Developing and Testing of an Upper Limb Exoskeleton for Stroke Patients

Objective: The main objective of this study was to determine functional and neuromuscular outcomes of stroke patients using their non-preferred hand with and without a 3D printed passive exoskeleton compared to controls using their non-preferred hand with and without the passive exoskeleton. Methods: Adults at least six months post stroke (Stroke, n = 5) and age- and sex- matched healthy controls (Control, n = 5) performed nine trials of a gross motor task while having their brain activity measured. The Fugl-Meyer and “Box and Block” test was used to measure the gross dexterity of the subjects with and without the exoskeleton. Strength testing, muscle activation and co-activation of the subjects’ forearms were measured during maximal voluntary contractions. Furthermore, EMG was measured during the Box and Block test and satisfaction and usability of the 3D printed exoskeleton were assessed using standardized questionnaires. Results: Separate two-way repeated ANOVAs were used to investigate the functional and neuromuscular outcomes. There was an interaction [F(1,4) = 41.60; p = .003, ηp2 = 0.912] with an observed power of 0.996. Decomposing the model, a dependent t-test (p = 0.004) showed the stroke subject’s preferred hand moved more blocks than the stroke subject’s non- preferred hand. The exoskeleton received an average QUEST score of 4.23 out of a maximum score of 5 and SUS score of 79.50 out of 100. Conclusion: The main finding showed the passive exoskeleton did not improve function or neuromuscular outcomes for the stroke patients

Biophysical and computational characterisation of the disorder-to-order structural transition of the small hydrophilic endoplasmic-reticulum associated protein, SHERP

This thesis explores the disorder-to-order structural transition of the small hydrophilic endoplasmic reticulum associated protein (SHERP). SHERP has been shown to be essential to the life cycle of Leishmania major, a parasite responsible for leishmaniasis which kills tens of thousands every year. The protein is almost entirely disordered in solution, but undergoes a dramatic increase in helicity upon binding to anionic lipids or detergents. Although the ordered structure of SHERP had previously been solved by solution nuclear magnetic resonance spectroscopy in the presence of sodium dodecyl sulphate (SDS), both the nature of the disordered ensemble of the protein and the organisation of the SHERP/detergent complex were unknown. Using a combination of synchrotron radiation circular dichroism spectroscopy (SRCD), small angle X-ray scattering (SAXS) and molecular dynamics (MD), several projects were carried out exploring the disorder-to-order structural transition of SHERP in the presence of SDS. The effectiveness of sequence-based predictors to estimate the effect of single mutants was explored, with a number of mutants expressed and characterised by SRCD and MD. A mutant, the “permutant”, was designed with the aim of decreasing the disorder of the protein in solution while maintaining amino acid composition, by introduction of multiple potential i → i4 salt bridges created by permutations of the wild-type sequence. Molecular dynamics simulations of the wild-type and “permutant” construct found a dramatic increase in salt bridge formation, and in vitro characterisation of the “permutant” construct showed it had significantly greater helical character than the wild-type in the absence of SDS. The disordered ensemble of SHERP was characterised by replica exchange MD, SRCD and SAXS. Good agreement was found between simulation and experiment, with a predominantly unfolded ensemble deficient in secondary structure described by our results. The changes that occur upon SHERP binding to SDS were also characterised. MD simulation of the SHERP-SDS complex showed that the protein bound among the head-groups of the SDS micelle, and the helical content and helix-turn-helix structure was retained. It also allowed identification of several cationic side-chains which formed stabilising salt bridges with the sulphates of SDS. The complex was then characterised in vitro, by SAXS and CD spectroscopy. The addition of the protein led to a doubling in micelle length, with multiple SHERP molecules found to bind to the anionic head-groups in the shell of the micelle. The residues identified during the MD simulation were substituted with alanine to make a series of mutants with increasing negative charge. Significant decreases in helicity, micelle length and the numbers of protein bound occurred as negative charge increased, possibly caused by decreased affinity of the protein for the micelle causing less protein molecules to bind per micelle, leading to a decreased chance of stabilising protein-protein interactions resulting in partial folding of the protein. These results demonstrate the importance of charge-charge interactions in the disorder-to-order structural transition of SHERP, and provide structural context for future functional work on this protein

Biophysical and computational characterisation of the disorder-to-order structural transition of the small hydrophilic endoplasmic-reticulum associated protein, SHERP

