Microarrays in molecular profiling of cancer - focus on head and neck squamous cell carcinoma

Microarrays have a wide range of applications in the biomedical field. From the beginning, arrays have mostly been utilized in cancer research, including classification of tumors into different subgroups and identification of clinical associations. In the microarray format, a collection of small features, such as different oligonucleotides, is attached to a solid support. The advantage of microarray technology is the ability to simultaneously measure changes in the levels of multiple biomolecules. Because many diseases, including cancer, are complex, involving an interplay between various genes and environmental factors, the detection of only a single marker molecule is usually insufficient for determining disease status. Thus, a technique that simultaneously collects information on multiple molecules allows better insights into a complex disease. Since microarrays can be custom-manufactured or obtained from a number of commercial providers, understanding data quality and comparability between different platforms is important to enable the use of the technology to areas beyond basic research. When standardized, integrated array data could ultimately help to offer a complete profile of the disease, illuminating mechanisms and genes behind disorders as well as facilitating disease diagnostics. In the first part of this work, we aimed to elucidate the comparability of gene expression measurements from different oligonucleotide and cDNA microarray platforms. We compared three different gene expression microarrays; one was a commercial oligonucleotide microarray and the others commercial and custom-made cDNA microarrays. The filtered gene expression data from the commercial platforms correlated better across experiments (r=0.78-0.86) than the expression data between the custom-made and either of the two commercial platforms (r=0.62-0.76). Although the results from different platforms correlated reasonably well, combining and comparing the measurements were not straightforward. The clone errors on the custom-made array and annotation and technical differences between the platforms introduced variability in the data. In conclusion, the different gene expression microarray platforms provided results sufficiently concordant for the research setting, but the variability represents a challenge for developing diagnostic applications for the microarrays. In the second part of the work, we performed an integrated high-resolution microarray analysis of gene copy number and expression in 38 laryngeal and oral tongue squamous cell carcinoma cell lines and primary tumors. Our aim was to pinpoint genes for which expression was impacted by changes in copy number. The data revealed that especially amplifications had a clear impact on gene expression. Across the genome, 14-32% of genes in the highly amplified regions (copy number ratio >2.5) had associated overexpression. The impact of decreased copy number on gene underexpression was less clear. Using statistical analysis across the samples, we systematically identified hundreds of genes for which an increased copy number was associated with increased expression. For example, our data implied that FADD and PPFIA1 were frequently overexpressed at the 11q13 amplicon in HNSCC. The 11q13 amplicon, including known oncogenes such as CCND1 and CTTN, is well-characterized in different type of cancers, but the roles of FADD and PPFIA1 remain obscure. Taken together, the integrated microarray analysis revealed a number of known as well as novel target genes in altered regions in HNSCC. The identified genes provide a basis for functional validation and may eventually lead to the identification of novel candidates for targeted therapy in HNSCC.

Non-linear flapping vibrations of rotating blades

The non-linear equations of motion of a rotating blade undergoing extensional and flapwise bending vibration are derived, including non-linearities up to O (ε3). The strain-displacement relationship derived is compared with expressions derived by earlier investigators and the errors and the approximations made in some of those are brought out. The equations of motion are solved under the inextensionality condition to obtain the influence of the amplitude on the fundamental flapwise natural frequency of the rotating blade. It is found that large finite amplitudes have a softening effect on the flapwise frequency and that this influence becomes stronger at higher speeds of rotation.

The missing link of crime analysis: A systematic approach to testing competing hypotheses

Crime analysts have traditionally received little guidance from academic researchers in key tasks in the analysis process, specifically the testing of multiple hypotheses and evaluating evidence in a scientific fashion. This article attempts to fill this gap by outlining a method (the Analysis of Competing Hypotheses) of systematically analysing multiple explanations for crime problems. The method is systematic, avoids many cognitive errors common in analysis, and is explicit. It is argued that the implementation of this approach makes analytic products audit-able, the reasoning underpinning them transparent, and provides intelligence managers a rational professional development tool for individual analysts.

