VictorJuiz/thesis huggingface dataset:
Diversity and competitive interactions in experimentally evolved bacterial populations
Keywords: experimental evolution
Biodiversity
competition

Laboratory bacterial populations provide ideal opportunities to experimentally test theories in ecology and evolutionary biology. I used a model laboratory microbial system, Pseudomonas fluorescens SBW25, to address an array of questions on the origin, maintenance, and functional role of biodiversity, and the evolution of biotic interactions. My thesis reports experiments with the following conclusions. (1) The extent of diversification in P. fluorescens populations is not affected by the presence of an interspecific competitor P. putida, although the early stage of the diversification in one environment (spatially homogeneous environment) could be speeded up by the competitor. (2) Niche and neutral mechanisms simultaneously contribute to the maintenance of phenotypic diversity in P. fluorescens populations; but the operation of niche processes does not lead to a positive effect of biodiversity on ecosystem functioning. (3) The competitive interactions among bacterial phenotypes are generally transitive, and competitive hierarchies inferred from pair-wise competition are fairly consistent to those from multi-species competition. (4) The niche complementarity and selection effects evaluated by random assembly biodiversity experiments can be used to predict the functional consequences of particular non-random species extinction scenarios. (5) P. fluorescens does not show an evolutionary trade-off in using several carbon substrates (glucose, galactose and trehalose), and evolution in environments containing these resources results in imperfect generalists; migration among populations may speed up fitness evolution of some generalists. (6) Biofilm formation at the air-broth interface by wrinkly spreader phenotypes in P. fluorescens is a cooperative behaviour which is costly to individuals but benefits the group; this behaviour could be exploited by smooth morph phenotypes. The cooperators and cheats in this system show reciprocal antagonistic coevolution in resistance and cheating performance.
Control and manipulation of cold atoms in optical tweezers
Keywords: Quantum Optics
Quantum Information Processing

The ability to address and manipulate individual information carriers in a deterministic, coherent, and scalable manner is a central theme in quantum information processing. Neutral atoms trapped by laser light are amongst the most promising candidates for storing and processing information in a quantum computer or simulator, so a scalable and flexible scheme for their control and manipulation is paramount.
This thesis demonstrates a fast and versatile method to address and dynamically control the position (the motional degrees of freedom) of neutral atoms trapped in optical tweezers. The tweezers are generated by using the direct image of a Spatial Light Modulator (SLM) which can control and shape a large number of optical dipole-force traps. Trapped atoms adapt to any change in the potential landscape, such that one can re-arrange and randomly access individual sites within atom-trap arrays. A diffraction limited imaging system is used to map the intensity distribution of the SLM onto a cloud of cold atoms captured and cooled using a Magneto Optical Surface Trap (MOST).
From German to Yiddish: adaptation strategies in the Kuhbukh and the Siben weisen mainster bichel
Keywords: Seven Sages of Rome
Book of Cows
Siben weisen mainster bichel
Kuhbukh
adaptation
Early modern

In light of often derogatory and unqualified assessments of Yiddish literature adapted from German narrative models, this thesis will propose a different approach to viewing these adaptations. Building on methodologies and frameworks of analyses developed in contemporary medieval scholarship, this thesis pushes for a re-assessment of this literature and suggests a flexible model of adaptation that views adaptation as a creative interaction between two texts.
In response to unsatisfactory approaches to judaizing strategies found in Yiddish texts adapted from German literature, this thesis also suggests a different approach. Judaizing processes can either be part of overall processes of adaptation aimed at coding the text as Jewish within an overarching framework of renewed cultural specificity; or, they can function as translation principles by achieving equivalence with the original model.
To illustrate both ends of this scale of adaptation, this thesis centres on two early modern Yiddish texts: the Kuhbukh (Verona, 1595) and the Siben weisen mainster bichel (Basel, 1602). The four chapters at the core of this thesis develop and apply extensive frameworks of literary analyses which enable us to rigorously assess the differing levels of adaptations (translation and Wiedererzählen) of both texts.
This thesis pushes for a future reassessment of other popular Yiddish narratives adapted from German models. This could ideally be achieved by a positioning of each individual Yiddish text based on German narratives on the proposed scale of adaptation. This should be backed by verifiable methodologies and analyses devoid of unjustifiably dismissive opinions. This would consequently move scholarship towards structured, methodological analyses of early Yiddish secular literature.
The use of online collaboration tools for employee volunteering: a case study of IBM’s CSC programme
Keywords: online collaboration
e-learning
IBM

