Corneal markers of diabetic neuropathy

Diabetic neuropathy is a significant clinical problem that currently has no effective therapy, and in advanced cases, leads to foot ulceration and lower limb amputation. The accurate detection, characterization and quantification of this condition are important in order to define at-risk patients, anticipate deterioration, monitor progression, and assess new therapies This review evaluates novel corneal methods of assessing diabetic neuropathy. Two new non-invasive corneal markers have emerged, and in cross-sectional studies have demonstrated their ability to stratify the severity of this disease. Corneal confocal microscopy allows quantification of corneal nerve parameters and non-contact corneal esthesiometry, the functional correlate of corneal structure, assesses the sensitivity of the cornea. Both these techniques are quick to perform, produce little or no discomfort for the patient, and are suitable for clinical settings. Each has advantages and disadvantages over traditional techniques for assessing diabetic neuropathy. Application of these new corneal markers for longitudinal evaluation of diabetic neuropathy has the potential to reduce dependence on more invasive, costly, and time-consuming assessments, such as skin biopsy.

Business process management : theory on progression and maturity

Business Process Management (BPM) is a topic that continues to grow in significance as organisations seek to gain and sustain competitive advantage in an increasingly global environment. Despite anecdotal evidence of organisations improving performance by pursuing a BPM approach, there is little theory that explains and substantiates this relationship. This study provides the first theory on the progression and maturity of BPM Initiatives within organisations and provides a vital starting block upon which future research in this area can build. The Researcher starts by clearly defining three key terms (BPM Initiative, BPM Progression and BPM Maturity), showing the relationship between these three concepts and proposing their relationship with Organisational Performance. The Researcher then combines extant literature and use of the Delphi Technique and the case study method to explore the progression and measurement of the BPM Initiatives within organisations. The study builds upon the principles of general theories including the Punctuated Equilibrium Model and Dynamic Capabilities to present theory on BPM Progression and BPM Maturity. Using the BPM Capability Framework developed through an international Delphi study series, the Researcher shows how the specific organisational context influences which capability areas an organisation chooses to progress. By comparing five separate organisations over an extended time the Researcher is able to show that, despite this disparity, there is some evidence of consistency with regard to the capability areas progressed. This suggests that subsequent identification of progression paths may be possible. The study also shows that the approach and scope taken to BPM within each organisation is a likely predictor of such paths. These outcomes result in the proposal of a formative model for measuring BPM Maturity.

Using ‘think aloud’ as a strategy for learning clinical reasoning in high fidelity case-based simulation for undergraduate nursing students

