Assessing the complementary information from an increased number of biologically relevant features in liquid biopsy-derived RNA-Seq data

Liquid biopsy-derived RNA sequencing (lbRNA-seq) exhibits significant promise for clinic-oriented cancer diagnostics due to its non-invasiveness and ease of repeatability. Despite substantial advancements, obstacles like technical artefacts and process standardisation impede seamless clinical integration. Alongside addressing technical aspects such as normalising fluctuating low-input material and establishing a standardised clinical workflow, the lack of result validation using independent datasets remains a critical factor contributing to the often low reproducibility of liquid biopsy-detected biomarkers. Considering the outlined drawbacks, our objective was to establish a workflow/methodology characterised by: 1. Harness the rich diversity of biological features accessible through lbRNA-seq data, encompassing a holistic range of molecular and functional attributes. These components are seamlessly integrated via a Machine Learning-based Ensemble Classification framework, enabling a unified and comprehensive analysis of the intricate information encoded within the data. 2. Implementing and rigorously benchmarking intra-sample normalisation methods to heighten their relevance within clinical settings. 3. Thoroughly assessing its efficacy across independent test sets to ascertain its robustness and potential utility. Using ten datasets from several studies comprising three different sources of biological material, we first show that while the best-performing normalisation methods depend strongly on the dataset and coupled Machine Learning method, the rather simple Counts Per Million method is generally very robust, showing comparable performance to cross-sample methods. Subsequently, we demonstrate that the innovative biofeature types introduced in this study, such as the Fraction of Canonical Transcript, harbour complementary information. Consequently, their inclusion consistently enhances prediction power compared to models relying solely on gene expression-based biofeatures. Finally, we demonstrate that the workflow is robust on completely independent datasets, generally from different labs and/or different protocols. Taken together, the workflow presented here outperforms generally employed methods in prediction accuracy and may hold potential for clinical diagnostics application due to its specific design.

Is non-medical use normal? Normalisation, medicalisation and pharmaceutical consumption

The theory of the normalisation of youth drug use in advanced capitalist societies has had an enduring legacy in contemporary drug scholarship. While the literature on the normalisation of 'illicit' drugs is well developed, less has been written about application of the theory to emerging discourse of pharmaceutical 'abuse', and how this might necessitate different thinking around what can be considered normal consumption. Pharmaceuticals are not directly associated with criminality, and their use does not traditionally attract stigma. In fact, social science scholarship has illustrated how many substances deemed illicit are normalised in the context of an ever-growing set of medical treatments. This paper explores the assumptions about legality, sociality and pleasure which sit behind the drug normalisation thesis, by reflecting on the relevance of drug normalisation in relation to pharmaceuticals, as well as examining scholarship on the medicalisation of society and qualitative research on non-medical use to illustrate the parallel processes of normalisation that apply to pharmaceuticals. The paper argues that questions of normalisation in relation to pharmaceutical use require a deeper engagement with the normative expectations we attach to pleasure, consumption and medicine, and the way this is structured by proximity to medical authority, whiteness and middle-classness.

Normalisation of SARS-CoV-2 concentrations in wastewater: The use of flow, electrical conductivity and crAssphage

Over the course of the Corona Virus Disease-19 (COVID-19) pandemic in 2020-2022, monitoring of the severe acute respiratory syndrome coronavirus 2 ribonucleic acid (SARS-CoV-2 RNA) in wastewater has rapidly evolved into a supplementary surveillance instrument for public health. Short term trends (2 weeks) are used as a basis for policy and decision making on measures for dealing with the pandemic. Normalisation is required to account for the dilution rate of the domestic wastewater that can strongly vary due to time- and location-dependent sewer inflow of runoff, industrial discharges and extraneous waters. The standard approach in sewage surveillance is normalisation using flow measurements, although flow based normalisation is not effective in case the wastewater volume sampled does not match the wastewater volume produced. In this paper, two alternative normalisation methods, using electrical conductivity and crAssphage have been studied and compared with the standard approach using flow measurements. For this, a total of 1116 24-h flow-proportional samples have been collected between September 2020 and August 2021 at nine monitoring locations. In addition, 221 stool samples have been analysed to determine the daily crAssphage load per person. Results show that, although crAssphage shedding rates per person vary greatly, on a population-level crAssphage loads per person per day were constant over time and similar for all catchments. Consequently, crAssphage can be used as a quantitative biomarker for populations above 5595 persons. Electrical conductivity is particularly suitable to determine dilution rates relative to dry weather flow concentrations. The overall conclusion is that flow normalisation is necessary to reliably determine short-term trends in virus circulation, and can be enhanced using crAssphage and/or electrical conductivity measurement as a quality check.

Papyrus: a large-scale curated dataset aimed at bioactivity predictions

With the ongoing rapid growth of publicly available ligand-protein bioactivity data, there is a trove of valuable data that can be used to train a plethora of machine-learning algorithms. However, not all data is equal in terms of size and quality and a significant portion of researchers' time is needed to adapt the data to their needs. On top of that, finding the right data for a research question can often be a challenge on its own. To meet these challenges, we have constructed the Papyrus dataset. Papyrus is comprised of around 60 million data points. This dataset contains multiple large publicly available datasets such as ChEMBL and ExCAPE-DB combined with several smaller datasets containing high-quality data. The aggregated data has been standardised and normalised in a manner that is suitable for machine learning. We show how data can be filtered in a variety of ways and also perform some examples of quantitative structure-activity relationship analyses and proteochemometric modelling. Our ambition is that this pruned data collection constitutes a benchmark set that can be used for constructing predictive models, while also providing an accessible data source for research.

A review and critical assessment of sedimentary metal indices used in determining the magnitude of anthropogenic change in coastal environments

The current critical review examines the application of 11 frequently used sedimentary metal indices in their ability to accurately assess the magnitude of human-induced change (enrichment) in the highly vulnerable and intensely developed coastal environment. The plethora and rapidly increasing number of sedimentary metal indices should, if not derived for special purposes, produce a consistent assessment on the basis that they use the same suite of metals and concentrations. Inconsistent numerical results produced by different index formulations should, when combined with their associated classification scheme, produce a common assessment of environmental condition. However, such a consistent outcome is seldom observed. Significant differences in assessment results are partly due to the historical evolution of indices and to the extraordinary diversity of background and reference values and materials being applied to account for pre-anthropogenic metal levels and confounding due to variable sediment characteristics. Size-normalised sample and background metal data used in the mCd and MEQ indices do not require reference values to account for textural variability and provide a quasi-direct measurement of enrichment with minimal computation (simple division). These priority indices should be combined into a single index (Enrichment Quotient, EQ). Results produced by the EF index were strongly correlated to mCd and MEQ and provide a similar classification and is recommended if normalised data are unavailable. Other indices assessed (MPI, PI, mPI, SEF, Igeo, PLI and Cf, original and current) provided a range of results, which either over- or under-estimated enrichment. The confusion concerning the choice and application of background and reference values in the assessment process is reviewed and their use in local and global assessment is clarified. Single- and combined-metal evaluations are recommended to provide detailed, local and more comprehensive assessments, respectively.

Follow, filter, filler? Social media usage and cosmetic procedure intention, acceptance, and normalization among young adults

Today, young people spend much of their lives online where they encounter abundant appearance-focused content. In light of the important role that social media platforms like Instagram play in young people's attitudes towards the cosmetic surgery industry, this study investigates passive and active social media usage in relation to young adults' perceptions of cosmetic procedures. In a cross-sectional survey study among 470 Instagram users aged 18-25 years (M_age = 21.00, SD_age = 2.26), young adults indicated a low cosmetic procedure intention themselves, but overestimated the prevalence of cosmetic procedures undertaken by others. Considering passive social media use, young adults who follow influencers who had undergone cosmetic procedures reported higher intentions to have cosmetic procedures themselves, and following influencers who had not undergone procedures was related to lower intentions. In terms of active social media usage, frequency of Instagram posting was generally insignificant in relation to acceptance of and intention to undergo cosmetic procedures. Yet, those who used filters to edit pictures more frequently reported increased cosmetic procedure acceptance and intention. Overall, this paper offers a nuanced perspective on the relation between young adults' perceptions of cosmetic procedures and their social media behaviors, highlighting the importance of specific appearance-oriented social media usage.

Energy cost of gait in children and the effect of speed, age, and body size

BACKGROUND

Energy cost (EC) of comfortable walking is often used in clinical evaluation of children with altered gait function. EC is presented as energy expenditure per kg bodyweight per meter, either in total (grossEC) or in addition to resting energy expenditure (netEC). GrossEC is considered more reliable and netEC less affected by between-subject variations in speed, age, and body size. However, the effect of the individual child's speed on EC is rarely considered, while altered gait function may affect both speed and EC.