This research study intends to find out about the use of online collaboration tools in supporting knowledge workers for the practice of employee volunteering. Online collaboration tools refer to the web-based technologies such as popular Web 2.0 tools like blogs or wikis and traditional online tools such as instant messenger, discussion forums, online chats and e-mail used by several individuals with the aim of achieving a common goal.
The employee volunteering program- called Corporate Service Corps (CSC) - is an employee volunteering program in which the IBM employees tackle the economic and societal issues of the less developed countries they have been sent to while getting involved in project-based learning activities. This study provides an insight into how online engagement enabled the continuation of non-formal workplace learning practices such as volunteering and opened up possibilities for new ways to contribute to the learning process of employees. When it comes to online communities there is a mixture of entanglements, partnerships, negotiations and resistances between these tools and human actors. This research study explores how online communities are created by employee volunteers and also provides an understanding of non-formal learning practices within such fluid settings; important issues for organizations interested in non-formal learning practices of their employees are also raised.
Today’s workplace settings are in constant need of recurrent learning processes interwoven with daily tasks on digital spaces. However, these digital spaces are not devoid of any issues and hence suggest the need for employees to be conscious of the emerging issues. The results from the case study are analysed by using participatory design methods in order to contribute to the understanding of the use of technology as both a single and collective experience.
This research identified the specific benefits of online collaboration tools, and explored how their usage has been appropriated by employee volunteers for their practice of volunteering and how they influenced the process of their meaning-making. By doing so, it raised an awareness of the digital tools that provide collections of traits through which individuals can get involved in non-formal learning practices by having digital interactions with others.
Strategy as the intentional structuration of practice: the translation of formal strategies into strategies-in-practice
Keywords: business enterprises
strategy-as-practice
decision making
management case studies
knowledge management

Acknowledging the difficulties of achieving effective strategic management in practice, this thesis investigates how formal strategies quite often succeed in conditioning organisational actions even in firms such as professional service firms, which may lack effective measures for coercing action and which often depend on distributed decision-making. The fundamental question posed in this investigation is: what are the social processes that make strategies work?
This thesis addresses that question by contributing to our understanding of strategy realisation as a continuing process of translating formal strategies into ‘strategies-in-practice’, i.e. the situated performance of strategies through choices, actions, and practices pertaining to the selection and accomplishment of concrete assignments. The thesis investigates this translation process in three small professional service firms, in which the responsibility for enacting the strategies lies with autonomous practitioners, making centralised strategy realisation difficult.
Searching for integration rather than further fragmentation of different strands of strategy research, the thesis make use of Porterian activity systems theory, Giddens’ structuration theory, Wittgensteinian theory of rule-following, Searlean theory of intentionality, and the strategy-as-practice approach, in order to understand the translation process as the intentional structuration of practice.
The thesis reports two main contributions, the first addressing a gap in strategy re-search, the second contradicting prevailing theories. The first contribution is an outline of a theory of strategy translation: how formal strategies are translated into strategies-in-practice, coping with insoluble strategic dilemmas, and achieving maintenance of strategic position and strategies-in-practice under pressure for unwanted change. Good strategies-in-practice are as much about managing dilemmas as about eliminating them.
Second, in contrast to prevailing strategic positioning theory and generic strategies, this study documents the potential benefits of straddling strategically distinct services within a single activity system, in terms of: learning opportunities; work variation; better opportunities for attracting, developing, and retaining talented people; the possibilities of capitalising on client relationships; and the dynamics of routinisation of once-novel services.
Structure and reactivity of transition metal clusters
Keywords: catalysis
cluster
transition metal

A range of computational and experimental techniques have been applied to the study of four metal cluster systems.
Decorated rhodium clusters RhnOm(N2O)+ (n=4−8,m=0−2) have been investigated both experimentally by IR-MPD and computationally using DFT. The effect of cluster size as well as oxygen coverage on the spectroscopy of the N2O bend are analyzed. The infrared-induced decomposition of N2O on RhnO+m is observed on all cluster sizes, with marked differences as a function of size and oxygen coverage, particularly in the case of Rh5(N2O)+.
The oxidation of CO was studied on the surface of small platinum cluster cations PtnO+m(n=3−7,m= 2,4) by IR-MPD at 400 – 2100cm−1. Spectroscopically, oxygen is found to be bound both dissociatively and molecularly on the cluster surface, while the CO band is found to red shift in cluster size, and blue shift with oxygen coverage. Oxidation of CO proceeds on all cluster sizes, with a constant branching ratio of 40% : 60% . DFT calculations identified key stationary points and barriers on the Pt4O2CO+ reaction pathway.
The one-colour Ta 2 photodissociation is studied by photoionization and VMI in the range 23500 – 24000cm−1 , finding clear evidence of a fragmentation process producing Ta , which is interpreted as fragmentation of cationic Ta+2at the two photon level. A majority of the observed channels produce either atomic (Ta(4F3/2)) or cationic (Ta+(5F1)) ground state. An improved value for the dissociation energy D0(Ta+2) is obtained, in agreement with computational predictions. The anisotropies observed show weak evidence of a perpendicular transition being involved in the photodissociation process.
Finally, the photodissociation dynamics of Cu2 are studied by spectroscopy in the range 36000 – 38200cm−1 as well as VMI. Clear evidence for resonant photolysis of Cu2 is obtained, as a result of both direct dissociation of the Cu+2 2Π ion state as well as dissociation of doubly excited Cu2 states, which leads to a determination of dimer dissociation energies. Finally, the production of Cu+2 is interpreted as evidence of photolysis of Cu3, from which a Cu3 dissociation energy is derived.
Predation and the evolution of multicellularity
Keywords: group size
Chlorophyceae
group formation
induced defense
multicellularity

