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Article ; Online: Development of a Rapid Identification Method for a Variety of Antibody Candidates Using High-throughput Sequencing.

Ito, Yuji

Yakugaku zasshi : Journal of the Pharmaceutical Society of Japan

2017 Volume 137, Issue 7, Page(s) 823–830

Abstract: As an alternative to hybridoma technology, the antibody phage library system can also be used for antibody selection. This method enables the isolation of antigen-specific binders through an in vitro selection process known as biopanning. While it has ... ...

Abstract	As an alternative to hybridoma technology, the antibody phage library system can also be used for antibody selection. This method enables the isolation of antigen-specific binders through an in vitro selection process known as biopanning. While it has several advantages, such as an avoidance of animal immunization, the phage cloning and screening steps of biopanning are time-consuming and problematic. Here, we introduce a novel biopanning method combined with high-throughput sequencing (HTS) using a next-generation sequencer (NGS) to save time and effort in antibody selection, and to increase the diversity of acquired antibody sequences. Biopannings against a target antigen were performed using a human single chain Fv (scFv) antibody phage library. VH genes in pooled phages at each round of biopanning were analyzed by HTS on a NGS. The obtained data were trimmed, merged, and translated into amino acid sequences. The frequencies (%) of the respective VH sequences at each biopanning step were calculated, and the amplification factor (change of frequency through biopanning) was obtained to estimate the potential for antigen binding. A phylogenetic tree was drawn using the top 50 VH sequences with high amplification factors. Representative VH sequences forming the cluster were then picked up and used to reconstruct scFv genes harboring these VHs. Their derived scFv-Fc fusion proteins showed clear antigen binding activity. These results indicate that a combination of biopanning and HTS enables the rapid and comprehensive identification of specific binders from antibody phage libraries.
MeSH term(s)	Amino Acid Sequence ; Animals ; Antibodies/isolation & purification ; Antigens ; Bacteriophages ; High-Throughput Nucleotide Sequencing/methods ; Humans ; Peptide Library ; Single-Chain Antibodies
Chemical Substances	Antibodies ; Antigens ; Peptide Library ; Single-Chain Antibodies
Language	Japanese
Publishing date	2017
Publishing country	Japan
Document type	Journal Article ; Review
ZDB-ID	200514-1
ISSN	1347-5231 ; 0031-6903 ; 0372-7750 ; 0919-2085 ; 0919-2131
ISSN (online)	1347-5231
ISSN	0031-6903 ; 0372-7750 ; 0919-2085 ; 0919-2131
DOI	10.1248/yakushi.16-00252-2
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Article ; Online: Stochastic Optimal Linear Control for Generalized Cost Functions With Time-Invariant Stochastic Parameters.

Ito, Yuji / Fujimoto, Kenji / Tadokoro, Yukihiro

IEEE transactions on cybernetics

2023 Volume PP

Abstract: This study presents the design of feedback controllers for generalized cost functions to deal with stochastic optimal control problems. Target linear systems contain time-invariant stochastic parameters that describe system uncertainty. The cost ... ...

Abstract	This study presents the design of feedback controllers for generalized cost functions to deal with stochastic optimal control problems. Target linear systems contain time-invariant stochastic parameters that describe system uncertainty. The cost functions involve nonlinear mappings and polynomial forms of the system states and inputs to express various performance metrics. Unfortunately, these properties cause difficulties in solving the problems. Conventional methods, such as the principle of optimality, are not employed to solve such problems owing to the time-invariant parameters. As opposed to the well-known quadratic functions, handling the generalized cost functions is a complicated task. This study overcomes these challenges by deriving an explicit relation between the cost function and the linear feedback gain of a controller. The derived relation enables the feedback gain to be optimized via a gradient method. A theoretical analysis ensures the convergence of the proposed gradient method. A suboptimal feedback controller is obtained to solve the problem, even for the generalized cost. Furthermore, the controller guarantees robust stability of the feedback system even with the stochastic parameters. It is demonstrated that the proposed cost function can express an expectation of a quadratic cost, risk-sensitive cost, polynomial cost, and input-to-state gain. A numerical simulation shows the effectiveness of the proposed method.
Language	English
Publishing date	2023-03-21
Publishing country	United States
Document type	Journal Article
ISSN	2168-2275
ISSN (online)	2168-2275
DOI	10.1109/TCYB.2023.3252673
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Article ; Online: Relationship between exercise habits and physical function in children aged 9-12 years.

