Seawater carbonate chemistry and Strongylocentrotus purpuratus body length and gene expression pattern changes during experiments, 2011

Extensive use of fossil fuels is leading to increasing CO2 concentrations in the atmosphere and causes changes in the carbonate chemistry of the oceans which represents a major sink for anthropogenic CO2. As a result, the oceans' surface pH is expected to decrease by ca. 0.4 units by the year 2100, a major change with potentially negative consequences for some marine species. Because of their carbonate skeleton, sea urchins and their larval stages are regarded as likely to be one of the more sensitive taxa. In order to investigate sensitivity of pre-feeding (2 days post-fertilization) and feeding (4 and 7 days post-fertilization) pluteus larvae, we raised Strongylocentrotus purpuratus embryos in control (pH 8.1 and pCO2 41 Pa e.g. 399 µatm) and CO2 acidified seawater with pH of 7.7 (pCO2 134 Pa e.g. 1318 µatm) and investigated growth, calcification and survival. At three time points (day 2, day 4 and day 7 post-fertilization), we measured the expression of 26 representative genes important for metabolism, calcification and ion regulation using RT-qPCR. After one week of development, we observed a significant difference in growth. Maximum differences in size were detected at day 4 (ca. 10 % reduction in body length). A comparison of gene expression patterns using PCA and ANOSIM clearly distinguished between the different age groups (Two way ANOSIM: Global R = 1) while acidification effects were less pronounced (Global R = 0.518). Significant differences in gene expression patterns (ANOSIM R = 0.938, SIMPER: 4.3% difference) were also detected at day 4 leading to the hypothesis that differences between CO2 treatments could reflect patterns of expression seen in control experiments of a younger larva and thus a developmental artifact rather than a direct CO2 effect. We found an up regulation of metabolic genes (between 10 to 20% in ATP-synthase, citrate synthase, pyruvate kinase and thiolase at day 4) and down regulation of calcification related genes (between 23 and 36% in msp130, SM30B, SM50 at day 4). Ion regulation was mainly impacted by up regulation of Na+/K+-ATPase at day 4 (15%) and down regulation of NHE3 at day 4 (45%). We conclude that in studies in which a stressor induces an alteration in the speed of development, it is crucial to employ experimental designs with a high time resolution in order to correct for developmental artifacts. This helps prevent misinterpretation of stressor effects on organism physiology.

Who is in charge? An L2 Discourse Intonation Study on Four Prosodic Parameters to Exert the Pragmatic Function of Dominance and Control in the Context of L2 Non-specialist Public Speaking

This paper reports the findings from a study of the learning of English intonation by Spanish speakers within the discourse mode of L2 oral presentation. The purpose of this experiment is, firstly, to compare four prosodic parameters before and after an L2 discourse intonation training programme and, secondly, to confirm whether subjects, after the aforementioned L2 discourse intonation training, are able to match the form of these four prosodic parameters to the discourse-pragmatic function of dominance and control. The study designed the instructions and tasks to create the oral and written corpora and Brazil’s Pronunciation for Advanced Learners of English was adapted for the pedagogical aims of the present study. The learners’ pre- and post-tasks were acoustically analysed and a pre / post- questionnaire design was applied to interpret the acoustic analysis. Results indicate most of the subjects acquired a wider choice of the four prosodic parameters partly due to the prosodically-annotated transcripts that were developed throughout the L2 discourse intonation course. Conversely, qualitative and quantitative data reveal most subjects failed to match the forms to their appropriate pragmatic functions to express dominance and control in an L2 oral presentation.

Is Our Students Learning - QuestionMark: Extending E-Assessment Systems for Adapative Marking and Feedback

Our key contribution is a flexible, automated marking system that adds desirable functionality to existing E-Assessment systems. In our approach, any given E-Assessment system is relegated to a data-collection mechanism, whereas marking and the generation and distribution of personalised per-student feedback is handled separately by our own system. This allows content-rich Microsoft Word feedback documents to be generated and distributed to every student simultaneously according to a per-assessment schedule.

The feedback is adaptive in that it corresponds to the answers given by the student and provides guidance on where they may have gone wrong. It is not limited to simple multiple choice which are the most prescriptive question type offered by most E-Assessment Systems and as such most straightforward to mark consistently and provide individual per-alternative feedback strings. It is also better equipped to handle the use of mathematical symbols and images within the feedback documents which is more flexible than existing E-Assessment systems, which can only handle simple text strings.

