Purpose: Monitor changes in force production, running economy (RE), and running kinematics (RK) in a highly trained marathon runner after beginning a strength training (ST) program. Methods: One marathon runner (M, 27 y, 165 cm, 53.3 kg, VO2pesk 67.43 ml/kg/min, PR 2:33:13) with no history of ST completed a 12-week block periodized ST program. Baseline and reliability testing was conducted over a two-month period prior to ST. The completed ST RPE and work (volume load*displacement) and running volume (km/wk) were monitored over the 12 weeks. The athlete performed an isometric mid-thigh pull to assess peak force (PF, N), rate of force development at 250 ms (RFD250), and net impulse at 250 ms (NI250) during baseline and throughout ST. The athlete performed a steady state test on a treadmill instrumented with the OptojumpTM optic sensor system to assess RE (ml/kg/km) and RK during baseline and throughout ST. Impact of the ST program was assessed by percent change of the variables during the taper from the baseline average and by the odds of a true change using the typical error and smallest worthwhile change. Results: PF improved (120:1 odds) by 17.11%, RFD250 improved (22:1 odds) by 24.73%, and NI250 improved (10:1 odds) by 16.70% before competition. Ground contact time decreased (7:1 odds) by 2.57%, flight time decreased (1:1 odds) by 1.49%, step rate increased (2:1 odds) by 2.28%, and step length decreased (57:1: odds) by 2.21%. RE improved (3:1 odds) by 2.09%. Conclusion: Improving a runner’s maximal strength and rate of force development may positively influence RK and RE.

The prostheses used by the majority of persons with upper limb amputations today offer a limited range of motion. Relative to anatomical joints transradial (below the elbow) prosthesis users lose at least two of the three degrees of freedom provided by the wrist and forearm. Some myoeletric prostheses currently allow for forearm pronation and supination (rotation about an axis parallel to the forearm) and the operation of a powered prosthetic hand. Body-powered prostheses, incorporating hooks and other cable driven terminal devices, have even fewer active degrees of freedom. In order to perform activities of daily living, an amputee must use a greater than normal range of movement from other anatomical body joints to compensate for the loss of movement caused by the amputation. By studying this compensatory motion of prosthetic users, the mechanics of how they adapt to the loss of range of motion in a given limb and specific tasks were analyzed. The purpose of this study is to create a robotic based kinematic model that can predict the compensatory motion of a given task using given subject data in select tasks. The tasks used in this study are the activities of daily living: opening a door, drinking from a cup, lifting a box, and turning a steering wheel. For the model the joint angles necessary to accomplish a task are calculated by a simulation for a set of prostheses and tasks. The simulation contains a set of configurations that are represented by parameters that consist of the joint degrees of freedom provided by each prosthesis, and a set of task information that includes joint constraints and trajectories. In the simulation the hand or prosthesis follows the trajectory to perform the task. Analysis of tasks is done by attaching prosthetic constraints to one of the arms of the upper body model in the simulation, other arm maintains an anatomical configuration. By running the model through this simulation with different configurations the compensatory motions were found. Results can then be used to select the best prosthesis for a given user, design prostheses that are more effective at selected tasks, and demonstrate some possible compensations given a set of residual joint limitations with certain prosthetic components, by optimizing the configuration of the prostheses to improve their performance.

Invasive species, such as the red lionfish, Pterois volitans, are damaging many ecosystems around the world by out-competing native species. However, little work has been done to determine if P. volitans have a direct influence on the feeding performance of native species with which they compete. This study examines the feeding performance in terms of suction pressure, kinematic timing, and excursion distances of spotted scorpionfish, Scorpaena plumieri. Through multiple trials it was examined how S. plumieri modulate their kinematic behavior in response to P. volitans and a conspecific. The creation of a smaller buccal cavity and a decrease in time of buccal expansion may allow individuals to create greater sub-ambient pressures to increase their prey-capture success. High-speed cinematography and pressure transducers were used to determine if S. plumieri modulate feeding performance in the presence of either P. volitans or a conspecific. The results of the study suggest that S. plumieri do not create larger subambient pressures or modulate their feeding kinematics in the presence of P. volitans or a conspecific.

