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Morinobu Seki, Akinori Uruha, Yuko Ohnuki, Sachiko Kamada, Tomoko Noda, Asako Onda, Masayuki Ohira, Aiko Isami, Sumie Hiramatsu, Makoto Hibino, Shunya Nakane, Seiya Noda, Sachiko Yutani, Akira Hanazono, Hiroshi Yaguchi, Masaki Takao, Takashi Shiina, Masahisa Katsuno, Jin Nakahara, Shiro Matsubara, Ichizo Nishino, Shigeaki Suzuki
OBJECTIVE: To characterize the inflammatory myopathy associated with programmed cell death 1 inhibitors (PD-1 myopathy). METHODS: We studied 19 Japanese patients with PD-1 myopathy (13 men and 6 women, mean age 70 years), who were referred to Keio University. As control groups, we used 68 patients with anti-signal recognition particle antibodies, 51 patients with anti-aminoacyl transfer RNA synthetase antibodies and 460 healthy subjects. RESULTS: In regard to muscle-disease severity, 10 patients showed a mild form of disease and 9 patients showed a severe form...
March 9, 2019: Journal of Autoimmunity
Rurina Watanuki, Tetsu Hayashida, Yuko Kawai, Masayuki Kikuchi, Ayako Nakashoji, Takamichi Yokoe, Tomoka Toyota, Tomoko Seki, Maiko Takahashi, Yuko Kitagawa
PURPOSE: In adjuvant settings of human epidermal growth factor receptor 2 (HER2)-positive breast cancer, anthracycline-based chemotherapy followed by taxane and trastuzumab is a standard regimen. Recent studies have reported the use of anthracycline-free adjuvant chemotherapy in selected HER2-positive breast cancer patients. We conducted a single-center retrospective study to identify the characteristics of HER2-positive breast cancer patients for whom anthracyclines can be safely omitted...
February 27, 2019: International Journal of Clinical Oncology
Y Nakamura, K Tanese, I Hirai, M Amagai, Y Kawakami, T Funakoshi
BACKGROUND: Extramammary Paget's disease (EMPD) is a rare intraepithelial adenocarcinoma affecting the genitals and axillary regions. As metastasis of these tumours is itself rare, solid disease management strategies have not been established. Serum carcinoembryonic antigen (CEA) and cytokeratin 19 fragment 21-1 (CYFRA 21-1) levels have been identified as candidate biomarkers for tumour progression in EMPD; however, neither the accuracy of, nor correlation between, these markers have been examined in EMPD patients...
February 21, 2019: British Journal of Dermatology
Sandra J Aedo, Helena R Ma, Mark P Brynildsen
The Keio single gene knockout collection comprises approximately 4000 mutants of E. coli K12 strain BW25113, where each mutant contains a kanamycin resistance cassette in place of a single nonessential gene. This mutant library has proven to be incredibly useful in the fields of bacteriology, chemical genomics, biotechnology, and systems biology, which is evidenced by the greater than 3800 citations that the article describing its construction has garnered in the approximate first 11 years since its publication...
2019: Methods in Molecular Biology
Hiroko Komatsu, Kaori Yagasaki, Kenro Hirata, Yasuo Hamamoto
PURPOSE: The objective of this qualitative study was to understand the perceived needs of advanced-stage cancer patients with chemotherapy-related hand-foot syndrome (HFS) and/or targeted therapy-related hand-foot skin reaction (HFSR). METHOD: Face-to-face interviews were conducted with 20 outpatients with advanced/recurrent cancer and chemotherapy-related HFS and/or targeted therapy-related HFSR using a semi-structured interview guide at Keio University Hospital, Tokyo, Japan...
February 2019: European Journal of Oncology Nursing: the Official Journal of European Oncology Nursing Society
Tokunori Kanazawa, Yasuhiro Minami, Masahiro Jinzaki, Masahiro Toda, Kazunari Yoshida, Hikaru Sasaki
The promoter methylation status of the O6 -methylguanine-DNA methyltransferase (MGMT) gene has been described as the most important predictor of chemotherapeutic response and patients' survival in glioblastomas (GBs). Therefore, prediction of the MGMT promoter methylation status by imaging would help to preoperatively decide the overall treatment strategy as well as surgical strategy. This study aimed to detect imaging parameters to predict MGMT promoter methylation in GBs by using a commercially available software...
January 23, 2019: Neurosurgical Review
Natalie Gugala, Kate Chatfield-Reed, Raymond J Turner, Gordon Chua
The diagnostic and therapeutic agent gallium offers multiple clinical and commercial uses including the treatment of cancer and the localization of tumors, among others. Further, this metal has been proven to be an effective antimicrobial agent against a number of microbes. Despite the latter, the fundamental mechanisms of gallium action have yet to be fully identified and understood. To further the development of this antimicrobial, it is imperative that we understand the mechanisms by which gallium interacts with cells...
