Biomedical subjects

Ryutaro Himeno

Publications and source records attributed to Ryutaro Himeno.

11 recordsLinked to original sources

PubMed2006

Exploration and grading of possible genes from 183 bacterial strains by a common protocol to identification of new genes: Gene Trek in Prokaryote Space (GTPS).

A large number of complete microorganism genomes has been sequenced and submitted to the public database and then incorporated into our complete genome database, Genome Information Broker (GIB, http://gib.genes.nig.ac.jp/). However, when comparative genomics is carried out, researchers must be aware that there are protein-coding genes not confirmed by homology or motif search and that reliable protein-coding genes are missing. Therefore, we developed a protocol (Gene Trek in Prokaryote Space, GTPS) for finding possible protein-coding genes in bacterial genomes. GTPS assigns a degree of reliability to predicted protein-coding genes. We first systematically applied the protocol to the complete genomes of all 123 bacterial species and strains that were publicly available as of July 2003, and then to those of 183 species and strains available as of September 2004. We found a number of incorrect genes and several new ones in the genome data in question. We also found a way to estimate the total number of orthologous genes in the bacterial world.

Bacteria↗

PubMed2006

Small airway changes in healthy and ovalbumin-treated mice during quasi-static lung inflation.

Previously, we developed a synchrotron radiation CT system to evaluate the morphometric changes (length and diameter, D) and small airway compliance (sC(aw)) of euthanized mice under quasi-static inflation [Sera, T., Uesugi, K., Yagi, N., 2005. Localized morphometric deformations of small airways and alveoli in intact mouse lungs under quasi-static inflation. Respir. Physiol. Neurobiol. 147, 51-63). Using this system, this study compared normal and asthmatic small airways. Ovalbumin-treated mice were used as an asthma model. Compared with the values at functional residual capacity, D of normal and asthmatic small airways (D<200microm) increased by 48% and 36% at the end of tidal inspiration. For larger airways (D>500microm), the increases were 23% and 20%, respectively. The ratio of the sC(aw) of asthmatic small airways to that of healthy small airways was 0.57, and the ratio was 0.70 for larger airways. The morphometric changes and sC(aw) in asthma model mice were significantly lower than those of healthy mice. The differences in sC(aw) between healthy and asthma model mice were greater for smaller airways.

Animals↗

PubMed2006

Influence of vision and static stretch of the calf muscles on postural sway during quiet standing.

The purpose of this experimental study was to evaluate the effects of vision and stretching of the calf muscles on postural sway during quiet standing. Under pre-stretch conditions, participants stood on a force plate for 30s and the sway of the ground reaction force center of pressure was recorded. The following postural sway variables were calculated off-line: sweep speed, sway speed, standard deviation, maximal mediolateral range, maximal anteroposterior range, mean mediolateral position and mean anteroposterior position. For post-stretch conditions, participants stood quietly on a device that was utilized to impose a static 3 min ankle joint dorsiflexion stretch. Immediately thereafter, participants moved onto the force platform where postural sway parameters were again recorded. Randomized eyes-open and eyes-closed conditions were tested in both cases. Results showed that postural sway significantly increased due to stretch (sweep speed, sway speed, standard deviation, maximal anteroposterior range, mean anteroposterior position), as well as eye closure (sweep speed, sway speed, standard deviation, maximal mediolateral range, maximal anteroposterior range). The interaction between stretch and eye closure was also significant (sweep speed, sway speed, standard deviation, maximal mediolateral range), suggesting that there were only minor increases in postural sway after stretch under the eyes-open condition. It was suggested that stretching of the calf muscles has the effect of increasing postural sway, although this effect can be greatly compensated for when vision is included.

Adult↗

PubMed2005

A numerical coupling model to analyze the blood flow, temperature, and oxygen transport in human breast tumor under laser irradiation.

The aim of this study is to investigate the variation of the blood perfusion rate and distribution of oxygen partial pressure (PO2) in human tumors by a coupling numerical model when laser irradiation is used as an adjuvant method in the treatment of cancer. A two-dimensional finite element (FE) thermal model of a human breast with a tumor was developed. The blood circulation inside the breast was modeled using one-dimensional non-linear equations of pulsatile fluid flow. The distribution of PO2 inside the capillaries, tumor vessels, and surrounding tissue was obtained by the Krogh analysis model. Finally, the variations of the average tumor temperature, blood perfusion, and PO2 during laser heating were computed by coupling the blood circulation, FE thermal, and oxygen transport models.

