Multi-resolution polymer Brownian dynamics with hydrodynamic interactions

A polymer model given in terms of beads, interacting through Hookean springs and hydrodynamic forces, is studied. Brownian dynamics description of this bead-spring polymer model is extended to multiple resolutions. Using this multiscale approach, a modeller can efficiently look at different regions of the polymer in different spatial and temporal resolutions with scalings given for the number of beads, statistical segment length and bead radius in order to maintain macro-scale properties of the polymer filament. The Boltzmann distribution of a Gaussian chain for differing statistical segment lengths gives a Langevin equation for the multi-resolution model with a mobility tensor for different bead sizes. Using the pre-averaging approximation, the translational diffusion coefficient is obtained as a function of the inverse of a matrix and then in closed form in the long-chain limit. This is then confirmed with numerical experiments.Comment: Submitted to Journal of Chemical Physic

Varying the resolution of the Rouse model on temporal and spatial scales: application to multiscale modelling of DNA dynamics

A multi-resolution bead-spring model for polymer dynamics is developed as a generalization of the Rouse model. A polymer chain is described using beads of variable sizes connected by springs with variable spring constants. A numerical scheme which can use different timesteps to advance the positions of different beads is presented and analyzed. The position of a particular bead is only updated at integer multiples of the timesteps associated with its connecting springs. This approach extends the Rouse model to a multiscale model on both spatial and temporal scales, allowing simulations of localized regions of a polymer chain with high spatial and temporal resolution, while using a coarser modelling approach to describe the rest of the polymer chain. A method for changing the model resolution on-the-fly is developed using the Metropolis-Hastings algorithm. It is shown that this approach maintains key statistics of the end-to-end distance and diffusion of the polymer filament and makes computational savings when applied to a model for the binding of a protein to the DNA filament.Comment: Submitted to Multiscale Modeling and Simulatio

Nutritional Ketoacidosis During Incremental Exercise in Healthy Athletes

Purpose: Ketosis, achieved through ingestion of ketone esters, may influence endurance exercise capacity by altering substrate metabolism. However, the effects of ketone consumption on acid-base status and subsequent metabolic and respiratory compensations are poorly described.Methods: Twelve athletically trained individuals completed an incremental bicycle ergometer exercise test to exhaustion following the consumption of either a ketone ester [(R)-3-hydroxybutyrate-(R)-1,3-butanediol] or a taste-matched control drink (bitter flavoured water) in a blinded, cross-over study. Respiratory gases and arterialised blood gas samples were taken at rest and at regular intervals during exercise.Results: Ketone ester consumption increased blood D-β-hydroxybutyrate concentration from 0.2 to 3.7 mM/L (p < 0.01), causing significant falls versus control in blood pH to 7.37 and bicarbonate to 18.5 mM/L before exercise. To compensate for ketoacidosis, minute ventilation was modestly increased (p < 0.05) with non-linearity in the ventilatory response to exercise (ventilatory threshold) occurring at a 22 W lower workload (p < 0.05). Blood pH and bicarbonate concentrations were the same at maximal exercise intensities. There was no difference in exercise performance having consumed the ketone ester or control drink.Conclusion: Athletes compensated for the greater acid load caused by ketone ester ingestion by elevating minute ventilation and earlier hyperventilation during incremental exercise

Effect of Fibre Supplementation on Body Weight and Composition, Frequency of Eating and Dietary Choice in Overweight Individuals

Fibre supplementation can potentially reduce energy intake and contribute to weight loss. The mechanism may be reduced frequency of eating, resulting in reduced food consumption. The objective of this research was to determine the effectiveness of fibre supplementation with PolyGlycopleX® (PGX®), on body weight and composition, frequency of eating and dietary intake in 118 overweight adults. In a three-arm, parallel, blind, randomised controlled trial participants were randomised to one of three groups; 4.5 g PGX as softgels (PGXS), 5 g PGX granules (PGXG) or 5 g rice flour (RF) control. Prior to supplementation and at 12 weeks, participants captured before and after images of all food and beverages consumed within 4 days using a mobile food record app (mFR). The mFR images were analysed for food group serving sizes and number of eating occasions. In the PGXG group, intention-to-treat analysis showed there was a significant reduction in waist circumference (2.5 cm; p = 0.003). Subgroup analysis showed that PGXG supplementation at the recommended dose resulted in a reduction in body weight (-1.4 ± 0.10 kg, p < 0.01), body mass index (BMI) reduction (-0.5 ± 0.10, p < 0.01), reduced number of eating occasions (-1.4 ± 1.2, p < 0.01) and a reduced intake of grain food (-1.52 ± 1.84 serves, p = 0.019). PGXG at the recommended dose resulted in a reduction in weight and BMI which was significantly greater than that for RF (p = 0.001). These results demonstrate the potential benefits of PGX fibre in controlling frequency of eating and in weight loss