As well as MCQs the system reliably and robustly handles Multiple Response, Text Matching and Numeric style questions in a more flexible manner than Questionmark: Perception and other E-Assessment Systems. It can also reliably handle multi-part questions where the response to an earlier question influences the answer to a later one and can adjust both scoring and feedback appropriately.

New question formats can be added at any time provided a corresponding marking method conforming to certain templates can also be programmed. Indeed, any question type for which a programmatic method of marking can be devised may be supported by our system. Furthermore, since the student’s response to each is question is marked programmatically, our system can be set to allow for minor deviations from the correct answer, and if appropriate award partial marks.

Organisational and systems factors impacting on patient safety in acute care organisations: lessons from four multi-site research studies

Background Patient safety is concerned with preventable harm in healthcare, a subject that became a focus for study in the UK in the late 1990s. How to improve patient safety, presented both a practical and a research challenge in the early 2000s, leading to the eleven publications presented in this thesis. Research question The overarching research question was: What are the key organisational and systems factors that impact on patient safety, and how can these best be researched? Methods Research was conducted in over 40 acute care organisations in the UK and Europe between 2006 and 2013. The approaches included surveys, interviews, documentary analysis and non-participant observation. Two studies were longitudinal. Results The findings reveal the nature and extent of poor systems reliability and its effect on patient safety; the factors underpinning cases of patient harm; the cultural issues impacting on safety and quality; and the importance of a common language for quality and safety across an organisation. Across the publications, nine key organisational and systems factors emerged as important for patient safety improvement. These include leadership stability; data infrastructure; measurement capability; standardisation of clinical systems; and creating an open and fair collective culture where poor safety is challenged. Conclusions and contribution to knowledge The research presented in the publications has provided a more complete understanding of the organisation and systems factors underpinning safer healthcare. Lessons are drawn to inform methods for future research, including: how to define success in patient safety improvement studies; how to take into account external influences during longitudinal studies; and how to confirm meaning in multi-language research. Finally, recommendations for future research include assessing the support required to maintain a patient safety focus during periods of major change or austerity; the skills needed by healthcare leaders; and the implications of poor data infrastructure.

Machine learning and data decompositions for complex networked dynamical systems

Thesis (Ph.D.)--University of Washington, 2016-08

Urban water sustainability: framework and application

Urban areas such as megacities (those with populations greater than 10 million) are hotspots of global water use and thus face intense water management challenges. Urban areas are influenced by local interactions between human and natural systems and interact with distant systems through flows of water, food, energy, people, information, and capital. However, analyses of water sustainability and the management of water flows in urban areas are often fragmented. There is a strong need to apply integrated frameworks to systematically analyze urban water dynamics and factors that influence these dynamics. We apply the framework of telecoupling (socioeconomic and environmental interactions over distances) to analyze urban water issues, using Beijing as a demonstration megacity. Beijing exemplifies the global water sustainability challenge for urban settings. Like many other cities, Beijing has experienced drastic reductions in quantity and quality of both surface water and groundwater over the past several decades; it relies on the import of real and virtual water from sending systems to meet its demand for clean water, and releases polluted water to other systems (spillover systems). The integrative framework we present demonstrates the importance of considering socioeconomic and environmental interactions across telecoupled human and natural systems, which include not only Beijing (the water-receiving system) but also water-sending systems and spillover systems. This framework helps integrate important components of local and distant human–nature interactions and incorporates a wide range of local couplings and telecouplings that affect water dynamics, which in turn generate significant socioeconomic and environmental consequences, including feedback effects. The application of the framework to Beijing reveals many research gaps and management needs. We also provide a foundation to apply the telecoupling framework to better understand and manage water sustainability in other cities around the world.

Memory effects and geometrical considerations in open quantum systems

This thesis discusses memory effects in open quantum systems with an emphasis on the Breuer, Laine, Piilo (BLP) measure of non-Markovianity. It is shown how the calculation of the measure can be simplifed and how quantum information protocols can bene t from memory e ects. The superdense coding protocol is used as an example of this. The quantum Zeno effect will also be studied from the point of view of memory e ects. Finally the geometric ideas used in simplifying the calculation of the BLP measure are applied in studying the amount of resources needed for detecting bipartite quantum correlations. It is shown that to decide without prior information if an unknown quantum state is entangled or not, an informationally complete measurement is required. The first part of the thesis contains an introduction to the theoretical ideas such as quantum states, closed and open quantum systems and necessary mathematical tools. The theory is then applied in the second part of the thesis as the results obtained in the original publications I-VI are presented and discussed.