January 9, 2019: Genes
Shinichi Goto, Mai Kimura, Yoshinori Katsumata, Shinya Goto, Takashi Kamatani, Genki Ichihara, Seien Ko, Junichi Sasaki, Keiichi Fukuda, Motoaki Sano
BACKGROUND: Patient with acute coronary syndrome benefits from early revascularization. However, methods for the selection of patients who require urgent revascularization from a variety of patients visiting the emergency room with chest symptoms is not fully established. Electrocardiogram is an easy and rapid procedure, but may contain crucial information not recognized even by well-trained physicians. OBJECTIVE: To make a prediction model for the needs for urgent revascularization from 12-lead electrocardiogram recorded in the emergency room...
2019: PloS One
Manato Akiyama, Kengo Sato, Yasubumi Sakakibara
A popular approach for predicting RNA secondary structure is the thermodynamic nearest-neighbor model that finds a thermodynamically most stable secondary structure with minimum free energy (MFE). For further improvement, an alternative approach that is based on machine learning techniques has been developed. The machine learning-based approach can employ a fine-grained model that includes much richer feature representations with the ability to fit the training data. Although a machine learning-based fine-grained model achieved extremely high performance in prediction accuracy, a possibility of the risk of overfitting for such a model has been reported...
December 2018: Journal of Bioinformatics and Computational Biology
Maya Hirohara, Yutaka Saito, Yuki Koda, Kengo Sato, Yasubumi Sakakibara
BACKGROUND: Previous studies have suggested deep learning to be a highly effective approach for screening lead compounds for new drugs. Several deep learning models have been developed by addressing the use of various kinds of fingerprints and graph convolution architectures. However, these methods are either advantageous or disadvantageous depending on whether they (1) can distinguish structural differences including chirality of compounds, and (2) can automatically discover effective features...
December 31, 2018: BMC Bioinformatics
Gabriela I Guzmán, Connor A Olson, Ying Hefner, Patrick V Phaneuf, Edward Catoiu, Lais B Crepaldi, Lucas Goldschmidt Micas, Bernhard O Palsson, Adam M Feist
BACKGROUND: Essentiality assays are important tools commonly utilized for the discovery of gene functions. Growth/no growth screens of single gene knockout strain collections are also often utilized to test the predictive power of genome-scale models. False positive predictions occur when computational analysis predicts a gene to be non-essential, however experimental screens deem the gene to be essential. One explanation for this inconsistency is that the model contains the wrong information, possibly an incorrectly annotated alternative pathway or isozyme reaction...
December 17, 2018: BMC Systems Biology
Masashi Takeuchi, Hirofumi Kawakubo, Shuhei Mayanagi, Yoshiyuki Suzuki, Koji Okabayashi, Toshiki Yamashita, Satoshi Kamiya, Tomoyuki Irino, Kazumasa Fukuda, Rieko Nakamura, Koichi Suda, Norihito Wada, Hiroya Takeuchi, Yuko Kitagawa
BACKGROUND: Although some predictive factors of long-term survival after a distal gastrectomy for gastric cancer have been reported, only few studies have predicted long-term outcomes based on preoperative parameters. We aimed to evaluate the reliability of perioperative risk calculator for predicting overall survival (OS) after distal gastrectomy in patients with gastric cancer. METHODS: Overall, 337 patients (225 males, 112 females) who had undergone a distal gastrectomy for gastric cancer at the Keio University Hospital, Tokyo, Japan, between January 2009 and December 2013 were enrolled in this study...
November 26, 2018: Gastric Cancer
Kiyotaka Uchiyama, Naoki Washida, Kaori Muraoka, Kohkichi Morimoto, Takahiro Kasai, Kentaro Yamaki, Kazutoshi Miyashita, Shu Wakino, Hiroshi Itoh
BACKGROUND: Muscle wasting, common and progressive in uremic patients, is associated with a high probability for morbidity, lower health-related quality of life (HRQOL), and mortality. However, exercise tolerance in peritoneal dialysis (PD) patients has not been fully elucidated. The aim of this study was to evaluate exercise capacity, its determinants, and its association with HRQOL in PD patients. METHODS: Outpatients treated with PD at Keio University Hospital from December 2016 to March 2018 were included in this single-center cross-sectional observational study...
November 25, 2018: Peritoneal Dialysis International: Journal of the International Society for Peritoneal Dialysis
Masahiro Yura, Hiroya Takeuchi, Kazumasa Fukuda, Rieko Nakamura, Koichi Suda, Norihito Wada, Hirofumi Kawakubo, Yuko Kitagawa
Aim: The aim of the present study was to clarify esophagogastric junction (EGJ) carcinoma patients who are at high risk of upper and middle mediastinal lymph node (MLN) metastasis. Methods: This was a retrospective study and included 110 consecutive patients with EGJ carcinoma who underwent R0/R1 resection at Keio University Hospital between January 2000 and December 2013. Results: Of the 110 patients, 18 (16.3%) had MLN metastasis, and the number increased to 23 (20...
