Calculating the Uncertainty of a Structure from Motion (SfM) Model, Cadman Quarry, Monroe, Washington

Structure from Motion (SfM) is a new form of photogrammetry that automates the rendering of georeferenced 3D models of objects using digital photographs and independently surveyed Ground Control Points (GCPs). This project seeks to quantify the error found in Digital Elevation Models (DEMs) produced using SfM. I modeled a rockslide found at the Cadman Quarry (Monroe, Washington) because the surface is vegetation-free, which is ideal for SfM and Terrestrial LiDAR Scanner (TLS) surveys. By using SfM, TLS, and GPS positioning at the same time, I attempted to find the deviation in the SfM model from the TLS model and GPS points. Using the deviation, I found the Root-Mean-Square Error (RMSE) between the SfM DEM and GPS positions. The RMSE of the SfM model when compared to surveyed GPS points is 17cm. I propagated the uncertainty of the GPS points with the RMSE of the SfM model to find the uncertainty of the SfM model compared to the NAD 1984 datum. The uncertainty of the SfM model compared to the NAD 1984 is 27cm. This study did not produce a model from the TLS that had sufficient resolution on horizontal surfaces to compare to surveyed GPS points.

Functionality, Robustness and Control of Nonlinear Network Dynamics: Modeling and Understanding the C. elegans Connectome

Thesis (Ph.D.)--University of Washington, 2016-06

Initiation of evasive manoeuvres during self-motion: a test of three hypotheses

To understand performance of evasive and interceptive actions it is important to know how people decide when to initiate a movement - initiating at the 'right' moment is often essential for successful performance. It has been proposed that initiation is triggered when a perceptually derived quantity reaches an invariant criterion value. Candidate quantities include time-to-collision (TTC), distance, and rate of image expansion ( ROE), all of which have received empirical support. We studied initiation of an evasive manoeuvre in a computer-simulated steering task in which the observer was required to steer through a stationary visual environment and avoid colliding with an obstacle in their path. The results could not be explained by hypotheses which propose that evasive manoeuvre initiation is based on a fixed criterion value of TTC or distance. The overall pattern was, however, consistent with the use of a criterion ROE value. This was further tested by analyses designed to directly evaluate whether the ROE value used to initiate the response was the same across experimental conditions. Only two of the six participants showed evidence for using the ROE strategy.

Hip strategy for balance control in quiet standing is reduced in people with low back pain

Study Design. Quiet stance on supporting bases with different lengths and with different visual inputs were tested in 24 study participants with chronic low back pain (LBP) and 24 matched control subjects. Objectives. To evaluate postural adjustment strategies and visual dependence associated with LBP. Summary of Background Data. Various studies have identified balance impairments in patients with chronic LBP, with many possible causes suggested. Recent evidence indicates that study participants with LBP have impaired trunk muscle control, which may compromise the control of trunk and hip movement during postural adjustments ( e. g., hip strategy). As balance on a short base emphasizes the utilization of the hip strategy for balance control, we hypothesized that patients with LBP might have difficulties standing on short bases. Methods. Subjects stood on either flat surface or short base with different visual inputs. A task was counted as successful if balance was maintained for 70 seconds during bilateral stance and 30 seconds during unilateral stance. The number of successful tasks, horizontal shear force, and center-of-pressure motion were evaluated. Results. The hip strategy was reduced with increased visual dependence in study participants with LBP. The failure rate was more than 4 times that of the controls in the bilateral standing task on short base with eyes closed. Analysis of center-of-pressure motion also showed that they have inability to initiate and control a hip strategy. Conclusions. The inability to control a hip strategy indicates a deficit of postural control and is hypothesized to result from altered muscle control and proprioceptive impairment.

Genomic organization of human arylamine N-acetyltransferase Type I reveals alternative promoters that generate different 5'-UTR splice variants with altered translational activities

