Operator and organizational maintenance manual : improved guided missile zero-length launcher M192E1 guided missile loading and storage pallet M1E2 and improved guided missile launching section control box AN/GSA-132A (X0-1), improved Hawk Air Defense Guided Missile System.

Includes index.

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

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

STAR: predicting recombination sites from amino acid sequence

Background: Designing novel proteins with site-directed recombination has enormous prospects. By locating effective recombination sites for swapping sequence parts, the probability that hybrid sequences have the desired properties is increased dramatically. The prohibitive requirements for applying current tools led us to investigate machine learning to assist in finding useful recombination sites from amino acid sequence alone. Results: We present STAR, Site Targeted Amino acid Recombination predictor, which produces a score indicating the structural disruption caused by recombination, for each position in an amino acid sequence. Example predictions contrasted with those of alternative tools, illustrate STAR'S utility to assist in determining useful recombination sites. Overall, the correlation coefficient between the output of the experimentally validated protein design algorithm SCHEMA and the prediction of STAR is very high (0.89). Conclusion: STAR allows the user to explore useful recombination sites in amino acid sequences with unknown structure and unknown evolutionary origin. The predictor service is available from http://pprowler.itee.uq.edu.au/star.

Characterization of a volume-sensitive chloride current in rat osteoblast-like (ROS 17/2.8) cells

1. During osmotic swelling, cultured osteoblastic cells (ROS 17/2.8) exhibited activation of large amplitude Cl- currents in the whole-cell configuration of the patch-clamp technique. Effects of hypotonic shock on cell volume and membrane conductance were rapidly reversed on return to isotonic conditions. 2. Voltage command pulses in the range -80 to +50 mV produce instantaneous activation of Cl- currents. At potentials more positive than +50 mV the current exhibited time-dependent inactivation. The instantaneous current-voltage relationship was outwardly rectifying. 3. The anion permeability sequence of the induced current was SCN- (2.2) > I- (1.9) > Br- (1.5) > Cl- (1.0) > F- (0.8) > gluconate- (0.2). This corresponds to Eisenman's sequence I. 4. The volume-sensitive Cl- current was effectively inhibited by the Cl- channel blockers 4,4'-diisothiocyanatostilbene-2,2-disulphonic acid (DIDS) and 5-nitro-2-(3-phenylpropylamino) benzoic acid (NPPB). Outward currents were more effectively suppressed by DIDS than inward currents. The concentrations for 50% inhibition (IC50) of outward and inward currents were 81 and 298 μM, respectively. NPPB was equally effective at inhibiting outward and inward currents (IC50 of 64 μM). The current was relatively insensitive to diphenylamine-2-carboxylate (DPC), 500 μM producing only 22.5 ± 4.0% inhibition. 5. Inhibitors of protein kinase A (H-89, 1 μM) and tyrosine kinase (tyrphostin A25, 200 μM) were without effect upon activation of Cl- currents in response to hypotonic shock. Under isotonic conditions, elevation of intracellular Ca2+ by ionomycin (1 μM) or activation of protein kinase C by 12-O-tetradecanoylphorbol 13-acetate (TPA, 0.1 μM) failed to evoke increases in basal Cl- conductance levels. 6. It is concluded that an outwardly rectifying Cl- conductance is activated upon osmotic swelling and may be involved in cell volume regulation of ROS 17/2.8 cells.

Present perspectives on the automated classification of the G-protein coupled receptors (GPCRs) at the protein sequence level

The G-protein coupled receptors--or GPCRs--comprise simultaneously one of the largest and one of the most multi-functional protein families known to modern-day molecular bioscience. From a drug discovery and pharmaceutical industry perspective, the GPCRs constitute one of the most commercially and economically important groups of proteins known. The GPCRs undertake numerous vital metabolic functions and interact with a hugely diverse range of small and large ligands. Many different methodologies have been developed to efficiently and accurately classify the GPCRs. These range from motif-based techniques to machine learning as well as a variety of alignment-free techniques based on the physiochemical properties of sequences. We review here the available methodologies for the classification of GPCRs. Part of this work focuses on how we have tried to build the intrinsically hierarchical nature of sequence relations, implicit within the family, into an adaptive approach to classification. Importantly, we also allude to some of the key innate problems in developing an effective approach to classifying the GPCRs: the lack of sequence similarity between the six classes that comprise the GPCR family and the low sequence similarity to other family members evinced by many newly revealed members of the family.

