Natural and engineered kallikrein inhibitors: an emerging pharmacopoeia

The kallikreins and kallikrein-related peptidases are serine proteases that control a plethora of developmental and homeostatic phenomena, ranging from semen liquefaction to skin desquamation and blood pressure. The diversity of roles played by kallikreins has stimulated considerable interest in these enzymes from the perspective of diagnostics and drug design. Kallikreins already have well-established credentials as targets for therapeutic intervention and there is increasing appreciation of their potential both as biomarkers and as targets for inhibitor design. Here, we explore the current status of naturally occurring kallikrein protease-inhibitor complexes and illustrate how this knowledge can interface with strategies for rational re-engineering of bioscaffolds and design of small-molecule inhibitors.

Grounded theory : a methodological spiral from positivism to postmodernism

Aim. Our aim in this paper is to explain a methodological/methods package devised to incorporate situational and social world mapping with frame analysis, based on a grounded theory study of Australian rural nurses' experiences of mentoring. Background. Situational analysis, as conceived by Adele Clarke, shifts the research methodology of grounded theory from being located within a postpositivist paradigm to a postmodern paradigm. Clarke uses three types of maps during this process: situational, social world and positional, in combination with discourse analysis. Method. During our grounded theory study, the process of concurrent interview data generation and analysis incorporated situational and social world mapping techniques. An outcome of this was our increased awareness of how outside actors influenced participants in their constructions of mentoring. In our attempts to use Clarke's methodological package, however, it became apparent that our constructivist beliefs about human agency could not be reconciled with the postmodern project of discourse analysis. We then turned to the literature on symbolic interactionism and adopted frame analysis as a method to examine the literature on rural nursing and mentoring as secondary form of data. Findings. While we found situational and social world mapping very useful, we were less successful in using positional maps. In retrospect, we would argue that collective action framing provides an alternative to analysing such positions in the literature. This is particularly so for researchers who locate themselves within a constructivist paradigm, and who are therefore unwilling to reject the notion of human agency and the ability of individuals to shape their world in some way. Conclusion. Our example of using this package of situational and social worlds mapping with frame analysis is intended to assist other researchers to locate participants more transparently in the social worlds that they negotiate in their everyday practice. © 2007 Blackwell Publishing Ltd.