In humans, a polymorphic gene encodes the drug-metabolizing enzyme NATI (arylamine N-acetyltransferase Type 1), which is widely expressed throughout the body. While the protein-coding region of NATI is contained within a single exon, examination of the human EST (expressed sequence tag) database at the NCBI revealed the presence of nine separate exons, eight of which were located in the 5'non-coding region of NATI. Differential splicing produced at least eight unique mRNA isoforms that could be grouped according to the location of the first exon, which suggested that NATI expression occurs from three alternative promoters. Using RT (reverse transcriptase)-PCR, we identified one major transcript in various epithelial cells derived from different tissues. In contrast, multiple transcripts were observed in blood-derived cell lines (CEM, THP-1 and Jurkat), with a novel variant, not identified in the EST database, found in CEM cells only. The major splice variant increased gene expression 9-11-fold in a luciferase reporter assay, while the other isoforrns were similar or slightly greater than the control. We examined the upstream region of the most active splice variant in a promoter-reporter assay, and isolated a 257 bp sequence that produced maximal promoter activity. This sequence lacked a TATA box, but contained a consensus Sp1 site and a CAAT box, as well as several other putative transcription-factor-binding sites. Cell-specific expression of the different NATI transcripts may contribute to the variation in NATI activity in vivo.

Acupressure for the in-patient treatment of nausea and vomiting in early pregnancy: A randomized control trial

Objective: The purpose of this study was to evaluate the efficacy of acupressure at the P6 point for the in-patient treatment of severe nausea and vomiting in early pregnancy. Study design: This was a prospective single-blind randomized control trial that involved 80 patients with nausea and vomiting plus ketonuria before 14 weeks of gestation. Results: There was no difference between length of stay, amount of medication, or fluid required between the acupressure and placebo groups, although acupressure reduced the number of patients who stayed >= 4 nights in the hospital. Acupressure was well tolerated and not associated with an increase in perinatal morbidity or death. Conclusion: The use of acupressure Lit the P6 point does not reduce the amount of antiemetric medication that is required, the requirement for intravenous fluid, and median duration of inpatient stay more than the use of placebo. A small reduction was seen in the number of women who required >= 4 days in the hospital. (c) 2006 Mosby, Inc. All rights reserved.

Improved joint control using a genetic algorithm for a humanoid robot

This paper describes experiments conducted in order to simultaneously tune 15 joints of a humanoid robot. Two Genetic Algorithm (GA) based tuning methods were developed and compared against a hand-tuned solution. The system was tuned in order to minimise tracking error while at the same time achieve smooth joint motion. Joint smoothness is crucial for the accurate calculation of online ZMP estimation, a prerequisite for a closedloop dynamically stable humanoid walking gait. Results in both simulation and on a real robot are presented, demonstrating the superior smoothness performance of the GA based methods.

Long-range translational coupling in single-stranded RNA bacteriophages: an evolutionary analysis

In coliphage MS2 RNA a long-distance interaction (LDI) between an internal segment of the upstream coat gene and the start region of the replicase gene prevents initiation of replicase synthesis in the absence of coat gene translation. Elongating ribosomes break up the repressor LDI and thus activate the hidden initiation site. Expression studies on partial MS2 cDNA clones identified base pairing between 1427-1433 and 1738-1744, the so-called Min Jou (MJ) interaction, as the molecular basis for the long-range coupling mechanism. Here, we examine the biological significance of this interaction for the control of replicase gene translation. The LDI was disrupted by mutations in the 3'-side and the evolutionary adaptation was monitored upon phage passaging. Two categories of pseudorevertants emerged. The first type had restored the MJ interaction but not necessarily the native sequence. The pseudorevertants of the second type acquired a compensatory substitution some 80 nt downstream of the MJ interaction that stabilizes an adjacent LDI. In one examined case we confirmed that the second site mutations had restored coat-replicase translational coupling. Our results show the importance of translational control for fitness of the phage. They also reveal that the structure that buries the replicase start extends to structure elements bordering the MJ interaction.

Colour and luminance interactions in the visual perception of motion

We sought to determine the extent to which red–green, colour–opponent mechanisms in the human visual system play a role in the perception of drifting luminance–modulated targets. Contrast sensitivity for the directional discrimination of drifting luminance–modulated (yellow–black) test sinusoids was measured following adaptation to isoluminant red–green sinusoids drifting in either the same or opposite direction. When the test and adapt stimuli drifted in the same direction, large sensitivity losses were evident at all test temporal frequencies employed (1–16 Hz). The magnitude of the loss was independent of temporal frequency. When adapt and test stimuli drifted in opposing directions, large sensitivity losses were evident at lower temporal frequencies (1–4 Hz) and declined with increasing temporal frequency. Control studies showed that this temporal–frequency–dependent effect could not reflect the activity of achromatic units. Our results provide evidence that chromatic mechanisms contribute to the perception of luminance–modulated motion targets drifting at speeds of up to at least 32°s-1. We argue that such mechanisms most probably lie within a parvocellular–dominated cortical visual pathway, sensitive to both chromatic and luminance modulation, but only weakly selective for the direction of stimulus motion.