The first step in the major evolutionary transition to multicellularity involves single cells forming a group. Why do cells form a group? Studies have shown that colony formation provides a benefit against predation. However, it is not well known whether this response is generic, or specific to certain prey-predator systems. We sought to assess this by measuring colony formation in nine 'algal-putative predator' combinations; the Chlorophyte algae Chlorella vulgaris, Chlorella sorokiniana and Scenedesmus obliquus as prey, and the flagellate Ochromonas spp., the ciliate Tetrahymena thermophila and the crustacean Daphnia magna as putative predators. We found that colony formation is a generic response of the algae C. sorokiniana, C. vulgaris and S. obliquus to predation by Ochromonas spp., T. thermophila or D. magna. Notably, the algae formed colonies regardless of whether the putative predator grazed upon the algae, indicating that predation by itself is not always a prerequisite for colony formation, but this response may have evolved in the algae as a defensive mechanism against potential predation. In six combinations, colonies could not be ingested by the predator, suggesting that colonies have a 'size benefit' against predation. These results outline the importance of predation as a generic factor driving colony formation and help enhance our understanding of the benefits and costs involved in colony formation, the first step in the evolution of multicellularity.
Supramolecular control of synthesis and electronic structure of porphyrin oligomers
Keywords: Self-Assembly
pi-Conjugation
OLED
SAXS
Template
Porphyrin
Supramolecular Cooperativity

The work described in this thesis demonstrates the use of supramolecular chemistry in the template-directed synthesis of porphyrin nanorings and as a tool to control conformation and topology of π-conjugated porphyrin oligomers. Particular emphasis is placed on changes to the electronic structure of these oligomers depending on their conformation.
Chapter 1 gives an overview of π-conjugated porphyrin oligomers and conjugated macrocycles in general, followed by an introduction into supramolecular cooperativity and small angle X-ray scattering in solution.
Chapter 2 describes advances in the synthesis, solution structure elucidation and optoelectronic properties of a fully conjugated cyclic porphyrin hexamer. The high rigidity and symmetry of this nanoring as well as its bent π-system lead to a significant decrease in its HOMO-LUMO gap. The resulting near-infrared emission was exploited in the fabrication of light emitting diodes, demonstrating the use of a bent topology for minimizing aggregation in thin films.
The synthesis of a [12]porphyrin nanoring using a hexadentate template is presented in Chapter 3. The concept of Vernier templating is introduced as a general strategy for the synthesis of large monodisperse macrocycles. The nanoring is characterized and its cooperative binding to two template molecules is studied. In Chapter 4 a bidentate ligand is used in the cooperative formation of a sandwich complex beween two nanorings.
Chapter 5 provides an analysis of the rigidity of the butadiyne linked porphyrin oligomers used throughout this thesis. A linear chain is significantly more flexible in solution than on a surface where it is confined within two dimensions. Analysis of the persistence length indicates that a porphyrin nanoring with more than around 20 units would not be significantly strained.
The supramolecular binding of linear porphyrin oligomers to carbon nanotubes is analyzed in Chapter 6. The binding strength increases sharply with oligomer length and binding is strongest with (8,6) and (7,5) tubes. The energy level alignment in these porphyrin CNT complexes appears to be favorable for an application in photovoltaics.
In Chapter 7 bisamidine-carboxylate salt bridges together with zinc-nitrogen coordination chemistry are used to access a variety of topologies in assemblies based on carboxylic acid functionalized porphyrin dimers.
A framework for processing correlated probabilistic data
Keywords: uncertain data
clustering
classification
correlations
probability computation
data mining
machine learning
probabilistic data
ENFrame