Rational design of serine protease inhibitors

Proteases regulate a spectrum of diverse physiological processes, and dysregulation of proteolytic activity drives a plethora of pathological conditions. Understanding protease function is essential to appreciating many aspects of normal physiology and progression of disease. Consequently, development of potent and specific inhibitors of proteolytic enzymes is vital to provide tools for the dissection of protease function in biological systems and for the treatment of diseases linked to aberrant proteolytic activity. The studies in this thesis describe the rational design of potent inhibitors of three proteases that are implicated in disease development. Additionally, key features of the interaction of proteases and their cognate inhibitors or substrates are analysed and a series of rational inhibitor design principles are expounded and tested. Rational design of protease inhibitors relies on a comprehensive understanding of protease structure and biochemistry. Analysis of known protease cleavage sites in proteins and peptides is a commonly used source of such information. However, model peptide substrate and protein sequences have widely differing levels of backbone constraint and hence can adopt highly divergent structures when binding to a protease’s active site. This may result in identical sequences in peptides and proteins having different conformations and diverse spatial distribution of amino acid functionalities. Regardless of this, protein and peptide cleavage sites are often regarded as being equivalent. One of the key findings in the following studies is a definitive demonstration of the lack of equivalence between these two classes of substrate and invalidation of the common practice of using the sequences of model peptide substrates to predict cleavage of proteins in vivo. Another important feature for protease substrate recognition is subsite cooperativity. This type of cooperativity is commonly referred to as protease or substrate binding subsite cooperativity and is distinct from allosteric cooperativity, where binding of a molecule distant from the protease active site affects the binding affinity of a substrate. Subsite cooperativity may be intramolecular where neighbouring residues in substrates are interacting, affecting the scissile bond’s susceptibility to protease cleavage. Subsite cooperativity can also be intermolecular where a particular residue’s contribution to binding affinity changes depending on the identity of neighbouring amino acids. Although numerous studies have identified subsite cooperativity effects, these findings are frequently ignored in investigations probing subsite selectivity by screening against diverse combinatorial libraries of peptides (positional scanning synthetic combinatorial library; PS-SCL). This strategy for determining cleavage specificity relies on the averaged rates of hydrolysis for an uncharacterised ensemble of peptide sequences, as opposed to the defined rate of hydrolysis of a known specific substrate. Further, since PS-SCL screens probe the preference of the various protease subsites independently, this method is inherently unable to detect subsite cooperativity. However, mean hydrolysis rates from PS-SCL screens are often interpreted as being comparable to those produced by single peptide cleavages. Before this study no large systematic evaluation had been made to determine the level of correlation between protease selectivity as predicted by screening against a library of combinatorial peptides and cleavage of individual peptides. This subject is specifically explored in the studies described here. In order to establish whether PS-SCL screens could accurately determine the substrate preferences of proteases, a systematic comparison of data from PS-SCLs with libraries containing individually synthesised peptides (sparse matrix library; SML) was carried out. These SML libraries were designed to include all possible sequence combinations of the residues that were suggested to be preferred by a protease using the PS-SCL method. SML screening against the three serine proteases kallikrein 4 (KLK4), kallikrein 14 (KLK14) and plasmin revealed highly preferred peptide substrates that could not have been deduced by PS-SCL screening alone. Comparing protease subsite preference profiles from screens of the two types of peptide libraries showed that the most preferred substrates were not detected by PS SCL screening as a consequence of intermolecular cooperativity being negated by the very nature of PS SCL screening. Sequences that are highly favoured as result of intermolecular cooperativity achieve optimal protease subsite occupancy, and thereby interact with very specific determinants of the protease. Identifying these substrate sequences is important since they may be used to produce potent and selective inhibitors of protolytic enzymes. This study found that highly favoured substrate sequences that relied on intermolecular cooperativity allowed for the production of potent inhibitors of KLK4, KLK14 and plasmin. Peptide aldehydes based on preferred plasmin sequences produced high affinity transition state analogue inhibitors for this protease. The most potent of these maintained specificity over plasma kallikrein (known to have a very similar substrate preference to plasmin). Furthermore, the efficiency of this inhibitor in blocking fibrinolysis in vitro was comparable to aprotinin, which previously saw clinical use to reduce perioperative bleeding. One substrate sequence particularly favoured by KLK4 was substituted into the 14 amino acid, circular sunflower trypsin inhibitor (SFTI). This resulted in a highly potent and selective inhibitor (SFTI-FCQR) which attenuated protease activated receptor signalling by KLK4 in vitro. Moreover, SFTI-FCQR and paclitaxel synergistically reduced growth of ovarian cancer cells in vitro, making this inhibitor a lead compound for further therapeutic development. Similar incorporation of a preferred KLK14 amino acid sequence into the SFTI scaffold produced a potent inhibitor for this protease. However, the conformationally constrained SFTI backbone enforced a different intramolecular cooperativity, which masked a KLK14 specific determinant. As a consequence, the level of selectivity achievable was lower than that found for the KLK4 inhibitor. Standard mechanism inhibitors such as SFTI rely on a stable acyl-enzyme intermediate for high affinity binding. This is achieved by a conformationally constrained canonical binding loop that allows for reformation of the scissile peptide bond after cleavage. Amino acid substitutions within the inhibitor to target a particular protease may compromise structural determinants that support the rigidity of the binding loop and thereby prevent the engineered inhibitor reaching its full potential. An in silico analysis was carried out to examine the potential for further improvements to the potency and selectivity of the SFTI-based KLK4 and KLK14 inhibitors. Molecular dynamics simulations suggested that the substitutions within SFTI required to target KLK4 and KLK14 had compromised the intramolecular hydrogen bond network of the inhibitor and caused a concomitant loss of binding loop stability. Furthermore in silico amino acid substitution revealed a consistent correlation between a higher frequency of formation and the number of internal hydrogen bonds of SFTI-variants and lower inhibition constants. These predictions allowed for the production of second generation inhibitors with enhanced binding affinity toward both targets and highlight the importance of considering intramolecular cooperativity effects when engineering proteins or circular peptides to target proteases. The findings from this study show that although PS-SCLs are a useful tool for high throughput screening of approximate protease preference, later refinement by SML screening is needed to reveal optimal subsite occupancy due to cooperativity in substrate recognition. This investigation has also demonstrated the importance of maintaining structural determinants of backbone constraint and conformation when engineering standard mechanism inhibitors for new targets. Combined these results show that backbone conformation and amino acid cooperativity have more prominent roles than previously appreciated in determining substrate/inhibitor specificity and binding affinity. The three key inhibitors designed during this investigation are now being developed as lead compounds for cancer chemotherapy, control of fibrinolysis and cosmeceutical applications. These compounds form the basis of a portfolio of intellectual property which will be further developed in the coming years.

