VictorJuiz/thesis huggingface dataset:
Enacting molecular complexity : data and health in the metabonomics laboratory

In this dissertation, I examine how biological data practices enable researchers to interact with and enact biological life in statistical ways, and how this poses challenges to the use and integration of biological knowledge with clinical practices. Instead of considering data as a pre-existing cognitive representation of the world, I combine scholarship on the anthropology of science with scholarship from science and technology studies to consider data as a form of material practice. I consider, in other words, how data is intertwined with technologies, people, and values, such that data is used to make normative and naturalized claims about biology and disease.
To explore the generation, interpretation, and use of biological data, I focus on the field of “metabonomics”—the post-genomic study of metabolism—as it is carried out within the Biomolecular Medicine Laboratory (BMM) at Imperial College London. In doing so, I examine how metabonomics researchers use biochemical techniques and multivariate statistics to investigate metabolism and disease.
After providing an overview of the literature, central questions, and methodology that frame this dissertation, I examine how multivariate statistical practices are central to the historical identity and epistemic culture of metabonomics research at the BMM. From there, I demonstrate how multivariate statistics require and enable metabonomics to enact metabolism as an inherently complex entity. Consequently, I examine how researchers struggle to assign the categories of “normal” and “abnormal” to dynamic notions of metabolism and health. I then explore how the translation of metabonomics knowledge into clinical practices places value on multivariate forms and large volumes of information, eclipsing the importance of human interpretation and judgment. Finally, I examine how metabonomics research is used to develop personalized medicine, but in ways that make it difficult to address the health of individual patients.

Keywords: bioinformatics
data
metabolomics
metabolism
statistics
post-genomic
laboratory
science and technology studies
Advisor: Ulijaszek, S
Cohn, S
Reclaiming experiment: geographies of experiment and experimental geographies

This thesis investigates the injunction to experiment in the social sciences and, more specifically, geography. This is both a geography of certain ways of thinking experiment, and an exploration of how particular strands of geographical thinking are being re-imagined and reworked as experimental under the influence of ideas and practices from within and beyond the discipline. Against the backdrop of recent debates about the status of experiment, it poses a number of key questions about what it means to be experimental, how experimental practices emerge and travel, and how these processes are inflected by the organization and atmospheres of particular sites of experimentation. These questions are addressed through a form of attentive participation at four key sites: The SenseLab and the Topological Media Lab in Montreal, the Institut für Raumexperimente in Berlin, and FoAM in Brussels. Based upon these encounters, and drawing upon the work of a range of exemplary experimentalists, the thesis develops the argument that there are new spaces of experiment which are worthy of such examination as part of a renewal of experimentation within geographical thinking. As such, the thesis outlines the logics of these forms of experiment and proposes the notion of ecologies of experiment. It also speculates on the possibilities for re-imagining what constitutes a geographical experiment, foregrounding the necessity of reactivating experiment as an ongoing ethos that needs careful cultivation and tending.

Keywords: research-creation
non-representational theory
experiment
cultural geography
Advisor: McCormack, D
Whatmore, S
Inventing the market. Smith, Hegel and political theory

This thesis analyses the constructions of the market in the thought of Adam Smith and Georg Wilhelm Friedrich Hegel and their relevance for contemporary political philosophy. Combining the history of ideas with systematic analysis, it contrasts Smith’s view of the market as a benevolently designed ‘contrivance of nature’ with Hegel’s view of the market as a ‘relic of the state of nature.’ In two interpretative chapters these two constructions of the market are discussed within the contexts of Smith’s and Hegel’s thought. In three systematic chapters, the relevance of these different constructions for the problems of identity and community, social justice, and different notions and dimensions of freedom is discussed. The first of these chapters argues that the conceptualization of the labour market as a market place for human capital or as a locus for the development of a professional ethos has a deep impact on how one thinks about the relation between individual and community, cutting across the debate between liberals and communitarians. The second systematic chapter shows that the market can be seen either as an instrument for addressing issues of social justice or as an institution against which social justice needs to be realized: for Smith, who thinks that free markets reward virtue and equalize income, it is the former, whereas for Hegel, who holds that free markets lead to unpredictable results and exacerbate social differences, it is the latter. The third systematic chapter addresses the relation between different aspects of liberty and the market. It shows that the market offers both chances and risks for liberty in the sense of individual autonomy, and analyses the relations of the market to positive liberty in a political sense. The concluding chapter draws some broader methodological lessons, arguing for a closer integration of economic and political theory at a ‘less-ideal’ level.

