Study of DNA Origami Dimerization and Dimer Dissociation Dynamics and of the Factors that Limit Dimerization

Organizing DNA origami building blocks into higher order structures is essential for fabrication of large structurally and functionally diverse devices and molecular machines. Unfortunately, the yields of origami building block attachment reactions are typically not sufficient to allow programed assembly of DNA devices made from more than a few origami building blocks. To investigate possible reasons for these low yields, a detailed single‐molecule fluorescence study of the dynamics of rectangular origami dimerization and origami dimer dissociation reactions is conducted. Reactions kinetics and yields are investigated at different origami and ion concentrations, for different ion types, for different lengths of bridging strands, and for the “sticky end” and “weaving welding” attachment techniques. Dimerization yields are never higher than 86%, which is typical for such systems. Analysis of the dynamic data shows that the low yield cannot be explained by thermodynamic instability or structural imperfections of the origami constructs. Atomic force microscopy and gel electrophoresis evidence reveal self‐dimerization of the origami monomers, likely via blunt‐end interactions made possible by the presence of bridging strands. It is suggested that this mechanism is the major factor that inhibits correct dimerization and means to overcome it are discussed.     

Adapting application execution in CMPs using helper threads

In parallel to the changes in both the architecture domain–the move toward chip multiprocessors (CMPs)–and the application domain–the move toward increasingly data-intensive workloads–issues such as performance, energy efficiency and CPU availability are becoming increasingly critical. The CPU availability can change dynamically due to several reasons such as thermal overload, increase in transient errors, or operating system scheduling. An important question in this context is how to adapt, in a CMP, the execution of a given application to CPU availability change at runtime. Our paper studies this problem, targeting the energy-delay product (EDP) as the main metric to optimize. We first discuss that, in adapting the application execution to the varying CPU availability, one needs to consider the number of CPUs to use, the number of application threads to accommodate and the voltage/frequency levels to employ (if the CMP has this capability). We then propose to use helper threads to adapt the application execution to CPU availability change in general with the goal of minimizing the EDP. The helper thread runs parallel to the application execution threads and tries to determine the ideal number of CPUs, threads and voltage/frequency levels to employ at any given point in execution. We illustrate this idea using four applications (Fast Fourier Transform, MultiGrid, LU decomposition and Conjugate Gradient) under different execution scenarios. The results collected through our experiments are very promising and indicate that significant EDP reductions are possible using helper threads. For example, we achieved up to 66.3%, 83.3%, 91.2%, and 94.2% savings in EDP when adjusting all the parameters properly in applications FFT, MG, LU, and CG, respectively. We also discuss how our approach can be extended to address multi-programmed workloads.     

Proteomic examination of Leishmania chagasi plasma membrane proteins: Contrast between avirulent and virulent (metacyclic) parasite forms

Purpose: About two million new cases of leishmaniasis with 50 000 associated deaths occur worldwide each year. Promastigotes of the causative Leishmania spp. develop from the procyclic stage to the highly virulent metacyclic stage within the sand fly vector. We hypothesized that proteins important for promastigote virulence might be uniquely represented in the plasma membrane of metacyclic, but not procyclic, promastigotes. Experimental design: Procyclic (logarithmic) promastigotes and purified metacyclic promastigotes from stationary phase cultures of Leishmania chagasi were used to prepare membrane preparations either by surface biotinylation‐streptavidin affinity separation or by octyl glucoside detergent extraction. Results: These membrane fractions were enriched over 130‐ and 250‐fold, respectively, as estimated by Western blotting for the plasma membrane's major surface protease. Hundreds or dozens of proteins were identified by LC‐MS/MS in the surface biotinylation or detergent extraction, respectively. Confocal microscopy suggested the difference between the lists was due to the fact that proteins localized both on the surface membrane and within the flagellar pocket were accessible to surface biotinylation, whereas only proteins on the membrane were obtained by detergent extraction. Using detergent extraction, we found different proteins were present in membranes of the procyclic stage compared to metacyclic stage promastigotes. Several dozen were stage specific. Conclusions and clinical relevance: These data provide a foundation for identifying virulence factors in the plasma membranes of Leishmania spp. promastigotes during metacyclogenesis.     

Modelling computational requirements of mobile robotic systems using zones and processing windows

Mobile robotic systems must sense constraints imposed by a dynamically changing environment and predictably react to those changes in real-time. Complexity arises in mobile robotic systems because the computing platform travels through the environment with which the system is interacting. These systems have spatio-temporal requirements in the sense that correct behavior is defined in terms of both space and time. The focus of this paper is mobile robotic platforms that must sense their environment and avoid obstacles as they navigate from one point to another. We present a design and analysis methodology for these platforms that integrates spatio-temporal attributes with fixed priority real-time scheduling through the use of zone and processing window abstractions.     

Leader’s dilemma game: An experimental design for cyber insider threat research

One of the problems with insider threat research is the lack of a complete 360° view of an insider threat dataset due to inadequate experimental design. This has prevented us from modeling a computational system to protect against insider threat situations. This paper provides a contemporary methodological approach for using online games to simulate insider betrayal for predictive behavioral research. The Leader’s Dilemma Game simulates an insider betrayal scenario for analyzing organizational trust relationships, providing an opportunity to examine the trustworthiness of focal individuals, as measured by humans as sensors engaging in computer-mediated communication. This experimental design provides a window into trustworthiness attribution that can generate a rigorous and relevant behavioral dataset, and contributes to building a cyber laboratory that advances future insider threat study.     