Introduction: Baseball pitching is considered one of the most intense aspects within the game of baseball, as well as the most complicated dynamic throwing task in all of sports. The biomechanics of pitching have been heavily investigated in an attempt to identify optimal pitching mechanics in terms of pitching performance. Previous quantified upper body kinetics research has concluded that improved muscle strength is needed in attempting to achieve adequate upper body kinetics and efficient pitching performances. Therefore, it is the purpose of this research study to compare the lower extremity muscle and upper extremity muscle activation patterns and kinematic variables associated with the curveball pitch and the fastball pitch when pitching from the wind-up and stretch position. Methods: Twelve skilled (competed at the NCAA collegiate level) baseball pitchers volunteered to be research subjects for this study. The participants were fitted with six surface electromyography (EMG) bipolar electrodes (Delsys Inc., Boston, Massachusetts) on the stride leg biceps femoris, medial gastrocnemius, ipsilateral side (throwing arm side) lower trapezius, upper trapezius, triceps brachii and biceps brachii. Each participant underwent maximum voluntary isometric contraction (MVIC) testing and then performed a pitching analysis. All EMG variables of interest were normalized using MVIC data and then compared between pitching types and pitch delivery. Shoulder rotation, shoulder abduction, elbow flexion and extension, elbow angular velocity and pelvis rotation were determined using motion capture (Motion Analysis Corp., Santa Rosa, SA) and Visual 3D software (C-Motion Inc., Germantown, MD). Paired t-tests and factorial analyses were performed using SPSS (p ≤ 0.05). Results and Discussion: Significant differences in the peak and mean muscle activity for the fastball and curveball pitched from wind-up and stretch position were observed. Significant differences in the kinematic variables between the fastball and curveball from the wind- up and stretch were also observed. These findings suggest that upper and lower muscle activity could be associated with enhanced pitching technique and pitching performance. Pitching kinematic differences associated with the diverse pitch types as well as the multiple pitch deliveries may impact the overall “wear and tear” on a pitcher’s health and pitching arm. Conclusions: Many differences were found, between both the pitching type and the pitching delivery as well as the kinematic variables. These findings suggest that upper and lower muscle activity could be associated with enhanced pitching technique and pitching performance to keep a baseball pitcher healthy and on the pitching mound longer into the season, decreasing the rate of injury. Shoulder rotation and pelvis rotation, as well as the elbow angular velocity and elbow flexion-extension, have an impact on the pitcher’s ability to stay off the disabled list and in the game longer. Determining pitch types along with delivery types that enhance the pitcher’s ability to stay active without injury will provide a way to make the game of baseball safer for the future generation of all stars.

The need to characterize normal and pathological human movement has consistently driven researchers to develop new tracking devices and to improve movement analysis systems. Movement has traditionally been captured by either optical, magnetic, mechanical, structured light, or acoustic systems. All of these systems have inherent limitations. Optical systems are costly, require fixed cameras in a controlled environment, and suffer from problems of occlusion. Similarly, acoustic and structured light systems suffer from the occlusion problem. Magnetic and radio frequency systems suffer from electromagnetic disturbances, noise and multipath problems. Mechanical systems have physical constraints that limit the natural body movement. Recently, the availability of low-cost wearable inertial sensors containing accelerometers, gyroscopes, and magnetometers has provided an alternative means to overcome the limitations of other motion capture systems. Inertial sensors can be used to track human movement in and outside of a laboratory, cannot be occluded, and are low cost. To calculate changes in orientation, researchers often integrate the angular velocity. However, a relatively small error or drift in the measured angular velocity leads to large integration errors. This restricts the time of accurate measurement and tracking to a few seconds. To compensate that drift, complementary data from accelerometers and magnetometers are normally integrated in tracking systems that utilize the Kalman filter (KF) or the extended Kalman filter (EKF) to fuse the nonlinear inertial data. Orientation estimates are only accurate for brief moments when the body is not moving and acceleration is only due to gravity. Moreover, success of using magnetometers to compensate drift about the vertical axis is limited by magnetic field disturbance. We combine kinematic models designed for control of robotic arms with state space methods to estimate angles of the human shoulder and elbow using two wireless wearable inertial measurement units. The same method can be used to track movement of other joints using a minimal sensor configuration with one sensor on each segment. Each limb is modeled as one kinematic chain. Velocity and acceleration are recursively tracked and propagated from one limb segment to another using Newton-Euler equations implemented in state space form. To mitigate the effect of sensor drift on the tracking accuracy, our system incorporates natural physical constraints on the range of motion for each joint, models gyroscope and accelerometer random drift, and uses zero-velocity updates. The combined effect of imposing physical constraints on state estimates and modeling the sensor random drift results in superior joint angles estimates. The tracker utilizes the unscented Kalman filter (UKF) which is an improvement to the EKF. This removes the need for linearization of the system equations which introduces tracking errors. We validate the performance of the inertial tracking system over long durations of slow, normal, and fast movements. Joint angles obtained from our inertial tracker are compared to those obtained from an optical tracking system and a high-precision industrial robot arm. Results show an excellent agreement between joint angles estimated by the inertial tracker and those obtained from the two reference systems.

