Application of Fluorescence Spectroscopy to Quantify Shear-Induced Protein Conformation Change

Rapid and robust methods are required to quantify the effect of hydrodynamic shear on protein conformation change. We evaluated such strategies in this work and found that the binding of the fluorescent probe 4,4'-dianilino-1, 1'-binaphthyl-5,5'-disulfonic acid (bis-ANS) to hydrophobic pockets in the blood protein von Willebrand factor (VWF) is enhanced upon the application of fluid shear to the isolated protein. Significant structural changes were observed when the protein was sheared at shear rates >= 6000/s for similar to 3.5 min. The binding of bis-ANS to multimeric VWF, but not dimeric VWF or control protein bovine serum albumin, was enhanced upon fluid shear application. Thus, high-molecular-weight VWF is more susceptible to conformation change upon tensile loading. Although bis-ANS itself did not alter the conformation of VWF, it stabilized protein conformation once it bound the sheared molecule. Bis-ANS binding to VWF was reduced when the sheared protein was allowed to relax before dye addition. Taken together with functional data in the literature, our results suggest that shear-induced conformation changes in VWF reported by bis-ANS correlate well with the normal function of the protein under physiological/pathological fluid flow conditions. Further, this study introduces the fluorescent dye bis-ANS as a tool that may be useful in studies of shear-induced protein conformation change.

Predicting the ecological impacts of a new freshwater invader:Functional responses and prey selectivity of the 'killer shrimp', Dikerogammarus villosus, compared to the native Gammarus pulex

The ability to predict the likely ecological impacts of invasive species in fresh waters is a pressing research requirement. Whilst comparisons of species traits and considerations of invasion history have some efficacy in this respect, we require robust methods that can compare the effects of native and invasive species. Here, we utilise comparative functional responses and prey selectivity experiments to understand and predict the ecological impact of an invader as compared to a native. We compared the predatory functional responses of an emerging invasive species in Europe, the 'killer shrimp', Dikerogammarus villosus, and an analogous native species, Gammarus pulex, towards three representative prey species: Asellus aquaticus, Daphnia magna and Chironomus sp. Furthermore, as ecological impact may be greater for invasive species with more indiscriminate feeding habits, we compared the selectivity for the three prey types between the invasive and native species. In both the presence and absence of experimental habitats, large D. villosus, and those matched for body size with G. pulex, generally showed higher (Type II) functional responses than G. pulex, with the invasive species exhibiting higher maximum feeding rates. Further, D. villosus exhibited significantly more indiscriminate prey selection compared with G. pulex, a trait that became more evident as the invader increased in size. Differences in functional responses and prey selectivity were prey species specific, with higher to lower predicted impacts in the order A. aquaticus, D. magna and Chironomus sp. This is in accord with the impact of this invasive species on macroinvertebrates in the field. We thus provide understanding of the known ecological impact of D. villosus and discuss the utility of the phenomenological use of comparative functional responses and resource use as a tool through which the potential ecological impacts of invasive species may be identified. © 2013 John Wiley & Sons Ltd.