Breast Neoplasms↗

PubMed2005

Development and validation of models for the investigation of blood clotting in idealized stenoses and cerebral aneurysms.

An in vitro model of blood clotting is presented using hypercoaguable milk as an analog for blood. Milk clot formation was studied for periods of 2, 5, 10, 20, and 30 min within an idealized stenosis geometry. Clot formation was recorded using photography, clot casting, and clot mass calculation. The distribution of clot within the fluid was seen to be in good agreement with a previous study that used a residence time model to predict areas of clot formation in thrombin solution. A numerical model was formulated within computational fluid dynamics package CFX that allowed local activation of blood clotting to be simulated. This model was applied to the analysis of an idealized cerebral aneurysm geometry. An idealized coil geometry was included within the aneurysm and clotting fluid concentration and fluid residence time were modeled using transport equations within CFX. The viscosity of the fluid was defined as a function of both residence time and clotting fluid concentration. The model was seen to produce features consistent with observations of thrombosis within cerebral aneurysms, while avoiding the unrealistic build up of clot in near-wall regions that is associated with a pure residence time model.

Animals↗

PubMed2005

Force, work and power output of lower limb muscles during human maximal-effort countermovement jumping.

The purpose of this study was to simulate human maximal-effort countermovement jumping with a three-dimensional neuromusculoskeletal model. The specific aim was to investigate muscle force, work and power output of major lower limb muscles during the motion. A neuromusculoskeletal model that has nine rigid body segments, 20 degrees of freedom, 32 Hill-type lower limb muscles was developed. The neural activation input signal was represented by a series of step functions with step duration of 0.05 s. The excitation-contraction dynamics of the contractile element, the tissues around the joints to limit the joint range of motion, as well as the foot-ground interaction were implemented. A simulation was started from a standing posture. Optimal pattern of the activation input signal was searched through numerical optimization with a goal of maximizing the height reached by the mass center of body after jumping up. As a result, feasible kinematics, ground reaction force profile and muscle excitation profile were generated. It was found that monoarticular muscles had major contributions of mechanical work and power output, whereas biarticular muscles had minor contributions. Hip adductors, abductors and external rotator muscles were vigorously activated, although their mechanical work and power output was minor because of their limited length change during the motion. Joint flexor muscles such as m. iliopsoas, m. biceps femoris short head and m. tibialis anterior were activated in the beginning of the motion with an effect of facilitating the generation of a countermovement.

Computer Simulation↗

PubMed2005

Rheological analyses of coagulation of blood from different individuals with special reference to procoagulant activity of erythrocytes.

In our previous papers, we reported that factor IX (FIX), when activated by erythrocyte membranes, causes coagulation. We have identified and characterized the FIX-activating enzyme located in normal human erythrocyte membranes. In this paper, to examine physiological and pathological significances of procoagulant activity of erythrocytes, coagulation of blood obtained from different individuals was analyzed by means of a rheological technique. In more than 65% of subjects including normals and patients, the initiation of coagulation seemed to be governed by erythrocytes. Coagulation of whole blood and platelet-free plasma supplemented with erythrocytes had a tendency to occur rapidly in the elderly. It was suggested that the concentration of FIX-activating enzyme on erythrocyte membranes for aged donors was somewhat higher than that for young ages. Propagation reactions on erythrocyte membranes (i.e. factor X activation leading to thrombin generation after FIX activation) was slower than that on platelet membranes. Moreover, the propagation reaction on erythrocyte membranes was greatly dependent on individuals, whereas that on platelet membranes was not so much. Our study demonstrates that the activation of FIX by erythrocytes and subsequent propagation reaction on platelet membranes may be important for initiating and controlling blood coagulation reactions.

Adult↗

PubMed2004

Purification, identification, and characterization of elastase on erythrocyte membrane as factor IX-activating enzyme.

