Statistical modelling and power analysis for detecting trends in total suspended sediment loads

The export of sediments from coastal catchments can have detrimental impacts on estuaries and near shore reef ecosystems such as the Great Barrier Reef. Catchment management approaches aimed at reducing sediment loads require monitoring to evaluate their effectiveness in reducing loads over time. However, load estimation is not a trivial task due to the complex behaviour of constituents in natural streams, the variability of water flows and often a limited amount of data. Regression is commonly used for load estimation and provides a fundamental tool for trend estimation by standardising the other time specific covariates such as flow. This study investigates whether load estimates and resultant power to detect trends can be enhanced by (i) modelling the error structure so that temporal correlation can be better quantified, (ii) making use of predictive variables, and (iii) by identifying an efficient and feasible sampling strategy that may be used to reduce sampling error. To achieve this, we propose a new regression model that includes an innovative compounding errors model structure and uses two additional predictive variables (average discounted flow and turbidity). By combining this modelling approach with a new, regularly optimised, sampling strategy, which adds uniformity to the event sampling strategy, the predictive power was increased to 90%. Using the enhanced regression model proposed here, it was possible to detect a trend of 20% over 20 years. This result is in stark contrast to previous conclusions presented in the literature. (C) 2014 Elsevier B.V. All rights reserved.

Sediment concentration prediction and statistical evaluation for annual load estimation

We consider the development of statistical models for prediction of constituent concentration of riverine pollutants, which is a key step in load estimation from frequent flow rate data and less frequently collected concentration data. We consider how to capture the impacts of past flow patterns via the average discounted flow (ADF) which discounts the past flux based on the time lapsed - more recent fluxes are given more weight. However, the effectiveness of ADF depends critically on the choice of the discount factor which reflects the unknown environmental cumulating process of the concentration compounds. We propose to choose the discount factor by maximizing the adjusted R-2 values or the Nash-Sutcliffe model efficiency coefficient. The R2 values are also adjusted to take account of the number of parameters in the model fit. The resulting optimal discount factor can be interpreted as a measure of constituent exhaustion rate during flood events. To evaluate the performance of the proposed regression estimators, we examine two different sampling scenarios by resampling fortnightly and opportunistically from two real daily datasets, which come from two United States Geological Survey (USGS) gaging stations located in Des Plaines River and Illinois River basin. The generalized rating-curve approach produces biased estimates of the total sediment loads by -30% to 83%, whereas the new approaches produce relatively much lower biases, ranging from -24% to 35%. This substantial improvement in the estimates of the total load is due to the fact that predictability of concentration is greatly improved by the additional predictors.

Process Analytical Technology Approach on Fluid Bed Granulation and Drying : Identifying Critical Relationships and Constructing the Design Space

Fluid bed granulation is a key pharmaceutical process which improves many of the powder properties for tablet compression. Dry mixing, wetting and drying phases are included in the fluid bed granulation process. Granules of high quality can be obtained by understanding and controlling the critical process parameters by timely measurements. Physical process measurements and particle size data of a fluid bed granulator that are analysed in an integrated manner are included in process analytical technologies (PAT). Recent regulatory guidelines strongly encourage the pharmaceutical industry to apply scientific and risk management approaches to the development of a product and its manufacturing process. The aim of this study was to utilise PAT tools to increase the process understanding of fluid bed granulation and drying. Inlet air humidity levels and granulation liquid feed affect powder moisture during fluid bed granulation. Moisture influences on many process, granule and tablet qualities. The approach in this thesis was to identify sources of variation that are mainly related to moisture. The aim was to determine correlations and relationships, and utilise the PAT and design space concepts for the fluid bed granulation and drying. Monitoring the material behaviour in a fluidised bed has traditionally relied on the observational ability and experience of an operator. There has been a lack of good criteria for characterising material behaviour during spraying and drying phases, even though the entire performance of a process and end product quality are dependent on it. The granules were produced in an instrumented bench-scale Glatt WSG5 fluid bed granulator. The effect of inlet air humidity and granulation liquid feed on the temperature measurements at different locations of a fluid bed granulator system were determined. This revealed dynamic changes in the measurements and enabled finding the most optimal sites for process control. The moisture originating from the granulation liquid and inlet air affected the temperature of the mass and pressure difference over granules. Moreover, the effects of inlet air humidity and granulation liquid feed rate on granule size were evaluated and compensatory techniques used to optimize particle size. Various end-point indication techniques of drying were compared. The ∆T method, which is based on thermodynamic principles, eliminated the effects of humidity variations and resulted in the most precise estimation of the drying end-point. The influence of fluidisation behaviour on drying end-point detection was determined. The feasibility of the ∆T method and thus the similarities of end-point moisture contents were found to be dependent on the variation in fluidisation between manufacturing batches. A novel parameter that describes behaviour of material in a fluid bed was developed. Flow rate of the process air and turbine fan speed were used to calculate this parameter and it was compared to the fluidisation behaviour and the particle size results. The design space process trajectories for smooth fluidisation based on the fluidisation parameters were determined. With this design space it is possible to avoid excessive fluidisation and improper fluidisation and bed collapse. Furthermore, various process phenomena and failure modes were observed with the in-line particle size analyser. Both rapid increase and a decrease in granule size could be monitored in a timely manner. The fluidisation parameter and the pressure difference over filters were also discovered to express particle size when the granules had been formed. The various physical parameters evaluated in this thesis give valuable information of fluid bed process performance and increase the process understanding.

