Improving management of summer weeds in dryland cropping systems with Cotton

In 2001 a scoping study (phase I) was commissioned to determine and prioritise the weed issues of cropping systems with dryland cotton. The main findings were that the weed flora was diverse, cropping systems complex, and weeds had a major financial and economical impact. Phase II 'Best weed management strategies for dryland cropping systems with cotton' focused on improved management of the key weeds, bladder ketmia, sowthistle, fleabane, barnyard grass and liverseed grass.In Phase III 'Improving management of summer weeds in dryland cropping systems with cotton', more information on the seed-bank dynamics of key weeds was gained in six pot and field studies. The studies found that these characteristics differed between species, and even climate in the case of bladder ketmia. Species such as sowthistle, fleabane and barnyard grass emerged predominately from the surface soil. Sweet summer grass was also in this category but also had a significant proportion emerging from 5 cm depth. Bladder ketmia in central Queensland emerged mainly from the top 2 cm, whereas in southern Queensland it emerged mainly from 5 cm. Liverseed grass had its highest emergence from 5 cm below the surface. In all cases the persistence of seed increased with increasing soil depth. Fleabane was also found to be sensitive to soil type with no seedlings emerging in the self-mulching black vertisol soil. A strategic tillage trial showed that burial of fleabane seed, using a disc or chisel plough, to a depth of greater than 2 cm can significantly reduce subsequent fleabane emergence. In contrast, tillage increased barnyard grass emergence and tended to decrease persistence. This research showed that weed management plans can not be blanketed across all weed species, rather they need to be targeted for each main weed species.This project has also resulted in an increased knowledge of how to manage fleabane from the eight experiments; one in wheat, two in sorghum, one in cotton and three in fallow on double knock. For summer crops, the best option is to apply a highly effective fallow treatment prior to sowing the crops. For winter crops, the strategy is the integration of competitive crops, residual herbicide followed by a knockdown to control survivors. This project explored further the usefulness of the double knock tactic for weed control and preventing seed set. Two field and one pot experiments have shown that this tactic was highly effective for fleabane control. Paraquat products provided good control when followed by glyphosate. When 2, 4-D was added in a tank mix with glyphosate and followed by paraquat products, 99-100% control was achieved in all cases. The ideal follow-up times for paraquat products after glyphosate were 5-7 days. The preferred follow-up times for 2, 4-D after glyphosate were on the same day and one day later. The pot trial, which compared a population from a cropping field with previous glyphosate exposure and a population from a non-cropping area with no previous glyphosate herbicide exposure, showed that the pervious herbicide exposure affected the response of fleabane to herbicidal control measures. The web-based brochure on managing fleabane has been updated.Knowledge on management of summer grasses and safe use of residual herbicides was derived from eight field and pot experiments. Residual grass and broadleaf weed control was excellent with atrazine pre-plant and at-planting treatments, provided rain was received within a short interval after application. Highly effective fallow treatments (cultivation and double knock), not only gave excellent grass control in the fallow, also gave very good control in the following cotton. In the five re-cropping experiments, there were no adverse impacts on cotton from atrazine, metolachlor, metsulfuron and chlorsulfuron residues following use in previous sorghum, wheat and fallows. However, imazapic residues did reduce cotton growth.The development of strategies to reduce the heavy reliance on glyphosate in our cropping systems, and therefore minimise the risk of glyphosate resistance development, was a key factor in the research undertaken. This work included identifying suitable tactics for summer grass control, such as double knock with glyphosate followed by paraquat and tillage. Research on fleabane also concentrated on minimising emergence through tillage, and applying the double knock tactic. Our studies have shown that these strategies can be used to prevent seed set with the goal of driving down the seed bank. Utilisation of the strategies will also reduce the reliance on glyphosate, and therefore reduce the risk of glyphosate resistance developing in our cropping systems.Information from this research, including ecological and management data were collected from an additional eight paddock monitoring sites, was also incorporated into the Weeds CRC seed bank model "Weed Seed Wizard", which will be able to predict the impact of different management options on weed populations in cotton and grain farming systems. Extensive communication activities were undertaken throughout this project to ensure adoption of the new strategies for improved weed management and reduced risk for glyphosate resistance.