Keywords: freedom
social justice
Smith
Hegel
capitalism
market
Advisor: Ryan, A
Philp, M
Prediction of NMR J-coupling in condensed matter

Nuclear magnetic resonance (NMR) is a popular spectroscopic method and has widespread use in many fields. Recent developments in solid-state NMR have increased interest in experiment and, alongside simultaneous developments in computational theory, have led to the field dubbed 'NMR crystallography.' This is a suite of methodologies, complementing the capabilities of other crystallographic methods in the determination of atomic structure, especially when large crystals cannot be made and when exploring materials with phenomena such as compositional, positional and dynamic disorder. NMR J-coupling is the indirect coupling between nuclear spins, which, when measured, can reveal a wealth of information about structure and bonding.
This thesis develops and applies the method of Joyce for the prediction of NMR J-coupling in condensed matter systems using plane-wave pseudopotential density-functional theory, an important requirement for efficient treatment of finite and infinite periodic systems. It describes the first-ever method for the use of ultrasoft pseudopotentials and inclusion of special relativistic effects in J-coupling prediction, allowing for the treatment of a wider range of materials systems and overall greater user friendliness, thus making the method more accessible and attractive to the wider scientific community.

Keywords: pseudopotentials
nuclear magnetic resonance
special relativity
density functional theory
Advisor: Yates, J
Evaluative language in Greek lyric and elegiac poetry and inscribed epigram to the end of the fifth century B.C.E

This dissertation is a study of the rhetorical uses of evaluative language in Greek lyric and elegiac poetry and inscribed epigram of the period from the seventh to the fifth century B.C.E. The discussion focuses on the poets' evaluations of human worth in three areas, each of which forms a separate chapter: martial valour, the relationship between physical appearance and inner virtue, and political or social values. Within each chapter, particular aspects of the subject under discussion are treated under separate headings.
Although the literary material has been treated in various ways in the past, the inclusion of inscribed epigram alongside the other literature in this case offers evidence from a related but distinct branch of poetic tradition for the development and expression of these values; divergences between the literary and the inscriptional tradition can be quite marked, as can the different approaches taken by poets of various genres within the literary material. The attempts of previous scholarship to define clear and consistent systems or codes of value represented in the poetry and to trace their development over this period have been generally unconvincing, but the poets' deployment of evaluative language does show some discernible patterns which appear to be related more to genre and poetic tradition than to the purely chronological processes of development that have been proposed by other scholars.
Theology and identity of the Egyptian Jewish diaspora in Septuagint of Isaiah

The Old Greek version of the Book of Isaiah (hereafter LXX-Is) should be studied not only as a translation but also as an interpretation reflecting the theology of the translator or translator’s community in Egypt. ‘Free’ translation in LXX-Is usually appears not to originate from any misunderstanding of the probable Hebrew Vorlage or from a different Vorlage, but deliberately and consciously. Also it is important that these Greek renderings should be dealt with in a broader context, not merely verse by verse; because the Septuagint seems to have been regarded as a religious text in itself, circulating among Jews in Egypt. The most conspicuous theme in Septuagint Isaiah is a bold declaration concerning their identity. According to this, the Jewish diaspora in Egypt is the true remnant, and their residence in Egypt should be regarded as due to God’s initiative, thus “Eisodos” instead of “Exodus” is emphasized. Such ideas may be understood as displaying an apologetic concern of the Jewish diaspora to defend their continued residence in Egypt, whereas the Bible states firmly that Jews are not to go down there. Judgments against Egypt appear more strongly than MT, and this is another expression of their identity. LXX-Is supplies a bold translation in 19:18: a temple in Egypt, called the ‘city of righteousness’. The writings of Josephus testify to the existence of the Temple of Onias in Heliopolis under the reign of Ptolemy Philometor who apparently showed great favour towards the Jews. The temple’s significance should be considered as more than a temporary shrine for local Jewish mercenaries. Rather, it aimed to be a new Jerusalem under a lawful Zadokite priest. In addition to this, LXX-Is shares some interesting and distinctive ideas with Hellenistic Jewish literature, including views on priests and sacrifice, and an attitude towards foreign kings shared by Hellenistic Jewish literature of the period. To conclude, through comparing with MT and investigating LXX-Is as it stands, this work shows that LXX-Is is not just a translation but a Hellenistic Jewish document reflecting a particular theology of at least some Jews in Egypt. LXX-Is is shown to have its place within Jewish Hellenistic literature.

