Search results for: Shohei Yokoyama

Authors: Ágnes Bogárdi-Mészöly, Takeshi Hashimoto, Shohei Yokoyama, Hiroshi Ishikawa

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The spread of Web 2.0 has caused user-generated content explosion. Users can tag resources to describe and organize them. Tag clouds provide rough impression of relative importance of each tag within overall cloud in order to facilitate browsing among numerous tags and resources. The goal of our paper is to enrich visualization of tag clouds. A font distribution algorithm has been proposed to calculate a novel metric based on frequency and content, and to classify among classes from this metric based on power law distribution and percentages. The suggested algorithm has been validated and verified on the tag cloud of a real-world thesis portal.

Keywords: tag cloud, font distribution algorithm, frequency-based, content-based, power law

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Authors: Siti Rahmah Shamsuri, Eiichiro Matsubara, Shohei Shiomi

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The 1D nanomaterial is far surpassed the 0D nanomaterial. It does not just offer most of the benefit of the 0D nanomaterial such as the large surface area, a great number of active site and an efficient interfacial charge transfer but also can assemble into free-standing and flexible electrode due to their high aspect ratio. Thus, it is essential to develop a simple and ease synthesis of this 1D nanomaterial for the practical application. Here, nickel nanowire/cellulose hybrid has been successfully fabricated via a simple liquid-phase method with the assist of the magnetic field. A finer nickel nanowire was heterogeneously nucleated on the surface of the cellulose fiber, which demonstrated the effect of the hydroxyl group on the cellulose structure. The result of the nickel nanowire size was found to vary from 66-114 nm. A detailed discussion on the mechanism of the nickel nanowire/ cellulose hybrid formation is also shown in this paper.

Keywords: cellulose nanofiber, liquid-phase reduction, metal nanowire, nano hybrid material

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Authors: Shohei Nakai, Yasuhiro Yamada

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Weed suppression and weeding are necessary measures for rice cultivation. Weed suppression precedes the process of weeding. It means suppressing the growth of young weeds and creating a weed-less environment. If we suppress the growth of weeds, we can reduce the number of weeds in a paddy field. This would result in a reduction of the weeding work load. In this paper, we will show how we developed a weed suppression robot for the purpose of reducing the weeding work load. The robot has a laser range finder for autonomous mobility and a robot arm for weed suppression. It travels along the rice rows without stepping on and injuring the rice plants in a paddy field. The robot arm applies force to the weed seedlings and thereby suppresses the growth of weeds. This paper will explain the methodology of the autonomous mobile, the experiment in weed suppression, and the method of controlling the robot’s posture on uneven ground.

Keywords: mobile robot, paddy field, robot arm, weed

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Authors: Mosaab A. Omar, Mohammad Saleh Al-Aboody, Mohmed A. Rizk, Shimaa M. Elsayed, Ahmed ElSify, Naoaki Yokoyama, Ikuo Igarashi

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Enoxacin is a broad-spectrum 6-fluoronaphthyridinone antibacterial agent (fluoroquinolones) structurally related to nalidixic acid used mainly in the treatment of urinary tract infections and gonorrhea. Also, it has been shown recently that it may have cancer inhibiting effect. The primary antibabesial effect of Enoxacin is due to inhibition of DNA gyrase subunit A, and DNA topoisomerase. In the present study, enoxacin was tested as a potent inhibitor against the in vitro growth of bovine and equine Piroplasms. The in vitro growth of five Babesia species that were tested was significantly inhibited (P<0.05) by micromolar concentrations of enoxacin (IC50 values= 13.5, 7.2, 7.5, and 24.2 µM for Babesia bovis, Babesia bigemina, Babesia caballi, and Theileria equi, respectively). Enoxacin IC50 values for Babesia and Theileria parasites were satisfactory as the drug is a potent antibacterial drug with minimum side effects. Therefore, enoxacin might be used for the treatment of Babesiosis and Theileriosis especially in case of mixed infections with bacterial diseases or in the case of animal sensitivity against diminazin toxicity.