Ecology and physical condition of red deer in the Iberian Peninsula: implications for management

The red deer (Cervus elaphus) is currently one of the most widespread and abundant wild ungulates in the Iberian Peninsula and is extremely important both ecologically, as a key species for the functioning of the ecosystems, and economically, as a major game species. In Iberia, red deer populations are subjected to different management systems that may affect the physical condition of the individuals, with further consequences for population dynamics. Studies investigating the effects of management practices and environmental conditions on the performance of red deer are still rare regarding Mediterranean ecosystems. Much of the knowledge concerning the ecology of red deer and the impact of management on its physical condition is based on studies conducted in northern and central regions of Europe, where climatological features and management practices differ from those observed in the Mediterranean areas of Iberia. Studies on a biogeographical scale can provide important insights into the relationships between species and a particular environment and contribute to the development of more targeted and appropriate management practices. The optimisation of sampling procedures and the fine-tuning of pre-existing analytical techniques are also fundamental to a more cost-effective monitoring and, therefore, are of enormous value to wildlife managers. In this context, the main aims of this thesis were: 1) to optimise the procedures used to assess the physical condition of red deer; and 2) to identify relevant management and environmental factors affecting the nutritional condition and stress physiology of red deer in the Mediterranean ecosystems of Iberia, as well as any potential interactions between those factors. Two studies with a methodological focus, presented in the first part of the thesis, demonstrated that the physical condition of red deer can be evaluated more simply, using more cost- and time-effective procedures than those traditionally used: i) it was shown that only one kidney and its associated fat is enough to assess nutritional condition in red deer; and ii) the feasibility of using near infrared spectroscopy to predict the concentrations of stress hormone metabolites was demonstrated using faeces of red deer for the first time. Subsequently, two large-scale observational studies, conducted in representative red deer populations found in Mediterranean Iberia, highlighted the importance of considering seasonal environmental variations and variables related to hunting management practices to better understand the nutritional and physiological ecology of red deer. High population densities had adverse effects on the nutritional condition of the deer and were associated with increased stress levels in natural populations without supplementary feeding. Massive hunting events involving the use of hounds were also identified as a potential source of chronic stress in red deer. The research presented in this thesis has clear implications regarding the management and monitoring of red deer populations in Mediterranean environments and is intended to help wildlife managers to implement more effective monitoring programmes and sustainable management practices.

Towards Proactive Context-aware Computing and Systems

A primary goal of context-aware systems is delivering the right information at the right place and right time to users in order to enable them to make effective decisions and improve their quality of life. There are three key requirements for achieving this goal: determining what information is relevant, personalizing it based on the users’ context (location, preferences, behavioral history etc.), and delivering it to them in a timely manner without an explicit request from them. These requirements create a paradigm that we term as “Proactive Context-aware Computing”. Most of the existing context-aware systems fulfill only a subset of these requirements. Many of these systems focus only on personalization of the requested information based on users’ current context. Moreover, they are often designed for specific domains. In addition, most of the existing systems are reactive - the users request for some information and the system delivers it to them. These systems are not proactive i.e. they cannot anticipate users’ intent and behavior and act proactively without an explicit request from them. In order to overcome these limitations, we need to conduct a deeper analysis and enhance our understanding of context-aware systems that are generic, universal, proactive and applicable to a wide variety of domains. To support this dissertation, we explore several directions. Clearly the most significant sources of information about users today are smartphones. A large amount of users’ context can be acquired through them and they can be used as an effective means to deliver information to users. In addition, social media such as Facebook, Flickr and Foursquare provide a rich and powerful platform to mine users’ interests, preferences and behavioral history. We employ the ubiquity of smartphones and the wealth of information available from social media to address the challenge of building proactive context-aware systems. We have implemented and evaluated a few approaches, including some as part of the Rover framework, to achieve the paradigm of Proactive Context-aware Computing. Rover is a context-aware research platform which has been evolving for the last 6 years. Since location is one of the most important context for users, we have developed ‘Locus’, an indoor localization, tracking and navigation system for multi-story buildings. Other important dimensions of users’ context include the activities that they are engaged in. To this end, we have developed ‘SenseMe’, a system that leverages the smartphone and its multiple sensors in order to perform multidimensional context and activity recognition for users. As part of the ‘SenseMe’ project, we also conducted an exploratory study of privacy, trust, risks and other concerns of users with smart phone based personal sensing systems and applications. To determine what information would be relevant to users’ situations, we have developed ‘TellMe’ - a system that employs a new, flexible and scalable approach based on Natural Language Processing techniques to perform bootstrapped discovery and ranking of relevant information in context-aware systems. In order to personalize the relevant information, we have also developed an algorithm and system for mining a broad range of users’ preferences from their social network profiles and activities. For recommending new information to the users based on their past behavior and context history (such as visited locations, activities and time), we have developed a recommender system and approach for performing multi-dimensional collaborative recommendations using tensor factorization. For timely delivery of personalized and relevant information, it is essential to anticipate and predict users’ behavior. To this end, we have developed a unified infrastructure, within the Rover framework, and implemented several novel approaches and algorithms that employ various contextual features and state of the art machine learning techniques for building diverse behavioral models of users. Examples of generated models include classifying users’ semantic places and mobility states, predicting their availability for accepting calls on smartphones and inferring their device charging behavior. Finally, to enable proactivity in context-aware systems, we have also developed a planning framework based on HTN planning. Together, these works provide a major push in the direction of proactive context-aware computing.

