First Online: 21 March 2016. 12 month embargo. / This paper presents cross-domain evidence that natural language makes use of (at least) two ways of individuating collective entities that differ in terms of how they cohere. The first kind, which I call swarm reference, picks out higher-order collective entities defined in terms of the spatial and temporal configuration of their constituent individuals. The second, which corresponds to canonical cases of group reference (e.g. committee, team, etc.), makes use of non-spatiotemporal notions. To motivate this distinction, I present systematic differences in how these two types of collective reference behave linguistically, both in the individual and event domains. These differences support two primary results. First, they are used as tests to isolate a new class of collective nouns that denote swarm individuals, both in English, as well as other languages like Romanian. I then consider a crosslinguistically common type of pluractionality, called event-internal in the previous literature (Cusic 1981, Wood 2007), and show that its properties are best explained if the relevant verbs denote swarm events. By reducing event-internal pluractionality to a type of collective reference also available for nouns, this work generates a new strong argument that pluractionality involves the same varieties of plural reference in the event domain that are seen in the individual domain.

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Influenza A virus (IAV) is one of the most common viruses circulating in the human population and is responsible for seasonal epidemics that affect millions of individuals worldwide. The need to develop new drugs and vaccines against IAVs led scientists to study the main IAV surface antigens hemagglutinin (HA) and neuraminidase (NA). In contrast to HA, which facilitates cell binding and entry of IAVs, NA plays a critical role in the release and spreading of the viral particles. The aim of this thesis was to study how the enzymatic head domain, the stalk and transmembrane domains have evolved to facilitate NA assembly into an enzymatically active homotetramer, and to determine how these regions have evolved together over time. Initially, we observed that the NA transmembrane domain (TMD) assists in the assembly of the head domain by tethering the stalk to the membrane in a tetrameric conformation. Upon examination of the available sequences for NA, we found that the subtype 1 (N1) TMDs have become more polar since 1918 while the subtype 2 (N2) TMDs have consistently retained the expected hydrophobicity of a TMD. Further analysis of the amino-acid sequences revealed a characteristic indicative of an amphipathic assembly for the N1 TMDs that were absent in the TMDs from N2. The function of the amphipathic assembly was examined by creating two viral chimeras, where the original TMD was replaced by another more polar or an engineered hydrophobic TMD. In both cases the viruses carrying the NA TMD chimeras showed reduced growth indicating that the TMD changes created an incompatibility with the head domain of NA. After prolonged passaging of these viruses, natural occurring mutations were observed in the TMD that were able to rescue the defects in viral growth, head domain folding and budding by creating a TMD with the appropriate polar or hydrophobic assembly properties. Interestingly, we observed that N1 and N2 have a great difference in the localization and length of amino-acid deletions occurring in the stalk region. In line with this observation, our data suggests that N1 supports large stalk deletions due to its strong TMD association, whereas N2 requires the presence of a strong oligomerizing stalk region to compensate for its weak TMD interaction. These results have demonstrated how important the NA TMD is for viral infectivity and how the three different domains have evolved in a cooperative manner to promote proper NA assembly / Influensa är en av de mest smittsamma sjukdomarna som drabbar människor och de flesta kan räkna med att bli infekterade många gånger under sin livstid. Influensaviruset attackerar främst luftvägarna, men kan även leda till t.ex. lunginflammation. De enskilda viruspartiklarna (virionerna) kan komma i olika former, men den vanligaste formen som används för att beskriva viruset är den sfäriska. På en virions yta så finns det två olika typer av membranproteiner, som kan liknas med två olika sorters spikar som sticker ut från viruset. Den ena ”spiken” kallas neuraminidas, eller bara kort för NA, och den andra för hemagglutinin (HA). När man har andats in ett influensavirus så kan viruset ta sig till de övre luftvägarna och vidare ner i luftstrupen för att där använda sig av HA för att ta sig in i en cell. Viruset använder sig sedan av cellen för att skapa många nya virioner, som tar sig ut ur cellen för att infektera fler celler. NA är det protein som virionerna använder sig av för att klyva sig loss från modercellen. Målet för avhandlingen var att studera NA och beskriva hur proteinet måste vara ihopsatt för att vara aktivt. NA har en uppbyggnad liknande en trädklunga, där fyra stycken identiska träd (med tillhörande rötter, stammar och trädkronor) går ihop och bildar en enda aktiv enhet, en s.k. tetramer. ”Rötterna” hos NA är den transmembrana domänen (TMD), den del av proteinet som sitter fast i influenaviruskroppen. ”Stammen”, eller stjälkdelen av NA, binder samman TMD