- 著者
- Fumihiro Asano Naofumi Shinagawa Takashi Ishida Akifumi Tsuzuku Motoko Tachihara Kenya Kanazawa Noriyuki Yamada Satoshi Oizumi Hiroshi Moriya
- 出版者
- The Japanese Society of Internal Medicine
- 雑誌
- Internal Medicine (ISSN:09182918)
- 巻号頁・発行日
- vol.54, no.9, pp.1021-1025, 2015 (Released:2015-05-01)
- 参考文献数
- 19
- 被引用文献数
- 6 27 4
Objective Bronchoscopy using radial-endobronchial ultrasound (R-EBUS) and virtual bronchoscopic navigation (VBN) is a promising method for diagnosing peripheral pulmonary lesions. We previously performed a randomized comparative trial (RCT) (i.e., VBN combined with EBUS RCT) involving patients with 30-mm or smaller peripheral pulmonary lesions and found that the addition of VBN to R-EBUS improved the diagnostic yield. In the present study, we performed a retrospective subanalysis in order to identify patients for whom VBN is useful. Methods The per-protocol population (194 cases) of the VBN combined with EBUS RCT was divided into subgroups based on the lesion size, lung lobe containing the lesion, lesion location, presence or absence of involved bronchi (bronchus sign) on thin-section CT and whether the lesion was detected on posterior-anterior (P-A) radiographs. The difference in the diagnostic yield between the VBN-assisted (VBNA) and non-VBN-assisted (NVBNA) groups was investigated. Results Within the bronchus sign-positive subgroup, the diagnostic yield in the VBNA and NVBNA groups was 94.4% (68/72) and 77.8% (56/72), respectively, showing a significantly higher yield in the VBNA group (p=0.004; odds ratio: 4.9). The yield was particularly high for lesions smaller than 20 mm (94.6% vs. 70.7%; p=0.006), lesions located in the peripheral third of the lung field (95.1% vs. 71.4%; p=0.005) and lesions invisible on P-A radiographs (90.0% vs. 41.7%; p=0.026). Conclusion VBN improves the diagnostic yield when combined with R-EBUS to assess lesions exhibiting involved bronchi on CT images.
- 著者
- Wisnu Ananta Kusuma Takashi Ishida Yutaka Akiyama
- 出版者
- Information Processing Society of Japan
- 雑誌
- IPSJ Transactions on Bioinformatics (ISSN:18826679)
- 巻号頁・発行日
- vol.4, pp.21-33, 2011 (Released:2011-11-04)
- 参考文献数
- 27
- 被引用文献数
- 2 2
De novo DNA sequence assembly is very important in genome sequence analysis. In this paper, we investigated two of the major approaches for de novo DNA sequence assembly of very short reads: overlap-layout-consensus (OLC) and Eulerian path. From that investigation, we developed a new assembly technique by combining the OLC and the Eulerian path methods in a hierarchical process. The contigs yielded by these two approaches were treated as reads and were assembled again to yield longer contigs. We tested our approach using three real very-short-read datasets generated by an Illumina Genome Analyzer and four simulated very-short-read datasets that contained sequencing errors. The sequencing errors were modeled based on Illumina's sequencing technology. As a result, our combined approach yielded longer contigs than those of Edena (OLC) and Velvet (Eulerian path) in various coverage depths and was comparable to SOAPdenovo, in terms of N50 size and maximum contig lengths. The assembly results were also validated by comparing contigs that were produced by assemblers with their reference sequence from an NCBI database. The results show that our approach produces more accurate results than Velvet, Edena, and SOAPdenovo alone. This comparison indicates that our approach is a viable way to assemble very short reads from next generation sequencers.
