Kinetic modeling of molecular motors: pause model and parameter determination from single-molecule experiments

Single-molecule manipulation experiments of molecular motors provide essential information about the rate and conformational changes of the steps of the reaction located along the manipulation coordinate. This information is not always sufficient to define a particular kinetic cycle. Recent single-molecule experiments with optical tweezers showed that the DNA unwinding activity of a Phi29 DNA polymerase mutant presents a complex pause behavior, which includes short and long pauses. Here we show that different kinetic models, considering different connections between the active and the pause states, can explain the experimental pause behavior. Both the two independent pause model and the two connected pause model are able to describe the pause behavior of a mutated Phi29 DNA polymerase observed in an optical tweezers single-molecule experiment. For the two independent pause model all parameters are fixed by the observed data, while for the more general two connected pause model there is a range of values of the parameters compatible with the observed data (which can be expressed in terms of two of the rates and their force dependencies). This general model includes models with indirect entry and exit to the long-pause state, and also models with cycling in both directions. Additionally, assuming that detailed balance is verified, which forbids cycling, this reduces the ranges of the values of the parameters (which can then be expressed in terms of one rate and its force dependency). The resulting model interpolates between the independent pause model and the indirect entry and exit to the long-pause state model

Risk from cattle trampling to nests of an endangered passerine evaluated using artificial nest experiments and simulations

Grasslands are often grazed by cattle and many grassland birds nest on the ground, potentially exposing nests to trampling. We tested for trampling risk introduced by cattle to nests of endangered Florida Grasshopper Sparrows (Ammodramus savannarum floridanus) using experimentally paired grids of artificial nests (i.e., clay targets) similar in size to nests of Florida Grasshopper Sparrows and counted the number of clay targets that were broken in paired grazed and ungrazed enclosures. Clay targets in grazed grids were trampled 3.9% more often than their respective ungrazed grids, and measurements of cattle presence or density were correlated with the number of broken clay targets, suggesting that excluding cattle during breeding is an important management recommendation for the Florida Grasshopper Sparrow. Trampling rates within grazed enclosures were spatially homogeneous with respect to cattle infrastructure such as supplemental feeding troughs and fences, and forests and stocking density were poor predictors of trampling rates when excluding ungrazed grids. We used population viability analysis to compare quasi-extinction rates, intrinsic growth rates, and median abundance in grazed and ungrazed Florida Grasshopper Sparrow aggregations to further understand the biological significance of management aimed at reducing trampling rates during the breeding season. Simulations indicated that trampling from grazing increased quasi-extinction rates by 41% while reducing intrinsic growth rates by 0.048, and reducing median abundance by an average of 214 singing males after 50 years. Management should avoid grazing enclosures occupied by Florida Grasshopper Sparrows during the nesting season to minimize trampling rates. Our methods that combine trampling experiments with population viability analysis provide a framework for testing effects from trampling on other grassland ground-nesting birds, and can directly inform conservation and management of the Florida Grasshopper Sparrow.

The paradoxes of risk management in the banking sector

This paper uses empirical evidence to examine the operational dynamics and paradoxical nature of risk management systems in the banking sector. It demonstrates how a core paradox of market versus regulatory demands and an accompanying variety of performance, learning and belonging paradoxes underlie evident tensions in the interaction between front and back office staff in banks. Organisational responses to such paradoxes are found to range from passive to proactive, reflecting differing organisational, departmental and individual risk culture(s), and performance management systems. Nonetheless, a common feature of regulatory initiatives designed to secure a more structurally independent risk management function is that they have failed to rectify a critical imbalance of power - with the back office control functions continuing to be dominated by front office trading and investment functions. Ultimately, viewing the 'core' of risk management systems as a series of connected paradoxes rather than a set of assured, robust practices, requires a fundamental switch in emphasis away from a normative, standards-based approach to risk management to one which gives greater recognition to its behavioural dimensions.