RESEARCH QUESTION

To what extent are grossEC and netEC affected by within-subject variation in speed and between-subject variations in speed, age, and body size?

METHODS

Forty-two typically developing children (7-15 y) were included in this cross-sectional study. Age, height, and bodyweight were obtained. Breath-to-breath gas-exchange measures of VO₂ and VCO₂ were conducted during rest and five over-ground gait conditions: walking at slow, comfortable, and fast speed, jogging and running. All conditions lasted 3-5 min. Body surface area, non-dimensional speed, grossEC, and netEC were calculated. Regression analyses and mixed model analyses were conducted to explain the effect of speed, age, and body size on variations in EC.

RESULTS

GrossEC showed a non-significant, concave up relation to within-subject variation in speed, with a minimum around comfortable/fast walking speed. NetEC had a strong positive linear relation to within-subject variation in speed. For each gait condition, grossEC was more affected by between-subject variations in speed, age, and body size compared to netEC. However, the effect of age and body size was not eliminated for netEC but was quadratic.

SIGNIFICANCE

Although normalised to speed and bodyweight, grossEC and netEC are still affected by those factors. However, they are affected differently for within- and between-subject variations. This must be considered when interpreting EC in children in relation to gait function.

Motivators of impulsivity to smoke waterpipe tobacco among Nigerian youth who smoke waterpipe tobacco: the moderating role of social media normalisation of waterpipe tobacco

Background

Impulsivity is a formidable cause of waterpipe tobacco smoking among youth, however, it is understudied among African youth. Using PRIME behavioural theory, this study aimed to develop a model that examines the motivators of impulsivity to smoke waterpipe tobacco in linkage to the moderating role of social media normalisation of waterpipe tobacco, specifically among youth in Nigeria who smoke waterpipe tobacco.

Methods

Data were drawn from 695 respondents who smoke waterpipe tobacco across six Nigerian universities in the South-West zone using the chain-referral sampling procedure. Descriptive analyses of the obtained data were carried out using the Statistical Package for Social Sciences (SPSS) version 25. The constructs in the developed model were validated through Partial Least Squares Structural Equation Modelling (PLS-SEM) in SmartPLS version 3.

Results

Among Nigerian youth who smoke waterpipe tobacco, intention (β = 0.442, P < 0.001) was the strongest motivator of impulsivity to smoke waterpipe tobacco as compared to positive evaluations (β = 0.302, P < 0.001). In addition, social media normalisation of waterpipe tobacco acted as a moderator that strengthened the relationship between intention and impulsivity (β = 0.287, P < 0.01), as well as, between positive evaluations and impulsivity (β = 0.186, P < 0.01) among youth.

Conclusion

Intention greatly instigates Nigerian youth’s impulsivity to smoke waterpipe tobacco, and social media normalisation of waterpipe tobacco also considerably increases their impulsivity to smoke waterpipe tobacco. Youth-focused educational waterpipe tobacco cessation-oriented programmes that utilise diverse constructive-based learning approaches like illustrative learning and counselling, can help to enlighten and encourage Nigerian youth on the importance of shunning the desirability to smoke waterpipe tobacco.

Young people in Australia discuss strategies for preventing the normalisation of gambling and reducing gambling harm

Background

The normalisation of gambling for young people has received considerable recent attention in the public health literature, particularly given the proliferation of gambling marketing aligned with sport. A range of studies and reports into the health and wellbeing of young people have recommended that they should be consulted and engaged in developing public health policy and prevention strategies. There are, however, very few opportunities for young people to have a say about gambling issues, with little consideration of their voices in public health recommendations related to gambling. This study aimed to address this gap by documenting young people’s perceptions about strategies that could be used to counter the normalisation of gambling and prevent gambling related harm.

Methods

This study took a critical qualitative inquiry approach, which acknowledges the role of power and social injustice in health issues. Qualitative interviews, using a constructivist approach, were conducted with 54 young people (11–17 years) in Australia. Reflexive thematic analysis was used to interpret the data.

Results

Five overall strategies were constructed from the data. 1) Reducing the accessibility and availability of gambling products; 2) Changing gambling infrastructure to help reduce the risks associated with gambling engagement; 3) Untangling the relationship between gambling and sport; 4) Restrictions on advertising; and 5) Counter-framing in commercial messages about gambling.

Conclusions

This study demonstrates that young people have important insights and provide recommendations for addressing factors that may contribute to the normalisation of gambling, including strategies to prevent gambling related harm. Young people hold similar views to public health experts about strategies aimed at de-normalising gambling in their local communities and have strong opinions about the need for gambling to be removed from sport.

Mental health status of medical staff in Xinjiang Province of China based on the normalisation of COVID-19 epidemic prevention and control

INTRODUCTION

The 2019 coronavirus disease (COVID-19) pandemic has burdened and threatened the psychological health of people around the world, especially those of front-line medical staff. This study aimed to explore the mental-health status and its associated factors amongst the medical workforce of Xinjiang province under the normalisation of the COVID-19 epidemic prevention and control.

METHODS

A total of 408 medical staff were recruited from February 20 to March 10, 2021. Symptom Checklist 90 (SCL-90) scale, Social support Scale, and Simplified Coping-Style Questionnaire were applied to assess their mental-health status and stress-coping tendency. Descriptive analyses, welch's T-test, chi-square test, and binary logistic regression were used to analyse the data.

RESULTS

The prevalence of mental-health problems was 20.25% (80/395) amongst the surveyed medical staff, and their total symptom mean score (1.31 ± 0.40) was lower than that of the general population (1.44 ± 0.43). Logistic regression analysis revealed that nurse, individual with poor health condition, those who lived with their elderly parents at home, those receiving less social support, and those with a negative stress-coping style were more likely to show psychological problems.

CONCLUSION

More attention should be paid to the mental state of the medical workforce during the COVID-19 pandemic. The government and professional institutes should facilitate social supportive activities and essential counselling services to help strengthen the psychological resilience of medical staff. Additionally, it is necessary for health administration committee and hospitals to make COVID-19 prevention practice guides and risk communication principles for improving the mental health of the front-line medical staff.

Building knowledge of university campus population dynamics to enhance near-to-source sewage surveillance for SARS-CoV-2 detection

Wastewater surveillance has been widely implemented for monitoring of SARS-CoV-2 during the global COVID-19 pandemic, and near-to-source monitoring is of particular interest for outbreak management in discrete populations. However, variation in population size poses a challenge to the triggering of public health interventions using wastewater SARS-CoV-2 concentrations. This is especially important for near-to-source sites that are subject to significant daily variability in upstream populations. Focusing on a university campus in England, this study investigates methods to account for variation in upstream populations at a site with highly transient footfall and provides a better understanding of the impact of variable populations on the SARS-CoV-2 trends provided by wastewater-based epidemiology. The potential for complementary data to help direct response activities within the near-to-source population is also explored, and potential concerns arising due to the presence of heavily diluted samples during wet weather are addressed. Using wastewater biomarkers, it is demonstrated that population normalisation can reveal significant differences between days where SARS-CoV-2 concentrations are very similar. Confidence in the trends identified is strongest when samples are collected during dry weather periods; however, wet weather samples can still provide valuable information. It is also shown that building-level occupancy estimates based on complementary data aid identification of potential sources of SARS-CoV-2 and can enable targeted actions to be taken to identify and manage potential sources of pathogen transmission in localised communities.

The Gambling Behaviour and Attitudes to Sports Betting of Sports Fans

Survey responses from a sample of nearly 15,000 Australian sports fans were used to study the determinants of: (i) gambling behaviour, including if a person does gamble and the type of gambling engaged with; (ii) the number of sports and non-sports bets made over a 12-month period; and (iii) attitudes towards betting on sports. The probability of betting on sports decreased with increasing age and was lower for women and people with a university education. This gender difference varied with age, with the greatest difference found among the young. Similar effects were observed for the number of sports bets made, which declined with age. The gender difference in the number of sports bets also varied with age with the greatest difference found among the young arising from the high propensity of young men to bet on sports. Attitudes to sports betting were also analysed, with a key finding that, within friendship circles, the views that sports betting is perceived as harmless, common and very much a part of enjoying sports were stronger among young men. These permissive attitudes were stronger among people who bet on sports and those who bet on sports more frequently. The analysis of sports fans provides insights into the characteristics of the target market most likely to bet on sports, which can be used to inform public health initiatives and harm reduction campaigns.

Scale-up of prevention programmes: sustained state-wide use of programme delivery software is explained by normalised self-organised adoption and non-adoption

Background

Population-level health promotion is often conceived as a tension between “top-down” and “bottom-up” strategy and action. We report behind-the-scenes insights from Australia’s largest ever investment in the “top-down” approach, the $45m state-wide scale-up of two childhood obesity programmes. We used Normalisation Process Theory (NPT) as a template to interpret the organisational embedding of the purpose-built software designed to facilitate the initiative. The use of the technology was mandatory for evaluation, i.e. for reporting the proportion of schools and childcare centres which complied with recommended health practices (the implementation targets). Additionally, the software was recommended as a device to guide the implementation process. We set out to study its use in practice.

