Binding free-energy calculation is a powerful tool for drug optimization: calculation and measurement of binding free energy for 7-azaindole derivatives to glycogen synthase kinase-3ß.

Present computational lead (drug)-optimization is lacking in thermodynamic tactics. To examine whether calculation of binding free-energy change (ΔG) is effective for the lead-optimization process, binding ΔGs of 7-azaindole derivatives to the ATP binding site of glycogen synthase kinase-3ß (GSK-3ß) were calculated. The result was a significant correlation coefficient of r = 0.895 between calculated and observed ΔGs. This indicates that calculated ΔG reflects the inhibitory activities of 7-azaindole derivatives. In addition to quantitative estimation of activity, ΔG calculation characterizes the thermodynamic behavior of 7-azaindole derivatives, providing also useful information for inhibitor optimization on affinity to water molecules.

The activation time-course of contractile elements estimated from in vivo fascicle behaviours during twitch contractions.

To better understand the cascade from neural activation up to force production within in vivo contracting muscle-tendon units, we estimated activation of contractile elements from experimentally measured human fascicle length change and force using a Hill-type muscle model. The experiment was conducted with respect to twitch contractions of the tibialis anterior muscle at three joint angles. As muscle contractile element force is a function of its length and velocity, the activation of contractile elements was calculated using a Hill-type muscle model and measured data. The results were able to reproduce the continuous rising activation of contractile elements after termination of electromyographic activity, the earlier shift of peak activation in time compared to twitch force, and the differences in time-course activation at three different joint angles. These findings are consistent with the predicted change in the activation of contractile elements from previous reports. Also, the results suggest that the time-course of the activation of contractile elements was greatly influenced by the change in force generating capacities related to both length and velocity, even in fixed end contractions, which could result from muscle-tendon interaction.

Three-dimensional microscopic elemental analysis using an automated high-precision serial sectioning system.

The elemental composition and microscopic-level shape of inclusions inside industrial materials are considered important factors in fracture analytical studies. In this work, a three-dimensional (3D) microscopic elemental analysis system based on a serial sectioning technique was developed to observe the internal structure of such materials. This 3D elemental mapping system included an X-ray fluorescence analyzer and a high-precision milling machine. Control signals for the X-ray observation process were automatically sent from a data I/O system synchronized with the precision positioning on the milling machine. Composite specimens were used to confirm the resolution and the accuracy of 3D models generated from this system. Each of the two specimens was composed of three metal wires of 0.5 mm diameter braided into a single twisted wire that was placed inside a metal pipe; the pipe was then filled with either epoxy resin or Sn. The milling machine was used to create a mirror-finish cross-sectional surface on these specimens, and elemental analyses were performed. The twisted wire structure was clearly observed in the resulting 3D models. This system enables automated investigation of the 3D internal structure of materials as well as the identification of their elemental components.

Application of MDGRAPE-3, a special purpose board for molecular dynamics simulations, to periodic biomolecular systems.

We describe the application of a special purpose board for molecular dynamics simulations, named MDGRAPE-3, to the problem of simulating periodic bio-molecular systems. MDGRAPE-3 is the latest board in a series of hardware accelerators designed to calculate the nonbonding long-range interactions much more rapidly than normal processors. So far, MDGRAPEs were mainly applied to isolated systems, where very many nonbonded interactions were calculated without any distance cutoff. However, in order to regulate the density and pressure during simulations of membrane embedded protein systems, one has to evaluate interactions under periodic boundary conditions. For this purpose, we implemented the Particle-Mesh Ewald (PME) method, and its approximation with distance cutoffs and charge neutrality as proposed by Wolf et al., using MDGRAPE-3. When the two methods were applied to simulations of two periodic biomolecular systems, a single MDGRAPE-3 achieved 30-40 times faster computation times than a single conventional processor did in the both cases. Both methods are shown to have the same molecular structures and dynamics of the systems.

Expression analysis for inverted effects of serotonin transporter inactivation.