Effectiveness factor for zeroth-order catalytic reactions with volume change and nonuniform catalyst activity profiles

Analytical solutions are presented for the effectiveness factor of a zeroth-order reaction with volume change and nonuniform catalyst activity profile in slab, cylinder and spherical pellets. The possibility of shape normalization is considered for a variety of activity profiles and pellet shapes. When the catalyst activity at the external surface of the pellet is non-zero, shape normalization is obtained, which makes the asymptotic behavior of the effectiveness factor identical for small and large values of Thiele modulus, however, the normalization can lead to significant errors, particularly for the case of activity profiles decreasing towards the outer surface of the catalyst.

A simple and fast two-locus quality control test to detect false positives due to batch effects in genome-wide association studies

The impact of erroneous genotypes having passed standard quality control (QC) can be severe in genome-wide association studies, genotype imputation, and estimation of heritability and prediction of genetic risk based on single nucleotide polymorphisms (SNP). To detect such genotyping errors, a simple two-locus QC method, based on the difference in test statistic of association between single SNPs and pairs of SNPs, was developed and applied. The proposed approach could detect many problematic SNPs with statistical significance even when standard single SNP QC analyses fail to detect them in real data. Depending on the data set used, the number of erroneous SNPs that were not filtered out by standard single SNP QC but detected by the proposed approach varied from a few hundred to thousands. Using simulated data, it was shown that the proposed method was powerful and performed better than other tested existing methods. The power of the proposed approach to detect erroneous genotypes was approximately 80% for a 3% error rate per SNP. This novel QC approach is easy to implement and computationally efficient, and can lead to a better quality of genotypes for subsequent genotype-phenotype investigations.

Satellite Telemetry and Long-Range Bat Movements.

Background: Understanding the long-distance movement of bats has direct relevance to studies of population dynamics, ecology, disease emergence, and conservation. Methodology/Principal Findings: We developed and trialed several collar and platform terminal transmitter (PTT) combinations on both free-living and captive fruit bats (Family Pteropodidae: Genus Pteropus). We examined transmitter weight, size, profile and comfort as key determinants of maximized transmitter activity. We then tested the importance of bat-related variables (species size/weight, roosting habitat and behavior) and environmental variables (day-length, rainfall pattern) in determining optimal collar/PTT configuration. We compared battery- and solar-powered PTT performance in various field situations, and found the latter more successful in maintaining voltage on species that roosted higher in the tree canopy, and at lower density, than those that roost more densely and lower in trees. Finally, we trialed transmitter accuracy, and found that actual distance errors and Argos location class error estimates were in broad agreement. Conclusions/Significance: We conclude that no single collar or transmitter design is optimal for all bat species, and that species size/weight, species ecology and study objectives are key design considerations. Our study provides a strategy for collar and platform choice that will be applicable to a larger number of bat species as transmitter size and weight continue to decrease in the future.

Fishing power and standardised catch rates: Implications of missing vessel-characteristic data from the Australian eastern king prawn fishery

Standardised time series of fishery catch rates require collations of fishing power data on vessel characteristics. Linear mixed models were used to quantify fishing power trends and study the effect of missing data encountered when relying on commercial logbooks. For this, Australian eastern king prawn (Melicertus plebejus) harvests were analysed with historical (from vessel surveys) and current (from commercial logbooks) vessel data. Between 1989 and 2010, fishing power increased up to 76%. To date, both forward-filling and, alternatively, omitting records with missing vessel information from commercial logbooks produce broadly similar fishing power increases and standardised catch rates, due to the strong influence of years with complete vessel data (16 out of 23 years of data). However, if gaps in vessel information had not originated randomly and skippers from the most efficient vessels were the most diligent at filling in logbooks, considerable errors would be introduced. Also, the buffering effect of complete years would be short lived as years with missing data accumulate. Given ongoing changes in fleet profile with high-catching vessels fishing proportionately more of the fleet’s effort, compliance with logbook completion, or alternatively ongoing vessel gear surveys, is required for generating accurate estimates of fishing power and standardised catch rates.

