An examination of the usefulness of single-species biomass models for the management of Lake Victoria fisheries

Nile perch (Lates niloticus), tilapia (Oreochromis spp), dagaa (Rastrineobola argentea, silver cyprinid), and haplochromines (Tribe Haplochromini) form the backbone of the commercial fishery on Lake Victoria. These fish stocks account for about 70% of the total catch in the three riparian states Uganda, Kenya, and Tanzania. The lake fisheries have been poorly managed, in part due to inadequate scientific analysis and management advice. The overall objective of this project was to model the stocks of the commercial fisheries of Lake Victoria with the view of determining reference points and current stock status. The Schaefer biomass model was fitted to available data for each stock (starting in the 1960s or later) in the form of landings, catch per unit effort, acoustic survey indices, and trawl survey indices. In most cases, the Schaefer model did not fit all data components very well, but attempts were made to find the best model for each stock. When the model was fitted to the Nile perch data starting from 1996, the estimated current biomass is 654 kt (95% CI 466–763); below the optimum of 692 kt and current harvest rate is 38% (33–73%), close to the optimum of 35%. At best, these can be used as tentative guidelines for the management of these fisheries. The results indicate that there have been strong multispecies interactions in the lake ecosystem. The findings from our study can be used as a baseline reference for future studies using more complex models, which could take these multispecies interactions into account.

Megabalanus azoricus (Pilsbry, 1916) : building a scientific basis for its management

Tese de Doutoramento, Biologia (Ciências do Mar), 5 de Julho de 2013, Universidade dos Açores.

Discovery and validation of serologic biomarkers for the diagnosis and prognosis of invasive candidiasis by computational immunomics

Invasive candidiasis (IC) is an opportunistic systemic mycosis caused by Candida species (commonly Candida albicans) that continues to pose a significant public health problem worldwide. Despite great advances in antifungal therapy and changes in clinical practices, IC remains a major infectious cause of morbidity and mortality in severely immunocompromised or critically ill patients, and further accounts for substantial healthcare costs. Its impact on patient clinical outcome and economic burden could be ameliorated by timely initiation of appropriate antifungal therapy. However, early detection of IC is extremely difficult because of its unspecific clinical signs and symptoms, and the inadequate accuracy and time delay of the currently available diagnostic or risk stratification methods. In consequence, the diagnosis of IC is often attained in advanced stages of infection (leading to delayed therapeutic interventions and ensuing poor clinical outcomes) or, unfortunately, at autopsy. In addition to the difficulties encountered in diagnosing IC at an early stage, the initial therapeutic decision-making process is also hindered by the insufficient accuracy of the currently available tools for predicting clinical outcomes in individual IC patients at presentation. Therefore, it is not surprising that clinicians are generally unable to early detect IC, and identify those IC patients who are most likely to suffer fatal clinical outcomes and may benefit from more personalized therapeutic strategies at presentation. Better diagnostic and prognostic biomarkers for IC are thus needed to improve the clinical management of this life-threatening and costly opportunistic fungal infection...

What lies beneath? : The pattern and abundance of the subterranean tuber bank of the invasive liana cat’s claw creeper, Macfadyena unguis-cati (Bignoniaceae)

Cat’s claw creeper, Macfadyena unguis-cati (L.) Gentry (Bignoniaceae) is a major environmental weed of riparian areas, rainforest communities and remnant natural vegetation in coastal Queensland and New South Wales, Australia. In densely infested areas, it smothers standing vegetation, including large trees, and causes canopy collapse. Quantitative data on the ecology of this invasive vine are generally lacking. The present study examines the underground tuber traits of M. unguis-cati and explores their links with aboveground parameters at five infested sites spanning both riparian and inland vegetation. Tubers were abundant in terms of density (~1000 per m2), although small in size and low in level of interconnectivity. M. unguis-cati also exhibits multiple stems per plant. Of all traits screened, the link between stand (stem density) and tuber density was the most significant and yielded a promising bivariate relationship for the purposes of estimation, prediction and management of what lies beneath the soil surface of a given M. unguis-cati infestation site. The study also suggests that new recruitment is primarily from seeds, not from vegetative propagation as previously thought. The results highlight the need for future biological-control efforts to focus on introducing specialist seed- and pod-feeding insects to reduce seed-output.