Keywords: enoxacin, Babesia, Theileria, IC50 and dimenazin

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Authors: Shohei Maruyama, Yasuo Matsuyama, Sachiyo Aburatani

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The development of the method to annotate unknown gene functions is an important task in bioinformatics. One of the approaches for the annotation is The identification of the metabolic pathway that genes are involved in. Gene expression data have been utilized for the identification, since gene expression data reflect various intracellular phenomena. However, it has been difficult to estimate the gene function with high accuracy. It is considered that the low accuracy of the estimation is caused by the difficulty of accurately measuring a gene expression. Even though they are measured under the same condition, the gene expressions will vary usually. In this study, we proposed a feature extraction method focusing on the variability of gene expressions to estimate the genes' metabolic pathway accurately. First, we estimated the distribution of each gene expression from replicate data. Next, we calculated the similarity between all gene pairs by KL divergence, which is a method for calculating the similarity between distributions. Finally, we utilized the similarity vectors as feature vectors and trained the multiclass SVM for identifying the genes' metabolic pathway. To evaluate our developed method, we applied the method to budding yeast and trained the multiclass SVM for identifying the seven metabolic pathways. As a result, the accuracy that calculated by our developed method was higher than the one that calculated from the raw gene expression data. Thus, our developed method combined with KL divergence is useful for identifying the genes' metabolic pathway.

Keywords: metabolic pathways, gene expression data, microarray, Kullback–Leibler divergence, KL divergence, support vector machines, SVM, machine learning

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Authors: Itsuo Yokoyama, Rikako Kikuti, Miti Sekikawa, Tosinori Asai, Sarai Tsuyoshi

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Introduction: Vascular access for hemodialysis therapy is often difficult, even for experienced medical personnel. Ultrasound guided needle placement have been performed occasionally but is not always helpful in certain cases with complicated vascular anatomy. Obtaining precise anatomical knowledge of the vascular structure is important to prevent access-related complications. With augmented reality (AR) device such as AR glasses, the virtual vascular structure is shown superimposed on the actual patient vessels, thus enabling the operator to maneuver catheter placement easily with free both hands. We herein report our method of AR guided vascular access method in dialysis treatment Methods: Three dimensional (3D) object of the arm with arteriovenous fistula is computer graphically created with 3D software from the data obtained by computer tomography, ultrasound echogram, and image scanner. The 3D vascular object thus created is viewed on the screen of the AR digital display device (such as AR glass or iPad). The picture of the vascular anatomical structure becomes visible, which is superimposed over the real patient’s arm, thereby the needle insertion be performed under the guidance of AR visualization with ease. By this method, technical difficulty in catheter placement for dialysis can be lessened and performed safely. Considerations: Virtual reality technology has been applied in various fields and medical use is not an exception. Yet AR devices have not been widely used among medical professions. Visualization of the virtual vascular object can be achieved by creation of accurate three dimensional object with the help of computer graphical technique. Although our experience is limited, this method is applicable with relative easiness and our accumulating evidence has suggested that our method of vascular access with the use of AR can be promising.

Keywords: abdominal-aorta, calcification, extraskeletal, dialysis, computer graphics, 3DCG, CT, calcium, phosphorus

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Authors: Werede Girmay Tesfasilasiea

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Three stratigraphic sections of the Antalo Limestone successions in Mekelle Outlier, northern Ethiopia (at Hagere-Selam, Messobo, and Wukro sections) have been investigated to distinguish their microfacies features, reservoir characterization, and their equivalent depositional environments. The Antalo Limestone successions were deposited in the Mekelle Outlier during the Upper Jurassic period as a result of flooding of the area by the Tethys Ocean toward the southeast direction. This study is based on field description and petrographic analysis to determine the depositional environment, age, and reservoir characteristics of the carbonate units. According to petrographical studies of 100 thin sections and field investigation, 14 microfacies types are recognized. These are grouped into 4 microfacies association of a tidal flat (MFT1-2), lagoons (MFL1-2), shoal (MFS1-4), and open marine environment (MFO1-6). Hence, the Antalo limestone successions are deposited in shallow carbonate ramps with a wide lateral and vertical distribution of facies. The carbonate units in the studied sections are affected by bioturbation, micritization, cementation, dolomitization, dissolution, silicification, and compaction type of early diagenetic alteration. Dissolution and dolomitization affected the type of rock, showing good reservoir quality, while cementation and compaction affected the type of rock, resulting in poor reservoir quality in the Antalo Limestone successions of the Mekelle outlier. Based on the abundant distribution of the Alveosepta jaccardi (Schrodt), Pseudocyclammina lituus (Yokoyama), Kurnubia palestiniensis (Henson), and Somalirhynchia africana in the studied sections the Antalo Limestone successions assigned to the Late Oxfordian-Kimmeridgian age.

