An Efficient User-Level Shared Memory Mechanism for Application-Specific Extensions

This paper focuses on an efficient user-level method for the deployment of application-specific extensions, using commodity operating systems and hardware. A sandboxing technique is described that supports multiple extensions within a shared virtual address space. Applications can register sandboxed code with the system, so that it may be executed in the context of any process. Such code may be used to implement generic routines and handlers for a class of applications, or system service extensions that complement the functionality of the core kernel. Using our approach, application-specific extensions can be written like conventional user-level code, utilizing libraries and system calls, with the advantage that they may be executed without the traditional costs of scheduling and context-switching between process-level protection domains. No special hardware support such as segmentation or tagged translation look-aside buffers (TLBs) is required. Instead, our ``user-level sandboxing'' mechanism requires only paged-based virtual memory support, given that sandboxed extensions are either written by a trusted source or are guaranteed to be memory-safe (e.g., using type-safe languages). Using a fast method of upcalls, we show how our mechanism provides significant performance improvements over traditional methods of invoking user-level services. As an application of our approach, we have implemented a user-level network subsystem that avoids data copying via the kernel and, in many cases, yields far greater network throughput than kernel-level approaches.

SymbolDesign: A User-centered Method to Design Pen-based Interfaces and Extend the Functionality of Pointer Input Devices

A method called "SymbolDesign" is proposed that can be used to design user-centered interfaces for pen-based input devices. It can also extend the functionality of pointer input devices such as the traditional computer mouse or the Camera Mouse, a camera-based computer interface. Users can create their own interfaces by choosing single-stroke movement patterns that are convenient to draw with the selected input device and by mapping them to a desired set of commands. A pattern could be the trace of a moving finger detected with the Camera Mouse or a symbol drawn with an optical pen. The core of the SymbolDesign system is a dynamically created classifier, in the current implementation an artificial neural network. The architecture of the neural network automatically adjusts according to the complexity of the classification task. In experiments, subjects used the SymbolDesign method to design and test the interfaces they created, for example, to browse the web. The experiments demonstrated good recognition accuracy and responsiveness of the user interfaces. The method provided an easily-designed and easily-used computer input mechanism for people without physical limitations, and, with some modifications, has the potential to become a computer access tool for people with severe paralysis.

Users & use: An exploration of the interaction between the user and the digital archive

This thesis will examine the interaction between the user and the digital archive. The aim of the study is to support an in-depth examination of the interaction process, with a view to making recommendations and tools, for system designers and archival professionals, to promote digital archive domain development. Following a comprehensive literature review process, an urgent requirement for models was identified. The Model of Contextual Interaction presented in this thesis, aims to provide a conceptual model through which the interaction process, between the user and the digital archive, can be examined. Using the five-phased research development framework, the study will present a structured account of its methods, using a multi-method methodology to ensuring robust data collection and analysis. The findings of the study are presented across the Model of Contextual Interaction, and provide a basis on which recommendations and tools for system designers have been made. The thesis concludes with a summary of key findings, and a reflective account of how the findings and the Model of Contextual Interaction have impacted digital provision within the archive domain and how the model could be applied to other domains.

Defining metabolically healthy obesity: role of dietary and lifestyle factors

Background: There is a current lack of consensus on defining metabolically healthy obesity (MHO). Limited data on dietary and lifestyle factors and MHO exist. The aim of this study is to compare the prevalence, dietary factors and lifestyle behaviours of metabolically healthy and unhealthy obese and non-obese subjects according to different metabolic health criteria. Method: Cross-sectional sample of 1,008 men and 1,039 women aged 45-74 years participated in the study. Participants were classified as obese (BMI ≥30kg/m2) and non-obese (BMI <30kg/m2). Metabolic health status was defined using five existing MH definitions based on a range of cardiometabolic abnormalities. Dietary composition and quality, food pyramid servings, physical activity, alcohol and smoking behaviours were examined. Results: The prevalence of MHO varied considerably between definitions (2.2% to 11.9%), was higher among females and generally increased with age. Agreement between MHO classifications was poor. Among the obese, prevalence of MH was 6.8% to 36.6%. Among the non-obese, prevalence of metabolically unhealthy subjects was 21.8% to 87%. Calorie intake, dietary macronutrient composition, physical activity, alcohol and smoking behaviours were similar between the metabolically healthy and unhealthy regardless of BMI. Greater compliance with food pyramid recommendations and higher dietary quality were positively associated with metabolic health in obese (OR 1.45-1.53 unadjusted model) and non-obese subjects (OR 1.37-1.39 unadjusted model), respectively. Physical activity was associated with MHO defined by insulin resistance (OR 1.87, 95% CI 1.19-2.92, p = 0.006).