Estimating winter crop area across seasons and regions using time-sequential MODIS imagery.

The wheat grain industry is Australia's second largest agricultural export commodity. There is an increasing demand for accurate, objective and near real-time crop production information by industry. The advent of the Moderate Resolution Imaging Spectroradiometer (MODIS) satellite platform has augmented the capability of satellite-based applications to capture reflectance over large areas at acceptable pixel scale, cost and accuracy. The use of multi-temporal MODIS-enhanced vegetation index (EVI) imagery to determine crop area was investigated in this article. Here the rigour of the harmonic analysis of time-series (HANTS) and early-season metric approaches was assessed when extrapolating over the entire Queensland (QLD) cropping region for the 2005 and 2006 seasons. Early-season crop area estimates, at least 4 months before harvest, produced high accuracy at pixel and regional scales with percent errors of -8.6% and -26% for the 2005 and 2006 seasons, respectively. In discriminating among crops at pixel and regional scale, the HANTS approach showed high accuracy. The errors for specific area estimates for wheat, barley and chickpea were 9.9%, -5.2% and 10.9% (for 2005) and -2.8%, -78% and 64% (for 2006), respectively. Area estimates of total winter crop, wheat, barley and chickpea resulted in coefficient of determination (R(2)) values of 0.92, 0.89, 0.82 and 0.52, when contrasted against the actual shire-scale data. A significantly high coefficient of determination (0.87) was achieved for total winter crop area estimates in August across all shires for the 2006 season. Furthermore, the HANTS approach showed high accuracy in discriminating cropping area from non-cropping area and highlighted the need for accurate and up-to-date land use maps. The extrapolability of these approaches to determine total and specific winter crop area estimates, well before flowering, showed good utility across larger areas and seasons. Hence, it is envisaged that this technology might be transferable to different regions across Australia.

Driving better vegetable irrigation through profitable practice change

The availability and quality of irrigation water has become an issue limiting productivity in many Australian vegetable regions. Production is also under competitive pressure from supply chain forces. Producers look to new technologies, including changing irrigation infrastructure, exploring new water sources, and more complex irrigation management, to survive these stresses. Often there is little objective information investigating which improvements could improve outcomes for vegetable producers, and external communities (e.g. meeting NRM targets). This has led to investment in inappropriate technologies, and costly repetition of errors, as business independently discover the worth of technologies by personal experience. In our project, we investigated technology improvements for vegetable irrigation. Through engagement with industry and other researchers, we identified technologies most applicable to growers, particularly those that addressed priority issues. We developed analytical tools for ‘what if’ scenario testing of technologies. We conducted nine detailed experiments in the Lockyer Valley and Riverina vegetable growing districts, as well as case studies on grower properties in southern Queensland. We investigated root zone monitoring tools (FullStop™ wetting front detectors and Soil Solution Extraction Tubes - SSET), drip system layout, fertigation equipment, and altering planting arrangements. Our project team developed and validated models for broccoli, sweet corn, green beans and lettuce, and spreadsheets for evaluating economic risks associated with new technologies. We presented project outcomes at over 100 extension events, including irrigation showcases, conferences, field days, farm walks and workshops. The FullStops™ were excellent for monitoring root zone conditions (EC, nitrate levels), and managing irrigation with poor quality water. They were easier to interpret than the SSET. The SSET were simpler to install, but required wet soil to be reliable. SSET were an option for monitoring deeper soil zones, unsuitable for FullStop™ installations. Because these root zone tools require expertise, and are labour intensive, we recommend they be used to address specific problems, or as a periodic auditing strategy, not for routine monitoring. In our research, we routinely found high residual N in horticultural soils, with subsequently little crop yield response to additional nitrogen fertiliser. With improved irrigation efficiency (and less leaching), it may be timely to re-examine nitrogen budgets and recommendations for vegetable crops. Where the drip irrigation tube was located close to the crop row (i.e. within 5-8 cm), management of irrigation was easier. It improved nitrogen uptake, water use efficiency, and reduced the risk of poor crop performance through moisture stress, particularly in the early crop establishment phases. Close proximity of the drip tube to the crop row gives the producer more options for managing salty water, and more flexibility in taking risks with forecast rain. In many vegetable crops, proximate drip systems may not be cost-effective. The next best alternative is to push crop rows closer to the drip tube (leading to an asymmetric row structure). The vegetable crop models are good at predicting crop phenology (development stages, time to harvest), input use (water, fertiliser), environmental impacts (nutrient, salt movement) and total yields. The two immediate applications for the models are understanding/predicting/manipulating harvest dates and nitrogen movements in vegetable cropping systems. From the economic tools, the major influences on accumulated profit are price and yield. In doing ‘what if’ analyses, it is very important to be as accurate as possible in ascertaining what the assumed yield and price ranges are. In most vegetable production systems, lowering the required inputs (e.g. irrigation requirement, fertiliser requirement) is unlikely to have a major influence on accumulated profit. However, if a resource is constraining (e.g. available irrigation water), it is usually most profitable to maximise return per unit of that resource.