A novel multilocus sequence typing scheme for the opportunistic pathogen Propionibacterium acnes and characterisation of type 1 cell surface-associated antigens

We have developed a novel multilocus sequence typing (MLST) scheme and database (http://pubmlst.org/pacnes/) for Propionibacterium acnes based on the analysis of seven core housekeeping genes. The scheme, which was validated against previously described antibody, single locus and random amplification of polymorphic DNA typing methods, displayed excellent resolution and differentiated 123 isolates into 37 sequence types (STs). An overall clonal population structure was detected with six eBURST groups representing the major clades I, II and III, along with two singletons. Two highly successful and global clonal lineages, ST6 (type IA) and ST10 (type IB1), representing 64?% of this current MLST isolate collection were identified. The ST6 clone and closely related single locus variants, which comprise a large clonal complex CC6, dominated isolates from patients with acne, and were also significantly associated with ophthalmic infections. Our data therefore support an association between acne and P. acnes strains from the type IA cluster and highlight the role of a widely disseminated clonal genotype in this condition. Characterization of type I cell surface-associated antigens that are not detected in ST10 or strains of type II and III identified two dermatan-sulphate-binding proteins with putative phase/antigenic variation signatures. We propose that the expression of these proteins by type IA organisms contributes to their role in the pathophysiology of acne and helps explain the recurrent nature of the disease. The MLST scheme and database described in this study should provide a valuable platform for future epidemiological and evolutionary studies of P. acnes.

Weakly Increasing Zero-Diminishing Sequences

The following problem, suggested by Laguerre’s Theorem (1884), remains open: Characterize all real sequences {μk} k=0...∞ which have the zero-diminishing property; that is, if k=0...n, p(x) = ∑(ak x^k) is any P real polynomial, then k=0...n, p(x) = ∑(μk ak x^k) has no more real zeros than p(x). In this paper this problem is solved under the additional assumption of a weak growth condition on the sequence {μk} k=0...∞, namely lim n→∞ | μn |^(1/n) < ∞. More precisely, it is established that the real sequence {μk} k≥0 is a weakly increasing zerodiminishing sequence if and only if there exists σ ∈ {+1,−1} and an entire function n≥1, Φ(z)= be^(az) ∏(1+ x/αn), a, b ∈ R^1, b =0, αn > 0 ∀n ≥ 1, ∑(1/αn) < ∞, such that µk = (σ^k)/Φ(k), ∀k ≥ 0.

Improving novice analyst performance in modeling the sequence diagram in systems analysis: A cognitive complexity approach

The Unified Modeling Language (UML) has quickly become the industry standard for object-oriented software development. It is being widely used in organizations and institutions around the world. However, UML is often found to be too complex for novice systems analysts. Although prior research has identified difficulties novice analysts encounter in learning UML, no viable solution has been proposed to address these difficulties. Sequence-diagram modeling, in particular, has largely been overlooked. The sequence diagram models the behavioral aspects of an object-oriented software system in terms of interactions among its building blocks, i.e. objects and classes. It is one of the most commonly-used UML diagrams in practice. However, there has been little research on sequence-diagram modeling. The current literature scarcely provides effective guidelines for developing a sequence diagram. Such guidelines will be greatly beneficial to novice analysts who, unlike experienced systems analysts, do not possess relevant prior experience to easily learn how to develop a sequence diagram. There is the need for an effective sequence-diagram modeling technique for novices. This dissertation reports a research study that identified novice difficulties in modeling a sequence diagram and proposed a technique called CHOP (CHunking, Ordering, Patterning), which was designed to reduce the cognitive load by addressing the cognitive complexity of sequence-diagram modeling. The CHOP technique was evaluated in a controlled experiment against a technique recommended in a well-known textbook, which was found to be representative of approaches provided in many textbooks as well as practitioner literatures. The results indicated that novice analysts were able to perform better using the CHOP technique. This outcome seems have been enabled by pattern-based heuristics provided by the technique. Meanwhile, novice analysts rated the CHOP technique more useful although not significantly easier to use than the control technique. The study established that the CHOP technique is an effective sequence-diagram modeling technique for novice analysts.

Improving Novice Analyst Performance in Modeling the Sequence Diagram in Systems Analysis: A Cognitive Complexity Approach

