ChromA: signal-based retention time alignment for chromatography–mass spectrometry data

Summary: We describe ChromA, a web-based alignment tool for chromatography–mass spectrometry data from the metabolomics and proteomics domains. Users can supply their data in open and standardized file formats for retention time alignment using dynamic time warping with different configurable local distance and similarity functions. Additionally, user-defined anchors can be used to constrain and speedup the alignment. A neighborhood around each anchor can be added to increase the flexibility of the constrained alignment. ChromA offers different visualizations of the alignment for easier qualitative interpretation and comparison of the data. For the multiple alignment of more than two data files, the center-star approximation is applied to select a reference among input files to align to

What are school leavers' priorities for festival preparation?

Published: 20 November 2013This paper reports on the findings from a qualitative research study that explored how young people prepared to minimise and/or avoid alcohol-related harm while attending a Schoolies Festival (SF). SFs are mass gatherings at which young people (schoolies) celebrate their graduation from high school. The attendance of schoolies, in various Australian communities, ranges between 10 000 and 30 000 individuals during the event. The literature suggests that schoolies are at higher than normal risk of harm at SF from misuse of alcohol, unsafe sex, aggressive behaviour, and other risk-taking factors. As a result of these concerns, SF organisers developed an infrastructure that treats alcohol-related harm, and provides on-site care (first aid stations) by St John Ambulance staff. This study used focus groups to identify strategies used by schoolies to avoid alcohol-related harm during SFs. Data revealed that schoolies did not actively seek health information before attending the event and did not display an interest in doing so. It is important to note that schoolies planned to use alcohol to celebrate and have a good time. Therefore a harm minimisation approach with a focus on providing the necessary infrastructure at SFs to minimise the dangers associated with excess alcohol use is important. Schoolies indicated that they had no desire for information about the hazards of alcohol ingestion. If any health messages were to be used by health authorities, it would be far more appropriate to promote the message of ‘take care of your mate’, to contribute to building a supportive environment at the event. This may be of more benefit to minimise harm at SFs than funding other health messages.Alison Hutton, Lynette Cusack, Lana Zannettino, Sarah J. M. Shaefer, Naomi Verdonk and Paul Arbo

Measuring the effectiveness of management interventions at regional scales by integrating ecological monitoring and modelling

Background: Because of site‐specific effects and outcomes, it is often difficult to know whether a management strategy for the control of pests has worked or not. Population dynamics of pests are typically spatially and temporally variable. Moreover, interventions at the scale of individual fields or farms are essentially unreplicated experiments; a decrease in a target population following management cannot safely be interpreted as success because, for example, it might simply be a poor year for that species. Here, we argue that if large‐scale data are available, population models can be used to measure outcomes against the prevailing mean and variance. We apply this approach to the problem of rotational management of the weed Alopecurus myosuroides. Results: We derived density‐structured population models for a set of fields that were not subject to rotational management (continuous winter wheat) and another group that were (rotated into spring barley to control A. myosuroides). We used these models to construct means and variances of the outcomes of management for given starting conditions, and to conduct transient growth analysis. We show that, overall, this management strategy is successful in reducing densities of weeds, albeit with considerable variance. However, we also show that one variant (rotation to spring barley along with variable sowing) shows little evidence for additional control. Conclusion: Our results suggest that rotational strategies can be effective in the control of this weed, but also that strategies require careful evaluation against a background of spatiotemporal variation

Overcoming: A Concept Analysis

Peer Reviewedhttp://deepblue.lib.umich.edu/bitstream/2027.42/86851/1/j.1744-6198.2011.00227.x.pd

Nursing judgement and decision-making using the Sedation Withdrawal Score (SWS) in children

