VictorJuiz/thesis huggingface dataset:
Implied licences in copyright law
Keywords: Copyright Law
Implied License
Implied Licence

Copyright licences can be implied when the doing of a restricted act is covered neither by the express licence of the copyright owner, nor by one of the statutory limitations and exceptions. The manner in which copyright licences are implied, therefore, holds the key to broadening the scope of permissible acts. In contrast to the rigidity of statutory limitations and exceptions, implied licences are more malleable in being able to respond to a diverse set of circumstances, as the need arises. Thus, implied licences can serve as a flexible and targeted mechanism to balance competing interests, including those of copyright owners and content users, especially in today’s dynamic technological environment. However, implication as a process is contentious, and there are no established rules for implying a licence. Implication of a copyright licence is even more complicated because the conceptualisation of a copyright licence is unsatisfactory. The resulting uncertainty has prevented implied licences from being embraced more readily by the courts. The objective of this thesis is, therefore, firstly, to reconceptualise a copyright licence that is broad enough to accommodate the diverse circumstances in which copyright licences arise, and certain enough to assist in finding their constituents; secondly, to propose frameworks for implying copyright licences in a methodical and transparent manner, based on three sources: the consent of the copyright owner; an established custom; and state intervention to achieve public policy goals. The frameworks are also customised differently for implied bare and implied contractual licences. The thesis demonstrates the robustness of these frameworks by rationalising them with the existing case law. Underscoring the contemporary relevance of implied licences, in conclusion, the thesis tests and validates the frameworks in relation to three essential and ubiquitous functions on the internet – browsing, hyperlinking and indexing.
Omnifarious octocoral observations: ecology and genetics of octocoral communities from Útila, Bay Islands, Honduras
Keywords: ALG11
diversity
mtmuts
octocoral
parasite
coral
ecology
Utila
habitat
host
COI
flamingo tongue snail
symbiosis
Cyphoma gibbous
phylogenetics
Caribbean
genetics
molecular
Mesoamerican Barrier Reef
biodiversity

The Oxford English Dictionary defines 'omnifarious' as 'comprising or relating to all sorts or varieties', which quite accurately captures the very nature of octocorals and this thesis. The research reported here, aims to describe undocumented communities of coral reef organisms – the octocorals – which are an emergent dominant component within their threatened ecosystem of the Caribbean. Within the last four decades, coral reefs worldwide have experienced a precipitous plunge in many ecosystem services they provide, and most notably in the Caribbean. The foundation to reef resilience is structured on the ecosystem’s ability to repair and restructure itself in the face of environmental shifts. These intricately complex strategies of resilience depend on repair mechanisms provided by a source of biodiversity, much of which remains poorly understood. This work explores many facets of the functioning within this potential future coral reef ecosystem. These reports are one of the most significant contributions to documenting and describing octocoral biodiversity (e.g. species, genetic, and community diversity) of the wider ecoregion of the Mesoamerican Barrier Reef System within the last three decades.
Lanthanide architectures, rotaxanes and responsive d-f assemblies
Keywords: supramolecular chemistry
click-chemistry
lanthanides
luminescence

This work describes the use of copper catalysed "Click" chemistry in the synthesis of lanthanide containing compounds and outlines the application of the products in modulation of luminescence, anion sensing, bioconjugation and multiemissive probes.
Chapter one discusses the fundamental properties of lanthanides with a focus on luminescence and magnetism. A brief literature review on the use of emissive lanthanide probes for sensing application is given. The chapter concludes with an overview on "click" chemistry and its use in the design of lanthanide containing architectures.
A redox switchable luminescent lanthanide complex using a ferrocene group as antenna is described in chapter 2. Insights into the mechanism of modulation of the luminescence signal are given. Other complexes containing redox active aryl chromophores were prepared and their luminescence properties elucidated.
In chapter three, a lanthanide complex is coupled with a rotaxane by Cu(I) "click" reaction. A detailed study of the anion sensing ability of this supramolecular structure follows.
Chapter 4 describes the synthesis of orthogonally functionalised synthons containing azide and alkyne groups that are amenable to form macrocyclic structures upon Cu(I) "click" reaction.
Chapter 5 describes the preparation and study of a novel class of lanthanide complexes containing an appended azide group, and their luminescence properties are studied. The chapter continues with the description of heterobimetallic f-f’ complexes prepared using Cu(I) "click" chemistry.
Chapter six describes the synthesis of lanthanide bioconjugates able to target the dopamine transporter (DAT) protein.
Chapter seven delineates the overarching conclusions from the thesis and possible future work in the field, while chapter eight provides experimental procedures.
Ecology and sustainability of the marine ornamental trade in Puerto Rico
Keywords: socio-economics
coral reef
Puerto Rico
aquarium trade
tropical fish