An exploratory study on the commercialisation of heat pump-fluidised bed drying technology

Fluidised bed-heat pump drying technology offers distinctive advantages over the existing drying technology employed in the Australian food industry. However, as is the case with many other examples of innovations that have had clear relative advantages, the rates of adoption and diffusion of this technology have been very slow. "Why does this happen?" is the theme of this research study that has been undertaken with an objective to analyse a range of issues related to the market acceptance of technological innovations. The research methodology included the development of an integrated conceptual model based on an extensive review of literature in the areas of innovation diffusion, technology transfer and industrial marketing. Three major determinants associated with the market acceptance of innovations were identified as the characteristics of the innovation, adopter information processing capability and the influence of the innovation supplier on the adoption process. This was followed by a study involving more than 30 small and medium enterprises identified as potential adopters of fluidised bed-heat pump drying technology in the Australian food industry. The findings revealed that judgment was the key evaluation strategy employed by potential adopters in the particular industry sector. Further, it was evidenced that the innovations were evaluated against a predetermined criteria covering a range of aspects with emphasis on a selected set of attributes of the innovation. Implication of these findings on the commercialisation of fluidised bed-heat pump drying technology was established, and a series of recommendations was made to the innovation supplier (DPI/FT) enabling it to develop an effective commercialisation strategy.

Expression Profiling of Nucleotide Metabolism-Related Genes in Human Breast Cancer Cells After Treatment with 5-Fluorouracil

5-Fluorouracil (5-FU) is one of the most widely used drugs for treatment of cancers, including breast cancer that exhibits its anticancer activity by inhibiting DNA synthesis and also incorporated into DNA and RNA. The objective of this investigation was to find out the total nucleotide metabolism genes regulated by 5-FU in breast cancer cell line. The breast cancer cell line MCF-7 was treated with the drug 5-FU. To analyze the expression of genes, we have conducted the experiment using 1.7k and 19k human microarray slide and confirmed the expression of genes by semiquantitative reverse transcription-polymerase chain reaction. The expression of 44 genes involved in the nucleotide metabolism pathway was quantified. Of these 44 genes analyzed, transcription of 6 genes were upregulated and 9 genes were downregulated. Earlier studies revealed that the transcription of genes for key enzymes like thymidylate synthase, thymidinekinase, and dihydropyrimidine dehydrogenase are regulated by 5-FU. This study identified some novel genes like thioredoxin reductase, ectonucleotide triphosphate dephosphorylase, and CTP synthase are regulated by 5-FU. The data also reveal large-scale perturbation in transcription of genes not involved directly in the known mechanism of action of 5-FU.

Runoff, sediment loss and water quality from forest roads in a southeast Queensland coastal plain Pinus plantation

Runoff and sediment loss from forest roads were monitored for a two-year period in a Pinus plantation in southeast Queensland. Two classes of road were investigated: a gravelled road, which is used as a primary daily haulage route for the logging area, and an ungravelled road, which provides the main access route for individual logging compartments and is intensively used as a haulage route only during the harvest of these areas (approximately every 30 years). Both roads were subjected to routine traffic loads and maintenance during the study. Surface runoff in response to natural rainfall was measured and samples taken for the determination of sediment and nutrient (total nitrogen, total phosphorus, dissolved organic carbon and total iron) loads from each road. Results revealed that the mean runoff coefficient (runoff depth/rainfall depth) was consistently higher from the gravelled road plot with 0.57, as compared to the ungravelled road with 0.38. Total sediment loss over the two-year period was greatest from the gravelled road plot at 5.7 t km−1 compared to the ungravelled road plot with 3.9 t km−1. Suspended solids contributed 86% of the total sediment loss from the gravelled road, and 72% from the ungravelled road over the two years. Nitrogen loads from the two roads were both relatively constant throughout the study, and averaged 5.2 and 2.9 kg km−1 from the gravelled and ungravelled road, respectively. Mean annual phosphorus loads were 0.6 kg km−1 from the gravelled road and 0.2 kg km−1 from the ungravelled road. Organic carbon and total iron loads increased in the second year of the study, which was a much wetter year, and are thought to reflect the breakdown of organic matter in roadside drains and increased sediment generation, respectively. When road and drain maintenance (grading) was performed runoff and sediment loss were increased from both road types. Additionally, the breakdown of the gravel road base due to high traffic intensity during wet conditions resulted in the formation of deep (10 cm) ruts which increased erosion. The Water Erosion Prediction Project (WEPP):Road model was used to compare predicted to observed runoff and sediment loss from the two road classes investigated. For individual rainfall events, WEPP:Road predicted output showed strong agreement with observed values of runoff and sediment loss. WEPP:Road predictions for annual sediment loss from the entire forestry road network in the study area also showed reasonable agreement with the extrapolated observed values.