Self-cutting and prospective repetition of self-harm: studies of emergency department presentations in Ireland

Background Self-harm places an individual at increased risk of future self-harm and suicide, and indicates distress and maladaptive coping. Those who present to hospital with self-cutting form a significant minority of self-harm patients who are at increased risk of prospective repetition of self-harm and suicide compared with those presenting with intentional overdose. In addition to increased risk, there is emerging evidence of demographic, psychological, clinical, and social differences between those presenting with self-cutting and those presenting with overdose. Aim and Key Objectives The aim of the current doctoral work was to examine in detail the association between presenting with self-cutting and risk of prospective repetition. The objectives were: to identify evidence-based risk factors for repetition of self-harm among those presenting to emergency departments with self-harm; to compare demographic and presentation characteristics and prospective repetition across presentations of self-cutting only, self-cutting plus intentional overdose, and intentional overdose only; to compare prospective repetition and other characteristics within self-cutting presentations based on the type of treatment received; to compare self-cutting and intentional overdose patients on psychological risk and protective factors for repetition; and to examine the lived experience of engaging in repeated overdose and self-cutting. Methods The current doctoral work used a mixed-methods approach and is comprised of one systematic review and four empirical studies. The empirical studies were two registry-based prospective studies of Irish hospital presentations of self-harm, one prospective structured interview study, and one qualitative study using Interpretative Phenomenological Analysis. Results The systematic review identified several consistent and emerging risk factors for repetition of self-harm, compared to which self-cutting had a medium-sized effect. The registry studies demonstrated that the involvement of self-cutting, particularly less medically severe selfcutting, confers an increased risk of 1-month and 12-month repetition among Irish index selfharm presentations. The structured psychological study detected higher hopelessness and lower non-reactivity to inner experience among those presenting with self-cutting, and higher depression among those who repeated self-harm. Repeaters had lower baseline levels of protective psychological factors than non-repeaters and continued to have higher depression and hopelessness at follow-up. Finally, the qualitative study indicated that self-harm is a purposeful action taken in response to an overwhelming situation and is evaluated afterwards in terms of personal and social effects. Chosen method of self-harm seemed to be influenced by the desired outcome of the self-harm act, capability, accessibility and previous experience. Conclusion Despite limitations in terms of recruitment rates, the work presented in this thesis is innovative in examining the issue of the association between self-cutting and repetition from multiple perspectives. No one factor can reliably predict all repetition but self-cutting represents one consistent and easily detected risk factor for repetition. Those who present with self-cutting exhibit significant differences on demographic, clinical, and psychological variables compared with those presenting with intentional overdose, and seem to exhibit a more vulnerable profile. However, those who present with self-cutting do not form a discrete or homogenous group, and self-harm methods and levels of suicidal intent are liable to fluctuate over time.

Survival of a Perverse Nation: Sexuality and Kinship in Post-Soviet Armenia

Survival of a Perverse Nation traces the ways in which contemporary Armenian anxieties are congealing into the figure of the “homosexual.” As in other post-Soviet republics, homosexuality has increasingly become defined as the crisis of the times, and is understood by many as a destructive force linked to European encroachment. In Armenia, a growing right-wing nationalist movement since 2012 has been targeting LGBT and feminist activists. I suggest that this movement has arisen out of Armenia’s concerns regarding proper social and biological reproduction in the face of high rates of emigration of especially men in search of work. Many in the country blame this emigration on a post-Soviet oligarchy, with close ties to the government. This oligarchy, having quickly and massively privatized and liquidated industry and land during the war over the region of Nagorno-Karabagh (1990-1994) with Azerbaijan, created widespread un(der)employment. A national narrative attributing the nation’s survival of the 1915 Genocide and dispersion of its populations to strong morality preserved by institutions such as the Church and the family has now, in the post-Soviet era, ruptured into one of moral “perversion.” This dissertation is based on 15 months of ethnographic research, during which I participated in the work of two local non-governmental organizations: Public Information and Need for Knowledge, an LGBT rights organization and Women’s Resource Center, a feminist organization. I also conducted interviews with 150 households across Yerevan, the capital city, and did in-depth interviews with other activists, right-wing nationalists and journalists. Through psychoanalytic frameworks, as well as studies of kinship, I show how sovereignty – the longed for dream for Armenians over the last century – is felt to have failed because of the moral corruption of the illegitimate figures that fill Armenian seats of authority. I, thus, examine the ways in which a missing father of the household is discursively linked to the lack of strong leadership by a corrupt government, producing a prevalent feeling of moral disintegration that nationalists displace onto the “homosexual.”

