Efficient HIV-1 inhibition by a 16 nt-long RNA aptamer designed by combining in vitro selection and in silico optimisation strategies

The human immunodeficiency virus type-1 (HIV-1) genome contains multiple, highly conserved structural RNA domains that play key roles in essential viral processes. Interference with the function of these RNA domains either by disrupting their structures or by blocking their interaction with viral or cellular factors may seriously compromise HIV-1 viability. RNA aptamers are amongst the most promising synthetic molecules able to interact with structural domains of viral genomes. However, aptamer shortening up to their minimal active domain is usually necessary for scaling up production, what requires very time-consuming, trial-and-error approaches. Here we report on the in vitro selection of 64 nt-long specific aptamers against the complete 5' -untranslated region of HIV-1 genome, which inhibit more than 75% of HIV-1 production in a human cell line. The analysis of the selected sequences and structures allowed for the identification of a highly conserved 16 nt-long stem-loop motif containing a common 8 nt-long apical loop. Based on this result, an in silico designed 16 nt-long RNA aptamer, termed RNApt16, was synthesized, with sequence 5'-CCCCGGCAAGGAGGGG-3-'. The HIV-1 inhibition efficiency of such an aptamer was close to 85%, thus constituting the shortest RNA molecule so far described that efficiently interferes with HIV-1 replication.

Analysis of Students’ Misconceptions and Error Patterns in Mathematics: The Case of Fractions

This study analyzed three fifth grade students’ misconceptions and error patterns when working with equivalence, addition and subtraction of fractions. The findings revealed that students used both conceptual and procedural knowledge to solve the problems. They used pictures, gave examples, and made connections to other mathematical concepts and to daily life topics. Error patterns found include using addition and subtraction of numerators and denominators, and finding the greatest common factor.

Seismic Response Analysis of a Full-Scale Base-Isolated Structure via Measurements and Modeling

The full-scale base-isolated structure studied in this dissertation is the only base-isolated building in South Island of New Zealand. It sustained hundreds of earthquake ground motions from September 2010 and well into 2012. Several large earthquake responses were recorded in December 2011 by NEES@UCLA and by GeoNet recording station nearby Christchurch Women's Hospital. The primary focus of this dissertation is to advance the state-of-the art of the methods to evaluate performance of seismic-isolated structures and the effects of soil-structure interaction by developing new data processing methodologies to overcome current limitations and by implementing advanced numerical modeling in OpenSees for direct analysis of soil-structure interaction.

This dissertation presents a novel method for recovering force-displacement relations within the isolators of building structures with unknown nonlinearities from sparse seismic-response measurements of floor accelerations. The method requires only direct matrix calculations (factorizations and multiplications); no iterative trial-and-error methods are required. The method requires a mass matrix, or at least an estimate of the floor masses. A stiffness matrix may be used, but is not necessary. Essentially, the method operates on a matrix of incomplete measurements of floor accelerations. In the special case of complete floor measurements of systems with linear dynamics, real modes, and equal floor masses, the principal components of this matrix are the modal responses. In the more general case of partial measurements and nonlinear dynamics, the method extracts a number of linearly-dependent components from Hankel matrices of measured horizontal response accelerations, assembles these components row-wise and extracts principal components from the singular value decomposition of this large matrix of linearly-dependent components. These principal components are then interpolated between floors in a way that minimizes the curvature energy of the interpolation. This interpolation step can make use of a reduced-order stiffness matrix, a backward difference matrix or a central difference matrix. The measured and interpolated floor acceleration components at all floors are then assembled and multiplied by a mass matrix. The recovered in-service force-displacement relations are then incorporated into the OpenSees soil structure interaction model.

Numerical simulations of soil-structure interaction involving non-uniform soil behavior are conducted following the development of the complete soil-structure interaction model of Christchurch Women's Hospital in OpenSees. In these 2D OpenSees models, the superstructure is modeled as two-dimensional frames in short span and long span respectively. The lead rubber bearings are modeled as elastomeric bearing (Bouc Wen) elements. The soil underlying the concrete raft foundation is modeled with linear elastic plane strain quadrilateral element. The non-uniformity of the soil profile is incorporated by extraction and interpolation of shear wave velocity profile from the Canterbury Geotechnical Database. The validity of the complete two-dimensional soil-structure interaction OpenSees model for the hospital is checked by comparing the results of peak floor responses and force-displacement relations within the isolation system achieved from OpenSees simulations to the recorded measurements. General explanations and implications, supported by displacement drifts, floor acceleration and displacement responses, force-displacement relations are described to address the effects of soil-structure interaction.

