Mining whole sample mass spectrometry proteomics data for biomarkers: an overview

In this paper we aim to provide a concise overview of designing and conducting an MS proteomics experiment in such a way as to allow statistical analysis that may lead to the discovery of novel biomarkers. We provide a summary of the various stages that make up such an experiment, highlighting the need for experimental goals to be decided upon in advance. We discuss issues in experimental design at the sample collection stage, and good practise for standardising protocols within the proteomics laboratory. We then describe approaches to the data mining stage of the experiment, including the processing steps that transform a raw mass spectrum into a useable form. We propose a permutation-based procedure for determining the significance of reported error rates. Finally, because of its general advantages in speed and cost, we suggest that MS proteomics may be a good candidate for an early primary screening approach to disease diagnosis, identifying areas of risk and making referrals for more specific tests without necessarily making a diagnosis in its own right. Our discussion is illustrated with examples drawn from experiments on bovine blood serum conducted in the Centre for Proteomic Research (CPR) at Southampton University

Exploring the anthelmintic properties of Australian native shrubs with respect to their potential role in livestock grazing systems

We measured in vitro anthelmintic activity in extracts from 85 species of Australian native shrub, with a view to identifying species able to provide a degree of worm control in grazing systems. Approximately 40% of the species showed significant activity in inhibiting development of Haemonchus contortus larvae. The most active extracts showed IC50 values of 60–300 mg/ml. Pre-incubation with polyvinylpolypyrrolidine removed the activity from some extracts, implicating tannins as the bioactive agent, while in other cases the pre-incubation had no effect, indicating the presence of other anthelmintic compounds. Plant reproductive maturity (onset of flowering or fruiting) was associated with increasing anthelmintic activity in some species. Variability was observed between plants of the same species growing in different environments, while variation between individual plants of the same species within a single field suggests the existence of distinct chemotypes. Significant activity against adult H. contortus worms in vitro was also demonstrated in a limited number of extracts tested against this life stage. Our study indicates that there is potential for Australian native shrubs to play an anthelmintic role in grazing systems, and highlights some plant biology factors which will need to be considered in order to maximize any anthelmintic effects.A. C. Kotze, J. O’Grady, J. Emms, A. F. Toovey, S. Hughes, P. Jessop, M. Bennell P. E. Vercoe and D. K. Revel

Stress-Activity Mapping: Physiological Responses During General Duty Police Encounters

Policing is a highly stressful and dangerous profession that involves a complex set of environmental, psychosocial, and health risks. The current study examined autonomic stress responses experienced by 64 police officers, during general duty calls for service (CFS) and interactions with the public. Advancing previous research, this study utilized GPS and detailed operational police records as objective evidence of specific activities throughout a CFS. These data were then used to map officers’ heart rate to both the phase of a call (e.g., dispatch, enroute) and incident factors (e.g., call priority, use-of-force). Furthermore, physical movement (i.e., location and inertia) was tracked and assisted in differentiating whether cardiovascular reactivity was due to physical or psychological stress. Officer characteristics, including years of service and training profiles, were examined to conduct a preliminary exploration of whether experience and relevant operational skills training impacted cardiovascular reactivity. Study results provide foundational evidence that CFS factors, specifically the phase of the call (i.e., arrival on scene, encountering a subject) and incident factors (i.e., call priority, weapons, arrest, use-of-force), influence physiologica

My joint pain, a web-based resource, effects on education and quality of care at 24 months

Objective: To evaluate the effects of the updated version of an evidence-based osteoarthritis (OA) resource and consumer hub, 'My Joint Pain' website, on health education and quality of care over 12 months.Methods: Using a classic quasi-experimental design, participants with symptomatic hip or knee OA were recruited across Australia to evaluate the 'My Joint Pain' website, compared to a control group of non-users from 12 to 24 months. Outcome measures included the Health Education Impact Questionnaire (HEIQ) and the OA Quality Indicator (OAQI) questionnaire. The changes from 12 to 24 months in the HEIQ were evaluated using a generalised linear model. The differences between users and non-users in the OAQI were evaluated using a chi-square test.Results: A total of 277 eligible participants with symptomatic hip or knee OA were recruited at baseline, and 122 participants completed the 24-month surveys (users: n = 35, non-users: n = 87). There was no significant difference between users and non-users for the HEIQ scores at 24 months after adjustments for age, sex and body mass index (BMI). Users had higher emotional distress scores than non-users in univariable analysis. When compared with non-users in the OAQI, users showed favourable changes in receiving information about "self-management" and "acetaminophen" and "non-steroidal anti-inflammatory drugs (NSAIDs)" from 12 to 24 months.Conclusion: The evaluation of the updated 'My Joint Pain' website didn't find significant improvements in terms of health education, but it may help delivering useful information about self-management and appropriate use of pharmacological treatments. More strategies are needed to facilitate the uptake of evidence-based self-management and education online resources for OA consumers

