono-cho, Moriguchi, Osaka, 570-8507, Japan, Tel +81-6-6992-1001, Fax +81-6-6993-9837, Email ishiura-@p2322.nsk.ne.jp; ishiuray@takii.kmu.ac.jpPurpose: The ‘treatable traits’ strategy for patients with chronic inflammatory airway diseases, especially asthma and chronic obstructive pulmonary disease (COPD), is a focus of interest, because it implements precision and personalized medicine. Asthma-COPD overlap (ACO), a phenotype involving both asthma and COPD, is an important disease entity because patients with ACO have significantly worse outcomes, conferring greater economical and social burdens. Some guidelines for ACO recommend add-on therapy of long-acting muscarinic antagonists to inhaled corticosteroids and long-acting β2 agonists. However, this approach is based on extrapolation from patients with asthma or COPD alone. Consequently, a ‘treatable traits’ approach suitable for ACO remains obscure.Methods: A 12-week open-label cross-over pilot study was conducted in patients with ACO to investigate the effect of tiotropium bromide (TIO) 5 μg/day add-on therapy to fluticasone propionate/formoterol fumarate (FP/FM) 500/20 μg/day compared with FP/FM 500/20 μg/day alone. A 4-week run-in period and two 4-week treatment periods were included.Results: A total of 18 male patients with stable ACO participated in this pilot study. All patients were ex-smokers. Mean values ± standard deviation (SD) for forced expiratory volume in 1 second (FEV1) were 1.21 ± 0.49 L after the run-in period, 1.20 ± 0.51 L after the FP/FM combination therapy period, and 1.30 ± 0.48 L after the TIO add-on therapy to FP/FM period. FEV1 values after the TIO add-on therapy FP/FM period were significantly higher than those after the run-in period (p < 0.01).Conclusion: TIO add-on therapy to FP/FM in patients with ACO, considered difficult to treat because of the presence of both asthma and COPD, resulted in improvements in lung function parameters in this real-world pilot study, indicating the potential value of TIO add-on therapy as a “treatable traits” option for standard treatment for ACO.Keywords: treatable trait, asthma-COPD overlap, tiotropium, fluticasone, formoterol, triple therapy

We have investigated the calcite growth mechanism by directly imaging atomic-scale structural changes at the growing step edges with high-speed frequency modulation atomic force microscopy (HS-FM-AFM). We compared the results with those previously obtained during dissolution, where a transition region (TR) consisting of a Ca(OH)

To prevent an increase in the frequency of antimicrobial resistance (AMR), the specific and rapid diagnosis of causative pathogens is important, as the results can be used to initiate appropriate antibiotics treatment. Recently, the highly sensitive rapid immunochromatographic assay of silver amplification technology was developed for the detection of Mycoplasma pneumoniae. We investigated the sensitivity and specificity of the silver amplification immunochromatographic assay in adolescent and adult patients. A total of 767 patients with respiratory tract infection (RTI) and 605 with pneumonia were assessed by the silver amplification assay and real-time polymerase chain reaction (PCR). M. pneumoniae was identified by PCR in 95 patients with RTI and in 30 patients with community-acquired pneumonia (CAP), but it was not identified in patients with nursing- and healthcare-associated pneumonia. Eighteen of the 95 RTI patients and 7 of the 30 CAP patients with PCR-positive M. pneumoniae were found to be infected with macrolide-resistant M. pneumoniae. When PCR was used as the control test, the sensitivity, specificity, and overall agreement with the silver amplification assay were 90.5%, 99.0%, and 97.9%, respectively, in RTI patients and 90.0%, 99.1%, and 98.7%, respectively, in pneumonia patients. Our results show that the silver amplification assay has excellent sensitivity and specificity compared with PCR despite being a rapid diagnostic method. The silver amplification assay may be helpful for initiating appropriate antibiotic treatment and preventing AMR.