Graded Exercise Therapy Guided Self-Help Trial for Patients with Chronic Fatigue Syndrome (GETSET): Protocol for a Randomized Controlled Trial and Interview Study

Background: Chronic fatigue syndrome, also known as myalgic encephalomyelitis (CFS/ME), is characterized by chronic disabling fatigue and other symptoms, which are not explained by an alternative diagnosis. Previous trials have suggested that graded exercise therapy (GET) is an effective and safe treatment. GET itself is therapist-intensive with limited availability. Objective: While guided self-help based on cognitive behavior therapy appears helpful to patients, Guided graded Exercise Self-help (GES) is yet to be tested. Methods: This pragmatic randomized controlled trial is set within 2 specialist CFS/ME services in the South of England. Adults attending secondary care clinics with National Institute for Health and Clinical Excellence (NICE)-defined CFS/ME (N=218) will be randomly allocated to specialist medical care (SMC) or SMC plus GES while on a waiting list for therapist-delivered rehabilitation. GES will consist of a structured booklet describing a 6-step graded exercise program, supported by up to 4 face-to-face/telephone/Skype™ consultations with a GES-trained physiotherapist (no more than 90 minutes in total) over 8 weeks. The primary outcomes at 12-weeks after randomization will be physical function (SF-36 physical functioning subscale) and fatigue (Chalder Fatigue Questionnaire). Secondary outcomes will include healthcare costs, adverse outcomes, and self-rated global impression change scores. We will follow up all participants until 1 year after randomization. We will also undertake qualitative interviews of a sample of participants who received GES, looking at perceptions and experiences of those who improved and worsened. Results: The project was funded in 2011 and enrolment was completed in December 2014, with follow-up completed in March 2016. Data analysis is currently underway and the first results are expected to be submitted soon. Conclusions: This study will indicate whether adding GES to SMC will benefit patients who often spend many months waiting for rehabilitative therapy with little or no improvement being made during that time. The study will indicate whether this type of guided self-management is cost-effective and safe. If this trial shows GES to be acceptable, safe, and comparatively effective, the GES booklet could be made available on the Internet as a practitioner and therapist resource for clinics to recommend, with the caveat that patients also be supported with guidance from a trained physiotherapist. The pragmatic approach in this trial means that GES findings will be generalizable to usual National Health Service (NHS) practice.

Exploring the effects of a universal classroom management training programme on teacher and child behaviour: a group randomised controlled trial and cost analysis

Teachers frequently struggle to cope with conduct problems in the classroom. The aim of this study was to assess the effectiveness of the Incredible Years Teacher Classroom Management Training Programme for improving teacher competencies and child adjustment. The study involved a group randomised controlled trial which included 22 teachers and 217 children (102 boys and 115 girls). The average age of children included in the study was 5.3 years (standard deviation = 0.89). Teachers were randomly allocated to an intervention group (n = 11 teachers; 110 children) or a waiting-list control group (n = 11; 107 children). The sample also included 63 ‘high-risk’ children (33 intervention; 30 control), who scored above the cut-off (>12) on the Strengths and Difficulties Questionnaire for abnormal socioemotional and behavioural difficulties. Teacher and child behaviours were assessed at baseline and 6 months later using psychometric and observational measures. Programme delivery costs were also analysed. Results showed positive changes in teachers’ self-reported use of positive classroom management strategies (effect size = 0.56), as well as negative classroom management strategies (effect size = −0.43). Teacher reports also highlight improvements in the classroom behaviour of the high-risk group of children, while the estimated cost of delivering the Incredible Years Teacher Classroom Management Training Programme was modest. However, analyses of teacher and child observations were largely non-significant. A need for further research exploring the effectiveness and cost-effectiveness of the Incredible Years Teacher Classroom Management Training Programme is indicated.

Effect of haptic guidance and error amplification robotic training interventions on the immediate improvement of timing among individuals that had a stroke