med den största delen, huvuddomänen som motsvarar ”trädkronan”. Det är just huvuddomänen som är ansvarig för att klyva loss viruspartiklar från en modercell. Vi har i våra studier sett att det kan vara väldigt viktigt att TMD-domänerna går ihop i grupper om fyra för att hela NA ska kunna gå ihop i en tetramer och aktivt kunna klyva loss viruspartiklarna. När vi studerade TMD från olika influensavirus så märkte vi att vissa egenskaper hos TMD krävs för att de skulle kunna gå ihop, men också att dessa egenskaper inte fanns hos alla influensavirus. Virusen har evolverat över lång tid och har anpassat sig efter värdorganismerna (inklusive människan) och har hittat olika lösningar på problemet med att behöva bilda en tetramer. När vi gjorde ändringar i en TMD som vanligtvis gick ihop till en tetramer, och därmed förhindrade detta, så noterade vi att huvuddomänens funktion påverkades vilket ledde till att influensaviruset hade svårt att spridas. Vidare så har våra pågående studier på stjälkdelen visat att även denna del kan ha stor betydelse för tetrameriseringen av NA, speciellt i de fall där TM-domänen saknar egenskaper för att gå ihop. Avhandlingen tillför inte bara ny och viktig information till influensaforskningen, utan även potentiellt för framställandet av nya influensavacciner/-mediciner. / <p>At the time of the doctoral defense, the following paper was unpublished and had a status as follows: Paper 4: Manuscript.</p>

A dissertation submitted to the Faculty of Engineering and the Built Environment, University of the Witwatersrand, Johannesburg, in fulfilment of the requirements for the degree of Master of Science in Engineering, 2016 / The work presented extends and contributes to the research of modelling lightning return stroke (RS) electromagnetic (EM) fields in the time domain. Although previous work in this area has focused on individual lightning electromagnetic pulse (LEMP) modelling techniques, there has not been an investigation into the strengths and weaknesses of different methods, as well as the implementation considerations of the models. This work critically compares three unique techniques (Finite Antenna, FDTD, and Single Cell FDTD) under the same ideal simulation parameters. The research presented will evaluate the EM fields in the range of 50m to 500m from the lightning channel. This range, often referred to as the near field distance, has a significant effect on lightning induced overvoltages on distribution lines, which are primarily created by the horizontal EM fields of the RS channel. These close distances have a significant effect on the model implementations, especially with the FDTD method. Each of these modelling methods is explained and tested through examples. The models are implemented in C++ and have been included in the Appendix to aid in future implementation. From the model simulations it is clear that the FDTD method is the most comprehensive model available. It allows for non-ideal ground planes, as well as complex simulation environments. However, FDTD has a number of numerical related errors that the Finite Antenna method does not suffer from. The Single Cell FDTD method is simple to implement and does not suffer from the same numerical errors as a full FDTD implementation, but is limited to simple simulation environments. This work contributes to the research field by comparing and evaluating three techniques and giving consideration to the implementation and the applicability to lightning EM simulations. / MT2017

Thesis advisor: Steven D. Bruner / Bacteria utilize complex enzymatic machinery to create diverse secondary metabolites. The architectural complexities of these small molecules are enhanced by nature’s ability to synthesize non-proteinogenic amino acids for incorporation into these scaffolds. Many of these natural products are utilized as therapeutic agents, and it would be advantageous to understand how the bacteria create various non-natural amino acid building blocks. With a greater understanding of these systems, engineering could be used to create libraries of potentially useful natural product analogs. The tyrosine aminomutase SgTAM from the soil bacteria Streptomyces globisporus catalyzes the formation of tyrosine to generate (S)-B-tyrosine. The precise mechanistic role of MIO in this novel family of aminomutases has not been established. We report the first X-ray crystal--> structure of an MIO based aminomutase and confirm the structural homology of SgTAM to ammonia lyases. Further work with mechanistic inhibitors provide structural evidence of the mechanism by which MIO dependent enzymes operate. We have also investigated LnmQ, an adenylation domain in the biosynthetic pathway of leinamycin. Leinamycin is an antitumor antibiotic that was isolated from soil samples in 1989. LnmQ is responsible for the specific recognition of D-alanine and subsequent activation as an aminoacyl adenylate species. We have cloned the gene into a DNA vector and expressed it in E. coli. Upon purification of the protein, crystallization conditions have been tested. Synthesis of an inhibitor that mimics the aminoacyl adenylate product catalyzed by LnmQ has been completed. Crystallization with this--> inhibitor will provide better quality crystals and a catalytically informative co-complex. / Thesis (PhD) — Boston College, 2008. / Submitted to: Boston College. Graduate School of Arts and Sciences. / Discipline: Chemistry.