Methods

Short-term, high-intensity ethnography with all 14 programme delivery teams across New South Wales was conducted, cross-sectionally, 4 years after scale-up began. The four key mechanisms of NPT (coherence/sensemaking, cognitive participation/engagement, collective action and reflexive monitoring) were used to describe the ways the technology had normalised (embedded).

Results

Some teams and practitioners embraced how the software offered a way of working systematically with sites to encourage uptake of recommended practices, while others rejected it as a form of “mechanisation”. Conscious choices had to be made at an individual and team level about the practice style offered by the technology—thus prompting personal sensemaking, re-organisation of work, awareness of choices by others and reflexivity about professional values. Local organisational arrangements allowed technology users to enter data and assist the work of non-users—collective action that legitimised opposite behaviours. Thus, the technology and the programme delivery style it represented were normalised by pathways of adoption and non-adoption. Normalised use and non-use were accepted and different choices made by local programme managers were respected. State-wide, implementation targets are being reported as met.

Conclusion

We observed a form of self-organisation where individual practitioners and teams are finding their own place in a new system, consistent with complexity-based understandings of fostering scale-up in health care. Self-organisation could be facilitated with further cross-team interaction to continuously renew and revise sensemaking processes and support diverse adoption choices across different contexts.

Association between community average body mass index and perception of overweight

Some evidence indicates under-perception of overweight is associated with lower levels of weight loss. This might be due to 'visual normalisation' of overweight through comparisons made in communities where average body mass index (BMI) is high, resulting in under-perception of overweight, which in turn, may protect against negative weight-related self-perceptions and/or reduce motivation to lose weight. Evidence in support of this hypothesis was found initially in a precision-weighted multilevel logistic regression analysis of 3729 overweight Australians aged >18 y, after adjusting for age, sex and area-level disadvantage. Participants whose BMI was -1 kg/m² or less than the community mean BMI had lower odds of weight-related dissatisfaction (OR = 0.64, 95%CI = 0.51-0.80) and perceived overweight (OR = 0.56, 95%CI = 0.45-0.70), compared with peers whose BMI was within ± 1 kg/m² of the community mean. Moreover, participants whose BMI was 1 kg/m² or greater than the community mean BMI had higher odds of weight-related dissatisfaction (OR = 1.97, 95%CI = 1.69-2.30) and perceived overweight (OR = 2.81, 95%CI = 2.41-3.28) when compared to the same reference group. These findings were consistent for men and women; however, they were attenuated towards the null and rendered statistically insignificant after adjustment for personal BMI. Overall, these results indicate that among adults who are overweight, personal BMI, rather than the relative difference between personal and community BMI, is the stronger determinant of weight-related perception and satisfaction.

Coping strategies and perceived barriers of women hospitality workplace employees to sexual harassment in Bahir Dar city, Ethiopia: a grounded theory approach

Background

Coping depicts how people detect, appraise, deal with, and learn from stressful encounters. Applying preferred coping strategies in various situations makes the issue a persistent agenda in hospitality workplaces, where women are unduly victims of sexual harassment. Thus, this study aimed to develop a context specific and data-driven coping strategy framework and barriers to coping strategy mechanisms for sexual harassment victimisation against women working in hospitality workplaces.

Methods

A qualitative, grounded theory approach was used. Data were collected from female employees, managers, cashiers, and customers. Semi-structured focus-group discussions and in-depth interview guides were employed. A constant comparative approach was used to describe the meanings and summarise the data. Data were coded, categorised, and networks were visualised using the ATLAS ti version 8.4.24 software package.

Results

In this study, six focus group discussions, ten in-depth interviews, and thirteen key informant interviews were conducted. The provided context specific coping strategic framework consists of four strictly interconnected dimensions with corresponding barriers practised by female hospitality employees. These were normalisation, engagement, help-seeking, and detachment. The normalisation dimension encompasses silence, acceptance, denial, refusal, grief, and tolerance. Confrontation, negotiation, retaliation/threatening, and discrimination of the perpetrators were included in the engagement dimension. Elements such as discussing with friends, complaining with supervisors, consulting professionals, and accusing perpetrators were in the help-seeking dimension. Lastly, job-hopping, job withdrawal, work withdrawal, and distancing were in the detachment dimension. Some barriers deterred all dimensions, some factors facilitated normalisation, and some adverse outcomes ended the engagement dimension.

Conclusion

Our study demonstrated that the coping capacities of sexual harassment among female hospitality employees have been apparent, providing space for stakeholders to intervene. Our new coping strategy framework can serve as a valuable guide for designing context-specific interventions. These interventions could help women and stakeholders prevent sexual harassment, decrease barriers, and alleviate these effects.

protGear: A protein microarray data pre-processing suite

Protein microarrays are versatile tools for high throughput study of the human proteome, but systematic and non-systematic sources of bias constrain optimal interpretation and the ultimate utility of the data. Published guidelines to limit technical variability whilst maintaining important biological variation favour DNA-based microarrays that often differ fundamentally in their experimental design. Rigorous tools to guide background correction, the quantification of within-sample variation, normalisation, and batch correction specifically for protein microarrays are limited, require extensive investigation and are not centrally accessible.

Here, we develop a generic one-stop-shop pre-processing suite for protein microarrays that is compatible with data from the major protein microarray scanners. Our graphical and tabular interfaces facilitate a detailed inspection of data and are coupled with supporting guidelines that enable users to select the most appropriate algorithms to systematically address bias arising in customized experiments. The localization and distribution of background signal intensities determine the optimal correction strategy. A novel function overcomes the limitations in the interpretation of the coefficient of variation when signal intensities are at the lower end of the detection threshold. We demonstrate essential considerations in the experimental design and their impact on a range of algorithms for normalization and minimization of batch effects.

Our user-friendly interactive web-based platform eliminates the need for prowess in programming. The open-source R interface includes illustrative examples, generates an auditable record, enables reproducibility, and can incorporate additional custom scripts through its online repository. This versatility will enhance its broad uptake in the infectious disease and vaccine development community.

Superimposing hip extension on knee flexion evokes higher activation in biceps femoris than knee flexion alone

Hamstring muscle function during knee flexion has been linked to hamstring injury and performance. However, it is unclear whether knee flexion alone (KF) requires similar hamstring electromyography (EMG) activity pattern to simultaneous hip extension and knee flexion (HE-KF), a combination that occurs in the late swing phase of sprinting. This study examined whether HE-KF maximal voluntary isometric contraction (MVIC) evokes higher (EMG) activity in biceps femoris long head (BFlh) and semitendinosus (ST) than KF alone. Effects of shank rotation angles were also tested. Twenty-one males performed the above-mentioned MVICs while EMG activity was measured along ST and BFlh. Conditions were compared using a one-way mixed functional ANOVA model under a fully Bayesian framework. Higher EMG activity was found in HE-KF in all shank rotation positions than in KF in the middle region of BFlh (highest in the 9th channel, by 0.022 mV [95%CrI 0.014 to 0.030] in neutral shank position). For ST, this was only observed in the neutral shank position and in the most proximal channel (by 0.013 mV [95%CrI 0.001 to 0.025]). We observed muscle- and region-specific responses to HE-KF. Future studies should examine whether hamstring activation in this task is related to injury risk and sprint performance.

Normalising the "new normal": Changing tech-driven work practices under pandemic time pressure

The COVID-19 pandemic has had massive implications for the nature of work and the role technology plays in the workplace. Organisations have been forced into rapid 'big bang' introduction of technology and 'tech-driven' practices in an unprecedented and time pressured manner. In many cases there has been little training or reflection on how the practices and associated technology should be introduced and integrated or adapted to suit the new workplace context. We argue that there is a need for a more reflective 'normalisation' of work practices and the role technology plays. The paper draws on normalisation process theory (NPT) and its underlying components of cohesion, cognitive participation, collective action and reflexive monitoring. As an exemplar, we focus on the changing nature of work and adoption of remote working practices. The paper uses NPT to examine current thinking and approaches and offering some guidelines to inform research and practice.