Takahashi, Daiki / Ito, Tadashi / Ito, Yuji / Natsume, Kentaro / Noritake, Koji / Ochi, Nobuhiko / Sugiura, Hideshi

Nagoya journal of medical science

2024 Volume 86, Issue 1, Page(s) 24–35

Abstract: Exercise improves physical health and positively impacts physical functions in children. Additionally, the habitual exercise established during childhood often continues into adulthood. Therefore, childhood is an important period for establishing healthy ...

Abstract	Exercise improves physical health and positively impacts physical functions in children. Additionally, the habitual exercise established during childhood often continues into adulthood. Therefore, childhood is an important period for establishing healthy habits. Investigating the relationship between the presence or absence of daily exercise and physical functions may provide important information to confirm poor physical function in children with poor exercise habits. Therefore, this study examined the relationship between exercise habits as defined by the Japanese Ministry of Health, Labor, and Welfare and physical function in children aged 9-12 years. Approximately 239 children were included in this study. Participants answered a questionnaire about their exercise habits. We evaluated the skeletal muscle mass index, grip strength, standing broad jump, one-leg standing time, and gait deviation index. Logistic regression analyses were performed to assess exercise habit association with skeletal muscle mass index, physical function, and gait deviation index after adjusting for sex. Of the 239 children, 75.5% (n = 178) had exercise habits. A significant association was noted between exercise habits and skeletal muscle mass index and standing broad jump (skeletal muscle mass index: OR, 1.84; 95% CI, 1.01-3.36 and p<0.05; standing long jump: OR, 1.02; 95% CI, 1.00-1.04 and p<0.05). In conclusion, exercise regardless of exercise level for at least 30 min per day, 2 days per week, for at least 1 year is important for skeletal muscle mass and instantaneous lower limb muscular strength development in school-aged children.
MeSH term(s)	Child ; Humans ; Exercise/physiology ; Hand Strength/physiology ; Surveys and Questionnaires ; Habits ; Muscle Strength/physiology ; Muscle, Skeletal/physiology
Language	English
Publishing date	2024-03-04
Publishing country	Japan
Document type	Journal Article
ZDB-ID	193148-9
ISSN	2186-3326 ; 0027-7622
ISSN (online)	2186-3326
ISSN	0027-7622
DOI	10.18999/nagjms.86.1.24
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Book ; Online: Second Moment Polytopic Systems

Ito, Yuji / Fujimoto, Kenji

Generalization of Uncertain Stochastic Linear Dynamics

2022

Abstract: This paper presents a new paradigm to stabilize uncertain stochastic linear systems. Herein, second moment polytopic (SMP) systems are proposed that generalize systems with both uncertainty and randomness. The SMP systems are characterized by second ... ...

Abstract	This paper presents a new paradigm to stabilize uncertain stochastic linear systems. Herein, second moment polytopic (SMP) systems are proposed that generalize systems with both uncertainty and randomness. The SMP systems are characterized by second moments of the stochastic system matrices and the uncertain parameters. Further, a fundamental theory for guaranteeing stability of the SMP systems is established. It is challenging to analyze the SMP systems owing to both the uncertainty and randomness. An idea to overcome this difficulty is to expand the SMP systems and exclude the randomness. Because the expanded systems contain only the uncertainty, their stability can be analyzed via robust stability theory. The stability of the expanded systems is equivalent to statistical stability of the SMP systems. These facts provide sufficient conditions for the stability of the SMP systems as linear matrix inequalities (MIs). In controller design for the SMP systems, the linear MIs reduce to cubic MIs whose solutions correspond to feedback gains. The cubic MIs are transformed into simpler quadratic MIs that can be solved using optimization techniques. Moreover, solving such non-convex MIs is relaxed into the iteration of a convex optimization. Solutions to the iterative optimization provide feedback gains that stabilize the SMP systems. As demonstrated here, the SMP systems represent linear dynamics with uncertain mean and covariance and other existing systems such as independently identically distributed dynamics and random polytopes. Finally, a numerical simulation shows the effectiveness of the proposed method. Comment: This work has been submitted to the IEEE for possible publication. Copyright may be transferred without notice, after which this version may no longer be accessible
Keywords	Mathematics - Optimization and Control ; Electrical Engineering and Systems Science - Systems and Control
Subject code	510
Publishing date	2022-07-12
Publishing country	us
Document type	Book ; Online
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Article ; Online: A Novel Strategy for Screening Tumor-Specific Variable Domain of Heavy-Chain Antibodies.