Ho Kwok Ching. / Thesis (M.Phil.)--Chinese University of Hong Kong, 2000. / Includes bibliographical references (leaves 107-111). / Abstracts in English and Chinese. / Content --- p.5 / Chapter 1 --- Introduction --- p.7 / Chapter 2 --- Background Theory --- p.9 / Chapter 2.1 --- Background history --- p.9 / Chapter 2.2 --- Finite Difference Time Domain Method --- p.10 / Chapter 2.2.1 --- Basic Formulation --- p.10 / Chapter 2.2.2 --- Finite Difference Expression: --- p.11 / Chapter 2.2.3 --- Courant Stability Criterion --- p.13 / Chapter 2.3 --- Absorbing Boundary Condition (PML) --- p.13 / Chapter 2.3.1 --- "Field -Splitting Modification of Maxwell's equation, TE case" --- p.14 / Chapter 2.3.2 --- Propagation of a TE Plane Wave in a PML Medium --- p.15 / Chapter 2.3.3 --- Transmission of a wave through PML-PML Interfaces --- p.19 / Chapter 2.3.4 --- PML for FDTD in 2D domain --- p.23 / Chapter 2.3.5 --- Extension to Three Dimension Case --- p.25 / Chapter 2.3.6 --- Obtaining S-parameters for General Microwave circuit --- p.26 / Chapter 2.4 --- Extended Finite Difference Time Domain Method --- p.29 / Chapter 2.4.1 --- Direct Implementation of Lumped Elements --- p.30 / Chapter 2.4.2 --- Equivalent-Source Techniques --- p.31 / Chapter 2.5 --- EMC --- p.37 / Chapter 3 --- Novel Techniques for Extended FDTD Method --- p.38 / Chapter 3.1 --- Introduction --- p.38 / Chapter 3.2 --- The Improved FDTD-SPICE Interface --- p.38 / Chapter 3.3 --- The Improved DC Bias Source --- p.48 / Chapter 3.4 --- The Improved DC Biasing Component --- p.50 / Chapter 3.5 --- Example --- p.51 / Chapter 3.6 --- Program Architecture --- p.55 / Chapter 3.7 --- Conclusion --- p.57 / Chapter 4 --- Example Design --- p.58 / Chapter 4.1 --- Introduction --- p.58 / Chapter 4.2 --- Internal Antenna Design --- p.58 / Chapter 4.2.1 --- Half-wavelength Patch --- p.58 / Chapter 4.2.2 --- Quarter-wavelength patch --- p.63 / Chapter 4.3 --- RF Power Amplifier Circuit Design --- p.73 / Chapter 4.4 --- Active Internal Antenna Design --- p.88 / Chapter 4.4.1 --- Design --- p.88 / Chapter 4.4.2 --- Surface Wave Analysis 一 Transient state analysis --- p.91 / Chapter 4.4.3 --- Surface wave analysis -AC analysis --- p.95 / Chapter 4.4.4 --- Far Field Pattern --- p.101 / Chapter 4.5 --- Conclusion --- p.105 / Chapter 5 --- Conclusion: --- p.106 / Chapter 6 --- Reference List --- p.107 / Publication --- p.111

by Wai-Chung Fung. / Thesis (M.Phil.)--Chinese University of Hong Kong, 1998. / Includes bibliographical references (leaves 121-124). / Abstract also in Chinese. / Acknowledgement --- p.i / Abstract --- p.ii / Table of contents / Chapter Chapter 1: --- Introduction --- p.1 / Chapter Chapter 2: --- Background Theories --- p.4 / Chapter 2.1 --- Introduction --- p.4 / Chapter 2.2 --- Maxwell's Equations --- p.5 / Chapter 2.3 --- Basic Formulation --- p.8 / Chapter 2.4 --- Plane Wave Formulation --- p.13 / Chapter 2.4.1 --- Total-Field / Scattered-Field Algorithm --- p.14 / Chapter 2.4.2 --- Pure Scattered-Field Algorithm --- p.16 / Chapter 2.4.2.1 --- Application to PEC Structures --- p.16 / Chapter 2.4.2.2 --- Application to Lossy Dielectric Structures --- p.17 / Chapter 2.5 --- Incident Plane Wave Components Generation --- p.20 / Chapter 2.6 --- Source and Termination Modeling in FD-TD model --- p.24 / Chapter 2.6.1 --- Resistive source --- p.25 / Chapter 2.6.2 --- Resistor Formulation --- p.27 / Chapter 2.7 --- PML Formulation --- p.28 / Chapter 2.7.1 --- Two-Dimensional TE Case --- p.28 / Chapter 2.7.2 --- Extension to the Full-vector Three-Dimension Case --- p.32 / Chapter 2.8 --- Time Domain Extrapolation --- p.33 / Chapter 2.8.1 --- Prony's Model --- p.34 / Chapter 2.8.2 --- Auto-regressive Model and Performance Comparison with Prony's Method --- p.36 / Chapter 2.9 --- Summary --- p.42 / Chapter Chapter 3: --- Verification of FD-TD Method --- p.43 / Chapter 3.1 --- Introduction --- p.43 / Chapter 3.2 --- Microstrip Patch Antenna: An Introduction --- p.44 / Chapter 3.2.1 --- Direct Fed Patch --- p.45 / Chapter 3.2.2 --- EMC Patch --- p.50 / Chapter 3.2.3 --- Aperture-Coupled Patch --- p.53 / Chapter 3.3 --- Verification of FD-TD: S11 Analysis --- p.55 / Chapter 3.3.1 --- Analysis of Direct Fed Rectangular Patch Antenna --- p.56 / Chapter 3.3.2 --- Analysis of EMC Patch Antenna --- p.60 / Chapter 3.3.3 --- Analysis of Aperture-Coupled Patch Antenna --- p.63 / Chapter 3.4 --- Verification of FD-TD: Radiation Pattern Analysis --- p.66 / Chapter 3.4.1 --- The Absolute and Relative Approaches --- p.67 / Chapter 3.4.2 --- The Inset Fed Patch Antenna --- p.69 / Chapter 3.5 --- Summary --- p.71 / Chapter Chapter 4: --- Space Diversity Design --- p.73 / Chapter 4.1 --- Introduction --- p.73 / Chapter 4.2 --- How Space Diversity Antenna Works --- p.74 / Chapter 4.3 --- Criteria for Evaluation and Optimization of Diversity Performance --- p.77 / Chapter 4.4 --- Simple Approach for Two-Patch Diversity Array --- p.82 / Chapter 4.4.1 --- Performance as a Function of Antenna Separation --- p.83 / Chapter 4.5 --- Novel Designs for Performance Improvement --- p.89 / Chapter 4.5.1 --- Shorting Post Isolation --- p.90 / Chapter 4.5.2 --- Offset-positioned Configuration --- p.101 / Chapter 4.6 --- Three-Patch Diversity Array --- p.106 / Chapter 4.6.1 --- Co-aligned Configurations --- p.107 / Chapter 4.6.2 --- Offset-Positioned Configurations --- p.112 / Chapter 4.7 --- Summary --- p.117 / Chapter Chapter 5: --- Conclusion --- p.118 / Appendix A: Publication --- p.121 / Appendix B: References List --- p.122

The acquisition of cellular adhesion machinery likely represented a key factor in the evolutionary transition from unicellular to multicellular organisms. Within metazoa, cellular adhesion is an integral aspect of organismal integrity through its regulation of a wide range of processes, including tissue patterning, cellular proliferation, and migration. As such, dysregulation of adhesion has been linked to diverse pathologies including cancers and neurodegenerative diseases. At the molecular level, adhesion is mediated by specific transmembrane cell adhesion molecules (CAMs) and intracellular complexes that create a dynamic link between the extracellular milieu and the intracellular cytoskeleton. At the sequence level, immunoglobulin domains act to mediate homo- and heterophilic interactions among CAMs and thus adhesion between neighboring cells. LIGs, a family of Ig-containing proteins that contain Leucine-rich repeats, represent candidates for novel CAMs with functions in axonal regeneration and synaptic pathfinding - all of which are highly dependent on cellular adhesion. In Drosophila, two LIG family members, Kekkon1 (Kek1) and Kekkon5 (Kek5) have been been implicated in EGF signaling, and