Ionophore-mediated transmembrane movement of divalent cations in small unilamellar liposomes: An evaluation of the chlortetracycline fluorescence technique and correlations with black lipid membrane studies

Conceptual advances in the field of membrane transport have, in the main, utilized artificial membranes, both planar and vesicular. Systems of biological interest,viz., cells and organelles, resemble vesicles in size and geometry. Methods are, therefore, required to extend the results obtained with planar membranes to liposome systems. In this report we present an analysis of a fluorescence technique, using the divalent cation probe chlortetracycline, in small, unilamellar vesicles, for the study of divalent cation fluxes. An ion carrier (X537 A) and a pore former (alamethicin) have been studied. The rate of rise of fluorescence signal and the transmembrane ion gradient have been related to transmembrane current and potential, respectively. A second power dependence of ion conduction-including the electrically silent portion thereof — on X537 A concentration, has been observed. An exponential dependence of ldquocurrentrdquo on ldquotransmembrane potentialrdquo in the case of alamethicin is also confirmed. Possible errors in the technique are discussed.

Econometric models of Finnish non-industrial private forest owners' timber supply and timber stock

This dissertation examines the short- and long-run impacts of timber prices and other factors affecting NIPF owners' timber harvesting and timber stocking decisions. The utility-based Faustmann model provides testable hypotheses of the exogenous variables retained in the timber supply analysis. The timber stock function, derived from a two-period biomass harvesting model, is estimated using a two-step GMM estimator based on balanced panel data from 1983 to 1991. Timber supply functions are estimated using a Tobit model adjusted for heteroscedasticity and nonnormality of errors based on panel data from 1994 to 1998. Results show that if specification analysis of the Tobit model is ignored, inconsistency and biasedness can have a marked effect on parameter estimates. The empirical results show that owner's age is the single most important factor determining timber stock; timber price is the single most important factor in harvesting decision. The results of the timber supply estimations can be interpreted using utility-based Faustmann model of a forest owner who values a growing timber in situ.

Uncertainty in forest simulators and forest planning systems

The forest simulator is a computerized model for predicting forest growth and future development as well as effects of forest harvests and treatments. The forest planning system is a decision support tool, usually including a forest simulator and an optimisation model, for finding the optimal forest management actions. The information produced by forest simulators and forest planning systems is used for various analytical purposes and in support of decision making. However, the quality and reliability of this information can often be questioned. Natural variation in forest growth and estimation errors in forest inventory, among other things, cause uncertainty in predictions of forest growth and development. This uncertainty stemming from different sources has various undesirable effects. In many cases outcomes of decisions based on uncertain information are something else than desired. The objective of this thesis was to study various sources of uncertainty and their effects in forest simulators and forest planning systems. The study focused on three notable sources of uncertainty: errors in forest growth predictions, errors in forest inventory data, and stochastic fluctuation of timber assortment prices. Effects of uncertainty were studied using two types of forest growth models, individual tree-level models and stand-level models, and with various error simulation methods. New method for simulating more realistic forest inventory errors was introduced and tested. Also, three notable sources of uncertainty were combined and their joint effects on stand-level net present value estimates were simulated. According to the results, the various sources of uncertainty can have distinct effects in different forest growth simulators. The new forest inventory error simulation method proved to produce more realistic errors. The analysis on the joint effects of various sources of uncertainty provided interesting knowledge about uncertainty in forest simulators.

