Practical Data Processing Approach for RNA Sequencing of Microorganisms

The rapid evolvement of sequencing technology has generated huge amounts of DNA/RNA sequences, even with the continuous performance acceleration. Due to the wide variety of basic studies and applications derived from the huge number of species and the microorganism diversity, the targets to be sequenced are also expanding. The huge amounts of data generated by recently developed high-throughput sequencers have required highly efficient data analysis algorithms using recently developed high-performance computers. We have developed a highly accurate and cost-effective mapping strategy that includes the exclusion of unreliable base calls and correction of the reference sequence through provisional mapping of RNA sequencing reads. The use of mapping software tools, such as HISAT and STAR, precisely aligned RNA-Seq reads to the genome of a filamentous fungus considering exon-intron boundaries. The accuracy of the expression analysis through the refinement of gene models was achieved by the results of mapped RNA-Seq reads in combination with ab initio gene finding tools using generalized hidden Markov models (GHMMs). Visualization of the mapping results greatly helps evaluate and improve the entire analysis in terms of both wet experiment and data processing. We believe that at least a portion of our approach is useful and applicable to the analysis of any microorganism

Risk Factors for Severe Obstructive Sleep Apnea Including Sleeping Position and its Gender Difference : A Retrospective Single-institute Study in Japan

Article信州医学雑誌 69(6) : 363-371(2021)departmental bulletin pape

Idiopathic Pneumonia Syndrome Refractory to Ruxolitinib after Post-Transplant Cyclophosphamide-based Haploidentical Hematopoietic Stem Cell Transplantation: Lung Pathological Findings from an Autopsy Case

A 69-year-old Japanese man with acute leukemia received post-transplant cyclophosphamide-based haploidentical stem cell transplantation (PTCY-haplo-SCT) but was readmitted with dyspnea and ground-glass-opacities of the lungs. Bronchoscopy showed inflammatory changes with no signs of infection. He received steroids but required intubation as his condition deteriorated. In addition to antithymocyte globulin and cyclophosphamide, we administered ruxolitinib but failed to save him. Autopsy findings revealed fibrotic nonspecific interstitial pneumonia (NSIP) without evidence of organizing pneumonia or infection. Thus, we diagnosed idiopathic pneumonia syndrome (IPS). As far as our knowledge, this is the first case of IPS with NSIP histology after PTCY-haplo-SCT

Acute Exacerbation of Pulmonary Fibrosis in Syndrome of Combined Pulmonary Fibrosis and Emphysema Following Lung Surgery : A Report of Two Cases

We herein report two cases of an acute exacerbation of pulmonary fibrosis in the syndrome of combined pulmonary fibrosis and emphysema (CPFE) following lung surgery, and also review the relevant literature. One is a 76-year-old man, who had been diagnosed with CPFE and lung cancer and undergone lobectomy. He was admitted to our hospital because of aggravation of dyspnea 50 days after lung surgery. The other is a 69-yearold man who had been diagnosed with pulmonary bulla, pulmonary emphysema and idiopathic interstitial pneumonia at 53 years old and was complicated by lung cancer. He underwent right lower lobectomy and presented with slight fever and desaturation 18 days after lung surgery. In both cases, chest computed tomography showed diffuse bilateral ground-glass opacities superimposed on preceding reticular opacities in the lower lung field. They were diagnosed as acute exacerbation of pulmonary fibrosis in CPFE.A strict followup is required, because the prevalence of lung cancer may be higher, and acute exacerbation may occur following lung surgery in CPFE patients. HRCT plays an important role in evaluating the occurrence of lung cancer at an early stage and for determining whether there is an acute exacerbation of pulmonary fibrosis in CPFE patients.Article信州医学雑誌 60(3): 149-156(2012)journal articl

Low-Mass Star Formation, Triggered by Supernova in Primordial Clouds

The evolution of a gas shell, swept by the supernova remnant of a massive first generation star, is studied with H_2 and HD chemistry taken into account. When a first-generation star explodes as a supernova, H_2 and HD molecules are formed in the swept gas shell and effectively cool the gas shell to temperatures of 32 K - 154 K. If the supernova remnant can sweep to gather the ambient gas, the gas shell comes to be dominated by its self-gravity, and hence, is expected to fragment. Our result shows that for a reasonable range of temperatures (200 K - 1000 K) of interstellar gas, the formation of second-generation stars can be triggered by a single supernova or hypernova.Comment: 38pages, 10 figures, The Astrophysical Journal, accepted 8 Dec. 200