Control circuits for avalanche photodiodes

Avalanche Photodiodes (APDs) have been used in a wide range of low light sensing applications such as DNA sequencing, quantum key distribution, LIDAR and medical imaging. To operate the APDs, control circuits are required to achieve the desired performance characteristics. This thesis presents the work on development of three control circuits including a bias circuit, an active quench and reset circuit and a gain control circuit all of which are used for control and performance enhancement of the APDs. The bias circuit designed is used to bias planar APDs for operation in both linear and Geiger modes. The circuit is based on a dual charge pumps configuration and operates from a 5 V supply. It is capable of providing milliamp load currents for shallow-junction planar APDs that operate up to 40 V. With novel voltage regulators, the bias voltage provided by the circuit can be accurately controlled and easily adjusted by the end user. The circuit is highly integrable and provides an attractive solution for applications requiring a compact integrated APD device. The active quench and reset circuit is designed for APDs that operate in Geiger-mode and are required for photon counting. The circuit enables linear changes in the hold-off time of the Geiger-mode APD (GM-APD) from several nanoseconds to microseconds with a stable setting step of 6.5 ns. This facilitates setting the optimal `afterpulse-free' hold-off time for any GM-APD via user-controlled digital inputs. In addition this circuit doesn’t require an additional monostable or pulse generator to reset the detector, thus simplifying the circuit. Compared to existing solutions, this circuit provides more accurate and simpler control of the hold-off time while maintaining a comparable maximum count-rate of 35.2 Mcounts/s. The third circuit designed is a gain control circuit. This circuit is based on the idea of using two matched APDs to set and stabilize the gain. The circuit can provide high bias voltage for operating the planar APD, precisely set the APD’s gain (with the errors of less than 3%) and compensate for the changes in the temperature to maintain a more stable gain. The circuit operates without the need for external temperature sensing and control electronics thus lowering the system cost and complexity. It also provides a simpler and more compact solution compared to previous designs. The three circuits designed in this project were developed independently of each other and are used for improving different performance characteristics of the APD. Further research on the combination of the three circuits will produce a more compact APD-based solution for a wide range of applications.

MyRoom: A user-centred model of affective responsive architecture

Can my immediate physical environment affect how I feel? The instinctive answer to this question must be a resounding “yes”. What might seem a throwaway remark is increasingly borne out by research in environmental and behavioural psychology, and in the more recent discipline of Evidence-Based Design. Research outcomes are beginning to converge with findings in neuroscience and neurophysiology, as we discover more about how the human brain and body functions, and reacts to environmental stimuli. What we see, hear, touch, and sense affects each of us psychologically and, by extension, physically, on a continual basis. The physical characteristics of our daily environment thus have the capacity to profoundly affect all aspects of our functioning, from biological systems to cognitive ability. This has long been understood on an intuitive basis, and utilised on a more conscious basis by architects and other designers. Recent research in evidence-based design, coupled with advances in neurophysiology, confirm what have been previously held as commonalities, but also illuminate an almost frightening potential to do enormous good, or alternatively, terrible harm, by virtue of how we make our everyday surroundings. The thesis adopts a design methodology in its approach to exploring the potential use of wireless sensor networks in environments for elderly people. Vitruvian principles of “commodity, firmness and delight” inform the research process and become embedded in the final design proposals and research conclusions. The issue of person-environment fit becomes a key principle in describing a model of continuously-evolving responsive architecture which makes the individual user its focus, with the intention of promoting wellbeing. The key research questions are: What are the key system characteristics of an adaptive therapeutic single-room environment? How can embedded technologies be utilised to maximise the adaptive and therapeutic aspects of the personal life-space of an elderly person with dementia?.

User experience of mobile cloud applications - current state and future directions

The increasing penetration rate of feature rich mobile devices such as smartphones and tablets in the global population has resulted in a large number of applications and services being created or modified to support mobile devices. Mobile cloud computing is a proposed paradigm to address the resource scarcity of mobile devices in the face of demand for more computing intensive tasks. Several approaches have been proposed to confront the challenges of mobile cloud computing, but none has used the user experience as the primary focus point. In this paper we evaluate these approaches in respect of the user experience, propose what future research directions in this area require to provide for this crucial aspect, and introduce our own solution.