How useful is expert opinion for predicting the distribution of a species within and beyond the region of expertise? A case study using brush-tailed rock-wallabiesPetrogale penicillata

1. Species' distribution modelling relies on adequate data sets to build reliable statistical models with high predictive ability. However, the money spent collecting empirical data might be better spent on management. A less expensive source of species' distribution information is expert opinion. This study evaluates expert knowledge and its source. In particular, we determine whether models built on expert knowledge apply over multiple regions or only within the region where the knowledge was derived. 2. The case study focuses on the distribution of the brush-tailed rock-wallaby Petrogale penicillata in eastern Australia. We brought together from two biogeographically different regions substantial and well-designed field data and knowledge from nine experts. We used a novel elicitation tool within a geographical information system to systematically collect expert opinions. The tool utilized an indirect approach to elicitation, asking experts simpler questions about observable rather than abstract quantities, with measures in place to identify uncertainty and offer feedback. Bayesian analysis was used to combine field data and expert knowledge in each region to determine: (i) how expert opinion affected models based on field data and (ii) how similar expert-informed models were within regions and across regions. 3. The elicitation tool effectively captured the experts' opinions and their uncertainties. Experts were comfortable with the map-based elicitation approach used, especially with graphical feedback. Experts tended to predict lower values of species occurrence compared with field data. 4. Across experts, consensus on effect sizes occurred for several habitat variables. Expert opinion generally influenced predictions from field data. However, south-east Queensland and north-east New South Wales experts had different opinions on the influence of elevation and geology, with these differences attributable to geological differences between these regions. 5. Synthesis and applications. When formulated as priors in Bayesian analysis, expert opinion is useful for modifying or strengthening patterns exhibited by empirical data sets that are limited in size or scope. Nevertheless, the ability of an expert to extrapolate beyond their region of knowledge may be poor. Hence there is significant merit in obtaining information from local experts when compiling species' distribution models across several regions.

Immunogenicity and protective efficacy of an anti-Streptococcus pyogenes vaccine candidate in multiple animal species

Streptococcus pyogenes, also known as Group A Streptococcus (GAS) has been associated with a range of diseases from the mild pharyngitis and pyoderma to more severe invasive infections such as streptococcal toxic shock. GAS also causes a number of non-suppurative post-infectious diseases such as rheumatic fever, rheumatic heart disease and glomerulonephritis. The large extent of GAS disease burden necessitates the need for a prophylactic vaccine that could target the diverse GAS emm types circulating globally. Anti-GAS vaccine strategies have focused primarily on the GAS M-protein, an extracellular virulence factor anchored to GAS cell wall. As opposed to the hypervariable N-terminal region, the C-terminal portion of the protein is highly conserved among different GAS emm types and is the focus of a leading GAS vaccine candidate, J8-DT/alum. The vaccine candidate J8-DT/alum was shown to be immunogenic in mice, rabbits and the non-human primates, hamadryas baboons. Similar responses to J8-DT/alum were observed after subcutaneous and intramuscular immunization with J8-DT/alum, in mice and in rabbits. Further assessment of parameters that may influence the immunogenicity of J8-DT demonstrated that the immune responses were identical in male and female mice and the use of alum as an adjuvant in the vaccine formulation significantly increased its immunogenicity, resulting in a long-lived serum IgG response. Contrary to the previous findings, the data in this thesis indicates that a primary immunization with J8-DT/alum (50ƒÊg) followed by a single boost is sufficient to generate a robust immune response in mice. As expected, the IgG response to J8- DT/alum was a Th2 type response consisting predominantly of the isotype IgG1 accompanied by lower levels of IgG2a. Intramuscular vaccination of rabbits with J8-DT/alum demonstrated that an increase in the dose of J8-DT/alum up to 500ƒÊg does not have an impact on the serum IgG titers achieved. Similar to the immune response in mice, immunization with J8-DT/alum in baboons also established that a 60ƒÊg dose compared to either 30ƒÊg or 120ƒÊg was sufficient to generate a robust immune response. Interestingly, mucosal infection of naive baboons with a M1 GAS strain did not induce a J8-specific serum IgG response. As J8-DT/alum mediated protection has been previously reported to be due to the J8- specific antibody formed, the efficacy of J8-DT antibodies was determined in vitro and in vivo. In vitro opsonization and in vivo passive transfer confirmed the protective potential of J8-DT antibodies. A reduction in the bacterial burden after challenge with a bioluminescent M49 GAS strain in mice that were passively administered J8-DT IgG established that protection due to J8-DT was mediated by antibodies. The GAS burden in infected mice was monitored using bioluminescent imaging in addition to traditional CFU assays. Bioluminescent GAS strains including the ‘rheumatogenic’ M1 GAS could not be generated due to limitations with transformation of GAS, however, a M49 GAS strain was utilized during BLI. The M49 serotype is traditionally a ‘nephritogenic’ serotype associated with post-streptococcal glomerulonephritis. Anti- J8-DT antibodies now have been shown to be protective against multiple GAS strains such as M49 and M1. This study evaluated the immunogenicity of J8-DT/alum in different species of experimental animals in preparation for phase I human clinical trials and provided the ground work for the development of a rapid non-invasive assay for evaluation of vaccine candidates.