Inférence robuste à la présence des valeurs aberrantes dans les enquêtes

Cette thèse comporte trois articles dont un est publié et deux en préparation. Le sujet central de la thèse porte sur le traitement des valeurs aberrantes représentatives dans deux aspects importants des enquêtes que sont : l’estimation des petits domaines et l’imputation en présence de non-réponse partielle. En ce qui concerne les petits domaines, les estimateurs robustes dans le cadre des modèles au niveau des unités ont été étudiés. Sinha & Rao (2009) proposent une version robuste du meilleur prédicteur linéaire sans biais empirique pour la moyenne des petits domaines. Leur estimateur robuste est de type «plugin», et à la lumière des travaux de Chambers (1986), cet estimateur peut être biaisé dans certaines situations. Chambers et al. (2014) proposent un estimateur corrigé du biais. En outre, un estimateur de l’erreur quadratique moyenne a été associé à ces estimateurs ponctuels. Sinha & Rao (2009) proposent une procédure bootstrap paramétrique pour estimer l’erreur quadratique moyenne. Des méthodes analytiques sont proposées dans Chambers et al. (2014). Cependant, leur validité théorique n’a pas été établie et leurs performances empiriques ne sont pas pleinement satisfaisantes. Ici, nous examinons deux nouvelles approches pour obtenir une version robuste du meilleur prédicteur linéaire sans biais empirique : la première est fondée sur les travaux de Chambers (1986), et la deuxième est basée sur le concept de biais conditionnel comme mesure de l’influence d’une unité de la population. Ces deux classes d’estimateurs robustes des petits domaines incluent également un terme de correction pour le biais. Cependant, ils utilisent tous les deux l’information disponible dans tous les domaines contrairement à celui de Chambers et al. (2014) qui utilise uniquement l’information disponible dans le domaine d’intérêt. Dans certaines situations, un biais non négligeable est possible pour l’estimateur de Sinha & Rao (2009), alors que les estimateurs proposés exhibent un faible biais pour un choix approprié de la fonction d’influence et de la constante de robustesse. Les simulations Monte Carlo sont effectuées, et les comparaisons sont faites entre les estimateurs proposés et ceux de Sinha & Rao (2009) et de Chambers et al. (2014). Les résultats montrent que les estimateurs de Sinha & Rao (2009) et de Chambers et al. (2014) peuvent avoir un biais important, alors que les estimateurs proposés ont une meilleure performance en termes de biais et d’erreur quadratique moyenne. En outre, nous proposons une nouvelle procédure bootstrap pour l’estimation de l’erreur quadratique moyenne des estimateurs robustes des petits domaines. Contrairement aux procédures existantes, nous montrons formellement la validité asymptotique de la méthode bootstrap proposée. Par ailleurs, la méthode proposée est semi-paramétrique, c’est-à-dire, elle n’est pas assujettie à une hypothèse sur les distributions des erreurs ou des effets aléatoires. Ainsi, elle est particulièrement attrayante et plus largement applicable. Nous examinons les performances de notre procédure bootstrap avec les simulations Monte Carlo. Les résultats montrent que notre procédure performe bien et surtout performe mieux que tous les compétiteurs étudiés. Une application de la méthode proposée est illustrée en analysant les données réelles contenant des valeurs aberrantes de Battese, Harter & Fuller (1988). S’agissant de l’imputation en présence de non-réponse partielle, certaines formes d’imputation simple ont été étudiées. L’imputation par la régression déterministe entre les classes, qui inclut l’imputation par le ratio et l’imputation par la moyenne sont souvent utilisées dans les enquêtes. Ces méthodes d’imputation peuvent conduire à des estimateurs imputés biaisés si le modèle d’imputation ou le modèle de non-réponse n’est pas correctement spécifié. Des estimateurs doublement robustes ont été développés dans les années récentes. Ces estimateurs sont sans biais si l’un au moins des modèles d’imputation ou de non-réponse est bien spécifié. Cependant, en présence des valeurs aberrantes, les estimateurs imputés doublement robustes peuvent être très instables. En utilisant le concept de biais conditionnel, nous proposons une version robuste aux valeurs aberrantes de l’estimateur doublement robuste. Les résultats des études par simulations montrent que l’estimateur proposé performe bien pour un choix approprié de la constante de robustesse.

Collaborative design procedures for architects and engineers

This book argues for novel strategies to integrate engineering design procedures and structural analysis data into architectural design. Algorithmic procedures that recently migrated into the architectural practice are utilized to improve the interface of both disciplines. Architectural design is predominately conducted as a negotiation process of various factors but often lacks rigor and data structures to link it to quantitative procedures. Numerical structural design on the other hand could act as a role model for handling data and robust optimization but it often lacks the complexity of architectural design. The goal of this research is to bring together robust methods from structural design and complex dependency networks from architectural design processes. The book presents three case studies of tools and methods that are developed to exemplify, analyze and evaluate a collaborative work flow.

Generative Temporal Planning with Complex Processes

Autonomous vehicles are increasingly being used in mission-critical applications, and robust methods are needed for controlling these inherently unreliable and complex systems. This thesis advocates the use of model-based programming, which allows mission designers to program autonomous missions at the level of a coach or wing commander. To support such a system, this thesis presents the Spock generative planner. To generate plans, Spock must be able to piece together vehicle commands and team tactics that have a complex behavior represented by concurrent processes. This is in contrast to traditional planners, whose operators represent simple atomic or durative actions. Spock represents operators using the RMPL language, which describes behaviors using parallel and sequential compositions of state and activity episodes. RMPL is useful for controlling mobile autonomous missions because it allows mission designers to quickly encode expressive activity models using object-oriented design methods and an intuitive set of activity combinators. Spock also is significant in that it uniformly represents operators and plan-space processes in terms of Temporal Plan Networks, which support temporal flexibility for robust plan execution. Finally, Spock is implemented as a forward progression optimal planner that walks monotonically forward through plan processes, closing any open conditions and resolving any conflicts. This thesis describes the Spock algorithm in detail, along with example problems and test results.