November 2018: Annals of Gastroenterological Surgery
Hideki Sonobe, Yoko Ogawa, Kentaro Yamada, Eisuke Shimizu, Yuichi Uchino, Mizuka Kamoi, Yumiko Saijo, Mio Yamane, Daniel Citterio, Koji Suzuki, Kazuo Tsubota
PURPOSE: To elucidate the correlation between lactoferrin concentration in the tear film and signs and symptoms of severe dry eye disease (DED) using a novel microfluidic paper-based analytical device (μPAD) and enzyme-linked immunosorbent assay (ELISA). METHODS: Twenty-four patients were recruited at the Keio University Hospital. Using a novel μPAD, lactoferrin concentrations were measured in 4 patients with GVHD-related DED, 3 patients with other type of dry eye and 2 controls (Group A)...
November 3, 2018: Ocular Surface
Goizeder Almagro, Alejandro M Viale, Manuel Montero, Francisco José Muñoz, Edurne Baroja-Fernández, Hirotada Mori, Javier Pozueta-Romero
ADP-glucose is the precursor of glycogen biosynthesis in bacteria, and a compound abundant in the starchy plant organs ingested by many mammals. Here we show that the enteric species Escherichia coli is capable of scavenging exogenous ADP-glucose for use as a glycosyl donor in glycogen biosynthesis and feed the adenine nucleotide pool. To unravel the molecular mechanisms involved in this process, we screened the E. coli single-gene deletion mutants of the Keio collection for glycogen content in ADP-glucose-containing culture medium...
October 19, 2018: Scientific Reports
Tomoyasu Nishimura, Masaki Ota, Masaaki Mori, Naoki Hasegawa, Hiroshi Kawabe, Seiya Kato
We estimated the latent tuberculosis infection (LTBI) rate for foreign-born students at Keio University, Tokyo, Japan, using an interferon-γ release assay. The LTBI rate for students from countries with estimated tuberculosis incidence >100 cases/100,000 persons was high (10.0%). Universities should screen for LTBI in students from countries with high tuberculosis incidence.
November 2018: Emerging Infectious Diseases
Muhammad Azman Zakaria, Mohd Zulkhairi Mohd Yusoff, Mohd Rafein Zakaria, Mohd Ali Hassan, Thomas K Wood, Toshinari Maeda
Pseudogenes in the Escherichia coli genome are assumed to be non-functional. In this study, Keio collection BW25113∆ yqiG and YqiG-producing strain (BW25113/pCA24N-YqiG) were used to evaluate the importance of pseudogene yqiG in hydrogen metabolism. Our results show pseudogene protein YqiG was identified as an essential protein in the production of biohydrogen from glucose. The mutant yqiG decreased biohydrogen production from 37 µmol mg-1 protein to 6 µmol mg-1 protein compared to the wild-type strain, and glucose consumption was reduced by 80%...
October 2018: 3 Biotech
Katsuyoshi Matsuoka, Shunsuke Hamada, Mikiko Shimizu, Kosaku Nanki, Shinta Mizuno, Hiroki Kiyohara, Mari Arai, Shinya Sugimoto, Yasushi Iwao, Haruhiko Ogata, Tadakazu Hisamatsu, Makoto Naganuma, Takanori Kanai, Mayumi Mochizuki, Masayuki Hashiguchi
Since anti-tumor necrosis factor (TNF)-α agents (TNF-α inhibitors) induce both clinical response and remission in patients with moderate to severe inflammatory bowel disease (IBD), the use of anti-TNF therapies has fundamentally changed the approach to treatment for patients with IBD. Infliximab (IFX) is a TNF-α inhibitor approved for the induction and remission of Crohn's disease (CD). However, even among patients who initially demonstrate a clinical response to IFX therapy, secondary loss of response occurs, although the reason remains unknown...
2018: PloS One
Enrique Martínez-Carranza, Luis Servín-González, Miguel Cocotl-Yañez, Gloria Soberón-Chávez
The understanding of why a gene is essential for a bacterium has implications in different research areas, such as bacterial evolution, synthetic biology and biotechnology, making the identification of essential genes a very active research field. Bacterial essential genes have been defined, among other criteria, by the inability to obtain viable mutants in such genes. In the case of Escherichia coli this approach led to the construction of the Keio collection of single-gene knockout mutants that contains deletions of all the open reading frames present in the genome with the exception of 303 genes that were found to be essential for the growth of this bacterium...
October 1, 2018: FEMS Microbiology Letters
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