Probiotics and diarrhoea management in enterally tube fed critically ill patients : what is the evidence?

Objective: The aim of this literature review is to identify the role of probiotics in the management of enteral tube feeding (ETF) diarrhoea in critically ill patients.---------- Background: Diarrhoea is a common gastrointestinal problem seen in ETF patients. The incidence of diarrhoea in tube fed patients varies from 2% to 68% across all patients. Despite extensive investigation, the pathogenesis surrounding ETF diarrhoea remains unclear. Evidence to support probiotics to manage ETF diarrhoea in critically ill patients remains sparse.---------- Method: Literature on ETF diarrhoea and probiotics in critically ill, adult patients was reviewed from 1980 to 2010. The Cochrane Library, Pubmed, Science Direct, Medline and the Cumulative Index of Nursing and Allied Health Literature (CINAHL) electronic databases were searched using specific inclusion/exclusion criteria. Key search terms used were: enteral nutrition, diarrhoea, critical illness, probiotics, probiotic species and randomised clinical control trial (RCT).---------- Results: Four RCT papers were identified with two reporting full studies, one reporting a pilot RCT and one conference abstract reporting an RCT pilot study. A trend towards a reduction in diarrhoea incidence was observed in the probiotic groups. However, mortality associated with probiotic use in some severely and critically ill patients must caution the clinician against its use.---------- Conclusion: Evidence to support probiotic use in the management of ETF diarrhoea in critically ill patients remains unclear. This paper argues that probiotics should not be administered to critically ill patients until further research has been conducted to examine the causal relationship between probiotics and mortality, irrespective of the patient's disease state or projected prophylactic benefit of probiotic administration.

Empirical comparison of machine learning algorithms for image texture classification with application to vegetation management in power line corridors

This paper reports on the empirical comparison of seven machine learning algorithms in texture classification with application to vegetation management in power line corridors. Aiming at classifying tree species in power line corridors, object-based method is employed. Individual tree crowns are segmented as the basic classification units and three classic texture features are extracted as the input to the classification algorithms. Several widely used performance metrics are used to evaluate the classification algorithms. The experimental results demonstrate that the classification performance depends on the performance matrix, the characteristics of datasets and the feature used.

Advances in vegetation management for power line corridor monitoring using aerial remote sensing techniques

This paper presents a comprehensive discussion of vegetation management approaches in power line corridors based on aerial remote sensing techniques. We address three issues 1) strategies for risk management in power line corridors, 2) selection of suitable platforms and sensor suite for data collection and 3) the progress in automated data processing techniques for vegetation management. We present initial results from a series of experiments and, challenges and lessons learnt from our project.

