Interaction of oligonucleotide-based amphiphilic block copolymers with cell membrane models

Oligonucleotides have unique molecular recognition properties, being involved in biological mechanisms such as cell-surface receptor recognition or gene silencing. For their use in human therapy for drug or gene delivery, the cell membrane remains a barrier, but this can be obviated by grafting a hydrophobic tail to the oligonucleotide. Here we demonstrate that two oligonucleotides, one consisting of 12 guanosine units (G(12)), and the other one consisting of five adenosine and seven guanosine (A(5)G(7)) units, when functionalized with poly(butadiene), namely PB-G(12) and PB-A(5)G(7), can be inserted into Langmuir monolayers of dipalmitoyl phosphatidyl choline (DPPC), which served as a cell membrane model. PB-G(12) and PB-A(5)G(7) were found to affect the DPPC monolayer even at high surface pressures. The effects from PB-G(12) were consistently stronger, particularly in reducing the elasticity of the DPPC monolayers, which may have important biological implications. Multilayers of DPPC and nucleotide-based copolymers could be adsorbed onto solid supports, in the form of Y-type LB films, in which the molecular-level interaction led to lower energies in the vibrational spectra of the nucleotide-based copolymers. This successful deposition of solid films opens the way for devices to be produced which exploit the molecular recognition properties of the nucleotides. (C) 2010 Elsevier Inc. All rights reserved.

Quantifying epistemic actions in human-computer interaction

As digital systems move away from traditional desktop setups, new interaction paradigms are emerging that better integrate with users’ realworld surroundings, and better support users’ individual needs. While promising, these modern interaction paradigms also present new challenges, such as a lack of paradigm-specific tools to systematically evaluate and fully understand their use. This dissertation tackles this issue by framing empirical studies of three novel digital systems in embodied cognition – an exciting new perspective in cognitive science where the body and its interactions with the physical world take a central role in human cognition. This is achieved by first, focusing the design of all these systems on a contemporary interaction paradigm that emphasizes physical interaction on tangible interaction, a contemporary interaction paradigm; and second, by comprehensively studying user performance in these systems through a set of novel performance metrics grounded on epistemic actions, a relatively well established and studied construct in the literature on embodied cognition. The first system presented in this dissertation is an augmented Four-in-a-row board game. Three different versions of the game were developed, based on three different interaction paradigms (tangible, touch and mouse), and a repeated measures study involving 36 participants measured the occurrence of three simple epistemic actions across these three interfaces. The results highlight the relevance of epistemic actions in such a task and suggest that the different interaction paradigms afford instantiation of these actions in different ways. Additionally, the tangible version of the system supports the most rapid execution of these actions, providing novel quantitative insights into the real benefits of tangible systems. The second system presented in this dissertation is a tangible tabletop scheduling application. Two studies with single and paired users provide several insights into the impact of epistemic actions on the user experience when these are performed outside of a system’s sensing boundaries. These insights are clustered by the form, size and location of ideal interface areas for such offline epistemic actions to occur, as well as how can physical tokens be designed to better support them. Finally, and based on the results obtained to this point, the last study presented in this dissertation directly addresses the lack of empirical tools to formally evaluate tangible interaction. It presents a video-coding framework grounded on a systematic literature review of 78 papers, and evaluates its value as metric through a 60 participant study performed across three different research laboratories. The results highlight the usefulness and power of epistemic actions as a performance metric for tangible systems. In sum, through the use of such novel metrics in each of the three studies presented, this dissertation provides a better understanding of the real impact and benefits of designing and developing systems that feature tangible interaction.

Interaction of the meso-tetrakis (4-N-methylpyridyl) porphyrin with gel and liquid state phospholipid vesicles

The interaction of the cationic meso-tetrakis 4-N-methylpyridyl porphyrin (TMPyP) with large unilamellar vesicles (LUVs) was investigated in the present study. LUVs were formed by mixtures of the zwitterionic 1,2-dipalmitoyl-sn-glycero-phosphatidylcholine (DPPC) and anionic 1,2-dipalmitoyl-sn-glycero-3-phosphoglycerol (DPPG) phospholipids, at different DPPG molar percentages. All investigations were carried out above (50 degrees C) and below (25 degrees C) the main phase transition temperature of the LUVs (similar to 41 degrees C). The binding constant values, K-b, estimated from the time-resolved fluorescence study, showed a significant increase of the porphyrin affinity at higher mol% DPPG. This affinity is markedly increased when the LUVs are in the liquid crystalline state. For both situations, the increase of the K-b value was also followed by a higher porphyrin fraction bound to the LUVs. The displacement of the vesicle-bound porphyrins toward the aqueous medium, upon titration with the salt potassium chloride (KCl), was also studied. Altogether, our steady-state and frequency-domain fluorescence quenching data results indicate that the TMPyP is preferentially located at the LUVs Stern layer. This is supported by the zeta potential studies, where a partial neutralization of the LUVs surface charge, upon porphyrin titration, was observed. Dynamic light scattering (DLS) results showed that, for some phospholipid systems, this partial neutralization leads to the LUVs flocculation. (C) 2012 Elsevier Inc. All rights reserved.

