Estuarine fish health assessment: evidence of wastewater impacts based on nitrogen isotopes and histopathology

Sewage effluent is a powerful agent of ecological change in estuaries. While the effects of sewage pollution on water quality are usually well documented, biological responses of exposed organisms are not. We quantified health impacts in the form of pathological tissue changes across multiple organs in estuarine fish exposed to elevated levels of treated wastewater. Structural pathologies were compared in wild populations of four fish species from two subtropical estuaries on the east coast of Australia that differ substantially in the amount of direct wastewater loadings. Uptake of sewage-derived  nitrogen by fish was traced with stable nitrogen isotopes. Pathologies were common in the liver, spleen, gill, kidney and muscle tissues, and included granulomas, melanomacrophage aggregates, and multiple deformities of the gill epithelia. Tissue deformities were more frequent in fish exposed directly to wastewater discharges. Mullet (Valamugil georgii) were most affected, with only a single specimen free of pathologies in the sewage-impacted estuary. Similarly, in those fish that had structural abnormalities, more deformities were generally found in individuals from sites receiving sewage. These spatial contrasts in impaired fish health correspond to significantly enriched δ₁₅N values in fish muscle as a consequence of fish assimilating sewage-N. Overall, the pattern of lower health and enriched δ₁₅N values in fish from sewage-impacted areas suggests that organism health is lowered by sewage inputs to estuaries. Measurements of organism health are required to understand the effects of sewage on estuarine ecosystems, and histopathology of fishes is a powerful tool to achieve this.

Agent-based hybrid framework for decision making on complex problems

Electronic commerce and the Internet have created demand for automated systems that can make complex decisions utilizing information from multiple sources. Because the information is uncertain, dynamic, distributed, and heterogeneous in nature, these systems require a great diversity of intelligent techniques including expert systems, fuzzy logic, neural networks, and genetic algorithms. However, in complex decision making, many different components or sub-tasks are involved, each of which requires different types of processing. Thus multiple such techniques are required resulting in systems called hybrid intelligent systems. That is, hybrid solutions are crucial for complex problem solving and decision making. There is a growing demand for these systems in many areas including financial investment planning, engineering design, medical diagnosis, and cognitive simulation. However, the design and development of these systems is difficult because they have a large number of parts or components that have many interactions. From a multi-agent perspective, agents in multi-agent systems (MAS) are autonomous and can engage in flexible, high-level interactions. MASs are good at complex, dynamic interactions. Thus a multi-agent perspective is suitable for modeling, design, and construction of hybrid intelligent systems. The aim of this thesis is to develop an agent-based framework for constructing hybrid intelligent systems which are mainly used for complex problem solving and decision making. Existing software development techniques (typically, object-oriented) are inadequate for modeling agent-based hybrid intelligent systems. There is a fundamental mismatch between the concepts used by object-oriented developers and the agent-oriented view. Although there are some agent-oriented methodologies such as the Gaia methodology, there is still no specifically tailored methodology available for analyzing and designing agent-based hybrid intelligent systems. To this end, a methodology is proposed, which is specifically tailored to the analysis and design of agent-based hybrid intelligent systems. The methodology consists of six models - role model, interaction model, agent model, skill model, knowledge model, and organizational model. This methodology differs from other agent-oriented methodologies in its skill and knowledge models. As good decisions and problem solutions are mainly based on adequate information, rich knowledge, and appropriate skills to use knowledge and information, these two models are of paramount importance in modeling complex problem solving and decision making. Follow the methodology, an agent-based framework for hybrid intelligent system construction used in complex problem solving and decision making was developed. The framework has several crucial characteristics that differentiate this research from others. Four important issues relating to the framework are also investigated. These cover the building of an ontology for financial investment, matchmaking in middle agents, reasoning in problem solving and decision making, and decision aggregation in MASs. The thesis demonstrates how to build a domain-specific ontology and how to access it in a MAS by building a financial ontology. It is argued that the practical performance of service provider agents has a significant impact on the matchmaking outcomes of middle agents. It is proposed to consider service provider agents' track records in matchmaking. A way to provide initial values for the track records of service provider agents is also suggested. The concept of ‘reasoning with multimedia information’ is introduced, and reasoning with still image information using symbolic projection theory is proposed. How to choose suitable aggregation operations is demonstrated through financial investment application and three approaches are proposed - the stationary agent approach, the token-passing approach, and the mobile agent approach to implementing decision aggregation in MASs. Based on the framework, a prototype was built and applied to financial investment planning. This prototype consists of one serving agent, one interface agent, one decision aggregation agent, one planning agent, four decision making agents, and five service provider agents. Experiments were conducted on the prototype. The experimental results show the framework is flexible, robust, and fully workable. All agents derived from the methodology exhibit their behaviors correctly as specified.