- 著者
- Hikaru Mamizu Takeshi Ohta Kensuke Yanai Ryo Yamazaki Maiko Mamizu Daisuke Ishikawa Hidenori Kawakami Toshiki Furukawa Takashi Ishida
- 出版者
- The Japanese Society of Internal Medicine
- 雑誌
- Internal Medicine (ISSN:09182918)
- 巻号頁・発行日
- pp.1302-22, (Released:2023-02-22)
- 参考文献数
- 22
We herein report a 75-year-old woman who presented with dyspnea and purpura. She was diagnosed with eosinophilic granulomatosis with polyangiitis (EGPA) based on axonal damage observed in the left tibial nerve and skin and lung pathologies. Lung pathology showed IgG4-positive plasma cells, considered a complication of IgG4-related disease (IgG4-RD). Computed tomography revealed thickening of the abdominal aorta and a poor contrast area in the left kidney, which was indicative of IgG4-RD. Steroid administration improved the IgG4-RD. However, the EGPA resisted treatment; therefore, immunosuppressive drugs and mepolizumab were administered. Refractory EGPA complicated with IgG4-RD showed different treatment responses for each organ.
- 著者
- Reira Suzuki Takashi Ueda Takuji Wada Masaki Ito Takashi Ishida Shinichiro Sawa
- 出版者
- Japanese Society for Plant Biotechnology
- 雑誌
- Plant Biotechnology (ISSN:13424580)
- 巻号頁・発行日
- vol.38, no.1, pp.1-8, 2021-03-25 (Released:2021-03-25)
- 参考文献数
- 45
- 被引用文献数
- 5
Root-knot nematodes (RKN; Meloidogyne incognita) are phytoparasitic nematodes that cause significant damage to crop plants worldwide. Recent studies have revealed that RKNs disrupt various physiological processes in host plant cells to induce gall formation. However, little is known about the molecular mechanisms of gall formation induced by nematodes. We have previously found that RNA expression levels of some of genes related to micro-RNA, cell division, membrane traffic, vascular formation, and meristem maintenance system were modified by nematode infection. Here we evaluated these genes importance during nematode infection by using Arabidopsis mutants and/or β-glucronidase (GUS) marker genes, particularly after inoculation with nematodes, to identify the genes involved in successful nematode infection. Our results provide new insights not only for the basic biology of plant–nematode interactions but also to improve nematode control in an agricultural setting.
- 著者
- Takashi Yoshida Takuto Tachita Haruna Fujinami Yoshiko Oshima Hirokazu Sasaki Yoshiaki Marumo Tomoko Narita Asahi Ito Masaki Ri Shigeru Kusumoto Takashi Ishida Hirokazu Komatsu Shinsuke Iida
- 出版者
- The Japanese Society of Internal Medicine
- 雑誌
- Internal Medicine (ISSN:09182918)
- 巻号頁・発行日
- pp.2082-18, (Released:2019-04-17)
- 参考文献数
- 27
- 被引用文献数
- 7
Infectious diseases, including those caused by fungi, remain important issues in patients receiving malignant lymphoma chemotherapy. We herein report a rare case of Exophiala dermatitidis fungemia during chemotherapy in a 67-year-old woman admitted to our hospital. She had a fever that could not be resolved despite antifungal therapy. Yeast-like fungi were detected in blood culture samples, but biochemical identification was difficult. E. dermatitidis, a black mold, was identified using time-of-flight mass spectrometry. The patient finally improved after her treatment was switched to voriconazole. Fungal infection is difficult to diagnose and treat, but this novel approach can improve patients' outcomes.
- 著者
- Keisuke Yanagisawa Takashi Ishida Yutaka Akiyama
- 出版者
- 一般社団法人 情報処理学会
- 雑誌
- IPSJ Transactions on Bioinformatics (ISSN:18826679)
- 巻号頁・発行日
- vol.8, pp.21-27, 2015 (Released:2015-08-19)
- 参考文献数
- 21
It is necessary to confirm that a new drug can be appropriately cleared from the human body. However, checking the clearance pathway of a drug in the human body requires clinical trials, and therefore requires large cost. Thus, computational methods for drug clearance pathway prediction have been studied. The proposed prediction methods developed previously were based on a supervised learning algorithm, which requires clearance pathway information for all drugs in a training set as input labels. However, these data are often insufficient in its numbers because of the high cost of their acquisition. In this paper, we propose a new drug clearance pathway prediction method based on semi-supervised learning, which can use not only labeled data but also unlabeled data. We evaluated the effectiveness of our method, focusing on the cytochrome P450 2C19 enzyme, which is involved in one of the major clearance pathways.