Reduced sampling efficiency causes degraded Vernier hyperacuity with normal aging: Vernier acuity in position noise

Vernier acuity, a form of visual hyperacuity, is amongst the most precise forms of spatial vision. Under optimal conditions Vernier thresholds are much finer than the inter-photoreceptor distance. Achievement of such high precision is based substantially on cortical computations, most likely in the primary visual cortex. Using stimuli with added positional noise, we show that Vernier processing is reduced with advancing age across a wide range of noise levels. Using an ideal observer model, we are able to characterize the mechanisms underlying age-related loss, and show that the reduction in Vernier acuity can be mainly attributed to the reduction in efficiency of sampling, with no significant change in the level of internal position noise, or spatial distortion, in the visual system.

Quality of work life and turnover intention in primary healthcare organisations : a cross-sectional study of registered nurses in Saudi Arabia

Purpose: The purpose of this study was to improve the retention of primary healthcare (PHC) nurses through exploring and assessing their quality of work life (QWL) and turnover intention. Design and methods: A cross-sectional survey design was used in this study. Data were collected using a questionnaire comprising four sections (Brooks’ survey of Quality of Nursing Work Life [QNWL], Anticipated Turnover Intention, open-ended questions and demographic characteristics). A convenience sample was recruited from 143 PHC centres in Jazan, Saudi Arabia. A response rate of 87% (n = 508/585) was achieved. The SPSS v17 for Windows and NVivo 8 were used for analysis purposes. Procedures and tests used in this study to analyse the quantitative data were descriptive statistics, t-test, ANOVA, General Linear Model (GLM) univariate analysis, standard multiple regression, and hierarchical multiple regression. Qualitative data obtained from responses to the open-ended questions were analysed using the NVivo 8. Findings: Quantitative findings suggested that PHC nurses were dissatisfied with their work life. Respondents’ scores ranged between 45 and 218 (mean = 139.45), which is lower than the average total score on Brooks’ Survey (147). Major influencing factors were classified under four dimensions. First, work life/home life factors: unsuitable working hours, lack of facilities for nurses, inability to balance work with family needs and inadequacy of vacations’ policy. Second, work design factors: high workload, insufficient workforce numbers, lack of autonomy and undertaking many non-nursing tasks. Third, work context factors: management practices, lack of development opportunities, and inappropriate working environment in terms of the level of security, patient care supplies and unavailability of recreation room. Finally, work world factors: negative public image of nursing, and inadequate payment. More positively, nurses were notably satisfied with their co-workers. Conversely, 40.4% (n = 205) of the respondents indicated that they intended to leave their current employment. The relationships between QWL and demographic variables of gender, age, marital status, dependent children, dependent adults, nationality, ethnicity, nursing tenure, organisational tenure, positional tenure, and payment per month were significant (p < .05). The eta squared test for these demographics indicates a small to medium effect size of the variation in QWL scores. Using the GLM univariate analysis, education level was also significantly related to the QWL (p < .05). The relationships between turnover intention and demographic variables including gender, age, marital status, dependent children, education level, nursing tenure, organisational tenure, positional tenure, and payment per month were significant (p < .05). The eta squared test for these demographics indicates a small to moderate effect size of the variation in the turnover intention scores. Using the GLM univariate analysis, the dependent adults’ variable was also significantly related to turnover intention (p < .05). Turnover intention was significantly related to QWL. Using standard multiple regression, 26% of the variance in turnover intention was explained by the QWL F (4,491), 43.71, p < .001, with R² = .263. Further analysis using hierarchical multiple regression found that the total variance explained by the model as a whole (demographics and QWL) was 32.1%, F (17.433) = 12.04, p < .001. QWL explained an additional 19% of the variance in turnover intention, after controlling for demographic variables, R squared change =.19, F change (4, 433) = 30.190, p < .001. The work context variable makes the strongest unique contribution (-.387) to explain the turnover intention, followed by the work design dimension (-.112). The qualitative findings reaffirmed the quantitative findings in terms of QWL and turnover intention. However, the home life/work life and work world dimensions were of great important to both QWL and turnover intention. The qualitative findings revealed a number of new factors that were not included in the survey questionnaire. These included being away from family, lack of family support, social and cultural aspects, accommodation facilities, transportation, building and infrastructure of PHC, nature of work, job instability, privacy at work, patients and community, and distance between home and workplace. Conclusion: Creating and maintaining a healthy work life for PHC nurses is very important to improve their work satisfaction, reduce turnover, enhance productivity and improve nursing care outcomes. Improving these factors could lead to a higher QWL and increase retention rates and therefore reinforcing the stabilisation of the nursing workforce. Significance of the research: Many countries are examining strategies to attract and retain the health care workforce, particularly nurses. This study identified factors that influence the QWL of PHC nurses as well as their turnover intention. It also determined the significant relationship between QWL and turnover intention. In addition, the present study tested Brooks’ survey of QNWL on PHC nurses for the first time. The qualitative findings of this study revealed a number of new variables regarding QWL and turnover intention of PHC nurses. These variables could be used to improve current survey instruments or to develop new research surveys. The study findings could be also used to develop and appropriately implement plans to improve QWL. This may help to enhance the home and work environments of PHC nurses, improve individual and organisational performance, and increase nurses’ commitment. This study contributes to the existing body of research knowledge by presenting new data and findings from a different country and healthcare system. It is the first of its kind in Saudi Arabia, especially in the field of PHC. It has examined the relationship between QWL and turnover intention of PHC nurses for the first time using nursing instruments. The study also offers a fresh explanation (new framework) of the relationship between QWL and turnover intention among PHC nurses, which could be used or tested by researchers in other settings. Implications for further research: Review of the extant literature reveals little in-depth research on the PHC workforce, especially in terms of QWL and organisational turnover in developing countries. Further research is required to develop a QWL tool for PHC nurses, taking into consideration the findings of the current study along with the local culture. Moreover, the revised theoretical framework of the current study could be tested in further research in other regions, countries or healthcare systems in order to identify its ability to predict the level of PHC nurses’ QWL and their intention to leave. There is a need to conduct longitudinal research on PHC organisations to gain an in-depth understanding of the determents of and changes in QWL and turnover intention of PHC nurses at various points of time. An intervention study is required to improve QWL and retention among PHC nurses using the findings of the current study. This would help to assess the impact of such strategies on reducing turnover of PHC nurses. Focusing on the location of the current study, it would be valuable to conduct another study in five years’ time to examine the percentage of actual turnover among PHC nurses compared with the reported turnover intention in the current study. Further in-depth research would also be useful to assess the impact of the local culture on the perception of expatriate nurses towards their QWL and their turnover intention. A comparative study is required between PHC centres and hospitals as well as the public and private health sector agencies in terms of QWL and turnover intention of nursing personnel. Findings may differ from sector to sector according to variations in health systems, working environments and the case mix of patients.