Dynamic Pricing for Vehicle Ferries: using Packing and Simulation to Optimize Revenues

We propose an heuristic approach to the vehicle ferry revenue management problem, where the aim is to maximize the revenue obtained from the sale of vehicle tickets by varying the prices charged to different vehicle types, each occupying a different amount of deck space. Customers arrive and purchase tickets according to their vehicle type and their willingness-to-pay, which typically increases over time because customers purchasing tickets closer to departure tend to accept higher prices. The optimization problem can be solved using dynamic programming but the possible states in the selling season are the set of all feasible vehicle mixes that fit onto the ferry. This makes the problem intractable as the number of vehicle types and ferry size increases. We propose a state space reduction, which uses a vehicle ferry loading simulator to map each vehicle mix to a remaining-space state. This reduces the state space of the dynamic program. Our approach allows the value function to be approximated rapidly and accurately with a relatively coarse discretization of states. We present simulations of the selling season using this reduced state space to validate the method. The vehicle ferry loading simulator was developed in collaboration with a vehicle ferry company and addresses real-world constraints such as manoeuvrability, elevator access, strategic parking gaps, vehicle height constraints and ease of implementation of the packing solutions

Voxel-Based Solution Approaches to the Three-Dimensional Irregular Packing Problem

Research on the three-dimensional (3D) packing problem has largely focused on packing boxes for the transportation of goods. As a result, there has been little focus on packing irregular shapes in the operational research literature. New technologies have raised the practical importance of 3D irregular packing problems and the need for efficient solutions. In this work, we address the variant of the problem where the aim is to place a set of 3D irregular items in a container, while minimizing the container height, analogous to the strip packing problem. In order to solve this problem, we need to address two critical components; efficient computation of the geometry and finding high-quality solutions. In this work, we explore the potential of voxels, the 3D equivalent of pixels, as the geometric representation of the irregular items. In this discretised space, we develop a geometric tool that extends the concept of the nofit polygon to the 3D case. This enables us to provide an integer linear programming formulation for this problem that can solve some small instances. For practical size problems, we design metaheuristic optimisation approaches. Because the literature is limited, we introduce new benchmark instances. Some are randomly generated and some represent realistic models from the additive manufacturing area. Our results on the literature benchmark data and on our new instances show that our metaheuristic techniques achieve the best known solutions for a wide variety of problems in practical computation times

Functional polymorphisms in the P2X7 receptor gene are associated with stress fracture injury

Context: Military recruits and elite athletes are susceptible to stress fracture injuries. Genetic predisposition has been postulated to have a role in their development. The P2X7 receptor (P2X7R) gene, a key regulator of bone remodelling, is a genetic candidate that may contribute to stress fracture predisposition. Objective: To evaluate the putative contribution of P2X7R to stress fracture injury in two separate cohorts, military personnel and elite athletes. Methods: In 210 Israeli Defence Forces (IDF) military conscripts, stress fracture injury was diagnosed (n=43) based on symptoms and a positive bone scan. In a separate cohort of 518 elite athletes, self-reported medical imaging scan-certified stress fracture injuries were recorded (n=125). Non-stress fracture controls were identified from these cohorts who had a normal bone scan or no history or symptoms of stress fracture injury. Study participants were genotyped for functional SNPs within the P2X7R gene using proprietary fluorescence-based competitive allele-specific PCR assay. Pearson Chi-square (χ2) tests, corrected for multiple comparisons, were used to assess associations in genotype frequencies. Results: The variant allele of P2X7R SNP rs3751143 (Glu496Ala- loss of function) was associated with stress fracture injury, while the variant allele of rs1718119 (Ala348Thr- gain of function) was associated with a reduced occurrence of stress fracture injury in military conscripts (P<0.05). The association of the variant allele of rs3751143 with stress fractures was replicated in elite athletes (P<0.05), whereas the variant allele of rs1718119 was also associated with reduced multiple stress fracture cases in elite athletes (P<0.05). Conclusions: The association between independent P2X7R polymorphisms with stress fracture prevalence supports the role of a genetic predisposition in the development of stress fracture injury

