VictorJuiz/thesis huggingface dataset:
The effect of ammonia on development in Dictyostelium discoideum

Upon starvation, individual amoebae of D. discoideum cooperate to produce a cell aggregate. The aggregate then elongates into a slug which moves chemotactically towards food sources. Culmination of the developmental cycle results in the formation of a fruiting body containing differentiated stalk and spore cells. Ammonia is produced naturally in the aggregates during starvation and is implicated in the regulation of the developmental cycle. Addition of excess ammonia leads to inhibition of aggregation, increased slug migration, delay of culmination and the promotion of spore formation.
This thesis examines the possible intracellular mechanism(s) through which ammonia might affect developmental processes. It has been postulated that ammonia might act by directly inhibiting a particular enzymatic activity, alternatively it could act as a weak base to raise the pH of the cytosol or an intracellular compartment. To investigate these possibilities, the effects of a variety of weak bases were tested on aggregation and culmination.
All of the weak bases tested inhibited development in a dose-dependent way, which argues against the notion that ammonia acts by direct enzyme inhibition since the bases are structurally distinct. In addition, the inhibition potencies of the bases varied according to their protonophoric activity: the most effective protonophores were also the most effective developmental inhibitors. This suggested that the bases were likely to be acting to neutralize an intracellular compartment in these experiments,a result which implicates acidic compartments in the control of development.
That weak bases can indeed dissipate the pH of intracellular vesicles was confirmed in vitro by monitoring acidification of isolated vesicles in the presence of the bases. In vivo experiments using 31P-NMR probes of the vesicular system confirmed this and showed that cytosolic pH was stable in the presence of bases.
Genetic evidence for the role of acidic compartments in development was also gathered. Both the acidification-defective (Hgr) mutants and a mutant created by antisense expression of a fraction of the B subunit cDNA of the vacuolar H+- ATPase were defective in development, displaying developmental behaviour reminiscent of weak base-treated wild-type strains. This shows that defective vacuolar acidification can mimic the effect of addition of ammonia and indicates that an acidic vesicle is the target of ammonia In vivo.

Advisor: Gross, J
Studies of the DNA repair proteins FANCD2/FANCI and DNA polymerase eta

Our genome is continuously under various sources of genotoxic stresses. Thus, human has developed several DNA repair pathways to deal with different types of DNA damage. This thesis contains two studies, one focusing on the Fanconi Anemia pathway, which is known to coordinate the DNA interstrand crosslink repair, and the other one on the regulation of translesion synthesis, which is responsible for replication at DNA lesion sites, e.g. UV induced pyrimidine dimers.
Fanconi Anemia (FA) is a genetic disorder caused by mutations in any of 15 FA genes, where patients usually have developmental defects and predisposition to cancers in addition to anemia, and all the patients and patient derived cell lines are hypersensitive to DNA crosslinking agents such as Mitomycin C (MMC) and Cisplatin. Of the 15 FA proteins, FANCD2 and FANCI are key players essential for the functionality of the pathway. Upon genotoxic stress, both proteins are phosphorylated, ubiquitinated, and quickly recruited to sites of DNA damage together with other DNA repair proteins. In this part of our studies, we present the structure of the full-length human FANCD2/FANCI heterodimer, and our attempts at generating ubiquitinated FANCD2/FANCI heterodimer.
Polymerase η is one of the Y-family polymerases that are involved in translesion synthesis. It is known that ubiquitination and phosphorylation are together regulating the recruitment of polymerase η. In this part of our studies, we identified several novel polymerase η interacting proteins, as well as two novel phosphorylation sites, which could participate in the process of polymerase η recruitment upon DNA damage.

Keywords: Polymerase eta
Fanconi Anemia
Advisor: Cohn, M
Lakin, N
Oil, culture &amp; economy: the reinvention of the Shetland way of life

Claims to historically-based identities and cultures have long been prevalent in Shetland, an island group bordering the North Sea and North Atlantic approximately 300 kilometres north of Aberdeen. In the early 1970s, however, oil and gas discoveries in the North Sea made Shetland an ideal location for oil infrastructure and ultimately the site of a major oil terminal and extensive oil-support and servicing activities. The prospect of such major developments, however, stirred fears regarding the disruption of a local culture and identity heavily based on historical elements. Discussed in this thesis are the elements and influences that led to the creation – sometimes intentionally – of Shetland’s sense of identity and culture and how the construction of the Sullom Voe Terminal and other oil support infrastructure impacted such perceptions. Not only did the actual externalities of development alter the ‘Shetland way of life’, but also in response, significantly, to fears about what the industrial growth in their midst would bring, Shetlanders’ understandings of their own cultures and identities were changed. Petroleum-related immigration and income both significantly altered the practicalities of Shetland life but did not wholly replace the cultural influences which had existed previously. Instead they fuelled the creation of new hybrid identities that largely embrace these modern influences while remaining grounded in the historical crofting and fishing ways of life, claims to Norse heritage, and a sense of island remoteness that have long characterised Shetlanders’ outlooks on the world and perceptions of self.