The VE-Cadherin/β-catenin signalling axis regulates immune cell infiltration into tumours

Vascular normalisation, the process that reverses the structural and functional abnormalities seen in tumour-associated vessels, is also accompanied by changes in leucocyte trafficking. Our previous studies have shown the normalisation effects of the agent CD5-2 which acts to stabilise VE-Cadherin leading to increased penetration of CD8⁺ T cells but decreased infiltration of neutrophils (CD11b⁺Gr1^hi) into tumour parenchyma. In the present study, we demonstrate that VE-Cadherin stabilisation through CD5-2 treatment of purified endothelial cells (ECs) results in a similar leucocyte-selective regulation of transmigration, suggesting the existence of an endothelial specific intrinsic mechanism. Further, we show by RNA sequencing (RNA-seq)-based transcriptomic analysis, that treatment of ECs with CD5-2 regulates chemokines known to be involved in leucocyte transmigration, including upregulation of CCL2 and CXCL10 that facilitate CD8⁺ T cell transmigration. Both in vitro and in vivo mechanistic studies revealed that the increased CCL2 expression was dependent on expression of VE-Cadherin and downstream activation of the AKT/GSK3β/β-catenin/TCF4 signalling pathway. CD5-2 treatment also contributed to the reorganisation of the cytoskeleton, inducing reorganisation of stress fibres to circumferential actin, which previously has been described as associated with the stabilisation of the endothelial barrier, and amplification of the transcellular migration of CD8⁺ T cells. Thus, we propose that promotion of endothelial junctional integrity during vascular normalisation not only inhibits vascular leak but also resets the endothelial dependent regulation of immune cell infiltration.

PAWER: protein array web exploreR

Background

Protein microarray is a well-established approach for characterizing activity levels of thousands of proteins in a parallel manner. Analysis of protein microarray data is complex and time-consuming, while existing solutions are either outdated or challenging to use without programming skills. The typical data analysis pipeline consists of a data preprocessing step, followed by differential expression analysis, which is then put into context via functional enrichment. Normally, biologists would need to assemble their own workflow by combining a set of unrelated tools to analyze experimental data. Provided that most of these tools are developed independently by various bioinformatics groups, making them work together could be a real challenge.

Results

Here we present PAWER, the online web tool dedicated solely to protein microarray analysis. PAWER enables biologists to carry out all the necessary analysis steps in one go. PAWER provides access to state-of-the-art computational methods through the user-friendly interface, resulting in publication-ready illustrations. We also provide an R package for more advanced use cases, such as bespoke analysis workflows.

Conclusions

PAWER is freely available at https://biit.cs.ut.ee/pawer.

Sediment metal enrichment and ecological risk assessment of ten ports and estuaries in the World Harbours Project

Ten global harbours were assessed for sediment quality by quantifying the magnitude of anthropogenic change and ecological risk. Anthropogenic change (enrichment) was high for Derwent River and Sydney estuary, moderate for Santander Harbour, Rio de Janeiro and Dublin Port, slight for Hong Kong, minimal for Darwin. All 10 enrichment indices used showed similar results. Derwent River sediment was rated at high ecological risk, followed by Sydney and Santander estuaries with moderate risk. Auckland and Darwin sediments exhibited minimal ecological risk and sediment in the remaining harbours (Dublin, Hong Kong, Ravenna, Ria de Vigo and Rio de Janeiro) were assessed at slight ecological risk. The extraordinary variety of environments and types/quantities/qualities of data investigated resulted in as much a critique and development of methodology, as an assessment of human impact, including unique techniques for elemental normalisation and contaminant classification. Recommendations for an improved technical framework for sediment quality assessment are provided.

The Demands of Beauty: Editors' Introduction

This article introduces a Special Issue comprising four papers emerging from the Beauty Demands Network project, and maps key issues in the beauty debate. The introduction first discusses the purpose of the Network; to consider the changing demands of beauty across disciplines and beyond academia. It then summarises the findings of the Network workshops, emphasising the complex place of notions of normality, and the different meanings and functions attached to ‘normal’ in the beauty context. Concerns are raised here about the use of normal to justify and motivate engaging in beauty practices such as cosmetic surgery and ‘non-invasive’ procedures. Other workshop findings included the recognition of beauty as increasingly a global value rather than a culturally distinct ideal, and the understanding that there is no clear distinction between beauty practices that are considered standard and those that are considered extreme. These themes, especially the concerns around understanding of normal, are reflected in the recommendations made by the Network in its Briefing Paper, which are presented next in this introduction. A further theme picked up by these recommendations is the extent to which individuals who are not traditionally vulnerable may be so in the beauty context. Finally, the introduction highlights the key matters covered in the four papers of the Special Issue: regulatory concerns around cosmetic surgery tourism; the impact of digitally altered images from psychological and philosophical perspectives; the ethics of genetic selection for fair skin; and the attraction and beauty of the contemporary athletic body.

Study protocol to investigate the efficacy of normalisation of Advance Care Planning (ACP) for people with chronic diseases in acute and community settings: a quasi-experimental design

BACKGROUND

Advanced care planning (ACP) is a process that involves thinking about what medical care one would like should individuals be seriously ill and cannot communicate decisions about treatment for themselves. The literature indicates that ACP leads to increased satisfaction from both patients and healthcare professionals. Despite the well-known benefits of ACP, it is still underutilised in Australia.

METHODS

The aim of this study is to investigate the effects of normalising ACP in acute and community settings with the use of specially trained normalisation agents. This is a quasi-experimental study, involving 16 sites (8 intervention and 8 control) in two health districts in Australia. A minimum of total 288 participants will be recruited (144 intervention, 144 control). We will train four registered nurses as normalisation agents in the intervention sites, who will promote and facilitate ACP discussions with adult patients with chronic conditions in hospital and community settings. An audit of the prevalence of ACP and Advanced Care Directives (ACDs) will be conducted before and after the 6-month intervention period at the 16 sites to assess the effects of the ACP service delivered by these agents. We will also collect interview and survey data from patients and families who participate, and healthcare professionals who are involved in this service to capture their experiences with ACP.

DISCUSSION

This study will potentially contribute to better patient outcomes with their health care services. Completion of ACDs will allow patients to express their wishes for care and receive the care that they wish for, as well as ease their family from the burden of making difficult decisions. The study will contribute to development of a new best practice model to normalise ACP that is sustainable and transferable in the processes of: 1) initiation of conversation; 2) discussion of important issues; 3) documentation of the wishes; 4) storage of the documented wishes; and 5) access and execution of the documented wishes. The study will generate new evidence on the challenges, strategies and benefits of normalising ACP into practice in acute and community settings.

TRIAL REGISTRATION

This project has been approved by the Hunter New England Human Research Ethics Committee (Approval No. 17/12/13/4.16). It has also been retrospectively registered on 3 October 2018 with the Australian New Zealand Clinical Trials Registry (Trial ID: ACTRN12618001627246 ). This study will operate in accordance with the National Health and Medical Research Council's National Statement on Ethical Conduct in Human Research (2007) and the CPMP/ICH Note for Guidance on Good Clinical Practice.

Soil quality index: Exploring options for a comprehensive assessment of land use impacts in LCA

Impacts associated with land use are increasingly recognized as important aspects to consider when conducting Life Cycle Assessment (LCA). Across the existing models accounting for land use activities in life cycle impact assessment, a balance is yet to be found between complexity and comprehensiveness on one hand, and applicability on the other hand. This work builds on the LANd use indicator value CAlculation (LANCA^®) model, assessing the impacts of land use activities on five soil properties, and aims at developing an aggregated index to improve its applicability. First a statistical analysis is conducted, leading to the shortlisting of the four most significant soil quality indicators. Then two options for aggregating the selected indicators are presented: the soil quality index (SQI), based on linear aggregation, and the normalisation-based soil quality index (NSQI), where the aggregation process involves normalisation integrated into the characterisation step. Country-specific and global average characterisation factors (CFs) are calculated for 57 land use types considering both land occupation and land transformation interventions with the two suggested approaches. The two indices present similar ranking of land use types but the relative contribution of the separate indicators to the aggregated index varies according to the approach adopted. The differences between the aggregation approaches suggested are discussed, together with the limitations related to both the LANCA^® model and the aggregation approaches. This work represents a first step towards the widespread application of a comprehensive and robust land use model at midpoint level in LCA. Finally, a number of recommendations for the future development of the LANCA^® model and of the related soil quality models are provided.

A mixed linear modelling characterisation of gender and speed related changes in spatiotemporal and kinematic characteristics of gait across a wide speed range in healthy adults

In exploring the relationship between the kinematics of gait and speed of progression individual variation in patterns and gender differences have not always been adequately taken into account. In the current study mixed linear modelling was used to isolate changes with speed from those associated with individual variation and gender. Three-dimensional motion analysis of 20 participants (10M/10F, 25.7 ± 5.1 years) walking at a wide range of speeds (normalised speeds 0.10-0.55 ∼0.41-2.26 m/s) was recorded (775 walks). Spatiotemporal (speed, cadence, step length, percentage of single and double support) and kinematic characteristics (pelvis through ankle) were determined. Significant between participant differences were highlighted in both intercept and slope of relationships. In addition females exhibiting different peak pelvic tilt and obliquity, hip flexion and internal rotation and ankle dorsiflexion compared to males. Spatiotemporal parameters exhibited non-linear relationships with normalised speed (R²> 0.5). Kinematic features exhibited significant relationships with normalised speed, varying from linear to cubic, from very weak to strong in fit (0.010 > R²> 0.672). Mixed linear modelling highlighted gender dependent, speed related changes in addition to inter-individual variation. Gender and speed are both important determinants of gait patterns, however, individual variations remain.

