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Article ; Online: Synthesis and fluorescence properties of butadiyne-linked linear and cyclic carbazole oligomers.

Ogawa, Kazuya / Tanaka, Shohei / Shimura, Kyosuke

RSC advances

2020 Volume 10, Issue 16, Page(s) 9657–9662

Abstract: Butadiyne-linked linear and cyclic carbazole oligomers were successfully synthesized. The intensity of the emission band in the 0-0 band of the highly planar macrocyclics decreased compared to that of the 0-1 band. Contrary to this, for larger ... ...

Abstract	Butadiyne-linked linear and cyclic carbazole oligomers were successfully synthesized. The intensity of the emission band in the 0-0 band of the highly planar macrocyclics decreased compared to that of the 0-1 band. Contrary to this, for larger macrocycles having reduced planarity, the intensity of the emission of the 0-0 band increased as in the cases of the linear compounds. This suggests that the emission color of the π-conjugated molecule can be controlled not only by the difference between the cyclic and chain structures but also by the control of the planarity, and is expected to be a new principle for molecular design in the development of fluorescent materials.
Language	English
Publishing date	2020-03-06
Publishing country	England
Document type	Journal Article
ISSN	2046-2069
ISSN (online)	2046-2069
DOI	10.1039/d0ra00830c
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Article ; Online: Unsupervised Predominant Sense Detection and Its Application to Text Classification

Attaporn Wangpoonsarp / Kazuya Shimura / Fumiyo Fukumoto

Applied Sciences, Vol 10, Iss 6052, p

2020 Volume 6052

Abstract: This paper focuses on the domain-specific senses of words and proposes a method for detecting predominant sense depending on each domain. Our Domain-Specific Senses (DSS) model is an unsupervised manner and detects predominant senses in each domain. We ... ...

Abstract	This paper focuses on the domain-specific senses of words and proposes a method for detecting predominant sense depending on each domain. Our Domain-Specific Senses (DSS) model is an unsupervised manner and detects predominant senses in each domain. We apply a simple Markov Random Walk (MRW) model to ranking senses for each domain. It decides the importance of a sense within a graph by using the similarity of senses. The similarity of senses is obtained by using distributional representations of words from gloss texts in the thesaurus. It can capture large semantic context and thus does not require manual annotation of sense-tagged data. We used the Reuters corpus and the WordNet in the experiments. We applied the results of domain-specific senses to text classification and examined how DSS affects the overall performance of the text classification task. We compared our DSS model with one of the word sense disambiguation techniques (WSD), Context2vec, and the results demonstrate our domain-specific sense approach gains 0.053 F1 improvement on average over the WSD approach.
Keywords	domain-specific sense ; Markov Random Walk ; text classification ; word sense disambiguation ; Technology ; T ; Engineering (General). Civil engineering (General) ; TA1-2040 ; Biology (General) ; QH301-705.5 ; Physics ; QC1-999 ; Chemistry ; QD1-999
Subject code	006
Language	English
Publishing date	2020-09-01T00:00:00Z
Publisher	MDPI AG
Document type	Article ; Online
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Article ; Online: A prospective multicenter study of endoscopic ultrasound-guided fine needle biopsy using a 22-gauge Franseen needle for pancreatic solid lesions.

Ishigaki, Kazunaga / Nakai, Yousuke / Sasahira, Naoki / Sugimori, Kazuya / Kitamura, Katsuya / Iwai, Tomohisa / Matsubara, Saburo / Shimura, Kenji / Itoi, Takao / Ryozawa, Shomei / Ushio, Jun / Doi, Shinpei / Imazu, Hiroo / Maetani, Iruru / Isayama, Hiroyuki

Journal of gastroenterology and hepatology

2021 Volume 36, Issue 10, Page(s) 2754–2761

Abstract: Background and aim: While encouraging data of endoscopic ultrasound (EUS)-guided fine-needle biopsy (EUS-FNB) using a 22-gauge Franseen needle have been reported, large-scale data of per pass and quantitative analyses are still lacking.: Methods: ... ...