Keywords: Shetland
tradition
oil
identity
culture
Advisor: Barry, A
The motion of an ion in an electron gas

We give a semi-classical treatment of the problem of electrical conduction around a charged impurity ion in a metal. As the electrons flow past the ion they are scattered by its screened Coulomb potential and so introduce a velocity dependent distribution of charge. This charge distribution leads, through the Poisson equation, to a modification of the potential surrounding the ion through which the electrons are initially scattered; we look for a self-consistent or simultaneous solution to the Boltzmann and Poisson equations. This final velocity dependent charge distribution induces an electric field at the ion, so exerting a force on that ion. We identify two effects: (i) a screening force acting so as to reduce the effect of the external field on the ion, (ii) a drift force resulting from the direct collisions between electron, and ion.
The process is described by a Boltzmann Transport equation which we solve at large distances from the ion. We derive the Green's Function for the equivalent integral equation, and then solve that equation by means of a Fourier Transform. In this technique we do not assume as in previous approaches that the ion is stationary or that its charge is small. The evaluation of the Green's Function does however involve the construction of an orbit model in which all scattered electrons pass through the ion itself and we do not expect this model to be of any use inside the screening radius.
We turn to a method of expansion by spherical harmonics, suggested by Das in his thesis, in the hope that it may be of use at short range. In understanding a paradox of the method we lose a criterion for convergence and our confidence in the method. To do this we consider the electron mean free path to be infinite in this short range region. In this limit a quantum mechanical calculation of the self-consistent field gives a result identical to that from a classical weak charge calculation due to Peierls, in the same limit, with the significant addition of a cut-off in momentum space at twice the Fermi-momentum. It is this cut-off, for which Peierls had argued on physical grounds, that eliminates a divergence at the origin. We use it to calculate the force.
We find that we may add Peierls' result where the Green's Function method is too insensitive. There are then three extra terms in the force, two due to drift and one to screening. However, the term we interpret as a screening correction may for large enough charge on the ion become greater than the direct field force. This may be due to an error in our interpretation as screening, or in the calculation itself. If it is the latter we propose a further calculation to check. In as far as the force on the ion derived in this thesis may be larger than the direct field force there is no disagreement with experimental data. Until we can understand the screening problem the result is not suitable for a detailed comparison with experiment.
Doing deals in a global law firm: the reciprocity of institutions and work

Since the early 1990s, institutional approaches to organizations have increasingly focused on explaining the role of agency in processes of institutional creation and transformation. The paradox of embedded agency, the question of how actors can become motivated and enabled to transform supposedly taken-for-granted practices, structures and norms has become the fundamental puzzle of contemporary institutional theory. Recent attempts to resolve this puzzle under the label of “institutional work” focus on practices aimed at creating, maintaining, and disrupting institutions, but portray them as planned, discrete episodes that unfold in isolation from everyday organizational or social life. Thereby, the label highlights institutionalists’ current neglect of work in its literal meaning as actors’ everyday occupational tasks and activities. The detachment of institutional work from practical work constitutes a significant blind spot in institutionalists’ understanding of agency and calls for research that examines the reciprocity of institutions and work. Drawing on illuminating constructs from theories of practice, this study extends existing field-level approaches to the paradox of embedded agency. It argues for a practice-based institutionalism that focuses on individual actors and the role of their collective micro-level praxis in constituting macro-level institutions. It re-connects institutional arguments to every-day activity rather than organizational or managerial action, unpacks the micro-practices and micro–politics by which actors negotiate institutional contradictions and demonstrates the reciprocity of institutions and work. The research addresses the detachment of institutional and practical work through a single-case study of a global law firm’s banking group. It explores what banking lawyers do when they ‘do deals’ and how their practical work may attain institutional relevance. Positioned at the intersec-tion of local laws, international financial markets, commercial and professional logics, banking lawyers operate across multiple institutional frameworks. Observations and accounts of their work provide particularly rich insights into the dynamics of institutional persistence and change, because they illustrate empirically how contradictory institutionalized concepts, practices and logics are experienced, negotiated, and constituted at work.