Maximising profitability with limited water in cotton farming systems

Diminishing water supply, changing weather patterns and pressure to enhance environmental flows are making it imperative to optimise water use efficiency (WUE) on cotton/grain farming systems. Growers are looking for better strategies to make the best use of limited water, but it is still not clear how to best use the available water at farm and field scale. This research project investigated the impact of management strategies to deal with limited water supplies on the yield and quality of irrigated cotton and wheat. The objectives were: (1) to develop irrigation management guidelines for the main irrigated crops on the Darling Downs for full- and deficitirrigation scenarios, taking into account the critical factors that affect irrigation decisions at the local level, (2) to quantify the evapotranspiration (ET) of Bollgard II cotton and wheat and its relationship to yield and quality under full- and deficit-irrigation scenarios, and (3) to increase industry awareness and education of farming systems practises for optimised economic water use efficiency.Objective (1) was addressed by (A) collaborating with ASPRU to develop the APSFarm model within APSIM to be able to perform multi-paddock simulations. APSFarm was then tested by conducting a case study at a farm near Dalby, and (B) conducting semi-structured interviews with individual farmers and crop consultants on the Darling Downs to document the strategies they are using to deal with limited water. Objective (2) was addressed by (A) building and installing 12 large (1 m x 1m x 1.5 m) weighing lysimeters to measure crop evapotranspiration. The lysimeters were installed at the Agri-Science Queensland research station at Kingsthorpe in November 2008, (B) conducting field experiments to measure crop evapotranspiration and crop development under four irrigation treatments, including dryland, deficit-irrigation, and full irrigation. Field experiments were conducted with cotton in 2007-08 and 2008-09, and with wheat in 2008 and 2009, and (C) collaborating with USQ on a PhD thesis to quantify the impact of crop stress on crop evapotranspiration and canopy temperature. Glasshouse experiments were conducted with wheat in 2008 and with cotton in 2008-09. Objective (3) was addressed by (A) conducting a field day at Kingsthorpe in 2009, which was attended by 80 participants, (B) presenting information in conferences in Australia and overseas, (D) presenting information at farmers meeting, (E) making presentations to crop consultants, and (F) preparing extension publications.As part of this project we contributed to the development of APSfarm, which has been successfully applied to evaluate the feasibility of practices at the whole-farm scale. From growers and crop consultants interviews we learned that there is a great variety of strategies, at different scales, that they are using to deal with limited water situation. These strategies will be summarised in the "e;Limited Water Guidelines for the Darling Downs"e; that we are currently preparing. As a result of this project, we now have a state-of-the-art lysimeter research facility (23 large weighing lysimeters) to be able to conduct replicated experiments to investigate daily water use of a variety of crops under different irrigation regimes and under different environments. Under this project, a series of field and glasshouse experiments were conducted with cotton and wheat, investigating aspects like: (A) quantification of daily and seasonal crop water use under nonstressed and stressed conditions, (B) impact of row configuration on crop water use, (C) impact of water stress on yield, evapotranspiration, crop vegetative and reproductive development, soil water extraction pattern, yield and yield quality. The information obtained from this project is now being used to develop web-based tools to help growers make planning and day-to-day irrigation decisions.

Genetic variation in tumour necrosis factor and lymphotoxin is not associated with endometriosis in an Australian sample

BACKGROUND Tumour necrosis factor (TNF) is a pleiotropic cytokine with a wide range of immunoregulatory effects. Variation in the promoter region of TNF and the neighbouring lymphotoxin alpha (LTA) gene might be associated with endometriosis. METHODS We examined the association between endometriosis and common single-nucleotide polymorphisms (SNPs) or haplotypes in the TNF/LTA region in an Australian sample by analysing 26 SNPs in 958 endometriosis cases and 959 unrelated controls. We selected functional SNPs in the coding and the promoter region of the TNF gene and HapMap tagging SNPs and typed them on a Sequenom MassARRAY platform. A key SNP (rs1800630) in the promoter region typed in previous studies did not give reliable results. Therefore, we also examined a statistically identical (r(2) = 1) SNP (siSNP) (rs2844482), identified using the web based program ssSNPer. RESULTS Genotype completion rate was 99.5% for SNPs spanning a region of 15.5 kb across the TNF/LTA locus. There was no evidence for association between endometriosis and TNF/LTA SNPs or SNP haplotypes in our case-control study. CONCLUSIONS Our data suggest both TNF and LTA genes are not major susceptibility genes for endometriosis.