The marine ornamental fishery (MOF), in which fish and invertebrates are harvested for the live aquarium trade, has been growing in the last years. It is a worldwide market where species are mainly harvested directly from coral reefs in tropical countries. In the island of Puerto Rico, in the US Caribbean, resource managers have little information about the impact of this harvest on the stock populations of the species in the trade. Due to concern about the potential for over-exploitation of the fishery, a regulation was passed in 2004 limiting the permitted species to be harvested and exported. This action caused significant conflict with ornamental fishers and exporters. In order to better manage the resource, more precise ecological and market information was needed, as well as a regulation that more accurately reflected the status of the resource. This study analyzed the marine ornamental trade in Puerto Rico, in order to provide baseline information and public policy recommendations. It evaluated management needs, enforcement, fishers' perspectives and practices, market forces, ecological assessment of the species, as well as explored a management tool for the commercial (edible species) fishery involving the ornamental trade.
The findings of the study are split into two broad topics, a) socio-economics and b) ecology. a) The number of dedicated ornamental fishers on the island is quite small, possibly allowing for the trade to become a seasonal alternative to commercial fishers during closed seasons for edible species. Certifications that promote correct harvesting and handling of the species were found to be of interest to fishermen and managers. b) Reef surveys of fish and invertebrates around Puerto Rico found associations of fish species with habitat characteristics including depth and rugosity. Fish and invertebrate richness and abundance did not vary markedly between different sites and regions around the island, and no evidence could be detected of ornamental fishing impacts. It is suggested that more species of fish could be added to the permitted species list, without damaging their population densities. From both ecological and market perspectives, MOF in Puerto Rico is a viable and sustainable small industry that could be expanded to benefit local people and international traders alike.
Investigating the psychological factors associated with obesity
Keywords: attachment
cognition
psychology
BMI
emotion regulation

Obesity is one of the most serious public health challenges of the 21st century, associated with a range of adverse physical, psychological, social and economic consequences. The aetiology of obesity is complex; however, the psychological factors associated with overweight and obesity remain poorly understood.
The first paper critically appraises evidence for three of the most developed psychological theories of obesity. Based on these findings, literature from the fields of emotion regulation and attachment are reviewed, and a novel developmental theory of obesity based on an integration of these theoretical constructs is proposed. Recommendations for future research based on a theoretical framework of emotion regulation are made, and implications for clinical practice including a focus on enhancing caregiver sensitivity are highlighted.
The second paper explores the applicability of an established cognitive model of Bulimia Nervosa (BN) and binge eating to an overweight and obese sample. Findings support the relevance of cognitive aspects of the model in an overweight and obese sample, and highlight the potential role of early attachment relationships in the formation of cognitions that make an individual vulnerable to overweight and obesity in later life. Theoretical and clinical implications based on the established cognitive model are considered. Limitations include reliance on self-report and the correlational nature of analyses used. Recommendations for future research with larger, more representative samples to address these limitations are made.
Overall, this dissertation makes a unique contribution to the psychological understanding of overweight and obesity, which has the potential to enhance treatment outcomes and suggests useful avenues for further research.
A compact borehole, thermal-infrared radiometer and infrared reflectometer for the characterization of subsurface habitability and presence of water ice on Mars
Keywords: NIR reflectometer
Mars Technologies
Thermal IR Radiometer

One of the most important steps in the search for life on Mars is to determine if a specific sub-surface location it is "habitable", or that it provides the conditions and requirements to support life as we know it. In this thesis, I present a miniature, thermal-IR radiometer and reflectometer designed to determine temperature, the presence of water ice, and the discrimination of minerals, all necessary for a habitable environment.
A dual use detector was selected for the thermal and five reflectance channels. The IR source is provided by five LEDs. These components were embedded in a thermally controlled aluminium block. Integrated electronics provided signal amplification and demodulation. This device will be suitable for drilling applications with less than 25 mm diameter boreholes and with limited available power (&LT;5watts).
Thermal testing was within a simulated borehole mounted in a thermal vacuum chamber. The results were compared to a theoretical model of the expected temperature. The maximum temperature error between predicted and measured was 0.21 K (&Tilde;0.08%). The total RMS error of all sources were calculated to be &LT;3%.
Reflectance testing in all five channels included a variety of minerals and a two point calibration method. The results were compared to the predicted reflectance values for the samples. The results of the reflectance channel testing demonstrated that the measured values matched the predicted values with a 2.5% measured error. The total RMS error was 6.1%.
Detection and discrimination of water ice and hydrated minerals included a non-linear mixing model and/or testing. The model predicted that water ice mixed in a pyroxene mineral matrix can be detected and discriminated from 5% to 60% concentration by weight. Testing with a hydrated mineral mixed within a non-hydrated mineral matrix demonstrated that the measured result matched the predicted result from 5-45% concentration by weight.
Video camera monitoring to detect changes in haemodynamics
Keywords: Patient monitoring
Signal processing