Sexuality in the lives of people with intellectual disabilities: A meta-ethnographic synthesis of qualitative studies

BACKGROUND

The normalisation movement calls for more recognition of the sexual rights of people with intellectual disabilities to challenge classically paradoxical cultural beliefs: 'hypersexual' versus 'asexual'.

AIMS

This meta-ethnographic qualitative synthesis aimed to explore the voices of people with intellectual disabilities in regards to their experiences and perceptions of sexuality using a Coordinated Management of Meaning framework to derive new conceptual understandings of how their sexuality exists within multiple contexts.

METHODS AND PROCEDURES

A systematic literature search and quality assessment yielded 16 studies that met the inclusion criteria and were synthesised following the method of meta-ethnography.

OUTCOMES AND RESULTS

Four core themes were identified; 'Sociocultural Norms'; 'Under Others Power'; 'Sexual Identity' and 'Sexual Experience'.

CONCLUSIONS AND IMPLICATIONS

Application of the hierarchical Coordinated Management of Meaning model suggested caregivers contextual beliefs about people with intellectual disabilities' sexuality inhibited or facilitated positive expressions of sexuality over and above individual needs and desires. Rights-based cultural messages provided the only context that led to positive sexuality outcomes and research that explores sexuality within this context is much needed. The Coordinated Management of Meaning model identified by this research may act as a framework to support the reflective-practice of caregivers.

Spatiotemporal and kinematic characteristics of gait initiation across a wide speed range

BACKGROUND

Gait initiation can be performed at a range of speeds. Those with disability tend to use a slower speed compared to those without disability. In assessing the spatiotemporal and kinematic characteristics of gait initiation it is therefore important to consider the effects of speed on outcomes.

RESEARCH QUESTION

What is the effect of speed of performance on spatiotemporal and kinematic characteristics of gait initiation?

METHODS

Spatiotemporal and kinematic characteristics were measured across a wide range of speeds from very slow to very fast (normalised initiating leg (swing or SW limb) step speed 0.1-0.5) for 20 health adults (10 men/10 women, 22-44 years) using three-dimensional motion analysis of the first two steps of gait.

RESULTS

Mixed linear modelling of 295 walking trials indicated differences between individuals, sexes and strong non-linear relationships between normalised initiating leg step speed and cadence and step lengths (R² > 0.5). Particular characteristics of joint kinematics (maxima and minima for both initiating (SW) and contralateral limb (stance or ST limb)) demonstrated significant non-linear (squared, cubic and power law) changes with speed. Moderate to strong relationships were identified for sagittal plane pelvis, hip and knee kinematics as well as hip adduction (0.3 < R² < 0.7).

SIGNIFICANCE

Gait initiation spatiotemporal and kinematic characteristics were quantified across the maximum range of speeds achievable, providing comprehensive characterisation of changes with speed. Significant, non-linear changes with speed were identified, suggesting different strategies are employed to modify speed at low and high speeds. The highlighted changes with speed illustrate the importance of taking speed into account when comparing outcomes between healthy adults and those with pathology.

NiftyPET: a High-throughput Software Platform for High Quantitative Accuracy and Precision PET Imaging and Analysis

We present a standalone, scalable and high-throughput software platform for PET image reconstruction and analysis. We focus on high fidelity modelling of the acquisition processes to provide high accuracy and precision quantitative imaging, especially for large axial field of view scanners. All the core routines are implemented using parallel computing available from within the Python package NiftyPET, enabling easy access, manipulation and visualisation of data at any processing stage. The pipeline of the platform starts from MR and raw PET input data and is divided into the following processing stages: (1) list-mode data processing; (2) accurate attenuation coefficient map generation; (3) detector normalisation; (4) exact forward and back projection between sinogram and image space; (5) estimation of reduced-variance random events; (6) high accuracy fully 3D estimation of scatter events; (7) voxel-based partial volume correction; (8) region- and voxel-level image analysis. We demonstrate the advantages of this platform using an amyloid brain scan where all the processing is executed from a single and uniform computational environment in Python. The high accuracy acquisition modelling is achieved through span-1 (no axial compression) ray tracing for true, random and scatter events. Furthermore, the platform offers uncertainty estimation of any image derived statistic to facilitate robust tracking of subtle physiological changes in longitudinal studies. The platform also supports the development of new reconstruction and analysis algorithms through restricting the axial field of view to any set of rings covering a region of interest and thus performing fully 3D reconstruction and corrections using real data significantly faster. All the software is available as open source with the accompanying wiki-page and test data.

Determination of stable reference genes for RT-qPCR expression data in mechanistic pain studies on pig dorsal root ganglia and spinal cord

RNA expression levels for genes of interest must be normalised with appropriate reference or "housekeeping" genes that are stably expressed across samples and treatments. This study determined the most stable reference genes from a panel of 6 porcine candidate genes: beta actin (ACTB), beta-2-microglobulin (B2M), eukaryotic elongation factor 1 gamma-like protein (eEF-1), glyceraldehyde-3-phosphate dehydrogenase (GAPDH), succinate dehydrogenase complex subunit A (SDHA), Ubiquitin C (UBC) in sacral dorsal root ganglia and spinal cord samples collected from 16 tail docked pigs (2/3rds of tail amputated) 1, 4, 8 and 16weeks after tail injury (4 pigs/time point). Total RNA from pooled samples was measured by SYBRgreen real-time quantitative PCR. Cycle threshold values were analysed using geNorm, BestKeeper and NormFinder PCR analysis software. Average expression stability and pairwise variation values were calculated for each candidate reference gene. GeNorm analysis identified the most stable genes for normalisation of gene expression data to be GAPDH>eEF-1>UBC>B2M>ACTB>SDHA for dorsal root ganglia and ACTB>SDHA>UBC>B2M>GAPDH>eEF-1 for spinal cord samples. Expression stability estimates were verified by BestKeeper and NormFinder analysis. Expression stability varied between genes within and between tissues. Validation of most stably expressed reference genes was performed by normalisation of calcitonin gene related polypeptide beta (CALCB). The results show similar patterns of CALCB expression when the best reference genes selected by all three programs were used. GAPDH, eEF-1 and UBC are suitable reference genes for porcine dorsal root ganglia samples, whereas ACTB, SDHA and UBC are more appropriate for spinal cord samples.

Undesirable properties of the dimensionless normalisation for spatio-temporal variables

We used theory and empirical data to demonstrate three undesirable properties of the dimensionless normalisation technique for gait spatio-temporal parameters. Firstly, it may not fully remove the correlation between leg length and spatio-temporal parameters. Secondly, it induces spurious correlation among spatio-temporal parameters, which might obscure their true correlation structure. Thirdly, it induces spurious correlation with external covariates, which complicates further statistical modelling. Therefore, depending on the objectives, we propose alternatives. If the objective is to compare datasets but remove the confounding effect of leg length, residualisation may be an alternative, although the generalisability of the residualisation is less well established than dimensionless normalisation. If the objective is to build a regression model, the raw spatio-temporal parameters could be used with leg length, or a function of leg length, as an explicit regressor to avoid spurious correlation. If correlation is the objective, partial correlation can be used instead.

The importance of body mass normalisation for ultrasound measurement of the transversus abdominis muscle: The effect of age, gender and sport practice

BACKGROUND

Some studies have not considered body mass as a confounder in TrA analysis, which may have led to improper interpretation of results.

OBJECTIVES

To assess the differences in the effect of age, gender and physical activity between normalised for body mass and actual values of the TrA as well as to establish the effect of age, gender and physical activity on normalised for body mass TrA thickness in adolescents.

DESIGN

The study was a cross-sectional study conducted at selected primary and secondary schools, and colleges in the Silesian region of Poland.

METHOD

A real-time ultrasound was used to obtain images of the TrA muscle. Body mass normalisation for TrA thickness was performed with allometric scaling and the following equation: Allometric-scaled TrA = TrA thickness/body mass^0.61.

RESULTS

Analysis has shown that boys have significantly thicker muscle by 0.27 mm (95% CI 0.04-0.50) than girls, and those who practise sports have thicker muscle by 0.30 mm (95% CI 0.06-0.52) than non-active individuals. For allometric-scaled TrA, there were no significant effects (p > 0.50). There was a significant correlation between participants age and the actual value of the TrA (r = 0.42, p < 0.05). The correlation between age and allometric-scaled TrA was insignificant and close to zero (r = -0.006, p = 0.93).