AIMS This paper reports on the implementation of a research project that trials an educational strategy implemented over six months of an undergraduate third year nursing curriculum. This project aims to explore the effectiveness of ‘think aloud’ as a strategy for learning clinical reasoning for students in simulated clinical settings. BACKGROUND Nurses are required to apply and utilise critical thinking skills to enable clinical reasoning and problem solving in the clinical setting [1]. Nursing students are expected to develop and display clinical reasoning skills in practice, but may struggle articulating reasons behind decisions about patient care. For students learning to manage complex clinical situations, teaching approaches are required that make these instinctive cognitive processes explicit and clear [2-5]. In line with professional expectations, nursing students in third year at Queensland University of Technology (QUT) are expected to display clinical reasoning skills in practice. This can be a complex proposition for students in practice situations, particularly as the degree of uncertainty or decision complexity increases [6-7]. The ‘think aloud’ approach is an innovative learning/teaching method which can create an environment suitable for developing clinical reasoning skills in students [4, 8]. This project aims to use the ‘think aloud’ strategy within a simulation context to provide a safe learning environment in which third year students are assisted to uncover cognitive approaches that best assist them to make effective patient care decisions, and improve their confidence, clinical reasoning and active critical reflection on their practice. MEHODS In semester 2 2011 at QUT, third year nursing students will undertake high fidelity simulation, some for the first time commencing in September of 2011. There will be two cohorts for strategy implementation (group 1= use think aloud as a strategy within the simulation, group 2= not given a specific strategy outside of nursing assessment frameworks) in relation to problem solving patient needs. Students will be briefed about the scenario, given a nursing handover, placed into a simulation group and an observer group, and the facilitator/teacher will run the simulation from a control room, and not have contact (as a ‘teacher’) with students during the simulation. Then debriefing will occur as a whole group outside of the simulation room where the session can be reviewed on screen. The think aloud strategy will be described to students in their pre-simulation briefing and allow for clarification of this strategy at this time. All other aspects of the simulations remain the same, (resources, suggested nursing assessment frameworks, simulation session duration, size of simulation teams, preparatory materials). RESULTS Methodology of the project and the challenges of implementation will be the focus of this presentation. This will include ethical considerations in designing the project, recruitment of students and implementation of a voluntary research project within a busy educational curriculum which in third year targets 669 students over two campuses. CONCLUSIONS In an environment of increasingly constrained clinical placement opportunities, exploration of alternate strategies to improve critical thinking skills and develop clinical reasoning and problem solving for nursing students is imperative in preparing nurses to respond to changing patient needs. References 1. Lasater, K., High-fidelity simulation and the development of clinical judgement: students' experiences. Journal of Nursing Education, 2007. 46(6): p. 269-276. 2. Lapkin, S., et al., Effectiveness of patient simulation manikins in teaching clinical reasoning skills to undergraduate nursing students: a systematic review. Clinical Simulation in Nursing, 2010. 6(6): p. e207-22. 3. Kaddoura, M.P.C.M.S.N.R.N., New Graduate Nurses' Perceptions of the Effects of Clinical Simulation on Their Critical Thinking, Learning, and Confidence. The Journal of Continuing Education in Nursing, 2010. 41(11): p. 506. 4. Banning, M., The think aloud approach as an educational tool to develop and assess clinical reasoning in undergraduate students. Nurse Education Today, 2008. 28: p. 8-14. 5. Porter-O'Grady, T., Profound change:21st century nursing. Nursing Outlook, 2001. 49(4): p. 182-186. 6. Andersson, A.K., M. Omberg, and M. Svedlund, Triage in the emergency department-a qualitative study of the factors which nurses consider when making decisions. Nursing in Critical Care, 2006. 11(3): p. 136-145. 7. O'Neill, E.S., N.M. Dluhy, and C. Chin, Modelling novice clinical reasoning for a computerized decision support system. Journal of Advanced Nursing, 2005. 49(1): p. 68-77. 8. Lee, J.E. and N. Ryan-Wenger, The "Think Aloud" seminar for teaching clinical reasoning: a case study of a child with pharyngitis. J Pediatr Health Care, 1997. 11(3): p. 101-10.

The development of a program to assist international nursing students to be prepared for clinical practice in the Australian health care context

Health education in Western Countries has grown considerably in the last decade and this has occurred for a number of reasons. Specifically Universities actively recruit International students as the health workforce becomes global; also it is much easier for students to move and study globally. Internationally there is a health workforce shortage and if students gain a degree in a reputable university their ability to work globally is improved significantly. However, when studying to practice in the health care field the student must undertake clinical practice in an acute or aged care setting. This can be a significant problem for students who are culturally and linguistically diverse in an English speaking country such as Australia. The issues that can arise stem from the language differences where communication, interpretation understanding and reading the cultural norms of the health care setting are major challenges for International students. To assist international students to be successful in their clinical education, an extra curriculum workshop program was developed to provide additional support. The program which runs twice each year includes on-campus interactive workshops that are complemented by targeted support provided for students and clinical staff who are supervising students’ practice experience in the workplace. As this is an English speaking country the workshop is based on practicing reading, writing, listening and speaking, as well as exploring basic health care concepts and cultural differences. This enables students to gain knowledge of and practice interpretation of cultural norms and expectations in a safe environment. This innovative series of interactive workshops in a highly student-centred learning environment combine education with role play and discussion with peers who are supported by culturally aware and competent Educators. Over the years it has been running, the program has been undertaken by an increasing number of students. In 2011, more than 100 students are expected to participate. Student evaluation of the program has confirmed that it has assisted the majority of them to be successful in their clinical studies. Effectiveness of the project is measured throughout the program and in follow up sessions. This ongoing information allows for continuous development of the program that serves to meet individual needs of the International student, the University and Service providers such as the hospitals. This feedback from students regarding their increased comprehension of the Australian colloquial Language, healthcare terminology, critical thinking and clinical skill development and a cultural awareness also enables them to maintain their feelings of self confidence and self esteem.