A survey addressing the fundamental matrix estimation problem

Epipolar geometry is a key point in computer vision and the fundamental matrix estimation is the only way to compute it. This article surveys several methods of fundamental matrix estimation which have been classified into linear methods, iterative methods and robust methods. All of these methods have been programmed and their accuracy analysed using real images. A summary, accompanied with experimental results, is given

A revised Tobit procedure for mitigating bias in the presence of non-zero censoring with an application to milk-market participation in the Ethiopian highlands

Fixed transactions costs that prohibit exchange engender bias in supply analysis due to censoring of the sample observations. The associated bias in conventional regression procedures applied to censored data and the construction of robust methods for mitigating bias have been preoccupations of applied economists since Tobin [Econometrica 26 (1958) 24]. This literature assumes that the true point of censoring in the data is zero and, when this is not the case, imparts a bias to parameter estimates of the censored regression model. We conjecture that this bias can be significant; affirm this from experiments; and suggest techniques for mitigating this bias using Bayesian procedures. The bias-mitigating procedures are based on modifications of the key step that facilitates Bayesian estimation of the censored regression model; are easy to implement; work well in both small and large samples; and lead to significantly improved inference in the censored regression model. These findings are important in light of the widespread use of the zero-censored Tobit regression and we investigate their consequences using data on milk-market participation in the Ethiopian highlands. (C) 2004 Elsevier B.V. All rights reserved.

Understanding and projecting sea level change

There is intense scientific and public interest in the Intergovernmental Panel on Climate Change (IPCC) projections of sea level for the twenty-first century and beyond. The Fourth Assessment Report (AR4) projections, obtained by applying standard methods to the results of the World Climate Research Programme Coupled Model Experiment, includes estimates of ocean thermal expansion, the melting of glaciers and ice caps (G&ICs), increased melting of the Greenland Ice Sheet, and increased precipitation over Greenland and Antarctica, partially offsetting other contributions. The AR4 recognized the potential for a rapid dynamic ice sheet response but robust methods for quantifying it were not available. Illustrative scenarios suggested additional sea level rise on the order of 10 to 20 cm or more, giving a wide range in the global averaged projections of about 20 to 80 cm by 2100. Currently, sea level is rising at a rate near the upper end of these projections. Since publication of the AR4 in 2007, biases in historical ocean temperature observations have been identified and significantly reduced, resulting in improved estimates of ocean thermal expansion. Models that include all climate forcings are in good agreement with these improved observations and indicate the importance of stratospheric aerosol loadings from volcanic eruptions. Estimates of the volumes of G&ICs and their contributions to sea level rise have improved. Results from recent (but possibly incomplete) efforts to develop improved ice sheet models should be available for the 2013 IPCC projections. Improved understanding of sea level rise is paving the way for using observations to constrain projections. Understanding of the regional variations in sea level change as a result of changes in ocean properties, wind-stress patterns, and heat and freshwater inputs into the ocean is improving. Recently, estimates of sea level changes resulting from changes in Earth's gravitational field and the solid Earth response to changes in surface loading have been included in regional projections. While potentially valuable, semi-empirical models have important limitations, and their projections should be treated with caution

Resistance to the first and second generation anticoagulant rodenticides: a new perspective

Warfarin resistance was first discovered among Norway rat (Rattus norvegicus) populations in Scotland in 1958 and further reports of resistance, both in this species and in others, soon followed from other parts of Europe and the United States. Researchers quickly defined the practical impact of these resistance phenomena and developed robust methods by which to monitor their spread. These tasks were relatively simple because of the high degree of immunity to warfarin conferred by the resistance genes. Later, the second generation anticoagulants were introduced to control rodents resistant to the warfarin-like compounds, but resistance to difenacoum, bromadiolone and brodifacoum is now reported in certain localities in Europe and elsewhere. However, the adoption of test methods designed initially for use with the first generation compounds to identify resistance to compounds of the second generation has led to some practical difficulties in conducting tests and in establishing meaningful resistance baselines. In particular, the results of certain test methodologies are difficult to interpret in terms of the likely impact on practical control treatments of the resistance phenomena they seek to identify. This paper defines rodenticide resistance in the context of both first and second generation anticoagulants. It examines the advantages and disadvantages of existing laboratory and field methods used in the detection of rodent populations resistant to anticoagulants and proposes some improvements in the application of these techniques and in the interpretation of their results.

