Sepsis: the LightCycler SeptiFast Test MGRADE®, SepsiTest™ and IRIDICA BAC BSI assay for rapidly identifying bloodstream bacteria and fungi – a systematic review and economic evaluation

Background: Sepsis can lead to multiple organ failure and death. Timely and appropriate treatment can reduce in-hospital mortality and morbidity. Objectives: To determine the clinical effectiveness and cost-effectiveness of three tests [LightCycler SeptiFast Test MGRADE® (Roche Diagnostics, Risch-Rotkreuz, Switzerland); SepsiTest™ (Molzym Molecular Diagnostics, Bremen, Germany); and the IRIDICA BAC BSI assay (Abbott Diagnostics, Lake Forest, IL, USA)] for the rapid identification of bloodstream bacteria and fungi in patients with suspected sepsis compared with standard practice (blood culture with or without matrix-absorbed laser desorption/ionisation time-offlight mass spectrometry). Data sources: Thirteen electronic databases (including MEDLINE, EMBASE and The Cochrane Library) were searched from January 2006 to May 2015 and supplemented by hand-searching relevant articles. Review methods: A systematic review and meta-analysis of effectiveness studies were conducted. A review of published economic analyses was undertaken and a de novo health economic model was constructed. A decision tree was used to estimate the costs and quality-adjusted life-years (QALYs) associated with each test; all other parameters were estimated from published sources. The model was populated with evidence from the systematic review or individual studies, if this was considered more appropriate (base case 1). In a secondary analysis, estimates (based on experience and opinion) from seven clinicians regarding the benefits of earlier test results were sought (base case 2). A NHS and Personal Social Services perspective was taken, and costs and benefits were discounted at 3.5% per annum. Scenario analyses were used to assess uncertainty. Results: For the review of diagnostic test accuracy, 62 studies of varying methodological quality were included. A meta-analysis of 54 studies comparing SeptiFast with blood culture found that SeptiFast had an estimated summary specificity of 0.86 [95% credible interval (CrI) 0.84 to 0.89] and sensitivity of 0.65 (95% CrI 0.60 to 0.71). Four studies comparing SepsiTest with blood culture found that SepsiTest had an estimated summary specificity of 0.86 (95% CrI 0.78 to 0.92) and sensitivity of 0.48 (95% CrI 0.21 to 0.74), and four studies comparing IRIDICA with blood culture found that IRIDICA had an estimated summary specificity of 0.84 (95% CrI 0.71 to 0.92) and sensitivity of 0.81 (95% CrI 0.69 to 0.90). Owing to the deficiencies in study quality for all interventions, diagnostic accuracy data should be treated with caution. No randomised clinical trial evidence was identified that indicated that any of the tests significantly improved key patient outcomes, such as mortality or duration in an intensive care unit or hospital. Base case 1 estimated that none of the three tests provided a benefit to patients compared with standard practice and thus all tests were dominated. In contrast, in base case 2 it was estimated that all cost per QALY-gained values were below £20,000; the IRIDICA BAC BSI assay had the highest estimated incremental net benefit, but results from base case 2 should be treated with caution as these are not evidence based. Limitations: Robust data to accurately assess the clinical effectiveness and cost-effectiveness of the interventions are currently unavailable. Conclusions: The clinical effectiveness and cost-effectiveness of the interventions cannot be reliably determined with the current evidence base. Appropriate studies, which allow information from the tests to be implemented in clinical practice, are required.

Barriers and facilitators to cooking from 'scratch' using basic or raw ingredients: A qualitative interview study

Background: Previous research has highlighted an ambiguity in understanding cooking related terminology and a number of barriers and facilitators to home meal preparation. However, meals prepared in the home still include convenience products (typically high in sugars, fats and sodium) which can have negative effects on health. Therefore, this study aimed to qualitatively explore: (1) how individuals define cooking from ‘scratch’, and (2) their barriers and facilitators to cooking with basic ingredients.
Methods: 27 semi-structured interviews were conducted with participants (aged 18-58 years) living on the island of Ireland, eliciting definitions of ‘cooking from scratch’ and exploring the reasons participants cook in a particular way. The interviews were professionally transcribed verbatim and Nvivo 10 was used for an inductive thematic analysis.
Results: Our results highlighted that although cooking from ‘scratch’ lacks a single definition, participants viewed it as optimal cooking. Barriers to cooking with raw ingredients included: 1) time pressures; (2) desire to save money; (3) desire for effortless meals; (4) family food preferences; and (5) effect of kitchen disasters. Facilitators included: 1) desire to eat for health and well-being; (2) creative inspiration; (3) ability to plan and prepare meals ahead of time; and (4) greater self-efficacy in one’s cooking ability.
Conclusions: Our findings contribute to understanding how individuals define cooking from ‘scratch’, and barriers and facilitators to cooking with raw ingredients. Interventions should focus on practical sessions to increase cooking self-efficacy; highlight the importance of planning ahead and teach methods such as batch cooking and freezing to facilitate cooking from scratch.