Interaction of chitosan and mucin in a biomembrane model environment

Chitosans have been widely exploited in biological applications, including drug delivery and tissue engineering, especially owing to their mucoadhesive properties, but the molecular-level mechanisms for the chitosan action are not known in detail. It is believed that chitosan could affect the mucus by interacting with the proteins mucins, in a process mediated by the cell membrane. In this study we used Langmuir monolayers of dimyristoylphosphatidic acid (DMPA) as simplified membrane models to investigate the interplay between the activity of mucins and chitosan. Surface pressure and surface potential measurements were performed with DMPA monolayers onto which chitosan and/or mucin was adsorbed. We found that the expanding effect from mucin was considerably reduced when chitosan was injected after mucin had been adsorbed on the DMPA monolayer. The results were consistent with the formation of complexes between mucin and chitosan, thus highlighting the importance of electrostatic interactions. Furthermore, chitosan could remove mucin that was co-deposited along with DMPA in Langmuir-Blodgett (LB) films, which could be ascribed to molecular-level interactions between chitosan and mucin inferred from the FTIR spectra of the LB films. In conclusion, the results with Langmuir and LB films suggest that electrostatic interactions are crucial for the mucoadhesive mechanism, which is affected by the complexation between chitosan and mucin. (C) 2012 Elsevier Inc. All rights reserved.

Interaction of p-cymene with beta-cyclodextrin

In this investigation, the study of inclusion complexes formation between p-cymene and beta-cyclodextrin using the methods of physical mixture, paste (PC) and slurry (SC), was evaluated. The results of DSC and TG/DTG showed that the products prepared by PC and SC methods were able to incorporate greater amounts of p-cymene, as evidenced by the weight loss of 7.15 and 3.97%, respectively, which occurred between 120 and 270 A degrees C. SEM images showed decreased size of the household, especially in the SC product. The absorption bands in the IR spectrum, characteristic of p-cymene, were also identified in the preparations, indicating the presence of the compound in the complex.

Inhibition of Reaper-induced apoptosis by interaction with inhibitor of apoptosis proteins (IAPs)

IAPs comprise a family of inhibitors of apoptosis found in viruses and animals. In vivo binding studies demonstrated that both baculovirus and Drosophila IAPs physically interact with an apoptosis-inducing protein of Drosophila, Reaper (RPR), through their baculovirus IAP repeat (BIR) region. Expression of IAPs blocked RPR-induced apoptosis and resulted in the accumulation of RPR in punctate perinuclear locations which coincided with IAP localization. When expressed alone, RPR rapidly disappeared from the cells undergoing RPR-induced apoptosis. Expression of P35, a caspase inhibitor, also blocked RPR-induced apoptosis and delayed RPR decline, but RPR remained cytoplasmic in its location. Mutational analysis of RPR demonstrated that caspases were not directly responsible for RPR disappearance. The physical interaction of IAPs with RPR provides a molecular mechanism for IAP inhibition of RPR’s apoptotic activity.

Evidence for functional and physical association between Caenorhabditis elegans SEL-10, a Cdc4p-related protein, and SEL-12 presenilin

Mutations in either of two human presenilin genes (PS1 and PS2) cause Alzheimer’s disease. Here we describe genetic and physical interactions between Caenorhabditis elegans SEL-10, a member of the Cdc4p family of proteins, and SEL-12, a C. elegans presenilin. We show that loss of sel-10 activity can suppress the egg-laying defective phenotype associated with reducing sel-12 activity, and that SEL-10 can physically complex with SEL-12. Proteins of the Cdc4p family have been shown to target proteins for ubiquitin-mediated turnover. The functional and physical interaction between sel-10 and sel-12 therefore offers an approach to understanding how presenilin levels are normally regulated.

