Point-and-shoot: rapid quantitative detection methods for on-site food fraud analysis – moving out of the laboratory and into the food supply chain

Major food adulteration and contamination events occur with alarming regularity and are known to be episodic, with the question being not if but when another large-scale food safety/integrity incident will occur. Indeed, the challenges of maintaining food security are now internationally recognised. The ever increasing scale and complexity of food supply networks can lead to them becoming significantly more vulnerable to fraud and contamination, and potentially dysfunctional. This can make the task of deciding which analytical methods are more suitable to collect and analyse (bio)chemical data within complex food supply chains, at targeted points of vulnerability, that much more challenging. It is evident that those working within and associated with the food industry are seeking rapid, user-friendly methods to detect food fraud and contamination, and rapid/high-throughput screening methods for the analysis of food in general. In addition to being robust and reproducible, these methods should be portable and ideally handheld and/or remote sensor devices, that can be taken to or be positioned on/at-line at points of vulnerability along complex food supply networks and require a minimum amount of background training to acquire information rich data rapidly (ergo point-and-shoot). Here we briefly discuss a range of spectrometry and spectroscopy based approaches, many of which are commercially available, as well as other methods currently under development. We discuss a future perspective of how this range of detection methods in the growing sensor portfolio, along with developments in computational and information sciences such as predictive computing and the Internet of Things, will together form systems- and technology-based approaches that significantly reduce the areas of vulnerability to food crime within food supply chains. As food fraud is a problem of systems and therefore requires systems level solutions and thinking.

An exploration of men’s experiences of undergoing active surveillance for favourable-risk prostate cancer: A mixed methods study protocol

Background
Prostate cancer is one of the most common male cancers worldwide. Active Surveillance (AS) has been developed to allow men with lower risk disease to postpone or avoid the adverse side effects associated with curative treatments until the disease progresses. Despite the medical benefits of AS, it is reported that living with untreated cancer can create a significant emotional burden for patients.

Methods/design
The aim of this study is to gain insight into the experiences of men eligible to undergo AS for favourable-risk PCa.

This study has a mixed-methods sequential explanatory design consisting of two phases: quantitative followed by qualitative. Phase 1 has a multiple point, prospective, longitudinal exploratory design. Ninety men diagnosed with favourable-risk prostate cancer will be assessed immediately post-diagnosis (baseline) and followed over a period of 12 months, in intervals of 3 month. Ninety age-matched men with no cancer diagnosis will also be recruited using peer nomination and followed up in the same 3 month intervals. Following completion of Phase 1, 10–15 AS participants who have reported both the best and worst psychological functioning will be invited to participate in semi-structured qualitative interviews. Phase 2 will facilitate further exploration of the quantitative results and obtain a richer understanding of participants’ personal interpretations of their illness and psychological wellbeing.

Discussion
To our knowledge, this is the first study to utilise early baseline measures; include a healthy comparison group; calculate sample size through power calculations; and use a mixed methods approach to gain a deeper more holistic insight into the experiences of men diagnosed with favourable-risk prostate cancer.

The effectiveness of a nurse practitioner-led pain management team in long-term care: A mixed methods study

BACKGROUND: Considering the high rates of pain as well as its under-management in long-term care (LTC) settings, research is needed to explore innovations in pain management that take into account limited resource realities. It has been suggested that nurse practitioners, working within an inter-professional model, could potentially address the under-management of pain in LTC.

OBJECTIVES: This study evaluated the effectiveness of implementing a nurse practitioner-led, inter-professional pain management team in LTC in improving (a) pain-related resident outcomes; (b) clinical practice behaviours (e.g., documentation of pain assessments, use of non-pharmacological and pharmacological interventions); and, (c) quality of pain medication prescribing practices.

METHODS: A mixed method design was used to evaluate a nurse practitioner-led pain management team, including both a quantitative and qualitative component. Using a controlled before-after study, six LTC homes were allocated to one of three groups: 1) a nurse practitioner-led pain team (full intervention); 2) nurse practitioner but no pain management team (partial intervention); or, 3) no nurse practitioner, no pain management team (control group). In total, 345 LTC residents were recruited to participate in the study; 139 residents for the full intervention group, 108 for the partial intervention group, and 98 residents for the control group. Data was collected in Canada from 2010 to 2012.

