http://hdl.handle.net/2144/978 2013-05-22T16:05:06Z 2013-05-22T16:05:06Z Oddsson, Lars IE Karlsson, Robin Konrad, Janusz Ince, Serdar Williams, Steve R Zemkova, Erika http://hdl.handle.net/2144/3347 2012-01-12T07:01:00Z 2007-07-10T00:00:00Z

A Rehabilitation Tool for Functional Balance using Altered Gravity and Virtual Reality Oddsson, Lars IE; Karlsson, Robin; Konrad, Janusz; Ince, Serdar; Williams, Steve R; Zemkova, Erika BACKGROUND There is a need for effective and early functional rehabilitation of patients with gait and balance problems including those with spinal cord injury, neurological diseases and recovering from hip fractures, a common consequence of falls especially in the elderly population. Gait training in these patients using partial body weight support (BWS) on a treadmill, a technique that involves unloading the subject through a harness, improves walking better than training with full weight bearing. One problem with this technique not commonly acknowledged is that the harness provides external support that essentially eliminates associated postural adjustments (APAs) required for independent gait. We have developed a device to address this issue and conducted a training study for proof of concept of efficacy. METHODS We present a tool that can enhance the concept of BWS training by allowing natural APAs to occur mediolaterally. While in a supine position in a 90 deg tilted environment built around a modified hospital bed, subjects wear a backpack frame that is freely moving on air-bearings (cf. puck on an air hockey table) and attached through a cable to a pneumatic cylinder that provides a load that can be set to emulate various G-like loads. Veridical visual input is provided through two 3-D automultiscopic displays that allow glasses free 3-D vision representing a virtual surrounding environment that may be acquired from sites chosen by the patient. Two groups of 12 healthy subjects were exposed to either strength training alone or a combination of strength and balance training in such a tilted environment over a period of four weeks. RESULTS Isokinetic strength measured during upright squat extension improved similarly in both groups. Measures of balance assessed in upright showed statistically significant improvements only when balance was part of the training in the tilted environment. Postural measures indicated less reliance on visual and/or increased use of somatosensory cues after training. CONCLUSION Upright balance function can be improved following balance specific training performed in a supine position in an environment providing the perception of an upright position with respect to gravity. Future studies will implement this concept in patients.

2007-07-10T00:00:00Z Shen, Yang Paschalidis, Ioannis Ch. Vakili, Pirooz Vajda, Sandor http://hdl.handle.net/2144/3041 2012-01-11T07:00:30Z 2008-10-10T00:00:00Z

Protein Docking by the Underestimation of Free Energy Funnels in the Space of Encounter Complexes Shen, Yang; Paschalidis, Ioannis Ch.; Vakili, Pirooz; Vajda, Sandor Similarly to protein folding, the association of two proteins is driven by a free energy funnel, determined by favorable interactions in some neighborhood of the native state. We describe a docking method based on stochastic global minimization of funnel-shaped energy functions in the space of rigid body motions (SE(3)) while accounting for flexibility of the interface side chains. The method, called semi-definite programming-based underestimation (SDU), employs a general quadratic function to underestimate a set of local energy minima and uses the resulting underestimator to bias further sampling. While SDU effectively minimizes functions with funnel-shaped basins, its application to docking in the rotational and translational space SE(3) is not straightforward due to the geometry of that space. We introduce a strategy that uses separate independent variables for side-chain optimization, center-to-center distance of the two proteins, and five angular descriptors of the relative orientations of the molecules. The removal of the center-to-center distance turns out to vastly improve the efficiency of the search, because the five-dimensional space now exhibits a well-behaved energy surface suitable for underestimation. This algorithm explores the free energy surface spanned by encounter complexes that correspond to local free energy minima and shows similarity to the model of macromolecular association that proceeds through a series of collisions. Results for standard protein docking benchmarks establish that in this space the free energy landscape is a funnel in a reasonably broad neighborhood of the native state and that the SDU strategy can generate docking predictions with less than 5 Å ligand interface Cα root-mean-square deviation while achieving an approximately 20-fold efficiency gain compared to Monte Carlo methods. Author SummaryProtein–protein interactions play a central role in various aspects of the structural and functional organization of the cell, and their elucidation is crucial for a better understanding of processes such as metabolic control, signal transduction, and gene regulation. Genomewide proteomics studies, primarily yeast two-hybrid assays, will provide an increasing list of interacting proteins, but only a small fraction of the potential complexes will be amenable to direct experimental analysis. Thus, it is important to develop computational docking methods that can elucidate the details of specific interactions at the atomic level. Protein–protein docking generally starts with a rigid body search that generates a large number of docked conformations with good shape, electrostatic, and chemical complementarity. The conformations are clustered to obtain a manageable number of models, but the current methods are unable to select the most likely structure among these models. Here we describe a refinement algorithm that, applied to the individual clusters, improves the quality of the models. The better models are suitable for higher-accuracy energy calculation, thereby increasing the chances that near-native structures can be identified, and thus the refinement increases the reliability of the entire docking algorithm.