Sediment and nutrient losses from exotic Pinus plantation management operations under simulated rainfall

Rainfall simulation experiments were carried out to measure runoff and soil water fluxes of suspended solids, total nitrogen, total phosphorus, dissolved organic carbon and total iron from sites in Pinus plantations on the coastal lowlands of south-eastern Queensland subjected to various operations (treatments). The operations investigated were cultivated and nil-cultivated site preparation, fertilised site preparation, clearfall harvesting and prescribed burning; these treatments were compared with an 8-y-old established plantation. Flow-weighted mean concentrations of total nitrogen and total phosphorus in surface runoff from the cultivated and nil-cultivated site-preparation, clearfall harvest, prescribed burning and 8-y-old established plantation treatments were very similar. However, both the soil water and the runoff from the fertilised site preparation treatment contained more nitrogen (N) and phosphorus (P) than the other treatments - with 3.10 mg N L-1 and 4.32 mg P L-1 (4 and 20 times more) in the runoff. Dissolved organic carbon concentrations in runoff from the nil-cultivated site-preparation and prescribed burn treatments were elevated. Iron concentrations were highest in runoff from the nil-cultivated site-preparation and 8-y-old established plantation treatments. Concentrations of suspended solids in runoff were higher from cultivated site preparation and prescribed burn treatments, and reflect the great disturbance of surface soil at these sites. The concentrations of all analytes were highest in initial runoff from plots, and generally decreased with time. Total nitrogen (mean 7.28, range 0.11-13.27 mg L-1) and total phosphorus (mean 11.60, range 0.06-83.99 mg L-1) concentrations in soil water were between 2 and 10 times greater than in surface runoff, which highlights the potential for nutrient fluxes in interflow (i.e. in the soil above the water table) through the general plantation area. Implications in regard to forest management are discussed, along with results of larger catchment-scale studies.

Gene expression profiling of cuticular proteins across the moult cycle of the crab Portunus pelagicus

Background: Crustaceans represent an attractive model to study biomineralization and cuticle matrix formation, as these events are precisely timed to occur at certain stages of the moult cycle. Moulting, the process by which crustaceans shed their exoskeleton, involves the partial breakdown of the old exoskeleton and the synthesis of a new cuticle. This cuticle is subdivided into layers, some of which become calcified while others remain uncalcified. The cuticle matrix consists of many different proteins that confer the physical properties, such as pliability, of the exoskeleton. Results: We have used a custom cDNA microarray chip, developed for the blue swimmer crab Portunus pelagicus, to generate expression profiles of genes involved in exoskeletal formation across the moult cycle. A total of 21 distinct moult-cycle related differentially expressed transcripts representing crustacean cuticular proteins were isolated. Of these, 13 contained copies of the cuticle_1 domain previously isolated from calcified regions of the crustacean exoskeleton, four transcripts contained a chitin_bind_4 domain (RR consensus sequence) associated with both the calcified and un-calcified cuticle of crustaceans, and four transcripts contained an unannotated domain (PfamB_109992) previously isolated from C. pagurus. Additionally, cryptocyanin, a hemolymph protein involved in cuticle synthesis and structural integrity, also displays differential expression related to the moult cycle. Moult stage-specific expression analysis of these transcripts revealed that differential gene expression occurs both among transcripts containing the same domain and among transcripts containing different domains. Conclusion: The large variety of genes associated with cuticle formation, and their differential expression across the crustacean moult cycle, point to the complexity of the processes associated with cuticle formation and hardening. This study provides a molecular entry path into the investigation of the gene networks associated with cuticle formation.

Hydrodynamic pressure on a dam with a periodically corrugated reservoir bed

The problem of determining the hydrodynamic pressure, caused by earthquake forces, on a dam with a vertical upstream face and a periodically corrugated reservoir bed is solved approximately by employing a Fourier cosine transform technique to the linearised equations of inviscid and incompressible flow. A particular case of the present problem giving rise to results valid for dams with flat reservoir beds is shown to produce known results as a check of the method used.

