Timesaving Double-Grid Method for Real-Space Electronic-Structure Calculations

We present a simple and efficient technique in ab initio electronic-structure calculation utilizing real-space double-grid with a high density of grid points in the vicinity of nuclei. This technique promises to greatly reduce the overhead for performing the integrals that involves non-local parts of pseudopotentials, with keeping a high degree of accuracy. Our procedure gives rise to no Pulay forces, unlike other real-space methods using adaptive coordinates. Moreover, we demonstrate the potential power of the method by calculating several properties of atoms and molecules.Comment: 4 pages, 5 figure

Clearance of Aspergillus fumigatus is impaired in the airway in allergic inflammation

Background Aspergillus fumigatus (Af) sometimes colonizes and persists within the respiratory tree in some patients with asthma. To date, the precise reasons why the clearance of Af is impaired in patients with asthma remain unknown. Objective To characterize the effects of allergic airway inflammation on clearance of Af. Methods Control and Dermatophagoides farinae (Df) allergen-sensitized BALB/c mice were intranasally infected with Af. After 2 and 9 days of infection, the pathology, fungal burden, and cytokine profile in lung tissue were compared. In a different set of experiments, the phagocytotic activity of alveolar macrophages and the expression of their pathogen recognition receptors also were determined. Results The Af conidia and neutrophilic airway inflammation disappeared by day 9 after infection in control mice. In Df-sensitized mice, Af conidia and neutrophilic and eosinophilic airway inflammation persisted at day 9 after infection. Compared with control mice, Df allergen-sensitized mice showed significant increases in interleukin (IL)-5 and decreases in IL-12 and interferon-γ in lung tissues at day 2 after infection. Most importantly, compared with Af-infected non-Df-sensitized mice, IL-17 in lung tissues was significantly decreased in Df allergen-sensitized Af-infected mice at day 2 after infection but was significantly increased at day 9. Alveolar macrophages isolated from Df allergen-sensitized mice exhibited significant decreases in phagocytotic activity and expression of Toll-like receptor-4 and dectin-1 compared with those from control mice. Conclusion In the airway of patients with allergy, T-helper cell type 2-dominant immunity potentially affects the expression of pathogen recognition receptors and attenuates cellular defense against Af. Prolonged IL-17 production also could play an important role

The whole blood transcriptional regulation landscape in 465 COVID-19 infected samples from Japan COVID-19 Task Force

「コロナ制圧タスクフォース」COVID-19患者由来の血液細胞における遺伝子発現の網羅的解析 --重症度に応じた遺伝子発現の変化には、ヒトゲノム配列の個人差が影響する--. 京都大学プレスリリース. 2022-08-23.Coronavirus disease 2019 (COVID-19) is a recently-emerged infectious disease that has caused millions of deaths, where comprehensive understanding of disease mechanisms is still unestablished. In particular, studies of gene expression dynamics and regulation landscape in COVID-19 infected individuals are limited. Here, we report on a thorough analysis of whole blood RNA-seq data from 465 genotyped samples from the Japan COVID-19 Task Force, including 359 severe and 106 non-severe COVID-19 cases. We discover 1169 putative causal expression quantitative trait loci (eQTLs) including 34 possible colocalizations with biobank fine-mapping results of hematopoietic traits in a Japanese population, 1549 putative causal splice QTLs (sQTLs; e.g. two independent sQTLs at TOR1AIP1), as well as biologically interpretable trans-eQTL examples (e.g., REST and STING1), all fine-mapped at single variant resolution. We perform differential gene expression analysis to elucidate 198 genes with increased expression in severe COVID-19 cases and enriched for innate immune-related functions. Finally, we evaluate the limited but non-zero effect of COVID-19 phenotype on eQTL discovery, and highlight the presence of COVID-19 severity-interaction eQTLs (ieQTLs; e.g., CLEC4C and MYBL2). Our study provides a comprehensive catalog of whole blood regulatory variants in Japanese, as well as a reference for transcriptional landscapes in response to COVID-19 infection