In our previous papers, we reported that factor IX (F-IX), when activated by erythrocyte membranes, causes coagulation. We report on purification, identification, and characterization of F-IX-activating enzyme extracted from human erythrocyte membranes. The enzyme whose amino acid sequence is almost in accord with neutrophil elastase was found in normal erythrocyte membrane. The molecular mass was slightly smaller than that of neutrophil elastase. The content of the enzyme in erythrocyte membranes was estimated to be 3.0-3.7 ng per 10(6)erythrocytes. The F-IX sites cleaved by the enzyme were slightly different from those by the ordinary coagulation reaction. The ability of F-IX cleaved by the enzyme to cause coagulation was estimated to be approximately 1/10 as high as that of the F-IX cleaved by activated F-XI. These findings provide evidence that F-IX is activated by erythrocyte membrane, which may serve as a triggering mechanism for blood coagulation.

Adult↗

PubMed2004

Localized compliance of small airways in excised rat lungs using microfocal X-ray computed tomography.

Airway compliance is a key factor in understanding lung mechanics and is used as a clinical diagnostic index. Understanding such mechanics in small airways physiologically and clinically is critical. We have determined the "morphometric change" and "localized compliance" of small airways under "near"-physiological conditions; namely, the airways were embedded in parenchyma without dehydration and fixation. Previously, we developed a two-step method to visualize small airways in detail by staining the lung tissue with a radiopaque solution and then visualizing the tissue with a cone-beam microfocal X-ray computed tomography system (Sera et al. J Biomech 36: 1587-1594, 2003). In this study, we used this technique to analyze changes in diameter and length of the same small airways ( approximately 150 microm ID) and then evaluated the localized compliance as a function of airway generation (Z). For smaller (<300-microm-diameter) airways, diameter was 36% larger at end-tidal inspiration and 89% larger at total lung capacity; length was 18% larger at end-tidal inspiration and 43% larger at total lung capacity than at functional residual capacity. Diameter, especially at smaller airways, did not behave linearly with V(1/3) (where V is volume). With increasing lung pressure, diameter changed dramatically at a particular pressure and length changed approximately linearly during inflation and deflation. Percentage of airway volume for smaller airways did not behave linearly with that of lung volume. Smaller airways were generally more compliant than larger airways with increasing Z and exhibited hysteresis in their diameter behavior. Airways at higher Z deformed at a lower pressure than those at lower Z. These results indicated that smaller airways did not behave homogeneously.

Animals↗

PubMed2003

Three-dimensional visualization and morphometry of small airways from microfocal X-ray computed tomography.

Physiological morphometry is a critical factor in the flow dynamics in small airways. In this study, we visualized and analyzed the three-dimensional structure of the small airways without dehydration and fixation. We developed a two-step method to visualize small airways in detail by staining the lung tissue with a radiopaque solution and then visualizing the tissue with a cone-beam microfocal X-ray computed tomographic (CT) system. To verify the applicability of this staining and CT imaging (SCT) method, we used the method to visualize small airways in excised rat lungs. By using the SCT method to obtain continuous CT images, three-dimensional branching and merging bronchi ranging from 500 to 150 microm (the airway generation=8-16) were successfully reconstructed. The morphometry of the small airways (diameter, length, branching angle and gravity angle between the gravity direction and airway vector) was analyzed using the three-dimensional thinning algorithm. The diameter and length exponentially decreased with the airway generation. The asymmetry of the bifurcation decreased with generation and one branching angle decided the other pair branching angle. The SCT method is the first reported method that yields faithful high-resolution images of soft tissue geometry without fixation and the three-dimensional morphometry of small airways is useful for studying the biomechanical dynamics in small airways.

Algorithms↗

PubMed2002

Time-accurate, parallel, multi-zone, multi-block solver to study the human cardio-vascular system.

A parallel, time-accurate flow solver is devised to study the human cardio-vascular system. The solver is capable of dealing with moving boundaries and moving grids. It is designed to handle complex, three-dimensional vascular systems. The computational domain is divided into multiple block subdomains. At each cross section the plane is divided into twelve sub-zones to allow flexibility for handling complex geometries and, if needed, appropriate parallel data partitioning. The unsteady, three-dimensional, incompressible Navier-Stokes equations are solved numerically. A second-order in time and third-order upwind finite volume method for solving time-accurate incompressible flows based on pseudo-compressibility and dual time-stepping technique is used. For parallel execution, the flow domain is partitioned. Communication between the subdomains of the flow on Riken's VPP/700E supercomputer is implemented using MPI message-passing library. A series of numerical simulations of biologically relevant flows is used to validate this code.

Biomechanical Phenomena↗