Monitoring behaviours and experiences before, during and after pregnancy in Ireland

Background: On-going surveillance of behaviours during pregnancy is an important but overlooked population health activity that is particularly lacking in Ireland. Few, if any, nationally representative estimates of most maternal behaviours and experiences are available. While on-going surveillance of maternal behaviours has not been a priority thus far in European countries including Ireland, on-going surveillance was identified as a key priority in the United States (US) during the 1980’s when the Pregnancy Risk Assessment Monitoring System (PRAMS), was established. Today, PRAMS is the only surveillance programme of maternal behaviours and experiences world-wide. Although on-going prevalence estimates are required in Ireland, studies which examine the offspring health effects of maternal behaviours are also required, since various questions regarding maternal exposures and their offspring health effects remain unanswered. Gestational alcohol consumption is one such important maternal exposure which is common in pregnancy, though its offspring health effects are unclear, particularly at lower or moderate levels. Thus, guidelines internationally have not reached consensus on safe alcohol recommendations for pregnant women. The aims of this thesis are to implement the PRAMS in Ireland (PRAMS Ireland), to describe the prevalence of health behaviours around the time of pregnancy in Ireland and to examine the effect of health behaviours on pregnancy and child outcomes (specifically the relationship between alcohol use during pregnancy and infant and child growth). Structure: In Chapter 1, a brief background and rationale for the work, as well as the thesis aims and objective is provided. A detailed description of the design and implementation of PRAMS Ireland is described in Chapter 2. Chapter 3 and Chapter 4 describe the methodological results of the implementation of the PRAMS Ireland pilot study and PRAMS Ireland main study. In Chapter 5, a comparison of alcohol prevalence in two Irish studies (PRAMS Ireland and Growing up in Ireland (GUI)) and one multi-centre prospective cohort study, Screening for Pregnancy Endpoints (SCOPE) Study is detailed. Chapter 6 describes findings on adherence to National Clinical Guidelines on health behaviours and nutrition around the time of pregnancy in PRAMS Ireland. Findings on exposure to alcohol use in pregnancy and infant growth outcomes are described in Chapter 7 and Chapter 8. The results of analysis conducted to examine the impact of gestational alcohol use on offspring growth trajectories to age ten are described in Chapter 9. Finally, a discussion of the findings, strengths and limitations of the thesis, direction for future research, policy, practice and public health implications are discussed in Chapter 10.Results: Implementation of PRAMS: PRAMS may be an effective system for the surveillance of health behaviours around the time of pregnancy in the Irish context. PRAMS Ireland had high response rates (67% and 61% response rates in the pilot and main study respectively), high item completion rates and valid prevalence estimates for many health behaviours. Examining prevalence of health behaviours: We found high levels of alcohol consumption before and during pregnancy, poor adherence to healthy diets and high levels of smoking before and during pregnancy among women in Ireland. Socially disadvantaged women had higher rates of deleterious health behaviours before pregnancy, although women with the most deleterious behaviour profiles before pregnancy appeared to experience the greatest gain in protective health behaviours during pregnancy. The impact of alcohol use on infant and offspring growth: We found that low and moderate levels of alcohol use did not impact on birth outcomes or offspring growth whereas heavy alcohol consumption resulted in reduced birth length and birth weight; however, this finding was not consistently observed across all studies. Selection, reporting and confounding biases which are common in observational research could be masking harmful effects. Conclusion: PRAMS is a valid and feasible method of surveillance of health behaviours around the time of pregnancy in Ireland. A surveillance program of maternal behaviours and experiences is immediately warranted due to high levels of deleterious health behaviours around the time of pregnancy in Ireland. Although our results do not indicate any evidence of harm, given the quality of evidence available, abstinence and advice of abstinence from alcohol may be the most prudent choice for patients and healthcare professionals respectively. Further studies of the effects of gestational alcohol use are required; particularly those which can reduce selection bias, reporting bias and confounding.

Practice-based personas: integrated user and practice models

Practices are routinised behaviours with social and material components and complex relationships over space and time. Practice-based design goes beyond interaction design to consider how these components and their relationships impact on the formation and enactment of a practice, where technology is just one part of the practice. Though situated user-centred design methods such as participatory design are employed for the design of practice, demand exists for additional methods and tools in this area. This paper introduces practice-based personas as an extension of the persona approach popular in interaction design, and demonstrates how a set of practice-based personas was developed for a given domain – academic practice. The three practice-based personas developed here are linked to a catalogue of forty practices, offering designers both a user perspective and a practice perspective when designing for the domain.

