High throughput determination of sequence-function relationships in protein and RNA

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

Transfer of resistance training to enhance rapid coordinated force production by older adults

The purpose of this study was to examine the capacity of resistance training to enhance the rapid and coordinated production of force by older people. Thirty adults (greater than or equal to 60 years) completed a visually guided aiming task that required the generation of isometric torque in 2 df about the elbow prior to and following a 4-week training period. Groups of six participants were allocated to two progressive ( 40 - 100% maximal voluntary contraction (MVC)) resistance-training (PRT) groups, to two constant low-load (10% MVC) training groups (CLO) and to one no-training control group. Training movements required the generation of either combined flexion and supination (FLESUP), or combined extension and supination (EXTSUP). In response to training, target acquisition times in the aiming task decreased for all groups; however, both the nature of the training load and the training movement influenced the pattern and magnitude of improvements (EXTSUP_ CLO: 36%, FLESUP_ PRT 26%, EXTSUP_ PRT 22%, FLESUP_ CLO 20%, CONTROL 15%). For one group that trained with progressively increasing loads, there arose a subsequent decrease in performance in one condition of the transfer task. For each group, these adaptations were accompanied by systematic changes in the coordination of muscles about the elbow joint, particularly the biceps brachii.

Trial of print and telephone delivered interventions to influence walking

Background. Both self-help print materials and telephone-assisted counseling have generally proved useful strategies to increase physical activity. This study examined their effectiveness in an intervention aimed specifically at promoting walking for specific purposes. Methods. Participants (n = 399) were randomly allocated to one of two 3-week intervention programs. The Print program comprised multiple mailing of brochures that emphasized walking within the local community environments. The Print plus Telephone program received the same brochures plus three telephone calls. Data collected via mailed self-completed surveys were analyzed by exploring outcomes related to walking for specific purposes. Results. There were no significant differences between the two programs in any of the walking measures. Both groups significantly increased time reported walking for exercise per week [Print: t(1,277) = -3.50, P < 0.001; Print plus telephone: t(1,106) = -2.44, P < 0.016]. Significantly, more participants in the Print plus Telephone group reported receiving and reading the materials (chi(2) = 20.11, P < 0.0001). Conclusions. The intervention programs were more successful at increasing walking for exercise than for any other purpose. The addition of brief telephone support was successful in focusing participants' attention on the print materials, but did not result in any additional increase in walking. (C) 2004 The Institute For Cancer Prevention and Elsevier Inc. All rights reserved.

Synthetic, EPR spectroscopic, magnetic and X-ray crystallographic structural studies on copper(II) complexes of the tridentate N2S donor ligand formed from 6-methyl-2-formylpyridine and S-methyldithiocarbazate (Hmpsme)

New copper(II) complexes of general empirical formula, Cu(mpsme)X center dot xCH(3)COCH(3) (mpsme = anionic form of the 6-methyl-2-formylpyridine Schiff base of S-methyldithiocarbazate; X = Cl, N-3, NCS, NO3; x = 0, 0.5) have been synthesized and characterized by IR, electronic, EPR and susceptibility measurements. Room temperature mu(eff) values for the complexes are in the range 1.75-2.1 mu(beta) typical of uncoupled or weakly coupled Cu(II) centres. The EPR spectra of the [Cu(mpsme)X] (X = Cl, N-3, NO3, NCS) complexes reveal a tetragonally distorted coordination sphere around the mononuclear Cu(II) centre. We have exploited second derivative EPR spectra in conjunction with Fourier filtering (sine bell and Hamming functions) to extract all of the nitrogen hyperfine coupling matrices. While the X-ray crystallography of [Cu(mpsme)NCS] reveals a linear polymer in which the thiocyanate anion bridges the two copper(II) ions, the EPR spectra in solution are typical of a magnetically isolated monomeric Cu(II) centres indicating dissociation of the polymeric chain in solution. The structures of the free ligand, Hmpsme and the {[Cu(mpsme)NO3] center dot 0.5CH(3)COCH(3)}(2) and [Cu(mpsme)NCS](n) complexes have been determined by X-ray diffraction. The {[Cu(mpsme)NO3]0.5CH(3)COCH(3)}(2) complex is a centrosymmetric dimer in which each copper atom adopts a five-coordinate distorted square-pyramidal geometry with an N2OS2 coordination environment, the Schiff base coordinating as a uninegatively charged tridentate ligand chelating through the pyridine and azomethine nitrogen atoms and the thiolate, an oxygen atom of a unidentate nitrato ligand and a bridging sulfur atom from the second ligand completing the coordination sphere. The [Cu(mpsme)(NCS)](n) complex has a novel staircase-like one dimensional polymeric structure in which the NCS- ligands bridge two adjacent copper(II) ions asymmetrically in an end-to-end fashion providing its nitrogen atom to one copper and the sulfur atom to the other. (c) 2005 Elsevier B.V. All rights reserved.