CONCLUSIONS

An analysis of TrA thickness without body mass normalisation can deliver improper interpretation of study results. Thus, it is recommended in future researches to analyse TrA thickness measurement after normalisation rather than actual values. In the adolescent population, there is no effect of gender, age and physical activity on allometric-scaled TrA thickness.

Determination of sediment metal background concentrations and enrichment in marine environments - A critical review

'Background' is the concentration of metals in pristine sediment, unaltered by human activity and 'enrichment' is the extent present-day sediment metal concentrations exceed pre-anthropogenic levels (the magnitude of human-induced change). Background and enrichment are becoming more frequently used for management measures to bring sediment and the environment back to near-pristine levels. Of the six empirical methods reviewed for determining background (global values, pristine marine and fluvial sediments, catchment soils and rocks), the use of sedimentary cores has the greatest advantage. Most of the eight statistical methods reviewed are adversely affected by the polymodality and an absence of normality or log-normality, however robust regression procedures are most commonly used. Sorption hypothesis techniques require further development. Indices used to determine enrichment incorporate background levels (enrichment indices) or do not (contamination indices). Of the 20 indices reviewed, the New Nemerow Index and the Mean Enrichment Quotient rate highly in performance, based on 5 beneficial attributes assessed: use of background and normalised data, provision of thresholds, a classification scheme, and inclusion of multiple metals. Variance in background metal concentrations determined in the 43 global projects reviewed is surprisingly moderate, however regional variability may be considerable due to local catchment mineralisation. Chemical analysis of sediment should not include metals bound in the mineral matrix and weak acid extractions are advisable. The use of appropriate and effective indicators of environmental condition are critical to the protection and restoration of marine regions and ensuring that human activities are carried out in a sustainable manner to promote safe, healthy and productive ecosystems.

The influence of marketing on the sports betting attitudes and consumption behaviours of young men: implications for harm reduction and prevention strategies

Background

Gambling can cause significant health and social harms for individuals, their families, and communities. While many studies have explored the individual factors that may lead to and minimise harmful gambling, there is still limited knowledge about the broader range of factors that may contribute to gambling harm. There are significant regulations to prevent the marketing of some forms of gambling but comparatively limited regulations relating to the marketing of newer forms of online gambling such as sports betting. There is a need for better information about how marketing strategies may be shaping betting attitudes and behaviours and the range of policy and regulatory responses that may help to prevent the risky or harmful consumption of these products.

Methods

We conducted qualitative, semi-structured interviews with 50 Australian men (aged 20–37 years) who gambled on sports. We explored their attitudes and opinions regarding sports betting marketing, the embedding of marketing within sports and other non-gambling community environments, and the implications this had for the normalisation of betting.

Results

Our findings indicate that most of the environments in which participants reported seeing or hearing betting advertisements were not in environments specifically designed for betting. Participants described that the saturation of marketing for betting products, including through sports-based commentary and sports programming, normalised betting. Participants described that the inducements offered by the industry were effective marketing strategies in getting themselves and other young men to bet on sports. Inducements were also linked with feelings of greater control over betting outcomes and stimulated some individuals to sign up with more than one betting provider.

Conclusions

This research suggests that marketing plays a strong role in the normalisation of gambling in sports. This has the potential to increase the risks and subsequent harms associated with these products. Legislators must begin to consider the cultural lag between an evolving gambling landscape, which supports sophisticated marketing strategies, and effective policies and practices which aim to reduce and prevent gambling harm.

Comparison of pre-processing methodologies for Illumina 450k methylation array data in familial analyses

Background

Human methylome mapping in health and disease states has largely relied on Illumina Human Methylation 450k array (450k array) technology. Accompanying this has been the necessary evolution of analysis pipelines to facilitate data processing. The majority of these pipelines, however, cater for experimental designs where matched ‘controls’ or ‘normal’ samples are available. Experimental designs where no appropriate ‘reference’ exists remain challenging. Herein, we use data generated from our study of the inheritance of methylome profiles in families to evaluate the performance of eight normalisation pre-processing methods. Fifty individual samples representing four families were interrogated on five 450k array BeadChips. Eight normalisation methods were tested using qualitative and quantitative metrics, to assess efficacy and suitability.

Results

Stratified quantile normalisation combined with ComBat were consistently found to be the most appropriate when assessed using density, MDS and cluster plots. This was supported quantitatively by ANOVA on the first principal component where the effect of batch dropped from p < 0.01 to p = 0.97 after stratified QN and ComBat. Median absolute differences between replicated samples were the lowest after stratified QN and ComBat as were the standard error measures on known imprinted regions. Biological information was preserved after normalisation as indicated by the maintenance of a significant association between a known mQTL and methylation (p = 1.05e-05).

Conclusions

A strategy combining stratified QN with ComBat is appropriate for use in the analyses when no reference sample is available but preservation of biological variation is paramount. There is great potential for use of 450k array data to further our understanding of the methylome in a variety of similar settings. Such advances will be reliant on the determination of appropriate methodologies for processing these data such as established here.

Electronic supplementary material

The online version of this article (doi:10.1186/s13148-016-0241-2) contains supplementary material, which is available to authorized users.

An international comparability study on quantification of mRNA gene expression ratios: CCQM-P103.1

Measurement of RNA can be used to study and monitor a range of infectious and non-communicable diseases, with profiling of multiple gene expression mRNA transcripts being increasingly applied to cancer stratification and prognosis. An international comparison study (Consultative Committee for Amount of Substance (CCQM)-P103.1) was performed in order to evaluate the comparability of measurements of RNA copy number ratio for multiple gene targets between two samples. Six exogenous synthetic targets comprising of External RNA Control Consortium (ERCC) standards were measured alongside transcripts for three endogenous gene targets present in the background of human cell line RNA. The study was carried out under the auspices of the Nucleic Acids (formerly Bioanalysis) Working Group of the CCQM. It was coordinated by LGC (United Kingdom) with the support of National Institute of Standards and Technology (USA) and results were submitted from thirteen National Metrology Institutes and Designated Institutes. The majority of laboratories performed RNA measurements using RT-qPCR, with datasets also being submitted by two laboratories based on reverse transcription digital polymerase chain reaction and one laboratory using a next-generation sequencing method. In RT-qPCR analysis, the RNA copy number ratios between the two samples were quantified using either a standard curve or a relative quantification approach. In general, good agreement was observed between the reported results of ERCC RNA copy number ratio measurements. Measurements of the RNA copy number ratios for endogenous genes between the two samples were also consistent between the majority of laboratories. Some differences in the reported values and confidence intervals (‘measurement uncertainties’) were noted which may be attributable to choice of measurement method or quantification approach. This highlights the need for standardised practices for the calculation of fold change ratios and uncertainties in the area of gene expression profiling.

The centre of rotation of the shoulder complex and the effect of normalisation

Shoulder motions consist of a composite movement of three joints and one pseudo-joint, which together dictate the humerothoracic motion. The purpose of this work was to quantify the location of the centre of rotation (CoR) of the shoulder complex as a whole. Dynamic motion of 12 participants was recorded using optical motion tracking during coronal, scapular and sagittal plane elevation. The instantaneous CoR was found for each angle of elevation using helical axes projected onto the three planes of motion. The location of an average CoR for each plane was evaluated using digitised and anthropometric measures for normalisation. When conducting motion in the coronal, scapular, and sagittal planes, respectively, the coefficients for locating the CoRs of the shoulder complex are −61%, −61%, and −65% of the anterior–posterior dimension – the vector between the midpoint of the incisura jugularis and the xiphoid process and the midpoint of the seventh cervical vertebra and the eighth thoracic vertebra; 0%, −1%, and −2% of the superior–inferior dimension – the vector between the midpoint of the acromioclavicular joints and the midpoint of the anterior superior iliac spines; and 57%, 57%, and 78% of the medial–lateral dimension −0.129 times the height of the participant. Knowing the location of the CoR of the shoulder complex as a whole enables improved participant positioning for evaluation and rehabilitation activities that involve movement of the hand with a fixed radius, such as those that employ isokinetic dynamometers.

Selection of reference genes for diurnal and developmental time-course real-time PCR expression analyses in lettuce

BACKGROUND

Real-time quantitative polymerase chain reaction (RT-qPCR) analysis is a low cost and sensitive technique that is widely used to measure levels of gene expression. Selecting and validating appropriate reference genes for normalising target gene expression should be the first step in any expression study to avoid inaccurate results.