Integration of CENA practice standards for postgraduate emergency nursing assessment

The use of professional competency standards to assess postgraduate nursing student’s clinical performance has been in place since 2004, at the Queensland University of Technology, School of Nursing & Midwifery (SONAM) when the Graduate Certificate in Emergency Nursing degree commenced. Emergency nursing students were assessed in their workplace, using a Clinical Performance Appraisal Tool or CPAT which was based on the Australian College of Critical Care Nurses (ACCCN) Competency Standards. With the subsequent formation of a separate Emergency Nursing Course advisory group in 2007, there was a review of clinical assessment course component. The release of the 2008 CENA revised Practice Standards for the Emergency Nursing Specialist’s, led to the emergency nursing course advisory committee supporting the integration of the CENA practice standards for assessment of emergency nurses in preference to the less relevant ACCCN competency standards. The SONAM emergency nursing study area team commenced the phasing in and progression of the CENA practice standards across the two Graduate Certificate units, and Graduate Diploma and Master of Nursing (emergency) clinical major options in 2009. As some units undertaken in the degree are available to nurses in other disciplines a separate CPAT was devised for the clinical assessments according to speciality context. The team has had to carefully consider how the professional standards are integrated into the teaching and assessment of the unit and not just applied instead of the ACCCN competency standards. Professional standards for the emergency context has also helped tailor course content and learning outcomes to be relevant across a number of emergency nursing contexts in Australia. The assessment of the CPAT is undertaken at the workplace by QUT appointed clinical lecturers. Clinical lecturers need to apply and have suitable postgraduate qualification to undertake the position. The clinical lecturer support role is well established at QUT. The integration of the new CENA practice standards has necessitated a review of the postgraduate assessment of emergency nurses. A clinical lecturer workshop has been organised to review role, scope and how to utilise the new look CENA based CPAT, clinical assessment format.

Training clinical psychologists : The current situation and a way forward [Guest Editorial]

In the past, training in clinical psychology in Australia and overseas has been dominated by definitions of input— hours of classes or supervision and of specific components. While prospective practitioners have been required to demonstrate the acquisition of generic competencies, satisfaction of these input driven criteria has been required for both accreditation and registration. Ironically, for a discipline that prides itself on requiring empirical bases for practice and communicating those to students (Calhoun, Moras, Pilkonis, & Rehm, 1998), training criteria have been primarily derived from accepted wisdom, rather than from a sound body of data. The situation has been remarkably like that of a treatment establishing standards of fidelity before its effective components are known—an action our profession has correctly criticised in the past (Herbert & Mueser, 1992).

The oral health of critically ill children : an observational cohort study

Aims and objectives: This study will describe the oral health status of critically ill children over time spent in the paediatric intensive care unit, examine influences on the development of poor oral health and explore the relationship between dysfunctional oral health and healthcare-associated infections. Background: The treatment modalities used to support children experiencing critical illness and the progression of critical illness may result in dysfunction in the oral cavity. In adults, oral health has been shown to worsen during critical illness as well as influence systemic health. Design: A prospective observational cohort design was used. Method: The study was undertaken at a single tertiary-referral Paediatric Intensive Care Unit. Oral health status was measured using the Oral Assessment Scale and culturing oropharyngeal flora. Information was also collected surrounding the use of supportive therapies, clinical characteristics of the children and the occurrence of healthcare-associated infections. Results: Of the 46 participants, 63% (n = 32) had oral dysfunction and 41% (n = 19) demonstrated pathogenic oropharyngeal colonisation during their critical illness. The potential systemic pathogens isolated from the oropharynx and included Candida sp., Staphylococcus aureus, Haemophilus influenzae, Enterococcus sp. and Pseudomonas aeruginosa. The severity of critical illness had a significant positive relationship (p < 0·05) with pathogenic and absent colonisation of the oropharynx. Sixty-three percent of healthcare-associated infections involved the preceding or simultaneous colonisation of the oropharynx by the causative pathogen. Conclusions: This study suggests paediatric oral health to be frequently dysfunctional and the oropharynx to repeatedly harbour potential systemic pathogens during childhood critical illness. Relevance to clinical practice: Given the frequency of poor oral health during childhood critical illness in this study and the subsequent potential systemic consequences, evidence based oral hygiene practices should be developed and validated to guide clinicians when nursing critically ill children.