Water balance in goats subjected to feed restriction

The effect of feed restriction on water balance and nutrient utilization was investigated in individually penned Boer x Saanen kids. Twenty-two male Boer x Saanen kids with an initial average live weight (LW) of 15 kg were used. Seven kids were slaughtered at the beginning of the experiment (reference animals) and the remainders were allocated to one of the three treatments (0, 30 and 60% restriction) and therefore there were five kids per treatment. The feed intake for the 0% restriction treatment animals determined the intake for the animals in the 30 and 60% restriction treatment. When the animals in the 0% restriction treatment group reached 25 kg LW, the animals in the 30 and 60% restriction treatment groups were also slaughtered. There was a negative relationship between DMI and water intake. The digestibility coefficients for DM, OM, carbohydrates, ash, ether extract, energy, NDF, ADF and lignin did not differ between treatments, whereas the digestibility coefficient for CP was different between treatment groups. The highest metabolic water production was in animals in the 0% restriction treatment group. No significant differences were observed in the composition of gastro-intestinal tract contents of the goats in the different treatments. Lower water retention was found in the animals in the 60% restriction treatment group. The study showed that feed restriction affected water intake, CP digestibility and water retention in the body of the kid goats. This experiment demonstrated that DM:water intake ratio changed when severe feed restriction was applied (60% restriction) and water was freely available. It shows a different pattern of behaviour of penned goats, particularly if feed intake is restricted and perhaps caution is needed to extrapolate results from nutritional and physiological trials in pens to goats at pasture. (c) 2005 Elsevier BX All rights reserved.

The analysis and case studies of successful express logistics companies

With the globalisation of world business, the border-crossing activities between organisations have substantially increased. Organisations not only need to handle supply functions, but also play a tremendous role in demand simulation through integration both inside the firm and outside with business partners and customers. Logistics has become more and more mature and sophisticated by taking on an external focus, incorporating suppliers and customers in the business processes, with all the supply chain functions integrated into a whole. By minimising the costs in the value chain or providing customised services, logistics acts as a major source of competitive advantages and profitability. To meet this goal, it would require the integration of activities to focus on customer-oriented measures. Customer service and logistics activities are a chain of interdependent activities that supplement each other to facilitate the flow of information, goods and cash within the value chain. The absence of one activity may imply some specific channels need to supplement another unit. Generally, this paper is to study the impact of corporate strategy, technology and customer satisfaction on the firm’s performance, filling the gap of good customer service effects on long-term profits. Two international delivery providers, UPS and FedEx, are studied to realise the critical success factors of express logistics.

From filters to features:Scale-space analysis of edge and blur coding in human vision

To make vision possible, the visual nervous system must represent the most informative features in the light pattern captured by the eye. Here we use Gaussian scale-space theory to derive a multiscale model for edge analysis and we test it in perceptual experiments. At all scales there are two stages of spatial filtering. An odd-symmetric, Gaussian first derivative filter provides the input to a Gaussian second derivative filter. Crucially, the output at each stage is half-wave rectified before feeding forward to the next. This creates nonlinear channels selectively responsive to one edge polarity while suppressing spurious or "phantom" edges. The two stages have properties analogous to simple and complex cells in the visual cortex. Edges are found as peaks in a scale-space response map that is the output of the second stage. The position and scale of the peak response identify the location and blur of the edge. The model predicts remarkably accurately our results on human perception of edge location and blur for a wide range of luminance profiles, including the surprising finding that blurred edges look sharper when their length is made shorter. The model enhances our understanding of early vision by integrating computational, physiological, and psychophysical approaches. © ARVO.

Applications of fractals to image data compression

Digital image processing is exploited in many diverse applications but the size of digital images places excessive demands on current storage and transmission technology. Image data compression is required to permit further use of digital image processing. Conventional image compression techniques based on statistical analysis have reached a saturation level so it is necessary to explore more radical methods. This thesis is concerned with novel methods, based on the use of fractals, for achieving significant compression of image data within reasonable processing time without introducing excessive distortion. Images are modelled as fractal data and this model is exploited directly by compression schemes. The validity of this is demonstrated by showing that the fractal complexity measure of fractal dimension is an excellent predictor of image compressibility. A method of fractal waveform coding is developed which has low computational demands and performs better than conventional waveform coding methods such as PCM and DPCM. Fractal techniques based on the use of space-filling curves are developed as a mechanism for hierarchical application of conventional techniques. Two particular applications are highlighted: the re-ordering of data during image scanning and the mapping of multi-dimensional data to one dimension. It is shown that there are many possible space-filling curves which may be used to scan images and that selection of an optimum curve leads to significantly improved data compression. The multi-dimensional mapping property of space-filling curves is used to speed up substantially the lookup process in vector quantisation. Iterated function systems are compared with vector quantisers and the computational complexity or iterated function system encoding is also reduced by using the efficient matching algcnithms identified for vector quantisers.