The amount of digitally-born data has surged in recent years. In many scenarios, this data is inherently uncertain (or: probabilistic), such as data originating from sensor networks, image and voice recognition, location detection, and automated web data extraction. Probabilistic data requires novel and different approaches to data mining and analysis, which explicitly account for the uncertainty and the correlations therein.
This thesis introduces ENFrame: a framework for processing and mining correlated probabilistic data. Using this framework, it is possible to express both traditional and novel algorithms for data analysis in a special user language, without having to explicitly address the uncertainty of the data on which the algorithms operate. The framework will subsequently execute the algorithm on the probabilistic input, and perform exact or approximate parallel probability computation. During the probability computation, correlations and provenance are succinctly encoded using probabilistic events.
This thesis contains novel contributions in several directions. An expressive user language – a subset of Python – is introduced, which allows a programmer to implement algorithms for probabilistic data without requiring knowledge of the underlying probabilistic model. Furthermore, an event language is presented, which is used for the probabilistic interpretation of the user program. The event language can succinctly encode arbitrary correlations using events, which are the probabilistic counterparts of deterministic user program variables. These highly interconnected events are stored in an event network, a probabilistic interpretation of the original user program. Multiple techniques for exact and approximate probability computation (with error guarantees) of such event networks are presented, as well as techniques for parallel computation.
Adaptations of multiple existing data mining algorithms are shown to work in the framework, and are subsequently subjected to an extensive experimental evaluation. Additionally, a use-case is presented in which a probabilistic adaptation of a clustering algorithm is used to predict faults in energy distribution networks. Lastly, this thesis presents techniques for integrating a number of different probabilistic data formalisms for use in this framework and in other applications.
Poverty dynamics: childhood experience on a low income
Keywords: British Household Panel Survey
quantitative
qualitative
child poverty

The UK government has pledged to end child poverty by 2020. It is not known how far the measure of child poverty used by the government corresponds to differences in children’s experiences. Qualitative research on poverty has not generally been informed by the insights of dynamic research, which investigates duration, timing and transitions, among other temporal topics. Qualitative and quantitative methods have not generally been combined in social policy research on poverty, which limits the explanatory power of both. The thesis presents an analysis of the correspondence or lack of correspondence between qualitative and quantitative research on child poverty as a temporal experience.
Semi-structured life history interviews were conducted with 15-21 year olds in Britain with experience of child poverty in the period 1997-2001. These were analysed alongside secondary analysis of the British Household Panel Survey (1991-2005). The qualitative respondents lived in households which took part in the survey, so there is a direct link between the two methods.
The assumptions, methods and findings of dynamic poverty research are in general found to be a simplified and decontexualised version, rather than a misrepresentation of, the qualitative findings. Time formed an important part of the experience of poverty for children. It was not possible to fully match together exits from poverty with perceived improvements in circumstances, and entries into poverty with perceived deteriorations in circumstances, though this was partly due to limited recall and lack of contemporaneous knowledge. Nor were these changes clearly placed in time by respondents, in terms of duration and timing. Although most respondents did not explicitly engage with the idea of poverty as a personal experience, poverty-like accounts of disadvantage and difference were found in the accounts of all respondents. Thus, there is evidence for and against the way child poverty is currently measured.
Structural studies of a membrane embedded chloride channel from E.Coli, a prokaryotic homologue of ClC channels
Keywords: prokaryote
ion channel
CLC
purification
Chloride channel
membrane protein
X-ray crystallography
structure

The ClC family of chloride channels are found throughout the eukaryotes and homologues are found among the prokaryotes. There are nine ClC chloride channels found in mammals that are expressed either ubiquitously or in specific tissues. They have a role in a broad spectrum of cellular functions, ranging from the control of electrical excitability of neurons and the maintenance of the balance of charge required in the acidification of organelles, to the regulation of cell volume. The physiological importance of these channels is often demonstrated by disease causing mutations. Mutations in ClC chloride channels cause myotonias, Becker’s Disease and have been implicated in the spread of cancer. The structural information on members of the ClC family is extremely limited. For this reason ClC prokaryotic homologues, ecClC1 and ecClC2 from E.coli, were cloned and expressed in the hope that this system would produce sufficient amounts of protein to grow crystals in order to obtain three-dimensional information. This information will provide a detailed mechanism of chloride conduction and molecular architecture of the channel necessary for the further physiological and pharmacological characterisation of this important family of chloride channels. The E.coli ClC chloride channel ecClC was cloned from E.coli genomic DNA and overexpressed in E.coli. The recombinant protein was purified from the E.coli membranes using detergents. Metal affinity and size exclusion chromatography were used to purify the protein to near homogeneity. Crystals of ecClC2 have been grown that diffract to 4Å and structural analysis is underway. This thesis describes the development of the purification protocol, the crystallisation of the protein and the preliminary analysis of the X-ray diffraction data.