Quantifying epistemic actions in human-computer interaction

As digital systems move away from traditional desktop setups, new interaction paradigms are emerging that better integrate with users’ realworld surroundings, and better support users’ individual needs. While promising, these modern interaction paradigms also present new challenges, such as a lack of paradigm-specific tools to systematically evaluate and fully understand their use. This dissertation tackles this issue by framing empirical studies of three novel digital systems in embodied cognition – an exciting new perspective in cognitive science where the body and its interactions with the physical world take a central role in human cognition. This is achieved by first, focusing the design of all these systems on a contemporary interaction paradigm that emphasizes physical interaction on tangible interaction, a contemporary interaction paradigm; and second, by comprehensively studying user performance in these systems through a set of novel performance metrics grounded on epistemic actions, a relatively well established and studied construct in the literature on embodied cognition. The first system presented in this dissertation is an augmented Four-in-a-row board game. Three different versions of the game were developed, based on three different interaction paradigms (tangible, touch and mouse), and a repeated measures study involving 36 participants measured the occurrence of three simple epistemic actions across these three interfaces. The results highlight the relevance of epistemic actions in such a task and suggest that the different interaction paradigms afford instantiation of these actions in different ways. Additionally, the tangible version of the system supports the most rapid execution of these actions, providing novel quantitative insights into the real benefits of tangible systems. The second system presented in this dissertation is a tangible tabletop scheduling application. Two studies with single and paired users provide several insights into the impact of epistemic actions on the user experience when these are performed outside of a system’s sensing boundaries. These insights are clustered by the form, size and location of ideal interface areas for such offline epistemic actions to occur, as well as how can physical tokens be designed to better support them. Finally, and based on the results obtained to this point, the last study presented in this dissertation directly addresses the lack of empirical tools to formally evaluate tangible interaction. It presents a video-coding framework grounded on a systematic literature review of 78 papers, and evaluates its value as metric through a 60 participant study performed across three different research laboratories. The results highlight the usefulness and power of epistemic actions as a performance metric for tangible systems. In sum, through the use of such novel metrics in each of the three studies presented, this dissertation provides a better understanding of the real impact and benefits of designing and developing systems that feature tangible interaction.

Tangible interfaces to explain Gaudi's use of ruled-surface geometries

This paper summarises the development of a machine-readable model series for explaining Gaudi's use of ruled surface geometry in the Sagrada Familia in Barcelona, Spain. The first part discusses the modeling methods underlying the columns of the cathedral and the techniques required to translate them into built structures. The second part discusses the design and development of a tangible machine-readable model to explain column-modeling methods interactively in educational contexts such as art exhibitions. It is designed to explain the principles underlying the column design by means of physical interaction without using mathematical terms or language.

Stomp : an interactive platform for people with intellectual disabilities

For people with intellectual disabilities there are significant barriers to inclusion in socially cooperative endeavours. This paper investigates the effectiveness of Stomp, a tangible user interface (TUI) designed to provide new participatory experiences for people with intellectual disability. Results from an observational study reveal the extent to which the Stomp system supports social and physical interaction. The tangible, spatial and embodied qualities of Stomp result in an experience that does not rely on the acquisition of specific competencies before interaction and engagement can occur.

Staying in touch and crafting mementoes

Designers of systems that attempt to support people in maintaining social connectedness should pay attention to the physical interaction characteristics of the systems they create. Systems today mostly accept the dominant computer interface configuration of screens, keyboards and mice, which are not always a good fit for settings outside the office, such as the home. We argue by reference to two design exemplars for a design philosophy that engages a broader range of people's abilities for skilled physical action when designing for social connectedness.

Pulse Gauntlets

To feel another person’s pulse is an intimate and physical interaction. In these prototypes we use near field communications to extend the tangible reach of our heart beat, so another person can feel our heart beat at a distance. The work is an initial experiment in near field haptic interaction, and is used to explore the quality of interactions resulting from feeling another persons pulse. The work takes the form of two feathered white gauntlets, to be worn on the fore arm. Each of the gauntlets contain a pulse sensor, radio transmitter and vibrator. The pulse of the wearer is transmitted to the other feathered gauntlet and transformed into haptic feedback. When there are two wearers, their heart beats are exchanged. To be felt by of each other without physical contact.