Potential Cost-effectiveness of Early Identification of Hospital-acquired Infection in Critically Ill Patients.

RATIONALE: Limitations in methods for the rapid diagnosis of hospital-acquired infections often delay initiation of effective antimicrobial therapy. New diagnostic approaches offer potential clinical and cost-related improvements in the management of these infections. OBJECTIVES: We developed a decision modeling framework to assess the potential cost-effectiveness of a rapid biomarker assay to identify hospital-acquired infection in high-risk patients earlier than standard diagnostic testing. METHODS: The framework includes parameters representing rates of infection, rates of delayed appropriate therapy, and impact of delayed therapy on mortality, along with assumptions about diagnostic test characteristics and their impact on delayed therapy and length of stay. Parameter estimates were based on contemporary, published studies and supplemented with data from a four-site, observational, clinical study. Extensive sensitivity analyses were performed. The base-case analysis assumed 17.6% of ventilated patients and 11.2% of nonventilated patients develop hospital-acquired infection and that 28.7% of patients with hospital-acquired infection experience delays in appropriate antibiotic therapy with standard care. We assumed this percentage decreased by 50% (to 14.4%) among patients with true-positive results and increased by 50% (to 43.1%) among patients with false-negative results using a hypothetical biomarker assay. Cost of testing was set at $110/d. MEASUREMENTS AND MAIN RESULTS: In the base-case analysis, among ventilated patients, daily diagnostic testing starting on admission reduced inpatient mortality from 12.3 to 11.9% and increased mean costs by $1,640 per patient, resulting in an incremental cost-effectiveness ratio of $21,389 per life-year saved. Among nonventilated patients, inpatient mortality decreased from 7.3 to 7.1% and costs increased by $1,381 with diagnostic testing. The resulting incremental cost-effectiveness ratio was $42,325 per life-year saved. Threshold analyses revealed the probabilities of developing hospital-acquired infection in ventilated and nonventilated patients could be as low as 8.4 and 9.8%, respectively, to maintain incremental cost-effectiveness ratios less than $50,000 per life-year saved. CONCLUSIONS: Development and use of serial diagnostic testing that reduces the proportion of patients with delays in appropriate antibiotic therapy for hospital-acquired infections could reduce inpatient mortality. The model presented here offers a cost-effectiveness framework for future test development.

Application of Numerical Methods to Study Arrangement and Fracture of Lithium-Ion Microstructure

The focus of this work is to develop and employ numerical methods that provide characterization of granular microstructures, dynamic fragmentation of brittle materials, and dynamic fracture of three-dimensional bodies.

We first propose the fabric tensor formalism to describe the structure and evolution of lithium-ion electrode microstructure during the calendaring process. Fabric tensors are directional measures of particulate assemblies based on inter-particle connectivity, relating to the structural and transport properties of the electrode. Applying this technique to X-ray computed tomography of cathode microstructure, we show that fabric tensors capture the evolution of the inter-particle contact distribution and are therefore good measures for the internal state of and electronic transport within the electrode.

We then shift focus to the development and analysis of fracture models within finite element simulations. A difficult problem to characterize in the realm of fracture modeling is that of fragmentation, wherein brittle materials subjected to a uniform tensile loading break apart into a large number of smaller pieces. We explore the effect of numerical precision in the results of dynamic fragmentation simulations using the cohesive element approach on a one-dimensional domain. By introducing random and non-random field variations, we discern that round-off error plays a significant role in establishing a mesh-convergent solution for uniform fragmentation problems. Further, by using differing magnitudes of randomized material properties and mesh discretizations, we find that employing randomness can improve convergence behavior and provide a computational savings.