Comparative study of coagulase negative Staphylococci (CoNS) from clinical isolates, skin and nasal sources

Staphylococci are important pathogenic bacteria responsible for a range of diseases in humans. The most frequently isolated microorganisms in a hospital microbiology laboratory are staphylococci. The general classification of staphylococci divides them into two major groups; Coagulase-positive staphylococci (e.g. Staphylococcus aureus) and Coagulase-negative staphylococci (e.g. Staphylococcus epidermidis). Coagulase-negative staphylococcal (CoNS) isolates include a variety of species and many different strains but are often dominated by the most important organism of this group, S. epidermidis. Currently, these organisms are regarded as important pathogenic organisms causing infections related to prosthetic materials and surgical wounds. A significant number of S. epidermidis isolates are also resistant to different antimicrobial agents. Virulence factors in CoNS are not very clearly established and not well documented. S. epidermidis is evolving as a resistant and powerful microbe related to nosocomial infections because it has different properties which independently, and in combination, make it a successful infectious agent, especially in the hospital environment. Such characteristics include biofilm formation, drug resistance and the evolution of genetic variables. The purpose of this project was to develop a novel SNP genotyping method to genotype S. epidermidis strains originating from hospital patients and healthy individuals. High-Resolution Melt Analysis was used to assign binary typing profiles to both clinical and commensal strains using a new bioinformatics approach. The presence of antibiotic resistance genes and biofilm coding genes were also interrogated in these isolates.

Clinical strategies for the alleviation of contractures from a predictive mathematical model of dermal repair

Hypertrophic scars arise when there is an overproduction of collagen during wound healing. These are often associated with poor regulation of the rate of programmed cell death(apoptosis) of the cells synthesizing the collagen or by an exuberant inflammatory response that prolongs collagen production and increases wound contraction. Severe contractures that occur, for example, after a deep burn can cause loss of function especially if the wound is over a joint such as the elbow or knee. Recently, we have developed a morphoelastic mathematical model for dermal repair that incorporates the chemical, cellular and mechanical aspects of dermal wound healing. Using this model, we examine pathological scarring in dermal repair by first assuming a smaller than usual apoptotic rate for myofibroblasts, and then considering a prolonged inflammatory response, in an attempt to determine a possible optimal intervention strategy to promote normal repair, or terminate the fibrotic scarring response. Our model predicts that in both cases it is best to apply the intervention strategy early in the wound healing response. Further, the earlier an intervention is made, the less aggressive the intervention required. Finally, if intervention is conducted at a late time during healing, a significant intervention is required; however, there is a threshold concentration of the drug or therapy applied, above which minimal further improvement to wound repair is obtained.