From Cash to Electronic Payments: Microeconomic, Macroeconomic, and Policy Aspects of Retail Payment Systems

This dissertation explores three aspects of the economics and policy issues surrounding retail payments (low-value frequent payments): the microeconomic aspect, by measuring costs associated with retail payment instruments; the macroeconomic aspect, by quantifying the impact of the use of electronic rather than paper-based payment instruments on consumption and GDP; and the policy aspect, by identifying barriers that keep countries stuck with outdated payment systems, and recommending policy interventions to move forward with payments modernization. Payment system modernization has become a prominent part of the financial sector reform agenda in many advanced and developing countries. Greater use of electronic payments rather than cash and other paper-based instruments would have important economic and social benefits, including lower costs and thereby increased economic efficiency and higher incomes, while broadening access to the financial system, notably for people with moderate and low incomes. The dissertation starts with a general introduction on retail payments. Chapter 1 develops a theoretical model for measuring payments costs, and applies the model to Guyana—an emerging market in the midst of the transition from paper to electronic payments. Using primary survey data from Guyanese consumers, the results of the analysis indicate that annual costs related to the use of cash by consumers reach 2.5 percent of the country’s GDP. Switching to electronic payment instruments would provide savings amounting to 1 percent of GDP per year. Chapter 2 broadens the analysis to calculate the macroeconomic impacts of a move to electronic payments. Using a unique panel dataset of 76 countries across the 17-year span from 1998 to 2014 and a pooled OLS country fixed effects model, Chapter 2 finds that on average, use of debit and credit cards contribute USD 16.2 billion to annual global consumption, and USD 160 billion to overall annual global GDP. Chapter 3 provides an in-depth assessment of the Albanian payment cards and remittances market and recommends a set of incentives and regulations (both carrots and sticks) that would allow the country to modernize its payment system. Finally, the conclusion summarizes the lessons of the dissertation’s research and brings forward issues to be explored by future research in the retail payments area.

RESULTADOS DO 13º CONTECSI USP – CONGRESSO INTERNACIONAL DE GESTÃO DA TECNOLOGIA E SISTEMAS DE INFORMAÇÃO; 36th WCARS – WORLD CONTINUOUS AUDITING AND REPORTING SYSTEMS SYMPOSIUM; 2º TOI ECA USP

In this document, we wish to describe statistics, data and the importance of the 13th CONTECSI – International Conference on Information Systems and Technology Management, which took place in the University of São Paulo, from June 1st through 3rd and was organized by TECSI/EAC/FEA/USP/ECA/POLI. This report presents statistics of the 13th CONTECSI, Goals and Objectives, Program, Plenary Sessions, Doctoral Consortium, Parallel Sessions, Honorable Mentions and Committees. We would like to point out the huge importance of the financial aid given by CAPES, CNPq, FAPESP, as well as the support of FEA USP, POLI USP, ECA USP, ANPAD, AIS, ISACA, UNINOVE, Mackenzie, Universidade do Porto, Rutgers School/USA, São Paulo Convention Bureau and CCINT-FEA-USP.

