Publications by authors named "Soichiro Tsuda"

In the current environment whereby new sources of proteins are extracted from plant material, it is also important to study the potential use of the resulting side streams. Although a number of studies have been conducted on various polysaccharides extracted from plant raw material, a polysaccharide fraction extracted from lupin bean is yet to be explored, in spite of the emerging interest in this crop as a source of food ingredients. In this work lupin soluble polysaccharide (LuPS) was obtained with a recovery as high as 46 % by extraction at pH 8, 120 °C, for 90 min.

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Endolysins, peptidoglycan hydrolases derived from bacteriophages (phages), are being developed as a promising alternative to conventional antibiotics. To obtain highly active endolysins, a diverse library of these endolysins is vital. We propose here microbial single-cell genome sequencing as an efficient tool to discover dozens of previously unknown endolysins, owing to its culture-independent sequencing method.

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Background: Iliopsoas impingement (IPI) is an important complication after total hip arthroplasty (THA), and anterior cup protrusion is believed to be its main cause; however, the relationship between the hip center of rotation (COR) and symptomatic IPI or cup protrusion remains poorly understood. Therefore, the present study investigated these relationships.

Methods: The medical records of 138 patients who underwent unilateral primary THA were retrospectively reviewed.

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Advances in culture-independent microbial analysis, such as metagenomics and single-cell genomics, have significantly increased our understanding of microbial lineages. While these methods have uncovered a large number of novel microbial taxa, many remain uncultured, and their function and mode of existence in the environment are still unknown. This study aims to explore the use of bacteriophage-derived molecules as probes for detecting and isolating uncultured bacteria.

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Crustacean aquaculture is expected to be a major source of fishery commodities in the near future. Hemocytes are key players of the immune system in shrimps; however, their classification, maturation, and differentiation are still under debate. To date, only discrete and inconsistent information on the classification of shrimp hemocytes has been reported, showing that the morphological characteristics are not sufficient to resolve their actual roles.

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Production of chimeric animals is often a necessity for the generation of genetically modified animals and has gained popularity in recent years in regenerative medicine for the reconstruction of xenogeneic organs. Aggregation and injection methods are generally used to produce chimeric mice. In the aggregation method, the chimeras are produced by co-culturing embryos and stem cells, and keeping them physically adhered, although it may not be an assured method for producing chimeric embryos.

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Current computers are limited by the von Neumann bottleneck, which constrains the throughput between the processing unit and the memory. Chemical processes have the potential to scale beyond current computing architectures as the processing unit and memory reside in the same space, performing computations through chemical reactions, yet their lack of programmability limits them. Herein, we present a programmable chemical processor comprising of a 5 by 5 array of cells filled with a switchable oscillating chemical (Belousov-Zhabotinsky) reaction.

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Evolution via natural selection is governed by the persistence and propagation of living things in an environment. The environment is important since it enabled life to emerge, and shapes evolution today. Although evolution has been widely studied in a variety of fields from biology to computer science, still little is known about the impact of environmental changes on an artificial chemical evolving system outside of computer simulations.

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Multi-drug strategies have been attempted to prolong the efficacy of existing antibiotics, but with limited success. Here we show that the evolution of multi-drug-resistant Escherichia coli can be manipulated in vitro by administering pairs of antibiotics and switching between them in ON/OFF manner. Using a multiplexed cell culture system, we find that switching between certain combinations of antibiotics completely suppresses the development of resistance to one of the antibiotics.

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Understanding ecosystem dynamics is crucial as contemporary human societies face ecosystem degradation. One of the challenges that needs to be recognized is the complex hierarchical dynamics. Conventional dynamic models in ecology often represent only the population level and have yet to include the dynamics of the sub-organism level, which makes an ecosystem a complex adaptive system that shows characteristic behaviors such as resilience and regime shifts.