Patients in hospital can be prone to sudden, life-threatening changes in their cardiovascular state. Haemodynamic parameters such as blood pressure, pulse transit time (PTT) and perfusion can be monitored in clinical situations to identify these changes as early as possible. Continuous blood pressure is usually monitored using a catheter placed into a major artery, but this is invasive and involves risk to the patient. In the last decade, the field of non-contact vital sign monitoring has emerged, with growing evidence that the remote photoplethysmogram (rPPG) signal can be used to estimate vital signs using video cameras. If the analysis of the rPPG signal can be expanded to include the estimation of haemodynamic parameters, it could result in methods for the continuous, non-contact monitoring of a subject's haemodynamic state.
In a physiology study, a series of video recordings were made of 43 healthy volunteers. The subjects sat in a purpose-built chamber, and the composition of the air was carefully adjusted to cause the subjects to experience large, controlled changes in blood oxygen levels. To validate the video camera algorithms, reference data were also collected. Along with the volunteer study, a clinical study was performed to acquire data in a challenging clinical environment. Data were collected from patients on haemodialysis in the Renal Unit, a population likely to experience sudden changes in haemodynamics.
The reference data from the Renal Unit study were analysed to determine the extent to which PTT and mean arterial pressure (MAP) are related. The correlation coefficients and linear fits were found on a global and a per-subject basis. In addition, the video recordings from the Physiology study were processed to derive rPPG signals, and these signals were analysed to obtain estimates for PTT. Local rPPG signals were also derived for different regions of interest, and the waveforms were analysed using a novel application of the technique of signal averaging to produce spatial maps of perfusion and blood flow.
The correlation between conventionally measured PTT and MAP was found to be weaker in the haemodialysis population than has been shown elsewhere in the literature, except for a sub-set of patients. The results of the video analysis showed that PTT could be estimated robustly and consistently, although direct validation of these estimates was not possible because of the different method used to calculate the reference PTT. For most subjects, the spatial mapping methods produced robust maps that were consistent over time. These results suggest that it is possible to detect changes in haemodynamics using a video camera, and that this could have applications in healthcare, providing that challenges such as subject movement and clinical validation can be overcome.
Algorithms and computer code for ab initio path integral molecular dynamics simulations
Keywords: AIPIMD
Constant pressure simulations
density functional theory
PIMD

This thesis presents i-PI, a new path integral molecular dynamics code designed to capture nuclear quantum effects in ab initio electronic structure calculations of condensed phase systems. This software has an implementation of estimators used to calculate a wide range of static and dynamical properties and of state-of-the-art techniques used to increase the computational efficiency of path integral simulations. i-PI has been designed in a highly modular fashion, to ensure that it is as simple as possible to develop and implement new algorithms to keep up with the research frontier, and so that users can take maximum advantage of the numerous electronic structure programs which are freely available without needing to rewrite large amounts of code.
Among the functionality of the i-PI code is a novel integrator for constant pressure dynamics, which is used to investigate the properties of liquid water at 750 K and 10 GPa, and efficient estimators for the calculation of single particle momentum distri- butions, which are used to study the properties of solid and liquid ammonia. These show respectively that i-PI can be used to make predictions about systems which are both difficult to study experimentally and highly non-classical in nature, and that it can illustrate the relative advantages and disadvantages of different theoretical methods and their ability to reproduce experimental data.
The impact of HLA-driven escape mutation on viral replicative capacity and immune control in HIV infection
Keywords: HLA-B*81:01
HLA-B*52:01
CTL response
viral replicative capacity
escape mutation
HLA-B*27:05
HLA-B*40:01
HIV
cellular immunity
HLA footprint
compensatory mutation
Gag