Calculation of dose kernels for radiotherapy applications using the GEANT 4 Monte Carlo toolkit

Dose kernels may be used to calculate dose distributions in radiotherapy (as described by Ahnesjo et al., 1999). Their calculation requires use of Monte Carlo methods, usually by forcing interactions to occur at a point. The Geant4 Monte Carlo toolkit provides a capability to force interactions to occur in a particular volume. We have modified this capability and created a Geant4 application to calculate dose kernels in cartesian, cylindrical, and spherical scoring systems. The simulation considers monoenergetic photons incident at the origin of a 3 m x 3 x 9 3 m water volume. Photons interact via compton, photo-electric, pair production, and rayleigh scattering. By default, Geant4 models photon interactions by sampling a physical interaction length (PIL) for each process. The process returning the smallest PIL is then considered to occur. In order to force the interaction to occur within a given length, L_FIL, we scale each PIL according to the formula: PIL_forced = L_FIL 9 (1 - exp(-PIL/PILo)) where PILo is a constant. This ensures that the process occurs within L_FIL, whilst correctly modelling the relative probability of each process. Dose kernels were produced for an incident photon energy of 0.1, 1.0, and 10.0 MeV. In order to benchmark the code, dose kernels were also calculated using the EGSnrc Edknrc user code. Identical scoring systems were used; namely, the collapsed cone approach of the Edknrc code. Relative dose difference images were then produced. Preliminary results demonstrate the ability of the Geant4 application to reproduce the shape of the dose kernels; median relative dose differences of 12.6, 5.75, and 12.6 % were found for an incident photon energy of 0.1, 1.0, and 10.0 MeV respectively.

A practical and theoretical definition of 'small field'

Introduction The consistency of measuring small field output factors is greatly increased by reporting the measured dosimetric field size of each factor, as opposed to simply stating the nominal field size [1] and therefore requires the measurement of cross-axis profiles in a water tank. However, this makes output factor measurements time consuming. This project establishes at which field size the accuracy of output factors are not affected by the use of potentially inaccurate nominal field sizes, which we believe establishes a practical working definition of a ‘small’ field. The physical components of the radiation beam that contribute to the rapid change in output factor at small field sizes are examined in detail. The physical interaction that dominates the cause of the rapid dose reduction is quantified, and leads to the establishment of a theoretical definition of a ‘small’ field. Methods Current recommendations suggest that radiation collimation systems and isocentre defining lasers should both be calibrated to permit a maximum positioning uncertainty of 1 mm [2]. The proposed practical definition for small field sizes is as follows: if the output factor changes by ±1.0 % given a change in either field size or detector position of up to ±1 mm then the field should be considered small. Monte Carlo modelling was used to simulate output factors of a 6 MV photon beam for square fields with side lengths from 4.0 to 20.0 mm in 1.0 mm increments. The dose was scored to a 0.5 mm wide and 2.0 mm deep cylindrical volume of water within a cubic water phantom, at a depth of 5 cm and SSD of 95 cm. The maximum difference due to a collimator error of ±1 mm was found by comparing the output factors of adjacent field sizes. The output factor simulations were repeated 1 mm off-axis to quantify the effect of detector misalignment. Further simulations separated the total output factor into collimator scatter factor and phantom scatter factor. The collimator scatter factor was further separated into primary source occlusion effects and ‘traditional’ effects (a combination of flattening filter and jaw scatter etc.). The phantom scatter was separated in photon scatter and electronic disequilibrium. Each of these factors was plotted as a function of field size in order to quantify how each affected the change in small field size. Results The use of our practical definition resulted in field sizes of 15 mm or less being characterised as ‘small’. The change in field size had a greater effect than that of detector misalignment. For field sizes of 12 mm or less, electronic disequilibrium was found to cause the largest change in dose to the central axis (d = 5 cm). Source occlusion also caused a large change in output factor for field sizes less than 8 mm. Discussion and conclusions The measurement of cross-axis profiles are only required for output factor measurements for field sizes of 15 mm or less (for a 6 MV beam on Varian iX linear accelerator). This is expected to be dependent on linear accelerator spot size and photon energy. While some electronic disequilibrium was shown to occur at field sizes as large as 30 mm (the ‘traditional’ definition of small field [3]), it has been shown that it does not cause a greater change than photon scatter until a field size of 12 mm, at which point it becomes by far the most dominant effect.

Playful interactions for people with intellectual disabilities

For people with intellectual disabilities, there are significant barriers to inclusion in socially cooperative endeavors. This paper investigates the effectiveness of Stomp, a tangible user interface (TUI) designed to provide new participatory experiences for people with intellectual disability. Results from an observational study reveal the extent to which the Stomp system supports social and physical interaction. The tangible, spatial, and embodied qualities of Stomp result in an experience that does not rely on the acquisition of specific competencies before interaction and engagement can occur.