On the fundamental mechanisms of active screen plasma nitriding

The nitriding mechanisms of conventional DC plasma treatments have been extensively studied and discussed, but no general agreement has been reached thus far. The sputtering and redeposition theory is among the most accepted ones but, even though this mechanism is feasible, its contribution to the nitriding effect is under question. Furthermore, the novel active screen plasma nitriding technique has been successful in treating samples left at floating potential, where sputtering can not be considered to play a major role. Therefore, it has been proposed that the material sputtered from the cathodic mesh of the active screen furnace (auxiliary cathode) and deposited onto the treated specimens is involved in the mass transfer of nitrogen. The contribution made by this transferred material is the focus of attention of the present study. The hardening effect on the treated specimens showed considerable correlation with the deposition layer, and the XRD analysis of this deposited material yielded possible FeN and FexN peaks. This finding supports the deposition of iron nitrides and their subsequent decomposition on the treated substrate as a mechanism of significance to the plasma nitriding treatments conducted in active screen experimental settings.

Feed intake, growth, plasma glucose and urea nitrogen concentration, and cacass traits of lambs fed isoenergetic amounts of canola meal, soybean meal, and fish meal with forage based diet.

This experiment was conducted to examine the effect of feeding small, isoenergetic amounts of supplements containing high protein and functional lipid components, rather than the greater amounts of cereal and/or legume grains usually fed during the dry season in Australia, on dry matter intake (DMI), growth performance, plasma metabolites, and fat deposition in lambs consuming low quality roughage. Thirty two crossbred wether lambs ([Merino × Border Leicester] × Poll Dorset) were divided into four groups by stratified randomization according to liveweight (26–33 kg). After a 7-day adaptation to a hay diet (lucerne hay:oaten hay; 30:70), lambs were allocated to four treatments consisting of (1) basal diet of lucerne hay:oat hay (20:80; metabolizable energy (ME) = 7.0 MJ/kg DM), Basal; (2) basal + canola meal (84 g per day), CM; (3) basal + soymeal (75 g per day), SM; or (4) basal + fishmeal (80 g per day), FM. Daily hay and supplement DMI, and weekly liveweight were recorded during a 53-day experimental study. Blood samples were taken on day 1 and pre- and post-feeding on days 30 and 53 to measure changes in plasma glucose and plasma urea nitrogen (PUN) concentration. At the end of the experiment, lambs were slaughtered and hot carcass weight (HCW) recorded; cold carcass fatness (total muscle and adipose tissue depth at 12th rib, 110 mm from midline; GR) was determined at 24 h postmortem. Total DMI was increased (P < 0.001) in CM, SM and FM treatments, but basal hay DMI intake was only increased (P < 0.01) in CM and FM treatments compared with Basal treatment. This resulted in significant (P < 0.01) increases in metabolizable energy (ME) and crude protein (CP) intakes in all supplemented treatments, with the highest intakes recorded in the FM treatment. Liveweight gain (LWG) was significantly increased in CM and SM (P < 0.05) and FM (P < 0.01) treatments but HCW was significantly (P < 0.01) heavier slaughter only in the FM treatment. Feed conversion efficiency (P < 0.001) and GR fat at depth (P < 0.05) was reduced in all supplement treatments compared with Basal. Plasma glucose concentration was significantly (P < 0.05) increased after feeding in all treatments but there was no treatment effect. PUN was significantly increased over time in the supplemented treatments compared with the Basal treatment; there was no significant difference between supplement treatments by day 53. Results show that feeding small amounts of high protein and lipid-containing supplements improves production responses and are beneficial in producing carcasses with more lean compared with carcasses from lambs fed a low quality hay diet.