The Thick Level-Set model is implemented to describe brittle media undergoing dynamic fragmentation as an alternative to the cohesive element approach. This non-local damage model features a level-set function that defines the extent and severity of degradation and uses a length scale to limit the damage gradient. In terms of energy dissipated by fracture and mean fragment size, we find that the proposed model reproduces the rate-dependent observations of analytical approaches, cohesive element simulations, and experimental studies.

Lastly, the Thick Level-Set model is implemented in three dimensions to describe the dynamic failure of brittle media, such as the active material particles in the battery cathode during manufacturing. The proposed model matches expected behavior from physical experiments, analytical approaches, and numerical models, and mesh convergence is established. We find that the use of an asymmetrical damage model to represent tensile damage is important to producing the expected results for brittle fracture problems.

The impact of this work is that designers of lithium-ion battery components can employ the numerical methods presented herein to analyze the evolving electrode microstructure during manufacturing, operational, and extraordinary loadings. This allows for enhanced designs and manufacturing methods that advance the state of battery technology. Further, these numerical tools have applicability in a broad range of fields, from geotechnical analysis to ice-sheet modeling to armor design to hydraulic fracturing.

Interpolated maps of pollen percentages in Europe over the last 15,000 years

Aim Palaeoecological reconstructions document past vegetation change with estimates of rapid rates of changing species distribution limits that are often not matched by model simulations of climate-driven vegetation dynamics. Genetic surveys of extant plant populations have yielded new insight into continental vegetation histories, challenging traditional interpretations that had been based on pollen data. Our aim is to examine an updated continental pollen data set from Europe in the light of the new ideas about vegetation dynamics emerging from genetic research and vegetation modelling studies. Location Europe Methods: We use pollen data from the European Pollen Database (EPD) to construct interpolated maps of pollen percentages documenting change in distribution and abundance of major plant genera and the grass family in Europe over the last 15,000 years. Results: Our analyses confirm high rates of postglacial spread with at least 1000 metres per year for Corylus, Ulmus and Alnus and average rates of 400 metres per year for Tilia, Quercus, Fagus and Carpinus. The late Holocene expansions of Picea and Fagus populations in many European regions cannot be explained by migrational lag. Both taxa shift their population centres towards the Atlantic coast suggesting that climate may have played a role in the timing of their expansions. The slowest rates of spread were reconstructed for Abies. Main conclusions: The calculated rates of postglacial plant spread are higher in Europe than those from North America, which may be due to more rapid shifts in climate mediated by the Gulf Stream and westerly winds. Late Holocene anthropogenic land use practices in Europe had major effects on individual taxa, which in combination with climate change contributed to shifts in areas of abundance and dominance. The high rates of spread calculated from the European pollen data are consistent with the common tree species rapidly tracking early Holocene climate change and contribute to the debate on the consequences of global warming for plant distributions.

(Table 1) Stable isotope record of Middle Cretaceous benthic foraminifera

Preservation of planktic foraminiferal calcite has received widespread attention in recent years, but the taphonomy of benthic foraminiferal calcite and its influence on the deep-sea palaeotemperature record have gone comparatively unreported. Numerical modeling indicates that the carbonate recrystallization histories of deep-sea sections are dominated by events in their early burial history, meaning that the degree of exchange between sediments and pore fluids during the early postburial phase holds the key to determining the palaeotemperature significance of diagenetic alteration of benthic foraminifera. Postburial sedimentation rate and lithology are likely to be important determinants of the paleoceanographic significance of this sediment-pore fluid interaction. Here we report an investigation of the impact of extreme change in sedimentation rate (a prolonged and widespread Upper Cretaceous hiatus in the North Atlantic Ocean) on the preservation and d18O of benthic foraminifera of Middle Cretaceous age (nannofossil zone NC10, uppermost Albian/lowermost Cenomanian, ~99 Ma ago) from multiple drill sites. At sites where this hiatus immediately overlies NC10, benthic foraminifera appear to display at least moderate preservation of the whole test. However, on closer inspection, these tests are shown to be extremely poorly preserved internally and yield d18O values substantially higher than those from contemporaneous better preserved benthic foraminifera at sites without an immediately overlying hiatus. These high d18O values are interpreted to indicate alteration close to the seafloor in cooler waters during the Late Cretaceous hiatus. Intersite differences in lithology modulate the diagenetic impact of this extreme change in sedimentation rate. Our results highlight the importance of thorough examination of benthic foraminiferal wall structures and lend support to the view that sedimentation rate and lithology are key factors controlling the paleoceanographic significance of diagenetic alteration of biogenic carbonates.