Abstract	Background and aim: While encouraging data of endoscopic ultrasound (EUS)-guided fine-needle biopsy (EUS-FNB) using a 22-gauge Franseen needle have been reported, large-scale data of per pass and quantitative analyses are still lacking. Methods: This was a multicenter prospective study of EUS-FNB using the 22-gauge Franseen needle for a pancreatic solid lesion. Cytological and histological analyses per pass were evaluated and semi-quantitative analyses were performed on core tissue and blood contamination. Primary end-point was diagnostic accuracy per session. Prognostic factors were analyzed for diagnostic accuracy, sensitivity, core tissue, and blood contamination. Results: A total of 629 passes were performed in 244 cases at 14 centers between 2018 and 2019. The median tumor size was 29 mm, and the puncture was transduodenal in 43%. The median pass number was 2. Diagnostic accuracy per session, at a first pass, and per pass were 93%, 90%, and 88%. In 198 cases with pancreatic cancer, diagnostic sensitivity per session, at a first pass, and per pass were 94%, 89%, and 89%. The rates of core tissue score of 4 and blood contamination score of 3 were 50% and 47%. The adverse event rate was 1.6%. In the multivariate analysis, tumor size ≤20 mm (odds ratio [OR] of 0.46, P = 0.03), transduodenal puncture (OR of 0.53, P = 0.04), and suction (OR of 0.16, P = 0.01) were associated with lower diagnostic accuracy. Conclusions: The EUS-FNB using the 22-gauge Franseen needle for pancreatic solid lesions showed high per pass and overall diagnostic accuracy.
MeSH term(s)	Endoscopic Ultrasound-Guided Fine Needle Aspiration ; Humans ; Needles ; Pancreas/diagnostic imaging ; Pancreatic Neoplasms/diagnostic imaging ; Prospective Studies
Language	English
Publishing date	2021-05-14
Publishing country	Australia
Document type	Journal Article ; Multicenter Study
ZDB-ID	632882-9
ISSN	1440-1746 ; 0815-9319
ISSN (online)	1440-1746
ISSN	0815-9319
DOI	10.1111/jgh.15534
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Zs.A 2180: Show issues			Location: Je nach Verfügbarkeit (siehe Angabe bei Bestand) bis Jg. 1994: Bestellungen von Artikeln über das Online-Bestellformular Jg. 1995 - 2021: Lesesall (1.OG) ab Jg. 2022: Lesesaal (EG)
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Article ; Online: Human retroviral antisense mRNAs are retained in the nuclei of infected cells for viral persistence.

Ma, Guangyong / Yasunaga, Jun-Ichirou / Shimura, Kazuya / Takemoto, Keiko / Watanabe, Miho / Amano, Masayuki / Nakata, Hirotomo / Liu, Benquan / Zuo, Xiaorui / Matsuoka, Masao

Proceedings of the National Academy of Sciences of the United States of America

2021 Volume 118, Issue 17

Abstract: Human retroviruses, including human T cell leukemia virus type 1 (HTLV-1) and HIV type 1 (HIV-1), encode an antisense gene in the negative strand of the provirus. Besides coding for proteins, the messenger RNAs (mRNAs) of retroviral antisense genes have ... ...

Abstract	Human retroviruses, including human T cell leukemia virus type 1 (HTLV-1) and HIV type 1 (HIV-1), encode an antisense gene in the negative strand of the provirus. Besides coding for proteins, the messenger RNAs (mRNAs) of retroviral antisense genes have also been found to regulate transcription directly. Thus, it has been proposed that retroviruses likely localize their antisense mRNAs to the nucleus in order to regulate nuclear events; however, this opposes the coding function of retroviral antisense mRNAs that requires a cytoplasmic localization for protein translation. Here, we provide direct evidence that retroviral antisense mRNAs are localized predominantly in the nuclei of infected cells. The retroviral 3' LTR induces inefficient polyadenylation and nuclear retention of antisense mRNA. We further reveal that retroviral antisense RNAs retained in the nucleus associate with chromatin and have transcriptional regulatory function. While HTLV-1 antisense mRNA is recruited to the promoter of C-C chemokine receptor type 4 (
MeSH term(s)	Basic-Leucine Zipper Transcription Factors/genetics ; Basic-Leucine Zipper Transcription Factors/metabolism ; Cell Line ; Cell Nucleus/metabolism ; Gene Expression/genetics ; Gene Expression Regulation, Viral/genetics ; HIV-1/genetics ; Human Immunodeficiency Virus Proteins/genetics ; Human Immunodeficiency Virus Proteins/metabolism ; Human T-lymphotropic virus 1/genetics ; Humans ; Primary Cell Culture ; Promoter Regions, Genetic/genetics ; Proviruses/genetics ; RNA, Antisense/genetics ; RNA, Antisense/metabolism ; RNA, Messenger/metabolism ; RNA, Viral/genetics ; Retroviridae Proteins/genetics ; Retroviridae Proteins/metabolism ; Terminal Repeat Sequences/genetics ; Transcription, Genetic/genetics ; Viral Envelope Proteins/genetics ; Viral Envelope Proteins/metabolism ; Viral Proteins/metabolism ; Virus Latency/genetics ; Virus Replication/genetics
Chemical Substances	ASP protein, HIV-1 ; Basic-Leucine Zipper Transcription Factors ; HBZ protein, human T-cell leukemia virus type I ; Human Immunodeficiency Virus Proteins ; RNA, Antisense ; RNA, Messenger ; RNA, Viral ; Retroviridae Proteins ; Viral Envelope Proteins ; Viral Proteins
Language	English
Publishing date	2021-11-18
Publishing country	United States
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	209104-5
ISSN	1091-6490 ; 0027-8424
ISSN (online)	1091-6490
ISSN	0027-8424
DOI	10.1073/pnas.2014783118
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Article ; Online: Impact of HIV-1 infection pathways on susceptibility to antiviral drugs and on virus spread.