Pre-clinical evaluation of amphiphilic silicone oligomers for scar remediation

The formation of hypertrophic scars is a frequent outcome of wound repair and often requires further therapy with treatments such as silicone gel sheets (SGS; Perkins et al., 1983). Although widely used, knowledge regarding SGS and their mechanism of action on hypertrophic scars is limited. Furthermore, SGS require consistent application for at least twelve hours a day for up to twelve consecutive months, beginning as soon as wound reepithelialisation has occurred. Preliminary research at QUT has shown that some species of silicone present in SGS have the ability to permeate into collagen gel skin mimetics upon exposure. An analogue of these species, GP226, was found to decrease both collagen synthesis and the total amount of collagen present following exposure to cultures of cells derived from hypertrophic scars. This silicone of interest was a crude mixture of silicone species, which resolved into five fractions of different molecular weight. These five fractions were found to have differing effects on collagen synthesis and cell viability following exposure to fibroblasts derived from hypertrophic scars (HSF), keloid scars (KF) and normal skin (nHSF and nKF). The research performed herein continues to further assess the potential of GP226 and its fractions for scar remediation by determining in more detail its effects on HSF, KF, nHSF, nKF and human keratinocytes (HK) in terms of cell viability and proliferation at various time points. Through these studies it was revealed that Fraction IV was the most active fraction as it induced a reduction in cell viability and proliferation most similar to that observed with GP226. Cells undergoing apoptosis were also detected in HSF cultures exposed to GP226 and Fraction IV using the Tunel assay (Roche). These investigations were difficult to pursue further as the fractionation process used for GP226 was labour-intensive and time inefficient. Therefore a number of silicones with similar structure to Fraction IV were synthesised and screened for their effect following application to HSF and nHSF. PDMS7-g-PEG7, a silicone-PEG copolymer of low molecular weight and low hydrophilic-lipophilic balance factor, was found to be the most effective at reducing cell proliferation and inducing apoptosis in cultures of HSF, nHSF and HK. Further studies investigated gene expression through microarray and superarray techniques and demonstrated that many genes are differentially expressed in HSF following treatment with GP226, Fraction IV and PDMS7-g-PEG7. In brief, it was demonstrated that genes for TGFβ1 and TNF are not differentially regulated while genes for AIFM2, IL8, NSMAF, SMAD7, TRAF3 and IGF2R show increased expression (>1.8 fold change) following treatment with PDMS7-g-PEG7. In addition, genes for αSMA, TRAF2, COL1A1 and COL3A1 have decreased expression (>-1.8 fold change) following treatment with GP226, Fraction IV and PDMS7-g-PEG7. The data obtained suggest that many different pathways related to apoptosis and collagen synthesis are affected in HSF following exposure to PDMS7-g-PEG7. The significance is that silicone-PEG copolymers, such as GP226, Fraction IV and PDMS7-g-PEG7, could potentially be a non-invasive substitute to apoptosis-inducing chemical agents that are currently used as scar treatments. It is anticipated that these findings will ultimately contribute to the development of a novel scar therapy with faster action and improved outcomes for patients suffering from hypertrophic scars.