Rafique, Abdur / Hichiwa, Genki / Jatnika, Muhammad Feisal / Ito, Yuji

International journal of molecular sciences

2023 Volume 24, Issue 13

Abstract: The properties of the variable domain of heavy-chain (VHH) antibodies are particularly relevant in cancer therapy. To isolate tumor cell-specific VHH antibodies, VHH phage libraries were constructed from multiple tumor cells. After enriching the ... ...

Abstract	The properties of the variable domain of heavy-chain (VHH) antibodies are particularly relevant in cancer therapy. To isolate tumor cell-specific VHH antibodies, VHH phage libraries were constructed from multiple tumor cells. After enriching the libraries against particular tumor cell lines, a next-generation sequencer was used to screen the pooled phages of each library for potential antibody candidates. Based on high amplification folds, 50 sequences from each library were used to construct phylogenetic trees. Several clusters with identical CDR3 were observed. Groups X, Y, and Z were assigned as common sequences among the different trees. These identical groups over the trees were considered to be cross-reactive antibodies. To obtain monoclonal antibodies, we assembled 200 sequences (top 50 sequences from each library) and rebuilt a combined molecular phylogenetic tree. Groups were categorized as A-G. For each group, we constructed a phagemid and determined its binding specificity with tumor cells. The phage-binding results were consistent with the phylogenetic tree-generated groups, which indicated particular tumor-specific clusters; identical groups showed cross-reactivity. The strategy used in the current study is effective for screening and isolating monoclonal antibodies. Specific antibodies can be identified, even when the target markers of cancer cells are unknown.
MeSH term(s)	Phylogeny ; Immunoglobulin Heavy Chains/genetics ; Antibodies, Monoclonal ; Cell Line, Tumor ; Gene Library ; Peptide Library
Chemical Substances	Immunoglobulin Heavy Chains ; Antibodies, Monoclonal ; Peptide Library
Language	English
Publishing date	2023-06-28
Publishing country	Switzerland
Document type	Journal Article
ZDB-ID	2019364-6
ISSN	1422-0067 ; 1422-0067 ; 1661-6596
ISSN (online)	1422-0067
ISSN	1422-0067 ; 1661-6596
DOI	10.3390/ijms241310804
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Article ; Online: Sensitive immunoassay of Legionella using multivalent conjugates of engineered VHHs.

Kiyose, Norihiko / Miyazaki, Nobuo / Furuhata, Katsunori / Ito, Yuji

Journal of biochemistry

2022 Volume 173, Issue 3, Page(s) 185–195

Abstract: VHH antibodies or nanobodies, which are antigen-binding domains of heavy chain antibodies from camelid species, have several advantageous characteristics, including compact molecular size, high productibility in bacteria and easy engineering for ... ...

Abstract	VHH antibodies or nanobodies, which are antigen-binding domains of heavy chain antibodies from camelid species, have several advantageous characteristics, including compact molecular size, high productibility in bacteria and easy engineering for functional improvement. Focusing on these advantages of VHHs, we attempted to establish an immunoassay system for detection of Legionella, the causative pathogen of Legionnaires' disease. A VHH phage display library was constructed using cDNA from B cells of alpacas immunized with Legionella pneumophila serogroup1 (LpSG1). Through biopanning, two specific VHH clones were isolated and used to construct a Legionella detection system based on the latex agglutination assay. After engineering the VHHs and improving the assay system, the sensitive detection system was successfully established for the LpSG1 antigen. The immunoassay developed in this study should be useful in easy and sensitive detection of Legionella, the causative agent of Legionnaires' disease, which is a potentially fatal pneumonia.
MeSH term(s)	Humans ; Legionella ; Legionnaires' Disease ; Antigens ; Immunoassay ; Immunoglobulin Heavy Chains ; Single-Domain Antibodies
Chemical Substances	Antigens ; Immunoglobulin Heavy Chains ; Single-Domain Antibodies
Language	English
Publishing date	2022-12-16
Publishing country	England
Document type	Journal Article
ZDB-ID	218073-x
ISSN	1756-2651 ; 0021-924X
ISSN (online)	1756-2651
ISSN	0021-924X
DOI	10.1093/jb/mvac102
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Article: Evaluation of Muscle Oxygen Dynamics in Children's Gait and Its Relationship with the Physiological Cost Index.