Motion, flash, and flicker:A unified spatiotemporal model of perceived edge sharpening

Blurred edges appear sharper in motion than when they are stationary. We proposed a model of this motion sharpening that invokes a local, nonlinear contrast transducer function (Hammett et al, 1998 Vision Research 38 2099-2108). Response saturation in the transducer compresses or 'clips' the input spatial waveform, rendering the edges as sharper. To explain the increasing distortion of drifting edges at higher speeds, the degree of nonlinearity must increase with speed or temporal frequency. A dynamic contrast gain control before the transducer can account for both the speed dependence and approximate contrast invariance of motion sharpening (Hammett et al, 2003 Vision Research, in press). We show here that this model also predicts perceived sharpening of briefly flashed and flickering edges, and we show that the model can account fairly well for experimental data from all three modes of presentation (motion, flash, and flicker). At moderate durations and lower temporal frequencies the gain control attenuates the input signal, thus protecting it from later compression by the transducer. The gain control is somewhat sluggish, and so it suffers both a slow onset, and loss of power at high temporal frequencies. Consequently, brief presentations and high temporal frequencies of drift and flicker are less protected from distortion, and show greater perceptual sharpening.

Computer control of machines utilising independent drive mechanisms

The thesis describes an investigation into methods for the specification, design and implementation of computer control systems for flexible manufacturing machines comprising multiple, independent, electromechanically-driven mechanisms. An analysis is made of the elements of conventional mechanically-coupled machines in order that the operational functions of these elements may be identified. This analysis is used to define the scope of requirements necessary to specify the format, function and operation of a flexible, independently driven mechanism machine. A discussion of how this type of machine can accommodate modern manufacturing needs of high-speed and flexibility is presented. A sequential method of capturing requirements for such machines is detailed based on a hierarchical partitioning of machine requirements from product to independent drive mechanism. A classification of mechanisms using notations, including Data flow diagrams and Petri-nets, is described which supports capture and allows validation of requirements. A generic design for a modular, IDM machine controller is derived based upon hierarchy of control identified in these machines. A two mechanism experimental machine is detailed which is used to demonstrate the application of the specification, design and implementation techniques. A computer controller prototype and a fully flexible implementation for the IDM machine, based on Petri-net models described using the concurrent programming language Occam, is detailed. The ability of this modular computer controller to support flexible, safe and fault-tolerant operation of the two intermittent motion, discrete-synchronisation independent drive mechanisms is presented. The application of the machine development methodology to industrial projects is established.

The dynamics and control of a remotely piloted plan-symmetric helicopter

Prior to the development of a production standard control system for ML Aviation's plan-symmetric remotely piloted helicopter system, SPRITE, optimum solutions to technical requirements had yet to be found for some aspects of the work. This thesis describes an industrial project where solutions to real problems have been provided within strict timescale constraints. Use has been made of published material wherever appropriate, new solutions have been contributed where none existed previously. A lack of clearly defined user requirements from potential Remotely Piloted Air Vehicle (RPAV) system users is identified, A simulation package is defined to enable the RPAV designer to progress with air vehicle and control system design, development and evaluation studies and to assist the user to investigate his applications. The theoretical basis of this simulation package is developed including Co-axial Contra-rotating Twin Rotor (CCTR), six degrees of freedom motion, fuselage aerodynamics and sensor and control system models. A compatible system of equations is derived for modelling a miniature plan-symmetric helicopter. Rigorous searches revealed a lack of CCTR models, based on closed form expressions to obviate integration along the rotor blade, for stabilisation and navigation studies through simulation. An economic CCTR simulation model is developed and validated by comparison with published work and practical tests. Confusion in published work between attitude and Euler angles is clarified. The implementation of package is discussed. dynamic adjustment of assessment. the theory into a high integrity software Use is made of a novel technique basing the integration time step size on error Simulation output for control system stability verification, cross coupling of motion between control channels and air vehicle response to demands and horizontal wind gusts studies are presented. Contra-Rotating Twin Rotor Flight Control System Remotely Piloted Plan-Symmetric Helicopter Simulation Six Degrees of Freedom Motion ( i i)

Design methodology for the servo control of high speed multi-axis machinery (BL): decoupling and synchronisation of a generic machine by blockwise decentralised MIMO control