Which components of heart failure programs are effective? A meta-analysis of the outcomes of structured telephone support or telemonitoring as the primary component of heart failure management in 9,560 patients (Abridged Cochrane Review)

Aims--Telemonitoring (TM) and structured telephone support (STS) have the potential to deliver specialised management to more patients with chronic heart failure (CHF), but their efficacy is still to be proven. Objectives To review randomised controlled trials (RCTs) of TM or STS on all- cause mortality and all-cause and CHF-related hospitalisations in patients with CHF, as a non-invasive remote model of specialised disease-management intervention.--Methods and Results--Data sources:We searched 15 electronic databases and hand-searched bibliographies of relevant studies, systematic reviews, and meeting abstracts. Two reviewers independently extracted all data. Study eligibility and participants: We included any randomised controlled trials (RCT) comparing TM or STS to usual care of patients with CHF. Studies that included intensified management with additional home or clinic visits were excluded. Synthesis: Primary outcomes (mortality and hospitalisations) were analysed; secondary outcomes (cost, length of stay, quality of life) were tabulated.--Results: Thirty RCTs of STS and TM were identified (25 peer-reviewed publications (n=8,323) and five abstracts (n=1,482)). Of the 25 peer-reviewed studies, 11 evaluated TM (2,710 participants), 16 evaluated STS (5,613 participants) and two tested both interventions. TM reduced all-cause mortality (risk ratio (RR 0•66 [95% CI 0•54-0•81], p<0•0001) and STS showed similar trends (RR 0•88 [95% CI 0•76-1•01], p=0•08). Both TM (RR 0•79 [95% CI 0•67-0•94], p=0•008) and STS (RR 0•77 [95% CI 0•68-0•87], p<0•0001) reduced CHF-related hospitalisations. Both interventions improved quality of life, reduced costs, and were acceptable to patients. Improvements in prescribing, patient-knowledge and self-care, and functional class were observed.--Conclusion: TM and STS both appear effective interventions to improve outcomes in patients with CHF.

The ecology of Bactrocera tryoni (Froggatt) (Diptera: Tephritdae) : what do we know to assist pest management?

The distribution, systematics and ecology of Bactrocera tryoni, the Queensland fruit fly are reviewed. Bactrocera tryoni is a member of the B. tryoni complex of species, which currently includes four named species, viz. B. tryoni s.s., B. neohumeralis, B. melas and B. aquilonis. The species status of B. melas and B. aquilonis are unclear (they may be junior synonyms of B. tryoni) and their validity, or otherwise, needs to be confirmed as a matter of urgency. While Queensland fruit fly is regarded as a tropical species, it cannot be assumed that its distribution will spread further south under climate change scenarios. Increasing aridity and hot dry summers, as well as more complex, indirect interactions resulting from elevated CO2, make predicting the future distribution and abundance of B. tryoni difficult. The ecology of B. tryoni is reviewed with respect to current control approaches (with the exception of Sterile Insect Technique which is covered in a companion paper). We conclude that there are major gaps in the knowledge required to implement most non-insecticide based management approaches. Priority areas for future research include host plant interactions, protein and cue-lure foraging and use, spatial dynamics, development of new monitoring tools, investigating the use of natural enemies and better integration of fruit flies into general horticultural IPM systems.

Host use and crop impacts of Oribius Marshall species (Coleoptera: Curculionidae) in Eastern Highlands Province, Papua New Guinea

Oribius species are small flightless weevils endemic to the island of New Guinea and far northern Cape York, Australia. The adults feed externally on leaves, developing fruit and green bark, but their impact as pests and general host use patterns are poorly known. Working in Eastern Highlands Province, Papua New Guinea, we carried out structured host use surveys, farmer surveys, shade-house growth trials, and on-farm and on-station impact trials to: (i) estimate the host range of the local Oribius species; (ii) understand adult daily activity patterns; (iii) elucidate feeding habits of the soil dwelling larvae; and (iv) quantify the impacts of adult feeding damage. Oribius inimicus and O. destructor accounted for nearly all the Oribius species encountered locally: of these two O. inimicus was the most abundant. Weevils were collected from 31 of 33 plants surveyed in the Aiyura Valley and a combination of farmer interviews and literature records provided evidence for the beetles being pestiferous on 43 crops currently or previously grown in the Highlands. Adult weevils had a distinct diurnal pattern of being in the upper plant canopy early in the morning and, to a lesser extent, again late in the afternoon. For the remainder of the day beetles resided within the canopy, or possibly off the plant. Movement of adults between plants appeared frequent. Pot trials confirmed the larvae are root feeders. Quantified impact studies showed that the weevils are damaging to a range of vegetable and orchard crops (broccoli, capsicum, celery, French bean, Irish potato, lettuce, orange and strawberry), causing average yield losses of around 30-40%, but up to 100% on citrus. Oribius weevils pose a significant and apparently growing problem for Highland’s agriculture.

