Single-cell sequencing techniques from individual to multiomics analyses

Yukie Kashima,Yoshitaka Sakamoto,Keiya Kaneko,Masahide Seki,Yutaka Suzuki,Ayako Suzuki 생화학분자생물학회 2020 Experimental and molecular medicine Vol.52 No.-

Here, we review single-cell sequencing techniques for individual and multiomics profiling in single cells. We mainly describe single-cell genomic, epigenomic, and transcriptomic methods, and examples of their applications. For the integration of multilayered data sets, such as the transcriptome data derived from single-cell RNA sequencing and chromatin accessibility data derived from single-cell ATAC-seq, there are several computational integration methods. We also describe single-cell experimental methods for the simultaneous measurement of two or more omics layers. We can achieve a detailed understanding of the basic molecular profiles and those associated with disease in each cell by utilizing a large number of single-cell sequencing techniques and the accumulated data sets.

Influence of Psychotropic Pro Re Nata Drug Use on Outcomes in Hospitalized Patients with Schizophrenia

Yoshitaka Kyou(Yoshitaka Kyou ),Satoru Oishi(Satoru Oishi ),Takeya Takizawa(Takeya Takizawa ),Yuki Yoshimura(Yuki Yoshimura ),Itsuki Hashimoto(Itsuki Hashimoto ),Ryutaro Suzuki(Ryutaro Suzuki ),Reina 대한정신약물학회 2023 CLINICAL PSYCHOPHARMACOLOGY AND NEUROSCIENCE Vol.21 No.2

Objective: In the treatment of patients with schizophrenia, pro re nata (PRN) drugs are commonly prescribed for medical indications such as agitation, acute psychiatric symptoms, insomnia, and anxiety. However, high-quality evidence supporting the use of PRN medications is lacking, and these drugs are administered on the basis of clinical experience and habits. Therefore, the actual use of psychotropic PRN drugs and its influence on the patients’ outcomes need to be investigated. Methods: This study included 205 patients who underwent inpatient treatment for schizophrenia. We investigated the prescription of psychotropic drugs before admission and at discharge, as well as the dosing frequency of PRN drugs during hospitalization. We also examined the influence of psychotropic PRN drug use on hospitalization days, antipsychotic polypharmacy, and readmission rates. Results: Patients who used psychotropic PRN drugs during hospitalization had significantly longer hospitalization days (p = 7.5 × 10−4) and significantly higher rates of antipsychotic polypharmacy (p = 2.4 × 10−4) at discharge than those who did not use psychotropic PRN drugs. Moreover, a higher number of psychotropic PRN drugs used per day was associated with higher readmission rates within 3 months of discharge (p = 4.4 × 10−3). Conclusion: Psychotropic PRN drug use is associated with prolonged hospitalization, antipsychotic polypharmacy, and increased readmission rates in inpatients with schizophrenia. Therefore, psychiatric symptoms should be stabilized with regularly prescribed medications without the extensive use of psychotropic PRN drugs. Moreover, a system for monitoring and reexamining PRN drug use needs to be established.

Outlier/Noise-Robust Partition of Unity Implicit Surface Reconstruction

Yukie Nagai,Yutaka Ohtake,Hiromasa Suzuki,Hideo Yokota (사)한국CDE학회 2010 한국CAD/CAM학회 국제학술발표 논문집 Vol.2010 No.8

In this paper, we propose an algorithm for outlier/noise-robust surface reconstruction based on a partition of unity (PU) approach. PU based surface reconstruction is a local method that covers an area including sampling points with spherical supports of local approximations, and then generates an approximation function whose zero-level sets approximate the surface. This algorithm has many advantages including representation of fine details, and fast and memory efficient computation. Many of these advantages are realized with the locality of PU however, it is also the reason of outlier/noise-instabilities. Unfortunately, scanned data generally contain much amount of noise, and hence improving the robustness of PU based algorithm is required. We achieve an outlier/noise-robust algorithm with integrating Graph-cut and diffusion of local approximations. Since the characteristics of outliers and noise are fundamentally different, overcoming these two with different approaches is reasonable. In our algorithm, first a spherical cover of an area containing input points is generated following the PU manner. And then Graph-cut is performed in order to determine spherical supports which are considered wrongly approximating affected by outliers. Finally, the PU approximation function is updated so that its gradient field smoothed. This smoothing is based on a diffusion of the local approximations. In this paper we show the effects of this integration approach for several scanned data sets.