Estimation of local forest attributes, utilizing two-phase sampling and auxiliary data

This thesis examines the feasibility of a forest inventory method based on two-phase sampling in estimating forest attributes at the stand or substand levels for forest management purposes. The method is based on multi-source forest inventory combining auxiliary data consisting of remote sensing imagery or other geographic information and field measurements. Auxiliary data are utilized as first-phase data for covering all inventory units. Various methods were examined for improving the accuracy of the forest estimates. Pre-processing of auxiliary data in the form of correcting the spectral properties of aerial imagery was examined (I), as was the selection of aerial image features for estimating forest attributes (II). Various spatial units were compared for extracting image features in a remote sensing aided forest inventory utilizing very high resolution imagery (III). A number of data sources were combined and different weighting procedures were tested in estimating forest attributes (IV, V). Correction of the spectral properties of aerial images proved to be a straightforward and advantageous method for improving the correlation between the image features and the measured forest attributes. Testing different image features that can be extracted from aerial photographs (and other very high resolution images) showed that the images contain a wealth of relevant information that can be extracted only by utilizing the spatial organization of the image pixel values. Furthermore, careful selection of image features for the inventory task generally gives better results than inputting all extractable features to the estimation procedure. When the spatial units for extracting very high resolution image features were examined, an approach based on image segmentation generally showed advantages compared with a traditional sample plot-based approach. Combining several data sources resulted in more accurate estimates than any of the individual data sources alone. The best combined estimate can be derived by weighting the estimates produced by the individual data sources by the inverse values of their mean square errors. Despite the fact that the plot-level estimation accuracy in two-phase sampling inventory can be improved in many ways, the accuracy of forest estimates based mainly on single-view satellite and aerial imagery is a relatively poor basis for making stand-level management decisions.

Quality Assessment of a Forest Inventory Based on Airborne Laser Scanning

In this study, a quality assessment method based on sampling of primary laser inventory units (microsegments) was analysed. The accuracy of a laser inventory carried out in Kuhmo was analysed as a case study. Field sample plots were measured on the sampled microsegments in the Kuhmo inventory area. Two main questions were considered. Did the ALS based inventory meet the accuracy requirements set for the provider and how should a reliable, cost-efficient and independent quality assessment be undertaken. The agreement between control measurement and ALS based inventory was analysed in four ways: 1) The root mean squared errors (RMSEs) and bias were calculated. 2) Scatter plots with 95% confidence intervals were plotted and the placing of identity lines was checked. 3) Bland-Altman plots were drawn so that the mean difference of attributes between the control method and ALS-method was calculated and plotted against average value of attributes. 4) The tolerance limits were defined and combined with Bland-Altman plots. The RMSE values were compared to a reference study from which the accuracy requirements had been set to the service provider. The accuracy requirements in Kuhmo were achieved, however comparison of RMSE values proved to be difficult. Field control measurements are costly and time-consuming, but they are considered to be robust. However, control measurements might include errors, which are difficult to take into account. Using the Bland-Altman plots none of the compared methods are considered to be completely exact, so this offers a fair way to interpret results of assessment. The tolerance limits to be set on order combined with Bland-Altman plots were suggested to be taken in practise. In addition, bias should be calculated for total area. Some other approaches for quality control were briefly examined. No method was found to fulfil all the required demands of statistical reliability, cost-efficiency, time efficiency, simplicity and speed of implementation. Some benefits and shortcomings of the studied methods were discussed.