Networks cities and ecological habitats

As the world’s rural populations continue to migrate from farmland to sprawling cities, transport networks form an impenetrable maze within which monocultures of urban form erupt from the spaces in‐between. These urban monocultures are as problematic to human activity in cities as cropping monocultures are to ecosystems in regional landscapes. In China, the speed of urbanisation is exacerbating the production of mono‐functional private and public spaces. Edges are tightly controlled. Barriers and management practices at these boundaries are discouraging the formation of new synergistic relationships, critical in the long‐term stability of ecosystems that host urban habitats. Some urban planners, engineers, urban designers, architects and landscape architects have recognised these shortcomings in contemporary Chinese cities. The ideology of sustainability, while critically debated, is bringing together thinking people in these and other professions under the umbrella of an ecological ethic. This essay aims to apply landscape ecology theory, a conceptual framework used by many professionals involved in land development processes, to a concept being developed by BAU International called Networks Cities: a city with its various land uses arranged in nets of continuity, adjacency, and superposition. It will consider six lesser‐known concepts in relation to creating enhanced human activity along (un)structured edges between proposed nets and suggest new frontiers that might be challenged in an eco‐city. Ecological theory suggests that sustaining biodiversity in regions and landscapes depends on habitat distribution patterns. Flora and fauna biologists have long studied edge habitats and have been confounded by the paradox that maximising the breadth of edges is detrimental to specialist species but favourable to generalist species. Generalist species of plants and animals tolerate frequent change in the landscape, frequenting two or more habitats for their survival. Specialist species are less tolerant of change, having specific habitat requirements during their life cycle. Protecting species richness then may be at odds with increasing mixed habitats or mixed‐use zones that are dynamic places where diverse activities occur. Forman (1995) in his book Land Mosaics however argues that these two objectives of land use management are entirely compatible. He postulates that an edge may be comprised of many small patches, corridors or convoluting boundaries of large patches. Many ecocentrists now consider humans to be just another species inhabiting the ecological environments of our cities. Hence habitat distribution theory may be useful in planning and designing better human habitats in a rapidly urbanising context like China. In less‐constructed environments, boundaries and edges provide important opportunities for the movement of multi‐habitat species into, along and from adjacent land use areas. For instance, invasive plants may escape into a national park from domestic gardens while wildlife may forage on garden plants in adjoining residential areas. It is at these interfaces that human interactions too flow backward and forward between land types. Spray applications of substances by farmers on cropland may disturb neighbouring homeowners while suburban residents may help themselves to farm produce on neighbouring orchards. Edge environments are some of the most dynamic and contested spaces in the landscape. Since most of us require access to at least two or three habitats diurnally, weekly, monthly or seasonally, their proximity to each other becomes critical in our attempts to improve the sustainability of our cities.

Improving accuracy and intelligibility of decisions

Intelligible and accurate risk-based decision-making requires a complex balance of information from different sources, appropriate statistical analysis of this information and consequent intelligent inference and decisions made on the basis of these analyses. Importantly, this requires an explicit acknowledgement of uncertainty in the inputs and outputs of the statistical model. The aim of this paper is to progress a discussion of these issues in the context of several motivating problems related to the wider scope of agricultural production. These problems include biosecurity surveillance design, pest incursion, environmental monitoring and import risk assessment. The information to be integrated includes observational and experimental data, remotely sensed data and expert information. We describe our efforts in addressing these problems using Bayesian models and Bayesian networks. These approaches provide a coherent and transparent framework for modelling complex systems, combining the different information sources, and allowing for uncertainty in inputs and outputs. While the theory underlying Bayesian modelling has a long and well established history, its application is only now becoming more possible for complex problems, due to increased availability of methodological and computational tools. Of course, there are still hurdles and constraints, which we also address through sharing our endeavours and experiences.