Thinking Pedagogically

Despite the dominancy of medical explanations for difficult child behavior, the shifting sands that lie beneath the ADHD construct provide an unstable foundation for educational practice. It can be somewhat liberating to remember that “attention deficit hyperactivity disorder” is a label (one of many, including minimal brain damage and hyperkinetic reaction of childhood) that the medical domain has coined to both group and describe certain challenging behaviors exhibited by children and young people (see Smith, Chapter 2). The label is but one conceptualization of what these behaviors mean and, despite the existence of powerful lobby groups, it may not be the best way forward. In what follows, I present an alternative typology to the medical conceptualization by describing some common issues that bring this group of children to attention. In an effort to introduce educationally useful responses to students who are difficult to teach, I will then outline what classroom teachers need to recognize in order to work with these students and realize their potential. To assist teachers in thinking pedagogically, these observations are coupled with well-known and relevant qualities of good teaching to remind teachers of what they already know and to reacquaint them with the power of that knowledge.

Go with the flow : optimal AUV path planning in coastal environments

This paper describes a novel optimum path planning strategy for long duration AUV operations in environments with time-varying ocean currents. These currents can exceed the maximum achievable speed of the AUV, as well as temporally expose obstacles. In contrast to most other path planning strategies, paths have to be defined in time as well as space. The solution described here exploits ocean currents to achieve mission goals with minimal energy expenditure, or a tradeoff between mission time and required energy. The proposed algorithm uses a parallel swarm search as a means to reduce the susceptibility to large local minima on the complex cost surface. The performance of the optimisation algorithms is evaluated in simulation and experimentally with the Starbug AUV using a validated ocean model of Brisbane’s Moreton Bay.

An improved chemically inducible gene switch that functions in the monocotyledonous plant sugar cane

Chemically inducible gene switches can provide precise control over gene expression, enabling more specific analyses of gene function and expanding the plant biotechnology toolkit beyond traditional constitutive expression systems. The alc gene expression system is one of the most promising chemically inducible gene switches in plants because of its potential in both fundamental research and commercial biotechnology applications. However, there are no published reports demonstrating that this versatile gene switch is functional in transgenic monocotyledonous plants, which include some of the most important agricultural crops. We found that the original alc gene switch was ineffective in the monocotyledonous plant sugar cane, and describe a modified alc system that is functional in this globally significant crop. A promoter consisting of tandem copies of the ethanol receptor inverted repeat binding site, in combination with a minimal promoter sequence, was sufficient to give enhanced sensitivity and significantly higher levels of ethanol inducible gene expression. A longer CaMV 35S minimal promoter than was used in the original alc gene switch also substantially improved ethanol inducibility. Treating the roots with ethanol effectively induced the modified alc system in sugar cane leaves and stem, while an aerial spray was relatively ineffective. The extension of this chemically inducible gene expression system to sugar cane opens the door to new opportunities for basic research and crop biotechnology.

Anatomy of sand beach ridges : evidence from severe Tropical Cyclone Yasi and its predecessors, northeast Queensland, Australia

[1] Four well-identified tropical cyclones over the past century have been responsible for depositing distinct units of predominantly quartzose sand and gravel to form the most seaward beach ridge at several locations along the wet tropical coast of northeast Queensland, Australia. These units deposited by tropical cyclones display a key sedimentary signature characterized by a sharp basal erosional contact, a coarser grain size than the underlying facies and a coarse-skewed trend toward the base. Coarse-skewed distributions with minimal change in mean grain size also characterize the upper levels of the high-energy deposited units at locations within the zone of maximum onshore winds during the tropical cyclone. These same coarse skew distributions are not apparent in sediments deposited at locations where predominantly offshore winds occurred during the cyclone, which in the case of northeast Australia is north of the eye-crossing location. These sedimentary signatures, along with the geochemical indicators and the degraded nature of the microfossil assemblages, have proven to be useful proxies to identify storm-deposited units within the study site and can also provide useful proxies in older beach ridges where advanced pedogenesis has obscured visual stratigraphic markers. As a consequence, more detailed long-term histories of storms and tropical cyclones can now be developed.

