Subdural electroencephalogram analysis for extracting discriminating measures in epileptogenic data

This dissertation introduces an integrated algorithm for a new application dedicated at discriminating between electrodes leading to a seizure onset and those that do not, using interictal subdural EEG data. The significance of this study is in determining among all of these channels, all containing interictal spikes, why some electrodes eventually lead to seizure while others do not. A first finding in the development process of the algorithm is that these interictal spikes had to be asynchronous and should be located in different regions of the brain, before any consequential interpretations of EEG behavioral patterns are possible. A singular merit of the proposed approach is that even when the EEG data is randomly selected (independent of the onset of seizure), we are able to classify those channels that lead to seizure from those that do not. It is also revealed that the region of ictal activity does not necessarily evolve from the tissue located at the channels that present interictal activity, as commonly believed.^ The study is also significant in terms of correlating clinical features of EEG with the patient's source of ictal activity, which is coming from a specific subset of channels that present interictal activity. The contributions of this dissertation emanate from (a) the choice made on the discriminating parameters used in the implementation, (b) the unique feature space that was used to optimize the delineation process of these two type of electrodes, (c) the development of back-propagation neural network that automated the decision making process, and (d) the establishment of mathematical functions that elicited the reasons for this delineation process. ^

Phylogenetic analysis of within -host serially-sampled viral data

The primary goal of this dissertation is the study of patterns of viral evolution inferred from serially-sampled sequence data, i.e., sequence data obtained from strains isolated at consecutive time points from a single patient or host. RNA viral populations have an extremely high genetic variability, largely due to their astronomical population sizes within host systems, high replication rate, and short generation time. It is this aspect of their evolution that demands special attention and a different approach when studying the evolutionary relationships of serially-sampled sequence data. New methods that analyze serially-sampled data were developed shortly after a groundbreaking HIV-1 study of several patients from which viruses were isolated at recurring intervals over a period of 10 or more years. These methods assume a tree-like evolutionary model, while many RNA viruses have the capacity to exchange genetic material with one another using a process called recombination. ^ A genealogy involving recombination is best described by a network structure. A more general approach was implemented in a new computational tool, Sliding MinPD, one that is mindful of the sampling times of the input sequences and that reconstructs the viral evolutionary relationships in the form of a network structure with implicit representations of recombination events. The underlying network organization reveals unique patterns of viral evolution and could help explain the emergence of disease-associated mutants and drug-resistant strains, with implications for patient prognosis and treatment strategies. In order to comprehensively test the developed methods and to carry out comparison studies with other methods, synthetic data sets are critical. Therefore, appropriate sequence generators were also developed to simulate the evolution of serially-sampled recombinant viruses, new and more through evaluation criteria for recombination detection methods were established, and three major comparison studies were performed. The newly developed tools were also applied to "real" HIV-1 sequence data and it was shown that the results represented within an evolutionary network structure can be interpreted in biologically meaningful ways. ^

Serial evolutionary networks of within-patient HIV-1 sequences reveal patterns of evolution of X4 strains

Background The HIV virus is known for its ability to exploit numerous genetic and evolutionary mechanisms to ensure its proliferation, among them, high replication, mutation and recombination rates. Sliding MinPD, a recently introduced computational method [1], was used to investigate the patterns of evolution of serially-sampled HIV-1 sequence data from eight patients with a special focus on the emergence of X4 strains. Unlike other phylogenetic methods, Sliding MinPD combines distance-based inference with a nonparametric bootstrap procedure and automated recombination detection to reconstruct the evolutionary history of longitudinal sequence data. We present serial evolutionary networks as a longitudinal representation of the mutational pathways of a viral population in a within-host environment. The longitudinal representation of the evolutionary networks was complemented with charts of clinical markers to facilitate correlation analysis between pertinent clinical information and the evolutionary relationships. Results Analysis based on the predicted networks suggests the following:: significantly stronger recombination signals (p = 0.003) for the inferred ancestors of the X4 strains, recombination events between different lineages and recombination events between putative reservoir virus and those from a later population, an early star-like topology observed for four of the patients who died of AIDS. A significantly higher number of recombinants were predicted at sampling points that corresponded to peaks in the viral load levels (p = 0.0042). Conclusion Our results indicate that serial evolutionary networks of HIV sequences enable systematic statistical analysis of the implicit relations embedded in the topology of the structure and can greatly facilitate identification of patterns of evolution that can lead to specific hypotheses and new insights. The conclusions of applying our method to empirical HIV data support the conventional wisdom of the new generation HIV treatments, that in order to keep the virus in check, viral loads need to be suppressed to almost undetectable levels.