Rational design of serine protease inhibitors

Proteases regulate a spectrum of diverse physiological processes, and dysregulation of proteolytic activity drives a plethora of pathological conditions. Understanding protease function is essential to appreciating many aspects of normal physiology and progression of disease. Consequently, development of potent and specific inhibitors of proteolytic enzymes is vital to provide tools for the dissection of protease function in biological systems and for the treatment of diseases linked to aberrant proteolytic activity. The studies in this thesis describe the rational design of potent inhibitors of three proteases that are implicated in disease development. Additionally, key features of the interaction of proteases and their cognate inhibitors or substrates are analysed and a series of rational inhibitor design principles are expounded and tested. Rational design of protease inhibitors relies on a comprehensive understanding of protease structure and biochemistry. Analysis of known protease cleavage sites in proteins and peptides is a commonly used source of such information. However, model peptide substrate and protein sequences have widely differing levels of backbone constraint and hence can adopt highly divergent structures when binding to a protease’s active site. This may result in identical sequences in peptides and proteins having different conformations and diverse spatial distribution of amino acid functionalities. Regardless of this, protein and peptide cleavage sites are often regarded as being equivalent. One of the key findings in the following studies is a definitive demonstration of the lack of equivalence between these two classes of substrate and invalidation of the common practice of using the sequences of model peptide substrates to predict cleavage of proteins in vivo. Another important feature for protease substrate recognition is subsite cooperativity. This type of cooperativity is commonly referred to as protease or substrate binding subsite cooperativity and is distinct from allosteric cooperativity, where binding of a molecule distant from the protease active site affects the binding affinity of a substrate. Subsite cooperativity may be intramolecular where neighbouring residues in substrates are interacting, affecting the scissile bond’s susceptibility to protease cleavage. Subsite cooperativity can also be intermolecular where a particular residue’s contribution to binding affinity changes depending on the identity of neighbouring amino acids. Although numerous studies have identified subsite cooperativity effects, these findings are frequently ignored in investigations probing subsite selectivity by screening against diverse combinatorial libraries of peptides (positional scanning synthetic combinatorial library; PS-SCL). This strategy for determining cleavage specificity relies on the averaged rates of hydrolysis for an uncharacterised ensemble of peptide sequences, as opposed to the defined rate of hydrolysis of a known specific substrate. Further, since PS-SCL screens probe the preference of the various protease subsites independently, this method is inherently unable to detect subsite cooperativity. However, mean hydrolysis rates from PS-SCL screens are often interpreted as being comparable to those produced by single peptide cleavages. Before this study no large systematic evaluation had been made to determine the level of correlation between protease selectivity as predicted by screening against a library of combinatorial peptides and cleavage of individual peptides. This subject is specifically explored in the studies described here. In order to establish whether PS-SCL screens could accurately determine the substrate preferences of proteases, a systematic comparison of data from PS-SCLs with libraries containing individually synthesised peptides (sparse matrix library; SML) was carried out. These SML libraries were designed to include all possible sequence combinations of the residues that were suggested to be preferred by a protease using the PS-SCL method. SML screening against the three serine proteases kallikrein 4 (KLK4), kallikrein 14 (KLK14) and plasmin revealed highly preferred peptide substrates that could not have been deduced by PS-SCL screening alone. Comparing protease subsite preference profiles from screens of the two types of peptide libraries showed that the most preferred substrates were not detected by PS SCL screening as a consequence of intermolecular cooperativity being negated by the very nature of PS SCL screening. Sequences that are highly favoured as result of intermolecular cooperativity achieve optimal protease subsite occupancy, and thereby interact with very specific determinants of the protease. Identifying these substrate sequences is important since they may be used to produce potent and selective inhibitors of protolytic enzymes. This study found that highly favoured substrate sequences that relied on intermolecular cooperativity allowed for the production of potent inhibitors of KLK4, KLK14 and plasmin. Peptide aldehydes based on preferred plasmin sequences produced high affinity transition state analogue inhibitors for this protease. The most potent of these maintained specificity over plasma kallikrein (known to have a very similar substrate preference to plasmin). Furthermore, the efficiency of this inhibitor in blocking fibrinolysis in vitro was comparable to aprotinin, which previously saw clinical use to reduce perioperative bleeding. One substrate sequence particularly favoured by KLK4 was substituted into the 14 amino acid, circular sunflower trypsin inhibitor (SFTI). This resulted in a highly potent and selective inhibitor (SFTI-FCQR) which attenuated protease activated receptor signalling by KLK4 in vitro. Moreover, SFTI-FCQR and paclitaxel synergistically reduced growth of ovarian cancer cells in vitro, making this inhibitor a lead compound for further therapeutic development. Similar incorporation of a preferred KLK14 amino acid sequence into the SFTI scaffold produced a potent inhibitor for this protease. However, the conformationally constrained SFTI backbone enforced a different intramolecular cooperativity, which masked a KLK14 specific determinant. As a consequence, the level of selectivity achievable was lower than that found for the KLK4 inhibitor. Standard mechanism inhibitors such as SFTI rely on a stable acyl-enzyme intermediate for high affinity binding. This is achieved by a conformationally constrained canonical binding loop that allows for reformation of the scissile peptide bond after cleavage. Amino acid substitutions within the inhibitor to target a particular protease may compromise structural determinants that support the rigidity of the binding loop and thereby prevent the engineered inhibitor reaching its full potential. An in silico analysis was carried out to examine the potential for further improvements to the potency and selectivity of the SFTI-based KLK4 and KLK14 inhibitors. Molecular dynamics simulations suggested that the substitutions within SFTI required to target KLK4 and KLK14 had compromised the intramolecular hydrogen bond network of the inhibitor and caused a concomitant loss of binding loop stability. Furthermore in silico amino acid substitution revealed a consistent correlation between a higher frequency of formation and the number of internal hydrogen bonds of SFTI-variants and lower inhibition constants. These predictions allowed for the production of second generation inhibitors with enhanced binding affinity toward both targets and highlight the importance of considering intramolecular cooperativity effects when engineering proteins or circular peptides to target proteases. The findings from this study show that although PS-SCLs are a useful tool for high throughput screening of approximate protease preference, later refinement by SML screening is needed to reveal optimal subsite occupancy due to cooperativity in substrate recognition. This investigation has also demonstrated the importance of maintaining structural determinants of backbone constraint and conformation when engineering standard mechanism inhibitors for new targets. Combined these results show that backbone conformation and amino acid cooperativity have more prominent roles than previously appreciated in determining substrate/inhibitor specificity and binding affinity. The three key inhibitors designed during this investigation are now being developed as lead compounds for cancer chemotherapy, control of fibrinolysis and cosmeceutical applications. These compounds form the basis of a portfolio of intellectual property which will be further developed in the coming years.