Differential expression profiling of components associated with exoskeletal hardening in crustaceans

Background: Exoskeletal hardening in crustaceans can be attributed to mineralization and sclerotization of the organic matrix. Glycoproteins have been implicated in the calcification process of many matrices. Sclerotization, on the other hand, is catalysed by phenoloxidases, which also play a role in melanization and the immunological response in arthropods. Custom cDNA microarrays from Portunus pelagicus were used to identify genes possibly associated with the activation pathways involved in these processes. Results: Two genes potentially involved in the recognition of glycosylation, the C-type lectin receptor and the mannose-binding protein, were found to display molt cycle-related differential expression profiles. C-type lectin receptor up-regulation was found to coincide with periods associated with new uncalcified cuticle formation, while the up-regulation of mannose-binding protein occurred only in the post-molt stage, during which calcification takes place, implicating both in the regulation of calcification. Genes presumed to be involved in the phenoloxidase activation pathway that facilitates sclerotization also displayed molt cycle-related differential expression profiles. Members of the serine protease superfamily, trypsin-like and chymotrypsin-like, were up-regulated in the intermolt stage when compared to post-molt, while trypsin-like was also up-regulated in pre-molt compared to ecdysis. Additionally, up-regulation in pre- and intermolt stages was observed by transcripts encoding other phenoloxidase activators including the putative antibacterial protein carcinin-like, and clotting protein precursor-like. Furthermore, hemocyanin, itself with phenoloxidase activity, displayed an identical expression pattern to that of the phenoloxidase activators, i.e. up-regulation in pre- and intermolt. Conclusion: Cuticle hardening in crustaceans is a complex process that is precisely timed to occur in the post-molt stage of the molt cycle. We have identified differential expression patterns of several genes that are believed to be involved in biomineralization and sclerotization and propose possible regulatory mechanisms for these processes based on their expression profiles, such as the potential involvement of C-type lectin receptors and mannose binding protein in the regulation of calcification.

Packed bed bioreactor for the isolation and expansion of placental-derived Mesenchymal Stromal Cells

Large numbers of Mesenchymal stem/stromal cells (MSCs) are required for clinical relevant doses to treat a number of diseases. To economically manufacture these MSCs, an automated bioreactor system will be required. Herein we describe the development of a scalable closed-system, packed bed bioreactor suitable for large-scale MSCs expansion. The packed bed was formed from fused polystyrene pellets that were air plasma treated to endow them with a surface chemistry similar to traditional tissue culture plastic. The packed bed was encased within a gas permeable shell to decouple the medium nutrient supply and gas exchange. This enabled a significant reduction in medium flow rates, thus reducing shear and even facilitating single pass medium exchange. The system was optimised in a small-scale bioreactor format (160 cm2) with murine-derived green fluorescent protein-expressing MSCs, and then scaled-up to a 2800 cm2 format. We demonstrated that placental derived MSCs could be isolated directly within the bioreactor and subsequently expanded. Our results demonstrate that the closed system large-scale packed bed bioreactor is an effective and scalable tool for large-scale isolation and expansion of MSCs.

Impacts of improved grazing land management on sediment yields, Part 1: Hillslope processes.

Summary Poor land condition resulting from unsustainable grazing practices can reduce enterprise profitability and increase water, sediment and associated nutrient runoff from properties and catchments. This paper presents the results of a 6 year field study that used a series of hillslope flume experiments to evaluate the impact of improved grazing land management (GLM) on hillslope runoff and sediment yields. The study was carried out on a commercial grazing property in a catchment draining to the Burdekin River in northern Australia. During this study average ground cover on hillslopes increased from ~35% to ~75%, although average biomass and litter levels are still relatively low for this landscape type (~60 increasing to 1100 kg of dry matter per hectare). Pasture recovery was greatest on the upper and middle parts of hillslopes. Areas that did not respond to the improved grazing management had <10% cover and were on the lower slopes associated with the location of sodic soil and the initiation of gullies. Comparison of ground cover changes and soil conditions with adjacent properties suggest that grazing management, and not just improved rainfall conditions, were responsible for the improvements in ground cover in this study. The ground cover improvements resulted in progressively lower runoff coefficients for the first event in each wet season, however, runoff coefficients were not reduced at the annual time scale. The hillslope annual sediment yields declined by ~70% on two out of three hillslopes, although where bare patches (with <10% cover) were connected to gullies and streams, annual sediment yields increased in response to higher rainfall in latter years of the study. It appears that bare patches are the primary source areas for both runoff and erosion on these hillslopes. Achieving further reductions in runoff and erosion in these landscapes may require management practices that improve ground cover and biomass in bare areas, particularly when they are located adjacent to concentrated drainage lines.

Freddy, Ursula, Elizabeth, Hal, Walter, and Kurt Gottschalk sharing a bed with their parents.

From left to right: Fred Gottschalk, grandma, Ursula Gottschalk, Elizabeth Gottschalk, grandpa, Hal Gottschalk, Walter Gottschalk, and Kurt Gottschalk

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.