Synergism between Wnt3a and heparin enhances osteogenesis via a phosphoinositide 3-kinase/Akt/RUNX2 pathway

A new strategy has emerged to improve healing of bone defects using exogenous glycosaminoglycans by increasing the effectiveness of bone-anabolic growth factors. Wnt ligands play an important role in bone formation. However, their functional interactions with heparan sulfate/heparin have only been investigated in non-osseous tissues. Our study now shows that the osteogenic activity of Wnt3a is cooperatively stimulated through physical interactions with exogenous heparin. N-Sulfation and to a lesser extent O-sulfation of heparin contribute to the physical binding and optimal co-stimulation of Wnt3a. Wnt3a-heparin signaling synergistically increases osteoblast differentiation with minimal effects on cell proliferation. Thus, heparin selectively reduces the effective dose of Wnt3a needed to elicit osteogenic, but not mitogenic responses. Mechanistically, Wnt3a-heparin signaling strongly activates the phosphoinositide 3-kinase/Akt pathway and requires the bone-related transcription factor RUNX2 to stimulate alkaline phosphatase activity, which parallels canonical beta-catenin signaling. Collectively, our findings establish the osteo-inductive potential of a heparin-mediated Wnt3a-phosphoinositide 3-kinase/Akt-RUNX2 signaling network and suggest that heparan sulfate supplementation may selectively reduce the therapeutic doses of peptide factors required to promote bone formation.

Remote sensing utility expansion through Earth Portal internet browser

A modular, graphic-oriented Internet browser has been developed to enable non-technical client access to a literal spinning world of information and remotely sensed. The Earth Portal (www.earthportal.net) uses the ManyOne browser (www.manyone.net) to provide engaging point and click views of the Earth fully tessellated with remotely sensed imagery and geospatial data. The ManyOne browser technology use Mozilla with embedded plugins to apply multiple 3-D graphics engines, e.g. ArcGlobe or GeoFusion, that directly link with the open-systems architecture of the geo-spatial infrastructure. This innovation allows for rendering of satellite imagery directly over the Earth's surface and requires no technical training by the web user. Effective use of this global distribution system for the remote sensing community requires a minimal compliance with protocols and standards that have been promoted by NSDI and other open-systems standards organizations.

De-Identification of health records using Anonym: Effectiveness and robustness across datasets

Objective Evaluate the effectiveness and robustness of Anonym, a tool for de-identifying free-text health records based on conditional random fields classifiers informed by linguistic and lexical features, as well as features extracted by pattern matching techniques. De-identification of personal health information in electronic health records is essential for the sharing and secondary usage of clinical data. De-identification tools that adapt to different sources of clinical data are attractive as they would require minimal intervention to guarantee high effectiveness. Methods and Materials The effectiveness and robustness of Anonym are evaluated across multiple datasets, including the widely adopted Integrating Biology and the Bedside (i2b2) dataset, used for evaluation in a de-identification challenge. The datasets used here vary in type of health records, source of data, and their quality, with one of the datasets containing optical character recognition errors. Results Anonym identifies and removes up to 96.6% of personal health identifiers (recall) with a precision of up to 98.2% on the i2b2 dataset, outperforming the best system proposed in the i2b2 challenge. The effectiveness of Anonym across datasets is found to depend on the amount of information available for training. Conclusion Findings show that Anonym compares to the best approach from the 2006 i2b2 shared task. It is easy to retrain Anonym with new datasets; if retrained, the system is robust to variations of training size, data type and quality in presence of sufficient training data.

Fatty acid uptake and incorporation into phospholipids in the rat lens

PURPOSE. Phospholipids are a major component of lens fiber cells and influence the activity of membrane proteins. Previous investigations of fatty acid uptake by the lens are limited. The purpose of the present study was thus to determine whether exogenous fatty acids could be taken up by the rat lens and incorporated into molecular phospholipids. METHODS. Lenses were incubated with fluorescently labeled palmitic acid and then analyzed by confocal microscopy. Concurrently, lenses incubated with either fluorescently labeled palmitic acid or the more physiologically relevant (13)C(18)-oleic acid were sectioned into nuclear and cortical regions and analyzed by highly sensitive and structurally selective electrospray ionization tandem mass spectrometry techniques. RESULTS. The detection of fluorescently labeled palmitic acid, even after 16 hours of incubation, was limited to approximately the outer 25% to 30% of the rat lens. Mass spectrometry also revealed the presence of free (13)C(18)-oleic acid in the cortex but not the nucleus. No evidence could be found for incorporation of fluorescently labeled palmitic acid into phospholipids; however, a low level of (13)C(18)-oleic acid incorporation into phosphatidylethanolamine (PE), specifically PE (PE 16:0/(13)C(18) 18:1) was detected in the lens cortex after 16 hours. CONCLUSIONS. These data demonstrate that uptake of exogenous (e.g., dietary fatty acids) by the lens and their incorporation into phospholipids is minimal, most likely occurring only during de novo synthesis in the outermost region of the lens. This finding adds support to the hypothesis that once synthesized there is no active remodeling or turnover of fiber cell phospholipids.