The effects of advanced practice nurses (APNs) as intensivists in a surgical intensive care unit (SICU) on patient outcomes, healthcare charges, and apn intensivist services in the SICU

Intensive Care Units (ICUs) account for over 10 percent of all US hospital beds, have over 4.4 million patient admissions yearly, approximately 360,000 deaths, and account for close to 30% of acute care hospital costs. The need for critical care services has increased due to an aging population and medical advances that extend life. The result is efforts to improve patient outcomes, optimize financial performance, and implement models of ICU care that enhance quality of care and reduce health care costs. This retrospective chart review study examined the dose effect of APN Intensivists in a surgical intensive care unit (SICU) on differences in patient outcomes, healthcare charges, SICU length of stay, charges for APN intensivist services, and frequency of APNs special initiatives when the SICU was staffed by differing levels of APN Intensivist staffing over four time periods (T1-T4) between 2009 and 2011. The sample consisted of 816 randomly selected (204 per T1-T4) patient chart data. Study findings indicated reported ventilator associated pneumonia (VAP) rates, ventilator days, catheter days and catheter associated urinary tract infection (CAUTI) rates increased at T4 (when there was the lowest number of APN Intensivists), and there was increased pressure ulcer incidence in first two quarters of T4. There was no statistically significant difference in post-surgical glycemic control (M = 142.84, SD = 40.00), t (223) = 1.40, p = .17, and no statistically significant difference in the SICU length of stay among the time-periods (M = 3.27, SD = 3.32), t (202) = 1.02, p = .31. Charges for APN services increased over the 4 time periods from $11,268 at T1 to $51,727 at T4 when a system to capture APN billing was put into place. The number of new APN initiatives declined in T4 as the number of APN Intensivists declined. Study results suggest a dose effect of APN Intensivists on important patient health outcomes and on the number of APNs initiatives to prevent health complications in the SICU. ^

Learning Data-Driven Models of Non-Verbal Behaviors for Building Rapport Using an Intelligent Virtual Agent

There is a growing societal need to address the increasing prevalence of behavioral health issues, such as obesity, alcohol or drug use, and general lack of treatment adherence for a variety of health problems. The statistics, worldwide and in the USA, are daunting. Excessive alcohol use is the third leading preventable cause of death in the United States (with 79,000 deaths annually), and is responsible for a wide range of health and social problems. On the positive side though, these behavioral health issues (and associated possible diseases) can often be prevented with relatively simple lifestyle changes, such as losing weight with a diet and/or physical exercise, or learning how to reduce alcohol consumption. Medicine has therefore started to move toward finding ways of preventively promoting wellness, rather than solely treating already established illness. Evidence-based patient-centered Brief Motivational Interviewing (BMI) interven- tions have been found particularly effective in helping people find intrinsic motivation to change problem behaviors after short counseling sessions, and to maintain healthy lifestyles over the long-term. Lack of locally available personnel well-trained in BMI, however, often limits access to successful interventions for people in need. To fill this accessibility gap, Computer-Based Interventions (CBIs) have started to emerge. Success of the CBIs, however, critically relies on insuring engagement and retention of CBI users so that they remain motivated to use these systems and come back to use them over the long term as necessary. Because of their text-only interfaces, current CBIs can therefore only express limited empathy and rapport, which are the most important factors of health interventions. Fortunately, in the last decade, computer science research has progressed in the design of simulated human characters with anthropomorphic communicative abilities. Virtual characters interact using humans’ innate communication modalities, such as facial expressions, body language, speech, and natural language understanding. By advancing research in Artificial Intelligence (AI), we can improve the ability of artificial agents to help us solve CBI problems. To facilitate successful communication and social interaction between artificial agents and human partners, it is essential that aspects of human social behavior, especially empathy and rapport, be considered when designing human-computer interfaces. Hence, the goal of the present dissertation is to provide a computational model of rapport to enhance an artificial agent’s social behavior, and to provide an experimental tool for the psychological theories shaping the model. Parts of this thesis were already published in [LYL+12, AYL12, AL13, ALYR13, LAYR13, YALR13, ALY14].

