La Trobe University

About: La Trobe University is a education organization based out in Melbourne, Victoria, Australia. It is known for research contribution in the topics: Population & Health care. The organization has 13370 authors who have published 41291 publications receiving 1138269 citations. The organization is also known as: LaTrobe University & LTU.

Sequence Artifacts in DNA from Formalin-Fixed Tissues: Causes and Strategies for Minimization

Abstract: BACKGROUND: Precision medicine is dependent on identifying actionable mutations in tumors. Accurate detection of mutations is often problematic in formalin-fixed paraffin-embedded (FFPE) tissues. DNA extracted from formalin-fixed tissues is fragmented and also contains DNA lesions that are the sources of sequence artifacts. Sequence artifacts can be difficult to distinguish from true mutations, especially in the context of tumor heterogeneity, and are an increasing interpretive problem in this era of massively parallel sequencing. Understanding of the sources of sequence artifacts in FFPE tissues and implementation of preventative strategies are critical to improve the accurate detection of actionable mutations. CONTENT: This mini-review focuses on DNA template lesions in FFPE tissues as the source of sequence artifacts in molecular analysis. In particular, fragmentation, base modification (including uracil and thymine deriving from cytosine deamination), and abasic sites are discussed as indirect or direct sources of sequence artifacts. We discuss strategies that can be implemented to minimize sequence artifacts and to distinguish true mutations from sequence artifacts. These strategies are applicable for the detection of actionable mutations in both single amplicon and massively parallel amplicon sequencing approaches. SUMMARY: Because FFPE tissues are usually the only available material for DNA analysis, it is important to maximize the accurate informational content from FFPE DNA. Careful consideration of each step in the work flow is needed to minimize sequence artifacts. In addition, validation of actionable mutations either by appropriate experimental design or by orthogonal methods should be considered.

Psychophysics: bees trade off foraging speed for accuracy.

Abstract: Bees have an impressive cognitive capacity1,2,3,4, but the strategies used by individuals in solving foraging tasks have been largely unexplored. Here we test bumblebees (Bombus terrestris) in a colour-discrimination task on a virtual flower meadow and find that some bees consistently make rapid choices but with low precision, whereas other bees are slower but highly accurate. Moreover, each bee will sacrifice speed in favour of accuracy when errors are penalized instead of just being unrewarded. To our knowledge, bees are the first example of an insect to show between-individual and within-individual speed– accuracy trade-offs.

The influence of childhood traffic‐related air pollution exposure on asthma, allergy and sensitization: a systematic review and a meta‐analysis of birth cohort studies

Abstract: The impact of early childhood traffic-related air pollution (TRAP) exposure on development of asthma and allergies remains unclear. Birth cohort studies are the best available study design to answer this question, but the evidence from such studies has not been synthesized to date. We conducted a systematic review and meta-analyses of published birth cohort studies to understand the association between early childhood TRAP exposure, and subsequent asthma, allergies and sensitization. Increased longitudinal childhood exposure to PM2.5 and black carbon was associated with increasing risk of subsequent asthma in childhood (PM2.5 : OR 1.14, 95%CI 1.00 to 1.30 per 2 μg/m(3) and black carbon: OR 1.20, 95%CI 1.05 to 1.38 per 1 × 10(-5) m(-1) ). Also, early childhood exposure to TRAP was associated with development of asthma across childhood up to 12 years of age. The magnitude of these associations increased with age, and the pattern was prominent for PM2.5 . Increasing exposure to PM2.5 was associated with sensitization to both aero- and food allergens. There was some evidence that TRAP was associated with eczema and hay fever. In summary, exposure to TRAP was related to asthma and allergic diseases. However, the substantial variability across studies warrants long-term birth cohort studies with regular repeated follow-ups to confirm these findings.

The Case for Using the Repeatability Coefficient When Calculating Test–Retest Reliability

Abstract: The use of standardised tools is an essential component of evidence-based practice. Reliance on standardised tools places demands on clinicians to understand their properties, strengths, and weaknesses, in order to interpret results and make clinical decisions. This paper makes a case for clinicians to consider measurement error (ME) indices Coefficient of Repeatability (CR) or the Smallest Real Difference (SRD) over relative reliability coefficients like the Pearson’s (r) and the Intraclass Correlation Coefficient (ICC), while selecting tools to measure change and inferring change as true. The authors present statistical methods that are part of the current approach to evaluate test–retest reliability of assessment tools and outcome measurements. Selected examples from a previous test–retest study are used to elucidate the added advantages of knowledge of the ME of an assessment tool in clinical decision making. The CR is computed in the same units as the assessment tool and sets the boundary of the minimal detectable true change that can be measured by the tool.