The complete genome sequence and phylogenetic analysis of the mitochondrial DNA of the wood-decaying fungus Fomitopsis palustris

Yuki Tanaka,Hideo Dohra,Tomohiro Suzuki,Takeshi Kurokura,Masayuki Iigo,Fubito Toyama,Naoto Habu,Naotake Konno 한국유전학회 2017 Genes & Genomics Vol.39 No.12

The complete mitochondrial genome sequence of the wood-decaying fungus Fomitopsis palustris (Basidiomycete, Agaricomycotina) was determined by next-generation sequencing technology. The complete sequence of the circular mitochondrial DNA of F. palustris was 63,479 bp in length with a 75.98% AT content. The mitochondrial genome encoded 14 conserved proteins, 2 ribosomal RNAs, 26 transfer RNAs, and 19 additional open reading frames. The coxI and cob genes contained six and one group I introns, respectively, and encoded eight open reading frames, including seven intron-encoded endonucleases. The complete mitochondrial genome of F. palustris presented herein represents the first such report for brown rot basidiomycetes. In addition, the BLAST score ratio and phylogenetic analysis may open new avenues to understanding the evolutionary status of this fungus.

Development of Seahorse Robot Capable of Expressing Happiness, Sadness and Anger

Keisuke Sayama,Yuki Suzuki,Hun-ok Lim 제어로봇시스템학회 2011 제어로봇시스템학회 국제학술대회 논문집 Vol.2011 No.10

This paper describes the mechanism and the control system of a seahorse robot that is able to express happiness, sadness and anger. MP motion sensors (Pyroelectric Motion Detection Sensor), force sensors, and color sensors are employed to express emotion. The seahorse robot consists of a base, a body and a head. It has 4 DOFs (2 DOFs in the head and 2 DOFs in the body) and it weighs 800 [g]. Emotion expression experiments are conducted to confirm the mechanism and the control system of the robot and are evaluated by ten subjects. After they watch the body color and motion), they select one of five emotions. The effectiveness of the mechanism and the control of the robot are verified through emotion experiments.

Free Posterior Interosseous Artery Flap for Treatment of First Web Space Contracture: Methods of Venous Anastomosis

Masao Fujiwara,Yuki Matsushita,Yoshikane Maeba,Ayano Suzuki,Hidekazu Fukamizu,Yoshiki Tokura 대한수부외과학회 2019 대한수부외과학회지 Vol.24 No.4

Purpose: First web space widening is crucial in the hand function. The skin on the dorsal side of the forearm can provide a thin and pliable skin suitable for first web space reconstruction. Although previous reports have described the use of the posterior interosseous artery (PIA) flap as a reverse-flow flap for treatment of first web space contracture, only a few have addressed its use as a free flap for this purpose. The caliber of the concomitant veins accompanying the PIA is usually small, which may give rise to a problem in the treatment.Methods: Seven patients with first web space contracture were treated with a free PIA flap and the details of the venous anastomosis method were elucidated.Results: Six of seven flaps survived. In a post-burn case, a flap was lost by late thrombosis. The PIA is anastomosed end-to-end to the dorsal branch of the radial artery. There are two choices for the recipient venous pedicle: concomitant veins of radial artery and a tributary of the cephalic vein. In our cases, there were four types of venous anastomosis. An average postoperative increase of the thumb radial abduction was 36° and that of the palmar abduction was 35°.Conclusion: Since the caliber of the concomitant veins accompanying the PIA is small, a careful scheme for venous anas-tomosis is essential in the treatment of first web space contracture using the free PIA flap.

Impact of Extra-Corporeal Membrane Oxygenation and Blood Purification Therapy on Early Mobilization in the Intensive Care Unit: Retrospective Cohort Study

Watanabe Shinichi,Iida Yuki,Hirasawa Jun,Naito Yuji,Mizutani Motoki,Uemura Akihiro,Nishimura Shogo,Suzuki Keisuke,Morita Yasunari 대한재활의학회 2023 Annals of Rehabilitation Medicine Vol.47 No.3