Managing chronic widespread pain in primary care : a qualitative study of patient perspectives and implications for treatment delivery

Funding The MUSICIAN trial was supported by an award from Arthritis Research UK, Chesterfield, UK. Grant number: 17292. The funding body approved the design of the study. They played no role in the collection, analysis, and interpretation of data or the writing of the manuscript.

Dosage form preference consultation study in children and young adults:paving the way for patient-centred and patient-informed dosage form development

Objectives: The current study aims to evaluate dosage form preferences in children and young adults together with identifying the key pragmatic dosage form characteristics that would enable appropriate formulation of orally disintegrating tablets (ODTs). Methods: International, multisite, cross-sectional questionnaire of children and young adults aged from 6 to 18 years. Eligibility was based on age, ability to communicate and previous experience in taking medications. The study was carried out at three locations: the UK, Saudi Arabia and Jordan. The questionnaire instrument was designed for participant self-completion under supervision of the study team.Results 104 questionnaires were completed by the study cohort (n=120, response rate 87%). Results: showed that ODTs were the most preferred oral dosage forms (58%) followed by liquids (20%), tablets (12%) and capsules (11%). The preferred colours were pink or white while the preferred size was small (<8 mm) with a round shape. With regard to flavour, strawberry was the most preferred (30.8%), while orange was the least preferred (5.8%). The results also showed that the most important physical characteristics of ODTs were disintegration time followed by taste, size and flavour, respectively. Conclusions: The results of our study support the WHO's claim for a shift of paradigm from liquid towards ODTs dosage forms for drug administration to young children older than 6 years. Data from this study will also equip formulators to prioritise development of key physical/performance attributes within the delivery system.

Lack of effect of lowering LDL cholesterol on cancer: meta-analysis of individual data from 175,000 people in 27 randomised trials of statin therapy

Background: Statin therapy reduces the risk of occlusive vascular events, but uncertainty remains about potential effects on cancer. We sought to provide a detailed assessment of any effects on cancer of lowering LDL cholesterol (LDL-C) with a statin using individual patient records from 175,000 patients in 27 large-scale statin trials. Methods and Findings: Individual records of 134,537 participants in 22 randomised trials of statin versus control (median duration 4.8 years) and 39,612 participants in 5 trials of more intensive versus less intensive statin therapy (median duration 5.1 years) were obtained. Reducing LDL-C with a statin for about 5 years had no effect on newly diagnosed cancer or on death from such cancers in either the trials of statin versus control (cancer incidence: 3755 [1.4% per year [py]] versus 3738 [1.4% py], RR 1.00 [95% CI 0.96-1.05]; cancer mortality: 1365 [0.5% py] versus 1358 [0.5% py], RR 1.00 [95% CI 0.93-1.08]) or in the trials of more versus less statin (cancer incidence: 1466 [1.6% py] vs 1472 [1.6% py], RR 1.00 [95% CI 0.93-1.07]; cancer mortality: 447 [0.5% py] versus 481 [0.5% py], RR 0.93 [95% CI 0.82-1.06]). Moreover, there was no evidence of any effect of reducing LDL-C with statin therapy on cancer incidence or mortality at any of 23 individual categories of sites, with increasing years of treatment, for any individual statin, or in any given subgroup. In particular, among individuals with low baseline LDL-C (<2 mmol/L), there was no evidence that further LDL-C reduction (from about 1.7 to 1.3 mmol/L) increased cancer risk (381 [1.6% py] versus 408 [1.7% py]; RR 0.92 [99% CI 0.76-1.10]). Conclusions: In 27 randomised trials, a median of five years of statin therapy had no effect on the incidence of, or mortality from, any type of cancer (or the aggregate of all cancer).

