A comparison of methods for classifying clinical samples based on proteomics data : a case study for statistical and machine learning approaches

The discovery of protein variation is an important strategy in disease diagnosis within the biological sciences. The current benchmark for elucidating information from multiple biological variables is the so called “omics” disciplines of the biological sciences. Such variability is uncovered by implementation of multivariable data mining techniques which come under two primary categories, machine learning strategies and statistical based approaches. Typically proteomic studies can produce hundreds or thousands of variables, p, per observation, n, depending on the analytical platform or method employed to generate the data. Many classification methods are limited by an n≪p constraint, and as such, require pre-treatment to reduce the dimensionality prior to classification. Recently machine learning techniques have gained popularity in the field for their ability to successfully classify unknown samples. One limitation of such methods is the lack of a functional model allowing meaningful interpretation of results in terms of the features used for classification. This is a problem that might be solved using a statistical model-based approach where not only is the importance of the individual protein explicit, they are combined into a readily interpretable classification rule without relying on a black box approach. Here we incorporate statistical dimension reduction techniques Partial Least Squares (PLS) and Principal Components Analysis (PCA) followed by both statistical and machine learning classification methods, and compared them to a popular machine learning technique, Support Vector Machines (SVM). Both PLS and SVM demonstrate strong utility for proteomic classification problems.

Helping understand nutritional gaps in the elderly (HUNGER) : a prospective study of patient factors associated with inadequate nutritional intake in older medical inpatients

BACKGROUND: Malnutrition, and poor intake during hospitalisation, are common in older medical patients. Better understanding of patient-specific factors associated with poor intake may inform nutritional interventions. AIMS: To measure the proportion of older medical patients with inadequate nutritional intake, and identify patient-related factors associated with this outcome. METHODS: Prospective cohort study enrolling consecutive consenting medical inpatients aged 65 years or older. Primary outcome was energy intake less than resting energy expenditure estimated using weight-based equations. Energy intake was calculated for a single day using direct observation of plate waste. Explanatory variables included age, gender, number of co-morbidities, number of medications, diagnosis, usual residence, nutritional status, functional and cognitive impairment, depressive symptoms, poor appetite, poor dentition, and dysphagia. RESULTS: Of 134 participants (mean age 80 years, 51% female), only 41% met estimated resting energy requirements. Mean energy intake was 1220 kcal/day (SD 440), or 18.1 kcal/kg/day. Factors associated with inadequate energy intake in multivariate analysis were poor appetite, higher BMI, diagnosis of infection or cancer, delirium and need for assistance with feeding. CONCLUSIONS: Inadequate nutritional intake is common, and patient factors contributing to poor intake need to be considered in nutritional interventions.

Communications materials on methods of development of revenue and cost estimates to non-technical audiences

This CDROM includes PDFs of presentations on the following topics: "TXDOT Revenue and Expenditure Trends;" "Examine Highway Fund Diversions, & Benchmark Texas Vehicle Registration Fees;" "Evaluation of the JACK Model;" "Future highway construction cost trends;" "Fuel Efficiency Trends and Revenue Impact"

Stability and convergence of implicit numerical methods for a class of fractional advection-dispersion models

In this paper, a class of fractional advection-dispersion models (FADM) is investigated. These models include five fractional advection-dispersion models: the immobile, mobile/immobile time FADM with a temporal fractional derivative 0 < γ < 1, the space FADM with skewness, both the time and space FADM and the time fractional advection-diffusion-wave model with damping with index 1 < γ < 2. They describe nonlocal dependence on either time or space, or both, to explain the development of anomalous dispersion. These equations can be used to simulate regional-scale anomalous dispersion with heavy tails, for example, the solute transport in watershed catchments and rivers. We propose computationally effective implicit numerical methods for these FADM. The stability and convergence of the implicit numerical methods are analyzed and compared systematically. Finally, some results are given to demonstrate the effectiveness of our theoretical analysis.

Malnutrition screening tools : comparison against two validated nutrition assessment methods in older medical inpatients

Objective Although several validated nutritional screening tools have been developed to “triage” inpatients for malnutrition diagnosis and intervention, there continues to be debate in the literature as to which tool/tools clinicians should use in practice. This study compared the accuracy of seven validated screening tools in older medical inpatients against two validated nutritional assessment methods. Methods This was a prospective cohort study of medical inpatients at least 65 y old. Malnutrition screening was conducted using seven tools recommended in evidence-based guidelines. Nutritional status was assessed by an accredited practicing dietitian using the Subjective Global Assessment (SGA) and the Mini-Nutritional Assessment (MNA). Energy intake was observed on a single day during first week of hospitalization. Results In this sample of 134 participants (80 ± 8 y old, 50% women), there was fair agreement between the SGA and MNA (κ = 0.53), with MNA identifying more “at-risk” patients and the SGA better identifying existing malnutrition. Most tools were accurate in identifying patients with malnutrition as determined by the SGA, in particular the Malnutrition Screening Tool and the Nutritional Risk Screening 2002. The MNA Short Form was most accurate at identifying nutritional risk according to the MNA. No tool accurately predicted patients with inadequate energy intake in the hospital. Conclusion Because all tools generally performed well, clinicians should consider choosing a screening tool that best aligns with their chosen nutritional assessment and is easiest to implement in practice. This study confirmed the importance of rescreening and monitoring food intake to allow the early identification and prevention of nutritional decline in patients with a poor intake during hospitalization.