Keywords: Antelo limestone successions, depositional environment, Mekelle outlier, microfacies analysis, diagenesis, reservoir quality

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Authors: Shohei Matsuo, Saki Mikai, Hiroshi Morita

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Objectives: Shochu is a popular Japanese distilled spirits. In the production of shochu, the filamentous fungus Aspergillus kawachii has traditionally been used. A. kawachii produces two types of starch hydrolytic enzymes, α-amylase (enzymatic liquefaction) and glucoamylase (enzymatic saccharification). Liquid culture system is a relatively easy microorganism to ferment with relatively low cost of production compared for solid culture. In liquid culture system, acid-unstable α-amylase (α-A) was produced abundantly, but, acid-stable α-amylase (Aα-A) was not produced. Since there is high enzyme productivity, most in shochu brewing have been adopted by a solid culture method. In this study, therefore, we investigated production of Aα-A in liquid culture system. Materials and methods: Microorganism Aspergillus kawachii NBRC 4308 was used. The mold was cultured at 30 °C for 7~14 d to allow formation of conidiospores on slant agar medium. Liquid Culture System: A. kawachii was cultured in a 100 ml of following altered SLS medium: 1.0 g of rice flour, 0.1 g of K2HPO4, 0.1 g of KCl, 0.6 g of tryptone, 0.05 g of MgSO4・7H2O, 0.001 g of FeSO4・7H2O, 0.0003 g of ZnSO4・7H2O, 0.021 g of CaCl2, 0.33 of citric acid (pH 3.0). The pH of the medium was adjusted to the designated value with 10 % HCl solution. The cultivation was shaking at 30 °C and 200 rpm for 72 h. It was filtered to obtain a crude enzyme solution. Aα-A assay: The crude enzyme solution was analyzed. An acid-stable α-amylase activity was carried out using an α-amylase assay kit (Kikkoman Corporation, Noda, Japan). It was conducted after adding 9 ml of 100 mM acetate buffer (pH 3.0) to 1 ml of the culture product supernatant and acid treatment at 37°C for 1 h. One unit of a-amylase activity was defined as the amount of enzyme that yielded 1 mmol of 2-chloro-4-nitrophenyl 6-azide-6-deoxy-b-maltopentaoside (CNP) per minute. Results and Conclusion: We experimented with co-culture of A. kawachii and lactobacillus in order to get control of pH in altered SLS medium. However, high production of acid-stable α-amylase was not obtained. We experimented with yoghurt or milk made an addition to liquid culture. The result indicated that high production of acid-stable α-amylase (964 U/g-substrate) was obtained when milk made an addition to liquid culture. Phosphate concentration in the liquid medium was a major cause of increased acid-stable α-amylase activity. In liquid culture, acid-stable α-amylase activity was enhanced by milk, but Fats and oils in the milk were oxidized. In addition, Tryptone is not approved as a food additive in Japan. Thus, alter SLS medium added to skim milk excepting for the fats and oils in the milk instead of tryptone. The result indicated that high production of acid-stable α-amylase was obtained with the same effect as milk.

Keywords: acid-stable α-amylase, liquid culture, milk, shochu

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Authors: Itsuo Yokoyama, Rika Kikuti, Naoko Watabe