A clustering based hybrid system for mass spectrometry data analysis

Recently, much attention has been given to the mass spectrometry (MS) technology based disease classification, diagnosis, and protein-based biomarker identification. Similar to microarray based investigation, proteomic data generated by such kind of high-throughput experiments are often with high feature-to-sample ratio. Moreover, biological information and pattern are compounded with data noise, redundancy and outliers. Thus, the development of algorithms and procedures for the analysis and interpretation of such kind of data is of paramount importance. In this paper, we propose a hybrid system for analyzing such high dimensional data. The proposed method uses the k-mean clustering algorithm based feature extraction and selection procedure to bridge the filter selection and wrapper selection methods. The potential informative mass/charge (m/z) markers selected by filters are subject to the k-mean clustering algorithm for correlation and redundancy reduction, and a multi-objective Genetic Algorithm selector is then employed to identify discriminative m/z markers generated by k-mean clustering algorithm. Experimental results obtained by using the proposed method indicate that it is suitable for m/z biomarker selection and MS based sample classification.

Process-based modelling of mass transport in the subsurface

Modern societies rely on natural water pathways that include subsurface flow of water and dissolved chemicals. The thesis presents a range of numerical and analytical models for simulating physical, chemical and biological processes in the subsurface, including coastal aquifers, the near-surface vadose zone, and solute transport in biogeochemically active aquifers.

Investigation of the postcure reaction and surface energy of epoxy resins using time-of-flight secondary ion mass spectrometry and contact-angle measurements

Time-of-flight secondary ion mass spectrometry (ToF-SIMS) was used to investigate correlations between the molecular changes and postcuring reaction on the surface of a diglycidyl ether of bisphenol A and diglycidylether of bisphenol F based epoxy resin cured with two different amine-based hardeners. The aim of this work was to present a proof of concept that ToF-SIMS has the ability to provide information regarding the reaction steps, path, and mechanism for organic reactions in general and for epoxy resin curing and postcuring reactions in particular. Contact-angle measurements were taken for the cured and postcured epoxy resins to correlate changes in the surface energy with the molecular structure of the surface. Principal components analysis (PCA) of the ToFSIMS positive spectra explained the variance in the molecular information, which was related to the resin curing and postcuring reactions with different hardeners and to the surface energy values. The first principal component captured information related to the chemical phenomena of the curing reaction path, branching, and network density based on changes in the relative ion density of the aliphatic hydrocarbon and the C₇H₇O⁺ positive ions. The second principal component captured information related to the difference in the surface energy, which was correlated to the difference in the relative intensity of the C_xH_yN_z⁺ ions of the samples. PCA of the negative spectra provided insight into the extent of consumption of the hardener molecules in the curing and postcuring reactions of both systems based on the relative ion intensity of the nitrogen-containing negative ions and showed molecular correlations with the sample surface energy.

Estimation of nitrogen and phosphorus in effluent from the striped catfish farming sector in the Mekong Delta, Vietnam

In this study an attempt is made to estimate nitrogen and phosphorus discharged to the environment from the striped catfish (Pangasianodon hypophthalmus) farming sector in the Mekong Delta (8°33̕–10°55̕ N, 104°30̕–106°50̕ E), South Vietnam. The sector accounted for 687,000 t production in 2007 and 1,094,879 t in 2008, with over 95% of the produce destined for export to over 100 countries. Commercial and farm-made feeds are used in catfish farming, currently the former being more predominant. Nitrogen discharge levels were similar for commercial feeds (median 46.0 kg/t fish) and farm-made feeds (median 46.8 kg/t fish); whilst, phosphorus discharge levels for commercial feeds (median 14.4 kg/t fish) were considerably lower than for farm-made feeds (median 18.4 kg/t fish). Based on the median nutrient discharge levels for commercial feeds, striped catfish production in the Mekong Delta discharged 31,602 t N and 9,893 t P, and 50,364 t N and 15,766 t P in 2007 and 2008, respectively. However, the amount of nutrients returned directly to the Mekong River may be substantially less than this as a significant proportion of the water used for catfish farming as well as the sludge is diverted to other agricultural farming systems. Striped catfish farming in the Mekong Delta compared favourably with other cultured species, irrespective of the type of feed used, when the total amounts of N and P discharged in the production of a tonne of production was estimated.