Rhipicephalus microplus serine protease inhibitor family: annotation, expression and functional characterisation assessment

Background: Rhipicephalus (Boophilus) microplus evades the host's haemostatic system through a complex protein array secreted into tick saliva. Serine protease inhibitors (serpins) conform an important component of saliva which are represented by a large protease inhibitor family in Ixodidae. These secreted and non-secreted inhibitors modulate diverse and essential proteases involved in different physiological processes. Methods: The identification of R. microplus serpin sequences was performed through a web-based bioinformatics environment called Yabi. The database search was conducted on BmiGi V1, BmiGi V2.1, five SSH libraries, Australian tick transcriptome libraries and RmiTR V1 using bioinformatics methods. Semi quantitative PCR was carried out using different adult tissues and tick development stages. The cDNA of four identified R. microplus serpins were cloned and expressed in Pichia pastoris in order to determine biological targets of these serpins utilising protease inhibition assays. Results: A total of four out of twenty-two serpins identified in our analysis are new R. microplus serpins which were named as RmS-19 to RmS-22. The analyses of DNA and predicted amino acid sequences showed high conservation of the R. microplus serpin sequences. The expression data suggested ubiquitous expression of RmS except for RmS-6 and RmS-14 that were expressed only in nymphs and adult female ovaries, respectively. RmS-19, and -20 were expressed in all tissues samples analysed showing their important role in both parasitic and non-parasitic stages of R. microplus development. RmS-21 was not detected in ovaries and RmS-22 was not identified in ovary and nymph samples but were expressed in the rest of the samples analysed. A total of four expressed recombinant serpins showed protease specific inhibition for Chymotrypsin (RmS-1 and RmS-6), Chymotrypsin / Elastase (RmS-3) and Thrombin (RmS-15). Conclusion: This study constitutes an important contribution and improvement to the knowledge about the physiologic role of R. microplus serpins during the host-tick interaction.

Contemplating Knudsen's Baseline: Where small is not so beautiful

Does the Internet's World Wide Web (the web) represent an opportunity or threat to the small firms of the world? In line with recent calls for entrepreneurship research to adopt a more evolutionary approach, this article considers the context, process, and possible outcomes of small place-based firms operating in a web-impacted environment. Despite initial optimism that the web would provide a level-playing field for firms of all sizes, little evidence exist to support such a notion. When the learning abilities deemed necessary to exploit the web are considered, it would seem that only the most entrepreneurial of small firms would likely adapt to web-impacted environments. It is concluded that the present rate of web-based change represents a unique and valuable research opportunity for entrepreneurship researchers.

An alternative view of small firm adaptation

Increasingly, small firms with a history tied to a specific geographic location are having their survival threatened by new and innovative web-based entrants. This paper considers the plight of such firms and proposes an alternative means to reflect on how they may or may not learn about such threats. Adopting an evolutionary perspective, the construct absorptive capacity is used to highlight the deficiencies of current market orientation theory to explain the process of firm learning. The conceptual model of evolutionary potential provides a framework through which both the firm and its owner/s' abilities to learn can be taken into account.

Small firm internet adoption: opportunities forgone, a journey not begun

This paper explores the endeavours of five small firms to develop web-based commerce capabilities within their existing operations. The focus is upon the strategic acquisition and exploitation of knowledge which underpins new value creating activates related to web-based commerce. A normative web-based commerce adoption model developed from a review of the extant literature related to electronic marketing, entrepreneurship, and the diffusion of new innovations was empirically tested. A multiple case study design enabled the exploration of contemporary marketing and entrepreneurship issues within the real life context of five small firms. The model aimed to emphasis best-practice adoption methods emphasizing the value of a firm's market orientation and entrepreneurial capabilities. A preliminary test of the model's theoretical contentions lent support to its overall focus, but found that the firm's existing learning capabilities were diminished during the adoption of web-based commerce, and that a lack of vision and prior knowledge produced sub-optimal adoption outcomes.