Keywords: Hellenistic Jewish literature
Temple of Onias
Old Testament
Isaiah
Septuagint
Advisor: Salvesen, A
La querelle Anglaise

This dissertation offers a study of the fifteenth century French polemical treatises written by authors such as Jean de Montreuil, Jean Juvénal des Ursins, Noël de Fribois and Robert Blondel, together with an edition of perhaps the most important of these works, Pour ce que plusieurs (1464). This treatise may have been written by Guillaume Cousinot II, who had been personally involved in the events surrounding the attack upon Fougères in 1449, a subject addressed in highly partial terms by this text; moreover, Cousinot had visited the Lancastrians in exile in Scotland, which might explain how Sir John Fortescue was able to learn of Jean Juvénal's Tres crestien, tres hault, tres puissant roy (1446), and how Pource que plusieurs in turn drew upon the pamphlets of Fortescue.
The polemical texts went beyond moral and chivalric discussion of the war, to address the complex legal and historical issues underpinning the conflict. In response to the English claim to the French throne, Jean de Montreuil adopted the Salic Law, a highly dubious and problematic authority, but one that achieved great fame particularly through the influence of Pour ce que plusieurs. Similarly, the polemical writers rejected English demands for Aquitaine and Normandy in full sovereignty by arguing that no French king could alienate the sovereign rights of the crown. In the sixteenth century, both of these principles were elevated to the status of Fundamental Laws.
These texts were not intended to serve as propaganda, but were generally produced by royal officials to serve as manuals for their fellow administrators and diplomats, and perhaps also for the king and other members of the court involved in negotiations with the English. Only in exceptional circumstances were such works disseminated beyond the narrow circles of the government and court, though royal officials did draw upon them when speaking at public assemblies.
Vacuum ultraviolet discharge excited lasers

The thesis concerns experimental studies of discharge excited lasers operating in the vacuum ultraviolet (VUV) region of the spectrum.
The known molecular fluorine laser operating at 157nm, on a bound- to-bound transition of the F2 molecule was selected for initial study. As a result of the work reported here the energy per pulse was increased by a factor of five (10mJ to 50mJ) from that of earlier F2 lasers. Similary the working lifetime of the gas mixture was increased from a few shots to several thousand by the application of cryogenic gas purification techniques. These improvements have resulted in the development of a practical commercial F2 laser. The performance characteristics of the fluorine laser and their relationship to the physical mechanisms are discussed.
With the objective of achieving laser action in the 110 to 130nm region of the VUV a novel scheme is investigated. The scheme involves the production of a population inversion between the v'=1 level of the b1πu state of molecular nitrogen and high lying levels of the X1Σg ground state. The excitation of the upper laser level involves production of N2 molecules in the a1πg state by means of a pulsed discharge. Transfer of population from this intermediate 'a' state to the upper level is accomplished by absorption of radiation at 308nm from a discharge excited xenon chloride laser. The practicality of this scheme has been investigated to the extent that populations of the order of 1013 molecules per cm3 have been produced in the 'a' state and laser induced fluorescence on the 'b' to 'X' band has been observed. Under the conditions of "the present experiments the potential VUV gain is too small (10-4cm-1>/sup>) to reach laser threshold. The problems of increasing the gain to reach threshold for a practical device are discussed.

Advisor: Webb, C
Functional characterization of the teleost multiple tissue (tmt) opsin family and their role in light detection.

In addition to a central circadian clock in the suprachiasmatic nucleus (SCN), zebrafish (Danio rerio) have local clock systems in their peripheral tissues. These peripheral tissues express a complement of clock genes that can be synchronized with the 24 h light/dark cycle and thus may be entrained by light. To date, teleost multiple tissue (tmt) opsin identified from Fugu rubripes and Danio rerio is the only opsin that has been proposed as a candidate to mediate this cellular photoentrainment (Moutsaki et al., 2003). Here we report the discovery of a multigene family of tmt opsins found not only in the teleost fishes, but in vertebrates,including amphibians, birds, reptiles, and some mammals.
Phylogenetic analysis demonstrated that this gene family consists of three main classes, tmtI, tmtII and tmtIII, with each duplicating further to give two paralogues in the zebrafish genome. Their predicted amino acid sequences contain most of the characteristic features for the function of a photopigment opsin, as well as seven transmembrane segments indicative of a G protein coupled receptor (GPCR) superfamily. Significantly, reverse transcription polymerase chain reaction (RT-PCR) reveals that the tmt opsin genes in zebrafish are both temporally and spatially regulated. To investigate if these tmt photopigments mediate light-activated currents in cells, each opsin was expressed in vitro and the responses characterised by calcium imaging, whole-cell patch clamp electrophysiology, UV-Vis spectrophotometric analysis, and bioluminescence reporter assay. Collectively, these data suggest that some of the opsin photoproteins signal via Gi-type G protein pathway. Interestingly, the spectral analysis obtained shows that most tmt opsins tested are UV-sensitive when reconstituted in vitro with 11-cis and all-trans retinal, indicating an intrinsic bistable dynamics. Using site directed mutagenesis on one of the tmt opsins, tmt10, the potential spectral tuning sites involved in UV detection were tested.
As part of this study, tmt opsin cDNAs were isolated from three populations of Mexican tetra (Astyanax mexicanus): surface, Pachon and Steinhardt. This allowed for a direct comparison between the tmt opsins present in the dark adapted species (cavefish) versus those of the light adapted species (zebrafish). It is hoped that the findings from this project will contribute to our understanding of non-visual light detection in fish and the evolution of their non-image forming photoreception.