Does an increase in body mass index over 10 years affect knee structure in a population-based cohort study of adult women?

Introduction : Although obesity is a modifiable risk factor for knee osteoarthritis (OA), the effect of weight gain on knee structure in young and healthy adults has not been examined. The aim of this study was to examine the relationship between body mass index (BMI), and change in BMI over the preceding 10-year period, and knee structure (cartilage defects, cartilage volume and bone marrow lesions (BMLs)) in a population-based sample of young to middle-aged females.

Methods : One hundred and forty-two healthy, asymptomatic females (range 30 to 49 years) in the Barwon region of Australia, underwent magnetic resonance imaging (MRI) during 2006 to 2008. BMI measured 10 years prior (1994 to 1997), current BMI and change in BMI (accounting for baseline BMI) over this period, was assessed for an association with cartilage defects and volume, and BMLs.

Results : After adjusting for age and tibial plateau area, the risk of BMLs was associated with every increase in one-unit of baseline BMI (OR 1.14 (95% CI 1.03 to 1.26) P = 0.009), current BMI (OR 1.13 (95% CI 1.04 to 1.23) P = 0.005), and per one unit increase in BMI (OR 1.14 (95% CI 1.03 to 1.26) P = 0.01). There was a trend for a one-unit increase in current BMI to be associated with increased risk of cartilage defects (OR 1.06 (95% CI 1.00 to 1.13) P = 0.05), and a suggestion that a one-unit increase in BMI over 10 years may be associated with reduced cartilage volume (-17.8 ml (95% CI -39.4 to 3.9] P = 0.10). Results remained similar after excluding those with osteophytes.

Conclusions : This study provides longitudinal evidence for the importance of avoiding weight gain in women during early to middle adulthood as this is associated with increased risk of BMLs, and trend toward increased tibiofemoral cartilage defects. These changes have been shown to precede increased cartilage loss. Longitudinal studies will show whether avoiding weight gain in early adulthood may play an important role in diminishing the risk of knee OA.

Prevalence of obesity and the relationship between the body mass index and body fat : cross-sectional, population-based data

Background: Anthropometric measures such as the body mass index (BMI) and waist circumference are widely used as convenient indices of adiposity, yet there are limitations in their estimates of body fat. We aimed to determine the prevalence of obesity using criteria based on the BMI and waist circumference, and to examine the relationship between the BMI and body fat.

Methodology/Principal Findings: This population-based, cross-sectional study was conducted as part of the Geelong Osteoporosis Study. A random sample of 1,467 men and 1,076 women aged 20–96 years was assessed 2001–2008. Overweight and obesity were identified according to BMI (overweight 25.0–29.9 kg/m2; obesity $30.0 kg/m2) and waist circumference (overweight men 94.0–101.9 cm; women 80.0–87.9 cm; obesity men $102.0 cm, women $88.0 cm); body fat mass was assessed using dual energy X-ray absorptiometry; height and weight were measured and lifestyle factors documented by self-report. According to the BMI, 45.1% (95%CI 42.4–47.9) of men and 30.2% (95%CI 27.4–33.0) of women were overweight and a further 20.2% (95%CI 18.0–22.4) of men and 28.6% (95%CI 25.8–31.3) of women were obese. Using waist circumference, 27.5% (95%CI 25.1–30.0) of men and 23.3% (95%CI 20.8–25.9) of women were overweight, and 29.3% (95%CI 26.9–31.7) of men and 44.1% (95%CI 41.2–47.1) of women, obese. Both criteria indicate that approximately 60% of the population exceeded recommended thresholds for healthy body habitus. There was no consistent pattern apparent between BMI and energy intake. Compared with women, BMI overestimated adiposity in men, whose excess weight was largely attributable to muscular body builds and greater bone mass. BMI also underestimated adiposity in the elderly. Regression models including gender, age and BMI explained 0.825 of the variance in percent body fat.

Conclusions/Significance: As the BMI does not account for differences in body composition, we suggest that gender- and age-specific thresholds should be considered when the BMI is used to indicate adiposity.