Investigating the purpose of an online discussion group for health professionals: a case example from forensic occupational therapy

Background: Thousands of health-related online discussion groups are active world-wide however, very little is known about the purpose and usefulness of such groups. In 2003 an online discussion group called ‘forensic occupational therapy' was established in the United Kingdom. This group was examined to gain an understanding of the purpose and use of online discussion groups for health professionals who may be practically and geographically isolated from others in similar areas of practice. Methods: Following a case study design, descriptive characteristics on members' locations and number of posts were collected from the forensic occupational therapy online discussion group. Eight years of posts (2003-2011) were examined using a theoretical thematic analysis process to identify and describe the purposes for which members were using the group. Results: Members from 20 countries contributed to the discussion group; the vast majority of posts being from members in the United Kingdom. Activity within the group was consistently high for the first five years however, activity within the group declined in the final three years. Six purposes for which members use the online discussion group were identified: seeking and giving advice, networking, requesting and sharing material resources, service development, defining the role of occupational therapists, and student learning. Conclusions: Findings suggest that health professionals in specialized and often isolated areas of practice are keen to connect with colleagues and learn from each other's experiences. The main purposes for which the online discussion group was used could be summarized as communication, information sharing and networking; though activity within the group declined significantly during the last three years of the data collection period. This raises questions about the sustainability of online discussion groups within the rapidly developing social media environment

The management of children with bronchiolitis in the Australasian hospital setting: Development of a clinical practice guideline

© 2018 The Author(s). Background: Bronchiolitis is the commonest respiratory infection in children less than 12 months and cause of hospitalisation in infants under 6 months of age in Australasia. Unfortunately there is substantial variation in management, despite high levels of supporting evidence. This paper reports on the process, strengths and challenges of the hybrid approach used to develop the first Australasian management guideline relevant to the local population. Method: An adaption of the nine steps recommended by the National Health and Medical Research Council (NHMRC) and the Grading of Recommendations Assessment, Development and Evaluation (GRADE) methodology were utilised. Following establishment of the Guideline Development Committee (GDC), we identified the population, intervention, comparator, outcomes and time of interest (PICOt) questions, undertook a systematic literature search and graded the evidence and recommendations using the NHMRC and GRADE processes. Using Nominal Group Techniques (NGT), consensus was sought in formulating the clinical practice recommendations and practice points. Key health professional bodies were consulted to ensure relevance in the Australasian emergency and ward settings. Results: From 33 PICOT questions, clinical recommendations for practice that were deemed relevant to the Australasian population were identified. Specific considerations for the management of Australian and New Zealand indigenous infants in relation to the use of azithromycin and risk factors for more serious illness are included. Using NGT, consensus demonstrated by a median Likert score > 8 for all recommendations was achieved. The guideline presents clinical guidance, followed by the key recommendations and evidence review behind each recommendation. Conclusion: Developing evidence-based clinical guidelines is a complex process with considerable challenges. Challenges included having committee members located over two countries and five time zones, large volume of literature and variation of member's knowledge of grading of evidence and recommendations. The GRADE and NHMRC processes provided a systematic and transparent approach ensuring a final structure including bedside interface, and a descriptive summary of the evidence base and tables for each key statement. Involvement of stakeholders who will ultimately be end-users as members of the GDC provided valuable knowledge. Lessons learnt during this guideline development process provide valuable insight for those planning development of evidence-based guidelines

Esophageal Cancer Related Gene-4 Is a Choroid Plexus-Derived Injury Response Gene: Evidence for a Biphasic Response in Early and Late Brain Injury