Introduction The treatment landscape of metastatic non-small-cell lung cancer (NSCLC) has changed dramatically in the last decade. Anaplastic lymphoma kinase (ALK) rearrangement has been a focus of interest since ALK inhibitors produced outstanding clinical results compared with chemotherapy with cytotoxic agents in patients with ALK-positive NSCLC. Case report We present the case of a 56-year-old woman with metastatic ALK-positive NSCLC and an inability to swallow capsules or tablets. Unfortunately, all ALK inhibitors are capsule or tablet formulations. Management and outcome We, therefore, decided to administer alectinib orally by opening the capsules and suspending the contents in water. Clinical imaging performed 12 months after initiating alectinib therapy indicated a complete response (CR). After 54 months of follow-up, CR has been maintained, and oral alectinib therapy has continued with no recurrence of the swallowing disturbance. Discussion There are no current guidelines for oral targeted therapy in patients with swallowing disturbance, but alectinib administered orally by opening the capsules and suspending the contents in water can be a treatment option in patients with ALK-positive NSCLC and swallowing difficulty.

Human leukocyte Ig-like receptors (LILR) LILRB1 and LILRB2 are immune checkpoint receptors that regulate a wide range of physiological responses by binding to diverse ligands, including HLA-G. HLA-G is exclusively expressed in the placenta, some immunoregulatory cells, and tumors and has several unique isoforms. However, the recognition of HLA-G isoforms by LILRs is poorly understood. In this study, we characterized LILR binding to the β2-microglobulin (β2m)-free HLA-G1 isoform, which is synthesized by placental trophoblast cells and tends to dimerize and multimerize. The multimerized β2m-free HLA-G1 dimer lacked detectable affinity for LILRB1, but bound strongly to LILRB2. We also determined the crystal structure of the LILRB1 and HLA-G1 complex, which adopted the typical structure of a classical HLA class I complex. LILRB1 exhibits flexible binding modes with the α3 domain, but maintains tight contacts with β2m, thus accounting for β2m-dependent binding. Notably, both LILRB1 and B2 are oriented at suitable angles to permit efficient signaling upon complex formation with HLA-G1 dimers. These structural and functional features of ligand recognition by LILRs provide novel insights into their important roles in the biological regulations.

The objective of this study was to clarify the clinical differences between nursing and healthcare-associated pneumonia (NHCAP) and community-acquired pneumonia (CAP) due to COVID-19. We also investigated the clinical characteristics to determine whether there is a difference between the variant and non-variant strain in patients with NHCAP due to COVID-19. In addition, we analyzed the clinical outcomes in NHCAP patients with mental disorders who were hospitalized in a medical institution for treatment of mental illness.This study was conducted at five institutions and assessed a total of 836 patients with COVID-19 pneumonia (154 cases were classified as NHCAP and 335 had lineage B.1.1.7.).No differences in patient background, clinical findings, disease severity, or outcomes were observed in patients with NHCAP between the non-B.1.1.7 group and B.1.1.7 group. The median age, frequency of comorbid illness, rates of intensive care unit stay, and mortality rate were significantly higher in patients with NHCAP than in those with CAP. Among the patients with NHCAP, the mortality rate was highest at 37.5% in patients with recent cancer treatment, followed by elderly or disabled patients receiving nursing care (24.3%), residents of care facilities (23.0%), patients receiving dialysis (13.6%), and patients in mental hospitals (9.4%).Our results demonstrated that there were many differences in the clinical characteristics between NHCAP patients and CAP patients due to COVID-19. It is necessary to consider the prevention and treatment content depending on the presence or absence of applicable criteria for NHCAP.

The Japanese Respiratory Society (JRS) scoring system is a useful tool for identifying Mycoplasma pneumoniae pneumonia. Most COVID-19 pneumonia in non-elderly patients (aged60 years) are classified as atypical pneumonia using the JRS scoring system. We evaluated whether physicians could distinguish between COVID-19 pneumonia and M. pneumoniae pneumonia using chest computed tomography (CT) findings. In addition, we investigated chest CT findings if there is a difference between the variant and non-variant strain.This study was conducted at five institutions and assessed a total of 823 patients with COVID-19 pneumonia (335 had lineage B.1.1.7.) and 100 patients with M. pneumoniae pneumonia.In COVID-19 pneumonia, at the first CT examination, peripheral, bilateral ground-glass opacity (GGO) with or without consolidation or crazy-paving pattern was observed frequently. GGO frequently had a round morphology (39.2%). No differences were observed in the radiological findings between the non-B.1.1.7 groups and B.1.1.7 groups. The frequency of pleural effusion, lymphadenopathy, bronchial wall thickening and nodules (tree-in-bud and centrilobular) was low. In contrast to COVID-19 pneumonia, bronchial wall thickening (84%) was observed most frequently, followed by nodules (81%) in M. pneumoniae pneumonia. These findings were significantly higher in M. pneumoniae pneumonia than COVID-19 pneumonia.Our results demonstrated that a combination of the JRS scoring system and chest CT findings is useful for the rapid presumptive diagnosis of COVID-19 pneumonia in patients aged60 years. However, this clinical and radiographic diagnosis is not adapted to elderly people.