An algebraic analysis of trivium ciphers based on the boolean satisfiability problem

Trivium is a stream cipher candidate of the eStream project. It has successfully moved into phase three of the selection process under the hardware category. No attacks faster than the exhaustive search have so far been reported on Trivium. Bivium-A and Bivium-B are simplified versions of Trivium that are built on the same design principles but with two registers. The simplified design is useful in investigating Trivium type ciphers with a reduced complexity and provides insight into effective attacks which could be extended to Trivium. This paper focuses on an algebraic analysis which uses the boolean satisfiability problem in propositional logic. For reduced variants of the cipher, this analysis recovers the internal state with a minimal amount of keystream observations.

Geometric sensitivity of patient-specific finite element models of the spine to variability in user-selected anatomical landmarks

Software to create individualised finite element (FE) models of the osseoligamentous spine using pre-operative computed tomography (CT) data-sets for spinal surgery patients has recently been developed. This study presents a geometric sensitivity analysis of this software to assess the effect of intra-observer variability in user-selected anatomical landmarks. User-selected landmarks on the osseous anatomy were defined from CT data-sets for three scoliosis patients and these landmarks were used to reconstruct patient-specific anatomy of the spine and ribcage using parametric descriptions. The intra-observer errors in landmark co-ordinates for these anatomical landmarks were calculated. FE models of the spine and ribcage were created using the reconstructed anatomy for each patient and these models were analysed for a loadcase simulating clinical flexibility assessment. The intra-observer error in the anatomical measurements was low in comparison to the initial dimensions, with the exception of the angular measurements for disc wedge and zygapophyseal joint (z-joint) orientation and disc height. This variability suggested that CT resolution may influence such angular measurements, particularly for small anatomical features, such as the z-joints, and may also affect disc height. The results of the FE analysis showed low variation in the model predictions for spinal curvature with the mean intra-observer variability substantially less than the accepted error in clinical measurement. These findings demonstrate that intra-observer variability in landmark point selection has minimal effect on the subsequent FE predictions for a clinical loadcase.

Evaluation of a pilot-scale oil extraction from microalgae for biodiesel production

Biodiesel derived from microalgae is one of a suite of potential solutions to meet the increasing demand for a renewable, carbon-neutral energy source. However, there are numerous challenges that must be addressed before algae biodiesel can become commercially viable. These challenges include the economic feasibility of harvesting and dewatering the biomass and the extraction of lipids and their conversion into biodiesel. Therefore, it is essential to find a suitable extraction process given these processes presently contribute significantly to the total production costs which, at this stage, inhibit the ability of biodiesel to compete financially with petroleum diesel. This study focuses on pilot-scale (100 kg dried microalgae) solvent extraction of lipids from microalgae and subsequent transesterification to biodiesel. Three different solvents (hexane, isopropanol (IPA) and hexane + IPA (1:1)) were used with two different extraction methods (static and Soxhlet) at bench-scale to find the most suitable solvent extraction process for the pilot-scale. The Soxhlet method extracted only 4.2% more lipid compared to the static method. However, the fatty acid profiles of different extraction methods with different solvents are similar, suggesting that none of the solvents or extraction processes were biased for extraction of particular fatty acids. Considering the cost and availability of the solvents, hexane was chosen for pilot-scale extraction using static extraction. At pilot-scale the lipid yield was found to be 20.3% of total biomass which is 2.5% less than from bench scale. Extracted fatty acids were dominated by polyunsaturated fatty acids (PUFAs) (68.94±0.17%) including 47.7±0.43 and 17.86±0.42% being docosahexaenoic acid (DHA) (C22:6) and docosapentaenoic acid (DPA) (C22:5, ω-3), respectively. These high amounts of long chain poly unsaturated fatty acids are unique to some marine microalgae and protists and vary with environmental conditions, culture age and nutrient status, as well as with cultivation process. Calculated physical and chemical properties of density, viscosity of transesterified fatty acid methyl esters (FAMEs) were within the limits of the biodiesel standard specifications as per ASTM D6751-2012 and EN 14214. The calculated cetane number was, however, significantly lower (17.8~18.6) compared to ASTM D6751-2012 or EN 14214-specified minimal requirements. We conclude that the obtained microalgal biodiesel would likely only be suitable for blending with petroleum diesel to a maximum of 5 to 20%.