The impact of user charges on patient choice of healthcare services in Ireland

This research assesses the impact of user charges in the context of consumer choice to ascertain how user charges in healthcare impact on patient behaviour in Ireland. Quantitative data is collected from a subset of the population in walk-in Urgent Care Clinics and General Practitioner surgeries to assess their responses to user charges and whether user charges are a viable source of part-funding healthcare in Ireland. Examining the economic theories of Becker (1965) and Grossman (1972), the research has assessed the impact of user charges on patient choice in terms of affordability and accessibility in healthcare. The research examined a number of private, public and part-publicly funded healthcare services in Ireland for which varying levels of user charges exist depending on patients’ healthcare cover. Firstly, the study identifies the factors affecting patient choice of privately funded walk-in Urgent Care Clinics in Ireland given user charges. Secondly, the study assesses patient response to user charges for a mainly public or part-publicly provided service; prescription drugs. Finally, the study examines patients’ attitudes towards the potential application of user charges for both public and private healthcare services when patient choice is part of a time-money trade-off, convenience choice or preference choice. These services are valued in the context of user charges becoming more prevalent in healthcare systems over time. The results indicate that the impact of user charges on healthcare services vary according to socio-economic status. The study shows that user charges can disproportionately affect lower income groups and consequently lead to affordability and accessibility issues. However, when valuing the potential application of user charges for three healthcare services (MRI scans, blood tests and a branded over a generic prescription drug), this research indicates that lower income individuals are willing to pay for healthcare services, albeit at a lower user charge than higher income earners. Consequently, this study suggests that user charges may be a feasible source of part-financing Irish healthcare, once the user charge is determined from the patients’ perspective, taking into account their ability to pay.

The Effects of Advanced Practice Nurses (APNs) as Intensivists in a Surgical Intensive Care Unit (SICU) on Patient Outcomes, Healthcare Charges, and APN Intensivist Services in the SICU

Intensive Care Units (ICUs) account for over 10 percent of all US hospital beds, have over 4.4 million patient admissions yearly, approximately 360,000 deaths, and account for close to 30% of acute care hospital costs. The need for critical care services has increased due to an aging population and medical advances that extend life. The result is efforts to improve patient outcomes, optimize financial performance, and implement models of ICU care that enhance quality of care and reduce health care costs. This retrospective chart review study examined the dose effect of APN Intensivists in a surgical intensive care unit (SICU) on differences in patient outcomes, healthcare charges, SICU length of stay, charges for APN intensivist services, and frequency of APNs special initiatives when the SICU was staffed by differing levels of APN Intensivist staffing over four time periods (T1-T4) between 2009 and 2011. The sample consisted of 816 randomly selected (204 per T1-T4) patient chart data. Study findings indicated reported ventilator associated pneumonia (VAP) rates, ventilator days, catheter days and catheter associated urinary tract infection (CAUTI) rates increased at T4 (when there was the lowest number of APN Intensivists), and there was increased pressure ulcer incidence in first two quarters of T4. There was no statistically significant difference in post-surgical glycemic control (M = 142.84, SD= 40.00), t (223) = 1.40, p = .17, and no statistically significant difference in the SICU length of stay among the time-periods (M= 3.27, SD = 3.32), t (202) = 1.02, p= .31. Charges for APN services increased over the 4 time periods from $11,268 at T1 to $51,727 at T4 when a system to capture APN billing was put into place. The number of new APN initiatives declined in T4 as the number of APN Intensivists declined. Study results suggest a dose effect of APN Intensivists on important patient health outcomes and on the number of APNs initiatives to prevent health complications in the SICU.