Keywords: institutional logics
embedded agency
situated change
global law firm
dialectical change
practice theory
professional service firm
law
Institutional theory
institutional change
Advisor: Morris, T
The relations of the Amampondo and the colonial authorities (1830-1886) with special reference to the role of the Wesleyan missionaries

South African historiography has tended to follow the Great Trek and to avoid the area between the Kei River and Natal. As a result, hardly any attention has been given to an unspectacular but significant chapter in the story of relations between black and white in the nineteenth century. The purpose of this thesis is to explore this by-way, and to examine the relations of the Amampondo and the Colonial authorities at the Cape and Natal between 1830 and 1886.
For the greater part of this period these relations were governed, nominally at least, by the Treaty of 1844, and an attempt has been made to assess its value as an Instrument regulating the dealings of a European power and a native tribe. The Treaty System, of which it formed a part, was the creature of a day. Built up between 1334 and 1844, it was swept away by the Frontier War of 1846 and the Bloemfontein Convention of 1854. It has therefore been necessary to ask why the Mpondo Treaty remained a living force for so many years after its counterparts had been abandoned.
[Please see pdf. for full abstract.]
Photodissociation of atmospherically important species

The photodissociation of ozone by ultraviolet light has a great impact on the photochemistry of the atmosphere. The relative quantum yield for the production of the singlet atomic fragment O(1D) has been determined in the wavelength region 306 to 327 nm for four temperatures between 227 K and 300 K. The technique of resonance enhanced multi photon ionisation (REMPI) was used to probe directly the O(1D) photolysis product. These relative measurements have been placed onto an absolute scale by the selection of a calibration point whose value has been agreed by the scientific community. The yields obtained are in good agreement with others reported during the time of the research reported in this thesis and clearly show that three mechanisms contribute to the final quantum yield. Below 310 nm, O(1D) is produced by a spin-allowed channel, above 320 nm the primary channel is a spin- forbidden one and at intermediate wavelengths photolysis of vibrationally excited ozone contributes to the O(1D) yield. Elements of the quantum yield data presented in this thesis are being included in a new recommendation for the temperature dependent O(1D) quantum yield.
Details of the dissociation kinetics, including further evidence confirming the spin-forbidden channel, is presented in time-of-flight studies of the O(1D) product. Time-of-flight profiles taken between 317 and 321 nm show evidence that, at room temperature, the O(1D) quantum yield is anti-correlated with the ozone absorption cross section. Excitation of the O2(a1Δg) co-fragment has been observed at wavelengths below 296 nm by monitoring the energies of the O(1D) formed. As the channel for the production of O2(a1Δg,andnbsp;vandnbsp;=andnbsp;1) opens, it is found that energy is preferentially partitioned into rotation of the O2 fragment rather than into translation. Initial studies on the O(1D) fragment have shown that the fragment is orbitally aligned and that the choice of REMPI transition can have a significant effect on the time-of-flight profiles and therefore on the measurements that are made from the profiles.
The time-of-flight profiles obtained by probing the O2(a1Δg) photofragment have shown that the O2(a1Δg) has an angular momentum polarisation that is J dependent, with the even J being strongly polarised and the odd J depolarised. This results in the shape of the time-of-flight profiles being a function of the REMPI laser polarisation; and the study of this behaviour has been used to confirm the assignments in highly perturbed REMPI spectra.

Advisor: Hancock, G
Measurements of the velocity-field characteristic of indium phosphide

The thesis describes measurements of the velocity-field characteristic of indium phosphide, below threshold by a direct method and above threshold by domain measurements. Comparisons, with good agreement, are made with microwave measurements, below threshold on material from the same slices, and above threshold on material with very similar properties.
A historical description of the Gunn effect and domain theory precedes a description of the structure of indium phosphide and a survey of published velocity-field calculations and measurements, showing the difference between 2- and 3-level conduction band models.
A value for the T valley deformation potential has previously been deduced from the temperature variation of low-field mobility by adding reciprocal mobilities due to different scattering processes. This method is examined and experimental results of other workers are shown consistent with a lower deformation potential than supposed.
Sub-threshold results agree closely with other, published, measurements, using various techniques. Extended to 77 K, the subthreshold method gave results agreeing reasonably with predictions for this temperature, and very well with extrapolations from other calculated and measured data.
Published high-field domain measurements made with a pointcontact probe differ greatly from others. Experiments to produce a point-contact probe and associated differentiator with a known performance, and analysis of a simple circuit model indicate that the specimen resistivity controls the probe response, necessitating different probe resistances for different material resistivities. The probe was still found fundamentally difficult to use and is suspected of causing specimen damage due to localised heating under the point.
Domain shapes measured agreed with published measurements from capacitive probes, but domain velocity was higher, giving a higher valley velocity (0.76 - 0.99 x 1O 7 cm/s). Comparison of the deduced velocity-field curve with published calculations strongly supports a 2-level transfer mechanism.