Objective: To investigate the effect on early mobilization in patients undergoing extra-corporeal membrane oxygenation (ECMO) and acute blood purification therapy in the intensive care unit (ICU).Methods: We conducted this multicenter retrospective cohort study by collecting data from six ICUs in Japan. Consecutive patients who were admitted to the ICU, aged ≥18 years, and received mechanical ventilation for >48 hours were eligible. The analyzed were divided into two groups: ECMO/blood purification or control group. Clinical outcomes; time to first mobilization, number of total ICU rehabilitations, mean and highest ICU mobility scale (IMS); and daily barrier changes were also investigated.Results: A total of 204 patients were included in the analysis, 43 in the ECMO/blood purification group and 161 in the control group. In comparison of clinical outcome, the ECMO/blood purification group had a significantly longer time to first mobilization: ECMO/blood purification group 6 vs. control group 4 (p=0.003), higher number of total ICU rehabilitations: 6 vs. 5 (p=0.042), lower mean: 0 vs. 1 (p=0.043) and highest IMS: 2 vs. 3 (p=0.039) during ICU stay. Circulatory factor were most frequently described as barriers to early mobilization on days 1 (51%), 2 (47%), and 3 (26%). On days 4 to 7, the most frequently described barrier was consciousness factors (21%, 16%, 19%, and 21%, respectively)Conclusion: The results of this study comparing the ECMO/blood purification group and the untreated group in the ICU showed that the ECMO/blood purification group had significantly longer days to mobilization and significantly lower mean and highest IMS.

A system for three-dimensional gaze fixation analysis using eye tracking glasses

Ryo Takahashi,Hiromasa Suzuki,Jouh Yeong Chew,Yutaka Ohtake,Yukie Nagai,Koichi Ohtomi 한국CDE학회 2018 Journal of computational design and engineering Vol.5 No.4

Eye tracking is a technology that has quickly become a commonplace tool for evaluating package and webpage design. In such design processes, static two-dimensional images are shown on a computer screen while a subject’s gaze where he or she looks is measured via an eye tracking device. The collected gaze fixation data are then visualized and analyzed via gaze plots and heat maps. Such evaluations using two-dimensional images are often too limited to analyze gaze on three-dimensional physical objects such as products because users look at them not from a single point of view but rather from various angles. Therefore in this study we propose methods for collecting gaze fixation data for a three-dimensional model of a given product and visualizing corresponding gaze plots and heat maps also in three dimen-sions. To achieve our goals, we used a wearable eye-tracking device, i.e., eye-tracking glasses. Further, we implemented a prototype system to demonstrate its advantages in comparison with two-dimensional gaze fixation methods.

Rapid Identification of blaIMP-1 and blaIMP-6 by Multiplex Amplification Refractory Mutation System PCR

Akiyo Nakano,Ryuichi Nakano,Yuki Suzuki,Kyoichi Saito,Kei Kasahara,Shiro Endo,Hisakazu Yano 대한진단검사의학회 2018 Annals of Laboratory Medicine Vol.38 No.4

Dear Editor, Carbapenem-resistant Enterobacteriaceae have acquired carbapenemase genes [1], which differ substantially across countries [2]. Transferable carbapenemase IMP-type metallo-β-lactamases, particularly IMP-1 and IMP-6, are commonly identified in the clinical setting in Japan [3, 4] and exhibit different substrate specificity despite having a difference of only one amino acid (IMP-6: Ser214Gly). IMP-1 producers are more resistant to imipenem than to meropenem, whereas IMP-6 producers are more resistant to meropenem [5]. We previously found that the susceptibility rate of IMP-6-positive Escherichia coli was higher for imipenem than for meropenem [3]. Thus, IMP-6-producing isolates may be erroneously categorized as imipenem-susceptible, which could lead to treatment failure in patients.

Flattening simulations of 3D thick sheets made of fiber composite materials

Morioka, Kotaro,Ohtake, Yutaka,Suzuki, Hiromasa,Nagai, Yukie,Hishida, Hiroyuki,Inagaki, Koichi,Nakamura, Takeshi,Watanabe, Fumiaki Society for Computational Design and Engineering 2015 Journal of computational design and engineering Vol.2 No.2

Recently, fiber composite materials have been attracting attention from industry because of their remarkable material characteristics, including light weight and high stiffness. However, the costs of products composed of fiber materials remain high because of the lack of effective manufacturing and designing technologies. To improve the relevant design technology, this paper proposes a novel simulation method for deforming fiber materials. Specifically, given a 3D model with constant thickness and known fiber orientation, the proposed method simulates the deformation of a model made of thick fiber-material. The method separates a 3D sheet model into two surfaces and then flattens these surfaces into two dimensional planes by a parameterization method with involves cross vector fields. The cross vector fields are generated by propagating the given fiber orientations specified at several important points on the 3D model. Integration of the cross vector fields gives parameterization with low-stretch and low-distortion.