Non-combinatorial library screening reveals subsite cooperativity and identifies new high-efficiency substrates for kallikrein-related peptidase 14

An array of substrates link the tryptic serine protease, kallikrein-related peptidase 14 (KLK14), to physiological functions including desquamation and activation of signaling molecules associated with inflammation and cancer. Recognition of protease cleavage sequences is driven by complementarity between exposed substrate motifs and the physicochemical signature of an enzyme's active site cleft. However, conventional substrate screening methods have generated conflicting subsite profiles for KLK14. This study utilizes a recently developed screening technique, the sparse matrix library, to identify five novel high-efficiency sequences for KLK14. The optimal sequence, YASR, was cleaved with higher efficiency (k(cat)/K(m)=3.81 ± 0.4 × 10(6) M(-1) s(-1)) than favored substrates from positional scanning and phage display by 2- and 10-fold, respectively. Binding site cooperativity was prominent among preferred sequences, which enabled optimal interaction at all subsites as indicated by predictive modeling of KLK14/substrate complexes. These simulations constitute the first molecular dynamics analysis of KLK14 and offer a structural rationale for the divergent subsite preferences evident between KLK14 and closely related KLKs, KLK4 and KLK5. Collectively, these findings highlight the importance of binding site cooperativity in protease substrate recognition, which has implications for discovery of optimal substrates and engineering highly effective protease inhibitors.

Is the unigram relevance model term independent? Classifying term dependencies in query expansion

This paper develops a framework for classifying term dependencies in query expansion with respect to the role terms play in structural linguistic associations. The framework is used to classify and compare the query expansion terms produced by the unigram and positional relevance models. As the unigram relevance model does not explicitly model term dependencies in its estimation process it is often thought to ignore dependencies that exist between words in natural language. The framework presented in this paper is underpinned by two types of linguistic association, namely syntagmatic and paradigmatic associations. It was found that syntagmatic associations were a more prevalent form of linguistic association used in query expansion. Paradoxically, it was the unigram model that exhibited this association more than the positional relevance model. This surprising finding has two potential implications for information retrieval models: (1) if linguistic associations underpin query expansion, then a probabilistic term dependence assumption based on position is inadequate for capturing them; (2) the unigram relevance model captures more term dependency information than its underlying theoretical model suggests, so its normative position as a baseline that ignores term dependencies should perhaps be reviewed.

Ocularcentric labour : ‘you don’t do this for money’

Building on the tradition of emotional labour and aesthetic labour, this study of fitness workers introduces the concept of “ocularcentric labour” (the worker seeking the adoring gaze of the client as the primary reward). It is a state in which labour’s quest for the psycho-social rewards gained from their own body image shapes the employment relationship (both the organization of work and the conditions of employment). We argue that for many fitness workers the goal is to gain access to the positional economy of the fitness centre to promote their celebrity. For this they are willing to trade-off standard conditions of employment, and exchange traditional employment rewards for the more intrinsic psycho-social rewards gained through the exposure of their physical capital to the adoration of their gazing clients. Significantly, with ocularcentric labour the worker becomes both the site of production and consumption.

Quality of work life among primary health care nurses in the Jazan region, Saudi Arabia : a crosssectional study

