Intratumor genetic heterogeneity in squamous cell carcinoma of the oral cavity

BackgroundWe sought to evaluate intratumor heterogeneity in squamous cell carcinoma of the oral cavity (OCC) and specifically determine the effect of physical separation and histologic differentiation within the same tumor.MethodsWe performed whole exome sequencing on five biopsy sites—two from well‐differentiated, two from poorly differentiated regions, and one from normal parenchyma—from five primary OCC specimens.ResultsWe found high levels of intratumor heterogeneity and, in four primary tumors, identified only 0 to 2 identical mutations in all subsites. We found that the heterogeneity inversely correlated with physical separation and that pairs of well‐differentiated samples were more similar to each other than analogous poorly differentiated specimens. Only TP53 mutations, but not other purported “driver mutations” in head and neck squamous cell carcinoma, were found in multiple biopsy sites.ConclusionThese data highlight the challenges to characterization of the mutational landscape of OCC with single site biopsy and have implications for personalized medicine.Peer Reviewedhttps://deepblue.lib.umich.edu/bitstream/2027.42/150549/1/hed25719.pdfhttps://deepblue.lib.umich.edu/bitstream/2027.42/150549/2/hed25719_am.pd

The reliability of postural balance measures in single and dual tasking in elderly fallers and non-fallers

BACKGROUND: The purpose of this study was to determine the reliability of a forceplate postural balance protocol in a group of elderly fallers and non-fallers. The measurements were tested in single and dual-task conditions, with and without vision. METHODS: 37 elderly (mean age 73 +/- 6 years) community-dwellers were included in this study. All were tested in a single (two-legged stance) and in a dual-task (two-legged stance while counting backwards aloud in steps of 7's) condition, with and without vision. A forceplate was used for registering postural variables: the maximal and the root-mean-square amplitude in medio-lateral (Max-ML, RMS-ML) and antero-posterior (Max-AP, RMS-AP) direction, mean velocity (MV), and the area of the 95% confidence ellipse (AoE). Reliability of the test protocol was expressed with intraclass correlation coefficients (ICC), with 95% limits of agreement (LoA), and with the smallest detectable difference (SDD). RESULTS: The ICCs for inter-rater reliability and test-retest reliability of the balance variables were r = 0.70-0.89. For the variables Max-AP and RMS-AP the ICCs were r = 0.52-0.74. The SDD values were for variable Max-ML and Max-AP between 0.37 cm and 0.83 cm, for MV between 0.48 cm/s and 1.2 cm/s and for AoE between 1.48 cm2 and 3.75 cm2. The LoA analysis by Bland-Altman plots showed no systematic differences between test-retest measurements. CONCLUSION: The study showed good reliability results for group assessment and no systematic errors of the measurement protocol in measuring postural balance in the elderly in a single-task and dual-task condition

Tracking reveals limited interactions between Campbell Albatross and fisheries during the breeding season

International audienceFisheries-related mortality has been influential in driving global declines in seabird populations. Understanding the overlap between seabird distribution and fisheries is one important element in assessing bycatch risk, and may be achieved by tracking the movements of individual birds and fishing vessels. Here, we assess the spatiotemporal overlap between the vulnerable Campbell Albatross Thalassarche impavida and large (>28 m) commercial fishing boats in New Zealand’s Exclusive Economic Zone (EEZ). We used a novel analytical approach, bivariate Gaussian bridge movement modelling, to compute spatiotemporal utilization distributions of bird-borne global positioning system (GPS) loggers and data from the Vessel Monitoring System. We tracked birds for 28,815 h during incubation and chick brooding, with half of this time spent within New Zealand’s EEZ, utilizing 6.7% of the available area. However, there was no evidence that albatrosses and fishing vessels were in the same location simultaneously. We accounted for the broader ecological footprint of fishing vessels by calculating the distance between GPS-fix locations for albatrosses and fishing vessels, revealing that albatrosses were within 30 km of fishing vessels in 8.4% of foraging trips. This highlights differences in estimated fine-scale spatiotemporal overlaps which may be due to the distance between albatrosses and vessels or the methods used. Overall, the low levels of spatial overlap could be a result of Campbell Albatross’ preference for foraging in areas without fishing activity or competitive exclusion by other species. Our results reinforce the importance of multi-scale, temporally explicit, and multi-national approaches to risk assessment, as Campbell Albatrosses spend approximately half of their time foraging outside New Zealand’s EEZ

Pan-cancer analysis of whole genomes

Cancer is driven by genetic change, and the advent of massively parallel sequencing has enabled systematic documentation of this variation at the whole-genome scale(1-3). Here we report the integrative analysis of 2,658 whole-cancer genomes and their matching normal tissues across 38 tumour types from the Pan-Cancer Analysis of Whole Genomes (PCAWG) Consortium of the International Cancer Genome Consortium (ICGC) and The Cancer Genome Atlas (TCGA). We describe the generation of the PCAWG resource, facilitated by international data sharing using compute clouds. On average, cancer genomes contained 4-5 driver mutations when combining coding and non-coding genomic elements; however, in around 5% of cases no drivers were identified, suggesting that cancer driver discovery is not yet complete. Chromothripsis, in which many clustered structural variants arise in a single catastrophic event, is frequently an early event in tumour evolution; in acral melanoma, for example, these events precede most somatic point mutations and affect several cancer-associated genes simultaneously. Cancers with abnormal telomere maintenance often originate from tissues with low replicative activity and show several mechanisms of preventing telomere attrition to critical levels. Common and rare germline variants affect patterns of somatic mutation, including point mutations, structural variants and somatic retrotransposition. A collection of papers from the PCAWG Consortium describes non-coding mutations that drive cancer beyond those in the TERT promoter(4); identifies new signatures of mutational processes that cause base substitutions, small insertions and deletions and structural variation(5,6); analyses timings and patterns of tumour evolution(7); describes the diverse transcriptional consequences of somatic mutation on splicing, expression levels, fusion genes and promoter activity(8,9); and evaluates a range of more-specialized features of cancer genomes(8,10-18).Peer reviewe

Harmful Elements in Estuarine and Coastal Systems

Estuaries and coastal zones are dynamic transitional systems which provide many economic and ecological benefits to humans, but also are an ideal habitat for other organisms as well. These areas are becoming contaminated by various anthropogenic activities due to a quick economic growth and urbanization. This chapter explores the sources, chemical speciation, sediment accumulation and removal mechanisms of the harmful elements in estuarine and coastal seawaters. It also describes the effects of toxic elements on aquatic flora and fauna. Finally, the toxic element pollution of the Venice Lagoon, a transitional water body located in the northeastern part of Italy, is discussed as a case study, by presenting the procedures adopted to measure the extent of the pollution, the impacts on organisms and the restoration activities