The Responsiveness, Content Validity, and Convergent Validity of the Measure Yourself Concerns and Wellbeing (MYCaW) Patient-Reported Outcome Measure

Objective Measure Yourself Concerns and Wellbeing (MYCaW) is a patient-centred questionnaire that allows cancer patients to identify and quantify the severity of their ‘Concerns’ and Wellbeing, as opposed to using a pre-determined list. MYCaW administration is brief and aids in prioritising treatment approaches. Our goal was to assess the convergent validity and responsiveness of MYCaW scores over time, the generalisability of the existing qualitative coding framework in different complementary and integrative healthcare settings and content validity. Methods Baseline and 6-week follow-up data (n=82) from MYCaW and FACIT-SpEx questionnaires were collected for a service evaluation of the ‘Living Well With The Impact of Cancer’ course at Penny Brohn Cancer Care. MYCaW construct validity was determined using Spearman's Rank Correlation test, and responsiveness indices assessed score changes over time. The existing qualitative coding framework was reviewed using a new dataset (n=158) and coverage of concern categories compared to items of existing outcome measures. Results Good correlation between MYCaW and FACIT-SpEx score changes were achieved (r= -0.57, p≥0.01). MYCaW Profile and Concern scores were highly responsive to change: SRM=1.02 and 1.08; effect size=1.26 and 1.22. MYCaW change scores showed the anticipated gradient of change according to clinically relevant degrees of change. Categories including ‘Spirituality’, ‘weight change’ and ‘practical concerns’ were added to the coding framework to improve generalisability. Conclusions MYCaW scores were highly responsive to change, allowing personalized patient outcomes to be quantified; the qualitative coding framework is generalisable across different oncology settings and has broader coverage of patient-identified concerns compared with existing cancer-related patient-reported outcome measures.

An R-package for the Estimation and Testing of Multiple Covariates and Biomarker Interactions for Survival Data Based on Local Partial Likelihood

When we study the variables that a ffect survival time, we usually estimate their eff ects by the Cox regression model. In biomedical research, e ffects of the covariates are often modi ed by a biomarker variable. This leads to covariates-biomarker interactions. Here biomarker is an objective measurement of the patient characteristics at baseline. Liu et al. (2015) has built up a local partial likelihood bootstrap model to estimate and test this interaction e ffect of covariates and biomarker, but the R code developed by Liu et al. (2015) can only handle one variable and one interaction term and can not t the model with adjustment to nuisance variables. In this project, we expand the model to allow adjustment to nuisance variables, expand the R code to take any chosen interaction terms, and we set up many parameters for users to customize their research. We also build up an R package called "lplb" to integrate the complex computations into a simple interface. We conduct numerical simulation to show that the new method has excellent fi nite sample properties under both the null and alternative hypothesis. We also applied the method to analyze data from a prostate cancer clinical trial with acid phosphatase (AP) biomarker.

Chemotherapy patient perception regarding communication with the healthcare staff

Purpose: To qualitatively explore the communication between healthcare professionals and oncology patients based on the perception of patients undergoing chemotherapy.Method: Qualitative and exploratory design. Participants were 14 adult patients undergoing chemotherapy at different stages of the disease. A socio-demographic and clinical data form was utilized along with semi-structured interviews. The interviews were audio-recorded, transcribed and content analysis was performed. Two independent judges evaluated the interview content in regards to emerging categories and obtained a Kappa index of 0.834.Results: Three categories emerged from the data: 1) Technical communication without emotional support, in which the information provided is composed of strictly technical information regarding the diagnosis, treatment and/or prognosis; 2) Technical communication, in which the information provided is oriented towards the technical aspects of the patient’s physical condition, while also providing psychological support for the patients’ subjective needs; and 3) Insufficient technical communication, win which there are gaps in the information provided causing confusion and suffering to the patient.Conclusions: Communication with emotional support contributes to greater satisfaction of chemotherapy patients. Practical implications: the results provide elements for the training of healthcare professionals regarding the importance of the emotional support that can be offered to cancer patients during their treatment.