Sensitive and specific detection of viable Mycobacterium avium subsp. paratuberculosis in raw milk by the Peptide-mediated magnetic separation (PMS)-phage assay

This study describes further validation of a previously described Peptide-mediated magnetic separation (PMS)-Phage assay, and its application to test raw cows’ milk for presence of viable Mycobacterium avium subsp. paratuberculosis (MAP). The inclusivity and exclusivity of the PMS-phage assay were initially assessed, before the 50% limit of detection (LOD50) was determined and compared with those of PMS-qPCR (targeting both IS900 and f57) and PMS-culture. These methods were then applied in parallel to test 146 individual milk samples and 22 bulk tank milk samples from Johne’s affected herds. Viable MAP were detected by the PMS-phage assay in 31 (21.2%) of 146 individual milk samples (mean plaque count of 228.1 PFU/50 ml, range 6-948 PFU/50 ml), and 13 (59.1%) of 22 bulk tank milks (mean plaque count of 136.83 PFU/50 ml, range 18-695 PFU/50 ml). In contrast, only 7 (9.1%) of 77 individual milks and 10 (45.4%) of 22 bulk tank milks tested PMS-qPCR positive, and 17 (11.6%) of 146 individual milks and 11 (50%) of 22 bulk tank milks tested PMS-culture positive. The mean 50% limits of detection (LOD50) of the PMS-phage, PMS-IS900 qPCR and PMS-f57 qPCR assays, determined by testing MAP-spiked milk, were 0.93, 135.63 and 297.35 MAP CFU/50 ml milk, respectively. Collectively, these results demonstrate that, in our laboratory, the PMS-phage assay is a sensitive and specific method to quickly detect the presence of viable MAP cells in milk. However, due to its complicated, multi-step nature, the method would not be a suitable MAP screening method for the dairy industry.

Development of A Flow Cytometry Assay for Measurement of CD4+ T Cell Proliferation

Thesis (Master's)--University of Washington, 2016-06

'Scratch' locative audio drama - report to BBC executives on trial at BBC FreeThinking 2008

‘Scratch’ investigates the use of physical space as a representation of narrative and dramatic structure. An audio-drama, it is a world-first in being location-sensitive without being tied to any particular place (preceding attempts by others have emphasised location-specific aspects of the genre). Developed in collaboration with and part-funded by BBC Radio Drama, it builds on research undertaken for ‘Dragons’ (output 4). It uses pre-recorded audio on GPS-enabled mobile devices allowing sounds to be virtually attached to locations in an outdoor space. As participants move, they encounter scenes forming a coherent drama which behave differently if the same place is visited more than once. This translocational approach opens novel artistic possibilities exploited through team expertise in narrative, sound design and advanced interaction. It is also significant in the economics of broadcast media as a more viable proposition than the many experimental locative experiences which have been site-specific: this was of great interest to the BBC. The public performance selected for BBC FreeThinking, 1-2 September 2008 in Liverpool as part of European Capital of Culture was reported in a co-authored 2009 conference presentation at ISEA, Belfast, 26-29 August 2009 and in a co-authored short chapter in Spierling and Szilas (eds.) Interactive Storytelling, Springer 2008. Boyd Davis directed the project and devised and undertook the evaluation with 40 trial listeners, reporting to BBC executives (http://researchonline.rca.ac.uk/1000/) for whom a second trial was also run in London in 2009. The evaluation used interview, video observation and a questionnaire combining an open question at the beginning with more specific questions later, avoiding channelling respondents' reactions immediately after the experience into issues which might not be uppermost in their minds, while also yielding data capable of rigorous analysis. The evaluation was to provide feedback to the makers of the drama and to guide policy at the BBC. [287] Participants were recruited principally through the publicity for FreeThinking 2008 – mainly via the festival website. The average age of participants was 40. The gender of participants was 20 males, 17 females and 3 null returns. The evaluation strategy was to combine an open question at the beginning with more specific questions later. In this way we avoided channeling respondents' initial opinions immediately after the experience into issues which might not be uppermost in their minds, while also yielding data capable of rigorous analysis. The purpose of the evaluation was to provide guidance for ourselves as the makers of the drama and to guide policy at the BBC on locative and other interactive media. The responses are analysed in the report.