This thesis explores the disorder-to-order structural transition of the small hydrophilic endoplasmic reticulum associated protein (SHERP). SHERP has been shown to be essential to the life cycle of Leishmania major, a parasite responsible for leishmaniasis which kills tens of thousands every year. The protein is almost entirely disordered in solution, but undergoes a dramatic increase in helicity upon binding to anionic lipids or detergents. Although the ordered structure of SHERP had previously been solved by solution nuclear magnetic resonance spectroscopy in the presence of sodium dodecyl sulphate (SDS), both the nature of the disordered ensemble of the protein and the organisation of the SHERP/detergent complex were unknown. Using a combination of synchrotron radiation circular dichroism spectroscopy (SRCD), small angle X-ray scattering (SAXS) and molecular dynamics (MD), several projects were carried out exploring the disorder-to-order structural transition of SHERP in the presence of SDS. The effectiveness of sequence-based predictors to estimate the effect of single mutants was explored, with a number of mutants expressed and characterised by SRCD and MD. A mutant, the “permutant”, was designed with the aim of decreasing the disorder of the protein in solution while maintaining amino acid composition, by introduction of multiple potential i → i4 salt bridges created by permutations of the wild-type sequence. Molecular dynamics simulations of the wild-type and “permutant” construct found a dramatic increase in salt bridge formation, and in vitro characterisation of the “permutant” construct showed it had significantly greater helical character than the wild-type in the absence of SDS. The disordered ensemble of SHERP was characterised by replica exchange MD, SRCD and SAXS. Good agreement was found between simulation and experiment, with a predominantly unfolded ensemble deficient in secondary structure described by our results. The changes that occur upon SHERP binding to SDS were also characterised. MD simulation of the SHERP-SDS complex showed that the protein bound among the head-groups of the SDS micelle, and the helical content and helix-turn-helix structure was retained. It also allowed identification of several cationic side-chains which formed stabilising salt bridges with the sulphates of SDS. The complex was then characterised in vitro, by SAXS and CD spectroscopy. The addition of the protein led to a doubling in micelle length, with multiple SHERP molecules found to bind to the anionic head-groups in the shell of the micelle. The residues identified during the MD simulation were substituted with alanine to make a series of mutants with increasing negative charge. Significant decreases in helicity, micelle length and the numbers of protein bound occurred as negative charge increased, possibly caused by decreased affinity of the protein for the micelle causing less protein molecules to bind per micelle, leading to a decreased chance of stabilising protein-protein interactions resulting in partial folding of the protein. These results demonstrate the importance of charge-charge interactions in the disorder-to-order structural transition of SHERP, and provide structural context for future functional work on this protein

Functional changes through the usage of 3D-printed transitional prostheses in children

Introduction: There is limited knowledge on the use of 3 D-printed transitional prostheses, as they relate to changes in function and strength. Therefore, the purpose of this study was to identify functional and strength changes after usage of 3 D-printed transitional prostheses for multiple weeks for children with upper-limb differences. Materials and methods: Gross manual dexterity was assessed using the Box and Block Test and wrist strength was measured using a dynamometer. This testing was conducted before and after a period of 24 ± 2.61 weeks of using a 3 D-printed transitional prosthesis. The 11 children (five girls and six boys; 3–15 years of age) who participated in the study, were fitted with a 3 D-printed transitional partial hand (n = 9) or an arm (n = 2) prosthesis. Results: Separate two-way repeated measures ANOVAs were performed to analyze function and strength data. There was a significant hand by time interaction for function, but not for strength. Conclusion and relevance to the study of disability and rehabilitation: The increase in manual gross dexterity suggests that the Cyborg Beast 2 3 D-printed prosthesis can be used as a transitional device to improve function in children with traumatic or congenital upper-limb differences. Implications for Rehabilitation Children’s prosthetic needs are complex due to their small size, rapid growth, and psychosocial development. Advancements in computer-aided design and additive manufacturing offer the possibility of designing and printing transitional prostheses at a very low cost, but there is limited knowledge on the function of this type of devices. The use of 3D printed transitional prostheses may improve manual gross dexterity in children after several weeks of using it

Coactivation index of children with congenital upper limb reduction deficiencies before and after using a wristdriven 3D printed partial hand prosthesis