RESULTS

In this study, ten candidate genes were tested for their suitability for use as reference genes in diurnal and developmental timecourse experiments in lettuce. The candidate reference genes were then used to normalise the expression pattern of the FLOWERING LOCUS T (FT) gene, one of key genes involved in the flowering time pathway whose expression is known to vary throughout the day and at different stages of development. Three reference genes, LsPP2A-1 (PROTEIN PHOSPHATASE 2A-1), LsPP2AA3 (PROTEIN PHOSPHATASE 2A REGULATORY SUBUNIT A3) and LsTIP41 (TAP42-INTERACTING PROTEIN OF 41 kDa), were the most stably expressed candidate reference genes throughout both the diurnal and developmental timecourse experiments. In the developmental experiment using just LsPP2A-1 and LsTIP41 as reference genes would be sufficient for accurate normalisation, whilst in the diurnal experiment all three reference genes, LsPP2A-1, LsPP2AA3 and LsTIP41, would be necessary. The FT expression pattern obtained demonstrates that the use of multiple and robust reference genes for RT-qPCR expression analyses results in a more accurate and reliable expression profile.

CONCLUSIONS

Reference genes suitable for use in diurnal and developmental timecourse experiments in lettuce were identified and used to produce a more accurate and reliable analysis of lsFT expression levels than previously obtained in such timecourse experiments.

The importance of selecting the appropriate reference genes for quantitative real time PCR as illustrated using colon cancer cells and tissue

Quantitative real-time reverse-transcription polymerase chain reaction (RT-qPCR) remains the most sensitive technique for nucleic acid quantification. Its popularity is reflected in the remarkable number of publications reporting RT-qPCR data. Careful normalisation within RT-qPCR studies is imperative to ensure accurate quantification of mRNA levels. This is commonly achieved through the use of reference genes as an internal control to normalise the mRNA levels between different samples. The selection of appropriate reference genes can be a challenge as transcript levels vary with physiology, pathology and development, making the information within the transcriptome flexible and variable. In this study, we examined the variation in expression of a panel of nine candidate reference genes in HCT116 and HT29 2-dimensional and 3-dimensional cultures, as well as in normal and cancerous colon tissue. Using normfinder we identified the top three most stable genes for all conditions. Further to this we compared the change in expression of a selection of PKC coding genes when the data was normalised to one reference gene and three reference genes. Here we demonstrated that there is a variation in the fold changes obtained dependent on the number of reference genes used. As well as this, we highlight important considerations namely; assay efficiency tests, inhibition tests and RNA assessment which should also be implemented into all RT-qPCR studies. All this data combined demonstrates the need for careful experimental design in RT-qPCR studies to help eliminate false interpretation and reporting of results.

The importance of selecting the appropriate reference genes for quantitative real time PCR as illustrated using colon cancer cells and tissue

Quantitative real-time reverse-transcription polymerase chain reaction (RT-qPCR) remains the most sensitive technique for nucleic acid quantification. Its popularity is reflected in the remarkable number of publications reporting RT-qPCR data. Careful normalisation within RT-qPCR studies is imperative to ensure accurate quantification of mRNA levels. This is commonly achieved through the use of reference genes as an internal control to normalise the mRNA levels between different samples. The selection of appropriate reference genes can be a challenge as transcript levels vary with physiology, pathology and development, making the information within the transcriptome flexible and variable. In this study, we examined the variation in expression of a panel of nine candidate reference genes in HCT116 and HT29 2-dimensional and 3-dimensional cultures, as well as in normal and cancerous colon tissue. Using normfinder we identified the top three most stable genes for all conditions. Further to this we compared the change in expression of a selection of PKC coding genes when the data was normalised to one reference gene and three reference genes. Here we demonstrated that there is a variation in the fold changes obtained dependent on the number of reference genes used. As well as this, we highlight important considerations namely; assay efficiency tests, inhibition tests and RNA assessment which should also be implemented into all RT-qPCR studies. All this data combined demonstrates the need for careful experimental design in RT-qPCR studies to help eliminate false interpretation and reporting of results.

Identification of stable reference genes for quantitative PCR in cells derived from chicken lymphoid organs

Quantitative polymerase chain reaction (qPCR) is a powerful technique for quantification of gene expression, especially genes involved in immune responses. Although qPCR is a very efficient and sensitive tool, variations in the enzymatic efficiency, quality of RNA and the presence of inhibitors can lead to errors. Therefore, qPCR needs to be normalised to obtain reliable results and allow comparison. The most common approach is to use reference genes as internal controls in qPCR analyses. In this study, expression of seven genes, including β-actin (ACTB), β-2-microglobulin (B2M), glyceraldehyde-3-phosphate dehydrogenase (GAPDH), β-glucuronidase (GUSB), TATA box binding protein (TBP), α-tubulin (TUBAT) and 28S ribosomal RNA (r28S), was determined in cells isolated from chicken lymphoid tissues and stimulated with three different mitogens. The stability of the genes was measured using geNorm, NormFinder and BestKeeper software. The results from both geNorm and NormFinder were that the three most stably expressed genes in this panel were TBP, GAPDH and r28S. BestKeeper did not generate clear answers because of the highly heterogeneous sample set. Based on these data we will include TBP in future qPCR normalisation. The study shows the importance of appropriate reference gene normalisation in other tissues before qPCR analysis.

Use of a pre-analysis osmolality normalisation method to correct for variable urine concentrations and for improved metabolomic analyses

Metabolomics analyses of urine have the potential to provide new information on the detection and progression of many disease processes. However, urine samples can vary significantly in total solute concentration and this presents a challenge to achieve high quality metabolomic datasets and the detection of biomarkers of disease or environmental exposures. This study investigated the efficacy of pre- and post-analysis normalisation methods to analyse metabolomic datasets obtained from neat and diluted urine samples from five individuals. Urine samples were extracted by solid phase extraction (SPE) prior to metabolomic analyses using a sensitive nanoflow/nanospray LC-MS technique and the data analysed by principal component analyses (PCA). Post-analysis normalisation of the datasets to either creatinine or osmolality concentration, or to mass spectrum total signal (MSTS), revealed that sample discrimination was driven by the dilution factor of urine rather than the individual providing the sample. Normalisation of urine samples to equal osmolality concentration prior to LC-MS analysis resulted in clustering of the PCA scores plot according to sample source and significant improvements in the number of peaks common to samples of all three dilutions from each individual. In addition, the ability to identify discriminating markers, using orthogonal partial least squared-discriminant analysis (OPLS-DA), was greatly improved when pre-analysis normalisation to osmolality was compared with post-analysis normalisation to osmolality and non-normalised datasets. Further improvements for peak area repeatability were observed in some samples when the pre-analysis normalisation to osmolality was combined with a post-analysis mass spectrum total useful signal (MSTUS) or MSTS normalisation. Future adoption of such normalisation methods may reduce the variability in metabolomics analyses due to differing urine concentrations and improve the discovery of discriminating metabolites associated with sample source.

Drug use and social control: The negotiation of moral ambivalence

Illicit drugs occupy an ambivalent position in late modern society; one that revolves around the twin themes of pleasure and disapproval. Drawing on Freudian psychoanalysis and Eliasian sociology this article considers how people, particularly those who use drugs, negotiate such ambivalence. Patterns of drug use and associated attitudes are examined on the basis of the Crime Survey for England and Wales and a specialist survey of largely recreational drug users in the United Kingdom. Although illicit drugs have become increasingly familiar, their use is still widely thought to be harmful and morally dubious, creating a series of challenges for those who engage in such behaviour. Ambivalence among drug users is evident in an awareness of potential costs as well as benefits; a tendency to avoid more harmful substances; a general emphasis on moderation; and a desire to use less. Building on previous work, which highlights the role of neutralisations in sustaining drug using behaviour, particular attention is paid to users' judgements about how their levels of consumption compare with other users. The analysis identifies a tendency among users to downplay their relative levels of use, which, it is argued, serves to shield them from some of the imperatives that may lead to decisions to cut down. As such, normalisation is said to be an intra-personal as well inter-personal process. The article concludes by discussing the potential of web-based personalised feedback as a harm reduction approach.

Assay for estimating total bacterial load: relative qPCR normalisation of bacterial load with associated clinical implications

Relative microorganism abundance is a parameter describing biodiversity, referring to how common a bacterial species is within the total bacterial flora. Anal, rectal, skin, mucal, and respiratory swabs are typical clinical samples where knowledge of relative bacterial abundance might make distinction between asymptomatic carriers and symptomatic cases. Assays trying to measure total bacterial load are usually based on the amplification of universal segments of 16S rRNA genes. Previous assays were not adoptable to "direct" PCR protocols, and/or they were not compatible with hydrolysis-based detection. Using the latest summary of universal 16S sequence motifs present in literature and testing our design with 500 liquid and 50 formed stool samples, we illustrate the performance characteristics of a new 16S quantitative PCR (qPCR) assay, which addresses well-known technical problems, including a) positive priming reaction in the absence of intended target due to self-priming and/or mispriming of unintended targets; b) amplification bias due to nonoptimal primer/probe coverage; and c) too large amplicons for clinical qPCR. Stool swabs ranked into bins of different bacterial loads show significant correlation with threshold cycle values of our new assay. To the best of our knowledge, this is the first description of qPCR assay measuring individual differences of total bacterial load present in human stool.