Abstract : Many individuals that had a stroke have motor impairments such as timing deficits that hinder their ability to complete daily activities like getting dressed. Robotic rehabilitation is an increasingly popular therapeutic avenue in order to improve motor recovery among this population. Yet, most studies have focused on improving the spatial aspect of movement (e.g. reaching), and not the temporal one (e.g. timing). Hence, the main aim of this study was to compare two types of robotic rehabilitation on the immediate improvement of timing accuracy: haptic guidance (HG), which consists of guiding the person to make the correct movement, and thus decreasing his or her movement errors, and error amplification (EA), which consists of increasing the person’s movement errors. The secondary objective consisted of exploring whether the side of the stroke lesion had an effect on timing accuracy following HG and EA training. Thirty-four persons that had a stroke (average age 67 ± 7 years) participated in a single training session of a timing-based task (simulated pinball-like task), where they had to activate a robot at the correct moment to successfully hit targets that were presented a random on a computer screen. Participants were randomly divided into two groups, receiving either HG or EA. During the same session, a baseline phase and a retention phase were given before and after each training, and these phases were compared in order to evaluate and compare the immediate impact of HG and EA on movement timing accuracy. The results showed that HG helped improve the immediate timing accuracy (p=0.03), but not EA (p=0.45). After comparing both trainings, HG was revealed to be superior to EA at improving timing (p=0.04). Furthermore, a significant correlation was found between the side of stroke lesion and the change in timing accuracy following EA (r[subscript pb]=0.7, p=0.001), but not HG (r[subscript pb]=0.18, p=0.24). In other words, a deterioration in timing accuracy was found for participants with a lesion in the left hemisphere that had trained with EA. On the other hand, for the participants having a right-sided stroke lesion, an improvement in timing accuracy was noted following EA. In sum, it seems that HG helps improve the immediate timing accuracy for individuals that had a stroke. Still, the side of the stroke lesion seems to play a part in the participants’ response to training. This remains to be further explored, in addition to the impact of providing more training sessions in order to assess any long-term benefits of HG or EA.

Elemental Anisotropic Growth and Atomic-Scale Structure of Shape-Controlled Octahedral Pt–Ni–Co Alloy Nanocatalysts

Multimetallic shape-controlled nanoparticles offer great opportunities to tune the activity, selectivity, and stability of electrocatalytic surface reactions. However, in many cases, our synthetic control over particle size, composition, and shape is limited requiring trial and error. Deeper atomic-scale insight in the particle formation process would enable more rational syntheses. Here we exemplify this using a family of trimetallic PtNiCo nanooctahedra obtained via a low-temperature, surfactant-free solvothermal synthesis. We analyze the competition between Ni and Co precursors under coreduction “one-step” conditions when the Ni reduction rates prevailed. To tune the Co reduction rate and final content, we develop a “two-step” route and track the evolution of the composition and morphology of the particles at the atomic scale. To achieve this, scanning transmission electron microscopy and energy dispersive X-ray elemental mapping techniques are used. We provide evidence of a heterogeneous element distribution caused by element-specific anisotropic growth and create octahedral nanoparticles with tailored atomic composition like Pt1.5M, PtM, and PtM1.5 (M = Ni + Co). These trimetallic electrocatalysts have been tested toward the oxygen reduction reaction (ORR), showing a greatly enhanced mass activity related to commercial Pt/C and less activity loss than binary PtNi and PtCo after 4000 potential cycles.

Woodturning for older learners : a real 'turn on'

The research reported in this study concerns older adults from Australia who voluntarily chose to learn the craft of woodturning. Semi-structured interviews and a survey questionnaire were distributed to members of a woodturning club to explore their motivations and the processes by which they learned how to woodturn. The findings indicated that participants’ motivation could be construed as both intrinsic and extrinsic. They used seven approaches to learning – structured courses, instruction from convenors, modelling/watching/demonstrations, guided practice and monitoring by convenors, trial and error with practice, advice and help from peers and reading. Finally, the positive climate of the organisation was found to be particularly important to the older learners.

Examining the use of bid information in predicting the contractor’s performance

Purpose – The purpose of this paper is to examine the use of bid information, including both price and non-price factors in predicting the bidder’s performance. Design/methodology/approach – The practice of the industry was first reviewed. Data on bid evaluation and performance records of the successful bids were then obtained from the Hong Kong Housing Department, the largest housing provider in Hong Kong. This was followed by the development of a radial basis function (RBF) neural network based performance prediction model. Findings – It is found that public clients are more conscientious and include non-price factors in their bid evaluation equations. With the input variables used the information is available at the time of the bid and the output variable is the project performance score recorded during work in progress achieved by the successful bidder. It was found that past project performance score is the most sensitive input variable in predicting future performance. Research limitations/implications – The paper shows the inadequacy of using price alone for bid award criterion. The need for a systemic performance evaluation is also highlighted, as this information is highly instrumental for subsequent bid evaluations. The caveat for this study is that the prediction model was developed based on data obtained from one single source. Originality/value – The value of the paper is in the use of an RBF neural network as the prediction tool because it can model non-linear function. This capability avoids tedious ‘‘trial and error’’ in deciding the number of hidden layers to be used in the network model. Keywords Hong Kong, Construction industry, Neural nets, Modelling, Bid offer spreads Paper type Research paper