Background: Co-contraction is the simultaneous activation of agonist and antagonist muscles that produces forces around a joint. It is unknown if the use of a wrist-driven 3D printed transitional prostheses has any influence on the neuromuscular motor control strategies of the affected hand of children with unilateral upper-limb reduction deficiencies. Thus, the purpose of the current investigation was to examine the coactivation index (CI) of children with congenital upper-limb reduction deficiencies before and after 6 months of using a wrist-driven 3D printed partial hand prosthesis. Methods: Electromyographic activity of wrist flexors and extensors (flexor carpi ulnaris and extensor digitorum) was recorded during maximal voluntary contraction of the affected and non-affected wrists. Co-contraction was calculated using the coactivation index and was expressed as percent activation of antagonist over agonist. Nine children (two girls and seven boys, 6 to 16 years of age) with congenital upper-limb deficiencies participated in this study and were fitted with a wrist-driven 3D printed prosthetic hand. From the nine children, five (two girls and three boys, 7 to 10 years of age) completed a second visit after using the wrist-driven 3D printed partial hand prosthesis for 6 months. Results: Separate two-way repeated measures ANOVAs were performed to analyze the coactivation index and strength data. There was a significant main effect for hand with the affected hand resulting in a higher coactivation index for flexion and extension than the non-affected hand. For wrist flexion there was a significant main effect for time indicating that the affected and non-affected hand had a significantly lower coactivation index after a period of 6 months. Conclusion: The use of a wrist-driven 3D printed hand prosthesis lowered the coactivation index by 70% in children with congenital upper limb reduction deficiencies. This reduction in coactivation and possible improvement in motor control strategies can potentially improve prosthetic rehabilitation outcomes

Racing Academy: A case study of a digital game for supporting students learning of physics and engineering

Racing Academy is a digital game, which is specifically designed to engage and motivate students in science and engineering. The aim of this chapter is to report a case study where the authors evaluated how effective Racing Academy is at supporting students’ learning of science and engineering. The study involved 219 students from five different courses in three further and higher educational institutions. They were given a pre-test a week before they started using Racing Academy. It consisted of an assessment of the students’ knowledge of engineering or physics and motivation towards engineering or physics. A week after they had used Racing Academy, they were given a post-test, which was the same as the pre-test, but it also included a measure of how motivating they found Racing Academy. The project found that after playing Racing Academy there is an increase in students’ knowledge and understanding in all five of the courses in which Racing Academy was used. The students found Racing Academy motivating to play, and 95% thought that Racing Academy was successful. The implications of these findings and the lessons learnt are discussed

Intercomparison of the representations of the atmospheric chemistry of pre-industrial methane and ozone in earth system and other global chemistry-transport models

An intercomparison has been set up to study the representation of the atmospheric chemistry of the pre-industrial troposphere in earth system and other global tropospheric chemistry-transport models. The intercomparison employed a constrained box model and utilised tropospheric trace gas composition data for the pre-industrial times at ninety mid-latitude surface locations. Incremental additions of four organic compounds: methane, ethane, acetone and propane, were used to perturb the constrained box model and generate responses in hydroxyl radicals and tropospheric ozone at each location and with each chemical mechanism. Although the responses agreed well across the chemical mechanisms from the selected earth system and other global tropospheric chemistry-transport models, there were differences in the detailed responses between the chemical mechanisms that could be tracked down by sensitivity analysis to differences in the representation of C1–C3 chemistry. Inter-mechanism ranges in NOx compensation points were about 0.17 ± 0.12 when expressed relative to the inter-mechanism average. Monte Carlo uncertainty analysis carried out with a single chemical mechanism put the intra-mechanism range a factor of three higher at 0.50 ± 0.12

Finishing the euchromatic sequence of the human genome

The sequence of the human genome encodes the genetic instructions for human physiology, as well as rich information about human evolution. In 2001, the International Human Genome Sequencing Consortium reported a draft sequence of the euchromatic portion of the human genome. Since then, the international collaboration has worked to convert this draft into a genome sequence with high accuracy and nearly complete coverage. Here, we report the result of this finishing process. The current genome sequence (Build 35) contains 2.85 billion nucleotides interrupted by only 341 gaps. It covers ∼99% of the euchromatic genome and is accurate to an error rate of ∼1 event per 100,000 bases. Many of the remaining euchromatic gaps are associated with segmental duplications and will require focused work with new methods. The near-complete sequence, the first for a vertebrate, greatly improves the precision of biological analyses of the human genome including studies of gene number, birth and death. Notably, the human enome seems to encode only 20,000-25,000 protein-coding genes. The genome sequence reported here should serve as a firm foundation for biomedical research in the decades ahead