Phylogenies reveal predictive power of traditional medicine in bioprospecting

There is controversy about whether traditional medicine can guide drug discovery, and investment in ethnobotanically led research has fluctuated. One view is that traditionally used plants are not necessarily efficacious and there are no robust methods for distinguishing the ones that are most likely to be bioactive when selecting species for further testing. Here, we reconstruct a genus-level molecular phylogeny representing the 20,000 species found in the floras of three disparate biodiversity hotspots: Nepal, New Zealand and the Cape of South Africa. Borrowing phylogenetic methods from community ecology, we reveal significant clustering of the 1,500 traditionally used species, and provide a direct measure of the relatedness of the three medicinal floras. We demonstrate shared phylogenetic patterns across the floras: related plants from these regions are used to treat medical conditions in the same therapeutic areas. This strongly suggests independent discovery of plant efficacy, an interpretation corroborated by the presence of a significantly greater proportion of known bioactive species in these plant groups than in a random sample. Phylogenetic cross-cultural comparison can focus screening efforts on a subset of traditionally used plants that are richer in bioactive compounds, and could revitalise the use of traditional knowledge in bioprospecting.

Rapid assessment of historic, current and future habitat quality for biodiversity around UK Natura 2000 sites

Changes in landscape composition and structure may impact the conservation and management of protected areas. Species that depend on specific habitats are at risk of extinction when these habitats are degraded or lost. Designing robust methods to evaluate landscape composition will assist decision- and policy-making in emerging landscapes. This paper describes a rapid assessment methodology aimed at evaluating landcover quality for birds, plants, butterflies and bees around seven UK Natura 2000 sites. An expert panel assigned quality values to standard Coordination of Information on the Environment (CORINE) landcover classes for each taxonomic group. Quality was assessed based on historical (1950, 1990), current (2000) and future (2030) land-cover data, the last projected using three alternative scenarios: a growth applied strategy (GRAS), a business-as-might-beusual (BAMBU) scenario, and sustainable European development goal (SEDG) scenario. A quantitative quality index weighted the area of each land-cover parcel with a taxa-specific quality measure. Land parcels with high quality for all taxonomic groups were evaluated for temporal changes in area, size and adjacency. For all sites and taxonomic groups, the rate of deterioration of land-cover quality was greater between 1950 and 1990 than current rates or as modelled using the alternative future scenarios (2000– 2030). Model predictions indicated land-cover quality stabilized over time under the GRAS scenario, and was close to stable for the BAMBU scenario. The SEDG scenario suggested an ongoing loss of quality, though this was lower than the historical rate of c. 1% loss per decade. None of the future scenarios showed accelerated fragmentation, but rather increases in the area, adjacency and diversity of high quality land parcels in the landscape.

Traditional medicine use by cancer patients in Thailand

Ethnobotanical relevance Cancer patients commonly use traditional medicines (TM) and in Thailand these are popular for both self-medication and as prescribed by TM practitioners, and are rarely monitored. A study was conducted at Wat Khampramong, a Thai Buddhist temple herbal medicine hospice, to document some of these practices as well as the hospice regime. Materials and methods Cancer patients (n=286) were surveyed shortly after admission as to which TMs they had previously taken and perceptions of effects experienced. They were also asked to describe their current symptoms. Treatment at the hospice is built upon an 11-herb anti-cancer formula, yod-ya-mareng, prescribed for all patients, and ideally, its effects would have been evaluated. However other herbal medicines and holistic practices are integral to the regime, so instead we attempted to assess the value of the patients׳ stay at the hospice by measuring any change in symptom burden, as they perceived it. Surviving patients (n=270) were therefore asked to describe their symptoms again just before leaving. Results 42% of patients (120/286; 95% CI 36.4%, 47.8%) had used herbal medicines before their arrival, with 31.7% (38/120; 95% CI 24%, 40.4%) using several at once. Mixed effects were reported for these products. After taking the herbal regime at Khampramong, 77% (208/270 95% CI; 71.7%, 81.7%) reported benefit, and a comparison of the incidence of the most common (pain, dyspepsia, abdominal or visceral pain, insomnia, fatigue) showed statistical significance (χ2 57.1, df 7, p<0.001). Conclusions A wide range of TMs is taken by cancer patients in Thailand and considered to provide more benefit than harm, and this perception extends to the temple regime. Patients reported a significant reduction in symptoms after staying at Khampramong, indicating an improvement in quality of life, the aim of hospices everywhere. Based on this evidence, it is not possible to justify the use of TM for cancer in general, but this study suggests that further research is warranted. The uncontrolled use of TMs, many of which are uncharacterised, raises concerns, and this work also highlights the fact that validated, robust methods of assessing holistic medical regimes are urgently needed.