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Introduction: It has been known that chronic kidney disease (CKD) patients can benefit from physical exercise during dialysis therapy improving aerobic capacity, muscle function, cardiovascular function, and overall health-related quality of life. This study aimed to evaluate the effectiveness of dialysis rehabilitation. Materials and Methods: A total of 55 patients underwent two-hour resistance exercise training during each hemodialysis session for three consecutive months. Various routine clinical data were collected, including the calculation of the planar dimension of the muscle area in both upper legs at the level of the ischial bone. This area calculation was possible in 26 patients who had yearly plain abdominal computed tomography (CT) scans. DICOM files from the CT scans were used with 3D Slicer software for area calculation. An age and sex-matched group of 26 patients without dialysis rehabilitation also had yearly CT scans during the study period for comparison. Clinical data were compared between the two groups: Group A (rehabilitation) and Group B (non-rehabilitation). Results: There were no differences in basic laboratory data between the two groups. The average muscle area before and after rehabilitation in Group A was 212 cm² and 216 cm², respectively. In Group B, the average areas were 230.0 cm² and 225.8 cm². While there was no significant difference in absolute values, the average percentage increase in muscle area was +1.2% (ranging from -7.6% to 6.54%) for Group A and -2.0% (ranging from -12.1% to 4.9%) for Group B, which was statistically significant. In Group A, 9 of 26 were diabetic (DM), and 13 of 26 in Group B were non-DM. The increase in muscle area for DM patients was 4.9% compared to -0.7% for non-DM patients, which was significantly different. There were no significant differences between the two groups in terms of nutritional assessment, Kt/V, or incidence of clinical complications such as cardiovascular events. Considerations: Dialysis rehabilitation has been reported to prevent muscle atrophy by increasing muscle fibers and capillaries. This study demonstrated that muscle volume increased after dialysis exercise, as evidenced by the increased muscle area in the thighs. Notably, diabetic patients seemed to benefit more from dialysis exercise than non-diabetics. Although this study is preliminary due to its relatively small sample size, it suggests that intradialytic physical training may improve insulin utilization in muscle fiber cells, particularly in type II diabetic patients where insulin receptor function and signaling are altered. Further studies are needed to investigate the detailed mechanisms underlying the muscle hypertrophic effects of dialysis exercise.

Keywords: dialysis, excercise, muscle, hypertrophy, diabetes, insulin

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Authors: Niklas Ravn-Boess, Nainita Bhowmick, Takamitsu Hattori, Shohei Koide, Christopher Park, Dimitris Placantonakis

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Background: Glioblastoma (GBM) is the most common and deadly primary brain malignancy in adults. Tumor propagation, brain invasion, and resistance to therapy critically depend on GBM stem-like cells (GSCs); however, the mechanisms that regulate GSC self-renewal are incompletely understood. Given the aggressiveness and poor prognosis of GBM, it is imperative to find biomarkers that could also translate into novel drug targets. Along these lines, we have identified a cell surface antigen, CD97 (ADGRE5), an adhesion G protein-coupled receptor (GPCR), that is expressed on GBM cells but is absent from non-neoplastic brain tissue. CD97 has been shown to promote invasiveness, angiogenesis, and migration in several human cancers, but its frequency of expression and functional role in regulating GBM growth and survival, and its potential as a therapeutic target has not been investigated. Design: We assessed CD97 mRNA and protein expression in patient derived GBM samples and cell lines using publicly available RNA-sequencing datasets and flow cytometry, respectively. To assess CD97 function, we generated shRNA lentiviral constructs that target a sequence in the CD97 extracellular domain (ECD). A scrambled shRNA (scr) with no predicted targets in the genome was used as a control. We evaluated CD97 shRNA lentivirally transduced GBM cells for Ki67, Annexin V, and DAPI. We also tested CD97 KD cells for their ability to self-renew using clonogenic tumorsphere formation assays. Further, we utilized synthetic Abs (sAbs) generated against the ECD of CD97 to test for potential antitumor effects using patient-derived GBM cell lines. Results: CD97 mRNA expression was expressed at high levels in all GBM samples available in the TCGA cohort. We found high levels of surface CD97 protein expression in 6/6 patient-derived GBM cell cultures, but not human neural stem cells. Flow cytometry confirmed downregulation of CD97 in CD97 shRNA lentivirally transduced cells. CD97 KD induced a significant reduction in cell growth in 3 independent GBM cell lines representing mesenchymal and proneural subtypes, which was accompanied by reduced (~20%) Ki67 staining and increased (~30%) apoptosis. Incubation of GBM cells with sAbs (20 ug/ ml) against the ECD of CD97 for 3 days induced GSC differentiation, as determined by the expression of GFAP and Tubulin. Using three unique GBM patient derived cultures, we found that CD97 KD attenuated the ability of GBM cells to initiate sphere formation by over 300 fold, consistent with an impairment in GSC self-renewal. Conclusion: Loss of CD97 expression in patient-derived GBM cells markedly decreases proliferation, induces cell death, and reduces tumorsphere formation. sAbs against the ECD of CD97 reduce tumorsphere formation, recapitulating the phenotype of CD97 KD, suggesting that sAbs that inhibit CD97 function exhibit anti-tumor activity. Collectively, these findings indicate that CD97 is necessary for the proliferation and survival of human GBM cells and identify CD97 as a promising therapeutically targetable vulnerability in GBM.

Keywords: adhesion GPCR, CD97, GBM stem cell, glioblastoma

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