Rule-based approach for identifying assertions in clinical free-text data

A rule-based approach for classifying previously identified medical concepts in the clinical free text into an assertion category is presented. There are six different categories of assertions for the task: Present, Absent, Possible, Conditional, Hypothetical and Not associated with the patient. The assertion classification algorithms were largely based on extending the popular NegEx and Context algorithms. In addition, a health based clinical terminology called SNOMED CT and other publicly available dictionaries were used to classify assertions, which did not fit the NegEx/Context model. The data for this task includes discharge summaries from Partners HealthCare and from Beth Israel Deaconess Medical Centre, as well as discharge summaries and progress notes from University of Pittsburgh Medical Centre. The set consists of 349 discharge reports, each with pairs of ground truth concept and assertion files for system development, and 477 reports for evaluation. The system’s performance on the evaluation data set was 0.83, 0.83 and 0.83 for recall, precision and F1-measure, respectively. Although the rule-based system shows promise, further improvements can be made by incorporating machine learning approaches.

Human corneal epithelial equivalents constructed on Bombyx mori silk fibroin membranes

Membranes prepared from a protein, fibroin, isolated from domesticated silkworm (Bombyx mori) silk, support the cultivation of human limbal epithelial (HLE) cells and thus display significant potential as biomaterials for ocular surface reconstruction. We presently extend this promising avenue of research by directly comparing the attachment, morphology and phenotype of primary HLE cell cultures grown on fibroin to that observed on donor amniotic membrane (AM), the current clinical standard substrate for HLE transplantation. Fibroin membranes measuring 6.3 ± 0.5 μm (mean ± sd) in thickness and permeable to FITC dextran of a molecular weight up to 70 kDa, were used. Attachment of HLE cells to fibroin was similar to that supported by tissue culture plastic but approximately 6-fold less than that observed on AM. Nevertheless, epithelia constructed from HLE on fibroin maintained evidence of corneal phenotype (K3/K12 expression) and displayed a comparable number and distribution of ΔNp63+ progenitor cells to that seen in cultures grown on AM. These results support the suitability of membranes constructed from Bombyx mori silk fibroin as substrata for HLE cultivation and encourage progression to studies of efficacy in preclinical models.

Wound healing angiogenesis : the clinical implications of a simple mathematical model

Nonhealing wounds are a major burden for health care systems worldwide. In addition, a patient who suffers from this type of wound usually has a reduced quality of life. While the wound healing process is undoubtedly complex, in this paper we develop a deterministic mathematical model, formulated as a system of partial differential equations, that focusses on an important aspect of successful healing: oxygen supply to the wound bed by a combination of diffusion from the surrounding unwounded tissue and delivery from newly formed blood vessels. While the model equations can be solved numerically, the emphasis here is on the use of asymptotic methods to establish conditions under which new blood vessel growth can be initiated and wound-bed angiogenesis can progress. These conditions are given in terms of key model parameters including the rate of oxygen supply and its rate of consumption in the wound. We use our model to discuss the clinical use of treatments such as hyperbaric oxygen therapy, wound bed debridement, and revascularisation therapy that have the potential to initiate healing in chronic, stalled wounds.