Traditional machinery for manufacturing processes are characterised by actuators powered and co-ordinated by mechanical linkages driven from a central drive. Increasingly, these linkages are replaced by independent electrical drives, each performs a different task and follows a different motion profile, co-ordinated by computers. A design methodology for the servo control of high speed multi-axis machinery is proposed, based on the concept of a highly adaptable generic machine model. In addition to the dynamics of the drives and the loads, the model includes the inherent interactions between the motion axes and thus provides a Multi-Input Multi-Output (MIMO) description. In general, inherent interactions such as structural couplings between groups of motion axes are undesirable and needed to be compensated. On the other hand, imposed interactions such as the synchronisation of different groups of axes are often required. It is recognised that a suitable MIMO controller can simultaneously achieve these objectives and reconciles their potential conflicts. Both analytical and numerical methods for the design of MIMO controllers are investigated. At present, it is not possible to implement high order MIMO controllers for practical reasons. Based on simulations of the generic machine model under full MIMO control, however, it is possible to determine a suitable topology for a blockwise decentralised control scheme. The Block Relative Gain array (BRG) is used to compare the relative strength of closed loop interactions between sub-systems. A number of approaches to the design of the smaller decentralised MIMO controllers for these sub-systems has been investigated. For the purpose of illustration, a benchmark problem based on a 3 axes test rig has been carried through the design cycle to demonstrate the working of the design methodology.

Pichia pastoris regulates its gene-specific response to different carbon sources at the transcriptional, rather than the translational, level

Background: The methylotrophic, Crabtree-negative yeast Pichia pastoris is widely used as a heterologous protein production host. Strong inducible promoters derived from methanol utilization genes or constitutive glycolytic promoters are typically used to drive gene expression. Notably, genes involved in methanol utilization are not only repressed by the presence of glucose, but also by glycerol. This unusual regulatory behavior prompted us to study the regulation of carbon substrate utilization in different bioprocess conditions on a genome wide scale. Results: We performed microarray analysis on the total mRNA population as well as mRNA that had been fractionated according to ribosome occupancy. Translationally quiescent mRNAs were defined as being associated with single ribosomes (monosomes) and highly-translated mRNAs with multiple ribosomes (polysomes). We found that despite their lower growth rates, global translation was most active in methanol-grown P. pastoris cells, followed by excess glycerol- or glucose-grown cells. Transcript-specific translational responses were found to be minimal, while extensive transcriptional regulation was observed for cells grown on different carbon sources. Due to their respiratory metabolism, cells grown in excess glucose or glycerol had very similar expression profiles. Genes subject to glucose repression were mainly involved in the metabolism of alternative carbon sources including the control of glycerol uptake and metabolism. Peroxisomal and methanol utilization genes were confirmed to be subject to carbon substrate repression in excess glucose or glycerol, but were found to be strongly de-repressed in limiting glucose-conditions (as are often applied in fed batch cultivations) in addition to induction by methanol. Conclusions: P. pastoris cells grown in excess glycerol or glucose have similar transcript profiles in contrast to S. cerevisiae cells, in which the transcriptional response to these carbon sources is very different. The main response to different growth conditions in P. pastoris is transcriptional; translational regulation was not transcript-specific. The high proportion of mRNAs associated with polysomes in methanol-grown cells is a major finding of this study; it reveals that high productivity during methanol induction is directly linked to the growth condition and not only to promoter strength.

Simplified PRBMs of spatial compliant multi-beam modules for planar motion

PRBMs (pseudo-rigid-body models) have been becoming important engineering technologies/methods in the field of compliant mechanisms to simplify the design and analysis through the use of the knowledge body of rigid-body mechanisms coupling with springs. This article addresses the PRBMs of spatial multi-beam modules for planar motion, which are composed of three or more symmetrical wire/slender beams parallel to each other where the planar twisting DOF (degree of freedom) is assumed to be very small for specific applications/loading conditions. Simplified PRBMs are firstly proposed through replacing each beam in spatial multi-beam module with a rigid-body link plus two identical spherical joints at its two ends. The characteristics factor, bending stiffness and twisting stiffness for the spherical joint are determined. Load-displacement equations are then derived for a class of spatial multi-beam modules and general spatial multi-beam modules using the virtual work principle and kinematic relationships. Finally, nonlinear FEA (finite element analysis) is employed with comparisons with the PRBMs. The present PRBMs have shown the ability to predict the primary nonlinear constraint characteristics such as load-stiffening effect, cross-axis coupling in the two primary translational directions and buckling load.