Bioreactor Systems for Tissue Engineering

The hydrodynamic environment “created” by bioreactors for the culture of a tissue engineered construct (TEC) is known to influence cell migration, proliferation and extra cellular matrix production. However, tissue engineers have looked at bioreactors as black boxes within which TECs are cultured mainly by trial and error, as the complex relationship between the hydrodynamic environment and tissue properties remains elusive, yet is critical to the production of clinically useful tissues. It is well known in the chemical and biotechnology field that a more detailed description of fluid mechanics and nutrient transport within process equipment can be achieved via the use of computational fluid dynamics (CFD) technology. Hence, the coupling of experimental methods and computational simulations forms a synergistic relationship that can potentially yield greater and yet, more cohesive data sets for bioreactor studies. This review aims at discussing the rationale of using CFD in bioreactor studies related to tissue engineering, as fluid flow processes and phenomena have direct implications on cellular response such as migration and/or proliferation. We conclude that CFD should be seen by tissue engineers as an invaluable tool allowing us to analyze and visualize the impact of fluidic forces and stresses on cells and TECs.

SwarmPS: Rapid, semi-automated single particle selection software

Single particle analysis (SPA) coupled with high-resolution electron cryo-microscopy is emerging as a powerful technique for the structure determination of membrane protein complexes and soluble macromolecular assemblies. Current estimates suggest that ∼104–105 particle projections are required to attain a 3 Å resolution 3D reconstruction (symmetry dependent). Selecting this number of molecular projections differing in size, shape and symmetry is a rate-limiting step for the automation of 3D image reconstruction. Here, we present SwarmPS, a feature rich GUI based software package to manage large scale, semi-automated particle picking projects. The software provides cross-correlation and edge-detection algorithms. Algorithm-specific parameters are transparently and automatically determined through user interaction with the image, rather than by trial and error. Other features include multiple image handling (∼102), local and global particle selection options, interactive image freezing, automatic particle centering, and full manual override to correct false positives and negatives. SwarmPS is user friendly, flexible, extensible, fast, and capable of exporting boxed out projection images, or particle coordinates, compatible with downstream image processing suites.

Performance control of distributed generation using digital estimation of signal parameters