Small firm internet adoption: A market oriented approach

Fundamental to the development of new customer value offerings via web-based commerce is a small firm's ability to strategically acquire and exploit knowledge. The focus of this paper is the empirical testing of a normative web-based commerce adoption model developed from a review of the extant literature related to electronic marketing, the Internet and the diffusion of new innovations. A preliminary test of the model's theoretical contentions lent support to its overall focus, but found that the firm's existing learning capabilities were diminished during the adoption of web-based commerce. Consequently, sub-optimal adoption outcomes were associated with insufficient knowledge development.

Computational Methods for Reconstruction and Analysis of Genome-Scale Metabolic Networks

Metabolism is the cellular subsystem responsible for generation of energy from nutrients and production of building blocks for larger macromolecules. Computational and statistical modeling of metabolism is vital to many disciplines including bioengineering, the study of diseases, drug target identification, and understanding the evolution of metabolism. In this thesis, we propose efficient computational methods for metabolic modeling. The techniques presented are targeted particularly at the analysis of large metabolic models encompassing the whole metabolism of one or several organisms. We concentrate on three major themes of metabolic modeling: metabolic pathway analysis, metabolic reconstruction and the study of evolution of metabolism. In the first part of this thesis, we study metabolic pathway analysis. We propose a novel modeling framework called gapless modeling to study biochemically viable metabolic networks and pathways. In addition, we investigate the utilization of atom-level information on metabolism to improve the quality of pathway analyses. We describe efficient algorithms for discovering both gapless and atom-level metabolic pathways, and conduct experiments with large-scale metabolic networks. The presented gapless approach offers a compromise in terms of complexity and feasibility between the previous graph-theoretic and stoichiometric approaches to metabolic modeling. Gapless pathway analysis shows that microbial metabolic networks are not as robust to random damage as suggested by previous studies. Furthermore the amino acid biosynthesis pathways of the fungal species Trichoderma reesei discovered from atom-level data are shown to closely correspond to those of Saccharomyces cerevisiae. In the second part, we propose computational methods for metabolic reconstruction in the gapless modeling framework. We study the task of reconstructing a metabolic network that does not suffer from connectivity problems. Such problems often limit the usability of reconstructed models, and typically require a significant amount of manual postprocessing. We formulate gapless metabolic reconstruction as an optimization problem and propose an efficient divide-and-conquer strategy to solve it with real-world instances. We also describe computational techniques for solving problems stemming from ambiguities in metabolite naming. These techniques have been implemented in a web-based sofware ReMatch intended for reconstruction of models for 13C metabolic flux analysis. In the third part, we extend our scope from single to multiple metabolic networks and propose an algorithm for inferring gapless metabolic networks of ancestral species from phylogenetic data. Experimenting with 16 fungal species, we show that the method is able to generate results that are easily interpretable and that provide hypotheses about the evolution of metabolism.

High-Rate Space-Time Coded Large-MIMO Systems: Low-Complexity Detection and Channel Estimation

In this paper, we present a low-complexity algorithm for detection in high-rate, non-orthogonal space-time block coded (STBC) large-multiple-input multiple-output (MIMO) systems that achieve high spectral efficiencies of the order of tens of bps/Hz. We also present a training-based iterative detection/channel estimation scheme for such large STBC MIMO systems. Our simulation results show that excellent bit error rate and nearness-to-capacity performance are achieved by the proposed multistage likelihood ascent search (M-LAS) detector in conjunction with the proposed iterative detection/channel estimation scheme at low complexities. The fact that we could show such good results for large STBCs like 16 X 16 and 32 X 32 STBCs from Cyclic Division Algebras (CDA) operating at spectral efficiencies in excess of 20 bps/Hz (even after accounting for the overheads meant for pilot based training for channel estimation and turbo coding) establishes the effectiveness of the proposed detector and channel estimator. We decode perfect codes of large dimensions using the proposed detector. With the feasibility of such a low-complexity detection/channel estimation scheme, large-MIMO systems with tens of antennas operating at several tens of bps/Hz spectral efficiencies can become practical, enabling interesting high data rate wireless applications.