Protein dynamics play an essential role in function regulation. In recent years, many experimental and theoretical studies have shown that changes in protein fluctuations in the backbone and side chains fulfill a pivotal role associated with amino acid mutations, chemical modifications, and ligand binding. The dynamic correlations between protein side chains have not been sufficiently studied, and no reliable analysis method has been available so far. Therefore, we developed a method to evaluate the dynamic correlation between protein side chains using mutual information and molecular dynamics simulations. To eliminate the structural superposition errors dealing with conventional analysis methods, and to accurately extract the intrinsic fluctuation properties of the side chains, we employed distance principal component analysis (distPCA). The motion of the side chain was then projected onto the eigenvector space obtained by distPCA, and the mutual information between the projected motions was calculated. The proposed method was then applied to a small protein “eglin c” and the mutants. The results show that even a single mutation significantly changed the dynamic correlations and also suggest that the dynamic change is deeply related to the stability. Those results indicate that our developed method could be useful for analyzing the molecular mechanism of allosteric communication in proteins.

In this paper we introduce a new camera localization strategy designed for image sequences captured in challenging industrial situations such as industrial parts inspection. To deal with peculiar appearances that hurt standard 3D reconstruction pipeline, we exploit pre-knowledge of the scene by selecting key frames in the sequence (called as anchors) which are roughly connected to a certain location. Our method then seek the location of each frame in time-order, while recursively updating an augmented 3D model which can provide current camera location and surrounding 3D structure. In an experiment on a practical industrial situation, our method can localize over 99% frames in the input sequence, whereas standard localization methods fail to reconstruct a complete camera trajectory., Comment: This paper have been accepted and will be appeared in the proceedings of 17th International Conference on Machine Vision Applications (MVA2021)

During the period from January to December 2015, 104 Streptococcus pneumoniae strains, 129 Haemophilus influenzae strains and 54 Moraxella catarrhalis strains isolated from clinical specimens of pediatric infections in the national 16 institutions, studied susceptibilities of total 28 antibiotics, the capsular serotype for S. pneumoniae, the capsular b type and β-lactamase production capability for H. influenzae, and the β-lactamase production capability for M. catarrhalis were measured. In S. pneumoniae, the results showed that 68 strains (65.4%) were PSSP, 32 (30.8%) were PISP, and 4 (3.8%) were PRSP. The susceptibilities of TBPM and GRNX among oral antibiotics, and PAPM among injectable antibiotics demonstrated the lowest value with MIC90 ≤ 0.06 μg/mL. The most frequent distribution of S. pneumoniae serotypes was seen in 15B, followed by 19A, and 35B. Serotype strains contained in 13-valent pneumococcal conjugate vaccine (PCV13) were 19 strains (18.3%). In H. influenzae, the results showed that BLNAS accounted for 40 strains (31.0%), BLNAI for 28 strains (21.7%), BLNAR for 47 strains (36.4%), β-lactamase producing for 14 strains (10.8%). The susceptibilities of quinolones demonstrated the lowest outcome among oral antibiotics with MIC90 ≤ 0.06 μg/mL, and CTRX and TAZ/PIPC (TAZ4 fixed) among injectable antibiotics with MIC of 0.25 μg/mL. There was no detection of capsular type b strains. In M. catarrhalis, all the isolates were β-lactamase producing strains. The susceptibilities of TBPM, CPFX, TFLX and GRNX among oral antibiotics, and TAZ/PIPC (TAZ4 fixed), PAPM, MEPM and DRPM among injectable antibiotics demonstrated the lowest outcome with MIC of ≤0.06 μg/mL.