Shimura, Kazuya / Miyazato, Paola / Oishi, Shinya / Fujii, Nobutaka / Matsuoka, Masao

Virology

2015 Volume 484, Page(s) 364–376

Abstract: The infection routes of HIV-1 can affect several viral properties, including dissemination, pathogenesis, and immune evasion. In this study, we evaluated the inhibitory activity of a wide variety of anti-HIV drugs, focusing on the impact that different ... ...

Abstract	The infection routes of HIV-1 can affect several viral properties, including dissemination, pathogenesis, and immune evasion. In this study, we evaluated the inhibitory activity of a wide variety of anti-HIV drugs, focusing on the impact that different infection pathways have on their efficacy. Compared to cell-free infection, inhibitory activities were reduced in cell-to-cell productive transmission for all drugs tested. We detected weak reporter-expressing target cells after cell-to-cell transmission in the presence of integrase strand transfer inhibitors (INSTIs). Further analysis revealed that this expression was mainly due to unintegrated circular HIV (cHIV) DNAs, consisting of 1-LTR and 2-LTR circles. When in vitro-constructed cHIV DNAs were introduced into cells, the production of infectious and intercellular transmittable virions was observed, suggesting that cHIV DNA could be a source of infectious virus. These results highlight some advantages of the cell-to-cell infection mode for viral expansion, particularly in the presence of anti-retroviral drugs.
MeSH term(s)	Anti-HIV Agents/pharmacology ; Cell Line ; HIV-1/drug effects ; HIV-1/physiology ; Humans ; Virus Internalization/drug effects ; Virus Release/drug effects ; Virus Replication/drug effects
Chemical Substances	Anti-HIV Agents
Language	English
Publishing date	2015-07-15
Publishing country	United States
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	200425-2
ISSN	1096-0341 ; 0042-6822
ISSN (online)	1096-0341
ISSN	0042-6822
DOI	10.1016/j.virol.2015.06.029
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Article ; Online: Elvitegravir: a new HIV integrase inhibitor.

Shimura, Kazuya / Kodama, Eiichi N

Antiviral chemistry & chemotherapy

2009 Volume 20, Issue 2, Page(s) 79–85

Abstract: Integration is a distinctive and essential process in the HIV infection cycle and thus represents an attractive antiviral drug target. Integrase inhibitors combined with other classes of drug might contribute to long-lasting suppression of HIV type-1 ( ... ...

Abstract	Integration is a distinctive and essential process in the HIV infection cycle and thus represents an attractive antiviral drug target. Integrase inhibitors combined with other classes of drug might contribute to long-lasting suppression of HIV type-1 (HIV-1) replication for many patients. Of the numerous potential integrase inhibitor leads that have been reported, few have reached clinical trials and only one, raltegravir, has been approved (in late 2007) for the treatment of HIV-1-infected patients. Another integrase inhibitor, elvitegravir, is currently showing promise in Phase III clinical studies. Once-daily administration of elvitegravir has a comparable antiviral activity to twice-daily of raltegravir in HIV-1-infected patients. Here, we highlight the salient features of elvitegravir: its chemical structure compared with representative integrase inhibitors, mechanism of action, in vitro and in vivo activity against HIV and other retroviruses, and the effect of integrase polymorphisms and resistance mutations on its anti-HIV activity.
MeSH term(s)	Drug Resistance, Neoplasm/genetics ; HIV Integrase Inhibitors/chemistry ; HIV Integrase Inhibitors/pharmacology ; Humans ; Quinolones/chemistry ; Quinolones/pharmacology ; Retroviridae/drug effects
Chemical Substances	HIV Integrase Inhibitors ; Quinolones ; elvitegravir (4GDQ854U53)
Language	English
Publishing date	2009-10-19
Publishing country	England
Document type	Journal Article ; Research Support, Non-U.S. Gov't ; Review
ZDB-ID	1033586-9
ISSN	2040-2066 ; 0956-3202
ISSN (online)	2040-2066
ISSN	0956-3202
DOI	10.3851/IMP1397
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Article ; Online: Correction: HTLV-1 bZIP Factor Enhances T-cell Proliferation by Impeding the Suppressive Signaling of Co-inhibitory Receptors.