The Unified Modeling Language (UML) has quickly become the industry standard for object-oriented software development. It is being widely used in organizations and institutions around the world. However, UML is often found to be too complex for novice systems analysts. Although prior research has identified difficulties novice analysts encounter in learning UML, no viable solution has been proposed to address these difficulties. Sequence-diagram modeling, in particular, has largely been overlooked. The sequence diagram models the behavioral aspects of an object-oriented software system in terms of interactions among its building blocks, i.e. objects and classes. It is one of the most commonly-used UML diagrams in practice. However, there has been little research on sequence-diagram modeling. The current literature scarcely provides effective guidelines for developing a sequence diagram. Such guidelines will be greatly beneficial to novice analysts who, unlike experienced systems analysts, do not possess relevant prior experience to easily learn how to develop a sequence diagram. There is the need for an effective sequence-diagram modeling technique for novices. This dissertation reports a research study that identified novice difficulties in modeling a sequence diagram and proposed a technique called CHOP (CHunking, Ordering, Patterning), which was designed to reduce the cognitive load by addressing the cognitive complexity of sequence-diagram modeling. The CHOP technique was evaluated in a controlled experiment against a technique recommended in a well-known textbook, which was found to be representative of approaches provided in many textbooks as well as practitioner literatures. The results indicated that novice analysts were able to perform better using the CHOP technique. This outcome seems have been enabled by pattern-based heuristics provided by the technique. Meanwhile, novice analysts rated the CHOP technique more useful although not significantly easier to use than the control technique. The study established that the CHOP technique is an effective sequence-diagram modeling technique for novice analysts.

Digital geometric-sequence control technique for bidirectional dual active bridge DC-DC converters used in future electric vehicles

Bidirectional DC-DC converters are widely used in different applications such as energy storage systems, Electric Vehicles (EVs), UPS, etc. In particular, future EVs require bidirectional power flow in order to integrate energy storage units into smart grids. These bidirectional power converters provide Grid to Vehicle (V2G)/ Vehicle to Grid (G2V) power flow capability for future EVs. Generally, there are two control loops used for bidirectional DC-DC converters: The inner current loop and The outer loop. The control of DAB converters used in EVs are proved to be challenging due to the wide range of operating conditions and non-linear behavior of the converter. In this thesis, the precise mathematical model of the converter is derived and non-linear control schemes are proposed for the control system of bidirectional DC-DC converters based on the derived model. The proposed inner current control technique is developed based on a novel Geometric-Sequence Control (GSC) approach. The proposed control technique offers significantly improved performance as compared to one for conventional control approaches. The proposed technique utilizes a simple control algorithm which saves on the computational resources. Therefore, it has higher reliability, which is essential in this application. Although, the proposed control technique is based on the mathematical model of the converter, its robustness against parameter uncertainties is proven. Three different control modes for charging the traction batteries in EVs are investigated in this thesis: the voltage mode control, the current mode control, and the power mode control. The outer loop control is determined by each of the three control modes. The structure of the outer control loop provides the current reference for the inner current loop. Comprehensive computer simulations have been conducted in order to evaluate the performance of the proposed control methods. In addition, the proposed control have been verified on a 3.3 kW experimental prototype. Simulation and experimental results show the superior performance of the proposed control techniques over the conventional ones.

Voltage and current spectra for matrix power converters

Matrix power converters are used for transforming one alternating-current power supply to another, with different peak voltage and frequency. There are three input lines, with sinusoidally varying voltages which are 120◦ out of phase one from another, and the output is to be delivered as a similar three-phase supply. The matrix converter switches rapidly, to connect each output line in sequence to each of the input lines in an attempt to synthesize the prescribed output voltages. The switching is carried out at high frequency and it is of practical importance to know the frequency spectra of the output voltages and of the input and output currents. We determine in this paper these spectra using a new method, which has significant advantages over the prior default method (a multiple Fourier series technique), leading to a considerably more direct calculation. In particular, the determination of the input current spectrum is feasible here, whereas it would be a significantly more daunting procedure using the prior method instead.

Teen Girls’ Perspectives on Their Current Dietary Habits and Food Choices: A Qualitative Study in Jeddah, Saudi Arabia

Rapid socioeconomic development in Saudi Arabia, as a result of oil revenues, has had profound effects on people’s lifestyles, including the transformation of people’s dietary habits. Such dietary transformations, known as the nutrition transition, are common in countries undergoing rapid socioeconomic changes. This transition is significant in Saudi Arabia as the traditional Saudi diet is considered a healthy one. Adoption of the Western diet has had negative health effects on the Saudi population, especially adolescents. As evidenced in many studies, adolescents are the most affected population when it comes to changes in dietary habits and physical activity. Adolescence is a vulnerable stage of life when dietary habits are developed, often lasting into adulthood, and may not be easily changed. In the case of Saudi Arabia, youth or adolescents represent almost 60% of the population; therefore, the eating habits they develop now could have profound consequences for population health in the future. To develop effective health promotion strategies, it is important to understand the sociocultural factors that influence the dietary habits and food choices of Saudi teens. I conducted two semi-structured, open-ended interviews, using photo-elicitation techniques, with 12 Saudi girls, aged 15-16 years. Analysis of the data shows four factors that pulled the participants toward eating home cooked traditional food and five factors that pushed participants away from eating home cooked traditional foods. The research suggests that despite the attractiveness of modern, Western ways of eating for Saudi teen girls, parents still play a key role in encouraging and supporting them to eat healthy food.