Statnote 10: the two-way analysis of variance

The two-way design has been variously described as a matched-sample F-test, a simple within-subjects ANOVA, a one-way within-groups ANOVA, a simple correlated-groups ANOVA, and a one-factor repeated measures design! This confusion of terminology is likely to lead to problems in correctly identifying this analysis within commercially available software. The essential feature of the design is that each treatment is allocated by randomization to one experimental unit within each group or block. The block may be a plot of land, a single occasion in which the experiment was performed, or a human subject. The ‘blocking’ is designed to remove an aspect of the error variation and increase the ‘power’ of the experiment. If there is no significant source of variation associated with the ‘blocking’ then there is a disadvantage to the two-way design because there is a reduction in the DF of the error term compared with a fully randomised design thus reducing the ‘power’ of the analysis.

Teenage mothers' experiences of stigma and formal support services

This research has two focal points: experiences of stigma and experiences of formal support services among teenage mothers. Twenty teenage mothers were interviewed in depth, ten from a one-to-one support service, and ten from a group based support service. Contributions to knowledge consisted of the following. First, regarding experiences of stigma, this research integrated concepts from the social psychology literature and established the effects of stigma which are experienced by teenage mothers, offering reasons for the same. Additionally, further coping mechanisms in response to being stigmatized were discovered and grouped into two new headings: active and passive coping mechanisms. It is acknowledged that for a minority of participants, stigma does have negative effects, however, the majority experiences no such serious negative effects. Secondly, regarding experiences of support services, this research was able to directly compare one-to-one with group based support for teenage mothers. Knowledge was unearthed as to influential factors in the selection of a mode of support and the functions of each of the modes of support, which were categorised under headings for ease of comparison. It was established that there is indeed a link between these two research foci in that both the one-to-one and group based support services fulfil a stigma management function, in which teenage mothers discuss the phenomenon, share experiences and offer advice to others. However, it was also established that this function is of minor importance compared to the other functions fulfilled by the support services.

Ocular response to silicone-hydrogel contact lenses

The thesis investigates the ocular response to silicone-hydrogel (SiH) contact lens wear, a relatively new contact lens material that has a higher modulus of rigidity and different surface coating than used in conventional hydrogel materials. The properties of SiH materials differ significantly from conventional hydrogels and, using subjective and objective means of assessment, the thesis examines how these properties affect reflection and biometry, ocular physiology, tear film characteristics, symptomatology, adverse events and complications. A range of standard and newly designed investigative techniques were employed, and latter involving novel imaging techniques, for the objective assessment of physiological changes which occur with contact lens wear. The study is the first to combine these techniques with biochemical analyses of the tear film composition. Forty-seven subjects were fitted with SiH lenses and randomly allocated to one of the two materials currently on the market (Lotrafilcon A or Balafilcon A) on an either daily or continuous wear basis. An additional control group of 14 age-matched non-contact lens wearers were monitored over the same period. Measurements were taken before and 1, 3, 6, 12 and 18 months after initial fitting. The findings reported in this thesis will enable contact lens practitioners and manufacturers to understand further the optical, physiological and biochemical nature of the ocular response to SiH contact lenses and hence facilitate the development of this important generation of contact lens material.

Disciplinary talk:a systemic functional exploration of university seminar discussions

Despite the growth of spoken academic corpora in recent years, relatively little is known about the language of seminar discussions in higher education. This thesis compares seminar discussions across three disciplinary areas. The aim of this thesis is to uncover the functions and patterns of talk used in different disciplinary discussions and to highlight language on a macro and micro level that would be useful for materials design and teaching purposes. A framework for identifying and analysing genres in spoken language based on Hallidayan Systemic Functional Linguistics (SFL) is used. Stretches of talk sharing a similar purpose and predictable functional staging, termed Discussion Macro Genres (DMGs) are identified. Language is compared across DMGs and across disciplines through use of corpus techniques in conjunction with SFL genre theory. Data for the study comprises just over 180,000 tokens and is drawn from the British Academic Spoken English corpus (BASE), recorded at two universities in the UK. The discipline areas investigated are Arts and Humanities, Social Sciences and Physical Sciences. Findings from this study make theoretical, empirical and methodological contributions to the field of spoken EAP. The empirical findings are firstly, that the majority of the seminar discussion can be assigned to one of the three main DMG in the corpus: Responding, Debating and Problem Solving. Secondly, it characterises each discipline area according to two DMGs. Thirdly, the majority of the discussion is non-oppositional in nature, suggesting that ‘debate’ is not the only form of discussion that students need to be prepared for. Finally, while some characteristics of the discussion are tied to the DMG and common across disciplines, others are discipline specific. On a theoretical level, this study shows that an SFL genre model for investigating spoken discourse can be successfully extended to investigate longer stretches of discourse than have previously been identified. The methodological contribution is to demonstrate how corpus techniques can be combined with SFL genre theory to investigate extended stretches of spoken discussion. The thesis will be of value to those working in the field of teaching spoken EAP/ ESAP as well as to materials developers.