The foot posture index, ankle lunge test, Beighton scale and the lower limb assessment score in healthy children: a reliability study

<p>Abstract</p> <p>Background</p> <p>Outcome measures are important when evaluating treatments and physiological progress in paediatric populations. Reliable, relevant measures of foot posture are important for such assessments to be accurate over time. The aim of the study was to assess the intra- and inter-rater reliability of common outcome measures for paediatric foot conditions.</p> <p>Methods</p> <p>A repeated measures, same-subject design assessed the intra- and inter-rater reliability of measures of foot posture, joint hypermobility and ankle range: the Foot Posture Index (FPI-6), the ankle lunge test, the Beighton scale and the lower limb assessment scale (LLAS), used by two examiners in 30 healthy children (aged 7 to 15 years). The Oxford Ankle Foot Questionnaire (OxAFQ-C) was completed by participants and a parent, to assess the extent of foot and ankle problems.</p> <p>Results</p> <p>The OxAFQ-C demonstrated a mean (SD) score of 6 (6) in adults and 7(5) for children, showing good agreement between parents and children, and which indicates mid-range (transient) disability. Intra-rater reliability was good for the FPI-6 (ICC = 0.93 - 0.94), ankle lunge test (ICC = 0.85-0.95), Beighton scale (ICC = 0.96-0.98) and LLAS (ICC = 0.90-0.98). Inter-rater reliability was largely good for each of the: FPI-6 (ICC = 0.79), ankle lunge test (ICC = 0.83), Beighton scale (ICC = 0.73) and LLAS (ICC = 0.78).</p> <p>Conclusion</p> <p>The four measures investigated demonstrated adequate intra-rater and inter-rater reliability in this paediatric sample, which further justifies their use in clinical practice.</p

RANK/RANKL/OPG pathway: genetic associations with stress fracture period prevalence in elite athletes

Context: The RANK/RANKL/OPG signalling pathway is important in the regulation of bone turnover, with single nucleotide polymorphisms (SNPs) in genes within this pathway associated with bone phenotypic adaptations. Objective: To determine whether four SNPs associated with genes in the RANK/RANKL/OPG signalling pathway were associated with stress fracture injury in elite athletes. Design, Participants, and Methods: Radiologically confirmed stress fracture history was reported in 518 elite athletes, forming the Stress Fracture Elite Athlete (SFEA) cohort. Data were analysed for the whole group, and were sub-stratified into male and cases of multiple stress fracture group. Genotypes were determined using proprietary fluorescence-based competitive allele-specific PCR assays. Results: SNPs rs3018362 (RANK) and rs1021188 (RANKL) were associated with stress fracture injury (p<0.05). 8.1% of stress fracture group and 2.8% of the non-stress fracture group were homozygote for the rare allele of rs1021188. Allele frequency, heterozygotes and homozygotes for the rare allele of rs3018362 were associated with stress fracture period prevalence (p<0.05). Analysis of the male only group showed 8.2% of rs1021188 rare allele homozygotes to have suffered a stress fracture while 2.5% of the non-stress fracture group were homozygous. In cases of multiple stress fractures, homozygotes for the rare allele of rs1021188, and individuals possessing at least one copy of the rare allele of rs4355801 (OPG) were shown to be associated with stress fracture injury (p<0.05). Conclusions: The data support an association between SNPs in the RANK/RANKL/OPG signalling pathway and the development of stress fracture injury. The association of rs3018362 (RANK) and rs1021188 (RANKL) with stress fracture injury susceptibility supports their role in the maintenance of bone health, and offers potential targets for therapeutic interventions