Body mass index, sexual difficulties and sexual satisfaction among people in regular heterosexual relationships : a population-based study

Background/Aims:  The aims of this study were to clarify the relationship between body mass index (BMI) and sexual difficulties and to investigate if BMI influenced sexual satisfaction, over and above the effects of sexual difficulties.

Methods:  Cross-sectional analyses of a nationally representative computer-assisted telephone interview. Eight thousand, six hundred and fifty-six respondents were recruited by random digit dialling in 2004–2005. Only those in a sexually active, heterosexual relationship were included in the current analyses.

Results:  After adjustments for demographic factors, both overweight and obese male and female participants were more likely to report worrying during sex about whether their body was unattractive. Among women, associations were also found between higher BMI and lack of interest in sex. No other significant associations between BMI and sexual difficulties were evident. There was an association between BMI and extreme physical pleasure for women but not men over and above the effects of sexual difficulties, with obese women being more likely than normal weight women to report extreme physical pleasure. No associations were found for either men or women between BMI and whether or not they reported extreme emotional or sexual satisfaction with their relationship.

Conclusions:  With the exception of body image difficulties, there is little association between BMI and self-reported sexual difficulties. Furthermore, extreme sexual and emotional satisfaction appeared to be associated with the presence or absence of sexual difficulties and not overly influenced by BMI. Overall, clinicians and patients should be aware that being overweight is not necessarily detrimental to sexual functioning.

Transcriptomics-based analysis using RNA-Seq of the coconut (Cocos nucifera) leaf in response to yellow decline phytoplasma infection

Invasive phytoplasmas wreak havoc on coconut palms worldwide, leading to high loss of income, food insecurity and extreme poverty of farmers in producing countries. Phytoplasmas as strictly biotrophic insect-transmitted bacterial pathogens instigate distinct changes in developmental processes and defence responses of the infected plants and manipulate plants to their own advantage; however, little is known about the cellular and molecular mechanisms underlying host–phytoplasma interactions. Further, phytoplasma-mediated transcriptional alterations in coconut palm genes have not yet been identified. This study evaluated the whole transcriptome profiles of naturally infected leaves of Cocos nucifera ecotype Malayan Red Dwarf in response to yellow decline phytoplasma from group 16SrXIV, using RNA-Seq technique. Transcriptomics-based analysis reported here identified genes involved in coconut innate immunity. The number of down-regulated genes in response to phytoplasma infection exceeded the number of genes up-regulated. Of the 39,873 differentially expressed unigenes, 21,860 unigenes were suppressed and 18,013 were induced following infection. Comparative analysis revealed that genes associated with defence signalling against biotic stimuli were significantly overexpressed in phytoplasma-infected leaves versus healthy coconut leaves. Genes involving cell rescue and defence, cellular transport, oxidative stress, hormone stimulus and metabolism, photosynthesis reduction, transcription and biosynthesis of secondary metabolites were differentially represented. Our transcriptome analysis unveiled a core set of genes associated with defence of coconut in response to phytoplasma attack, although several novel defence response candidate genes with unknown function have also been identified. This study constitutes valuable sequence resource for uncovering the resistance genes and/or susceptibility genes which can be used as genetic tools in disease resistance breeding.

Mass spectrometry-based proteomic data for cancer diagnosis using interval type-2 fuzzy system

An interval type-2 fuzzy logic system is introduced for cancer diagnosis using mass spectrometry-based proteomic data. The fuzzy system is incorporated with a feature extraction procedure that combines wavelet transform and Wilcoxon ranking test. The proposed feature extraction generates feature sets that serve as inputs to the type-2 fuzzy classifier. Uncertainty, noise and outliers that are common in the proteomic data motivate the use of type-2 fuzzy system. Tabu search is applied for structure learning of the fuzzy classifier. Experiments are performed using two benchmark proteomic datasets for the prediction of ovarian and pancreatic cancer. The dominance of the suggested feature extraction as well as type-2 fuzzy classifier against their competing methods is showcased through experimental results. The proposed approach therefore is helpful to clinicians and practitioners as it can be implemented as a medical decision support system in practice.