Kinosada, Haruka / Yasunaga, Jun-Ichirou / Shimura, Kazuya / Miyazato, Paola / Onishi, Chiho / Iyoda, Tomonori / Inaba, Kayo / Matsuoka, Masao

PLoS pathogens

2017 Volume 13, Issue 2, Page(s) e1006228

Abstract: This corrects the article DOI: 10.1371/journal.ppat.1006120.]. ...

Abstract	[This corrects the article DOI: 10.1371/journal.ppat.1006120.].
Language	English
Publishing date	2017-02-23
Publishing country	United States
Document type	Published Erratum
ZDB-ID	2205412-1
ISSN	1553-7374 ; 1553-7366
ISSN (online)	1553-7374
ISSN	1553-7366
DOI	10.1371/journal.ppat.1006228
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Article ; Online: Sporadic on/off switching of HTLV-1 Tax expression is crucial to maintain the whole population of virus-induced leukemic cells.

Mahgoub, Mohamed / Yasunaga, Jun-Ichirou / Iwami, Shingo / Nakaoka, Shinji / Koizumi, Yoshiki / Shimura, Kazuya / Matsuoka, Masao

Proceedings of the National Academy of Sciences of the United States of America

2018 Volume 115, Issue 6, Page(s) E1269–E1278

Abstract: Viruses causing chronic infection artfully manipulate infected cells to enable viral persistence in vivo under the pressure of immunity. Human T-cell leukemia virus type 1 (HTLV-1) establishes persistent infection mainly in CD4+ T cells in vivo and ... ...

Abstract	Viruses causing chronic infection artfully manipulate infected cells to enable viral persistence in vivo under the pressure of immunity. Human T-cell leukemia virus type 1 (HTLV-1) establishes persistent infection mainly in CD4+ T cells in vivo and induces leukemia in this subset. HTLV-1-encoded Tax is a critical transactivator of viral replication and a potent oncoprotein, but its significance in pathogenesis remains obscure due to its very low level of expression in vivo. Here, we show that Tax is expressed in a minor fraction of leukemic cells at any given time, and importantly, its expression spontaneously switches between on and off states. Live cell imaging revealed that the average duration of one episode of Tax expression is ∼19 hours. Knockdown of Tax rapidly induced apoptosis in most cells, indicating that Tax is critical for maintaining the population, even if its short-term expression is limited to a small subpopulation. Single-cell analysis and computational simulation suggest that transient Tax expression triggers antiapoptotic machinery, and this effect continues even after Tax expression is diminished; this activation of the antiapoptotic machinery is the critical event for maintaining the population. In addition, Tax is induced by various cytotoxic stresses and also promotes HTLV-1 replication. Thus, it seems that Tax protects infected cells from apoptosis and increases the chance of viral transmission at a critical moment. Keeping the expression of Tax minimal but inducible on demand is, therefore, a fundamental strategy of HTLV-1 to promote persistent infection and leukemogenesis.
MeSH term(s)	Gene Expression Regulation, Viral ; Gene Products, tax/genetics ; Gene Products, tax/metabolism ; HTLV-I Infections/genetics ; HTLV-I Infections/metabolism ; HTLV-I Infections/virology ; Human T-lymphotropic virus 1/pathogenicity ; Humans ; Leukemia-Lymphoma, Adult T-Cell/genetics ; Leukemia-Lymphoma, Adult T-Cell/metabolism ; Leukemia-Lymphoma, Adult T-Cell/virology ; Single-Cell Analysis ; T-Lymphocytes/virology ; Virus Activation ; Virus Replication
Chemical Substances	Gene Products, tax ; tax protein, Human T-lymphotrophic virus 1
Language	English
Publishing date	2018-01-22
Publishing country	United States
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	209104-5
ISSN	1091-6490 ; 0027-8424
ISSN (online)	1091-6490
ISSN	0027-8424
DOI	10.1073/pnas.1715724115
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Article ; Online: Impaired oxidative endoplasmic reticulum stress response caused by deficiency of thyroid hormone receptor α.