Contextual factors affecting task distribution in two participatory ergonomic interventions: a qualitative study

This article provides an analysis of the evolution of the division of labour in participatory ergonomics (PE) programmes in two worksites. The analysis is based on interviews and field observations in the worksites. In both settings there was meaningful participation by both worker and management members of ergonomic change teams (ECTs) in the hazard assessment and solution identification stages, but as the teams moved to the implementation stage, worker representatives were marginalised and the participatory nature of the programmes was severely curtailed. The removal of workers from the process was the outcome of the interplay among the type of activities pursued in the implementation stage, the skills and knowledge required to carry out those activities, and workers' limited influence in the organisational hierarchies. Findings highlight the salience of the social context in which participatory programmes are located and the importance of examining participatory programmes as they evolve over time. STATEMENT OF RELEVANCE: This article contributes to a growing literature on the process and implementation of PE programmes. The article's focus on social and organisational factors that affect the division of labour and attention to the evolution of involvement over time extend current understandings of participation in ergonomics programmes.     

Optimization of Geoscience Laser Altimeter System waveform metrics to support vegetation measurements

The Geoscience Laser Altimeter System (GLAS) has collected over 250 million measurements of vegetation height over forests globally. Accurate vegetation heights can be determined using waveform metrics that include vertical extent and extent of the waveform's trailing and leading edges. All three indices are highly dependent upon the signal strength, background noise and signal-to-noise ratio of the waveform, as the background noise contribution to the waveforms has to be removed before their calculation. Over the last six years, GLAS has collected data during thirteen observation periods using illumination from three different lasers. The power levels of these lasers have changed over time, resulting in variable signal power and noise characteristics. Atmospheric conditions vary continuously, also influencing signal power and noise.To minimize these effects, we optimized a noise coefficient which could be constant or vary according to observation period or noise metric. This parameter is used with the mean and standard deviation of the background noise to determine a noise level threshold that is removed from each waveform. An optimization analysis was used with a global dataset of waveforms that are near-coincident with waveforms from other observation periods; the goal of the optimization was to minimize the difference in vertical extent between spatially overlapping GLAS observations. Optimizations based on absolute difference in height led to situations in which the total extent was minimized as well; further optimizations reduced a normalized difference in height extent. The simplest optimizations were based on a constant value to be applied to all observations; noise coefficients of 2.7, 3.2, 3.4 and 4.0 were determined for datasets consisting of global forests, global vegetation, forest in the legal Amazon basin and boreal forests respectively. Optimizations based on the power level or the signal-to-noise ratio of waveforms best minimized differences in waveform extent, decreasing the percent root mean squared height difference by 25-54% over the constant value approach. Further development of methods to ensure temporal consistency of waveform indices will be necessary to support long-term satellite lidar missions and will result in more accurate and precise estimates of canopy height.     

Kinematics of heelstrike during walking and carrying: implications for slip resistance testing

Slip resistance measurements of shoes and floors are used to evaluate the potential for slip and fall injuries. These measurements are believed to have increased validity when they more closely reflect actual heelstrike biomechanics during locomotion. The purpose of this study was to describe heelstrike kinematics during load carrying to provide data towards improved slip resistance testing. Foot kinematics during load carrying (unladen and carrying from 0 to 13.5 kg) at various cadences (70, 90, 100 steps/min) was recorded. Measures before, during and after heelstrike were analysed. Cadence was an important predictor for all variables measured, associated with changes from 13% to over 100%. The load carried was an important predictor for only the heel slip distance after heelstrike, but this effect needs to be investigated further. These results can be used to improve the fidelity of slip resistance measurements, which is critical to reduce slip and fall injuries in the workplace or during activities of daily living.     

Large displays enhance optical flow cues and narrow the gender gap in 3-D virtual navigation

OBJECTIVE: Existing reports suggest that males significantly outperform females in navigating 3-D virtual environments. Although researchers have recognized that this may be attributable to males and females possessing different spatial abilities, most work has attempted to reduce the gender gap by providing more training for females. In this paper, we explore using large displays to narrow the gender gap within these tasks. BACKGROUND: While evaluating various interaction techniques, we found that large displays affording wider fields of view seemed to improve virtual navigation performance in general and, additionally, to narrow the gender gap that existed on standard desktop displays. METHOD: We conducted two experiments (32 and 22 participants) exploring the individual contributions of display and geometric fields of view to the observed effects as well as isolating factors explaining performance increases seen on the large displays. RESULTS: We show that wider fields of view on large displays not only increase performance of all users on average but also benefit females to such a degree as to allow them to perform as well as males do. We further demonstrate that these benefits can be attributed to better optical flow cues offered by the large displays. CONCLUSION: These findings provide a significant contribution, including recommendations for the improved presentation of 3-D environments, backed by empirical data demonstrating performance benefits during navigation tasks. APPLICATION. Results can be used to design systems that narrow the gender gap in domains such as teleoperation and virtual environments for entertainment, virtual training, or information visualization.