Shirai, Yuya / Ito, Tadashi / Ito, Yuji / Matsunaga, Naomichi / Noritake, Koji / Ochi, Nobuhiko / Sugiura, Hideshi

Healthcare (Basel, Switzerland)

2023 Volume 11, Issue 2

Abstract: The response of muscle oxygen saturation, which is an index for the energy metabolism of muscles during walking in children, and its relationship to the physiological cost index, which indicates walking efficiency, are unknown. This study aimed to ... ...

Abstract	The response of muscle oxygen saturation, which is an index for the energy metabolism of muscles during walking in children, and its relationship to the physiological cost index, which indicates walking efficiency, are unknown. This study aimed to evaluate muscle oxygen saturation in lower extremity muscles during walking in children, its changes with age, and the relationship between the physiological cost index. The oxygen saturation was measured by the amount of change during a two-minute walk, and the physiological cost index was calculated from the change in heart rate before and after exercise and walking speed. Results were compared for each muscle, and the correlation between the two was examined. Changes in muscle oxygen saturation were greater in the lower leg muscles, significantly greater in the tibialis anterior at six to seven years, and in the gastrocnemius medial head at eight to ten years. The physiological cost index was significantly correlated with changes in muscle oxygen saturation in the tibialis anterior (r = 0.44, p < 0.001). The lower leg muscles were metabolically active in children’s gait, and their response varied with age. Moreover, the muscle oxygenation dynamics of the tibialis anterior may influence walking efficiency.
Language	English
Publishing date	2023-01-11
Publishing country	Switzerland
Document type	Journal Article
ZDB-ID	2721009-1
ISSN	2227-9032
ISSN	2227-9032
DOI	10.3390/healthcare11020221
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Article ; Online: A knowledge-based simple education program for patients with epilepsy in Japan: Effects sustained after the program implementation.

Morita, Takenori / Motooka, Hiromichi / Ito, Yuji / Yasumoto, Shingo / Uchimura, Naohisa / Murotani, Kenta / Ozone, Motohiro

Epilepsy & behavior : E&B

2023 Volume 145, Page(s) 109341

Abstract: Purpose: To investigate the effects of an original education program on patients with epilepsy (PWE). The effects on knowledge about epilepsy, attitude to epilepsy, depression scales, and quality of life were investigated.: Method: Thirty-five PWE ... ...

Abstract	Purpose: To investigate the effects of an original education program on patients with epilepsy (PWE). The effects on knowledge about epilepsy, attitude to epilepsy, depression scales, and quality of life were investigated. Method: Thirty-five PWE participated in a lecture-style educational program using an original knowledge-oriented textbook. All patients were administered a total of four rating scales: the Knowledge about Epilepsy Scale (KES), the Attitude toward Epilepsy Scale (AES), and the Japanese version of the Quality of Life in Epilepsy Inventory (QOLIE-31-P), the Beck Depression Inventory (BDI). The KES and AES of patients (pKES and pAES) were compared to those of medical students (St) and residents (Rd). Results: After education, pKES improved and showed significant differences among pre-and post-education and six months later. Before education, pKES was inferior to St and Rd. However, after education, pKES changed and became superior to St and Rd. Six months later, the advantage was lost, but not significantly. PAES also improved after education, with significant differences before, after, and six months later after education. PAES was statistically inferior to St and Rd before education, but the difference disappeared after education, and the effect persisted after six months. The non-depressed (BDI < 20) and depressed groups (BDI ≧ 20) improved in the KES after education. About the AES, the non-depressive group has a statistical tendency, but not the depressive group. At six months, the depressed group's AES is significantly lower than the non-depressed group. Conclusion: While correct knowledge about epilepsy can improve attitudes and perceptions of epilepsy in PWE, special measures are needed for PWE with depression.
MeSH term(s)	Humans ; Depression/etiology ; Quality of Life ; Japan ; Epilepsy ; Educational Status
Language	English
Publishing date	2023-07-12
Publishing country	United States
Document type	Journal Article
ZDB-ID	2010587-3
ISSN	1525-5069 ; 1525-5050
ISSN (online)	1525-5069
ISSN	1525-5050
DOI	10.1016/j.yebeh.2023.109341
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Article ; Online: Prediction of antigen-responding VHH antibodies by tracking the evolution of antibody along the time course of immunization.