By virtue of its ability to regulate the composition of cerebrospinal fluid (CSF), the choroid plexus (CP) is ideally suited to instigate a rapid response to traumatic brain injury (TBI) by producing growth regulatory proteins. For example, Esophageal Cancer Related Gene-4 (Ecrg4) is a tumor suppressor gene that encodes a hormone-like peptide called augurin that is present in large concentrations in CP epithelia (CPe). Because augurin is thought to regulate senescence, neuroprogenitor cell growth and differentiation in the CNS, we evaluated the kinetics of Ecrg4 expression and augurin immunoreactivity in CPe after CNS injury. Adult rats were injured with a penetrating cortical lesion and alterations in augurin immunoreactivity were examined by immunohistochemistry. Ecrg4 gene expression was characterized by in situ hybridization. Cell surface augurin was identified histologically by confocal microscopy and biochemically by sub-cellular fractionation. Both Ecrg4 gene expression and augurin protein levels were decreased 24–72 hrs post-injury but restored to uninjured levels by day 7 post-injury. Protein staining in the supraoptic nucleus of the hypothalamus, used as a control brain region, did not show a decrease of auguin immunoreactivity. Ecrg4 gene expression localized to CPe cells, and augurin protein to the CPe ventricular face. Extracellular cell surface tethering of 14 kDa augurin was confirmed by cell surface fractionation of primary human CPe cells in vitro while a 6–8 kDa fragment of augurin was detected in conditioned media, indicating release from the cell surface by proteolytic processing. In rat CSF however, 14 kDa augurin was detected. We hypothesize the initial release and proteolytic processing of augurin participates in the activation phase of injury while sustained Ecrg4 down-regulation is dysinhibitory during the proliferative phase. Accordingly, augurin would play a constitutive inhibitory function in normal CNS while down regulation of Ecrg4 gene expression in injury, like in cancer, dysinhibits proliferation

Studying partially ordered systems using stochastic differential equations

This thesis looks at two different problems in the field of partially ordered systems - modelling biopolymers on multiple scales as well as modelling two-dimensional nematic liquid crystal wells - and seeks to gain insight using stochastic differential equations, through mathematical analysis and numerical simulations. In the field of biopolymers, we generalize existing models for a coarse-grained polymer to multiple resolutions, which allows for faster computations while maintaining a high level of detail in regions of interest. This is done for two bead spring models; the Rouse model, which does not account for hydrodynamic interactions, as well as the bead-spring model with hydrodynamic interactions. For both models mathematical analysis is done to find expressions for global statistics to derive scaling laws for the models. This is implemented by generalizing existing algorithms using a multi-resolution approach which utilizes multiple spatial and temporal scales. These simulations show that the scaling laws for multiple resolutions match expected analytic results through simulations. For the Rouse model, a model for the binding of a protein to DNA is introduced, along with a mechanism for changing resolutions along the filament on-the-fly. Within reasonable error, the results for the chain in multiple resolutions matches the chain modelled entirely in high-resolution. The work on nematic liquid crystals is concerned with a stochastic dynamics model of nematic liquid crystals contained within a square well, looking at their behaviour under Brownian motion using the Gay-Berne potential. In particular, we are interested in the parameter regimes which are responsible for different types of steady states to form in the system and whether steady states suggested by continuum modelling are stable.</p

Studying partially ordered systems using stochastic differential equations

This thesis looks at two different problems in the field of partially ordered systems - modelling biopolymers on multiple scales as well as modelling two-dimensional nematic liquid crystal wells - and seeks to gain insight using stochastic differential equations, through mathematical analysis and numerical simulations. In the field of biopolymers, we generalize existing models for a coarse-grained polymer to multiple resolutions, which allows for faster computations while maintaining a high level of detail in regions of interest. This is done for two bead spring models; the Rouse model, which does not account for hydrodynamic interactions, as well as the bead-spring model with hydrodynamic interactions. For both models mathematical analysis is done to find expressions for global statistics to derive scaling laws for the models. This is implemented by generalizing existing algorithms using a multi-resolution approach which utilizes multiple spatial and temporal scales. These simulations show that the scaling laws for multiple resolutions match expected analytic results through simulations. For the Rouse model, a model for the binding of a protein to DNA is introduced, along with a mechanism for changing resolutions along the filament on-the-fly. Within reasonable error, the results for the chain in multiple resolutions matches the chain modelled entirely in high-resolution. The work on nematic liquid crystals is concerned with a stochastic dynamics model of nematic liquid crystals contained within a square well, looking at their behaviour under Brownian motion using the Gay-Berne potential. In particular, we are interested in the parameter regimes which are responsible for different types of steady states to form in the system and whether steady states suggested by continuum modelling are stable.</p

Multiscale modelling of mesoscopic polymer dynamics

Non UBCUnreviewedAuthor affiliation: University of OxfordGraduat