How employer and employee satisfaction affect customer satisfaction:an application to franchise services

In small-service settings, how do owner satisfaction, front-line employee satisfaction, and customer satisfaction relate to one another? The authors use generalized exchange theory (GET) to examine how satisfaction levels of these three constituents are reciprocated. The authors examine a European franchise system comprising 50 outlets, 933 employees, and 20,742 customers. Their results show two important findings. First, the effect of owner-franchisee's satisfaction on customer satisfaction is fully mediated by front-line employee satisfaction. Thus, managers of a service outlet can strongly impact the satisfaction and behavioral intentions of their customer base, even without direct contact with them. Second, the link between customer satisfaction and purchase intention is moderated by employee satisfaction at an outlet. The link between customer satisfaction and customer purchase intentions is almost twice as strong when employees are satisfied than when they are not. Thus, there is a "doublepositive effect:" not only does higher employee satisfaction at an outlet directly lead to higher customer satisfaction but it also indirectly strengthens the association between customer satisfaction and their repurchase intentions.

QT interval prolongation related to psychoactive drug treatment:a comparison of monotherapy versus polytherapy

Background - Several antipsychotic agents are known to prolong the QT interval in a dose dependent manner. Corrected QT interval (QTc) exceeding a threshold value of 450 ms may be associated with an increased risk of life threatening arrhythmias. Antipsychotic agents are often given in combination with other psychotropic drugs, such as antidepressants, that may also contribute to QT prolongation. This observational study compares the effects observed on QT interval between antipsychotic monotherapy and psychoactive polytherapy, which included an additional antidepressant or lithium treatment. Method - We examined two groups of hospitalized women with Schizophrenia, Bipolar Disorder and Schizoaffective Disorder in a naturalistic setting. Group 1 was composed of nineteen hospitalized women treated with antipsychotic monotherapy (either haloperidol, olanzapine, risperidone or clozapine) and Group 2 was composed of nineteen hospitalized women treated with an antipsychotic (either haloperidol, olanzapine, risperidone or quetiapine) with an additional antidepressant (citalopram, escitalopram, sertraline, paroxetine, fluvoxamine, mirtazapine, venlafaxine or clomipramine) or lithium. An Electrocardiogram (ECG) was carried out before the beginning of the treatment for both groups and at a second time after four days of therapy at full dosage, when blood was also drawn for determination of serum levels of the antipsychotic. Statistical analysis included repeated measures ANOVA, Fisher Exact Test and Indipendent T Test. Results - Mean QTc intervals significantly increased in Group 2 (24 ± 21 ms) however this was not the case in Group 1 (-1 ± 30 ms) (Repeated measures ANOVA p < 0,01). Furthermore we found a significant difference in the number of patients who exceeded the threshold of borderline QTc interval value (450 ms) between the two groups, with seven patients in Group 2 (38%) compared to one patient in Group 1 (7%) (Fisher Exact Text, p < 0,05). Conclusions - No significant prolongation of the QT interval was found following monotherapy with an antipsychotic agent, while combination of these drugs with antidepressants caused a significant QT prolongation. Careful monitoring of the QT interval is suggested in patients taking a combined treatment of antipsychotic and antidepressant agents.

The multiple pheromone ant clustering algorithm and its application to real world domains

The Multiple Pheromone Ant Clustering Algorithm (MPACA) models the collective behaviour of ants to find clusters in data and to assign objects to the most appropriate class. It is an ant colony optimisation approach that uses pheromones to mark paths linking objects that are similar and potentially members of the same cluster or class. Its novelty is in the way it uses separate pheromones for each descriptive attribute of the object rather than a single pheromone representing the whole object. Ants that encounter other ants frequently enough can combine the attribute values they are detecting, which enables the MPACA to learn influential variable interactions. This paper applies the model to real-world data from two domains. One is logistics, focusing on resource allocation rather than the more traditional vehicle-routing problem. The other is mental-health risk assessment. The task for the MPACA in each domain was to predict class membership where the classes for the logistics domain were the levels of demand on haulage company resources and the mental-health classes were levels of suicide risk. Results on these noisy real-world data were promising, demonstrating the ability of the MPACA to find patterns in the data with accuracy comparable to more traditional linear regression models. © 2013 Polish Information Processing Society.