Inactivation of serotonin transporter (HTT) by pharmacologically in the neonate or genetically increases risk for depression in adulthood, whereas pharmacological inhibition of HTT ameliorates symptoms in depressed patients. The differing role of HTT function during early development and in adult brain plasticity in causing or reversing depression remains an unexplained paradox. To address this we profiled the gene expression of adult Htt knockout (Htt KO) mice and HTT inhibitor-treated mice. Inverted profile changes between the two experimental conditions were seen in 30 genes. Consistent results of the upstream regulatory element search and the co-localization search of these genes indicated that the regulation may be executed by Pax5, Pax7 and Gata3, known to be involved in the survival, proliferation, and migration of serotonergic neurons in the developing brain, and these factors are supposed to keep functioning to regulate downstream genes related to serotonin system in the adult brain.

Development of high-resolution 4D in vivo-CT for visualization of cardiac and respiratory deformations of small animals.

The interest in small animal models of human diseases has generated a need to design a computed tomography (CT) system that operates at a microscopic level. It is particularly important to be able to visualize the dramatic rhythmical motion of organs such as the heart and lungs. In order to evaluate the motion of the heart and lungs of small animals (rats and mice), we developed in the present study a high-resolution 4D in vivo-CT system for small animals that uses synchrotron radiation. To reduce motion artifacts and the radiation dose, the projections were synchronized with airway pressure, the ECG, the x-ray shutter and the CCD shutter. For cardiovascular imaging, a blood pool contrast agent was injected and the data sets were acquired at several ECG points during the end-expiratory phase. For imaging of the lungs, the data sets were acquired at several airway pressures during diastole. The dynamic motion of the cardiovascular system (the ventricles and coronary arteries) and small airways (diameter > 250 microm of rats and 125 microm of mice) was visualized. This high-resolution imaging tool may be very useful for the development of novel drugs in murine models, in addition to its use in the study of cardiovascular and respiratory physiology.

Finite element analysis of blood flow and heat transfer in an image-based human finger.

The human finger is said to be the extension of the brain and can convey the information on mechanical, thermal, and tissue damaging. The quantitative prediction of blood flow rate and heat generation are of great importance for diagnosing blood circulation illness and for the noninvasive measurement of blood glucose. In this study, we developed a coupled thermofluid model to simulate blood flow in large vessels and living tissue. The finite element (FE) model to analyze the blood perfusion and heat transport in the human finger was developed based on the transport theory in porous media. With regard to the blood flow in the large arteries and veins, the systemic blood circulation in the upper limb was modeled based on the one-dimensional flow in an elastic tube. The blood pressure and velocity in each vessel were first computed and the corresponding values for the large vessels in the finger were subsequently transferred to the FE model as the boundary conditions. The realistic geometric model for the human finger was constructed based on the MRI image data. After computing the capillary pressure and blood velocity in the tissue, the temperatures in the large vessels and the tissue of the finger were computed simultaneously by numerically solving the energy equation in porous media. The computed blood flow in tissues is in agreement with the anatomical structure and the measurement. It is believed that this analysis model will have extensive applications in the prediction of peripheral blood flow, temperature variation, and mass transport.

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.

In vivo behavior of muscle fascicles and tendinous tissues in human tibialis anterior muscle during twitch contraction.

In this study we investigated the time course of length and velocity of muscle fascicles and tendinous tissues (TT) during isometric twitch contraction, and examined how their interaction relates to the time course of external torque and muscle fascicle force generation. From seven males, supra-maximal twitch contractions (singlet) of the tibialis anterior muscle were induced at 30 degrees , 10 degrees and -10 degrees plantar flexed positions. The length and velocity of fascicles and TT were determined from a series of their transverse ultrasound images. The maximal external torque appeared when the shortening velocity of fascicles was zero. The fascicle and TT length, and external torque showed a 10-30 ms delay of each onset, with a significant difference in half relaxation times at -10 degrees . The time course of TT elongation, and fascicle and tendinous velocities did not differ between joint angles. Curvilinear length-force properties, whose slope of quasi-linear part was ranged from -15.0 to -5.9 N/mm for fascicles and 5.4 to 14.3N/mm for TT, and a loop-like pattern of velocity-force properties, in which the mean power was ranged from 0.14 to 0.80 W for fascicles, and 0.14 to 0.81 W for TT were also observed. These results were attributed to the muscle-tendon interaction, depending on the slack and non-linearity of length-force relationship of compliant TT. We conclude that the mechanical interaction between fascicles and TT, are significant determinants of twitch force and time characteristics.