Activity concentrations of radionuclides in 5 short cores taken in 2007-2008 measured by ICP-MS and HPGe gamma spectrometry

Natural radionuclides and man-made 137Cs were analyzed in five short sediment cores taken in northern part of the Gulf of Eilat (Gulf of Aqaba) in order to provide information on sedimentation and mixing rates and sediment sources. The maximum estimates of sedimentation rates based on excess 210Pb were found to vary between 0.105 ± 0.020 and 0.35 ± 0.23 cm · year**-1. Even the lowest estimates are significantly higher than those expected from dust deposition, suggesting other sources and processes being responsible for most of the allochthonous material accumulation, including periodical floods following heavy rain events, internal erosion or triggers, like earthquakes. In 137Cs depth profiles no 1963 related nuclear weapon test maxima were found; instead, the activities decrease monotonically, suggesting that a major process leading to radionuclides' depth distribution might be mixing. The mixing rates calculated from 137Cs, excess 210Pb and excess 228Th reach values up to 2.18 ± 0.69 cm**2 · year**-1.

On the feasibility of time-lapse superconducting gravimetry for reservoir monitoring

The feasibility of monitoring fluid flow subsurface processes that result in density changes, using the iGrav superconducting gravimeter, is investigated. Practical targets include steam-assisted gravity drainage (SAGD) bitumen depletion and water pumping from aquifers, for which there is currently a void in low-impact, inexpensive monitoring techniques. This study demonstrates that the iGrav has the potential to be applied to multi-scale and diverse reservoirs. Gravity and gravity gradient signals are forward modeled for a real SAGD reservoir at two time steps, and for surface-fed and groundwater-fed aquifer pumping models, to estimate signal strength and directional dependency of water flow. Time-lapse gravimetry on small-scale reservoirs exhibits two obstacles, namely, a µgal sensitivity requirement and high noise levels in the vicinity of the reservoir. In this study, both limitations are overcome by proposing (i) a portable superconducting gravimeter, and (ii) a pair of instruments under various baseline geometries. This results in improved spatial resolution for locating depletion zones, as well as the cancellation of noise common in both instruments. Results indicate that a pair of iGrav superconducting gravimeters meet the sensitivity requirements and the spatial focusing desired to monitor SAGD bitumen migration at the reservoir scales. For SAGD reservoirs, the well pair separation, reservoir depth, and survey sampling determine the resolvability of individual well pair depletion patterns during the steam chamber rising phase, and general reservoir depletion patterns during the steam chamber spreading phase. Results show that monitoring water table elevation changes due to pumping and tracking whether groundwater or surface water is being extracted are feasible.

As assessment of the Competition Commission Report and subsequent outcomes

Following the Office of Fair Trading's review of the British deregulated bus market as a whole in 2009, the issues raised were referred to the Competition Commission. Its final report was published in December 2011. Subsequently, the House of Commons Transport Committee carried out an enquiry into the Commission's report, and reactions to it by the operating industry, user groups, and other bodies, which was published in September 2012. A number of major issues have been raised, including the extent to which price competition may be effective, the appropriate rate of return on capital that would be expected within the industry (and appropriate actions where this is excessive in practice), and industry structure. The importance of competition per se, as distinct from attributes of direct concern to users (such as reliability, frequency, and fares) has also been debated. This paper reviews the issues raised, and outcomes to date, in the light of further evidence on the industry's performance. It is demonstrated similar rates of return could be attained through very different operating strategies, which in turn have very different implications for changes in consumer surplus. The alternative uses made of such profits (for example through reinvestment) may also have markedly different impacts effects on users. Rather than focussing on the dangers of excessive rates of return on capital, the outcomes for service users should be the main issue.