RESULTS: Implementing a nurse practitioner-led pain team in LTC significantly reduced residents' pain and improved functional status compared to usual care without access to a nurse practitioner. Positive changes in clinical practice behaviours (e.g., assessing pain, developing care plans related to pain management, documenting effectiveness of pain interventions) occurred over the intervention period for both the nurse practitioner-led pain team and nurse practitioner-only groups; these changes did not occur to the same extent, if at all, in the control group. Qualitative analysis highlighted the perceived benefits of LTC staff about having access to a nurse practitioner and benefits of the pain team, along with barriers to managing pain in LTC.

CONCLUSIONS: The findings from this study showed that implementing a nurse practitioner-led pain team can significantly improve resident pain and functional status as well as clinical practice behaviours of LTC staff. LTC homes should employ a nurse practitioner, ideally located onsite as opposed to an offsite consultative role, to enhance inter-professional collaboration and facilitate more consistent and timely access to pain management.

A comparison of three methods for detecting KRAS mutations in formalin-fixed colorectal cancer specimens.

BACKGROUND: KRAS mutation testing is required to select patients with metastatic colorectal cancer (CRC) to receive anti-epidermal growth factor receptor antibodies, but the optimal KRAS mutation test method is uncertain. METHODS: We conducted a two-site comparison of two commercial KRAS mutation kits - the cobas KRAS Mutation Test and the Qiagen therascreen KRAS Kit - and Sanger sequencing. A panel of 120 CRC specimens was tested with all three methods. The agreement between the cobas test and each of the other methods was assessed. Specimens with discordant results were subjected to quantitative massively parallel pyrosequencing (MPP). DNA blends were tested to determine detection rates at 5% mutant alleles. RESULTS: Reproducibility of the cobas test between sites was 98%. Six mutations were detected by cobas that were not detected by Sanger, and five were confirmed by MPP. The cobas test detected eight mutations which were not detected by the therascreen test, and seven were confirmed by MPP. Detection rates with 5% mutant DNA blends were 100% for the cobas and therascreen tests and 19% for Sanger. CONCLUSION: The cobas test was reproducible between sites, and detected several mutations that were not detected by the therascreen test or Sanger. Sanger sequencing had poor sensitivity for low levels of mutation.

Application of self-quenched JH consensus primers for real-time quantitative PCR of IGH gene to minimal residual disease evaluation in multiple myeloma.

Monitoring multiple myeloma patients for relapse requires sensitive methods to measure minimal residual disease and to establish a more precise prognosis. The present study aimed to standardize a real-time quantitative polymerase chain reaction (PCR) test for the IgH gene with a JH consensus self-quenched fluorescence reverse primer and a VDJH or DJH allele-specific sense primer (self-quenched PCR). This method was compared with allele-specific real-time quantitative PCR test for the IgH gene using a TaqMan probe and a JH consensus primer (TaqMan PCR). We studied nine multiple myeloma patients from the Spanish group treated with the MM2000 therapeutic protocol. Self-quenched PCR demonstrated sensitivity of >or=10(-4) or 16 genomes in most cases, efficiency was 1.71 to 2.14, and intra-assay and interassay reproducibilities were 1.18 and 0.75%, respectively. Sensitivity, efficiency, and residual disease detection were similar with both PCR methods. TaqMan PCR failed in one case because of a mutation in the JH primer binding site, and self-quenched PCR worked well in this case. In conclusion, self-quenched PCR is a sensitive and reproducible method for quantifying residual disease in multiple myeloma patients; it yields similar results to TaqMan PCR and may be more effective than the latter when somatic mutations are present in the JH intronic primer binding site.

Minimal residual disease monitoring in multiple myeloma: a comparison between allelic-specific oligonucleotide real-time quantitative polymerase chain reaction and flow cytometry.