Advisor: Minakovic, B
Developing powers: modernization, economic development, and governance in Cold War Afghanistan

In the last decade, scholars have recognized economic development and modernization as crucial themes in the history of the twentieth century and the ‘global Cold War.’ Yet while historians have written lucid histories of the role of the social sciences in American foreign policy in the Third World, far less is known on the Soviet Union’s ideological and material support during the same period for countries like Egypt, India, Ethiopia, Angola, or – most prominently – Afghanistan.
This dissertation argues that the Soviet intervention in Afghanistan is best understood as the final and most costly of a series developmental interventions staged in that country during the latter half of the twentieth century by Afghans, Soviets, Americans, Germans and others. Cold War-era Afghanistan is best understood as a laboratory for ideas about the nation-state and the idea of a ‘national economy.’ One can best understand Afghanistan during that period less through a common but ahistorical ‘graveyard of empires’ narrative, and more in terms of the history of the social sciences, the state system in South and Central Asia, and the ideological changes in ideas about the state and the economy in 20th century economic thought.
Four chapters explore this theme, looking at the history of the Soviet social sciences, developmental interventions in Afghanistan prior to 1978, a case study of Soviet advisors in eastern Afghanistan, and Soviet interventions to protect Afghan women. Making use of new materials from Soviet, German, and American archives, and dozens of interviews with former Soviet advisors, this dissertation makes a new and meaningful contribution to the historical literature on the Soviet Union, Central Asia, and international history.

Keywords: international history
Afghanistan
development
central Asia
women's studies
Soviet Union
Advisor: Morrison, A
Kelly, C
The impact of prior experience on acquisition behaviour and performance

The objective of the thesis is to advance the concept of learning by explicating the mechanisms contributing to knowledge accumulation and its transfer to new situations. On the basis of 44 case studies, the framework is refined to accurately capture the unique features and outcomes of experiential knowledge in acquisitions. Feedback from the performance of prior acquisitions was found to enrich representations of action-outcome linkages and modify procedures in search and valuation. Inferential transfer though depended on similar kinds of features emerging in subsequent decisions. Outcomes therefore reflected the integration of feedback processes and similarity judgments. From the case studies, a set of hypotheses was developed and their plausibility tested, using another data set on the acquisitions of 687 managers. The research finds that the performance of prior decisions and the similarity to prior experiences materially impact behaviour. Poor performance in prior, similar acquisitions led to a reduction in subsequent risk behaviour, illustrated by the extent of risk management and by the lessening of commitment to specific transactions. The impact of performance feedback was also extant in the similarity of choice to prior experiences. The results illustrate that although feedback shapes perceptions of likelihood and expected value, similarity judgments moderate the impact of prior performance on behaviour. Given the impact on acquisition behaviour, the research also illustrates that prior experiences do not necessarily increase performance. Adaptation from prior failures was not unambiguously linked to positive returns, suggesting limitations from feedback mechanisms. Rather, the extent and similarity of acquisition experience led to a reduction in the variability of performance. By providing a framework for selecting planning procedures, greater experience tended to reduce surprises post-acquisition.

Keywords: Risk management
Escalation of commitment
Experiential knowledge
Adaptation
Similarity judgment
Performance feedback
Strategic management
Mergers &amp; acquisitions
Advisor: Angwin, D
Physiognomic and taphonomic studies in New Zealand and Australia

Measurements of surface uplift rate potentially hold the key to understanding the tectonics of mountain belts and areas of uplift. Wolfe (1993) compiled a multicharacter data set (CLAMP) of the physiognomy of woody dicotyledon leaves with a view to using it to extract climatic information from fossil floras. The limited extent of this data set, along with the anomalous behaviour of some outliers cause me to question the global relationship between physiognomy and climate which has been implicitly assumed in all analyses of the data conducted to date.
Additional data collected from native vegetation in New Zealand and Australia are compared to the CLAMP data set. These data include samples along altitudinal transects and from different forest types growing in the same climatic regime. In addition taphonomic samples were collected from lake bottom sediments and their physiognomic signals compared to those of the adjacent living vegetation.
The possibility that the relationship between climate and physiognomy is sufficiently non-linear that only local relationships should be sought is investigated. To estimate the climate at a certain flora, resemblance functions are used to select physiognomically similar sites. Estimations of climate are formed using only these sites. The power of this approach to estimate mean annual temperature, mean annual precipitation, mean growing season precipitation, and moist enthalpy is investigated using the modern sites, and varying the number of nearest neighbours and dimensions used as well as the type of ordination.
The collection of altitudinal transects has allowed the study of physiognomic change with altitude. Because these transects were collected over a very restricted area it was possible to observe this change without the superimposed effects of changing continentality and variation in latitude. In addition studies made of adjacent floras in similar climatic regimes and taphonomic studies of leaves in lacustrine sediments has allowed the beginning of a realistic assessment of possible errors in climate estimation for fossil sites.
Fossil sites examined using CLAMP and related methods are re-examined using the nearest neighbour approach.