Linking Unit Tests and Properties

QuickCheck allows us to verify software against particular proper- ties. A property can be regarded as an abstraction over many unit tests. QuickCheck uses generated random input data to test such properties. If a counterexample is found, it becomes immediately clear what we have tested. This is not the case when all tests pass, since we do not (and shall not) see the actual generated test cases. How can we be sure about what is tested? QuickCheck has the ability to gather statistics about the test cases, which is insightful. But still it does not tell us whether the particular unit test scenarios we have in mind are included. For this reason, we have developed a tool that can answer this question. It checks if a given unit test can be generated by a property, making it easier to judge the property’s quality. We have applied our tool to an industrial use case of testing the AUTOSAR basic software modules and shows that it can handle complex models and large unit tests

Quaternary structural evolution and seismic hazards of the onshore Ventura basin, southern California, USA

Fault interactions cause variations in patterns of deformation and stress distribution, which control the location and magnitude of earthquakes and can also have a significant impact on the evolution of the landscape. Consequently, a better understanding of how patterns of deformation vary in time and space and the timescales over which fault interactions occur is of critical importance to a sizeable amount of the global population who live within earthquake-prone regions. Devastating earthquakes can occur on well-studied faults, or faults that are either blind or unknown prior to an earthquake. Furthermore, there are several recent examples where large-magnitude earthquakes are attributed to synchronous ruptures of multiple faults with complex subsurface geometry and kinematics. For example, the 2016 Mw 7.8 Kaikoura earthquake is thought to have ruptured up to twelve major faults, at least two of which were unknown before the event occurred. The observation that such complex earthquake ruptures can occur brings into focus the need to use geologic and geomorphic field data to accurately characterize parameters such as subsurface fault geometry and fault slip rates. Additional information on tectonic activity and patterns of deformation can also be acquired from a quantitative analysis of landscape morphology. However, even in well-studied areas such as southern California, fundamental data such as fault slip rates or subsurface fault geometry are often poorly understood, which undermines a complete analysis of seismic hazards. This thesis integrates a multi-disciplinary approach incorporating geomorphic mapping, multiple cosmogenic isotope techniques to establish dates and rates of Earth surface processes, landscape topographic analysis, structural geology, and static Coulomb stress modelling. I investigate the degree to which patterns of deformation over multiple earthquakes cycles are variable in time and space and examine how potential variability in deformation controls the morphology of the landscape and impacts our interpretation of seismic hazards. I focus on the Ventura basin, southern California, USA, which is an ideal location to address such questions because despite an abundance of active reverse and thrust faults in proximity to major population centres, the subsurface geometry and slip rates for several key faults are not well quantified and there are few data on how the numerous active faults have shaped the evolution of the landscape. III First, I investigate evidence for a proposed blind fault in the Ventura basin, the Southern San Cayetano fault (SSCF), and the potential role of the SSCF in stress transfer between the Ventura fault and the San Cayetano fault in potential large-magnitude (Mw 7.5–8.0) multi-fault earthquakes. I examine late Quaternary alluvial fans and river terraces using field mapping, high-resolution lidar topographic data, 10Be surface exposure dating, and subsurface well data to provide evidence for a young, active SSCF. I calculate a Holocene reverse slip rate of 1.3 +0.5/-0.3 mm yr-1 and suggest that displacement rates for the SSCF have not varied significantly since the onset of activity on the SSCF around ~58 ka. I hypothesize that the SSCF could potentially act as a rupture pathway between the Ventura and San Cayetano faults in large-magnitude, multi-fault earthquakes in southern California. In the second part of the thesis, I examine the subsurface geometry of the SSCF and the potential structural connectivity and stress interactions between the SSCF and neighbouring faults. I present a series of structural cross sections along strike of the SSCF and a 3D fault model for the SSCF. These results provide evidence for a low-angle SSCF that dips ~15° north and connects with the western San Cayetano fault (WSCF) around 1.5–3.5 km depth. I incorporate the 3D fault model for the SSCF in static Coulomb stress modelling and find that triggered seismicity may occur on the SSCF and the WSCF because of ruptures on the eastern section of the San Cayetano fault. However, my results indicate that the role of static Coulomb stress transfer in the potential occurrence of multi-fault earthquakes in the Ventura basin is critically dependent on fault model adopted for the deep structure of faults. The results demonstrate that an accurate characterization of three-dimensional subsurface fault geometry is important for reducing uncertainties when assessing future patterns of regional seismicity and highlight the importance of integrating field observations, surface data, and subsurface data to create realistic fault inputs when modelling static Coulomb stress transfer. In the last section of the thesis, I investigate how fault evolution has controlled patterns of topographic relief development, channel morphology, and erosion in the Ventura basin. I employ cosmogenic isotope isochron burial dating of an important, yet poorly dated, Quaternary strain marker, the Saugus Formation, to reduce uncertainties in the assessment of rates of tectonic processes. My results confirm that the Saugus Formation increases in age from west to east along the axis of the Ventura basin with ages for the top of the exposed Saugus Formation of 0.38 +.017/-0.23 Ma at Ventura and 2.49 +0.25/-0.29 Ma in the eastern Ventura basin. The burial ages for the base of shallow marine sands, which underlie the Saugus Formation throughout the basin are 0.55 +0.80/-0.10 Ma at Ventura and 3.30 +0.30/-0.42 Ma in the eastern Ventura basin. Burial ages for the Saugus Formation in conjunction with published fault offsets suggest long-term slip rates of 7.1 +/- 1.0 mm yr-1 for the San Cayetano fault since ~1.54 Ma. In addition, I calculate 10Be-derived catchment-averaged erosion rates and compare erosion rates with fault displacement rates and the results of a morphometric landscape analysis. The comparison indicates a transient landscape response to tectonic forcing in the Ventura basin, where the erosion signal in fault hanging walls is not yet fully adjusted to various tectonic perturbations over the last ~1.5 Ma. These data demonstrate that on the local scale with uniform climate, such as the hanging wall of the San Cayetano, Ventura, and Southern San Cayetano faults, tectonic perturbations are the main drivers in patterns of topographic relief developments and highest stream gradients for periods up to 106 years. Overall, my results demonstrate that patterns of deformation can demonstrate significant spatial variability on timescales between 103 to 106 years. I find that fault interactions and the migration of deformation exert significant control on rates of fault activity and landscape morphology, and that patterns of deformation must be accurately modelled for a robust analysis of seismic hazards.Open Acces