Aims: The aim of the study was to evaluate registered children’s nurses’ approaches to the assessment and management of withdrawal syndrome in children. Background: Assessment of withdrawal syndrome is undertaken following critical illness when the child’s condition may be unstable with competing differential diagnoses. Assessment tools aim to standardize and improve recognition of withdrawal syndrome. Making the right decisions in complex clinical situations requires a degree of mental effort and it is not known how nurses make decisions when undertaking withdrawal assessments. Design: Cognitive interviews with clinical vignettes. Methods: Interviews were undertaken with 12 nurses to explore the cognitive processes they used when assessing children using the Sedation Withdrawal Score (SWS) tool. Interviews took place in Autumn 2013. Findings: Each stage of decision-making—noticing, interpreting and responding— presented cognitive challenges for nurses. When defining withdrawal behaviours nurses tended to blur the boundaries between Sedation Withdrawal Score signs. Challenges in interpreting behaviours arose from not knowing if the patient’s behaviour was a result of withdrawal or other co-morbidities. Nurses gave a range of diagnoses when interpreting the vignettes, despite being provided with identical information. Treatment responses corresponded to definite withdrawal diagnoses, but varied when nurses were unsure of the diagnosis. Conclusion: Cognitive interviews with vignettes provided insight into nurses’ judgement and decision-making. The SWS does not standardize the assessment of withdrawal due to the complexity of the context where assessments take place and the difficulties of determining the cause of equivocal behaviours in children recovering from critical illness

Bacteria clustering by polymers induces the expression of quorum sense controlled phenotypes

Bacteria deploy a range of chemistries to regulate their behaviour and respond to their environment. Quorum sensing is one mean by which bacteria use chemical reactions to modulate pre-infection behaviour such as surface attachment. Polymers that can interfere with bacterial adhesion or the chemical reactions used for quorum sensing are thus a potential means to control bacterial population responses. Here we report how polymeric "bacteria sequestrants", designed to bind to bacteria through electrostatic interactions and thus inhibit bacterial adhesion to surfaces, induce the expression of quorum sensing controlled phenotypes as a consequence of cell clustering. A combination of polymer and analytical chemistry, biological assays and computational modelling has been used to characterise the feedback between bacteria clustering and quorum sensing signaling. We have also derived design principles and chemical strategies for controlling bacterial behaviour at the population leve

Helicobacter pylori versus the Host: Remodeling of the Bacterial Outer Membrane Is Required for Survival in the Gastric Mucosa

Modification of bacterial surface structures, such as the lipid A portion of lipopolysaccharide (LPS), is used by many pathogenic bacteria to help evade the host innate immune response. Helicobacter pylori, a gram-negative bacterium capable of chronic colonization of the human stomach, modifies its lipid A by removal of phosphate groups from the 1- and 4′-positions of the lipid A backbone. In this study, we identify the enzyme responsible for dephosphorylation of the lipid A 4′-phosphate group in H. pylori, Jhp1487 (LpxF). To ascertain the role these modifications play in the pathogenesis of H. pylori, we created mutants in lpxE (1-phosphatase), lpxF (4′-phosphatase) and a double lpxE/F mutant. Analysis of lipid A isolated from lpxE and lpxF mutants revealed lipid A species with a 1 or 4′-phosphate group, respectively while the double lpxE/F mutant revealed a bis-phosphorylated lipid A. Mutants lacking lpxE, lpxF, or lpxE/F show a 16, 360 and 1020 fold increase in sensitivity to the cationic antimicrobial peptide polymyxin B, respectively. Moreover, a similar loss of resistance is seen against a variety of CAMPs found in the human body including LL37, β-defensin 2, and P-113. Using a fluorescent derivative of polymyxin we demonstrate that, unlike wild type bacteria, polymyxin readily associates with the lpxE/F mutant. Presumably, the increase in the negative charge of H. pylori LPS allows for binding of the peptide to the bacterial surface. Interestingly, the action of LpxE and LpxF was shown to decrease recognition of Helicobacter LPS by the innate immune receptor, Toll-like Receptor 4. Furthermore, lpxE/F mutants were unable to colonize the gastric mucosa of C57BL/6J and C57BL/6J tlr4 -/- mice when compared to wild type H. pylori. Our results demonstrate that dephosphorylation of the lipid A domain of H. pylori LPS by LpxE and LpxF is key to its ability to colonize a mammalian host