Directional genetic differentiation and relative migration

Understanding the population structure and patterns of gene flow within species is of fundamental importance to the study of evolution. In the fields of population and evolutionary genetics, measures of genetic differentiation are commonly used to gather this information. One potential caveat is that these measures assume gene flow to be symmetric. However, asymmetric gene flow is common in nature, especially in systems driven by physical processes such as wind or water currents. As information about levels of asymmetric gene flow among populations is essential for the correct interpretation of the distribution of contemporary genetic diversity within species, this should not be overlooked. To obtain information on asymmetric migration patterns from genetic data, complex models based on maximum-likelihood or Bayesian approaches generally need to be employed, often at great computational cost. Here, a new simpler and more efficient approach for understanding gene flow patterns is presented. This approach allows the estimation of directional components of genetic divergence between pairs of populations at low computational effort, using any of the classical or modern measures of genetic differentiation. These directional measures of genetic differentiation can further be used to calculate directional relative migration and to detect asymmetries in gene flow patterns. This can be done in a user-friendly web application called divMigrate-online introduced in this study. Using simulated data sets with known gene flow regimes, we demonstrate that the method is capable of resolving complex migration patterns under a range of study designs.

Temperature and the synchrony of plant-insect interactions

Increasing temperatures resulting from climate change have within recent years been shown to advance phenological events in a large number of species worldwide. Species can differ in their response to increasing temperatures, and understanding the mechanisms that determine the response is therefore of great importance in order to understand and predict how a warming climate can influence both individual species, but also their interactions with each other and the environment. Understanding the mechanisms behind responses to increasing temperatures are however largely unexplored. The selected study system consisting of host plant species of the Brassicaceae family and their herbivore Anthocharis cardamines, is assumed to be especially vulnerable to climatic variations. Through the use of this study system, the aim of this thesis is to study differences in the effect of temperature on development to start of flowering within host plant species from different latitudinal regions (study I), and among host plant species (study II). We also investigate whether different developmental phases leading up to flowering differ in sensitivity to temperature (study II), and if small-scale climatic variation in spring temperature influence flowering phenology and interactions with A. cardamines (study III). Finally, we investigate if differences in the timing of A. cardamines relative to its host plants influence host species use and the selection of host individuals differing in phenology within populations (study IV). Our results showed that thermal reaction norms differ among regions along a latitudinal gradient, with the host plant species showing a mixture of co-, counter- and mixed gradient patterns (study I). We also showed that observed differences in the host plant species order of flowering among regions and years might be caused by both differences in the distribution of warm days during development and differences in the sensitivity to temperature in different phases of development (study II). In addition, we showed that small-scale variations in temperature led to variation in flowering phenology among and within populations of C. pratensis, impacting the interactions with the butterfly herbivore A. cardamines. Another result was that the less the mean plant development stage of a given plant species in the field deviated from the stage preferred by the butterfly for oviposition, the more used was the species as a host by the butterfly (study IV). Finally, we showed that the later seasonal appearance of the butterflies relative to their host plants, the higher butterfly preference for host plant individuals with a later phenology, corresponding to a preference for host plants in earlier development stages (study IV). For our study system, this thesis suggest that climate change will lead to changes in the interactions between host plants and herbivore, but that differences in phenology among host plants combined with changes in host species use of the herbivore might buffer the herbivore against negative effects of climate change. Our work highlights the need to understand the mechanisms behind differences in the responses of developmental rates to temperature between interacting species, as well as the need to account for differences in temperature response for interacting organisms from different latitudinal origins and during different developmental phases in order to understand and predict the consequences of climate change.