Single-cell western blotting.

To measure cell-to-cell variation in protein-mediated functions, we developed an approach to conduct ∼10(3) concurrent single-cell western blots (scWesterns) in ∼4 h. A microscope slide supporting a 30-μm-thick photoactive polyacrylamide gel enables western blotting: settling of single cells into microwells, lysis in situ, gel electrophoresis, photoinitiated blotting to immobilize proteins and antibody probing. We applied this scWestern method to monitor single-cell differentiation of rat neural stem cells and responses to mitogen stimulation. The scWestern quantified target proteins even with off-target antibody binding, multiplexed to 11 protein targets per single cell with detection thresholds of <30,000 molecules, and supported analyses of low starting cell numbers (∼200) when integrated with FACS. The scWestern overcomes limitations of antibody fidelity and sensitivity in other single-cell protein analysis methods and constitutes a versatile tool for the study of complex cell populations at single-cell resolution

Anonymising Clinical Data for Secondary Use

Secondary use of data already collected in clinical studies has become more and more popular in recent years, with the commitment of the pharmaceutical industry and many academic institutions in Europe and the US to provide access to their clinical trial data. Whilst this clearly provides societal benefit in helping to progress medical research, this has to be balanced against protection of subjects' privacy. There are two main scenarios for sharing subject data: within Clinical Study Reports and Individual Patient Level Data, and these scenarios have different associated risks and generally require different approaches. In any data sharing scenario, there is a trade-off between data utility and the risk of subject re-identification, and achieving this balance is key. Quantitative metrics can guide the amount of de-identification required and new technologies may also start to provide alternative ways to achieve the risk-utility balance.Comment: 25 page

Fragmentary embeddedness: Challenges for alternative food networks in Guangzhou, China

Alternative food networks (AFNs) have been viewed as being more deeply embedded in the fabric of places and the social relations of their food systems than conventional food networks, and have been regarded as ‘spaces of hope’ for addressing sustainability challenges associated with global food systems. This paper argues that embeddedness, however, is contingent and shifting rather than an intrinsic quality, and is shaped by the cultures of production, trade, and consumption in particular places. This paper evaluates challenges that emerging AFNs in Guangzhou, China, are confronting relating to their embeddedness in place. The paper is underpinned by research involving interviews and focus groups with key food system actors and stakeholders in Guangzhou, including government officials, organic farmers, retailers, and non-governmental organizations. It demonstrates that AFNs in Guangzhou achieve only ‘fragmentary embeddedness’ in local cultures and systems of production, retail, and consumption. Despite strong social relationships established by a few successful farms and their loyal consumer groups, AFNs more broadly have struggled to embed themselves in the social and cultural fabric of the city and its commercial foodscapes. In terms of territorial embeddedness, the association of AFNs with western values, which do not always translate into Guangzhou's production and retail systems, can limit their embeddedness and scaling up in this context. The split between ‘new’ farmers (i.e., educated and urban-rooted producers ‘returning to the land’) and common farmers (i.e., local peasants) further exacerbates the difficulty of integrating AFNs in rural communities. Regarding social embeddedness, AFNs struggle to meet local consumer preferences regarding food appearances, quality, and taste, and therefore consumer trust in them is limited. In terms of institutional embeddedness, AFNs lack government policy support, despite the alignment of their missions with national strategies. More efforts are needed to deepen the embeddedness of AFNs in Guangzhou's food system and cultures if they are to respond effectively to China's food crisis and wider sustainability issues