Eliot Glacier is a small (1.6 km2), relatively well-studied glacier on Mount Hood, Oregon. Since 1901, glacier area decreased from 2.03 ± 0.16 km2 to 1.64 ± 0.05 km2 by 2004, a loss of 19%, and the terminus retreated about 600 m. Mount Hood's glaciers as a whole have lost 34% of their area. During the first part of the 20th century the glacier thinned and retreated, then thickened and advanced between the 1940s and 1960s because of cooler temperatures and increased winter precipitation and has since accelerated its retreat, averaging about 1.0 m a-1 thinning and a 20 m a-1 retreat rate by 2004. Surface velocities at a transverse profile reflect ice thickness over time, reaching a low of 1.4 m a-1 in 1949 before increasing to 6.9 ± 1.7 m a-1 from the 1960s to the 1980s. Velocities have since slowed to about 2.3 m a-1 , about the 1940 speed.

The overall objective of this thesis is to build an integrated, inexpensive, human-sized humanoid robot from scratch that looks and behaves like a human. More specifically, my goal is to build an android robot called Marie Curie robot that can act like a human actor in the Portland Cyber Theater in the play Quantum Debate with a known script of every robot behavior. In order to achieve this goal, the humanoid robot need to has degrees of freedom (DOF) similar to human DOFs. Each part of the Curie robot was built to achieve the goal of building a complete humanoid robot. The important additional constraints of this project were: 1) to build the robot from available components, 2) to minimize costs, and 3) to be simple enough that the design can be replicated by non-experts, so they can create robot theaters worldwide. Furthermore, the robot appears lifelike because it executes two main behaviors like a human being. The first behavior is tracking where the humanoid robot uses a tracking algorithm to follow a human being. In other words, the tracking algorithm allows the robot to control its neck using the information taken from the vision system to look at the nearest human face. In addition, the robot uses the same vision system to track labeled objects. The second behavior is grasping where the inverse kinematics (IK) is calculated so the robot can move its hand to a specific coordinate in the surrounding space. IK gives the robot the ability to move its end-effector (hand) closer to how humans move their hands.

Introduction: The Vestibulo-ocular reflex (VOR) is quantified by computing the ratio of head angular velocity and eye angular velocity (VOR Gain). This measure only includes head angular movements; linear translations are not accounted for. These investigations postulate an alternative method of VOR quantification, one that assesses retinal image stability during head angular and linear movements (Foveal fixation (FF)). This method was used to assess the role of vision in balance reactions. Methods: Experiment 1 : Ten Young subjects were fitted with an eye tracker linked to an EM kinematic recording system. This allowed for the recording of head, trunk and eye kinematics during the performance of gaze stabilization tasks. Subjects fixated an LED target while performing head flexion and extension exercises at four frequencies. Point-of-gaze analysis was performed by transforming eye-in-head and head-in-space data into eye-in-space data, which were compared to the known location of the targets. The distance between the eye vector target plane intersection and the target location provided an error that could be used to calculate the estimated image location on the retina. FF and VOR gain were compared with head angular velocities to determine correlations. Experiment 2: Balance was assessed in Young and Elderly following a series of perturbations. Dependent variables included: step latency, head and trunk angular velocity, VOR Gain, FF. Results: Correlations between head angular velocity and FF showed that retinal image stability degraded as head angular velocity increased. Elderly showed a more rapid degradation of FF with higher overall head angular velocities. Comparisons between rate of change of VOR and FF over velocity spectrum indicated a greater change in FF response. A negative linear correlation between FF and Step Latency was observed: there was no relationship between VOR gain and Step Latency. Conclusion: FF is a more sensitive measure of VOR than Gain as it accounts for angular and translational head movements. Its correlation with Step Latency suggests the importance of image stability in formulating responses following perturbation.

Clinicians working on motor skill learning interventions often find that improvements observed during training are not sustained and do not transfer to very similar tasks. Research suggests that strategies such as real-time biofeedback and learner's focus of attention seem to facilitate motor skill learning. However, research on the implications of these strategies in rehabilitation is limited and has not been investigated in healthy individuals. The motor learning effects of these strategies need to be assessed as they offer the possibility of enhancing rehabilitation regimens. The purpose of this study was to investigate the generalizability of real-time biofeedback and learner's focus of attention to a treadmill gait retraining program aimed at correcting knee hyperextension insidious gait patterns in healthy young women. Assessing the acquisition, retention, and transfer of kinematic improvements was the focus of this study. 1.Knee sagittal plane kinematics could be influenced with dynamic gait training using real-time biofeedback. Gained proficiency in controlling knee hyperextension during treadmill training was evident during overground walking immediately and 1 month after training. 2.The effectiveness of real-time biofeedback in improving performance does not seem to be influenced by the focus of attention, internal or external, induced during treadmill training. Participants in both intervention groups improved in a similar way as a consequence of practice. However, there were trends in the data that pointed that the external focus of attention group had better long-term retention. It is not known if participants actively switched to an external focus of attention despite the instructions provided during training. Tests to ensure instructional compliance should be used. 3.A treadmill gait retraining program using learner's focus of attention indicated that that there were not differences in learning acquisition, short and long-term retention, and transfer to overground walking and obstacle crossing between intervention groups. It is not known if these changes persist beyond the 4-month follow-up included in this study. The results of this study will help to reduce knee hyperextension gait patterns in women. Future studies may also use the methodology used in this study to further investigate the implications of learner's focus of attention in rehabilitation. Similarly, the findings of this study could offer an additional strategy for rehabilitation regimens.