Background: Quality of work life (QWL) is defined as the extent to which employee is satisfied with personal and working needs through participating in the workplace while achieving the organisation’s goals. QWL has been found to influence the commitment and productivity of employees in healthcare organisations, as well as in other industries. However, reliable information on the QWL of PHC nurses is limited. The purpose of this study was to assess the QWL among PHC nurses in the Jazan region, Saudi Arabia. Methods: A descriptive research design, namely, a cross-sectional survey was used in this study. Data were collected using Brooks’ survey of quality of nursing work life (QNWL) and demographic questions. A convenience sample was recruited from 143 PHC centres in Jazan, Saudi Arabia. The Jazan region is located in the southern part of Saudi Arabia. A response rate of 91% (N = 532/585) was achieved (effective RR = 87%, n = 508). Data analysis consisted of descriptive statistics, t-test and one way-analysis of variance. Total scores and sub-scores for QWL Items and item summary statistics were computed and reported, using SPSS version 17 for Windows. Results: Findings suggested that the respondents were dissatisfied with their work life. The major influencing factors were unsuitable working hours/shifts, lack of facilities for nurses, inability to balance work with family needs, inadequacy of family-leave time, poor staffing, management and supervision practices, lack of professional development opportunities, and inappropriate working environment in terms of the level of security, patient care supplies and equipment, and recreation facilities (Break-area). Other essential factors include the community’s view of nursing and inadequate salary. More positively, the majority of nurses were satisfied with their co-workers, satisfied to be nurses and had a sense of belonging in their workplaces. Significant differences were found according to gender, age, marital status, dependent children, dependent adults, nationality, ethnicity, nursing tenure, organisational tenure, positional tenure, and payment per month. No significant differences were found according to education level and location of PHC. Conclusions: These findings can be used by PHC managers and policy makers for developing and appropriately implementing successful plans to improve the QWL. This will help to enhance the home and work environments, improve individual and organisation performance and increase nurses’ commitment.

Average structure of an An (sub 48) plagioclase from the Hogarth Ranges

The average structure (CI) of a volcanic plagioclase megacryst with composition Ano, from the Hogarth Ranges, Australia, has been determined using three-dimensional, singlecrystal neutron and X-ray diffraction data. Least squaresr efinements, incorporating anisotropic thermal motion of all atoms and an extinction correction, resulted in weighted R factors (based on intensities) of 0.076 and 0.056, respectively, for the neutron and X-ray data. Very weak e reflections could be detected in long-exposure X-ray and electron diffraction photographs of this crystal, but the refined average structure is believed to be unaffected by the presence of such a weak superstructure. The ratio of the scattering power of Na to that of Ca is different for X ray and neutron radiation, and this radiation-dependence of scattering power has been used to determine the distribution of Na and Ca over a split-atom M site (two sites designated M' and M") in this Ano, plagioclase. Relative peak-height ratios M'/M", revealed in difference Fourier sections calculated from neutron and X-ray data, formed the basis for the cation-distribution analysis. As neutron and X-ray data sets were directly compared in this analysis, it was important that systematic bias between refined neutron and X-ray positional parameters could be demonstrated to be absent. In summary, with an M-site model constrained only by the electron-microprobedetermined bulk composition of the crystal, the following values were obtained for the M-site occupanciesN: ar, : 0.29(7),N ar. : 0.23(7),C ar, : 0.15(4),a nd Car" : 0.33(4). These results indicate that restrictive assumptions about M sites, on which previous plagioclase refinements have been based, are not applicable to this Ano, and possibly not to the entire compositional range. T-site ordering determined by (T-O) bond-length variation-t,o : 0.51(l), trm = t2o = t2m = 0.32(l)-is weak, as might be expectedf rom the volcanic origin of this megacryst.

Making a point of difference : the glocalised ecology of the International Baccalaureate Diploma in Australian schools

The International Baccalaureate Diploma is an independent, globally available curriculum currently enjoying rapid uptake in government systems as an alternative curriculum. This paper explores the logic of its consumption in three case study schools across different states of Australia, and the relational ‘points of difference’ it creates in each local context and its curricular market. The analysis uses a typology of goods to describe the nature and dynamics of the IBD’s glocalised ecology of in each site. The conclusion argues the success of the IBD as a curricular alternative risks eroding its appeal as a positional good.