DOCK2 is involved in the host genetics and biology of severe COVID-19

「コロナ制圧タスクフォース」COVID-19疾患感受性遺伝子DOCK2の重症化機序を解明 --アジア最大のバイオレポジトリーでCOVID-19の治療標的を発見--. 京都大学プレスリリース. 2022-08-10.Identifying the host genetic factors underlying severe COVID-19 is an emerging challenge. Here we conducted a genome-wide association study (GWAS) involving 2, 393 cases of COVID-19 in a cohort of Japanese individuals collected during the initial waves of the pandemic, with 3, 289 unaffected controls. We identified a variant on chromosome 5 at 5q35 (rs60200309-A), close to the dedicator of cytokinesis 2 gene (DOCK2), which was associated with severe COVID-19 in patients less than 65 years of age. This risk allele was prevalent in East Asian individuals but rare in Europeans, highlighting the value of genome-wide association studies in non-European populations. RNA-sequencing analysis of 473 bulk peripheral blood samples identified decreased expression of DOCK2 associated with the risk allele in these younger patients. DOCK2 expression was suppressed in patients with severe cases of COVID-19. Single-cell RNA-sequencing analysis (n = 61 individuals) identified cell-type-specific downregulation of DOCK2 and a COVID-19-specific decreasing effect of the risk allele on DOCK2 expression in non-classical monocytes. Immunohistochemistry of lung specimens from patients with severe COVID-19 pneumonia showed suppressed DOCK2 expression. Moreover, inhibition of DOCK2 function with CPYPP increased the severity of pneumonia in a Syrian hamster model of SARS-CoV-2 infection, characterized by weight loss, lung oedema, enhanced viral loads, impaired macrophage recruitment and dysregulated type I interferon responses. We conclude that DOCK2 has an important role in the host immune response to SARS-CoV-2 infection and the development of severe COVID-19, and could be further explored as a potential biomarker and/or therapeutic target

The role of preoperative glycemic control in decreasing surgical site infections in lower extremity fractures

Abstract Background Postoperative surgical site infections (SSIs) are an important complication to prevent in surgical treatment. Patients with diabetes mellitus (DM) have a higher risk of SSIs. Preoperative glycemic control is required. For patients with orthopedic trauma, the duration of preoperative glycemic control is limited because delaying operative treatment is difficult. However, whether preoperative glycemic control would decrease the risk of SSIs in diabetic patients with lower extremity fractures is unclear. The first aim of this study was to investigate the rate of SSIs among patients with DM who had undergone preoperative glycemic control, compared with that of patients without DM. As the secondary aim, we sought to demonstrate among patients with DM whether preoperative glycemic control would affect the development of SSIs between patients with controlled DM and patients with poorly controlled DM. Methods In this retrospective cohort study, 1510 patients treated surgically for lower extremity fractures were enrolled. Data collected were patient age, sex, body mass index, history of DM, development of SSIs, tobacco use, the presence of an open fracture, the period between the day of injury and the operation, the length of surgery, and blood glucose levels on admission and on the day before surgery. Results The rate of total SSIs was 6.0% among patients with DM and 4.4% among patients without DM (p = 0.31). Multivariate logistic regression revealed a significant association between the development of SSIs and the presence of DM (odds ratio, 1.79; 95% confidence interval 1.01–3.19; p = 0.047). The results of the secondary study revealed that the rate of early SSIs was significantly higher in the poorly controlled DM group than in the controlled DM group (5.9% vs. 1.5%; p = 0.032). However, multivariate logistic regression revealed that control levels of DM were not significantly associated with the development of SSIs. Conclusions Even though patients with DM had undergone preoperative glycemic control, SSIs were significantly associated with DM, especially when the patients had poorly controlled DM. This finding suggested that continuous glycemic control is important preoperatively and postoperatively to prevent SSIs

Catalytic Asymmetric Synthesis of Chiral 2‑Vinylindole Scaffolds by Friedel–Crafts Reaction

A chiral bis­(imidazolidine)­pyridine (PyBidine)–Ni­(OTf)₂ complex smoothly catalyzed an asymmetric Friedel–Crafts reaction of 2-vinylindoles with nitroalkenes to give chiral indoles in a highly enantioselective manner while maintaining the 2-vinyl functionality. The chiral 2-vinylindoles offer unique chiral scaffolds for diverse transformations

Cysteinyl leukotriene receptor antagonist regulates allergic airway inflammation in an organ- and cytokine-specific manner

Background: Cysteinyl leukotrienes (cys-LTs) are very important factors in the pathophysiology of bronchial asthma. Cys-LT receptor antagonists (LTRAs) decrease allergic airway inflammation. The aim of the present study was to determine the differential effects of LTRAs and corticosteroids on allergic airway inflammation and allergen-specific cytokine production from lymphoid tissues using a murine model of asthma. Material/Methods: Four groups of female BALB/c mice [control (Cont); Dermatophagoides farinae allergen-sensitized (AS); pranlukast (Prl), an LTRA-treated AS; and dexamethasone (Dex)-treated AS] were examined. Lung pathology and cytokine production by prepared mononuclear cells isolated from mediastinal lymph nodes (MLNs) and spleen were compared among these groups. Results: AS mice exhibited allergic airway inflammation and significant increases in allergen-specific Th1 and Th2 cytokines in MLNs and spleen. Prl-treated mice showed significant attenuation of allergic airway inflammation concomitant with reduction of Th2 cytokines and IFN-g in MLNs but not in spleen. In contrast, Dex significantly decreased Th1 and Th2 cytokines in MLNs and also decreased them (except IL-13 and IL-2) in spleen. Conclusions: The inflammatory effects of cys-LTs could differ in lymphoid organs. LTRAs potentially regulate allergic airway inflammation in an organ- and cytokine-specific manner, while systemic corticosteroid shows nonspecific effects