Genetic sequences are being collected at an ever increasing rate due to rapid cost reductions; however, experimental approaches to determine the structure and function of the protein(s) each gene codes are not keeping pace. Therefore, computational methods to augment experimental structures with comparative (i.e. homology) models using physics-based methods for building residues, loops and domains are needed to thread new sequences onto homologous structures. In addition, even experimental structure determination relies on analogous first principles structure refinement and prediction algorithms to place structural elements that are not defined by the data alone. Computational methods developed to find the global free energy minimum of an amino acid sequence (i.e. the protein folding problem) are increasingly successful, but limitations in accuracy and efficiency remain. Optimization efforts have focused on subsets of systems and environments by utilizing potential energy functions ranging from fixed charged force fields (Fiser, Do, & Sali, 2000; Jacobson et al., 2004), statistical or knowledge based potentials (Das & Baker, 2008) and/or potentials incorporating experimental data (Brunger, 2007; Trabuco, Villa, Mitra, Frank, & Schulten, 2008). Although these methods are widely used, limitations include 1) a target function global minimum that does not correspond to the actual free energy minimum and/or 2) search protocols that are inefficient or not deterministic due to rough energy landscapes characterized by large energy barriers between multiple minima. Our Global Optimization Using Metadynamics and a Polarizable Force Field (GONDOLA) approach tackles the first limitation by incorporating experimental data (i.e. from X-ray crystallography, CryoEM or NMR experiments) into a hybrid target function that also includes information from a polarizable molecular mechanics force field (Lopes, Roux, & MacKerell, 2009; Ponder & Case, 2003). The second limitation is overcome by driving the sampling of conformational space by adding a time-dependent bias to the objective function, which pushes the search toward unexplored regions (Alessandro Barducci, Bonomi, & Parrinello, 2011; Zheng, Chen, & Yang, 2008). The GONDOLA approach incorporates additional efficiency constructs for search space exploration that include Monte Carlo moves and fine grained minimization. Furthermore, the dimensionality of the search is reduced by fixing atomic coordinates of known structural regions while atoms of interest explore new coordinate positions. The overall approach can be used for optimization of side-chains (i.e. set side-chain atoms active while constraining backbone atoms), residues (i.e. side-chain atoms and backbone atoms active), ligand binding pose (i.e. set atoms along binding interface active), protein loops (i.e. set atoms connecting two terminating residues active) or even entire protein domains or complexes. Here we focus on using the GONDOLA general free energy driven optimization strategy to elucidate the structural details of missing protein loops, which are often missing from experimental structures due to conformational heterogeneity and/or limitations in the resolution of the data. We first show that the correlation between experimental data and AMOEBA (i.e. a polarizable force field) structural minima is stronger than that for OPLS-AA (i.e. a fixed charge force field). This suggests that the higher order multipoles and polarization of the AMOEBA force field more accurately represented the true crystalline environment than the simpler OPLS-AA model. Thus, scoring and optimization of loops with AMOEBA is more accurate than with OPLS-AA, albeit at a slightly increased computational cost. Next, missing PDZ domain protein loops and protein loops from a loop decoy data set were optimized for 5 ns using the GONDOLA approach (i.e. under the AMOEBA polarizable force field) as well as a commonly used global optimization procedure (i.e. simulated annealing under the OPLS-AA fixed charge force field). The GONDOLA procedure was shown to provide more accurate structures in terms of both experimental metrics (i.e. lower Rfree values) and structural metrics (i.e. using the MolProbity structure validation tool). In terms of Rfree, only one out of seven simulated annealing results was better than the Gondola global optimization. Similarly, one simulated anneal loop had a better MolProbity score, but none of the simulated annealing loops were better in both categories. On average, GONDOLA achieved an Rfree value 19.48 and simulated annealing saw an average Rfree value of 19.63, and the average MolProbity scores were 1.56 for GONDOLA and 1.75 for simulated annealing. In addition to providing more accurate predictions, GONDOLA was shown to converge much faster than the simulated annealing protocol. Ten separate 5 ns optimizations of the 4 residue loop missing from one of the PDZ domains were conducted. Five were done using GONDOLA and five with the simulated annealing protocol. The fastest four converging results belonged to the GONDOLA approach. Thus, this work demonstrates that GONDOLA is well-suited to refine or predict the coordinates of missing residues and loops because it is both more accurate and converges more rapidly.