The expression, regulation and function of kallikrein 4 in prostate cancer

Prostate cancer is a significant health problem faced by aging men. Currently, diagnostic strategies for the detection of prostate cancer are either unreliable, yielding high numbers of false positive results, or too invasive to be used widely as screening tests. Furthermore, the current therapeutic strategies for the treatment of the disease carry considerable side effects. Although organ confined prostate cancer can be curable, most detectable clinical symptoms occur in advanced disease when primary tumour cells have metastasised to distant sites - usually lymph nodes and bone. Many growth factors and steroids assist the continued growth and maintenance of prostatic tumour cells. Of these mitogens, androgens are important in the development of the normal prostate but are also required to sustain the growth of prostate cancer cells in the early stage of the disease. Not only are androgens required in the early stage of disease, but also many other growth factors and hormones interact to cause uncontrolled proliferation of malignant cells. The early, androgen sensitive phase of disease is followed by an androgen insensitive phase, whereby androgens are no longer required to stimulate the growth of the tumour cells. Growth factors such as transforming growth factor  and  (TGF/), epidermal growth factor (EGF), basic fibroblast growth factor (bFGF), insulin-like growth factors (IGFs), Vitamin D and thyroid hormone have been suggested to be important at this stage of disease. Interestingly, some of the kallikrein family of genes, including prostate specific antigen (PSA), the current serum diagnostic marker for prostate cancer, are regulated by androgens and many of the aforementioned growth factors. The kallikrein gene family is a group of serine proteases that are involved in a diverse range of physiological processes: regulation of local blood flow, angiogenesis, tissue invasion and mitogenesis. The earliest members of the kallikrein gene family (KLK1-KLK3) have been strongly associated with general disease states, such as hypertension, inflammation, pancreatitis and renal disease, but are also linked to various cancers. Recently, this family was extended to include 15 genes (KLK1-15). Several newer members of the kallikrein family have been implicated in the carcinogenesis and tumour metastasis of hormone-dependent cancers such as prostate, breast, endometrial and ovarian cancer. The aims of this project were to investigate the expression of the newly identified kallikrein, KLK4, in benign and malignant prostate tissues, and prostate cancer cell lines. This thesis has demonstrated the elevated expression of KLK4 mRNA transcripts in malignant prostate tissue compared to benign prostates. Additionally, expression of the full length KLK4 transcript was detected in the androgen dependent prostate cancer cell line, LNCaP. Based on the above finding, the LNCaP cell line was chosen to assess the potential regulation of full length KLK4 by androgen, thyroid hormone and epidermal growth factor. KLK4 mRNA and protein was found to be up-regulated by androgen and a combination of androgen and thyroid hormone. Thyroid hormone alone produced no significant change in KLK4 mRNA or protein over the control. Epidermal growth factor treatment also resulted in elevated expression levels of KLK4 mRNA and protein. To assess the potential functional role(s) of KLK4/hK4 in processes associated with tumour progression, full length KLK4 was transfected into PC-3 cells - a prostate cancer cell line originally derived from a secondary bone lesion. The KLK4/hK4 over-expressing cells were assessed for their proliferation, migration, invasion and attachment properties. The KLK4 over-expressing clones exhibited a marked change in morphology, indicative of a more aggressive phenotype. The KLK4 clones were irregularly shaped with compromised adhesion to the growth surface. In contrast, the control cell lines (parent PC-3 and empty vector clones) retained a rounded morphology with obvious cell to cell adhesion, as well as significant adhesion to their growth surface. The KLK4 clones exhibited significantly greater attachment to Collagen I and IV than native PC-3s and empty vector controls. Over a 12 hour period, in comparison to the control cells, the KLK4 clones displayed an increase in migration towards PC-3 native conditioned media, a 3 fold increase towards conditioned media from an osteoblastic cell line (Saos-2) and no change in migration towards conditioned media from neonatal foreskin fibroblast cells or 20% foetal bovine serum. Furthermore, the increase in migration exhibited by the KLK4 clones was partially blocked by the serine protease inhibitor, aprotinin. The data presented in this thesis suggests that KLK4/hK4 is important in prostate carcinogenesis due to its over-expression in malignant prostate tissues, its regulation by hormones and growth factors associated with prostate disease and the functional consequences of over-expression of KLK4/hK4 in the PC-3 cell line. These results indicate that KLK4/hK4 may play an important role in tumour invasion and bone metastasis via increased attachment to the bone matrix protein, Collagen I, and enhanced migration due to soluble factors produced by osteoblast cells. This suggestion is further supported by the morphological changes displayed by the KLK4 over-expressing cells. Overall, this data suggests that KLK4/hK4 should be further studied to more fully investigate the potential value of KLK4/hK4 as a diagnostic/prognostic biomarker or in therapeutic applications.