Bone Morphogenetic Protein signaling as well as cellular adhesion, respectively. To investigate the putative role of Kek5 as a CAM, characterization of Kek5 activity was carried out at the cellular and molecular level. From this it was discovered that Kek5 is able to induce a dramatic upregulation of the adherens junction component Armadillo, in addition to epithelial extrusion and cell enlargement. Together, the studies presented within support a model in which Kek5 acts in a homophilic fashion to upregulate Arm and that this activity is functionally separable from other observed effects (epithelial extrusion and cell enlargement).

Cu+-ATPases receive Cu+ from specific chaperones via ligand exchange and subsequently drive the metal efflux from the cell cytoplasms. Cu+-ATPases have two transmembrane metal binding/transport sites (TM-MBS) and various cytoplasmic domains: the actuator (A-domain) and ATP binding domains (ATPBD), and regulatory N-terminal metal binding domains (N-MBD). Archaeoglobus fulgidus CopA, the Cu+-ATPase used in these studies, contains a single N-MBD and an apparently non-functional C-terminal MBD. The Cu+ dependent interaction of N-MBD and ATPBD was postulated as a possible mechanism for enzyme regulation. The Cu+ transfer from the chaperone to CopA is independent of the N-MBD capability to bind Cu+. Therefore, we hypothesized that ligand (Cu+ or nucleotide) binding to cytoplasmic domains might affect the interactions between the cytoplasmic domains. To test these ideas, the interactions among isolated cytoplasmic domains were characterized. Studies using isolated domains showed that while the N-MBD interacts with ATPBD, the presence of Cu+ or nucleotide (ADP) prevents this interaction. The N-MBD does not interact with the A domain. Alternatively, the C-MBD interacts with both ATPBD and A-domains in a ligand independent fashion. Only one Cu+ is transferred to CopA in absence of nucleotides, while the presence of ADP allows full loading of TM-MBS. These results suggest that the ligand binding affects the interactions between the cytoplasmic domains, and also change the conformation of CopA to help it accept the second Cu+ from chaperone.

This project looks at using diagrammatic reasoning to prove mathematical theorems. The work is motivated by a need for theorem provers whose reasoning is readily intelligible to human beings. It should also have practical applications in mathematics teaching. We focus on the continuous domain of analysis - a geometric subject, but one which is taught using a dry algebraic formalism which many students find hard. The geometric nature of the domain makes it suitable for a diagram-based approach. However it is a difficult domain, and there are several problems, including handling alternating quantifiers, sequences and generalisation. We developed representations and reasoning methods to solve these. Our diagram logic isn't complete, but does cover a reasonable range of theorems. It utilises computers to extend diagrammatic reasoning in new directions – including using animation. This work is tested for soundness, and evaluated empirically for ease of use. We demonstrate that computerised diagrammatic theorem proving is not only possible in the domain of real analysis, but that students perform better using it than with an equivalent algebraic computer system.