Computation of the kinematics and the minimum peak joint moments of sit-to-stand movements.

BACKGROUND: A sit-to-stand (STS) movement requires muscle strength higher than that of other daily activities. There are many elderly people, who experience difficulty when standing up from a chair. The muscle strength required (or the load on the joints) during a STS task is determined by the kinematics (movement pattern). The purpose of this study was to evaluate the kinematics and resultant joint moments of people standing up from a chair in order to determine the minimum peak joint moments required for a STS task. METHODS: This study consisted of three steps. In the first step, kinematic data of lower extremity joint angles (hip, knee and ankle) during STS movements were experimentally collected from human subjects. Eighty-five sets of STS kinematic data were obtained. In the second step, the experimentally collected kinematic data and a link segment model of the human body were used to generate more than 5,000,000 computed STS movements. In the third step, using inverse dynamics method, joint moments of the lower extremity were calculated for all movements obtained through the preceding steps. From the outputs of the third step, the optimal kinematics (movement pattern) in terms of minimized peak joint moment for the hip, knee and ankle was determined. RESULTS: The peak hip joint moment ranged from 0.24 to 1.92 N.m/kg. The peak knee joint moment ranged from 0.51 to 1.97 N.m/kg, and the peak ankle joint moment ranged from -0.11 to 1.32 N.m/kg. The optimal movement patterns differed depending on which minimized joint moment index was selected (hip, knee or ankle). However, the sum of the peak hip joint moment and peak knee joint moment was always approximately 1.53 N.m/kg regardless of which minimized joint moment index was selected. CONCLUSION: The most important finding of this study was that the relation between the peak joint moments at the hip and knee joints was complementary and the sum of those moments needed to be greater than 1.53 N.m/kg in order to perform a successful STS. A combined hip-knee value of 1.5 N.m/kg or lower may indicate the need for physical rehabilitation and/or exercise to increase muscular force.

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.

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.

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.

Cardiovascular disease-induced thermal responses during passive heat stress: an integrated computational study.

The cardiovascular system plays a crucial role in human thermoregulation; cardiovascular diseases may lead to significantly degrading the thermoregulation ability for patients during exposure to heat stress. To evaluate the thermal responses of patients with common chronic cardiovascular diseases, we here propose an integrated computational model by coupling a two-node thermoregulation model with a closed-loop, multi-compartment, lumped-parameter cardiovascular model. This bioheat transfer model is validated, capable to predict cardiovascular functions and thermal responses under varying environmental conditions. Our results demonstrate that the cardiovascular disease-induced reduction in cardiac output and skin blood flow causes extra elevation in core temperature during hyperthermic challenges. In addition, a combination of aging, obesity, and cardiovascular diseases shows a pronounced increase in core temperature during heat exposure, which implies that such combined effect may increase the risk of heat-related morbidity and mortality. Copyright © 2016 John Wiley & Sons, Ltd.

Analysis of the equine ovarian structure during the first twelve months of life by three-dimensional internal structure microscopy.

A three-dimensional internal structure microscopy (3D-ISM) can clarify the anatomical arrangement of internal structures of equine ovaries. In this study, morphological changes of the equine ovary over the first 12 months of life were investigated by 3D-ISM in 59 fillies and by histological analysis in 2 fillies. The weight and volume of the paired ovaries initially decreased from 0 to 1 months to 2 to 3 months of age and then significantly increased at 8 to 12 months of age. The ovulation fossa was first observed around the 3rd month and became evident after the 6th month. The number of follicles with a diameter of ≥10 mm and the diameter of the largest follicle increased gradually after 6 months of age. On a volume basis, the medulla accounted for nearly 90% of the whole ovary at 0 to 1 months of age, but significantly decreased from 2 to 3 months of age. The volume of the cortex increased progressively after birth and reached approximately 60% of the total volume at 8 to 12 months of age. This significant development of the cortex coincided with the increased number and size of large follicles observed from 6 months of age. These results suggest that the development of the cortex plays a role in the maturation of the follicles and the equine ovary undergoes substantial morphological changes postnatally until puberty.

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.

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.

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.

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.

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.