Ecology, physiology and performance in high-rate anaerobic digestion

The design demands on water and sanitation engineers are rapidly changing. The global population is set to rise from 7 billion to 10 billion by 2083. Urbanisation in developing regions is increasing at such a rate that a predicted 56% of the global population will live in an urban setting by 2025. Compounding these problems, the global water and energy crises are impacting the Global North and South alike. High-rate anaerobic digestion offers a low-cost, low-energy treatment alternative to the energy intensive aerobic technologies used today. Widespread implementation however is hindered by the lack of capacity to engineer high-rate anaerobic digestion for the treatment of complex wastes such as sewage. This thesis utilises the Expanded Granular Sludge Bed bioreactor (EGSB) as a model system in which to study the ecology, physiology and performance of high-rate anaerobic digestion of complex wastes. The impacts of a range of engineered parameters including reactor geometry, wastewater type, operating temperature and organic loading rate are systematically investigated using lab-scale EGSB bioreactors. Next generation sequencing of 16S amplicons is utilised as a means of monitoring microbial ecology. Microbial community physiology is monitored by means of specific methanogenic activity testing and a range of physical and chemical methods are applied to assess reactor performance. Finally, the limit state approach is trialled as a method for testing the EGSB and is proposed as a standard method for biotechnology testing enabling improved process control at full-scale. The arising data is assessed both qualitatively and quantitatively. Lab-scale reactor design is demonstrated to significantly influence the spatial distribution of the underlying ecology and community physiology in lab-scale reactors, a vital finding for both researchers and full-scale plant operators responsible for monitoring EGSB reactors. Recurrent trends in the data indicate that hydrogenotrophic methanogenesis dominates in high-rate anaerobic digestion at both full- and lab-scale when subject to engineered or operational stresses including low-temperature and variable feeding regimes. This is of relevance for those seeking to define new directions in fundamental understanding of syntrophic and competitive relations in methanogenic communities and also to design engineers in determining operating parameters for full-scale digesters. The adoption of the limit state approach enabled identification of biological indicators providing early warning of failure under high-solids loading, a vital insight for those currently working empirically towards the development of new biotechnologies at lab-scale.

Secular and tidal evolution of circumbinary systems

We investigate the secular dynamics of three-body circumbinary systems under the effect of tides. We use the octupolar non-restricted approximation for the orbital interactions, general relativity corrections, the quadrupolar approximation for the spins, and the viscous linear model for tides. We derive the averaged equations of motion in a simplified vectorial formalism, which is suitable to model the long-term evolution of a wide variety of circumbinary systems in very eccentric and inclined orbits. In particular, this vectorial approach can be used to derive constraints for tidal migration, capture in Cassini states, and stellar spin–orbit misalignment. We show that circumbinary planets with initial arbitrary orbital inclination can become coplanar through a secular resonance between the precession of the orbit and the precession of the spin of one of the stars. We also show that circumbinary systems for which the pericenter of the inner orbit is initially in libration present chaotic motion for the spins and for the eccentricity of the outer orbit. Because our model is valid for the non-restricted problem, it can also be applied to any three-body hierarchical system such as star–planet–satellite systems and triple stellar systems.

Context dependency of trait repeatability and its relevance for management and conservation of fish populations

Repeatability of behavioural and physiological traits is increasingly a focus for animal researchers, for which fish have become important models. Almost all of this work has been done in the context of evolutionary ecology, with few explicit attempts to apply repeatability and context dependency of trait variation toward understanding conservation-related issues. Here, we review work examining the degree to which repeatability of traits (such as boldness, swimming performance, metabolic rate and stress responsiveness) is context dependent. We review methods for quantifying repeatability (distinguishing between within-context and across-context repeatability) and confounding factors that may be especially problematic when attempting to measure repeatability in wild fish. Environmental factors such temperature, food availability, oxygen availability, hypercapnia, flow regime and pollutants all appear to alter trait repeatability in fishes. This suggests that anthropogenic environmental change could alter evolutionary trajectories by changing which individuals achieve the greatest fitness in a given set of conditions. Gaining a greater understanding of these effects will be crucial for our ability to forecast the effects of gradual environmental change, such as climate change and ocean acidification, the study of which is currently limited by our ability to examine trait changes over relatively short time scales. Also discussed are situations in which recent advances in technologies associated with electronic tags (biotelemetry and biologging) and respirometry will help to facilitate increased quantification of repeatability for physiological and integrative traits, which so far lag behind measures of repeatability of behavioural traits.

High-stakes testing and Educational Governance – insights and innovations in European school systems. Special Issue Editorial

International research with regard to the intended as well as to the unintended outcomes and effects of high-stakes testing shows that the impact of high-stakes tests has important consequences for the participants involved in the respective educational systems. The purpose of this special issue is to examine the implementation of high-stakes testing in different national school systems and to refer to the effects in view of the concept of Educational Governance. (DIPF/Orig.)