BACKGROUND AND OBJECTIVES: Minimal residual disease (MRD) studies are useful in multiple myeloma (MM). However, the definition of the best technique and clinical utility are still unresolved issues. The aim of this study was to analyze and compare the clinical utility of MRD studies in MM with two different techniques: allelic-specific oligonucleotide real-time quantitative PCR (ASO-RQ-PCR), and flow cytometry (FCM). DESIGN AND METHODS: Bone marrow samples from 32 MM patients who had achieved complete response after transplantation were evaluated by ASO-RQ-PCR, using TaqMan technology, and multiparametric FCM. RESULTS: ASO-RQ-PCR was only applicable in 75% of patients for a variety of technical reasons, while FCM was applicable in up to 90%. Therefore, simultaneous PCR/FCM analysis was possible in only 24 patients. The number of residual tumor cells identified by both techniques was very similar (mean=0.29%, range=0.001-1.61%, correlation coefficient=0.861). However, RQ-PCR was able to detect residual myelomatous cells in 17 patients while FCM only did so in 11; thus, 6 cases were FCM negative but PCR positive, all of them displaying a very low number of clonal cells (median=0.014%, range=0.001-0.11). Using an MRD threshold of 0.01% (10(-4)) two risk groups with significantly different progression-free survival could be identified by either PCR (34 vs. 15m, p=0.04) or FCM (27 vs. 10m, p=0.05). INTERPRETATION AND CONCLUSIONS: Although MRD evaluation by ASO-RQ-PCR is slightly more sensitive and specific than FCM, it is applicable in a lower proportion of MM patients and is more time-consuming, while both techniques provide similar prognostic information.

Complexity of risk: Mixed methods approach to understanding youth risk and insecurity in post-conflict settings

In settings of intergroup conflict, identifying contextually-relevant risk factors for youth development in an important task. In Vukovar, Croatia, a city devastated during the war in former Yugoslavia, ethno-political tensions remain. The current study utilized a mixed method approach to identify two salient community-level risk factors (ethnic tension and general antisocial behavior) and related emotional insecurity responses (ethnic and non-ethnic insecurity) among youth in Vukovar. In Study 1, focus group discussions (N=66) with mother, fathers, and adolescents 11 to 15-years-old were analyzed using the Constant Comparative Method, revealing two types of risk and insecurity responses. In Study 2, youth (N=227, 58% male, M=15.88 SD=1.12 years old) responded to quantitative scales developed from the focus groups; discriminate validity was demonstrated and path analyses established predictive validity between each type of risk and insecurity. First, community ethnic tension (i.e., threats related to war/ethnic identity) significantly predicted ethnic insecurity for all youth (β=.41, p<.001). Second, experience with community antisocial behavior (i.e., general crime found in any context) predicted non-ethnic community insecurity for girls (β=.32, p<.05), but not for boys. These findings are the first to show multiple forms of emotional insecurity at the community level; implications for future research are discussed.

The effect of changing the built environment on physical activity: a quantitative review of the risk of bias in natural experiments.

BACKGROUND:
Evidence regarding the association of the built environment with physical activity is influencing policy recommendations that advocate changing the built environment to increase population-level physical activity. However, to date there has been no rigorous appraisal of the quality of the evidence on the effects of changing the built environment. The aim of this review was to conduct a thorough quantitative appraisal of the risk of bias present in those natural experiments with the strongest experimental designs for assessing the causal effects of the built environment on physical activity.

METHODS:
Eligible studies had to evaluate the effects of changing the built environment on physical activity, include at least one measurement before and one measurement of physical activity after changes in the environment, and have at least one intervention site and non-intervention comparison site. Given the large number of systematic reviews in this area, studies were identified from three exemplar systematic reviews; these were published in the past five years and were selected to provide a range of different built environment interventions. The risk of bias in these studies was analysed using the Cochrane Risk of Bias Assessment Tool: for Non-Randomized Studies of Interventions (ACROBAT-NRSI).

RESULTS:
Twelve eligible natural experiments were identified. Risk of bias assessments were conducted for each physical activity outcome from all studies, resulting in a total of fifteen outcomes being analysed. Intervention sites included parks, urban greenways/trails, bicycle lanes, paths, vacant lots, and a senior citizen's centre. All outcomes had an overall critical (n = 12) or serious (n = 3) risk of bias. Domains with the highest risk of bias were confounding (due to inadequate control sites and poor control of confounding variables), measurement of outcomes, and selection of the reported result.

CONCLUSIONS:
The present review focused on the strongest natural experiments conducted to date. Given this, the failure of existing studies to adequately control for potential sources of bias highlights the need for more rigorous research to underpin policy recommendations for changing the built environment to increase physical activity. Suggestions are proposed for how future natural experiments in this area can be improved.