Non-linear refined finite element elastic analysis of steel frames with generalized transverse member loads

In the finite element modelling of steel frames, external loads usually act along the members rather than at the nodes only. Conventionally, when a member is subjected to these transverse loads, they are converted to nodal forces which act at the ends of the elements into which the member is discretised by either lumping or consistent nodal load approaches. For a contemporary geometrically non-linear analysis in which the axial force in the member is large, accurate solutions are achieved by discretising the member into many elements, which can produce unfavourable consequences on the efficacy of the method for analysing large steel frames. Herein, a numerical technique to include the transverse loading in the non-linear stiffness formulation for a single element is proposed, and which is able to predict the structural responses of steel frames involving the effects of first-order member loads as well as the second-order coupling effect between the transverse load and the axial force in the member. This allows for a minimal discretisation of a frame for second-order analysis. For those conventional analyses which do include transverse member loading, prescribed stiffness matrices must be used for the plethora of specific loading patterns encountered. This paper shows, however, that the principle of superposition can be applied to the equilibrium condition, so that the form of the stiffness matrix remains unchanged with only the magnitude of the loading being needed to be changed in the stiffness formulation. This novelty allows for a very useful generalised stiffness formulation for a single higher-order element with arbitrary transverse loading patterns to be formulated. The results are verified using analytical stability function studies, as well as with numerical results reported by independent researchers on several simple structural frames.

Distamycin A affects the stability of NF-kappaB p50-DNA complexes in a sequence-dependent manner

The effect of two different DNA minor groove binding molecules, Hoechst 33258 and distamycin A, on the binding kinetics of NF-κB p50 to three different specific DNA sequences was studied at various salt concentrations. Distamycin A was shown to significantly increase the dissociation rate constant of p50 from the sequences PRDII (5′-GGGAAATTCC-3′) and Ig-κ B (5′-GGGACTTTCC-3′) but had a negligible effect on the dissociation from the palindromic target-κB binding site (5′-GGGAATTCCC-3′). By comparison, the effect of Hoechst 33258 on binding of p50 to each sequence was found to be minimal. The dissociation rates for the protein–DNA complexes increased at higher potassium chloride concentrations for the PRDII and Ig-κB binding motifs and this effect was magnified by distamycin A. In contrast, p50 bound to the palindromic target-κB site with a much higher intrinsic affinity and exhibited a significantly reduced salt dependence of binding over the ionic strength range studied, retaining a KD of less than 10 pM at 150 mM KCl. Our results demonstrate that the DNA binding kinetics of p50 and their salt dependence is strongly sequence-dependent and, in addition, that the binding of p50 to DNA can be influenced by the addition of minor groove-binding drugs in a sequence-dependent manner.

Transient expression vectors for functional genomics, quantification of promoter activity and RNA silencing in plants

Background We describe novel plasmid vectors for transient gene expression using Agrobacterium, infiltrated into Nicotiana benthamiana leaves. We have generated a series of pGreenII cloning vectors that are ideally suited to transient gene expression, by removing elements of conventional binary vectors necessary for stable transformation such as transformation selection genes. Results We give an example of expression of heme-thiolate P450 to demonstrate effectiveness of this system. We have also designed vectors that take advantage of a dual luciferase assay system to analyse promoter sequences or post-transcriptional regulation of gene expression. We have demonstrated their utility by co-expression of putative transcription factors and the promoter sequence of potential target genes and show how orthologous promoter sequences respond to these genes. Finally, we have constructed a vector that has allowed us to investigate design features of hairpin constructs related to their ability to initiate RNA silencing, and have used these tools to study cis-regulatory effect of intron-containing gene constructs. Conclusion In developing a series of vectors ideally suited to transient expression analysis we have provided a resource that further advances the application of this technology. These minimal vectors are ideally suited to conventional cloning methods and we have used them to demonstrate their flexibility to investigate enzyme activity, transcription regulation and post-transcriptional regulatory processes in transient assays.

Accelerometer data reduction : a comparison of four reduction algorithms on select outcome variables

Purpose Accelerometers are recognized as a valid and objective tool to assess free-living physical activity. Despite the widespread use of accelerometers, there is no standardized way to process and summarize data from them, which limits our ability to compare results across studies. This paper a) reviews decision rules researchers have used in the past, b) compares the impact of using different decision rules on a common data set, and c) identifies issues to consider for accelerometer data reduction. Methods The methods sections of studies published in 2003 and 2004 were reviewed to determine what decision rules previous researchers have used to identify wearing period, minimal wear requirement for a valid day, spurious data, number of days used to calculate the outcome variables, and extract bouts of moderate to vigorous physical activity (MVPA). For this study, four data reduction algorithms that employ different decision rules were used to analyze the same data set. Results The review showed that among studies that reported their decision rules, much variability was observed. Overall, the analyses suggested that using different algorithms impacted several important outcome variables. The most stringent algorithm yielded significantly lower wearing time, the lowest activity counts per minute and counts per day, and fewer minutes of MVPA per day. An exploratory sensitivity analysis revealed that the most stringent inclusion criterion had an impact on sample size and wearing time, which in turn affected many outcome variables. Conclusions These findings suggest that the decision rules employed to process accelerometer data have a significant impact on important outcome variables. Until guidelines are developed, it will remain difficult to compare findings across studies