Delivering mobile cloud services to the user: description, discovery, and consumption

The mobile cloud computing paradigm can offer relevant and useful services to the users of smart mobile devices. Such public services already exist on the web and in cloud deployments, by implementing common web service standards. However, these services are described by mark-up languages, such as XML, that cannot be comprehended by non-specialists. Furthermore, the lack of common interfaces for related services makes discovery and consumption difficult for both users and software. The problem of service description, discovery, and consumption for the mobile cloud must be addressed to allow users to benefit from these services on mobile devices. This paper introduces our work on a mobile cloud service discovery solution, which is utilised by our mobile cloud middleware, Context Aware Mobile Cloud Services (CAMCS). The aim of our approach is to remove complex mark-up languages from the description and discovery process. By means of the Cloud Personal Assistant (CPA) assigned to each user of CAMCS, relevant mobile cloud services can be discovered and consumed easily by the end user from the mobile device. We present the discovery process, the architecture of our own service registry, and service description structure. CAMCS allows services to be used from the mobile device through a user's CPA, by means of user defined tasks. We present the task model of the CPA enabled by our solution, including automatic tasks, which can perform work for the user without an explicit request.

Evaluation of Altered Kras Codon Bias and NOS Inhibition During Lung Tumorigenesis

The small GTPases HRAS, NRAS and KRAS are mutated in approximately one-third of all human cancers, rendering the proteins constitutively active and oncogenic. Lung cancer is the leading cause of cancer deaths worldwide, and more than 20% of human lung cancers harbor mutations in RAS, with 98% of those occurring in the KRAS isoform. While there have been many advances in the understanding of KRAS–driven lung tumorigenesis, it remains a therapeutic challenge. To further this understanding and assess novel approaches for treatment, I have investigated two aspects of Kras–driven tumorigenesis in the lung:

(I) Despite nearly identical protein sequences, the three RAS proto-oncogenes exhibit divergent codon usage. Of the three isoforms, KRAS contains the most rare codons resulting in lower levels of KRAS protein expression relative to HRAS and NRAS. To determine the consequences of rare codon bias during de novo tumorigenesis, we created a knock-in Krasex3op mouse in which synonymous mutations in exon 3 converted codons from rare to common. These mice had reduced tumor burden and fewer oncogenic mutations in the Krasex3op allele following carcinogen exposure. The reduction in tumorigenesis appeared to be a product of rare codons affecting both the oncogenic and non–oncogenic alleles. Converting rare codons to common codons yielded a more potent oncogenic allele that promoted growth arrest and enhanced tumor suppression by the non-oncogenic allele. Thus, rare codons play an integral role in Kras tumorigenesis.

(II) Lung cancer patients exhale higher levels of NO and iNOS-/- mice are resistant to chemically induced lung tumorigenesis. I hypothesize that NO promotes Kras–driven lung adenocarcinoma, and NOS inhibition may decrease Kras–driven lung tumorigenesis. To test this hypothesis, I assessed efficacy of the NOS inhibitor L–NAME in a genetically engineered mouse model of Kras-driven lung adenocarcinoma. Adenoviral Cre recombinase was delivered into the lungs intranasally, resulting in expression of oncogenic KrasG12D and dominant-negative Trp53R172H in lung epithelial cells. L–NAME treatment was provided in the water and continued until survival endpoints. In this model, L–NAME treatment decreased tumor growth and prolonged survival. These data establish a potential clinical role for NOS inhibition in lung cancer treatment.

Barriers to and facilitators of interventions to counter publication bias: thematic analysis of scholarly articles and stakeholder interviews.

BACKGROUND: When the nature and direction of research results affect their chances of publication, a distortion of the evidence base - termed publication bias - results. Despite considerable recent efforts to implement measures to reduce the non-publication of trials, publication bias is still a major problem in medical research. The objective of our study was to identify barriers to and facilitators of interventions to prevent or reduce publication bias. METHODS: We systematically reviewed the scholarly literature and extracted data from articles. Further, we performed semi-structured interviews with stakeholders. We performed an inductive thematic analysis to identify barriers to and facilitators of interventions to counter publication bias. RESULTS: The systematic review identified 39 articles. Thirty-four of 89 invited interview partners agreed to be interviewed. We clustered interventions into four categories: prospective trial registration, incentives for reporting in peer-reviewed journals or research reports, public availability of individual patient-level data, and peer-review/editorial processes. Barriers we identified included economic and personal interests, lack of financial resources for a global comprehensive trial registry, and different legal systems. Facilitators identified included: raising awareness of the effects of publication bias, providing incentives to make data publically available, and implementing laws to enforce prospective registration and reporting of clinical trial results. CONCLUSIONS: Publication bias is a complex problem that reflects the complex system in which it occurs. The cooperation amongst stakeholders to increase public awareness of the problem, better tailoring of incentives to publish, and ultimately legislative regulations have the greatest potential for reducing publication bias.