An evaluation of the theoretical potential and practical opportunity for using greywater for domestic purposes in Ghana

Assessments concerning the effects of climate change, water resource availability and water deprivation in West Africa have not frequently considered the positive contribution to be derived from collecting and reusing water for domestic purposes. Where the originating water is taken from a clean water source and has been used the first time for washing or bathing, this water is commonly called “greywater”. Greywater is a prolific resource that is generated wherever people live. Treated greywater can be used for domestic cleaning, for flushing toilets where appropriate, for washing cars, sometimes for watering kitchen gardens, and for clothes washing prior to rinsing. Therefore, a large theoretical potential exists to increase total water resource availability if greywater were to be widely reused. Locally treated greywater reduces the distribution network requirement, lower construction effort and cost and, wherever possible, minimising the associated carbon footprint. Such locally treated greywater offers significant practical opportunities for increasing the total available water resources at a local level. The reuse of treated greywater is one important action that will help to mitigate the reducing availability of clean water supplies in some areas, and the expected mitigation required in future aligns well with WHO/UNICEF (2012) aspirations. The evaluation of potential opportunities for prioritising greywater systems to support water reuse takes into account the availability of water resources, water use indicators and published estimates in order to understand typical patterns of water demand. The approach supports knowledge acquisition regarding local conditions for enabling capacity building for greywater reuse, the understanding of systems that are most likely to encourage greywater reuse, and practices and future actions to stimulate greywater infrastructure planning, design and implementation. Although reuse might be considered to increase the uncertainty of achieving a specified quality of the water supply, robust methods and technologies are available for local treatment. Resource strategies for greywater reuse have the potential to consistently improve water efficiency and availability in water impoverished and water stressed regions of Ghana and West Africa. Untreated greywater is referred to as “greywater”; treated greywater is referred to as “treated greywater” in this paper.

A regionally informed abundance index for supporting integrative analyses across butterfly monitoring schemes

1. The rapid expansion of systematic monitoring schemes necessitates robust methods to reliably assess species' status and trends. Insect monitoring poses a challenge where there are strong seasonal patterns, requiring repeated counts to reliably assess abundance. Butterfly monitoring schemes (BMSs) operate in an increasing number of countries with broadly the same methodology, yet they differ in their observation frequency and in the methods used to compute annual abundance indices. 2. Using simulated and observed data, we performed an extensive comparison of two approaches used to derive abundance indices from count data collected via BMS, under a range of sampling frequencies. Linear interpolation is most commonly used to estimate abundance indices from seasonal count series. A second method, hereafter the regional generalized additive model (GAM), fits a GAM to repeated counts within sites across a climatic region. For the two methods, we estimated bias in abundance indices and the statistical power for detecting trends, given different proportions of missing counts. We also compared the accuracy of trend estimates using systematically degraded observed counts of the Gatekeeper Pyronia tithonus (Linnaeus 1767). 3. The regional GAM method generally outperforms the linear interpolation method. When the proportion of missing counts increased beyond 50%, indices derived via the linear interpolation method showed substantially higher estimation error as well as clear biases, in comparison to the regional GAM method. The regional GAM method also showed higher power to detect trends when the proportion of missing counts was substantial. 4. Synthesis and applications. Monitoring offers invaluable data to support conservation policy and management, but requires robust analysis approaches and guidance for new and expanding schemes. Based on our findings, we recommend the regional generalized additive model approach when conducting integrative analyses across schemes, or when analysing scheme data with reduced sampling efforts. This method enables existing schemes to be expanded or new schemes to be developed with reduced within-year sampling frequency, as well as affording options to adapt protocols to more efficiently assess species status and trends across large geographical scales.

Formação de agenda e formulação de uma política pública no Brasil: o caso do Fundo Social do Pré-Sal

Entender o processo que engendra o Fundo Social do Pré-Sal demanda compreender a nova regulação do petróleo, aprovada em 2010. Esta tese empreende análise da trajetória da regulação do petróleo no Brasil, partindo da aprovação da Lei do Petróleo (1997), e avalia como ideias e interesses interagem com instituições vigentes, ação política e condições econômicas, para gerar nova configuração setorial. Combinando visão abrangente do institucionalismo histórico aos métodos robustos do institucionalismo da escolha racional para determinação das preferências dos atores, este trabalho aponta para a determinação histórica das escolhas dos agentes. Em termos empíricos, mostra como as condições econômicas foram determinantes na permeabilidade da política econômica brasileira aos interesses representados pelas instituições multilaterais, esclarece a importância do volume de reservas de petróleo na determinação do novo marco regulatório; e aponta razão para a escalada de valor da Petrobras após 1997.