Supplementary material for the article: Beškoski, V. P.; Yamamoto, A.; Nakano, T.; Yamamoto, K.; Matsumura, C.; Motegi, M.; Beškoski, L. S.; Inui, H. Defluorination of Perfluoroalkyl Acids Is Followed by Production of Monofluorinated Fatty Acids. Science of the Total Environment 2018, 636, 355–359. https://doi.org/10.1016/j.scitotenv.2018.04.243

Supplementary material for: [https://doi.org/10.1016/j.scitotenv.2018.04.243]Related to published version: [http://cherry.chem.bg.ac.rs/handle/123456789/2168

Supplementary material for the article: Beškoski, V. P.; Yamamoto, A.; Nakano, T.; Yamamoto, K.; Matsumura, C.; Motegi, M.; Beškoski, L. S.; Inui, H. Defluorination of Perfluoroalkyl Acids Is Followed by Production of Monofluorinated Fatty Acids. Science of the Total Environment 2018, 636, 355–359. https://doi.org/10.1016/j.scitotenv.2018.04.243

Supplementary material for: [https://doi.org/10.1016/j.scitotenv.2018.04.243]Related to published version: [http://cherry.chem.bg.ac.rs/handle/123456789/2168

Efficiency of Incentive Spirometry for Video-Assisted Thoracoscopic Surgery for Esophagectomy

Transthoracic subtotal esophagectomy for esophageal cancer is a highly invasive procedure, associated with high mortality and morbidity rates. We examined the use of video-assisted thoracoscopic and laparoscopic surgery for esophagectomy (VATS-E). Further, incentive spirometry (IS) is commonly used in perioperative rehabilitation for esophagectomy. We investigated whether pulmonary complications after VATS-E are related to changes in the perioperative IS volumes and whether such changes could be predictive of these complications. This study included 63 patients who underwent VATS-E from June 2008 to December 2009. IS volumes before and after surgery were recorded for all patients. The perioperative IS volumes and clinicopathological factors were correlated with the incidence of postoperative pneumonia and atelectasis. Nine patients (14.5%) had postoperative pneumonia, and thirteen (22.2%) had atelectasis. Univariate analysis showed an increased risk of atelectasis in patients with diabetes and an increased risk of pneumonia in patients with a long operating time and for whom the lung was adhered to the thoracic wall. The vital capacity (VC) correlation coefficient was 0.674. Further, the risk of pneumonia was high in patients with 13% less than the minimum IS volume/preoperative VC ratio and 22% with less than the average IS volume/preoperative VC ratio. Multivariate regression models for pneumonia showed the same results regarding the IS volume/VC ratio. The results indicated that IS volumes could be used to predict the incidence of complications after VATS-E, and thereby facilitate early application of interventions to prevent pulmonary complications

Relationship between changes in quality of life and genitourinary toxicity grade after brachytherapy with I-125 alone for localised prostate cancer

Background: The relationship between the grading of toxicities based on toxicity criteria and longitudinal changes in quality of life (QOL) scores after permanent prostate brachytherapy (PPB) for localized prostate cancer remains unclear. This study aimed to evaluate these relationships. Materials and methods: We assessed 107 patients treated with PPB using Iodine-125 alone from May 2007 to April 2010. Disease-specific QOL scores before PPB and at 1, 3, 6, 12, and 24 months after PPB were retrospectively evaluated with the Expanded Prostate Cancer Index Composite (EPIC), focusing on urinary domains. Toxicities were graded using the Radiation therapy oncology group and the European organization for research and treatment of cancer toxicity criteria. Results: The median follow-up duration was 116 (range 18–148) months. Thirty-four patients (31.8%) developed grade ≥ 2 acute genitourinary (GU) toxicities; six (5.6%) developed grade ≥ 2 late GU toxicities. The general urinary domain score dropped significantly at 1 month (77.1 ± 14.1) post-PPB compared to the baseline score (92.2 ± 8.2), and then gradually returned to the baseline level by 12 months (93.7 ± 8.3) post-PPB. Reductions in the general urinary domain scores, including its subscale scores at 1, 3, and 6-months post-PPB were significantly greater among patients with grade ≥ 2 GU toxicity than among those with grade 0–1 GU toxicity. Changes in urinary domain scores demonstrated a close relationship with acute GU toxicity grades after PPB. Conclusions: Longitudinal assessments of the EPIC QOL scores provided additional information regarding time-course changes in GU toxicities after PPB.

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

High-grade neuroepithelial tumor with BCL6 corepressor-alteration presenting pathological and radiological calcification: A case report

A 5-year-old girl presented with headache and vomiting. Head computed tomography and magnetic resonance imaging showed a right frontal lobe tumor with marked calcification. The patient underwent resection surgery with suspicion of anaplastic ependymoma, and the tumor was gross totally removed. Pathological examination revealed areas of dense tumor cells with a high nucleocytoplasmic ratio and myxoid areas consisting of tumor cells with a round-shaped nucleus and eosinophilic cytoplasm. Perivascular pseudorosette, necrosis, circumscribed growth, and microcalcification were also observed. Immunohistochemistry demonstrated negative staining for glial fibrillary protein and epithelial membrane antigen. Diagnosis of a high-grade neuroepithelial tumor (HGNET) with BCL6 corepressor (BCOR) alteration was made based on pathological findings and internal tandem duplication in the exon 15 of BCOR. Although calcification on radiological and pathological examination is not typical, it would be essential to recognize that calcification could appear in HGNET-BCOR