2008-10-10T00:00:00Z Upile, Tahwinder Jerjes, Waseem Sterenborg, Henricus JCM El-Naggar, Adel K Sandison, Ann Witjes, Max JH Biel, Merrill A Bigio, Irving Wong, Brian JF Gillenwater, Ann MacRobert, Alexander J Robinson, Dominic J Betz, Christian S Stepp, Herbert Bolotine, Lina McKenzie, Gordon Mosse, Charles Alexander Barr, Hugh Chen, Zhongping Berg, Kristian D'Cruz, Anil K Stone, Nicholas Kendall, Catherine Fisher, Sheila Leunig, Andreas Olivo, Malini Richards-Kortum, Rebecca Soo, Khee Chee Bagnato, Vanderlei Choo-Smith, Lin-Ping Svanberg, Katarina Tan, I Bing Wilson, Brian C Wolfsen, Herbert Yodh, Arjun G Hopper, Colin http://hdl.handle.net/2144/2818 2012-01-10T07:01:51Z 2009-07-13T00:00:00Z

Head & Neck Optical Diagnostics: Vision of the Future of Surgery Upile, Tahwinder; Jerjes, Waseem; Sterenborg, Henricus JCM; El-Naggar, Adel K; Sandison, Ann; Witjes, Max JH; Biel, Merrill A; Bigio, Irving; Wong, Brian JF; Gillenwater, Ann; MacRobert, Alexander J; Robinson, Dominic J; Betz, Christian S; Stepp, Herbert; Bolotine, Lina; McKenzie, Gordon; Mosse, Charles Alexander; Barr, Hugh; Chen, Zhongping; Berg, Kristian; D'Cruz, Anil K; Stone, Nicholas; Kendall, Catherine; Fisher, Sheila; Leunig, Andreas; Olivo, Malini; Richards-Kortum, Rebecca; Soo, Khee Chee; Bagnato, Vanderlei; Choo-Smith, Lin-Ping; Svanberg, Katarina; Tan, I Bing; Wilson, Brian C; Wolfsen, Herbert; Yodh, Arjun G; Hopper, Colin Review paper and Proceedings of the Inaugural Meeting of the Head and Neck Optical Diagnostics Society (HNODS) on March 14th 2009 at University College London. The aim of our research must be to provide breakthrough translational research which can be applied clinically in the immediate rather than the near future. We are fortunate that this is indeed a possibility and may fundamentally change current clinical and surgical practice to improve our patients' lives.

2009-07-13T00:00:00Z Campbell, David K Singh, R. R. P Sandvik, A. W http://hdl.handle.net/2144/986 2009-10-29T14:59:02Z 1997-06-05T00:00:00Z

Quantum Monte Carlo in the Interaction Representation --- Application to a Spin-Peierls Model Campbell, David K; Singh, R. R. P; Sandvik, A. W A quantum Monte Carlo algorithm is constructed starting from the standard perturbation expansion in the interaction representation. The resulting configuration space is strongly related to that of the Stochastic Series Expansion (SSE) method, which is based on a direct power series expansion of exp(-beta*H). Sampling procedures previously developed for the SSE method can therefore be used also in the interaction representation formulation. The new method is first tested on the S=1/2 Heisenberg chain. Then, as an application to a model of great current interest, a Heisenberg chain including phonon degrees of freedom is studied. Einstein phonons are coupled to the spins via a linear modulation of the nearest-neighbor exchange. The simulation algorithm is implemented in the phonon occupation number basis, without Hilbert space truncations, and is exact. Results are presented for the magnetic properties of the system in a wide temperature regime, including the T-->0 limit where the chain undergoes a spin-Peierls transition. Some aspects of the phonon dynamics are also discussed. The results suggest that the effects of dynamic phonons in spin-Peierls compounds such as GeCuO3 and NaV2O5 must be included in order to obtain a correct quantitative description of their magnetic properties, both above and below the dimerization temperature.

1997-06-05T00:00:00Z