Matsuda, Tomonari / Akazawa-Ogawa, Yoko / Komaba, Lilian-Kaede / Kiyose, Norihiko / Miyazaki, Nobuo / Mizuguchi, Yusaku / Fukuta, Tetsuo / Ito, Yuji / Hagihara, Yoshihisa

Frontiers in immunology

2024 Volume 14, Page(s) 1335462

Abstract: Antibody maturation is the central function of the adaptive immune response. This process is driven by the repetitive selection of mutations that increase the affinity toward antigens. We hypothesized that a precise observation of this process by high- ... ...

Abstract	Antibody maturation is the central function of the adaptive immune response. This process is driven by the repetitive selection of mutations that increase the affinity toward antigens. We hypothesized that a precise observation of this process by high-throughput sequencing along the time course of immunization will enable us to predict the antibodies reacting to the immunized antigen without any additional
MeSH term(s)	Animals ; Single-Domain Antibodies ; Camelids, New World ; Immunization ; Vaccination ; Antigens ; Immunoglobulin G
Chemical Substances	Single-Domain Antibodies ; Antigens ; Immunoglobulin G
Language	English
Publishing date	2024-01-16
Publishing country	Switzerland
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	2606827-8
ISSN	1664-3224 ; 1664-3224
ISSN (online)	1664-3224
ISSN	1664-3224
DOI	10.3389/fimmu.2023.1335462
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Article ; Online: COVID-19 symptom-onset to diagnosis and diagnosis to treatment intervals are significant predictors of disease progression and hospitalization in high-risk patients: A real world analysis.

Shimizu, Hideyasu / Kawase, Jin / Hayashi, Masamichi / Imaizumi, Kazuyoshi / Ito, Yuji / Okazawa, Mitsushi

Respiratory investigation

2023 Volume 61, Issue 2, Page(s) 220–229

Abstract: Background: Coronavirus disease (COVID-19) is overwhelming healthcare systems worldwide. This study aimed to elucidate factors that influence disease progression to pneumonia and hospitalization before and after antiviral treatment for COVID-19 in an ... ...

Abstract	Background: Coronavirus disease (COVID-19) is overwhelming healthcare systems worldwide. This study aimed to elucidate factors that influence disease progression to pneumonia and hospitalization before and after antiviral treatment for COVID-19 in an outpatient setting. Methods: A total of 206 high-risk patients with COVID-19 were treated with sotrovimab, remdesivir, and molnupiravir at the Toshiwakai clinic between January 4 and April 30, 2022. Of these, 49 patients visited the Toshiwakai clinic directly and were treated immediately after diagnosis (Toshiwakai-clinic study group). The remaining patients were diagnosed elsewhere, and of these, 102 patients were quarantined at home (health-center study group) and 55 at designated facilities (quarantine-facility study group) before being referred to Toshiwakai clinic. Patients were categorized into those with mild and moderate COVID-19, based on the presence of pneumonia at the initial visit to Toshiwakai clinic. Results: The symptom-onset-to-diagnosis and diagnosis-to-treatment intervals were significant predictors of moderate disease. Age, dyspnea, and diagnosis-to-treatment interval at the first visit to Toshiwakai clinic were significant predictors for hospitalization even after antiviral treatment. Although the symptom-onset-to-diagnosis interval did not differ among the three study groups, the diagnosis-to-treatment and symptom-onset-to-treatment intervals were significantly longer in the health-center and quarantine-facility study groups than in the Toshiwakai-clinic study group. Conclusion: The symptom-onset-to-diagnosis and diagnosis-to-treatment intervals reflect diagnostic and interventional delays, respectively, which are closely related to the current COVID-19 clinical management protocol. Easy access to the clinics and immediate antiviral treatment after diagnosis may be the best methods to prevent disease progression and hospitalization in high-risk patients.
MeSH term(s)	Humans ; COVID-19 ; SARS-CoV-2 ; Hospitalization ; Disease Progression ; Antiviral Agents ; COVID-19 Testing
Chemical Substances	Antiviral Agents
Language	English
Publishing date	2023-02-01
Publishing country	Netherlands
Document type	Journal Article
ZDB-ID	2660821-2
ISSN	2212-5353 ; 2212-5345
ISSN (online)	2212-5353
ISSN	2212-5345
DOI	10.1016/j.resinv.2023.01.002
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