Keywords: Photopigment
Photosensory
Transduction
Multiple Tissue expression
Opsin
G protein-coupled receptor
Biological rhythms
Advisor: Hankins, MW
Geodetic observation and modelling of continental deformation in Iran and Turkey

In this thesis I use Interferometric Synthetic Aperture Radar (InSAR) and GPS geodetic observations, along with numerical models, to examine the distribution of strain, assess seismic hazard, and study the dynamics of deformation across Turkey and Iran.
I measure interseismic strain accumulation across the Ashkabad fault using InSAR, and find that atmospheric corrections using MERIS (Medium Resolution Imaging Spectrometer) data are necessary in order to retrieve the tectonic signal in the presence of large atmospheric delays. I estimate a slip rate of 5-12 mm/yr for the Ashkabad fault which is faster than previous geodetic estimates. I also attempt to validate atmospheric corrections derived from the ERA-Interim numerical weather model and find that they do not work satisfactorily for this region.
I produce InSAR-derived velocity maps for five overlapping tracks in Eastern Turkey, covering both the North Anatolian Fault (NAF) and East Anatolian Fault (EAF), and measure slip rates for the NAF and EAF of 20+/-3 mm/yr and 10+/-2 mm/yr respectively. I calculate a velocity field for Eastern Turkey from these InSAR data and a compilation of GPS data, and find that strain is mainly localised across the NAF and EAF and that there is negligible differential vertical motion across the Anatolian Plateau.
I construct a thin viscous sheet model for Iran and find that the GPS velocity field is well described by deformation of a ductile lithosphere. Contrary to previous suggestions, a rigid central Iran is not required to match the kinematics of Iranian deformation, but buoyancy forces acting in the lithosphere are found to play an important role. I develop a new method to assess slip rates and therefore seismic hazard on major faults in Iran from this continuum model.
In this thesis I have measured slip rates across three major strike-slip faults using InSAR; the first time this has been achieved for the Ashkabad fault and the EAF. I have demonstrated the importance of atmospheric correction for these results, and have shown that Iran deforms as a continuous medium.

Keywords: active tectonics
interseismic
earthquakes
geodesy
geophysics
Middle East
InSAR
Advisor: Parsons, B
England, P
Wright, T
Theory of meaning

This thesis examines Michael Dummett's form of a theory of meaning for natural language. I argue that Dummett's extension of Frege's formal techniques to the semantics of natural language, based on the categories of sense, force and tone, and the centrality of truth, provides an inadequate theoretical account of linguistic competence.
Part One examines the celebrated sense-force distinction. Dummett's schematic model of force-indicators and sentence-radicals ignores or mishandles semantic features of numerous ordinary expressions and linguistic forms. In many cases the distinction is blurred, and worse, univocity is sacrificed. A chief culprit is the restrictive nature of true-false polarity. The principal thesis that force attaches only to complete sentences is compromised, and Dummett's handling of force-indication fails to account for the distinct elements of word-order, verbal mood and intonation contour.
In Part Two I attempt to distinguish genuine varieties of tone, inspecting the different differences among e.g., 'lift'-'elevator', 'cheekbone'-'zygoma', 'ere'- 'before 1 , 'Chinese'-'Chink', 'and'-'but 1 and others, as well as the contribution of adverbs like 'still' and 'almost'. Both Frege and Dummett consign to this general category many expressions which do not belong; for some other cases, tonality is a matter of use, but not meaning. Minimally, the sense-tone boundary needs redrawing. More accurately, the notion of sense, identified with the determination of truth-conditions, must either be broadened to incorporate some non-truth-conditional aspects of word-meaning, or else be replaced by another term possessing the broader role.
In Part Three a single general characterization of meaning is advanced which accommodates both individual expressions and linguistic forms. I support the idea that a formulation in terms of a primitive notion of 'making things out to be a certain way', aligned with the poles of correctness and incorrectness, captures in a systematic way the expressions and forms which proved resistant to Dummett's canonical form of explanation.