In this paper, we present a robust and efficient Structure from Motion pipeline for accurate 3D reconstruction under challenging environments by leveraging the camera pose information from a visual-inertial odometry. Specifically, we propose a geometric verification method to filter out mismatches by considering the prior geometric configuration of candidate image pairs. Furthermore, we introduce an efficient and scalable reconstruction approach that relies on batched image registration and robust bundle adjustment, both leveraging the reliable local odometry estimation. Extensive experimental results show that our pipeline performs better than the state-of-the-art SfM approaches in terms of reconstruction accuracy and robustness for challenging sequential image collections., Comment: This manuscript was accepted and presented in the 22th IEEE International Conference on Industrial Technology (ICIT2021)

Pipe inspection is a critical task for many industries and infrastructure of a city. The 3D information of a pipe can be used for revealing the deformation of the pipe surface and position of the camera during the inspection. In this paper, we propose a 3D pipe reconstruction system using sequential images captured by a monocular endoscopic camera. Our work extends a state-of-the-art incremental Structure-from-Motion (SfM) method to incorporate prior constraints given by the target shape into bundle adjustment (BA). Using this constraint, we can minimize the scale-drift that is the general problem in SfM. Moreover, our method can reconstruct a pipe network composed of multiple parts including straight pipes, elbows, and tees. In the experiments, we show that the proposed system enables more accurate and robust pipe mapping from a monocular camera in comparison with existing state-of-the-art methods., Comment: This manuscript was accepted and presented in the 29th IEEE International Symposium on Industrial Electronics (ISIE2020)

Fulminant type 1 diabetes mellitus (T1DM) is idiopathic T1DM with the rapid destruction of pancreatic β-cells. We herein report a 48-year-old man who developed fulminant T1DM complicated with a life-threatening electrolyte abnormality and abnormal electrocardiogram findings. He had no remarkable medical history, but one day, he developed general fatigue. His blood glucose level and HbA1c were 806 mg/dL and 6.3%, and his insulin secretion was markedly suppressed. He had ketoacidosis, hyponatremia and hyperkalemia. Furthermore, a life-threatening abnormality was noted on electrocardiogram. After fluid infusion and insulin therapy, the abnormality disappeared. In conclusion, we should bear in mind the possibility of fulminant T1DM in patients complaining of general malaise.

To evaluate scoring systems to predict Legionella pneumonia and therapeutic efficacy against Legionella pneumonia, the Japanese Society of Chemotherapy Legionella committee has collected data on cases of Legionella pneumonia from throughout Japan. We analyzed 176 patients with Legionella pneumonia and compared them with 217 patients with Streptococcus pneumoniae pneumonia and 202 patients with Mycoplasma pneumoniae pneumonia. We evaluated four scoring systems, the Winthrop-University Hospital score, Community-Based Pneumonia Incidence Study Group score, and Japan Respiratory Society score, but they demonstrated limited sensitivity and specificity for predicting Legionella pneumonia. Using six clinical and laboratory parameters (high fever, high C-reactive protein, high lactate dehydrogenase, thrombocytopenia, hyponatremia, and unproductive cough) reported by Fiumefreddo and colleagues, only 6% had Legionnella pneumonia when less than 2 parameters were present. The efficacy rates of antibiotics at the time of termination were 94.6% for intravenous antibiotics, including ciprofloxacin and pazufloxacin, and 95.5% for oral antibiotics, including ciprofloxacin, levofloxacin, garenoxacin, moxifloxacin, and clarithromycin. Our results suggested that the previously reported clinical scoring systems to predict Legionnella pneumonia are not useful, but 6 simple diagnostic score accurately ruled out Legionnella pneumonia, which may help to optimize initial empiric therapy. Quinolones and clarithromycin still showed good clinical efficacy against Legionella pneumonia.