Patient-reported quality-of-life analysis of radium-223 dichloride from the phase III ALSYMPCA study

BACKGROUND: Radium-223 dichloride (radium-223), a first-in-class α-emitting radiopharmaceutical, is recommended in both pre- and post-docetaxel settings in patients with castration-resistant prostate cancer (CRPC) and symptomatic bone metastases based on overall survival benefit demonstrated in the phase III ALSYMPCA study. ALSYMPCA included prospective measurements of health-related quality of life (QOL) using two validated instruments: the general EuroQoL 5D (EQ-5D) and the disease-specific Functional Assessment of Cancer Therapy-Prostate (FACT-P).

PATIENTS AND METHODS: Analyses were conducted to determine treatment effects of radium-223 plus standard of care (SOC) versus placebo plus SOC on QOL using FACT-P and EQ-5D. Outcomes assessed were percentage of patients experiencing improvement, percentage of patients experiencing worsening, and mean QOL scores during the study.

RESULTS: Analyses were carried out on the intent-to-treat population of patients randomized to receive radium-223 (n = 614) or placebo (n = 307). The mean baseline EQ-5D utility and FACT-P total scores were similar between treatment groups. A significantly higher percentage of patients receiving radium-223 experienced meaningful improvement in EQ-5D utility score on treatment versus placebo {29.2% versus 18.5%, respectively; P = 0.004; odds ratio (OR) = 1.82 [95% confidence interval (CI) 1.21-2.74]}. Findings were similar for FACT-P total score [24.6% versus 16.1%, respectively; P = 0.020; OR = 1.70 (95% CI 1.08-2.65)]. A lower percentage of patients receiving radium-223 experienced meaningful worsening versus placebo measured by EQ-5D utility score and FACT-P total score. Prior docetaxel use and current bisphosphonate use did not affect these findings. Treatment was a significant predictor of EQ-5D utility score, with radium-223 associated with higher scores versus placebo (0.56 versus 0.50, respectively; P = 0.002). Findings were similar for FACT-P total score (99.08 versus 95.22, respectively; P = 0.004).

CONCLUSIONS: QOL data from ALSYMPCA demonstrated that improved survival with radium-223 is accompanied by significant QOL benefits, including a higher percentage of patients with meaningful QOL improvement and a slower decline in QOL over time in patients with CRPC.

Outlier effects on robust joint modelling of longitudinal and survival data

Robust joint modelling is an emerging field of research. Through the advancements in electronic patient healthcare records, the popularly of joint modelling approaches has grown rapidly in recent years providing simultaneous analysis of longitudinal and survival data. This research advances previous work through the development of a novel robust joint modelling methodology for one of the most common types of standard joint models, that which links a linear mixed model with a Cox proportional hazards model. Through t-distributional assumptions, longitudinal outliers are accommodated with their detrimental impact being down weighed and thus providing more efficient and reliable estimates. The robust joint modelling technique and its major benefits are showcased through the analysis of Northern Irish end stage renal disease patients. With an ageing population and growing prevalence of chronic kidney disease within the United Kingdom, there is a pressing demand to investigate the detrimental relationship between the changing haemoglobin levels of haemodialysis patients and their survival. As outliers within the NI renal data were found to have significantly worse survival, identification of outlying individuals through robust joint modelling may aid nephrologists to improve patient's survival. A simulation study was also undertaken to explore the difference between robust and standard joint models in the presence of increasing proportions and extremity of longitudinal outliers. More efficient and reliable estimates were obtained by robust joint models with increasing contrast between the robust and standard joint models when a greater proportion of more extreme outliers are present. Through illustration of the gains in efficiency and reliability of parameters when outliers exist, the potential of robust joint modelling is evident. The research presented in this thesis highlights the benefits and stresses the need to utilise a more robust approach to joint modelling in the presence of longitudinal outliers.