Field Evaluation of a Competitive Lateral-flow Assay for Detection of Alternaria brassicae in Vegetable Brassica Crops

On-site detection of inoculum of polycyclic plant pathogens could potentially contribute to management of disease outbreaks. A 6-min, in-field competitive immunochromatographic lateral flow device (CLFD) assay was developed for detection of Alternaria brassicae (the cause of dark leaf spot in brassica crops) in air sampled above the crop canopy. Visual recording of the test result by eye provides a detection threshold of approximately 50 dark leaf spot conidia. Assessment using a portable reader improved test sensitivity. In combination with a weather-driven infection model, CLFD assays were evaluated as part of an in-field risk assessment to identify periods when brassica crops were at risk from A. brassicae infection. The weather-driven model overpredicted A. brassicae infection. An automated 7-day multivial cyclone air sampler combined with a daily in-field CLFD assay detected A. brassicae conidia air samples from above the crops. Integration of information from an in-field detection system (CLFD) with weather-driven mathematical models predicting pathogen infection have the potential for use within disease management systems.

AMBIENTE DE PROGRAMAÇÃO SCRATCH VOLTADA PARA CRIANÇAS SOB A PERSPECTIVA DA ENGENHARIA SEMIÓTICA

Neste atual cenário mundial, em que as mudanças acontecem em uma velocidade espantosa, novos desafios, novas tecnologias e novos atores aparecem e participam ativamente dessas mudanças. Esta pesquisa apresenta exatamente um desses novos atores, as crianças, as quais interagem cada vez mais cedo com essa diversidade tecnológica. A participação das crianças nesse cenário passa a ser mais ativa quando as mesmas começam a aprender linguagem de programação através de ambientes computacionais. Esses ambientes são avaliados através de sua metacomunicação com aplicação de métodos da Engenharia Semiótica. Assim, a pesquisa tenta compreender e avaliar o processo de metacomunicação usuário-sistema e a contribuição do mesmo no processo de aprendizagem infantil. Com o objetivo de verificarmos essas ocorrências de rupturas entre o ambiente de programação Scratch e seu público-alvo específico, aplicamos a metodologia denominada MAC – Método de Avaliação da Comunicabilidade –, uma técnica conhecida pela Engenharia Semiótica desde 1999. Diversos resultados foram percebidos, porém um merece destaque especial, em que percebemos que as mensagens foram, em sua maioria, identificadas e interpretadas pelos usuários finais. Por outro lado, ocorreram rupturas de comunicação em todos os voluntários, mesmo para aqueles que concluíram todas as tarefas.

Relation between DNA damage measured by comet assay and OGG1 Ser326Cys polymorphism in antineoplastic drugs biomonitoring

Antineoplastic drugs are hazardous chemical agents used mostly in the treatment of patients with cancer, however health professionals that handle and administer these drugs can become exposed and develop DNA damage. Comet assay is a standard method for assessing DNA damage in human biomonitoring and, combined with formamidopyrimidine DNA glycosylase (FPG) enzyme, it specifically detects DNA oxidative damage. The aim of this study was to investigate genotoxic effects in workers occupationally exposed to cytostatics (n = 46), as compared to a control group with no exposure (n = 46) at two Portuguese hospitals, by means of the alkaline comet assay. The potential of the OGG1 Ser326Cys polymorphism as a susceptibility biomarker was also investigated. Exposure was evaluated by investigating the contamination of surfaces and genotoxic assessment was done by alkaline comet assay in peripheral blood lymphocytes. OGG1 Ser326Cys (rs1052133) polymorphism was studied by Real Time PCR. As for exposure assessment, there were 121 (37%) positive samples out of a total of 327 samples analysed from both hospitals. No statistically significant differences (Mann-Whitney test, p > 0.05) were found between subjects with and without exposure, regarding DNA damage and oxidative DNA damage, nevertheless the exposed group exhibited higher values. Moreover, there was no consistent trend regarding the variation of both biomarkers as assessed by comet assay with OGG1 polymorphism. Our study was not statistically significant regarding occupational exposure to antineoplastic drugs and genetic damage assessed by comet assay. However, health professionals should be monitored for risk behaviour, in order to ensure that safety measures are applied and protection devices are used correctly.