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Three dimensional (3D) printing is actively sought after in recent years as a promising novel technology to construct complex objects, which scope spans from nano- to over millimeter scale. Previously we utilized Fused deposition modeling (FDM)-based 3D printer to construct complex 3D chemical fluidic systems, and here we demonstrate the construction of 3D milli-fluidic structures for programmable liquid handling and control of biological samples. Basic fluidic operation devices, such as water-in-oil (W/O) droplet generators for producing compartmentalized mono-disperse droplets, sensor-integrated chamber for online monitoring of cellular growth, are presented.

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Lipid vesicles, in particular Giant Unilamellar Vesicles (GUVs), have been increasingly important as compartments of artificial cells to reconstruct living cell-like systems in a bottom-up fashion. Here, we report shape transformations of lipid vesicles induced by polyethylene glycol-lipid conjugate (PEG lipids). Statistical analysis of deformed vesicle shapes revealed that shapes vesicles tend to deform into depended on the concentration of the PEG lipids.

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The control and prediction of complex chemical systems is a difficult problem due to the nature of the interactions, transformations and processes occurring. From self-assembly to catalysis and self-organization, complex chemical systems are often heterogeneous mixtures that at the most extreme exhibit system-level functions, such as those that could be observed in a living cell. In this paper, we outline an approach to understand and explore complex chemical systems using an automated droplet maker to control the composition, size and position of the droplets in a predefined chemical environment.

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We here present a method to reconstruct effective free energy landscapes (FELs) of lipid vesicles from the statistical analysis of a large number of microscope images. This method, not only allows us to define possible energy landscapes, but also highlights minority vesicle shapes that were otherwise hidden in the majority. When compared with temporal evolution of deforming lipid vesicles, it was found that the trajectory of deforming vesicles was in accordance with the reconstructed landscape, in which the minority shapes play a key role.

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This paper describes the utilization of giant unilamellar vesicles (GUVs) as a platform for handling chemical and biochemical reagents. GUVs with diameters of 5 to 10 µm and containing chemical/biochemical reagents together with inert polymers were fused with electric pulses (electrofusion). After reagent mixing, the fused GUVs spontaneously deformed to a budding shape, separating the mixed solution into sub-volumes.

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High-dose melphalan has been gaining recognition as a highly emetogenic agent used in hematopoietic stem cell transplantation (HSCT). The aim of this retrospective study was to elucidate the efficacy of aprepitant in preventing high-dose melphalan-induced emesis. Sixty patients who received melphalan (70 mg/m(2)/day, 2 days) and fludarabine (125 mg/m(2)/day, 5 days) as conditioning for allogeneic HSCT for hematological malignancies, and who received ondansetron and methylprednisolone as an antiemetic prophylaxis, were eligible.

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We show how an array of ion-sensitive-field-effect-transistors can be used to both spatially and temporally image the oscillating pH/ion waves produced by the Belousov-Zhabotinsky (BZ) reaction with high resolution.

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The regeneration process of contractile oscillation in the plasmodium of Physarum polycephalum is investigated experimentally and modelled computationally. When placed in a well, the Physarum cell restructures the body (fusion of small granule-like cells) and shows various complex oscillation patterns. After it completed the restructuring and regained synchronized oscillation within the body, the cell shows bilateral oscillation or rotating wave pattern.

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Electrical impedance tomography is an imaging technology that spatially characterizes the electrical properties of an object. We present a miniaturized electrical impedance tomography system that can image the electrical conductivity distribution within a two-dimensional cell culture. A chip containing a circular 16-electrode array was fabricated using printed circuit board developing technology and used to inject current and to measure spatial voltage across the object.

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At present there exists a large gap in size, performance, adaptability and robustness between natural and artificial information processors for performing coherent perception-action tasks under real-time constraints. Even the simplest organisms have an enviable capability of coping with an unknown dynamic environment. Robots, in contrast, are still clumsy if confronted with such complexity.

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There have been many attempts for realization of emergent computing, but the notion of emergent computing is still ambiguous. In an open system, emergence and an error cannot be specified distinctly, because they are dependent on the dis-equilibration process between local and global behaviors. To manifest such an aspect, we implement a Boolean gate as a biological device made of slime mold Physarum polycephalum.

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