Afatinib versus gefitinib as first-line treatment of patients with EGFR mutation-positive non-small-cell lung cancer (LUX-Lung 7): a phase 2B, open-label, randomised controlled trial

Background The irreversible ErbB family blocker afatinib and the reversible EGFR tyrosine kinase inhibitor gefitinib are approved for first-line treatment of EGFR mutation-positive non-small-cell lung cancer (NSCLC). We aimed to compare the efficacy and safety of afatinib and gefitinib in this setting. Methods This multicentre, international, open-label, exploratory, randomised controlled phase 2B trial (LUX-Lung 7) was done at 64 centres in 13 countries. Treatment-naive patients with stage IIIB or IV NSCLC and a common EGFR mutation (exon 19 deletion or Leu858Arg) were randomly assigned (1:1) to receive afatinib (40 mg per day) or gefitinib (250 mg per day) until disease progression, or beyond if deemed beneficial by the investigator. Randomisation, stratified by EGFR mutation type and status of brain metastases, was done centrally using a validated number generating system implemented via an interactive voice or web-based response system with a block size of four. Clinicians and patients were not masked to treatment allocation; independent review of tumour response was done in a blinded manner. Coprimary endpoints were progression-free survival by independent central review, time-to-treatment failure, and overall survival. Efficacy analyses were done in the intention-to-treat population and safety analyses were done in patients who received at least one dose of study drug. This ongoing study is registered with ClinicalTrials.gov, number NCT01466660. Findings Between Dec 13, 2011, and Aug 8, 2013, 319 patients were randomly assigned (160 to afatinib and 159 to gefitinib). Median follow-up was 27·3 months (IQR 15·3–33·9). Progression-free survival (median 11·0 months [95% CI 10·6–12·9] with afatinib vs 10·9 months [9·1–11·5] with gefitinib; hazard ratio [HR] 0·73 [95% CI 0·57–0·95], p=0·017) and time-to-treatment failure (median 13·7 months [95% CI 11·9–15·0] with afatinib vs 11·5 months [10·1–13·1] with gefitinib; HR 0·73 [95% CI 0·58–0·92], p=0·0073) were significantly longer with afatinib than with gefitinib. Overall survival data are not mature. The most common treatment-related grade 3 or 4 adverse events were diarrhoea (20 [13%] of 160 patients given afatinib vs two [1%] of 159 given gefitinib) and rash or acne (15 [9%] patients given afatinib vs five [3%] of those given gefitinib) and liver enzyme elevations (no patients given afatinib vs 14 [9%] of those given gefitinib). Serious treatment-related adverse events occurred in 17 (11%) patients in the afatinib group and seven (4%) in the gefitinib group. Ten (6%) patients in each group discontinued treatment due to drug-related adverse events. 15 (9%) fatal adverse events occurred in the afatinib group and ten (6%) in the gefitinib group. All but one of these deaths were considered unrelated to treatment; one patient in the gefitinib group died from drug-related hepatic and renal failure. Interpretation Afatinib significantly improved outcomes in treatment-naive patients with EGFR-mutated NSCLC compared with gefitinib, with a manageable tolerability profile. These data are potentially important for clinical decision making in this patient population.

Understanding Connectivity between Groundwater Chemistry Data and Geological Stratigraphy via 3D Sub-surface Visualization and Analysis

This paper describes the 3D Water Chemistry Atlas - an open source, Web-based system that enables the three-dimensional (3D) sub-surface visualization of ground water monitoring data, overlaid on the local geological model. Following a review of existing technologies, the system adopts Cesium (an open source Web-based 3D mapping and visualization interface) together with a PostGreSQL/PostGIS database, for the technical architecture. In addition a range of the search, filtering, browse and analysis tools were developed that enable users to interactively explore the groundwater monitoring data and interpret it spatially and temporally relative to the local geological formations and aquifers via the Cesium interface. The result is an integrated 3D visualization system that enables environmental managers and regulators to assess groundwater conditions, identify inconsistencies in the data, manage impacts and risks and make more informed decisions about activities such as coal seam gas extraction, waste water extraction and re-use.