Ventilation distribution in rats : part 2 – a comparison of electrical impedance tomography and hyperpolarised helium magnetic resonance imaging

Background: Hyperpolarised helium MRI (He3 MRI) is a new technique that enables imaging of the air distribution within the lungs. This allows accurate determination of the ventilation distribution in vivo. The technique has the disadvantages of requiring an expensive helium isotope, complex apparatus and moving the patient to a compatible MRI scanner. Electrical impedance tomography (EIT) a non-invasive bedside technique that allows constant monitoring of lung impedance, which is dependent on changes in air space capacity in the lung. We have used He3MRI measurements of ventilation distribution as the gold standard for assessment of EIT. Methods: Seven rats were ventilated in supine, prone, left and right lateral position with 70% helium/30% oxygen for EIT measurements and pure helium for He3 MRI. The same ventilator and settings were used for both measurements. Image dimensions, geometric centre and global in homogeneity index were calculated. Results: EIT images were smaller and of lower resolution and contained less anatomical detail than those from He3 MRI. However, both methods could measure positional induced changes in lung ventilation, as assessed by the geometric centre. The global in homogeneity index were comparable between the techniques. Conclusion: EIT is a suitable technique for monitoring ventilation distribution and inhomgeneity as assessed by comparison with He3 MRI.

Capturing complex, non-linear team behaviours during competitive football performance

This study investigated changes in the complexity (magnitude and structure of variability) of the collective behaviours of association football teams during competitive performance. Raw positional data from an entire competitive match between two professional teams were obtained with the ProZone® tracking system. Five compound positional variables were used to investigate the collective patterns of performance of each team including: surface area, stretch index, team length, team width, and geometrical centre. Analyses involve the coefficient of variation (%CV) and approximate entropy (ApEn), as well as the linear association between both parameters. Collective measures successfully captured the idiosyncratic behaviours of each team and their variations across the six time periods of the match. Key events such as goals scored and game breaks (such as half time and full time) seemed to influence the collective patterns of performance. While ApEn values significantly decreased during each half, the %CV increased. Teams seem to become more regular and predictable, but with increased magnitudes of variation in their organisational shape over the natural course of a match.

Structural characterization of glycerophospholipids by combinations of ozone- and collision-induced dissociation mass spectrometry: The next step towards "top-down" lipidomics

The complete structural elucidation of complex lipids, including glycerophospholipids, using only mass spectrometry represents a major challenge to contemporary analytical technologies. Here, we demonstrate that product ions arising from the collision-induced dissociation (CID) of the [M + Na] + adduct ions of phospholipids can be isolated and subjected to subsequent gas-phase ozonolysis-known as ozone-induced dissociation (OzID)-in a linear ion-trap mass spectrometer. The resulting CID/OzID experiment yields abundant product ions that are characteristic of the acyl substitution on the glycerol backbone (i.e., sn-position). This approach is shown to differentiate sn-positional isomers, such as the regioisomeric phosphatidylcholine pair of PC 16:0/18:1 and PC 18:1/16:0. Importantly, CID/OzID provides a sensitive diagnostic for the existence of an isomeric mixture in a given sample. This is of very high value for the analysis of tissue extracts since CID/OzID analyses can reveal changes in the relative abundance of isomeric constituents even within different tissues from the same animal. Finally, we demonstrate the ability to assign carbon-carbon double bond positions to individual acyl chains at specific backbone positions by adding subsequent CID and/or OzID steps to the workflow and that this can be achieved in a single step using a hybrid triple quadrupole-linear ion trap mass spectrometer. This unique approach represents the most complete and specific structural analysis of lipids by mass spectrometry demonstrated to date and is a significant step towards comprehensive top-down lipidomics. This journal is © The Royal Society of Chemistry 2014. Grant Number ARC/DP0986628, ARC/FT110100249, ARC/LP110200648

Novelty-based visual obstacle detection in agriculture

This paper describes a novel obstacle detection system for autonomous robots in agricultural field environments that uses a novelty detector to inform stereo matching. Stereo vision alone erroneously detects obstacles in environments with ambiguous appearance and ground plane such as in broad-acre crop fields with harvested crop residue. The novelty detector estimates the probability density in image descriptor space and incorporates image-space positional understanding to identify potential regions for obstacle detection using dense stereo matching. The results demonstrate that the system is able to detect obstacles typical to a farm at day and night. This system was successfully used as the sole means of obstacle detection for an autonomous robot performing a long term two hour coverage task travelling 8.5 km.