Takahashi, Kazuya / Furuya, Fumihiko / Shimura, Hiroki / Kaneshige, Masahiro / Kobayashi, Tetsuro

The Journal of biological chemistry

2014 Volume 289, Issue 18, Page(s) 12485–12493

Abstract: Thyroid hormone receptor α (TRα) is critical to postnatal pancreatic β-cell maintenance. To investigate the association between TRα and the survival of pancreatic β-cells under endoplasmic reticulum (ER) stress, the expression of endogenous TRα was ... ...

Abstract	Thyroid hormone receptor α (TRα) is critical to postnatal pancreatic β-cell maintenance. To investigate the association between TRα and the survival of pancreatic β-cells under endoplasmic reticulum (ER) stress, the expression of endogenous TRα was inhibited by infection with an adenovirus expressing double-stranded short hairpin RNA against TRα (AdshTRα). In control adenovirus-infected pancreatic β-cells, palmitate enhanced the expression of activating transcription factor 4 (ATF4) and heme oxygenase 1, which facilitates adaptation to oxidative ER stress. However, in AdshTRα-infected pancreatic β-cells, palmitate did not induce ATF4-mediated integrated stress response, and oxidative stress-associated apoptotic cell death was significantly enhanced. TRα-deficient mice or wild-type mice (WT) were fed a high fat diet (HFD) for 30 weeks, and the effect of oxidative ER stress on pancreatic β-cells was analyzed. HFD-treated TRα-deficient mice had high blood glucose levels and low plasma insulin levels. In HFD-treated TRα-deficient mice, ATF4 was not induced, and apoptosis was enhanced compared with HFD-treated WT mice. Furthermore, the expression level of 8-hydroxydeoxyguanosine, an oxidative stress marker, was enhanced in the β-cells of HFD-treated TRα-deficient mice. These results indicate that endogenous TRα plays an important role for the expression of ATF4 and facilitates reduced apoptosis in pancreatic β-cells under ER stress.
MeSH term(s)	8-Hydroxy-2'-Deoxyguanosine ; Activating Transcription Factor 4/genetics ; Activating Transcription Factor 4/metabolism ; Animals ; Apoptosis/drug effects ; Apoptosis/genetics ; Apoptosis/physiology ; Blood Glucose/metabolism ; Blotting, Western ; Cell Line, Tumor ; Deoxyguanosine/analogs & derivatives ; Deoxyguanosine/metabolism ; Diet, High-Fat ; Dietary Fats/pharmacology ; Endoplasmic Reticulum Stress/genetics ; Endoplasmic Reticulum Stress/physiology ; Immunohistochemistry ; Insulin/blood ; Insulin-Secreting Cells/drug effects ; Insulin-Secreting Cells/metabolism ; Insulinoma/genetics ; Insulinoma/metabolism ; Insulinoma/pathology ; Mice ; Mice, Inbred C57BL ; Mice, Knockout ; Oxidative Stress ; Pancreatic Neoplasms/genetics ; Pancreatic Neoplasms/metabolism ; Pancreatic Neoplasms/pathology ; RNA Interference ; Reverse Transcriptase Polymerase Chain Reaction ; Thyroid Hormone Receptors alpha/deficiency ; Thyroid Hormone Receptors alpha/genetics
Chemical Substances	Atf4 protein, mouse ; Blood Glucose ; Dietary Fats ; Insulin ; Thyroid Hormone Receptors alpha ; Activating Transcription Factor 4 (145891-90-3) ; 8-Hydroxy-2'-Deoxyguanosine (88847-89-6) ; Deoxyguanosine (G9481N71RO)
Language	English
Publishing date	2014-03-18
Publishing country	United States
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	2997-x
ISSN	1083-351X ; 0021-9258
ISSN (online)	1083-351X
ISSN	0021-9258
DOI	10.1074/jbc.M113.544122
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Article ; Online: Correction

Haruka Kinosada / Jun-Ichirou Yasunaga / Kazuya Shimura / Paola Miyazato / Chiho Onishi / Tomonori Iyoda / Kayo Inaba / Masao Matsuoka

PLoS Pathogens, Vol 13, Iss 2, p e

HTLV-1 bZIP Factor Enhances T-cell Proliferation by Impeding the Suppressive Signaling of Co-inhibitory Receptors.

2017 Volume 1006228

Abstract: This corrects the article DOI:10.1371/journal.ppat.1006120.]. ...

Abstract	[This corrects the article DOI:10.1371/journal.ppat.1006120.].
Keywords	Immunologic diseases. Allergy ; RC581-607 ; Biology (General) ; QH301-705.5
Language	English
Publishing date	2017-02-01T00:00:00Z
Publisher	Public Library of Science (PLoS)
Document type	Article ; Online
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