Novel application of a discrete choice experiment to identify preferences for a national healthcare-associated infection surveillance programme: A cross-sectional study

Objective: To identify key stakeholder preferences and priorities when considering a national healthcare-associated infection (HAI) surveillance programme through the use of a discrete choice experiment (DCE). Setting: Australia does not have a national HAI surveillance programme. An online web-based DCE was developed and made available to participants in Australia. Participants: A sample of 184 purposively selected healthcare workers based on their senior leadership role in infection prevention in Australia. Primary and secondary outcomes: A DCE requiring respondents to select 1 HAI surveillance programme over another based on 5 different characteristics (or attributes) in repeated hypothetical scenarios. Data were analysed using a mixed logit model to evaluate preferences and identify the relative importance of each attribute. Results: A total of 122 participants completed the survey (response rate 66%) over a 5-week period. Excluding 22 who mismatched a duplicate choice scenario, analysis was conducted on 100 responses. The key findings included: 72% of stakeholders exhibited a preference for a surveillance programme with continuous mandatory core components (mean coefficient 0.640 (p<0.01)), 65% for a standard surveillance protocol where patient-level data are collected on infected and non-infected patients (mean coefficient 0.641 (p<0.01)), and 92% for hospital-level data that are publicly reported on a website and not associated with financial penalties (mean coefficient 1.663 (p<0.01)). Conclusions: The use of the DCE has provided a unique insight to key stakeholder priorities when considering a national HAI surveillance programme. The application of a DCE offers a meaningful method to explore and quantify preferences in this setting.

Designing a blended learning model for primary school language learning

In Finland, there is a desperate need for flexible, reliable and functional multi-e-learning settings for pupils aged 11-13. Southern Finland has several ongoing e-learning projects, but none that develop a multiple setting, with learning and teaching occurring between more than two schools. In 2006, internet connections were not broadband and data transfer was mainly audio data. Connections and technical problems occurred, which were an obstacle to multi-e-learning. Internet connections today enable web-based learning in major parts of
Lapland and by 2015, broadband will reach even the remotest villages up north. Therefore, it is important to research the possibilities of multi-e-learning and to build collaborative, learner-centred, versatile network models for primary school-aged pupils. The resulting model will facilitate distance learning to extend education to rural, sparsely populated areas, and it will give a model of using mobile devices in language portfolios. This will promote regional equality and prevent exclusion. Working with portfolios provides the opportunity to develop mobility from a pedagogical point of view. It is important to study the pros and cons of mobile devices in producing artefacts on portfolios in e-learning and language learning settings.
The current study represents a design-based research approach. The design research approach includes two important aspects concerning the current research: ‘a teacher as researcher’ aspect, which means there is the possibility to be strongly involved in developing processes and an obstacle-aspect, which means that problems while developing, are seen as a
promoter in evolving the designed model, as apposed to negative results.

Designing a blended learning model for primary school language learning

In Finland, there is a desperate need for flexible, reliable and functional multi-e-learning settings for pupils aged 11-13. Southern Finland has several ongoing e-learning projects, but none that develop a multiple setting, with learning and teaching occurring between more than two schools. In 2006, internet connections were not broadband and data transfer was mainly audio data. Connections and technical problems occurred, which were an obstacle to multi-e-learning. Internet connections today enable web-based learning in major parts of Lapland and by 2015, broadband will reach even the remotest villages up north. Therefore, it is important to research the possibilities of multi-e-learning and to build collaborative, learner-centred, versatile network models for primary school-aged pupils. The resulting model will facilitate distance learning to extend education to rural, sparsely populated areas, and it will give a model of using mobile devices in language portfolios. This will promote regional equality and prevent exclusion. Working with portfolios provides the opportunity to develop mobility from a pedagogical point of view. It is important to study the pros and cons of mobile devices in producing artefacts on portfolios in e-learning and language learning settings. The current study represents a design-based research approach. The design research approach includes two important aspects concerning the current research: ‘a teacher as researcher’ aspect, which means there is the possibility to be strongly involved in developing processes and an obstacle-aspect, which means that problems while developing, are seen as a promoter in evolving the designed model, as apposed to negative results.