Comet assay as a human biomonitoring tool: application in occupational exposure to antineoplastic drugs

Antineoplastic drugs are a heterogeneous group of chemicals used in the treatment of cancer, and have been proved by IARC to be mutagens, carcinogens and teratogens agents. In general, chemicals that interact directly with DNA by biding covalently or by intercalating, or indirectly by interfering with DNA synthesis, were among the first chemotherapeutics developed. Also, these drugs can induce reactive oxygen species that can lead to DNA damage and, consequently, mutations. These drugs are often used in combination to achieve synergistic effects on tumour cells resulting from their differing modes of action. However, most if not all of these chemical agents are generally nonselective and, along with tumour cells, normal cells may undergo cytotoxic/genotoxic damage. The in vivo exposure to antineoplastic drugs has been shown to induce different types of lesions in DNA, depending on the particular stage of cell cycle at the time of treatment. Besides the patients that use these drugs as a treatment, workers that handle and/or administer these drugs can be exposed to these substances; namely pharmacy, and nursing personnel in hospital context.

Validation of a novel assay for cardiology drug screening using hESC-derived cardiomyocyte spheroids - “mini-hearts”

This is an abstract of a presented talk at the European Biotechnology Conference held in Latvia during 05–07 May 2016

The cytokinesis-block micronucleus (CBMN) assay in human populations exposed to styrene: a systematic review and meta-analysis

Styrene is a building-block of several compounds used in a wide array of materials and products. The most important human exposure to this substance occurs in industrial settings, especially among reinforced-plastics industry workers. The effect of occupational exposure to styrene on cytogenetics biomarkers has been previously reviewed with positive association observed for chromosomal aberrations, and inconclusive data for the micronucleus assay. Some limitations were noted in those studies, including inadequate exposure assessment and poor epidemiological design. Furthermore, in earlier studies micronuclei frequency was measured with protocols not as reliable as cytokinesis-block micronucleus (CBMN) assay. Aim of the present systematic review and meta-analysis is to investigate genomic instability and DNA damage as measured by the CBMN assay in lymphocytes of subjects exposed to styrene. A total of 11 studies published between 2004 and 2012 were included in the meta-analysis encompassing 479 styrene-exposed workers and 510 controls. The quality of each study was estimated by a quality scoring system which ranked studies according to the consideration of major confounders, exposure characterization, and technical parameters. An overall increase of micronuclei frequencies was found in styrene-exposure workers when compared to referents (meta-MR 1.34; 95% CI 1.18–1.52), with significant increases achieved in six individual studies. The consistency of results in individual studies, the independence of this result from major confounding factors and from the quality of the study strengthens the reliability of risk estimates and supports the use of the CBMN assay in monitoring genetic risk in styrene workers.

A mitochondrial species identification assay for Australian blacktip sharks (Carcharhinus tilstoni, C. limbatus and C. amblyrhynchoides) using real-time PCR and high-resolution melt analysis

Tropical Australian shark fisheries target two morphologically indistinguishable blacktip sharks, the Australian blacktip (Carcharhinus tilstoni) and the common blacktip (C. limbatus). Their relative contributions to northern and eastern Australian coastal fisheries are unclear because of species identification difficulties. The two species differ in their number of precaudal vertebrae, which is difficult and time consuming to obtain in the field. But, the two species can be distinguished genetically with diagnostic mutations in their mitochondrial DNA ND4 gene. A third closely related sister species, the graceful shark C. amblyrhynchoides, can also be distinguished by species-specific mutations in this gene. DNA sequencing is an effective diagnostic tool, but is relatively expensive and time consuming. In contrast, real-time high-resolution melt (HRM) PCR assays are rapid and relatively inexpensive. These assays amplify regions of DNA with species-specific genetic mutations that result in PCR products with unique melt profiles. A real-time HRM PCR species-diagnostic assay (RT-HRM-PCR) has been developed based on the mtDNA ND4 gene for rapid typing of C. tilstoni, C. limbatus and C. amblyrhynchoides. The assay was developed using ND4 sequences from 66 C. tilstoni, 33. C. limbatus and five C. amblyrhynchoides collected from Indonesia and Australian states and territories; Western Australia, the Northern Territory, Queensland and New South Wales. The assay was shown to be 100% accurate on 160 unknown blacktip shark tissue samples by full mtDNA ND4 sequencing.