Legionella species are consistently identified as some of the most common causative agents of severe community-acquired pneumonia (CAP) or nosocomial pneumonia. Although the number of reported Legionella infection cases is gradually increasing in Japan, most cases are diagnosed by a urinary antigen test, which identifies only L. pneumophila serogroup 1. Therefore, assessment of pneumonia-causing Legionella species and serogroups would be important. The Japan Society for Chemotherapy Legionella committee has collected the isolates and clinical information on cases of sporadic community-acquired Legionella pneumonia throughout Japan. Between December 2006 and March 2019, totally 140 sporadic cases were identified, in which L. pneumophila was the most frequently isolated species (90.7%) followed by L. bozemanae (3.6%), L. dumofii (3.6%), L. micdadei (1.4%), and L. longbeachae (0.7%). Among 127 isolates of L. pneumophila, 111 isolates were of serogroup 1, two of serogroup 2, four of serogroup 3, one of serogroup 4, one of serogroup 5, seven of serogroup 6, and one was of serogroup 10. We also assessed in vitro activity of antibiotics against these isolates and showed that quinolones and macrolides have potent anti-Legionella activity. Our study showed that pneumonia-causing Legionella species and serogroup distribution was comparable to that reported in former surveillances. L. pneumophila was the most common etiologic agent in patients with community-acquired Legionella pneumonia, and L. pneumophila serogroup 1 was the predominant serogroup.

This paper reviews various enhanced conformational sampling methods and explicit/implicit solvent/membrane models, as well as their recent applications to the exploration of the structure and dynamics of membranes and membrane proteins. Molecular dynamics simulations have become an essential tool to investigate biological problems, and their success relies on proper molecular models together with efficient conformational sampling methods. The implicit representation of solvent/membrane environments is reasonable approximation to the explicit all-atom models, considering the balance between computational cost and simulation accuracy. Implicit models can be easily combined with replica-exchange molecular dynamics methods to explore a wider conformational space of a protein. Other molecular models and enhanced conformational sampling methods are also briefly discussed. As application examples, we introduce recent simulation studies of glycophorin A, phospholamban, amyloid precursor protein, and mixed lipid bilayers and discuss the accuracy and efficiency of each simulation model and method. This article is part of a Special Issue entitled: Membrane Proteins edited by J.C. Gumbart and Sergei Noskov.

It is unclear whether in the treatment of community-acquired pneumonia (CAP) beta-lactam plus macrolide antibiotics lead to better survival than beta-lactam alone. We report a systematic review and meta-analysis. Trials and observational studies published in English were included, if they provided sufficient data on odds ratio for all-cause mortality for a beta-lactam plus macrolide regimen compared with beta-lactam alone. Two investigators independently searched for eligible articles. Of 514 articles screened, 14 were included: two open-label randomized controlled trials (RCTs) comprising 1975 patients, one non-RCT interventional study comprising 1011 patients and 11 observational studies comprising 33 332 patients. Random-model meta-analysis yielded an odds ratio for all-cause death for beta-lactam plus macrolide compared with beta-lactam alone of 0.80 (95% CI 0.69-0.92, P = 0.002) with substantial heterogeneity (I(2) = 59%, P for heterogeneity = 0.002). Severity-based subgroup analysis and meta-regression revealed that adding macrolide had a favourable effect on mortality only for severe CAP. Of the two RCTs, one suggested that macrolide plus beta-lactam lead to better outcome compared with beta-lactam alone, while the other did not. Subgrouping based on study design, that is, RCT versus non-RCT, which was almost identical to subgrouping based on severity, revealed substantial inter-subgroup heterogeneity. Compared with beta-lactam alone, beta-lactam plus macrolide may decrease all-cause death only for severe CAP. However, this conclusion is tentative because this was based mainly on observational studies.

Rapid diagnostic tests are useful tools in the early diagnosis of respiratory tract infections (RTIs) caused by a specific pathogens. We investigated the sensitivity and specificity of a rapid and simple antigen test for the detection of Mycoplasma pneumoniae, Ribotest Mycoplasma(®) in adolescent and adult patients with RTIs. In addition, we evaluated the accuracy of clinical and laboratory findings for the early presumptive diagnosis of M. pneumoniae RTI. We compared 55 cases with laboratory-confirmed M. pneumoniae infection using serology, culture, and polymerase chain reaction (PCR) and 346 cases without laboratory-confirmed M. pneumoniae infection. Pneumonia cases were excluded in this study. Among patients with M. pneumoniae infection, the incidences of cough, sore throat, and sputum production were high, with rates of 98%, 61%, and 67%, respectively, but the specificity was low. The prevalence of nasal symptoms was significantly lower in patients with M. pneumoniae infection (9%) than in non-M. pneumoniae infection (70%; p