The Queensland University of Technology (QUT) allows the presentation of a thesis for the Degree of Doctor of Philosophy in the format of published or submitted papers, where such papers have been published, accepted or submitted during the period of candidature. This thesis is composed of seven published/submitted papers, of which one has been published, three accepted for publication and the other three are under review. This project is financially supported by an Australian Research Council (ARC) Discovery Grant with the aim of proposing strategies for the performance control of Distributed Generation (DG) system with digital estimation of power system signal parameters. Distributed Generation (DG) has been recently introduced as a new concept for the generation of power and the enhancement of conventionally produced electricity. Global warming issue calls for renewable energy resources in electricity production. Distributed generation based on solar energy (photovoltaic and solar thermal), wind, biomass, mini-hydro along with use of fuel cell and micro turbine will gain substantial momentum in the near future. Technically, DG can be a viable solution for the issue of the integration of renewable or non-conventional energy resources. Basically, DG sources can be connected to local power system through power electronic devices, i.e. inverters or ac-ac converters. The interconnection of DG systems to power system as a compensator or a power source with high quality performance is the main aim of this study. Source and load unbalance, load non-linearity, interharmonic distortion, supply voltage distortion, distortion at the point of common coupling in weak source cases, source current power factor, and synchronism of generated currents or voltages are the issues of concern. The interconnection of DG sources shall be carried out by using power electronics switching devices that inject high frequency components rather than the desired current. Also, noise and harmonic distortions can impact the performance of the control strategies. To be able to mitigate the negative effect of high frequency and harmonic as well as noise distortion to achieve satisfactory performance of DG systems, new methods of signal parameter estimation have been proposed in this thesis. These methods are based on processing the digital samples of power system signals. Thus, proposing advanced techniques for the digital estimation of signal parameters and methods for the generation of DG reference currents using the estimates provided is the targeted scope of this thesis. An introduction to this research – including a description of the research problem, the literature review and an account of the research progress linking the research papers – is presented in Chapter 1. One of the main parameters of a power system signal is its frequency. Phasor Measurement (PM) technique is one of the renowned and advanced techniques used for the estimation of power system frequency. Chapter 2 focuses on an in-depth analysis conducted on the PM technique to reveal its strengths and drawbacks. The analysis will be followed by a new technique proposed to enhance the speed of the PM technique while the input signal is free of even-order harmonics. The other techniques proposed in this thesis as the novel ones will be compared with the PM technique comprehensively studied in Chapter 2. An algorithm based on the concept of Kalman filtering is proposed in Chapter 3. The algorithm is intended to estimate signal parameters like amplitude, frequency and phase angle in the online mode. The Kalman filter is modified to operate on the output signal of a Finite Impulse Response (FIR) filter designed by a plain summation. The frequency estimation unit is independent from the Kalman filter and uses the samples refined by the FIR filter. The frequency estimated is given to the Kalman filter to be used in building the transition matrices. The initial settings for the modified Kalman filter are obtained through a trial and error exercise. Another algorithm again based on the concept of Kalman filtering is proposed in Chapter 4 for the estimation of signal parameters. The Kalman filter is also modified to operate on the output signal of the same FIR filter explained above. Nevertheless, the frequency estimation unit, unlike the one proposed in Chapter 3, is not segregated and it interacts with the Kalman filter. The frequency estimated is given to the Kalman filter and other parameters such as the amplitudes and phase angles estimated by the Kalman filter is taken to the frequency estimation unit. Chapter 5 proposes another algorithm based on the concept of Kalman filtering. This time, the state parameters are obtained through matrix arrangements where the noise level is reduced on the sample vector. The purified state vector is used to obtain a new measurement vector for a basic Kalman filter applied. The Kalman filter used has similar structure to a basic Kalman filter except the initial settings are computed through an extensive math-work with regards to the matrix arrangement utilized. Chapter 6 proposes another algorithm based on the concept of Kalman filtering similar to that of Chapter 3. However, this time the initial settings required for the better performance of the modified Kalman filter are calculated instead of being guessed by trial and error exercises. The simulations results for the parameters of signal estimated are enhanced due to the correct settings applied. Moreover, an enhanced Least Error Square (LES) technique is proposed to take on the estimation when a critical transient is detected in the input signal. In fact, some large, sudden changes in the parameters of the signal at these critical transients are not very well tracked by Kalman filtering. However, the proposed LES technique is found to be much faster in tracking these changes. Therefore, an appropriate combination of the LES and modified Kalman filtering is proposed in Chapter 6. Also, this time the ability of the proposed algorithm is verified on the real data obtained from a prototype test object. Chapter 7 proposes the other algorithm based on the concept of Kalman filtering similar to those of Chapter 3 and 6. However, this time an optimal digital filter is designed instead of the simple summation FIR filter. New initial settings for the modified Kalman filter are calculated based on the coefficients of the digital filter applied. Also, the ability of the proposed algorithm is verified on the real data obtained from a prototype test object. Chapter 8 uses the estimation algorithm proposed in Chapter 7 for the interconnection scheme of a DG to power network. Robust estimates of the signal amplitudes and phase angles obtained by the estimation approach are used in the reference generation of the compensation scheme. Several simulation tests provided in this chapter show that the proposed scheme can very well handle the source and load unbalance, load non-linearity, interharmonic distortion, supply voltage distortion, and synchronism of generated currents or voltages. The purposed compensation scheme also prevents distortion in voltage at the point of common coupling in weak source cases, balances the source currents, and makes the supply side power factor a desired value.

Kiss

In an age of mobile phones, Facebook, Twitter and online dating, interactions in mediated environments often outnumber face to face encounters. Kiss is an interactive light artwork by artists Priscilla Bracks & Gavin Sade. Kiss reacts to people standing in front of the artwork looking at each other - the moment before kissing. Without interaction the work generates a seductive, ambient, red lighting display, that creates the restful sense of staring into a fire. A fleeting response of white light – like sparks flying in the air – occurs the moment before two faces touch. These sparks are visible in peripheral vision, but fade when the kissing couple turns to look at the work. This moment - as two people look at each other - is a primal moment when two people recognise each other. Face to face encounters with another person are a privileged phenomenon in which the other person's presence and proximity are strongly felt. Kiss does not respond to every instance of a kiss or a look. Its recognition algorithms are fussy, selecting some faces and not others. As in life it’s difficult to tell why sparks fly with some people but not with others. For some this will be felt as a glitch. “This machine should be part of my social life!” But it does promote trial and error, asking viewers to be intimate in public and look at each other for longer than otherwise socially normal. 10 minutes continuous eye contact is said in most cases to arouse sexual feelings in both parties. But even if we don’t look that long, a short time may be all that is needed to explore the face of the person we are looking at. We see that they are human like us. We experience beauty, difference, discomfort, perhaps even nervous laughing, before turning to a more intimate moment of recognition.