Despite the introduction of antiretroviral therapy, the HIV/HIV epidemic remains an unsolved global health problem. Amongst all the host defence mechanisms, HLA class I molecules have shown the strongest genetic association with delayed disease progression, in particular HLA-B alleles. Numerous studies have shown that the HLAmediated CD8+ T cell responses play a central role in the immune control of HIV. Yet our understanding of HLA-mediated immune control of HIV remains incomplete, even when considering the best-defined epitopes restricted by the protective HLA alleles at a population level.
The studies I have conducted and describe herein focus on two well-charaterised protective HLA-B molecules, HLA-B*81:01 and HLA-B*27:05; a third protective molecule, HLA-B*52:01, that has not been well-studied hitherto; and finally the most prevalent HLAB allele in many Asian populations such as Taiwan, HLA-B*40:01, which has an apparently neutral effect on viral replication. This thesis is centred on the Gag-specific immune response, since previous studies have shown the benefits of CD8+ T-cell responses targeting this conserved and immunogenic region of the HIV proteome, in particular the p24 capsid protein. I have investigated here HLA footprints driven by CD8+ T-cell pressure on HIV that are evident in the viral sequences of individuals expressing these HLA molecules. These footprints include novel escape and putative compensatory mutations. The impact of these variants on viral replicative capacity (VRC) and on HIV disease outcome clinical outcomes was examined via fitness assays. These studies identified several escape mutations that effectively cripple HIV. The distinct compensatory pathways available to the virus to mitigate the fitness cost of particular escape mutations were evaluated. In the course of these analyses I have demonstrated the critical influence of the viral backbone, including HIV clade, in combination with particular viral variants, on VRC. Computational modelling analysis has been applied to facilitate understanding of the mechanism by which certain mutants affect the stability of interactions between HLA and viral capsid protein. This thesis offers novel insights into immune control of the key HIV subtypes – B- and C-clade – and of the most severely affected populations – in Africa (South Africa) and Asia (India and Taiwan) – within the global epidemic. This work helps to better define the viral mutation landscape that is essential both for future vaccines designed to corner the virus, and for successful HIV cure strategies.
Investigating resistance of glioblastoma multiforme to radiotherapy and chemotherapy
Keywords: Temozolomide
CD24
Radio-resistance
MGMT
Glioblastoma multiforme
Radiation
IGF-1R
Chemo-resistance

Glioblastoma multiforme (GBM) is the most common and aggressive type of brain tumour. Despite treatment with surgery, radiotherapy and temozolomide (TMZ) chemotherapy, patient survival remains poor, suggesting that GBM cells evade and resist these therapies. The insulin-like growth factor 1 receptor (IGF-1R) is a receptor tyrosine kinase that signals towards cellular survival, proliferation and motility. Previous work from our laboratory showed that IGF-1R inhibition sensitises other tumour types to ionising radiation (IR) and TMZ. The first aim of this project was to assess IGF-1R expression in brain tumour tissue microarrays by immunohistochemistry. IGF-1R was found to be upregulated in adult and paediatric tumours relative to normal brain. In paediatric brain tumour patients, higher IGF-1R expression was found to associate with reduced patient survival, but no association was observed for adult brain tumour patients. The second aim sought to assess the effect of IGF-1R inhibition on the sensitivities of GBM cell lines to IR and TMZ. Adult and paediatric GBM cells showed varied expression and activation of IGF-1R and downstream signalling components. Use of two IGF-1R axis inhibitors showed that paediatric, but not adult GBM cells were sensitive to IGF-1R inhibition. In addition, there was evidence that IGF-1R inhibition sensitised paediatric GBM cells to IR. These results suggest that the IGF-1R could be an important target in paediatric GBM. However, sensitisation to TMZ was not observed. The third aim of this project was to assess the effects of repeated TMZ or IR treatment on adult GBM cells in order to identify mediators of treatment resistance. Repeated treatment with TMZ allowed previously sensitive cells that lacked O6-alkylguanine-DNA alkyltransferase (MGMT) to acquire different degrees of resistance to TMZ. Characterisation of the induced resistance sublines showed detectable MGMT expression. However, unlike the TMZ resistance detected in two cell lines that expressed endogenous MGMT, the induced TMZ resistance in the repeatedly treated cells did not depend on MGMT activity. These MGMT-independent resistant cells may be useful to investigate novel strategies to overcome TMZ resistance. Finally, two repeatedly irradiated GBM sublines were established and characterised. One subline developed relative resistance to IR, the other developed a more motile phenotype. Microarray analysis showed differential expression of 122 genes across both cell line pairs, including upregulation of the stem cell marker CD24 in the more motile repeatedly irradiated subline. CD24 upregulation was validated at the mRNA and protein levels. Further investigation of differentially expressed genes may provide insights into novel mechanisms by which GBM cells evade or resist radiotherapy, and may help to guide development of new targeted treatments for GBM patients.