The hygienic efficacy of different hand-drying methods : a review of the evidence

The transmission of bacteria is more likely to occur from wet skin than from dry skin; therefore, the proper drying of hands after washing should be an integral part of the hand hygiene process in health care. This article systematically reviews the research on the hygienic efficacy of different hand-drying methods. A literature search was conducted in April 2011 using the electronic databases PubMed, Scopus, and Web of Science. Search terms used were hand dryer and hand drying. The search was limited to articles published in English from January 1970 through March 2011. Twelve studies were included in the review. Hand-drying effectiveness includes the speed of drying, degree of dryness, effective removal of bacteria, and prevention of cross-contamination. This review found little agreement regarding the relative effectiveness of electric air dryers. However, most studies suggest that paper towels can dry hands efficiently, remove bacteria effectively, and cause less contamination of the washroom environment. From a hygiene viewpoint, paper towels are superior to electric air dryers. Paper towels should be recommended in locations where hygiene is paramount, such as hospitals and clinics.

Understanding teachers' reporting of child sexual abuse : measurement methods matter

The present study considered factors influencing teachers' reporting of child sexual abuse (CSA). Conducted in three Australian jurisdictions with different reporting laws and policies, the study focused on teachers' actual past and anticipated future reporting of CSA. A sample of 470 teachers within randomly selected rural and urban schools was surveyed, to identify training and experience; knowledge of reporting legislation and policy; attitudes; and reporting practices. Factors influencing actual past reporting and anticipated future reporting were identified using logistic regression modelling. This is the first study to simultaneously examine the effect of important influences in reporting practice using both retrospective and prospective approaches across jurisdictions with different reporting laws. Teachers who have actually reported CSA in the past are more likely have higher levels of policy knowledge, and hold more positive attitudes towards reporting CSA along three specific dimensions: commitment to the reporting role; confidence in the system's effective response to their reporting; and they are more likely to be able to override their concerns about the consequences of their reporting. Teachers indicating intention to report hypothetical scenarios are more likely to hold reasonable grounds for suspecting CSA, to recognise that significant harm has been caused to the child, to know that their school policy requires a report, and to be able to override their concerns about the consequences of their reporting.

Novel methods and the maximum likelihood estimation technique for estimating traffic critical gap

Most unsignalised intersection capacity calculation procedures are based on gap acceptance models. Accuracy of critical gap estimation affects accuracy of capacity and delay estimation. Several methods have been published to estimate drivers’ sample mean critical gap, the Maximum Likelihood Estimation (MLE) technique regarded as the most accurate. This study assesses three novel methods; Average Central Gap (ACG) method, Strength Weighted Central Gap method (SWCG), and Mode Central Gap method (MCG), against MLE for their fidelity in rendering true sample mean critical gaps. A Monte Carlo event based simulation model was used to draw the maximum rejected gap and accepted gap for each of a sample of 300 drivers across 32 simulation runs. Simulation mean critical gap is varied between 3s and 8s, while offered gap rate is varied between 0.05veh/s and 0.55veh/s. This study affirms that MLE provides a close to perfect fit to simulation mean critical gaps across a broad range of conditions. The MCG method also provides an almost perfect fit and has superior computational simplicity and efficiency to the MLE. The SWCG method performs robustly under high flows; however, poorly under low to moderate flows. Further research is recommended using field traffic data, under a variety of minor stream and major stream flow conditions for a variety of minor stream movement types, to compare critical gap estimates using MLE against MCG. Should the MCG method prove as robust as MLE, serious consideration should be given to its adoption to estimate critical gap parameters in guidelines.

Near infrared spectroscopy for non-destructive evaluation of articular cartilage

There is a need for an accurate real-time quantitative system that would enhance decision-making in the treatment of osteoarthritis. To achieve this objective, significant research is required that will enable articular cartilage properties to be measured and categorized for health and functionality without the need for laboratory tests involving biopsies for pathological evaluation. Such a system would provide the capability of access to the internal condition of the cartilage matrix and thus extend the vision-based arthroscopy that is currently used beyond the subjective evaluation of surgeons. The system required must be able to non-destructively probe the entire thickness of the cartilage and its immediate subchondral bone layer. In this thesis, near infrared spectroscopy is investigated for the purpose mentioned above. The aim is to relate it to the structure and load bearing properties of the cartilage matrix to the near infrared absorption spectrum and establish functional relationships that will provide objective, quantitative and repeatable categorization of cartilage condition outside the area of visible degradation in a joint. Based on results from traditional mechanical testing, their innovative interpretation and relationship with spectroscopic data, new parameters were developed. These were then evaluated for their consistency in discriminating between healthy viable and degraded cartilage. The mechanical and physico-chemical properties were related to specific regions of the near infrared absorption spectrum that were identified as part of the research conducted for this thesis. The relationships between the tissue's near infrared spectral response and the new parameters were modeled using multivariate statistical techniques based on partial least squares regression (PLSR). With significantly high levels of statistical correlation, the modeled relationships were demonstrated to possess considerable potential in predicting the properties of unknown tissue samples in a quick and non-destructive manner. In order to adapt near infrared spectroscopy for clinical applications, a balance between probe diameter and the number of active transmit-receive optic fibres must be optimized. This was achieved in the course of this research, resulting in an optimal probe configuration that could be adapted for joint tissue evaluation. Furthermore, as a proof-of-concept, a protocol for obtaining the new parameters from the near infrared absorption spectra of cartilage was developed and implemented in a graphical user interface (GUI)-based software, and used to assess cartilage-on-bone samples in vitro. This conceptual implementation has been demonstrated, in part by the individual parametric relationship with the near infrared absorption spectrum, the capacity of the proposed system to facilitate real-time, non-destructive evaluation of cartilage matrix integrity. In summary, the potential of the optical near infrared spectroscopy for evaluating articular cartilage and bone laminate has been demonstrated in this thesis. The approach could have a spin-off for other soft tissues and organs of the body. It builds on the earlier work of the group at QUT, enhancing the near infrared component of the ongoing research on developing a tool for cartilage evaluation that goes beyond visual and subjective methods.