[LAST-Q: Adaptation and normalisation in Quebec of the Language Screening Test]

The goal of the present study was to adapt and to establish normative data for the recently developed Language Screening Test (LAST; Flamand-Roze et al., 2011) in the French-Canadian population according to age and level of education. After an adaptation process, 100 French-Canadian speakers were evaluated with the LAST-Q. As expected, a perfect score of 15/15 was obtained for all high level education participants, and a score of 14/15 was obtained for all participants with a lowest level of education or aged 80 years or more. Thanks to this adaptation, LAST-Q can be used in acute patients in stroke unit in Quebec.

The stories we tell: qualitative research interviews, talking technologies and the 'normalisation' of life with HIV

Since the earliest days of the HIV/AIDS epidemic, talking about the virus has been a key way affected communities have challenged the fear and discrimination directed against them and pressed for urgent medical and political attention. Today, HIV/AIDS is one of the most prolifically and intimately documented of all health conditions, with entrenched infrastructures, practices and technologies--what Vinh-Kim Nguyen has dubbed 'confessional technologies'--aimed at encouraging those affected to share their experiences. Among these technologies, we argue, is the semi-structured interview: the principal methodology used in qualitative social science research focused on patient experiences. Taking the performative nature of the research interview as a talking technology seriously has epistemological implications not merely for how we interpret interview data, but also for how we understand the role of research interviews in the enactment of 'life with HIV'. This paper focuses on one crucial aspect of this enactment: the contemporary 'normalisation' of HIV as 'just another' chronic condition--a process taking place at the level of individual subjectivities, social identities, clinical practices and global health policy, and of which social science research is a vital part. Through an analysis of 76 interviews conducted in London (2009-10), we examine tensions in the experiential narratives of individuals living with HIV in which life with the virus is framed as 'normal', yet where this 'normality' is beset with contradictions and ambiguities. Rather than viewing these as a reflection of resistances to or failures of the enactment of HIV as 'normal', we argue that, insofar as these contradictions are generated by the research interview as a distinct 'talking technology', they emerge as crucial to the normative (re)production of what counts as 'living with HIV' (in the UK) and are an inherent part of the broader performative 'normalisation' of the virus.

Normalisation method can affect gluteus medius electromyography results during weight bearing exercises in people with hip osteoarthritis (OA): a case control study

Surface electromyography (sEMG) is used to assess muscle activation during therapeutic exercise, but data are significantly affected by inter-individual variability and requires normalisation of the sEMG signal to enable comparison between individuals. The purpose of this study was to compare two normalisation methods, a maximal method (maximum voluntary isometric contraction (MVIC)) and non-maximal peak dynamic method (PDM), on gluteus medius (GMed) activation using sEMG during three weight-bearing exercises in people with hip osteoarthritis (OA) and healthy controls. Thirteen people with hip OA and 20 controls performed three exercises (Squat, Step-Up, Step-Down). Average root-mean squared EMG amplitude based on MVIC and PDM normalisation was compared between groups for both involved and uninvolved hips using Mann-Whitney tests. Using MVIC normalisation, significantly higher normalised GMed EMG amplitudes were found in the OA group during all Step-up and down exercises on the involved side (p=0.02-0.001) and most of the Step exercises on the uninvolved side (p=0.03-0.04), but not the Squat (p>0.05), compared to controls. Using PDM normalisation, significant between-group differences occurred only for Ascending Squat (p=0.03) on the involved side. MVIC normalisation demonstrated higher inter-trial relative reliability (ICCs=0.78-0.99) than PDM (ICCs=0.37-0.84), but poorer absolute reliability using Standard Error of Measurement. Normalisation method can significantly affect interpretation of EMG amplitudes. Although MVIC-normalised amplitudes were more sensitive to differences between groups, there was greater variability using this method, which raises concerns regarding validity. Interpretation of EMG data is strongly influenced by the normalisation method used, and this should be considered when applying EMG results to clinical populations.

[Polynesian adaptation of the Mini-Mental State Examination]

This study aimed to develop and validate a Polynesian version of the MMSE (Mini-Mental State Examination). For this study a sample (n=112) of healthy people were evaluated with the French version of the consensual version of the MMSE, to target and modify some inadequate items for French Polynesia. Subsequently, a second sample (n=112) with the same characteristics (age, educational level) as well as 46 healthy people aged 60 years and more were evaluated with the adaptive version of the MMSE (P-MMSE). This version was then applied to 17 participants with Alzheimer disease. The control subjects were selected according to their age and educational level. The variables gender and evaluation sites were checked. An analysis of the results showed a significant dissociation between the two versions as well as a meaningful effect on global performance of the variables age (r=-0.45) and educational level (r=-0.25). Cut-off scores taking into consideration these variables were defined. The sensitivity and specificity values of the new cut-off scores were much greater than 0.5. Various global cut-off scores were also analyzed. A general cut-off score (≤23) was defined and yielded 82 % sensitivity and 75 % specificity in detecting Alzheimer disease.

Genetic Interaction Scoring Procedure for Bacterial Species

A genetic interaction occurs when the phenotype of an organism carrying two mutant genes differs from what should have been observed given their independent influence. Such unexpected outcome indicates a mechanistic connection between the perturbed genes, providing a key source of functional information about the cell. Large-scale screening for genetic interactions involves measuring phenotypes of single and double mutants, which for microorganisms is usually done by automated analysis of images of ordered colonies. Obtaining accurate colony sizes, and using them to identify genetic interactions from such screens remains a challenging and time-consuming task. Here, we outline steps to compute genetic interaction scores in E. coli by measuring colony sizes from plate images, performing normalisation, and quantifying the strength of the effect.

The use of regression and normalisation for the comparison of spatio-temporal gait data in children

Spatio-temporal parameters (STPs) are fundamental gait measures often used to compare children of different ages or gait ability. In the first case, non-dimensional normalisation (ND) of STPs using either leg-length or height is frequently conducted even though the process may not remove known inter-subject variability. STPs of children with and without disability can be compared through matched databases or using regression driven prediction. Unfortunately, database assignment is largely arbitrary and previous regressions have employed too few parameters to be successful. Therefore, the aims of this study were to test how well actual and ND STPs could be predicted from anthropometrics and speed and to assess if self-selected speed could be predicted from anthropometrics using multivariate regression in a cohort of eighty-nine typically developing children. Equations were validated on an extraneous dataset. We found that equations for actual step length, stride length, and cadence explained more than 84% of the variance compared to their ND counterparts. Moreover, only leg-length ND versions of these parameters were linearly proportional to speed. Prediction of single and double limb support times was weaker (R(2)=0.69 and 0.72, respectively) and we were unable to predict self-selected speed (R(2)<0.16) suggesting the use of anthropometrics is inappropriate for this purpose. Validation was successful for most STPs except in children lying near or outside the normal ranges and for gait speed. Clinically, regression could be used to quantify the difference between a patient's actual and theoretical STPs, allowing for monitoring of progress pre- and post intervention.

The role of leisure and delinquency in frequent cannabis use and dependence trajectories among young adults

BACKGROUND

The link between leisure and cannabis use has been widely studied, but less so for young adults, and rarely with a focus on frequent cannabis use. Also, little is known about how changes in leisure develop over time and how they are related to transitions in cannabis use and dependence.

METHOD

As part of a 3-year longitudinal project, in a qualitative study 47 frequent male and female young adult cannabis users with (n=23) and without (n=24) dependence at baseline were interviewed in-depth after 1.5 and 3 years.

RESULTS

Frequent cannabis users (at baseline ≥3 days per week in the past 12 months) are involved in similar leisure activities as the general young adult population and live rather conventional lives, generally away from a delinquent subculture. They mostly regulate their cannabis use to leisure time, to enhance other leisure activities, including socialising and video gaming. While they often give precedence to responsibilities (e.g. work and study), dependent and non-dependent users differed in whether they actively adapted their leisure activities to their cannabis use, or their cannabis use to their leisure time. Both types of and time spent on leisure activities were associated with transitions in use and dependence.

CONCLUSIONS

While our findings generally support the normalisation thesis, it is questionable whether frequent but non-problematic cannabis use is socially accepted in wider society. This study also questions the diagnostic dependence vs. non-dependence dichotomy, and adds finer distinctions to the concept of cannabis dependence. Implications for prevention and treatment include facilitating structured spending of leisure time (e.g. sports), and targeting frequent users who spent much leisure time video gaming at home.